bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychometric evaluation of the Thai version of the Early Childhood Oral Health Impact Scale (Th-ECOHIS): a cross sectional validation study
Authors: Leelataweewud Pattarawadee , Jirarattanasopha Varangkanar , Ungchusak Chantana , Vejvithee Warangkana
Published: February 2021

Background

Early childhood caries (ECC) is prevalent in Thailand, but no appropriate tool has been available to measure its impact on children’s quality of life. This study translated the Early Childhood Oral Health Impact Scale (ECOHIS), a widely used proxy-reported questionnaire developed in the United States for measuring the oral health-related quality of life of preschool children and their families, into Thai (Th-ECOHIS). The scale’s psychometric properties were investigated in Thai caregivers and their children.

Methods

Cultural adaptation for the scale development within the Thai context was processed using forward–backward translation by experts. A face and content validation was conducted among 20 Thai caregivers to attain the final Th-ECOHIS. Psychometric testing was done on 3-year-old child-caregiver pairs in Bangkok using the interviewer-administered mode. Children’s oral health was determined by caries experience (decayed, missing and filled primary teeth, dmft) and treatment need. The caregivers answered the Th-ECOHIS and global questions regarding their perception of the children’s oral health. Across-items reliability was assessed by internal consistency using the Cronbach’s alpha coefficient. Test-retest reliability was managed at a 2-week interval in 10% of the sample using the intraclass correlation coefficient calculated by two-way analysis of variance. The discriminant validity was tested by the relationship between the severity of dental caries, treatment need and Th-ECOHIS scores, using the Kruskal-Wallis test.

Results

A total of 214 child-caregiver pairs participated. Twenty-two percent had ECC (dmft 1–3) and 17.3% had severe ECC (dmft 4 or higher) with mean (SD) dmft 1.63 (2.92). All items in the original ECOHIS were retained in the Thai version. The test-retest reliability of Th-ECOHIS was 0.87; internal consistency was 0.85; the total Th-ECOHIS scores were significantly correlated with the global rating of oral health question (r = 0.604). Th-ECOHIS scores in both child and family impact sections and the total were significantly associated with the severity of caries (p <  0.001) and treatment need (p <  0.001).

Conclusions

Th-ECOHIS demonstrated good reliability and validity. It could be used on caregivers to assess the impacts of ECC on quality of life of Thai pre-school children and compared to other countries.
Oral health knowledge and dental behavior among individuals with autism in Jordan: a case–control study
Authors: Alshatrat Sabha Mahmoud , Al-Bakri Isra Abdelkarim , Al-Omari Wael Mousa , Al Mortadi Noor Abdullah
Published: February 2021

Background

Oral care is acknowledged as an integral component of general health and plays an essential role in establishing the desired level of quality of life for individuals with autism spectrum disorder (ASD).

Purpose

To investigate oral health knowledge and dental behaviors in individuals with ASD in comparison with individuals without ASD in Jordan.

Methods

A case–control study was carried out among 296 caregivers of individuals with ASD (n = 147) and control (n = 149) groups. A closed ended, validated self-designed questionnaire was distributed. The questionnaire included questions addressing participant’s oral health knowledge and behaviour. Data were analyzed using SPSS® software Version 22 with a 0.05 level of significance. A Chi-square test and contingency-table analysis were performed.

Results

Individuals with ASD in Jordan were significantly less knowledgeable about different oral health aspects than individuals without ASD (p < 0.05). Fewer individuals in the ASD group brushed their teeth once or twice daily (89%), compared to the control group (93%). Only 15% of the ASD participants could brush their teeth without help. The use of fluoridated toothpaste and the frequency of using mouth rinse demonstrated a significant difference between groups (p < 0.05).

Conclusion

ASD individuals in Jordan suffer from a significant lack of oral knowledge comparing to their controls, leading to a misunderstanding of the basic and highly important dental health aspects. Indicating that the knowledge was not enough to influence their dental behaviors. Children with ASD and their families should receive appropriate education in special need oral health care given by oral health professionals to reduce the risk of having dental problems and oral disease and enhance their quality of life.
A thematic network for factors affecting the choice of specialty education by medical students: a scoping study in low-and middle-income countries
Authors: Sarikhani Yaser , Ghahramani Sulmaz , Bayati Mohsen , Lotfi Farhad , Bastani Peivand
Published: February 2021

Background

Medical specialty selection is a complex phenomenon that can affect the performance of health systems, community health, and physicians’ lives. It is essential to identify the key factors influencing the choice of specialty for evidence-based policymaking. This scoping review aimed to provide a comprehensive map of evidence regarding the factors influencing the choice of specialty by medical students (MS) in low-and middle-income countries (LMICs) and also to determine knowledge gaps.

Methods

We carried out a systematic search on six online databases from January 2000 to May 2020. We used a five-step scoping review method proposed by Arksey and O’Malley. We synthesized the data using a quantitative content analysis approach. Then, we developed a thematic network as a conceptual map for a better understanding of the concept.

