bluuebunny/crossref_metadata_2025 huggingface dataset:
Protection Generated by Prior Exposure to Pathogens Depends on both Priming and Challenge Dose
Authors: Weitzman Chava L. , Ceja Guadalupe , Leon Ariel E. , Hawley Dana M.
Published: January 2022

Free-living hosts encounter pathogens at a wide range of frequencies and concentrations, including low doses that are largely aclinical, creating a varied landscape of exposure history and reinfection likelihood. While several studies show that higher priming doses result in stronger immunological protection against reinfection, it remains unknown how the reinfection challenge dose and priming dose interact to determine the likelihood and severity of reinfection.
The Conceptualization of Quantitative Reasoning among Introductory Biology Faculty
Authors: Cleveland Ann , Sezen-Barrie Asli , Marbach-Ad Gili
Published: January 2022

Quantitative reasoning (QR) skills have become a critical competency for undergraduate biology students, and recommendations for curricular reform urge QR training throughout undergraduate biology programs. Much research has been directed at course design, pedagogy, and student challenges in QR, but less research has been directed toward understanding how biology faculty conceptualize the QR skills they are called upon to teach.
Herpesviruses and Inflammasomes: One Sensor Does Not Fit All
Authors: Kumar Ayush , Stavrakis Georgia , Karaba Andrew H.
Published: January 2022

Herpesviruses are ubiquitous double-stranded DNA viruses that cause lifelong infections and are associated with a variety of diseases. While they have evolved multiple mechanisms to evade the immune system, they are all recognized by the innate immune system, which can lead to both localized and systemic inflammation.
Acyl-Coenzyme A Synthetase Long-Chain Family Member 4 Is Involved in Viral Replication Organelle Formation and Facilitates Virus Replication via Ferroptosis
Authors: Kung Yu-An , Chiang Huan-Jung , Li Mei-Ling , Gong Yu-Nong , Chiu Hsin-Ping , Hung Chuan-Tien , Huang Peng-Nien , Huang Sheng-Yu , Wang Pei-Yu , Hsu Tsu-An , Brewer Gary , Shih Shin-Ru
Published: January 2022

We provide the first evidence for the role of ACSL4 in enterovirus replication organelle formation. Moreover, both enteroviruses and coronaviruses induce ferroptosis via ACSL4. These findings establish a novel regulatory mechanism for viral replication. The inhibition of ACSL4 by ferroptosis inhibitors can reduce viral yields of enteroviruses and coronaviruses, including SARS-CoV-2, implying that ACSL4-mediated ferroptosis is a promising therapeutic target for viral diseases.
Genetic Dissection of Antibiotic Adjuvant Activity
Authors: Bailey J. , Gallagher L. , Barker W. T. , Hubble V. B. , Gasper J. , Melander C. , Manoil C.
Published: January 2022

One strategy to confront the antibiotic resistance crisis is through the development of adjuvant compounds that increase the efficacy of established drugs. A key step in the development of a natural product adjuvant as a drug is identifying the resistance process it undermines to enhance antibiotic activity.
Human Nasal Epithelial Cells Sustain Persistent SARS-CoV-2 Infection
In Vitro
, despite Eliciting a Prolonged Antiviral Response
Authors: Gamage Akshamal M. , Tan Kai Sen , Chan Wharton O. Y. , Lew Zhe Zhang Ryan , Liu Jing , Tan Chee Wah , Rajagopalan Deepa , Lin Quy Xiao Xuan , Tan Le Min , Venkatesh Prasanna Nori , Ong Yew Kwang , Thong Mark , Lin Raymond Tzer Pin , Prabhakar Shyam , Wang De Yun , Wang Lin-Fa
Published: January 2022

Increasing medical attention has been drawn to the persistence of symptoms (long-COVID syndrome) or live virus shedding from subsets of COVID-19 patients weeks to months after the initial onset of symptoms.
In vitro
approaches to model viral or symptom persistence are needed to fully dissect the complex and likely varied mechanisms underlying these clinical observations. We show that
in vitro
differentiated human NECs are persistently infected with SARS-CoV-2 for up to 28 dpi.
High-Level Acquisition of Maternal Oral Bacteria in Formula-Fed Infant Oral Microbiota
Authors: Kageyama Shinya , Furuta Michiko , Takeshita Toru , Ma Jiale , Asakawa Mikari , Yamashita Yoshihisa
Published: January 2022

Acquisition of oral bacteria during infancy can affect the subsequent formation of stable oral microbiota. This study focused on the mother-to-infant transmission of oral bacteria, a major acquisition route of infant oral microbiota, and demonstrated that most infants acquired oral bacteria from their biological mother even at the single-nucleotide level.
Unmasking of CgYor1-Dependent Azole Resistance Mediated by Target of Rapamycin (TOR) and Calcineurin Signaling in Candida glabrata
Authors: Kumari Sonam , Kumar Mohit , Esquivel Brooke D. , Wasi Mohd , Pandey Ajay Kumar , Kumar Khandelwal Nitesh , Mondal Alok K. , White Theodore C. , Prasad Rajendra , Gaur Naseem A.
Published: January 2022

