bluuebunny/crossref_metadata_2025 huggingface dataset:
Typhoon eye effect versus ripple effect: the role of family size on mental health during the COVID-19 pandemic in Pakistan
Authors: Lateef Tooba , Chen Jiyao , Tahir Muhammad , Lateef Teba Abdul , Chen Bryan Z. , Li Jizhen , Zhang Stephen X.
Published: March 2021

Background

The recent outbreak of COVID-19 has impacted adversely upon the mental health of millions of people worldwide. Impacts on the mental health conditions and the associated predictors relating to adults in Pakistan, the fifth most populous country in the world, during the COVID-19 remain understudied. Our aim was to investigate distress, anxiety, and overall mental health and their associated predictors among Pakistani adults in this pandemic. We specifically examine mental health issues based on the distance from the epicenter, (a predictor that has revealed opposing evidence in other countries) based on the theories of typhoon eye effect and ripple effect. The sample consisted of 601 adults who were surveyed online about 2.5 months into the outbreak across Pakistan with varying distances from the epicenter of COVID-19 of Karachi.

Results

The results showed that 9.2 and 19.0% of the participants surpassed the cut-off criteria for distress and anxiety disorders, respectively. Overall, the distance from the epicenter positively predicted the mental health of adults in Pakistan, and family size negatively moderated this effect. The distance from the epicenter negatively predicted distress and anxiety disorders for adults in large families, which are quite common in Pakistan.

Conclusion

The evidence of the study interestingly finds that the prediction of the mental health of people by their distance from the epicenter depends on family size. The evidence of this study can help to provide initial indicators for mental health care providers to screen vulnerable groups in Pakistan, a populous country that continues struggling to cope with the COVID-19 pandemic.
Correction to: Survivorship and prognostic factors for pleomorphic liposarcoma: a population-based study
Authors: Wan Lu , Tu Chao , Qi Lin , Li Zhihong
Published: March 2021

An amendment to this paper has been published and can be accessed via the original article.
A review of epigenetic changes in asthma: methylation and acetylation
Authors: Sheikhpour Mojgan , Maleki Mobina , Ebrahimi Vargoorani Maryam , Amiri Vahid
Published: March 2021

Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
Reduced metagenome sequencing for strain-resolution taxonomic profiles
Authors: Snipen Lars , Angell Inga-Leena , Rognes Torbjørn , Rudi Knut
Published: March 2021

Background

Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data.

Results

We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time.

Conclusion

We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.
Practices and strategies for enhancing learning through collaboration between vocational teacher training institutions and workplaces
Authors: Arinaitwe Dinavence
Published: March 2021

The study aimed to identify and understand practices and strategies for enhancing learning through collaboration among a master’s degree in vocational pedagogy (MVP) program, vocational teacher training institutions (VTIs), and workplaces. Using in-depth semi-structured individual and focus group interviews, data were obtained from administrators, mentors, supervisors, students, teachers, officers/managers of the MVP, two VTIs, and four workplaces from central and eastern parts of Uganda. The data analysis was based on Engestrom’s cultural-historical activity theory (CHAT) particularly the concept of expansive learning for resolving contradictions within human activity systems. The findings revealed a need for involving actors in timely planning and disseminating the activity plans, increasing duration for collaborative activities as well as involving the students in the tracking of MVP activity record in fostering the institutional capacity to plan and implement collaborative activities. To strengthen the institutional capacity to supervise learning under collaborative activities, findings indicated a need to engaging workplace mentors and facilitators in learning at the MVP as well as joint supervision and collaborative development of supervision guidelines. To foster the communication between partners, the findings revealed a need to institute a collaboration focal person, providing feedback to collaborating actors and government support on a policy encouraging workplaces’ involvement in vocational training. Relationship issues revealed a need to initiate collaboration based on a signed memorandum of understanding as well as organising workshops and symposiums to equip and orient actors to MVP work methods and practices. Due to contradicting learning cultures and traditions amongst the activity systems, some of the suggested strategies required renegotiating the system especially the university before being implemented to minimise further challenges.
User profile correlation-based similarity (UPCSim) algorithm in movie recommendation system
Authors: Widiyaningtyas Triyanna , Hidayah Indriana , Adji Teguh B.
Published: March 2021