Results

The analysis led to the development of five main themes, including personal determinants, life fulfillment aspects, influential career aspects, educational determinants, and interpersonal effects. Moreover, the most frequent sub-themes were specific personal factors, controllable lifestyle, quality of working life, and future working conditions.

Conclusion

This review provided evidence on the factors influencing the choice of specialties. In order to support physician workforce policy with more precise evidence, it is necessary to explore the weight and ranking of these factors based on the socioeconomic contexts of the countries. This study also indicated that factors such as ethical values, various aspects of medical philosophy, and immigration tendencies are areas for further investigations.
The economic burden of coronavirus disease 2019 (COVID-19): evidence from Iran
Authors: Ghaffari Darab Mohsen , Keshavarz Khosro , Sadeghi Elnaz , Shahmohamadi Javad , Kavosi Zahra
Published: February 2021

This study aimed to estimate both direct medical and indirect costs of treating the Coronavirus disease 2019 (COVID-19) from a societal perspective in the patients at a referral hospital in Fars province as well as the economic burden of COVID-19 in Iran in 2020.

Methods

This study is a partial economic evaluation and a cross-sectional cost-description study conducted based on the data of the COVID-19 patients referred to a referral university hospital in Fars province between March and July 2020. The data were collected by examining the patients’ records and accounting information systems. The subjects included all the inpatients with COVID-19 (477 individuals) who admitted to the medical centre during the 4 months. Bottom-up costing (also called micro-costing approach), incidence-based and income-based human capital approaches were used as the main methodological features of this study.

Results

The direct medical costs were estimated to be 28,240,025,968 Rials ($ 1,791,172) in total with mean cost of 59,203,409 Rials ($ 3755) per person (SD = 4684 $/ 73,855,161 Rials) in which significant part (41%) was that of intensive and general care beds (11,596,217,487 Rials equal to $ 735,510 (M = 24,310,728 Rials or $ 1542, SD = 34,184,949 Rials or $ 2168(. The second to which were the costs of medicines and medical consumables (28%). The mean indirect costs, including income loss due to premature death, economic production loss due to hospitalization and job absenteeism during recovery course were estimated to be 129,870,974 Rials ($ 11,634) per person. Furthermore, the economic burden of the disease in the country for inpatient cases with the definitive diagnosis was 22,688,925,933,095 Rials equal to $ 1,439,083,784.

Conclusion

The results of this study showed that the severe status of the disease would bring about the extremely high cost of illness in this case. It is estimated that the high prevalence rate of COVID-19 has been imposing a heavy economic burden on the country and health system directly that may result in rationing or painful cost-control approaches.
High intake of vegetables is linked to lower white blood cell profile and the effect is mediated by the gut microbiome
Authors: Menni Cristina , Louca Panayiotis , Berry Sarah E. , Vijay Amrita , Astbury Stuart , Leeming Emily R. , Gibson Rachel , Asnicar Francesco , Piccinno Gianmarco , Wolf Jonathan , Davies Richard , Mangino Massimo , Segata Nicola , Spector Tim D. , Valdes Ana M.
Published: February 2021

Background

Chronic inflammation, which can be modulated by diet, is linked to high white blood cell counts and correlates with higher cardiometabolic risk and risk of more severe infections, as in the case of COVID-19.

Methods

Here, we assessed the association between white blood cell profile (lymphocytes, basophils, eosinophils, neutrophils, monocytes and total white blood cells) as markers of chronic inflammation, habitual diet and gut microbiome composition (determined by sequencing of the 16S RNA) in 986 healthy individuals from the PREDICT-1 nutritional intervention study. We then investigated whether the gut microbiome mediates part of the benefits of vegetable intake on lymphocyte counts.

Results

Higher levels of white blood cells, lymphocytes and basophils were all significantly correlated with lower habitual intake of vegetables, with vegetable intake explaining between 3.59 and 6.58% of variation in white blood cells after adjusting for covariates and multiple testing using false discovery rate (q < 0.1). No such association was seen with fruit intake. A mediation analysis found that 20.00% of the effect of vegetable intake on lymphocyte counts was mediated by one bacterial genus, Collinsella, known to increase with the intake of processed foods and previously associated with fatty liver disease. We further correlated white blood cells to other inflammatory markers including IL6 and GlycA, fasting and post-prandial glucose levels and found a significant relationship between inflammation and diet.

Conclusion

A habitual diet high in vegetables, but not fruits, is linked to a lower inflammatory profile for white blood cells, and a fifth of the effect is mediated by the genus Collinsella.

Trial registration

The ClinicalTrials.gov registration identifier is NCT03479866.
Pathological findings in rotation thromboelastometry associated with thromboembolic events in COVID-19 patients
Authors: Boss Kristina , Kribben Andreas , Tyczynski Bartosz
Published: February 2021

Background

Severe thromboembolic events are one of the major complications associated with COVID-19 infection, especially among critically ill patients. We analysed ROTEM measurements in COVID-19 patients with a severe disease course and in patients with severe sepsis.