The increasing incidence of
Candida glabrata
infections in the last 40 years is a serious concern worldwide. These infections are usually associated with intrinsic azole resistance and increasing echinocandin resistance.
The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids
Authors: Rajer Fredrika , Sandegren Linus
Published: January 2022

Multiresistance plasmids are one of the main drivers of antibiotic resistance development and spread. Their evolutionary success through the accumulation and mobilization of resistance genes is central to resistance evolution.
Cross-Reactive Antibody Responses against Nonpoliovirus Enteroviruses
Authors: Rosenfeld Amy B. , Shen Edmund Qian Long , Melendez Michaela , Mishra Nischay , Lipkin W. Ian , Racaniello Vincent R.
Published: January 2022

Enteroviruses (EVs) are common human pathogens. Although infection with EVs leads to cross-reactive antibodies, the clinical relevance of these antibodies is unclear given the estimated incidence of EV infections in the general population of one per year.
CRISPR Interference Reveals That All-
Trans
-Retinoic Acid Promotes Macrophage Control of Mycobacterium tuberculosis by Limiting Bacterial Access to Cholesterol and Propionyl Coenzyme A
Authors: Babunovic Gregory H. , DeJesus Michael A. , Bosch Barbara , Chase Michael R. , Barbier Thibault , Dickey Amy K. , Bryson Bryan D. , Rock Jeremy M. , Fortune Sarah M.
Published: January 2022

Tuberculosis, caused by the bacterium
Mycobacterium tuberculosis
, is a leading cause of death due to infectious disease. Improving the immune response to tuberculosis holds promise for fighting the disease but is limited by our lack of knowledge as to how the immune system kills
M. tuberculosis
.
Vaccinating Children against COVID-19: Commentary and Mathematical Modeling
Authors: Hawkes Michael T. , Good Michael F.
Published: January 2022

Countries have recently begun implementation of childhood vaccination against SARS-CoV-2 with the Pfizer/BioNTech mRNA vaccine in children 5 to 11 years of age. Because SARS-CoV-2 disease severity is remarkably age dependent, vaccinating children may have modest public health benefits, relative to the unequivocal benefit of vaccinating vulnerable older adults.
Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes
Authors: Moller Abraham G. , Petit Robert A. , Read Timothy D.
Published: January 2022

Staphylococcus aureus
is a widespread, hospital- and community-acquired pathogen that is commonly antibiotic resistant. It causes diverse diseases affecting both the skin and internal organs.
Eruption dynamics leading to a volcanic thunderstorm—The January 2020 eruption of Taal volcano, Philippines
Authors: Van Eaton Alexa R. , Smith Cassandra M. , Pavolonis Michael , Said Ryan
Published: January 2022

Advances in global lightning detection have provided novel ways to characterize explosive volcanism. However, researchers are still at the early stages of understanding how volcanic plumes become electrified on different spatial and temporal scales. We deconstructed the phreatomagmatic eruption of Taal volcano (Philippines) on 12 January 2020 to investigate the origin of its powerful volcanic thunderstorm. Satellite analysis indicated that the water-rich plume rose >10 km high before creating lightning detected by Vaisala's global lightning data set (GLD360). Flash rates increased with plume heights and cloud expansion over time, producing >70 flashes min–1. Photographs revealed a highly electrified region at the base of the umbrella cloud, where we infer strong convective updrafts and icy collisions enhanced the electrical activity. These findings inform a conceptual model with overlapping regimes of charge generation in wet eruptions—initially due to ash particle collisions near the vent, followed by thunderstorm-like electrification in icy regions of the upper plume. Despite the wide reach of Taal's ash cloud, most of the lightning occurred within 20–30 km of the volcano, producing thousands of hazardous cloud-to-ground flashes over a densely populated area. The eruption demonstrates that volcanic lightning can pose a hazard in its own right, embedded within the broader hazards of explosive volcanism in an urban setting.
Case of retained guide wires traversing anatomical boundaries with neurological and cardiac morbidity
Authors: Omoregbee Benjamin , Haqzad Yama , Zicho David , Ngaage Dumbor
Published: January 2022

A 69-year-old woman with a history of multiple hospital attendances for cardiac and neurological symptoms, presented with multifocal cerebral infarcts due to embolisation from retained guide wires and was referred for retrieval of two wires. One was intracardiac and the other had migrated through major vascular structures, breeching anatomical boundaries. Just before surgery, she half-expectorated a 35 cm wire that was removed with a video laryngoscope. Three days later, the second wire had traversed the right ventricular myocardium in an attempt to exteriorise, and a 7 cm wire was removed by emergency left anterior mini-thoracotomy. Her recovery was uneventful.
COVID-19 in two children with new-onset diabetes: case reports
Authors: Lança Ana , Rodrigues Cláudia , Diamantino Catarina , Fitas Ana Laura
Published: January 2022