Collaborative filtering is one of the most widely used recommendation system approaches. One issue in collaborative filtering is how to use a similarity algorithm to increase the accuracy of the recommendation system. Most recently, a similarity algorithm that combines the user rating value and the user behavior value has been proposed. The user behavior value is obtained from the user score probability in assessing the genre data. The problem with the algorithm is it only considers genre data for capturing user behavior value. Therefore, this study proposes a new similarity algorithm – so-called User Profile Correlation-based Similarity (UPCSim) – that examines the genre data and the user profile data, namely age, gender, occupation, and location. All the user profile data are used to find the weights of the similarities of user rating value and user behavior value. The weights of both similarities are obtained by calculating the correlation coefficients between the user profile data and the user rating or behavior values. An experiment shows that the UPCSim algorithm outperforms the previous algorithm on recommendation accuracy, reducing MAE by 1.64% and RMSE by 1.4%.
Similarity assessment by multivariate statistics method based on the distance between biosimilar and originator
Authors: Xu Jian , Shao Zhihui , Han Xiaoxiong , Huang Yingfeng , Zou Xun , Shen Yaling
Published: March 2021

The development of biosimilar products or follow-on biologics has been flourishing in recent years because of their lower price than the originators. In this study, a multivariate data analysis method based on JMP software was proposed to assess the glycosylation pattern similarity of antibody candidates from different conditions in optimization experiments with a reference. A specific distance was generated by this method and indicated the glycoform similarity between the biosimilar and the reference. This method can be applied to analyze the similarity of other physicochemical and functional characteristics between follow-on biologics and originators. Then, the design of experimental methods can be realized to optimize the conditions of cell culture to attain similar antibody candidates. A higher concentration of GlcNAc added to the basal media made the glycan of the antibody more similar to the glycan of the reference in this study.
An organizational approach to the Philippine migration industry: recruiting, matching and tailoring migrant domestic workers
Authors: Debonneville Julien
Published: March 2021

This article analyses how organizations shape migration trajectories. More specifically, by looking at the Philippine migration industry, this ethnographic research highlights how organizations such as recruitment agencies, and governmental organizations, frame migration trajectories in terms of directionality, spatiality, but also by marketing migrants in the case of domestic workers. By looking at organization’s rationalities, it shows how migration flows have become institutionalized and ruled by organizations based on economic and protection rationalities in order to remain competitive on the global domestic labor market. Moreover, it underlines the crucial role played by these organizations to ensure the matching between the employers and the employee. This article highlights thus how agencies proceed by mobilizing migrant sociodemographic data to market skills such as docility, hardworking and flexibility. In addition, this research describes in detail how age, religion, marital status become key information mobilized by agencies in order to market migrants, meet employers’ expectations, and remain competitive on the global market of domestic labor. Finally, this article emphasizes the contribution of the organizational approach in the field of migration studies.
Correction to: Korea hypertension fact sheet 2020: analysis of nationwide population-based data
Authors:   for the Korean Society of Hypertension (KSH) – Hypertension Epidemiology Research Working Group, Kim Hyeon Chang , Cho So Mi Jemma , Lee Hokyou , Lee Hyeok-Hee , Baek Jongmin , Heo Ji Eun
Published: March 2021

An amendment to this paper has been published and can be accessed via the original article.
Telegenetics for inherited retinal diseases in the COVID-19 environment
Authors: Al-Moujahed Ahmad , Kumar Aarushi , Chemudupati Teja , Tsang Stephen H. , Mahajan Vinit B.
Published: March 2021

Inherited retinal diseases (IRDs) are visually debilitating conditions that affect families worldwide. They require extensive clinical testing, examination, and patient and family counseling, which are frequently accomplished over single-day extended clinic visits. However, the COVID-19 pandemic has limited the number of patients and staff allowed in clinics, leading to interruptions in care. We therefore developed telehealth management protocols for complete or hybrid virtual visits. The three main components of our telegenetics approach included reviewing the diagnostic tests results remotely, in-person or virtual video visits with a retina specialist, and virtual genetic testing using saliva kits. During the first 5 months of the program, telegenetic care was provided for 80 patients, including 3 international patients, and a spectrum of retinal dystrophies were diagnosed and managed. In conclusion, telegenetic virtual visits ensure continuity of care while reducing patient and provider exposure to SARS-CoV-2 and may continue and expand into other medical genetic conditions long after the pandemic.
Breast edema, from diagnosis to treatment: state of the art
Authors: Verbelen Hanne , Tjalma Wiebren , Dombrecht Dorien , Gebruers Nick
Published: March 2021

Introduction

Breast edema can arise from different etiologies; however, it is mostly seen after breast conserving surgery and/or radiotherapy. Combining breast conserving surgery and radiotherapy can cause damage to the lymphatic system and reactions to surrounding tissues, which can lead to breast edema; hereby, the breast size can increase by more than one cup size. Swelling of the breast is not the only criterion associated with breast edema. Other common criteria found in literature are peau d’orange, heaviness of the breast, skin thickening, breast pain, redness of the skin, hyperpigmented skin pores and a positive pitting sign. Despite the benefits of breast conserving surgery, breast edema can be uncomfortable, and can negatively influence quality of life in suffering patients. In contrast to lymphedema of the arm, which is well known in clinical practice and in research, breast edema is often underestimated and far less explored in literature. Currently, many aspects still need to be reviewed.