Methods

In this study, data obtained by extended analysis of haemostasis with standard laboratory tests and thromboelastometry of 20 patients with severe course of COVID-19 were retrospectively analysed and compared with similar data from 20 patients with severe sepsis but no COVID-19.

Results

The thromboelastometry values obtained from 20 sepsis patients contained a maximum clot firmness above the normal range but among COVID-19 patients, hypercoagulability was much more pronounced, with significantly higher maximum clot firmness (FIBTEM: 38.4 ± 10.1 mm vs. 29.6 ± 10.8 mm; P  = 0.012; EXTEM: 70.4 ± 10.4 mm vs. 60.6 ± 14.8 mm; P  = 0.022). Additionally, fibrinogen levels were significantly higher among COVID-19 patients (757 ± 135 mg/dl vs. 498 ± 132 mg/dl, P < 0.0001). Furthermore, thromboelastometry showed fibrinolysis shutdown among COVID-19 patients with significantly lower maximum of lysis than among sepsis patients (EXTEM: 0.6 ± 1.2 % vs. 3.3 ± 3.7 %; P  = 0.013). Seven of 20 COVID-19 patients experienced thromboembolic events, whereas no patient in the sepsis group experienced such events.

Conclusions

ROTEM analysis showed significantly different pathological findings characterized by hypercoagulability and fibrinolysis shutdown among COVID-19 patients with a severe disease course compared to patients with severe sepsis. These abnormalities seem to be associated with thromboembolic events.
A landscape analysis of health technology assessment capacity in the Association of South-East Asian Nations region
Authors: Sharma Manushi , Teerawattananon Yot , Dabak Saudamini Vishwanath , Isaranuwatchai Wanrudee , Pearce Fiona , Pilasant Songyot , Sabirin Junainah , Mayxay Mayfong , Guerrero Melissa , Phuong Nguyen Khanh , Sastroasmoro Sudigdo , Htoo Thant Sin
Published: February 2021

Background

Progress towards achieving Universal Health Coverage and institutionalizing healthcare priority setting through health technology assessment (HTA) in the Association of South-East Asian Nations (ASEAN) region varies considerably across countries because of differences in healthcare expenditure, political support, access to health information and technology infrastructure. To explore the status and capacity of HTA in the region, the ASEAN Secretariat requested for member countries to be surveyed to identify existing gaps and to propose solutions to help countries develop and streamline their priority-setting processes for improved healthcare decision-making.

Methods

A mixed survey questionnaire with open- and closed-ended questions relating to HTA governance, HTA infrastructure, supply and demand of HTA and global HTA networking opportunities in each country was administered electronically to representatives of HTA nodal agencies of all ASEAN members. In-person meetings or email correspondence were used to clarify or validate any unclear responses. Results were collated and presented quantitatively.

Results

Responses from eight out of ten member countries were analysed. The results illustrate that countries in the ASEAN region are at different stages of HTA institutionalization. While Malaysia, Singapore and Thailand have well-established processes and methods for priority setting through HTA, other countries, such as Cambodia, Indonesia, Lao PDR, Myanmar, the Philippines and Vietnam, have begun to develop HTA systems in their countries by establishing nodal agencies or conducting ad-hoc activities.

Discussion and conclusion

The study provides a general overview of the HTA landscape in ASEAN countries. Systematic efforts to mitigate the gaps between the demand and supply of HTA in each country are required while ensuring adequate participation from stakeholders so that decisions for resource allocation are made in a fair, legitimate and transparent manner and are relevant to each local context.
The unmet needs for modern family planning methods among postpartum women in Sub-Saharan Africa: a systematic review of the literature
Authors: Gahungu Jumaine , Vahdaninia Mariam , Regmi Pramod R.
Published: February 2021

Background

Sub-Saharan Africa has the highest fertility rate in the world, with the highest unmet need for family planning (FP). Yet, there is a lack of knowledge about the determinants for non-utilisation of modern contraceptive methods among women of reproductive age. This systematic review of literature assessed factors affecting the unmet need and reasons for non-utilisation of modern contraceptive methods during the postpartum period in Sub-Saharan African women.

Methods

An online literature search was conducted in several databases: MEDLINE, Cochrane Review, PubMed, Elsevier's Science Direct and Web of Science. The search was completed by hand searching. Data were extracted and summarised using the Arksey and O’Malley methodology.

Results

In total, 19 studies were included; one qualitative study, seventeen quantitative, and one used a mixed-methods approach. Studies were conducted in Ethiopia (n = 11), Nigeria (n = 3), Kenya (n = 2), Malawi (n = 2) and Uganda (n = 1). Factors affecting the unmet need for modern contraceptive methods were described at three levels: (a) individual; (b) household; and (c) healthcare facility level. Reasons for non-use of FP included: fear of side effects; husband’s disapproval; the absence of menses; abstinence; and low perception of risk of pregnancy.