Delayed diagnosis, low socioeconomic status and infection have been associated with diabetic ketoacidosis (DKA) at type 1 diabetes mellitus presentation. A teenager from a low socioeconomic status family, with longstanding weight loss, polyphagia, polyuria, vomiting and abdominal pain, attended the emergency department, also complaining of anosmia and odynophagia. He was diagnosed with COVID-19 and new-onset DKA. The second child had 2 weeks of diabetes symptoms and was admitted with new-onset mild DKA. SARS-CoV-2 RT-PCR test was positive, although asymptomatic. Persistent hyperglycaemia with high insulin requirements was a common feature to both patients. Both cases support that SARS-CoV-2 may have an association with rapidly increasing insulin daily needs. In case one, not only fear of COVID-19 delayed hospital attendance but also the setting of a low socioeconomic status family appears to have enhanced the risk for late diagnosis and challenging disease management.
Profiling the tackle and its injury characteristics in premier New Zealand club rugby union players over a complete season
Authors: Takamori Sohei , Hamlin Michael John , King Doug , Hume Patria A , Tachikawa Kosuke , Koyanagi Ryuta , Yoshida Toru
Published: January 2022

Objectives

RugbySmart is a safe tackle technique education programme. Our objective was to identify whether the RugbySmart-recommended safe tackle technique was exhibited by club rugby players and whether tackle-related injuries showed poor tackle technique characteristics.

Methods

The prospective cohort design enabled 28 senior club based amateur male rugby union players from New Zealand to be followed over 18 matches in the 2017 rugby season. Game video analysis by three analysts provided categorisation of tackle technique into type, approach, foot contact, leading foot and rear foot position, face and head position. Injuries were diagnosed by the same sports medicine physician.

Results

In the 18 matches, 28 players completed a combined total of 3006 tackles, with only six tackle-related injuries sustained. Notable findings included: (1) forwards complete more tackles than backs; (2) shoulder tackles were the most prevalent tackle; (3) good tackle technique as promoted by RugbySmart was demonstrated in 57.9% of all tackles and (4) of the six tackle-related injuries, two occurred despite RugbySmart desired tackle techniques.

Conclusion

This is the first study to investigate whether players were performing the recommended ‘safe tackle technique’ proposed by New Zealand Rugby’s RugbySmart programme. As two of six tackle-related injuries occurred despite the RugbySmart preferred technique being performed, further technique analysis and a larger sample are needed to determine what techniques reduce risk of injury during tackles. As only 57.9% of tackles were performed with RugbySmart head and foot positions, further research and education regarding tackle technique recommendations are needed.
Military provision of maternal care in humanitarian and disaster relief operations
Authors: Bishop Alexander , Dewhurst H
Published: January 2022

With three-quarters of the 80 million people in need of humanitarian assistance being women or children in 2014, maternal care makes up a significant burden of medical care in humanitarian assistance and disaster relief operations. Due to lack of infrastructure and up to 80% of these displaced people being located in developing countries, mothers are often extremely vulnerable to disease, abuse and malnutrition. This can lead to late presentations of severe disease and birthing complications that would usually be easily manageable, but are far more complex due to the physical condition of the mother and lack of available resources. The British Armed Forces are often involved in humanitarian assistance and disaster relief either intentionally or due to the nature of the operations they carry out. However, it is not always possible to predict the requirement of maternal care. This humanitarian special edition article focuses on the factors impacting the maternal patient in a humanitarian environment, also looking at common pathologies and ways of managing these in a Role 1 facility. This is a paper commissioned as a part of the Humanitarian and Disaster Relief Operations special issue ofBMJ Military Health.
Simplified data science approach to extract social and behavioural determinants: a retrospective chart review
Authors: Teng Andrew , Wilcox Adam
Published: January 2022

Objectives

We aim to extract a subset of social factors from clinical notes using common text classification methods.

Design

Retrospective chart review.

Setting

We collaborated with a local level I trauma hospital located in an underserved area that has a housing unstable patient population of about 6.5% and extracted text notes related to various social determinants for acute care patients.

Participants

Notes were retrospectively extracted from 43 798 acute care patients.

Methods

We solely use open source Python packages to test simple text classification methods that can potentially be easily generalisable and implemented. We extracted social history text from various sources, such as admission and emergency department notes, over a 5-year timeframe and performed manual chart reviews to ensure data quality. We manually labelled the sentiment of the notes, treating each text entry independently. Four different models with two different feature selection methods (bag of words and bigrams) were used to classify and predict housing stability, tobacco use and alcohol use status for the extracted clinical text.

Results

From our analysis, we found overall positive results and metrics in applying open-source classification techniques; the accuracy scores were 91.2%, 84.7%, 82.8% for housing stability, tobacco use and alcohol use, respectively. There were many limitations in our analysis including social factors not present due to patient condition, multiple copy-forward entries and shorthand. Additionally, it was difficult to translate usage degrees for tobacco and alcohol use. However, when compared with structured data sources, our classification approach on unstructured notes yielded more results for housing and alcohol use; tobacco use proved less fruitful for unstructured notes.
Determining feasibility of incorporating consumer engagement into implementation activities: study protocol of a hybrid effectiveness-implementation type II pilot
Authors: Woodward Eva N , Willging Cathleen , Landes Sara J , Hausmann Leslie R M , Drummond Karen L , Ounpraseuth Songthip , Ball Irenia A , Kirchner JoAnn E
Published: January 2022

Introduction

Implementation researchers could draw from participatory research to engage patients (consumers of healthcare) in implementation processes and possibly reduce healthcare disparities. There is a little consumer involvement in healthcare implementation, partially because no formal guidance exists. We will create and pilot a toolkit of methods to engage consumers from the US’ Veterans Health Administration (VHA) in selecting and tailoring implementation strategies. This toolkit, Consumer Voice, will provide guidance on what, when, where, how and why an implementer might engage consumers in implementing treatments. We will pilot the toolkit by implementing Safety Planning Intervention for suicide prevention with rural veterans, a population with suicide disparities. Safety Planning Intervention is effective for reducing suicidal behaviours.