Purpose and importance to practice

This masterclass aims at providing the state of the art of breast edema for all health care workers and researchers involved in the treatment and monitoring of breast cancer patients. It includes current and future perspectives on its diagnosis, longitudinal course and treatment. Furthermore, recommendations for clinical practice and future research are discussed.

Clinical implications

It is recommended to closely monitor those patients in whom breast edema symptoms do not decline within 6 months after termination of radiotherapy and provide them with the appropriate therapy. Since evidence concerning the treatment of breast edema is currently lacking, we recommend the complex decongestive therapy (CDT) to the utmost extent, by analogy with the lymphedema treatment of the extremities. This treatment involves skin care, exercise therapy and compression. Additionally, all patients should be informed about the normal course of breast edema development.

Future research priorities

A consensus should be reached among clinicians and researchers concerning the definition, assessment methods and best treatment of breast edema. Furthermore, high quality studies are necessary to prove the effectiveness of the CDT for breast edema.
Explaining persistence in online courses in higher education: a difference-in-differences analysis
Authors: Lakhal Sawsen , Khechine Hager , Mukamurera Joséphine
Published: March 2021

The aim of this study was to verify if the UTAUT model, enriched with anxiety and factors relating to students characteristics and to the specificities of online courses, influences persistence in online courses. A theoretical model encompassing 13 variables was tested. Three moderating variables (gender, age and prior online course experience) were taken into account in the analyses. Data was collected among a sample of 759 students from Université Laval and Université de Sherbrooke using an online questionnaire. The results indicate that the main driver of persistence in online courses are: anxiety, satisfaction, effort expectancy, engagement, behavioral intention, employer encouragement, facilitating conditions and performance expectancy. The structural model was further examined according to gender, age and prior online course experience groups. Findings indicate that the model explains 21.4% to 37.1% of the variance in persistence in online courses. Moreover, as expected, the results indicated different patterns in the strength and significant relationships between groups and for the overall model, suggesting that gender, age and prior online course experience play a moderating role. The discussion links the results of this study to those of previous studies and suggests areas for improvement that could be implemented by academic administrators and instructors in order to enhance persistence in online courses.
Organic matter-driven electrical resistivity of immature lacustrine oil-prone shales
Authors: Jia Jianliang , Zhou Renjie , Liu Zhaojun , Han Xuehui , Gao Yuan
Published: March 2021

Organic matter (OM) and minerals are major particle components in lacustrine organic-rich shales. Their association and distribution control the development of the primary pore space. The response of OM-driven conduction by modifying the pore-space volume and structure in organic-rich shales of the virgin zone is still unclear. Based on a detailed study of geochemical, mineralogical, and geophysical properties from immature lacustrine oil-prone shales of the Songliao Basin (Northeast China), we have observed a novel continuous variation of electrical resistivity driven by large ranges of total-organic-carbon (TOC) content (0.64–24.51 wt%). The reduced resistivity at low TOC content ([Formula: see text]) and then enhanced resistivity at high TOC content ([Formula: see text]) are present in our immature shales. These variations in electrical resistivity are confirmed by fluid (S1) and solid organic compounds (S2). Furthermore, clay and detrital minerals in shales contribute to the variation of electrical resistivity as well as OMs at low and high TOC content. The electrical resistivity of shales is closely related to the pore-space volume and structure for the electrical flow pathway. Two resistivity trends are highlighted by pore parameters such as the pore volume, throat/pore ratio, pore diameter, and bulk density. Although reduced amounts and the arrangement of large pores for low TOC content cannot decrease the conduction, the enhanced additional clay conduction and low OM concentration reduce the resistivity of shales. Moreover, increased amounts of nonconductive fluid and solid organic compounds and the effect of OM filling on pore space during high TOC content enhance the resistivity of shales. Thus, modified minerals and pore space driven by various OMs affect the electrical resistivity of immature shales. These results improve the understanding of OM-driven conduction in shales and contribute to the evaluation of source rocks using a well-log method.
Automatic seismic phase picking based on unsupervised machine-learning classification and content information analysis
Authors: Cano Eduardo Valero , Akram Jubran , Peter Daniel B.
Published: March 2021