Conclusion

Unmet needs in postpartum FP in women from Sub-Saharan Africa were associated with health-system and socio-demographic determinants. We suggest that there is a need to improve the awareness of modern contraceptive methods through effective interventions. Further research is needed for under-studied countries in this continent.
Changes in opioid-related deaths following increased access to opioid substitution treatment
Authors: Andersson Lisa , Håkansson Anders , Berge Jonas , Johnson Björn
Published: February 2021

Background

Opioid-related mortality is high and increasing in the Western world, and interventions aimed at reducing opioid-related deaths represent an important area of study. In Skåne County, Sweden, a patient choice reform resulted in increased access to opioid substitution treatment (OST). In addition, a gradual shift towards less restrictive terms for exclusion from OST has been implemented. The aim of this study was to assess the impact of these policy changes on opioid-related deaths.

Methods

Detailed data on opioid-related deaths in Skåne during the 2 years prior to and following the policy change were obtained from forensic records and from health care services. Data on overdose deaths for Skåne and the rest of Sweden were obtained using publicly available national register data. Time periods were used as the predictor for opioid-related deaths in the forensic data. The national level data were used in a natural experiment design in which rates of overdose deaths were compared between Skåne and the rest of Sweden before and after the intervention.

Results

There was no significant difference in the number of deaths in Skåne between the data collection periods (RR: 1.18 95% CI:0.89–1.57, p= 0.251). The proportion of deaths among patients enrolled in OST increased between the two periods (2.61, 1.12–6.10, p= 0.026). There was no change in deaths related to methadone or buprenorphine in relation to deaths due to the other opioids included in the study (0.92, 0.51–1.63, p= 0.764). An analysis of national mortality data showed an annual relative decrease in unintentional drug deaths in Skåne compared to the rest of Sweden following the onset of the reform (0.90, 0.84–0,97, p= 0.004).

Conclusions

Opioid-related deaths, as assessed using forensic data, has not changed significantly in Skåne following a change to lower-threshold OST. By contrast, national level data indicate that the policy change has been associated with decreased overdose deaths. The discrepancy between these results highlights the need for more research to elucidate this issue. The result that more patients die during ongoing OST following an increase in access to treatment underlines the need for further preventive interventions within the OST treatment setting.
Turner’s syndrome mosaicism in girls with neurodevelopmental disorders: a cohort study and hypothesis
Authors: Vorsanova Svetlana G. , Kolotii Alexey D. , Kurinnaia Oksana S. , Kravets Victor S. , Demidova Irina A. , Soloviev Ilya V. , Yurov Yuri B. , Iourov Ivan Y.
Published: February 2021

Background

Turner’s syndrome is associated with either monosomy or a wide spectrum of structural rearrangements of chromosome X. Despite the interest in studying (somatic) chromosomal mosaicism, Turner’s syndrome mosaicism (TSM) remains to be fully described. This is especially true for the analysis of TSM in clinical cohorts (e.g. cohorts of individuals with neurodevelopmental disorders). Here, we present the results of studying TSM in a large cohort of girls with neurodevelopmental disorders and a hypothesis highlighting the diagnostic and prognostic value.

Results

Turner’s syndrome-associated karyotypes were revealed in 111 (2.8%) of 4021 girls. Regular Turner’s syndrome-associated karyotypes were detected in 35 girls (0.9%). TSM was uncovered in 76 girls (1.9%). TSM manifested as mosaic aneuploidy (45,X/46,XX; 45,X/47,XXX/46,XX; 45,X/47,XXX) affected 47 girls (1.2%). Supernumerary marker chromosomes derived from chromosome X have been identified in 11 girls with TSM (0.3%). Isochromosomes iX(q) was found in 12 cases (0.3%); one case was non-mosaic. TSM associated with ring chromosomes was revealed in 5 girls (0.1%).

Conclusion

The present cohort study provides data on the involvement of TSM in neurodevelopmental disorders among females. Thus, TSM may be an element of pathogenic cascades in brain diseases (i.e. neurodegenerative and psychiatric disorders). Our data allowed us to propose a hypothesis concerning ontogenetic variability of TSM levels. Accordingly, it appears that molecular cytogenetic monitoring of TSM, which is a likely risk factor/biomarker for adult-onset multifactorial diseases, is required.
ESCO2 promotes lung adenocarcinoma progression by regulating hnRNPA1 acetylation
Authors: Zhu Hui-er , Li Tao , Shi Shengnan , Chen De-xiong , Chen Weiping , Chen Hui
Published: February 2021

Background

Emerging evidence indicates that metabolism reprogramming and abnormal acetylation modification play an important role in lung adenocarcinoma (LUAD) progression, although the mechanism is largely unknown.