Methods and analysis

In Aim 1, we will use participatory approaches and user-centred design to develop Consumer Voice and its methods. In Aim 2, we will pilot Consumer Voice by implementing the Safety Planning Intervention in two clinics serving rural VHA patients. One site will receive a current implementation strategy (Implementation Facilitation) only; the second will receive Implementation Facilitation plus Consumer Voice. We will use mixed methods to assess feasibility and acceptability of Consumer Voice. We will compare sites on preliminary implementation (reach, adoption, fidelity) and clinical outcomes (depression severity, suicidal ideation, suicidal behaviour). In Aim 3, we will evaluate Aim 2 outcomes at 20 months to assess sustained impact. We will gather qualitative data on sustainability of the Safety Planning Intervention.

Ethics and dissemination

These studies are overseen by the Institutional Review Board at the Central Arkansas Veterans Healthcare System. We plan to use traditional academic modalities of dissemination (eg, conferences, publications). We plan to disseminate findings through meetings with other trainers in implementation practice so they may adopt Consumer Voice. We plan to share results with local community boards.
External validation and recalibration of an incidental meningioma prognostic model – IMPACT: protocol for an international multicentre retrospective cohort study
Authors: Islim Abdurrahman I , Millward Christopher P , Piper Rory J , Fountain Daniel M , Mehta Shaveta , Kolamunnage-Dona Ruwanthi , Ali Usama , Koszdin Shelli Diane , Georgious Theo , Mills Samantha J , Brodbelt Andrew R , Mathew Ryan K , Santarius Thomas , Jenkinson Michael D
Published: January 2022

Introduction

Due to the increased use of CT and MRI, the prevalence of incidental findings on brain scans is increasing. Meningioma, the most common primary brain tumour, is a frequently encountered incidental finding, with an estimated prevalence of 3/1000. The management of incidental meningioma varies widely with active clinical-radiological monitoring being the most accepted method by clinicians. Duration of monitoring and time intervals for assessment, however, are not well defined. To this end, we have recently developed a statistical model of progression risk based on single-centre retrospective data. The model Incidental Meningioma: Prognostic Analysis Using Patient Comorbidity and MRI Tests (IMPACT) employs baseline clinical and imaging features to categorise the patient with an incidental meningioma into one of three risk groups: low, medium and high risk with a proposed active monitoring strategy based on the risk and temporal trajectory of progression, accounting for actuarial life expectancy. The primary aim of this study is to assess the external validity of this model.

Methods and analysis

IMPACT is a retrospective multicentre study which will aim to include 1500 patients with an incidental intracranial meningioma, powered to detect a 10% progression risk. Adult patients ≥16 years diagnosed with an incidental meningioma between 1 January 2009 and 31 December 2010 will be included. Clinical and radiological data will be collected longitudinally until the patient reaches one of the study endpoints: intervention (surgery, stereotactic radiosurgery or fractionated radiotherapy), mortality or last date of follow-up. Data will be uploaded to an online Research Electronic Data Capture database with no unique identifiers. External validity of IMPACT will be tested using established statistical methods.

Ethics and dissemination

Local institutional approval at each participating centre will be required. Results of the study will be reported through peer-reviewed articles and conferences and disseminated to participating centres, patients and the public using social media.
Joint position statement of the International Federation of Sports Medicine (FIMS) and European Federation of Sports Medicine Associations (EFSMA) on the IOC framework on fairness, inclusion and non-discrimination based on gender identity and sex variations
Authors: Pigozzi Fabio , Bigard Xavier , Steinacker Juergen , Wolfarth Bernd , Badtieva Victoriya , Schneider Christian , Swart Jeroen , Bilzon James Lee John , Constantinou Demitri , Dohi Michiko , Di Luigi Luigi , Fossati Chiara , Bachl Norbert , Li Guoping , Papadopoulou Theodora , Casasco Maurizio , Janse van Rensburg Dina Christina (Christa) , Kaux Jean-François , Rozenstoka Sandra , Casajus Jose-Antonio , Zelenkova Irina , Ak Emre , Ulkar Bulent , Arroyo Francisco , Ionescu Anca , Pedrinelli André , Miller Mike , Singleton Patrick , Shroff Malav , Webborn Nick , Barrett James , Hamilton Blair , Geistlinger Michael , Beltrami Gianfranco , Migliorini Sergio , Dienstbach-Wech Lenka , Bermon Stéphane , Pitsiladis Yannis P
Published: January 2022