Accurate identification and picking of P- and S-wave arrivals is important in earthquake and exploration seismology. Often, existing algorithms are lacking in automation, multiphase classification and picking, as well as performance accuracy. We have developed a new fully automated four-step workflow for efficient classification and picking of P- and S-wave arrival times on microseismic data sets. First, time intervals with possible arrivals on waveform recordings are identified using the fuzzy c-means clustering algorithm. Second, these intervals are classified as corresponding to P-, S-, or unidentified waves using the polarization attributes of the waveforms contained within. Third, the P-, S-, and unidentified-waves arrival times are picked using the Akaike information criterion picker on the corresponding intervals. Fourth, unidentified waves are classified as P or S based on the arrivals moveouts. The application of the workflow on synthetic and real microseismic data sets indicates that it yields accurate arrival picks for high and low signal-to-noise ratio waveforms.
Velocity model building for single-offset VSP data via deformable-layer tomography: A Texas salt dome example
Authors: Wo Yukai , Zong Jingjing , Hu Hao , Zhou Hua-Wei , Stewart Robert R.
Published: March 2021

We have applied multiscale deformable-layer tomography (DLT) to build a laterally varying velocity model, using a single-offset vertical seismic profile (VSP) data set acquired for a salt proximity survey in southern Texas. The purpose of the VSP survey is to delineate the 2D salt flank using the P-wave reflections. Previous study has identified an anhydrate layer as the cap rock of the salt dome. The large impedance contrasts of this anhydrite layer generate strong downgoing P (sediment)-S (anhydrite)-P (salt) waves recorded by downhole geophones. Incidentally, the P-S-P-waves have traveltimes similar to those of the P-wave salt flank reflections, thus contaminating the imaging of the salt flank. Identifying shear-mode contamination requires an accurate velocity model of anhydrite. However, the extremely poor coverage of the single-offset VSP greatly challenges tomographic techniques to determine the lateral velocity variation. We tackle this problem using multiscale DLT, which characterizes the velocity field by a set of deformable layers. We constrain the layer velocities using the check-shot data and invert for the geometric variation. The inverted model indicates that the anhydrite layer has a “thick-thin-thick” lateral variation with offset, and the S-wave in the anhydrite layer helps in imaging the P-S-P-waves along the well track. The estimated anhydrite layer geometry is validated by the kinematic accuracies of P-waves in the data domain and P-S-P-waves in the image domain. Some in-salt dipping structures are determined by multiscale DLT as well. This field data example indicates that multiscale DLT is feasible for estimating velocities using VSP data of the single-offset situation. An accurate velocity model is the key for modeling and adaptive subtraction of the shear-mode contamination related to the salt geometry.
Understanding how overpressure affects the physical properties of sandstones
Authors: Han Tongcheng , Liu Shengbiao , Fu Li-Yun , Yan Han
Published: March 2021

Overpressure is one of the major difficulties that we have to face when exploring the deep earth. Geophysical remote sensing methods, especially seismic and electrical methods, are widely used to predict overpressure for derisking the drilling of deep boreholes in the earth’s crust. However, there are major uncertainties in relating the measured geophysical parameters to the physical properties of crustal rocks, needed for reliable overpressure estimation. We address this knowledge gap through dedicated laboratory measurements of elastic velocity, electrical conductivity, and porosity with increasing pore pressure and the analyses and interpretation of the experimental results. We find a linear increase in the porosity and an exponential increase and decrease in the electrical conductivity and compressional wave velocity, respectively, with the increasing pore pressure. We also find an exponential reduction in the cementation exponent and effective pore aspect ratio (PAR) inverted from the pore pressure induced electrical conductivity and compressional wave velocity, respectively. We further determine that electrical and elastic rock properties are affected more significantly by the changing cementation exponent and effective PAR by increasing the pore pressure rather than by dilating porosity. The results not only strengthen our understanding of the influencing mechanism of overpressure on the physical properties of crustal rocks, but also provide new insights for the more reliable detection of overpressure zones from geophysical remote sensing.
Seismic attributes for characterization and prediction of carbonate faulted karst reservoirs in the Tarim Basin, China
Authors: Wang Li , Yang Ruizhao , Li Dewei , Meng Lingbin , Xiao Zhiwei
Published: March 2021