Methods

Here, we used three public databases (Oncomine, Gene Expression Omnibus [GEO], The Cancer Genome Atlas [TCGA]) to analyze ESCO2 (establishment of cohesion 1 homolog 2) expression in LUAD. The biological function of ESCO2 was studiedusing cell proliferation, colony formation, cell migration, and invasion assays in vitro, and mouse xenograft models in vivo. ESCO2 interacting proteins were searched using gene set enrichment analysis (GSEA) and mass spectrometry. Pyruvate kinase M1/2 (PKM) mRNA splicing assay was performed using RT-PCR together with restriction digestion. LUAD cell metabolism was studied using glucose uptake assays and lactate production. ESCO2 expression was significantly upregulated in LUAD tissues, and higher ESCO2 expression indicated worse prognosis for patients with LUAD.

Results

We found that ESCO2 promoted LUAD cell proliferation and metastasis metabolic reprogramming in vitro and in vivo. Mechanistically, ESCO2 increased hnRNPA1 (heterogeneous nuclear ribonucleoprotein A1) binding to the intronic sequences flanking exon 9 (EI9) of PKM mRNA by inhibiting hnRNPA1 nuclear translocation, eventually inhibiting PKM1 isoform formation and inducing PKM2 isoform formation.

Conclusions

Our findings confirm that ESCO2 is a key factor in promoting LUAD malignant progression and suggest that it is a new target for treating LUAD.
M.I.C.E—Mental Health Intervention for Children with Epilepsy: a randomised controlled, multi-centre clinical trial evaluating the clinical and cost-effectiveness of MATCH-ADTC in addition to usual care compared to usual care alone for children and young people with common mental health disorders and epilepsy—study protocol
Authors:   MICE Study Team, Bennett Sophie D. , Cross J. Helen , Coughtrey Anna E. , Heyman Isobel , Ford Tamsin , Chorpita Bruce , Moss-Morris Rona , Byford Sarah , Dalrymple Emma , Reilly Colin , Stephenson Terence , Doré Caroline , Varadkar Sophia , Blackstone James , Chowdhury Kashfia , Ganguli Poushali , Deane Liz , Shafran Roz
Published: February 2021

Background

Mental health disorders in the context of long-term conditions in children and young people are currently overlooked and undertreated. Evidence-based psychological treatments for common childhood mental health disorders (anxiety, depression and disruptive behaviour disorders) have not been systematically evaluated in young people with epilepsy despite their high prevalence in this population. The aim of this multi-site randomised controlled trial is to determine the clinical and cost-effectiveness of adding a modular psychological intervention to usual care for the mental health disorders in comparison to assessment-enhanced usual care alone.

Methods

In total, 334 participants aged 3–18 years attending epilepsy services will be screened for mental health disorders with the Strengths and Difficulties Questionnaire (SDQ) and the diagnostic Development and Wellbeing Assessment (DAWBA). Those identified as having a mental health disorder and consenting to the trial will be randomised to either receive up to 22 sessions of the modular psychological intervention (MATCH-ADTC) delivered over the telephone over 6 months by non-mental health professionals in addition to usual care or to assessment-enhanced usual care alone. Outcomes will be measured at baseline, 6 months and 12 months post-randomisation. It is hypothesised that MATCH-ADTC plus usual care will be superior to assessment-enhanced usual care in improving emotional and behavioural symptoms. The primary outcome is the SDQ reported by parents at 6 months. Secondary outcomes include parent-reported mental health measures such as the Revised Children’s Anxiety and Depression Scale, quality of life measures such as the Paediatric Quality of Life Inventory and physical health measures such as the Hague Seizure Severity Scale. Outcome assessors will be blinded to group assignment. Qualitative process evaluations and a health economic evaluation will also be completed.

Discussion

This trial aims to determine whether a systematic and integrated approach to the identification and treatment of mental health disorders in children and young people with epilepsy is clinically and cost-effective. The findings will contribute to policies and practice with regard to addressing mental health needs in children and young people with other long-term conditions.

Trial registration

ISRCTNISRCTN57823197. Registered on 25 February 2019.
NOAA/NCEI and University of Colorado candidate models for IGRF-13
Authors: Alken P. , Chulliat A. , Nair M.
Published: February 2021

The International Geomagnetic Reference Field (IGRF) is a set of parameters representing the large-scale internal part of Earth’s magnetic field. The 13th generation IGRF requested candidate models for a definitive main field for 2015.0, a provisional main field for 2020.0, and a predictive secular variation covering the period 2020.0–2025.0. The University of Colorado (CU) and the National Centers for Environmental Information (NCEI), part of the National Oceanic and Atmospheric Administration (NOAA), have produced these three candidate models for consideration in IGRF-13. In this paper, we present the methodology used to derive our candidate models. Our candidates were built primarily from Swarm satellite data, and also relied on geomagnetic indices derived from the ground observatory network. The ground observatories played a crucial role as independent data in validating our candidates. This paper also provides a retrospective assessment of the CU/NCEI candidate model to the previous IGRF (IGRF-12) and discusses the impact of differences between candidate and final IGRF models on global model errors.
Geomagnetic secular variation forecast using the NASA GEMS ensemble Kalman filter: A candidate SV model for IGRF-13
Authors: Tangborn Andrew , Kuang Weijia , Sabaka Terence J. , Yi Ce
Published: February 2021