The IOC recently published its framework on fairness, inclusion and non-discrimination based on gender identity and sex variations. This framework is drafted mainly from a human rights perspective, with less consideration for medical/scientific issues. The framework places the onus for gender eligibility and classification entirely on the International Federations (IFs), even though most will not have the capacity to implement the framework. The position of no presumption of advantage is contrary to the 2015 IOC consensus. Implementation of the 2021 framework will be a major challenge for IFs that have already recognised the inclusion of trans and women athletes with differences of sexual development (DSD) using a scientific/medical solution. The potential consequences for sports that need to prioritise fairness or safety could be one of two extremes (1) exclusion of all transgender or DSD athletes on the grounds of advantage or (2) self-identification that essentially equates to no eligibility rules. Exclusion of all transgender or DSD athletes is contrary to the Olympic charter and unlawful in many countries. While having no gender eligibility rules, sport loses its meaning and near-universal support. Athletes should not be under pressure to undergo medical procedures or treatment to meet eligibility criteria. However, if an athlete is fully informed and consents, then it is their free choice to undergo carefully considered or necessary interventions for gender classification for sport to compete fairly and safely in their chosen gender. Free choice is a fundamental human right, but so is the right to fair and safe competition.
Results of histopathological revisions of major salivary gland neoplasms in routine clinical practice
Authors: Reerds Sam T H , Uijen Maike J M , Van Engen-Van Grunsven Adriana C H , Marres Henri A M , van Herpen Carla M L , Honings Jimmie
Published: January 2022

Aims

Salivary gland neoplasms are rare and are characterised by overlapping histopathological aspects. Therefore, the assessment of the correct histopathological diagnosis can be challenging. This study evaluated the frequency of pathology consultations and revisions for salivary gland neoplasms during routine clinical practice in the Netherlands. Furthermore, the concordance and discordance rates of these revisions are presented.

Methods

The Dutch Pathology Registry (PALGA) was searched for patients that underwent a resection of a major salivary gland neoplasm between 2006 and 2016. Frequencies of pathology consultations and revisions are presented and, in order to calculate the rates of concordance and discordance, the results of the initial histopathological review were compared with the results of the revision.

Results

Between 2006 and 2016, 13 441 major salivary gland neoplasms were resected in the Netherlands. 90% (n=12 082) of these tumours were diagnosed as benign and 10% (n=1359) as malignant. The initial pathologist requested a consultation in 3.3% of resections (n=439). Revision of the histopathological specimen was performed in 2.6% (n=350) of cases. Revisions were discordant in 8.3%; including 5.8% of the initially benign diagnosed lesions reclassified as malignant by the second expert pathologist and 8% of the revised malignant tumours that underwent a subtype change.

Conclusions

The number of discordant histopathological revisions (8.3%) emphasises the complexity of the histopathological diagnosis of salivary gland neoplasms. An increase in consultations may improve the accuracy of the initial diagnosis and thus treatment in salivary gland tumours while lowering the need for revisions and the number of discordant revisions.
Marketing of flavour capsule cigarettes: a systematic review
Authors: Kyriakos Christina N , Zatoński Mateusz Zygmunt , Filippidis Filippos T
Published: January 2022

Objective

This systematic review aims to identify marketing elements of flavour capsule variants (FCVs), cigarettes that release flavour when a capsule(s) embedded in the filter is crushed.

Data sources

A search of original research without restrictions in publication year, population, study design or language using a combination of cigarette and capsule terms was conducted across four databases (Medline, Embase, Web of Science and Scopus), indexed until 13 December 2021, along with a citation search.

Study selection

Studies were included if they presented original research relevant to marketing features of FCVs.

Data extraction

One author performed data extraction and coded outcomes based on ‘4Ps’ of marketing mix theory: product, place, price and promotion. The second author conducted a cross-check.

Data synthesis

Of 2436 unduplicated database records and 30 records from other sources, 40 studies were included in the review. Studies were published between 2009 and 2021. Study methodologies primarily included content analysis of cigarette packs/sticks, review of tobacco industry documents and content analysis of advertising information. Findings suggest FCVs are marketed using a mix of strategies, particularly characterised by product innovation, timing market launches around tobacco policies, point-of-sale advertising and packaging to communicate a high-tech, customisable and flavourful product.

Conclusion

Findings illuminate the marketing strategies of FCVs that are likely driving their global growth, particularly among young people and in low and middle-income countries. Comprehensive tobacco control regulations are needed to close loopholes and curb industry efforts to circumvent existing policies in order to mitigate uptake of FCVs and other product innovations.
Accuracy of body composition measurement techniques across the age span
Authors: Rose Grace L. , Farley Morgan J. , Ward Leigh C. , Slater Gary J. , Skinner Tina L. , Keating Shelley E. , Schaumberg Mia A.
Published: January 2022

This study investigated the acceptable accuracy of common body composition techniques compared with the reference 4-compartment (4C-R) model, which has not been investigated in a sample with diverse characteristics, including age and sex. Techniques included components of the 4C-R model [dual-energy X-ray absorptiometry, air displacement plethysmography, deuterium dilution (DD)] and surrogate compartment models, which utilised bioelectrical impedance spectroscopy (BIS) rather than DD. Men and women (sex = 1:1, 18–85 years, n = 90) completed body composition testing under best-practice guidance. For measurement of individuals, only the reference 3-compartment (3C-R) equation met acceptable error limits (<5% error among individuals) within the a priori cut-point (80%) for fat-free mass (FFM; CV = 0.52%) and fat mass (FM; CV = 1.61%). However, all investigated techniques reached equivalency to the 4C-R model for FFM on average (CV = 0.52–4.31%), but for FM only the 3C and 4C equations that included quantification of total body water (TBW) by DD or BIS reached equivalency overall (CV = 1.61–6.68%). Sex and age minimally influenced accuracy. Only the 3C-R or 4C-R equations are supported for acceptable individual accuracy for both FFM and FM. For group estimates any investigated technique could be used with acceptable accuracy for FFM; however, for FM, inclusion of TBW measurement within a compartment model is necessary.