An ultradeep, faulted karst reservoir of Ordovician carbonate was discovered in the Shunbei area of the Tarim Basin. Fractured-cavity reservoirs buried beneath the large thickness of upper Ordovician mudstone were formed along the fault-karst belts. The hydrocarbon accumulation in these reservoirs is controlled by the fault system, and the oil-gas accumulation was affected by karstification and hydrothermal reformation. Previous studies and 2D modeling revealed that the reservoirs had “bright spot” amplitude responses like “string beads,” and they have developed along the strike-slip faults. However, describing such a complex fault-controlled karst system is still a difficult problem that has not been well addressed. We have sought to instruct the attribute expression of faulted karst reservoirs in the northern part of the Tarim Basin. We applied coherence and fault likelihood (FL) seismic attributes to image faults and fractures zones. We then used a trend analysis method to calculate the residual impedance from the impedance of the acoustic inversion, using the fact that residual impedance has higher lateral resolution in reservoir predictions. Finally, we integrated the coherence, FL, and residual impedance attributes into a new seismic attribute, the “fault-vuggy body,” with a certain fusion coefficient. The fault-vuggy body attribute establishes a connection between faults and karst cavities. This method could help in the characterization and prediction of carbonate faulted karst reservoirs. Available drilling data were used to validate that the fused fault-vuggy body attribute was an effective reservoir prediction method. As the seismic sections and slices along the layer help delineate, the distribution of bright spots and strike-slip faults indicates that the main strike-slip fault zones are the most favorable reservoirs in the Shunbei Oil and Gas Field.
Mutations in BRCA1/2 and Other Panel Genes in Patients With Metastatic Breast Cancer —Association With Patient and Disease Characteristics and Effect on Prognosis
Authors: Fasching Peter A. , Yadav Siddhartha , Hu Chunling , Wunderle Marius , Häberle Lothar , Hart Steven N. , Rübner Matthias , Polley Eric C. , Lee Kun Y. , Gnanaolivu Rohan D. , Hadji Peyman , Hübner Hanna , Tesch Hans , Ettl Johannes , Overkamp Friedrich , Lux Michael P. , Ekici Arif B. , Volz Bernhard , Uhrig Sabrina , Lüftner Diana , Wallwiener Markus , Müller Volkmar , Belleville Erik , Untch Michael , Kolberg Hans-Christian , Beckmann Matthias W. , Reis André , Hartmann Arndt , Janni Wolfgang , Wimberger Pauline , Taran Florin-Andrei , Fehm Tanja N. , Wallwiener Diethelm , Brucker Sara Y. , Schneeweiss Andreas , Hartkopf Andreas D. , Couch Fergus J.
Published: March 2021

PURPOSE

Among patients with metastatic breast cancer (mBC), the frequency of germline mutations in cancer susceptibility genes and the clinical relevance of these mutations are unclear. In this study, a prospective cohort of patients with mBC was used to determine mutation rates for breast cancer (BC) predisposition genes, to evaluate the clinical characteristics of patients with mutations, and to assess the influence of mutations on patient outcome.

PATIENTS AND METHODS

Germline DNA from 2,595 patients with mBC enrolled in the prospective PRAEGNANT registry was evaluated for mutations in cancer predisposition genes. The frequencies of mutations in known BC predisposition genes were compared with results from a prospective registry of patients with nonmetastatic BC sequenced using the same QIAseq method and with public reference controls. Associations between mutation status and tumor characteristics, progression-free survival, and overall survival were assessed.

RESULTS

Germline mutations in 12 established BC predisposition genes (including BRCA1 and BRCA2) were detected in 271 (10.4%) patients. A mutation in BRCA1 or BRCA2 was seen in 129 patients (5.0%). BRCA1 mutation carriers had a higher proportion of brain metastasis (27.1%) compared with nonmutation carriers (12.8%). Mutations were significantly enriched in PRAEGNANT patients with mBC compared with patients with nonmetastatic BC (10.4% v 6.6%, P < .01). Mutations did not significantly modify progression-free survival or overall survival for patients with mBC.

CONCLUSION

Multigene panel testing may be considered in all patients with mBC because of the high frequency of germline mutations in BRCA1/2 and other BC predisposition genes. Although the prognosis of mutation carriers and nonmutation carriers with mBC was similar, differences observed in tumor characteristics have implications for treatment and for future studies of targeted therapies.
Barriers to Prescribing Targeted Therapies for Patients With NSCLC With Highly Actionable Gene Variants in the Veterans Affairs National Precision Oncology Program
Authors: Vashistha Vishal , Armstrong Jenna , Winski David , Poonnen Pradeep J. , Hintze Bradley , Price Meghan , Snowdon Jane L. , Weeraratne Dilhan , Brotman David , Jackson Gretchen P. , Kelley Michael J.
Published: March 2021

PURPOSE:

Next-generation sequencing (NGS) gene panels are frequently completed for patients with advanced non–small-cell lung cancer (NSCLC). Patients with highly actionable gene variants have improved outcomes and reduced toxicities with the use of corresponding targeted agents. We sought to identify barriers to targeted agent use within the Veterans Health Affairs' National Precision Oncology Program (NPOP).

METHODS:

A retrospective evaluation of patients with NSCLC who underwent NGS multigene panels through NPOP between July 2015 and February 2019 was conducted. Patients who were assigned level 1 or 2A evidence for oncogenic gene variants by an artificial intelligence offering (IBM Watson for Genomics [WfG]) and NPOP staff were selected. Antineoplastic drug prescriptions and provider notes were reviewed. Reasons for withholding targeted treatments were categorized.