We have produced a 5-year mean secular variation (SV) of the geomagnetic field for the period 2020–2025. We use the NASA Geomagnetic Ensemble Modeling System (GEMS), which consists of the NASA Goddard geodynamo model and ensemble Kalman filter (EnKF) with 400 ensemble members. Geomagnetic field models are used as observations for the assimilation, including gufm1 (1590–1960), CM4 (1961–2000) and CM6 (2001–2019). The forecast involves a bias correction scheme that assumes that the model bias changes on timescales much longer than the forecast period, so that they can be removed by successive forecast series. The algorithm was validated on the time period 2010-2015 by comparing with CM6 before being applied to the 2020–2025 time period. This forecast has been submitted as a candidate predictive model of IGRF-13 for the period 2020–2025.

Graphical abstract
Innovative seismic imaging of volcanogenic massive sulfide deposits, Neves-Corvo, Portugal — Part 2: Surface array
Authors: Donoso George A. , Malehmir Alireza , Brodic Bojan , Pacheco Nelson , Carvalho João , Araujo Vitor
Published: February 2021

Seismic methods are an affordable and effective way of studying the subsurface for mineral exploration. With the goal of testing new technologies for mineral exploration in highly challenging mining areas, in early 2019, an innovative seismic survey was conducted at the Neves-Corvo mine, south Portugal. We have focused on the data and results from the surface array data, whereas other work deals with the underground seismic data. The surface seismic survey consisted of two perpendicular 2D profiles positioned above the known world-class tier-1 Lombador deposit. Simultaneously, a survey inside the active underground mine took place, being unique because it included the testing of a prototype system that enabled accurate GPS-time (microsecond accuracy) synchronization inside the mine tunnels, approximately 650 m below the surface profiles. Due to the active mining operations, the surface data are noisy. To handle this, a carefully tailored processing algorithm was developed and applied to enhance reflections in the data, interpreted to originate from lithologic contacts and the Lombador deposit. The results and interpretations from 2D processing were validated taking advantage of the known deposit geometry using 3D exploding reflector modeling and pseudo-3D cross-dip analysis. These analyses suggest that there is an out-of-plane signature of the Lombador deposit on the surface data. Additionally, source points activated in the exploration tunnels and simultaneously recorded on the surface profiles allowed for the creation of a 2D velocity model that was used for migration and time-to-depth conversion, providing a reliable 2D seismic section of the subsurface under the surface profiles. We determine that limited surface coverage 2D surveys and a velocity model derived from the tunnel-to-surface seismic recordings allow for imaging of key subsurface geologic structures and delineating mineral deposits of economic interest.
Identification of regulatory elements required for Stra8 expression in fetal ovarian germ cells of the mouse
Authors: Feng Chun-Wei , Burnet Guillaume , Spiller Cassy M. , Cheung Fiona Ka Man , Chawengsaksophak Kallayanee , Koopman Peter , Bowles Josephine
Published: February 2021

In mice, the entry of germ cells into meiosis crucially depends on the expression of stimulated by retinoic acid gene 8 (Stra8). Stra8 is expressed specifically in pre-meiotic germ cells of females and males, at fetal and postnatal stages, respectively, but the mechanistic details of its spatiotemporal regulation are yet to be defined. In particular, there has been considerable debate regarding whether retinoic acid is required, in vivo, to initiate Stra8 expression in the mouse fetal ovary. We show that the distinctive anterior-to-posterior pattern of Stra8 initiation, characteristic of germ cells in the fetal ovary, is faithfully recapitulated when 2.9 kb of the Stra8 promoter is used to drive eGFP expression. Using in vitro transfection assays of cutdown and mutant constructs, we identified two functional retinoic acid responsive elements (RAREs) within this 2.9 kb regulatory element. We also show that the transcription factor DMRT1 enhances Stra8 expression, but only in the presence of RA and the most proximal RARE. Finally, we used CRISPR/Cas9-mediated targeted mutation studies to demonstrate that both RAREs are required for optimal Stra8 expression levels in vivo.
Long-term Outcomes After Surgical Resection of Pancreatic Metastases from Renal Clear-Cell Carcinoma
Authors: Malleo Giuseppe , Salvia Roberto , Maggino Laura , Marchegiani Giovanni , D’Angelica Michael , DeMatteo Ronald , Kingham Peter , Pulvirenti Alessandra , Sereni Elisabetta , Jarnagin William R. , Bassi Claudio , Allen Peter J. , Butturini Giovanni
Published: February 2021

Background

Pancreatic metastases (PM) from renal cell carcinoma (RCC) are uncommon. We herein describe the long-term outcomes associated with pancreatectomy at two academic institutions, with a specific focus on 10-year survival.

Methods

This investigation was limited to patients undergoing pancreatectomy for PM between 2000 and 2008 at the University of Verona and Memorial Sloan Kettering Cancer Center, allowing a potential for 10 years of surveillance. The probabilities of further RCC recurrence and RCC-related death were estimated using a competing risk analysis (method of Fine and Gray) to account for patients who died of other causes during follow-up.