Novelty: Only the referent 3C and 4C models (including deuterium dilution) provide accurate body composition results that are acceptable for measurement of individuals in the general population. For group estimates of lean mass in the general population, compartments models that include TBW must be used for accurate measurement.
Bacterial community of reindeer lichens differs between northern and southern lichen woodlands
Authors: Alonso-García Marta , Villarreal A. Juan Carlos
Published: January 2022

Lichens cover nearly 7% of the earth’s surface, and in eastern Canada, lichen woodlands occupy over 300 000 km2. Reindeer lichens (genus Cladonia) are the main component of lichen woodlands and they play a crucial role in boreal forest ecology. We study, for the first time, the bacterial community of four species of reindeer lichens from eastern North America’s boreal forests. Using the 16S rRNA gene, we characterize the bacterial community of 189 lichen samples. We aim to analyse the effect of geography and host identity in the bacterial community composition and structure, verify the presence of a common core bacteria, and identify the most abundant core taxa. Our results suggest that host-lichen identity does not determine bacterial community composition and structure in reindeer lichens, but we confirm the influence of geography in shaping the diversity and abundance of bacteria associated with Cladonia stellaris. We also reveal that reindeer lichens share a reduced common core bacteria composed exclusively by Alphaproteobacteria. Northern lichen woodlands exhibit a significantly higher diversity and abundance of bacteria associated with C. stellaris than southern lichen woodlands do. The presence of the species Methylorosula polaris in the core bacteria is evident and may have a particular importance for reindeer lichens.
Proposed changes to the soil family taxon within the Canadian System of Soil Classification
Authors: Warren C. James , Saurette Daniel D.
Published: January 2022

The soil family was developed in the 1960s as the fourth level of taxa within the hierarchical structure of the Canadian System of Soil Classification. The original aim of the soil family category was to provide a framework for checking and establishing limits for soil series while providing a link between the series and the subgroup level. Its intended use was to define and group numerous soil series based on soil characteristics important for the purpose of applying appropriate management practices. In the current Canadian System of Soil Classification, taxa at the family level represent subdivisions of the subgroups. Classification of mineral soils at the family level is based on properties of the parent materials which include particle size; soil mineralogy; reaction (soil pH); calcareousness; depth to bedrock and permafrost; as well as climactic factors: soil temperature and soil moisture regimes. The soil family particle-size classes were originally intended as a compromise between both agronomic and engineering influences; however, the resulting product has limited functionality because of differences in definitions between engineering and agronomic grain sizes and non-alignment with soil textural classes. Consequently, classification and use of the family taxon have largely been ignored. Some adjustments to the family taxon for mineral soils and terric layers in organic soils are proposed including realignment of classes in the current family particle-size triangle to follow the divisions of the soil textural classes. Minor adjustments to mineralogy classes and depth to bedrock are also proposed.
A cautionary tale of decorrelating theory uncertainties
Authors: Ghosh Aishik , Nachman Benjamin
Published: January 2022

A variety of techniques have been proposed to train machine learning classifiers that are independent of a given feature. While this can be an essential technique for enabling background estimation, it may also be useful for reducing uncertainties. We carefully examine theory uncertainties, which typically do not have a statistical origin. We will provide explicit examples of two-point (fragmentation modeling) and continuous (higher-order corrections) uncertainties where decorrelating significantly reduces the apparent uncertainty while the true uncertainty is much larger. These results suggest that caution should be taken when using decorrelation for these types of uncertainties as long as we do not have a complete decomposition into statistically meaningful components.
A spinning construction for virtual 1-knots and 2-knots, and the fiberwise and welded equivalence of virtual 1-knots
Authors: Kauffman Louis H. , Ogasa Eiji , Schneider Jonathan
Published: January 2022

Spun-knots (respectively, spinning tori) in [Formula: see text] made from classical 1-knots compose an important class of 2-knots (respectively, embedded tori) contained in [Formula: see text]. Virtual 1-knots are generalizations of classical 1-knots. We generalize these constructions to the virtual 1-knot case by using what we call, in this paper, the spinning construction of submanifolds. The construction proceeds as follows: For a virtual 1-knot [Formula: see text], take an embedded circle [Formula: see text] contained in (a closed oriented surface [Formula: see text])×(a closed interval [Formula: see text]), where [Formula: see text] is called a representing surface in virtual 1-knot theory. Embed [Formula: see text] in [Formula: see text] by an embedding map [Formula: see text], and let [Formula: see text] stand for [Formula: see text] Regard the tubular neighborhood of [Formula: see text] in [Formula: see text] as the result of rotating [Formula: see text] around [Formula: see text]. Rotate [Formula: see text] together then with [Formula: see text]. When [Formula: see text], we obtain an embedded torus [Formula: see text]. We prove the following: The embedding type [Formula: see text] in [Formula: see text] depends only on [Formula: see text], and does not depend on [Formula: see text]. Furthermore, the submanifolds, [Formula: see text] and “the embedded torus made from [Formula: see text] by using Satoh’s method”, of [Formula: see text] are isotopic.