RESULTS:

Of 1,749 patients with NSCLC who successfully underwent NGS gene panel testing, 112 (6.4%) patients were assigned level 1 and/or 2A evidence for available targeted treatments by WfG and NPOP staff. All highly actionable gene variants were within ALK, BRAF, EGFR, ERBB2, MET, RET, and ROS1. Of these, 36 (32.1%) patients were not prescribed targeted agents. The three most common reasons were (1) patient did not carry a diagnosis of metastatic disease (33.3%), (2) treating provider did not comment on the NGS results (25.0%), and (3) provider felt that patient could not tolerate therapy (19.4%). No patients were denied access to level 1 or 2A targeted drugs because of rejection of a nonformulary drug request.

CONCLUSION:

A substantial minority of patients with NSCLC bearing highly actionable gene variants are not prescribed targeted agents. Further provider- and pathologist-directed educational efforts and implementation of health informatics systems to provide real-time decision support for test ordering and interpretation are needed.
Against the New Normal
Authors: Cubitt Sean
Published: March 2021

COVID-19 is now part of the resources out of which any future must be made. The temptation is to curl back into private misery and fatalism. The opportunity is to further the design of neonationalist, neoliberal returns to pre-1917 norms of extreme wealth, extreme poverty, and unmitigated exploitation of technical and ecological resources. The challenge is to build a future of public health, wealth, education, and environmental justice.
The Power of Social Pensions: Evidence from China's New Rural Pension Scheme
Authors: Huang Wei , Zhang Chuanchuan
Published: March 2021

This paper utilizes the county-by-county rollout of China's New Rural Pension Scheme (NRPS) and finds that, among age-eligible people, the pension scheme leads to higher household income and food expenditure, less farmwork, better health, and lower mortality. In addition, the NRPS shifts age-ineligible adults from farmwork to nonfarmwork but does not significantly affect their income, expenditure, or health. No significant evidence shows that the NRPS affects private transfers or health behaviors. These findings provide relevant evidence of the impacts of social pensions on individual behaviors and welfare for developing countries today and developed countries in the past. (JEL H55, J14, I38, O18, P25, P36)
MIREyA: a computational approach to detect miRNA-directed gene activation
Authors: Elizarova Anna , Ozturk Mumin , Guler Reto , Medvedeva Yulia A.
Published: March 2021

Emerging studies demonstrate the ability of microRNAs (miRNAs) to activate genes via different mechanisms. Specifically, miRNAs may trigger an enhancer promoting chromatin remodelling in the enhancer region, thus activating the enhancer and its target genes. Here we present MIREyA, a pipeline developed to predict such miRNA-gene-enhancer trios based on an expression dataset which obviates the need to write custom scripts. We applied our pipeline to primary murine macrophages infected by Mycobacterium tuberculosis (HN878 strain) and detected Mir22, Mir221, Mir222, Mir155 and Mir1956, which could up-regulate genes related to immune responses. We believe that MIREyA is a useful tool for detecting putative miRNA-directed gene activation cases. MIREyA is available from: https://github.com/veania/MIREyA
Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim
Authors: Menardo Fabrizio , Rutaihwa Liliana K. , Zwyer Michaela , Borrell Sonia , Comas Iñaki , Conceição Emilyn Costa , Coscolla Mireia , Cox Helen , Joloba Moses , Dou Horng-Yunn , Feldmann Julia , Fenner Lukas , Fyfe Janet , Gao Qian , García de Viedma Darío , Garcia-Basteiro Alberto L. , Gygli Sebastian M. , Hella Jerry , Hiza Hellen , Jugheli Levan , Kamwela Lujeko , Kato-Maeda Midori , Liu Qingyun , Ley Serej D. , Loiseau Chloe , Mahasirimongkol Surakameth , Malla Bijaya , Palittapongarnpim Prasit , Rakotosamimanana Niaina , Rasolofo Voahangy , Reinhard Miriam , Reither Klaus , Sasamalo Mohamed , Silva Duarte Rafael , Sola Christophe , Suffys Philip , Batista Lima Karla Valeria , Yeboah-Manu Dorothy , Beisel Christian , Brites Daniela , Gagneux Sebastien
Published: March 2021

Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied.

Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection.

Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates.

Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.
Mechanism, spectrum, consequences and management of hyponatremia in tuberculous meningitis
Authors: Misra Usha K. , Kalita Jayantee ,   Tuberculous Meningitis International Research Consortium
Published: March 2021

Hyponatremia is the commonest electrolyte abnormality in hospitalized patients and is associated with poor outcome. Hyponatremia is categorized on the basis of serum sodium into severe (< 120 mEq/L), moderate (120-129 mEq/L) and mild (130-134mEq/L) groups. Serum sodium has an important role in maintaining serum osmolality, which is maintained by the action of antidiuretic hormone (ADH) secreted from the posterior pituitary, and natriuretic peptides such as atrial natriuretic peptide and brain natriuretic peptide. These peptides act on kidney tubules via the renin angiotensin aldosterone system. Hyponatremia <120mEq/L or a rapid decline in serum sodium can result in neurological manifestations, ranging from confusion to coma and seizure. Cerebral salt wasting (CSW) and syndrome of inappropriate secretion of ADH (SIADH) are important causes of hyponatremia in tuberculosis meningitis (TBM). CSW is more common than SIADH. The differentiation between CSW and SIADH is important because treatment of one may be detrimental for the other; evidence of hypovolemia in CSW and euvolemia or hypervolemia in SIADH is used for differentiation. In addition, evidence of dehydration, polyuria, negative fluid balance as assessed by intake output chart, weight loss, laboratory evidence and sometimes central venous pressure are helpful in the diagnosis of these disorders. Volume contraction in CSW may be more protracted than hyponatremia and may contribute to border zone infarctions in TBM. Hyponatremia should be promptly and carefully treated by saline and oral salt, while 3% saline should be used in severe hyponatremia with coma and seizure. In refractory patients with hyponatremia, fludrocortisone helps in early normalization of serum sodium without affecting polyuria or functional outcome. In SIADH, V2 receptor antagonist conivaptan or tolvaptan may be used if the patient is not responding to fluid restriction. Fluid restriction in SIADH has not been found to be beneficial in TBM and should be avoided.
Occasional Speech Acts
Authors: Korobkina N.
Published: March 2021

Speech acts are considered as minimal units of speech activity and as a three-component structure consisting of ilocution, locution and perlocution. Varieties of speech acts are distinguished depending on a statement illocutionary purpose: assertives, commissives, directives, expressives, declarations (according to J. Searle). The possibility of these speech acts occasional nature is emphasized. A speech act occasionality is achieved by using a nomination in a corresponding communicative situation. This nomination has novelty over time and outside the conditions of its speech generation, the absence of a wide (frequency) situational functioning, created on occasion, often with an author’s intention. Specific examples of communicative situations containing a kind of an occasional speech act are given. It is noted that occasional speech acts are a key point in the study of a pragmatic approach to language phenomena, when a producer intensity – to produce a certain speech action – comes to the fore.
Problems of Perception of Linguistic Landscape
Authors: Goncharova Lyubov
Published: March 2021

The article describes the problems of perception of linguistic landscape. The concept of linguistic landscape is clarified, its components are described, and the communicative impact of the urban environment on a person is evaluated. The author identifies the communicative factors and linguocultural elements of the linguistic landscape. The communicative elements of the urban environment are analyzed on the example of Kaliningrad region photo materials collected in the framework of the scientific project "Linguistic landscape as a mechanism of state policy: socio-cultural and communicative aspects".
Monitoring observations of meteor echo at the EKB ISTP SB RAS radar: algorithms, validation, statistics
Authors: Fedorov Roman , Berngardt Oleg
Published: March 2021

The paper considers the implementation of algorithms for automatic search for signals scattered by meteor trails according to EKB ISTP SB RAS radar data. In general, the algorithm is similar to the algorithms adopted in specialized meteor systems. The algorithm is divided into two stages: detecting a meteor echo and determining its parameters. We show that on the day of the maximum Geminid shower, December 13, 2016, the scattered signals detected by the algorithm are foreshortening and correspond to scattering by irregularities extended in the direction of the meteor shower radiant. This confirms that the source of the signals detected by the algorithm is meteor trails. We implement an additional program for indirect trail height determination. It uses a decay time of echo and the NRLMSIS-00 atmosphere model to estimate the trail height. The dataset from 2017 to 2019 is used for further testing of the algorithm. We demonstrate a correlation in calculated Doppler velocity between the new algorithm and FitACF. We present a solution of the inverse problem of reconstructing the neutral wind velocity vector from the data obtained by the weighted least squares method. We compare calculated speeds and directions of horizontal neutral winds, obtained in the three-dimensional wind model, and the HWM-14 horizontal wind model. The algorithm allows real-time scattered signal processing and has been put into continuous operation at the EKB ISTP SB RAS radar.
On possible relation of earthquakes with the sign change of the interplanetary magnetic field radial component
Authors: Zotov Oleg , Guglielmi Anatol , Silina Aleksandra
Published: March 2021