Results

The study population consisted of 69 patients, mostly with isolated metachronous PM (77%). The median interval from nephrectomy to pancreatic metastasectomy was 109 months, whereas the median post-pancreatectomy follow-up was 141 months. The 10-year cumulative incidence of new RCC recurrence was 62.7%. In the adjusted analysis, the relative risk of repeated recurrence was significantly higher in PM synchronous to the primary RCC (sHR = 1.27) and in patients receiving extended pancreatectomy (sHR = 3.05). The 10-year cumulative incidence of disease-specific death was 25.5%. The only variable with an influence on disease-specific death was the recurrence-free interval following metastasectomy (sHR = 0.98). In patients with repeated recurrence, the 10-year cumulative incidence of RCC-related death was 35.4%.

Conclusion

In a selected group of patients followed for a median of 141 months and mostly with isolated metachronous PM, resection was associated with a high possibility of long-term disease control in surgically fit patients with metastases confined to the pancreas.
The clinical effectiveness of reconstructing 18F-sodium fluoride PET/CT bone using Bayesian penalized likelihood algorithm for evaluation of metastatic bone disease in obese patients
Authors: Usmani Sharjeel , Ahmed Najeeb , Gnanasegaran Gopinath , Rasheed Rashid , Marafi Fahad , Alnaaimi Mashari , Omar Mohammad , Musbah Ahmed , al Kandari Fareeda , De Schepper Stijn , Van den Wyngaert Tim
Published: February 2021

Objective:

A new Bayesian penalized likelihood reconstruction algorithm for positron emission tomography (PET) (Q.Clear) is now in clinical use for fludeoxyglucose (FDG) PET/CT. However, experience with non-FDG tracers and in special patient populations is limited. This pilot study aims to compare Q.Clear to standard PET reconstructions for 18F sodium fluoride (18F-NaF) PET in obese patients.

Methods:

30 whole body 18F-NaF PET/CT scans (10 patients with BMI 30–40 Kg/m2 and 20 patients with BMI >40 Kg/m2) and a NEMA image quality phantom scans were analyzed using ordered subset expectation maximization (OSEM) and Q.Clear reconstructions methods with B400, 600, 800 and 1000. The images were assessed for overall image quality (IQ), noise level, background soft tissue, and lesion detectability, contrast recovery (CR), background variability (BV) and contrast-to-noise ratio (CNR) for both algorithms.

Results:

CNR for clinical cases was higher for Q.Clear than OSEM (p < 0.05). Mean CNR for OSEM was (21.62 ± 8.9), and for Q.Clear B400 (31.82 ± 14.6), B600 (35.54 ± 14.9), B800 (39.81 ± 16.1), and B1000 (40.9 ± 17.8). As the β value increased the CNR increased in all clinical cases. B600 was the preferred β value for reconstruction in obese patients. The phantom study showed Q.Clear reconstructions gave lower CR and lower BV than OSEM. The CNR for all spheres was significantly higher for Q.Clear (independent of β) than OSEM (p < 0.05), suggesting superiority of Q.Clear.

Conclusion:

This pilot clinical study shows that Q.Clear reconstruction algorithm improves overall IQ of 18F-NaF PET in obese patients. Our clinical and phantom measurement results demonstrate improved CNR and reduced BV when using Q.Clear. A β value of 600 is preferred for reconstructing 18F-NaF PET/CT with Q.Clear in obese patients.

Advances in knowledge:

18F-NaF PET/CT is less susceptible to artifacts induced by body habitus. Bayesian penalized likelihood reconstruction with18F-NaF PET improves overall IQ in obese patients.
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Authors: Mehta Subina , Crane Marie , Leith Emma , Batut Bérénice , Hiltemann Saskia , Arntzen Magnus Ø , Kunath Benoit J. , Delogu Francesco , Sajulga Ray , Kumar Praveen , Johnson James E. , Griffin Timothy J. , Jagtap Pratik D.
Published: February 2021

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.
Keep calm and read fantasy novels
Authors:   Southern Federal University, Vinnik Evgeniya
Published: February 2021

Данное учебное пособие основано на трех произведениях британской прозы XX века в жанре фэнтези: «Лев, колдунья и платяной шкаф» К.С. Льюиса, «Гарри Поттер и философский камень» Дж. Роулинг, «Звездная пыль» Н. Геймана. Пособие состоит из трех модулей, каждый из которых содержит комплекс упражнений, который позволит усовершенствовать знание английского языка, поможет разрешить возникающие вопросы и трудности при работе с оригинальным текстом, развить восприятие английской речи на слух и привыкнуть к правилам употребления грамматических конструкций в естественных условиях функционирования языка. Пособие будет интересно и полезно всем, кто знает и изучает английский язык с преподавателем или самостоятельно. Рекомендуется студентам – бакалаврам, специалистам, магистрантам факультетов иностранных языков продолжающих изучать английский язык (уровень В1-В2 – Intermediate-Upper-Intermediate).
Methodological Support of the Work of Primary Schoolchildren with Information Presented in the Form of Diagrams
Authors: Pichugin S.
Published: February 2021