Fiberwise equivalence of diagrams refers to fiberwise equivalence of tori in 4-space that lie over the diagrams. We prove that two virtual 1-knot diagrams [Formula: see text] and [Formula: see text] are fiberwise equivalent if and only if [Formula: see text] and [Formula: see text] are rotational welded equivalent (see the body of the paper for this definition).

We generalize the construction in the virtual 1-knot case written in the first paragraph, and we also succeed to make a consistent construction of one-dimensional-higher submanifolds from any virtual two-dimensional knot. Note that Satoh’s method says nothing about the virtual 2-knot case. Rourke’s interpretation of Satoh’s method is that one puts “fiber-circles” on each point of each virtual 1-knot diagram. If there is no virtual branch point in a virtual 2-knot diagram, our way gives such fiber-circles to each point of the virtual 2-knot diagram. Furthermore we prove the following: If a virtual 2-knot diagram [Formula: see text] has a virtual branch point, [Formula: see text] cannot be covered by such fiber-circles. Hence Rourke’s method cannot be generalized to the virtual 2-knot case. Only the spinning construction introduced in this paper works for now.
Analyzing Trajectory Gaps to Find Possible Rendezvous Region
Authors: Sharma Arun , Shekhar Shashi
Published: January 2022

Given trajectory data with gaps, we investigate methods to identify possible rendezvous regions. The problem has societal applications such as improving maritime safety and regulatory enforcement. The challenges come from two aspects. First, gaps in trajectory data make it difficult to identify regions where moving objects may have rendezvoused for nefarious reasons. Hence, traditional linear or shortest path interpolation methods may not be able to detect such activities, since objects in a rendezvous may have traveled away from their usual routes to meet. Second, user detecting a rendezvous regions involve a large number of gaps and associated trajectories, making the task computationally very expensive. In preliminary work, we proposed a more effective way of handling gaps and provided examples to illustrate potential rendezvous regions. In this article, we are providing detailed experiments with both synthetic and real-world data. Experiments on synthetic data show that the accuracy improved by 50 percent, which is substantial as compared to the baseline approach. In this article, we propose a refined algorithm Temporal Selection Search for finding a potential rendezvous region and finding an optimal temporal range to improve computational efficiency. We also incorporate two novel spatial filters: (i) a Static Ellipse Intersection Filter and (ii) a Dynamic Circle Intersection Spatial Filter. Both the baseline and proposed approaches account for every possible rendezvous pattern. We provide a theoretical evaluation of the algorithms correctness and completeness along with a time complexity analysis. Experimental results on synthetic and real-world maritime trajectory data show that the proposed approach substantially improves the area pruning effectiveness and computation time over the baseline technique. We also performed experiments based on accuracy and precision on synthetic dataset on both proposed and baseline techniques.
Supply-Demand-aware Deep Reinforcement Learning for Dynamic Fleet Management
Authors: Zheng Bolong , Ming Lingfeng , Hu Qi , Lü Zhipeng , Liu Guanfeng , Zhou Xiaofang
Published: January 2022

Online ride-hailing platforms have reduced significantly the amounts of the time that taxis are idle and that passengers spend on waiting. As a key component of these platforms, the fleet management problem can be naturally modeled as a Markov Decision Process, which enables us to use the deep reinforcement learning. However, existing studies are proposed based on simplified problem settings that fail to model the complicated supply-dynamics and restrict the performance in the real traffic environment. In this article, we propose a supply-demand-aware deep reinforcement learning algorithm for taxi dispatching, where we use a deep Q-network with action sampling policy, called AS-DQN, to learn an optimal dispatching policy. Furthermore, we utilize a dueling network architecture, called AS-DDQN, to improve the performance of AS-DQN. Extensive experiments on real-world datasets offer insight into the performance of our model and show that it is capable of outperforming the baseline approaches.
Integrating Algorithmic Sampling-Based Motion Planning with Learning in Autonomous Driving
Authors: Zhang Yifan , Zhang Jinghuai , Zhang Jindi , Wang Jianping , Lu Kejie , Hong Jeff
Published: January 2022

Sampling-based motion planning (SBMP) is a major algorithmic trajectory planning approach in autonomous driving given its high efficiency and outstanding performance in practice. However, driving safety still calls for further refinement of SBMP. In this article we organically integrate algorithmic motion planning with learning models to improve SBMP in highway traffic scenarios from the following two perspectives. First, given the number of points to be sampled, we develop a new model to sample “important” points for SBMP by predicting the intention of surrounding vehicles and learning the distribution of human drivers’ trajectory. Second, we empirically study the relationship between the number of sample points and the environment, which is largely ignored in conventional SBMP. Then, we provide a guideline to select the appropriate number of points to be sampled under different scenarios to guarantee efficiency. The simulation experiments are conducted based on the vehicle trajectory dataset NGSIM. The results show that the proposed sampling strategy outperforms existing sampling strategies in terms of the computing time, traveling time, and smoothness of the trajectory.
A Comprehensive Exploration of Languages for Parallel Computing
Authors: Ciccozzi Federico , Addazi Lorenzo , Asadollah Sara Abbaspour , Lisper Björn , Masud Abu Naser , Mubeen Saad
Published: January 2022