This work is devoted to an experimental study of the possible relationship between earthquakes and interplanetary magnetic field (IMF) variations. For the analysis, we use world and regional catalogs of earthquakes and a catalog containing data on the IMF sector structure for several decades. The main methodological technique consists in a comparative analysis of the occurrence rate of earthquakes on the days when Earth crosses the boundary between IMF sectors with the days when Earth is inside the sector. The sign of the IMF radial component is utilized as an indicator of the events on which the oscillation mode of Earth's magnetosphere depends. The sign reversal signals the probable crossing of the boundary between the IMF sectors by Earth, or, in other words, the crossing of the heliospheric current sheet by Earth. The hypothesis about the relationship between IMF variations and seismic activity is that IMF fluctuations, penetrating into the magnetosphere, excite ULF electromagnetic oscillations in the magnetosphere, which, in principle, can affect the physical processes in upcoming earthquake sources. We have found a weak, but statistically significant relationship between IMF variations and seismic activity. We also consider other IMF parameters that control ultra-low-frequency oscillations of the geomagnetic field.
Healthcare Encounter and Financial Impact of COVID‐19 on Children's Hospitals
Authors: Synhorst David C , Bettenhausen Jessica L , Hall Matt , Thurm Cary , Shah Samir S , Auger Katherine A , Williams Derek J , Morse Rustin , Berry Jay G
Published: March 2021

Children's hospitals responded to COVID‐19 by limiting nonurgent healthcare encounters, conserving personal protective equipment, and restructuring care processes to mitigate viral spread. We assessed year‐over‐year trends in healthcare encounters and hospital charges across US children's hospitals before and during the COVID‐19 pandemic. We performed a retrospective analysis, comparing healthcare encounters and inflation‐adjusted charges from 26 tertiary children's hospitals reporting to the PROSPECT database from February 1 to June 30 in 2019 (before the COVID‐19 pandemic) and 2020 (during the COVID‐19 pandemic). All children's hospitals experienced similar trends in healthcare encounters and charges during the study period. Inpatient bed‐days, emergency department visits, and surgeries were lower by a median 36%, 65%, and 77%, respectively, per hospital by the week of April 15 (the nadir) in 2020 compared with 2019. Across the study period in 2020, children's hospitals experienced a median decrease of $276 million in charges.
Third-Party Consequences of Changes in Managerial Fiduciary Duties: The Case of Auditors’ Going Concern Opinions
Authors: Tan Liang , Ramalingegowda Santhosh , Yu Yong
Published: March 2021

This study examines the effect of managerial fiduciary duties on the likelihood of firms receiving going concern (GC) opinions from their auditors. We exploit an influential 1991 legal ruling that expanded fiduciary duties of corporate directors and officers in favor of creditors for near-insolvent Delaware firms. Our difference-in-differences test reveals an increase in GC opinions following the ruling for near-insolvent Delaware firms. Further tests indicate an increase in type I audit opinion errors and no change in audit risk after the ruling. Additional analysis shows that, after the ruling, near-insolvent Delaware firms are less likely to dismiss their auditors following the receipt of a GC report. Overall, our findings are consistent with managers and directors with increased fiduciary duties toward creditors exerting less pressure on auditors and allowing them to reveal more GC opinions. Our results highlight important third-party consequences of changes in managerial fiduciary duties.

This paper was accepted by Shiva Rajagopal, accounting.
A Large-Scale Optimization Model for Replicating Portfolios in the Life Insurance Industry
Authors: Adelmann Maximilian , Fernandez-Arjona Lucio , Mayer Janos , Schmedders Karl
Published: March 2021

Replicating Portfolios for Economic Capital Calculations
Design of experiments for the optimization of SOFI super-resolution microscopy imaging
Authors: Cevoli Dario , Vitale Raffaele , Vandenberg Wim , Hugelier Siewert , Van den Eynde Robin , Dedecker Peter , Ruckebusch Cyril
Published: March 2021

Super-resolution optical fluctuation imaging (SOFI) is a well-known super-resolution technique appreciated for its versatility and broad applicability. However, even though an extended theoretical description is available, it is still not fully understood how the interplay between different experimental parameters influences the quality of a SOFI image. We investigated the relationship between five experimental parameters (measurement time, on-time ton, off-time toff, probe brightness, and out of focus background) and the quality of the super-resolved images they yielded, expressed as Signal to Noise Ratio (SNR). Empirical relationships were modeled for second- and third-order SOFI using data simulated according to a D-Optimal design of experiments, which is an ad-hoc design built to reduce the experimental load when the total number of trials to be conducted becomes too high for practical applications. This approach proves to be more reliable and efficient for parameter optimization compared to the more classical parameter by parameter approach. Our results indicate that the best image quality is achieved for the fastest emitter blinking (lowest ton and toff), lowest background level, and the highest measurement duration, while the brightness variation does not affect the quality in a statistically significant way within the investigated range. However, when the ranges spanned by the parameters are constrained, a different set of optimal conditions may arise. For example, for second-order SOFI, we identified situations in which the increase of toff can be beneficial to SNR, such as when the measurement duration is long enough. In general, optimal values of ton and toff have been found to be highly dependent from each other and from the measurement duration.