Software-intensive systems in most domains, from autonomous vehicles to health, are becoming predominantly parallel to efficiently manage large amount of data in short (even real-) time. There is an incredibly rich literature on languages for parallel computing, thus it is difficult for researchers and practitioners, even experienced in this very field, to get a grasp on them. With this work we provide a comprehensive, structured, and detailed snapshot of documented research on those languages to identify trends, technical characteristics, open challenges, and research directions. In this article, we report on planning, execution, and results of our systematic peer-reviewed as well as grey literature review, which aimed at providing such a snapshot by analysing 225 studies.
A Survey of Evaluation Metrics Used for NLG Systems
Authors: Sai Ananya B. , Mohankumar Akash Kumar , Khapra Mitesh M.
Published: January 2022

In the last few years, a large number of automatic evaluation metrics have been proposed for evaluating Natural Language Generation (NLG) systems. The rapid development and adoption of such automatic evaluation metrics in a relatively short time has created the need for a survey of these metrics. In this survey, we (i) highlight the challenges in automatically evaluating NLG systems, (ii) propose a coherent taxonomy for organising existing evaluation metrics, (iii) briefly describe different existing metrics, and finally (iv) discuss studies criticising the use of automatic evaluation metrics. We then conclude the article highlighting promising future directions of research.
Level-5 Autonomous Driving—Are We There Yet? A Review of Research Literature
Authors: Khan Manzoor Ahmed , Sayed Hesham El , Malik Sumbal , Zia Talha , Khan Jalal , Alkaabi Najla , Ignatious Henry
Published: January 2022

Autonomous vehicles are revolutionizing transport and next-generation autonomous mobility. Such vehicles are promising to increase road safety, improve traffic efficiency, reduce vehicle emission, and improve mobility. However, for these vehicles to live up to their full potentials, there are significant research, technological and urgent organizational issues that need to be addressed to reach the highest level of automation, i.e., level 5. Sensors, communication, mobile edge computing, machine learning, data analytic, distributed learning, and so on, are examples of the building blocks technologies and concepts constituting the end-to-end solution. This survey discusses these technologies and concepts and maps their roles to the end-to-end solution. It highlights the challenges for each technology. Moreover, this survey provides an analysis of different solution approaches proposed by relevant stakeholders, utilizing these technologies aiming to achieve level-5 autonomy. Finally, the article details two use cases to present the interplay of the building blocks technologies.
Orchestration in Fog Computing: A Comprehensive Survey
Authors: Costa Breno , Bachiega Joao , de Carvalho Leonardo Rebouças , Araujo Aleteia P. F.
Published: January 2022

Fog computing is a paradigm that brings computational resources and services to the network edge in the vicinity of user devices, lowering latency and connecting with cloud computing resources. Unlike cloud computing, fog resources are based on constrained and heterogeneous nodes whose connectivity can be unstable. In this complex scenario, there is a need to define and implement orchestration processes to ensure that applications and services can be provided, considering the settled agreements. Although some publications have dealt with orchestration in fog computing, there are still some diverse definitions and functional intersection with other areas, such as resource management and monitoring. This article presents a systematic review of the literature with focus on orchestration in fog computing. A generic architecture of fog orchestration is presented, created from the consolidation of the analyzed proposals, bringing to light the essential functionalities addressed in the literature. This work also highlights the main challenges and open research questions.
Zero-One Laws for Existential First-Order Sentences of Bounded Quantifier Depth
Authors: Podder Moumanti , Zhukovskii Maksim
Published: January 2022

For any fixed positive integer
k
, let α

k

denote the smallest α ∈ (0,1) such that the random graph sequence {
G
(
n, n
-α
)}

n

does not satisfy the zero-one law for the set ε

k

of all existential first-order sentences that are of quantifier depth at most
k
. This article finds upper and lower bounds on α

k

, showing that as
k
→ ∞, we have α

k

= (
k
- 2 -
t
(
k
))
-1
for some function
t
(
k
) = Θ (
k
-2
). We also establish the precise value of α

k

when
k
= 4.
Biomedical Question Answering: A Survey of Approaches and Challenges
Authors: Jin Qiao , Yuan Zheng , Xiong Guangzhi , Yu Qianlan , Ying Huaiyuan , Tan Chuanqi , Chen Mosha , Huang Songfang , Liu Xiaozhong , Yu Sheng
Published: January 2022

Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access, and understand complex biomedical knowledge. There have been tremendous developments of BQA in the past two decades, which we classify into five distinctive approaches: classic, information retrieval, machine reading comprehension, knowledge base, and question entailment approaches. In this survey, we introduce available datasets and representative methods of each BQA approach in detail. Despite the developments, BQA systems are still immature and rarely used in real-life settings. We identify and characterize several key challenges in BQA that might lead to this issue, and we discuss some potential future directions to explore.