The article outlines a range of methodological problems that arise when teaching younger schoolchildren, the ability to use information presented in the form of diagrams. Modern textbooks of mathematics for elementary school and methodological recommendations to them related to the topic “Diagrams” of the section “Working with information” are analyzed. Since the development in younger schoolchildren of the skills of working with visual sign-symbolic means of graphical presentation of information is one of the requirements of the Federal State Educational Standard of Primary General Education for meta-subject learning outcomes, the author proposes methodological techniques and a system of assignments that allow to eliminate the current and potential difficulties of primary school students when mastering charts.
Methodology for Teaching Third Graders to Distinguish and Compose Monologue Texts of Different Types
Authors: Starchikova G.
Published: February 2021

Using the example of conducting a Russian language lesson in the third grade, the article reveals the methodology of forming the ability of younger students to independently construct monologue texts. The author has demonstrated the effectiveness of using a set of methodological techniques that contribute to the development of students’ ability to analyze and distinguish between texts of different types: narration, description, reasoning. This allows third graders to create their own texts, taking into account the characteristics of the type to which they belong. Taking into account the tendency of primary school children to play, research activities and dialogue with peers, the teacher offers them didactic play, educational dialogue and discussion during the lesson.
Improving the Quality of Functional Literacy of Primary Schoolchildren in the Process of Extracurricular Activities
Authors: Belousova G.
Published: February 2021

The article discusses the problem of organizing extracurricular activities of younger schoolchildren by a teacher, focused on the formation of their experience of using the skills of functional literacy in various imaginary situations. The author reveals the special importance of director’s play in improving the quality of functional literacy, gives examples of playful imaginary situations that are used in class with fourth grade students as part of an integrated extracurricular activity course, designed to develop their mathematical literacy and achieve higher meta-subject learning outcomes.
Formation of Adequate Self-Esteem in a Younger Schoolchild to Eliminate Manifestations of Deceit
Authors: Pavlova N.
Published: February 2021

The article highlights the actual psychological and pedagogical problem of manifestation of a tendency to lie in children of primary school age. Based on the study of scientific literature on this topic and the results of an experimental study conducted in the second grades of primary school, the reasons for this communicative phenomenon and its relationship with the level of self-esteem of the child are analyzed. The formation of an adequate self-esteem in a younger student is seen as a means of eliminating his manifestations of deceit. The conditions, methods and techniques of pedagogical activity aimed at the formation of an adequate self-esteem of a younger student, and the role of a teacher in this process are revealed.
Guidelines for Developing Listening Skills of Chinese Students in Business Russian
Authors: Koneva Natalya , Zhigulskaia Daria
Published: February 2021

Currently the Russian language is becoming increasingly popular in China, that’s why there is an increase in demand for the Chinese, who speak Russian. This leads to higher demand for developing materials tailored to Chinese students, who study business Russian. This article addresses the importance of developing listening skills in “Business Russian”, provides methodological guidelines and suggests exercises for developing listening skills (level B1).
Exact Facetial Odd-Cycle Separation for Maximum Cut and Binary Quadratic Optimization
Authors: Jünger Michael , Mallach Sven
Published: February 2021

The exact solution of the NP-hard (nondeterministic polynomial-time hard) maximum cut problem is important in many applications across, for example, physics, chemistry, neuroscience, and circuit layout—which is also due to its equivalence to the unconstrained binary quadratic optimization problem. Leading solution methods are based on linear or semidefinite programming and require the separation of the so-called odd-cycle inequalities. In their groundbreaking research, F. Barahona and A. R. Mahjoub have given an informal description of a polynomial-time algorithm for this problem. As pointed out recently, however, additional effort is necessary to guarantee that the inequalities obtained correspond to facets of the cut polytope. In this paper, we shed more light on a so enhanced separation procedure and investigate experimentally how it performs in comparison with an ideal setting where one could even employ the sparsest, most violated, or geometrically most promising facet-defining odd-cycle inequalities.

Summary of Contribution: This paper aims at a better capability to solve binary quadratic optimization or maximum cut problems and their various applications using integer programming techniques. To this end, the paper describes enhancements to a well-known algorithm for the central separation problem arising in this context; it is demonstrated experimentally that these enhancements are worthwhile from a computational point of view. The linear relaxations of the aforementioned problems are typically solved using fewer iterations and cutting planes than with a nonenhanced approach. It is also shown that the enhanced procedure is only slightly inferior to an ideal, enumerative, and, in practice, intractable global cutting-plane selection.
A Responsive-Pricing Retailer Sourcing from Competing Suppliers Facing Disruptions
Authors: Shan Xi , Li Tao , Sethi Suresh P.
Published: February 2021

Problem definition: We study a problem of a retailer that orders from competing strategic suppliers subject to independent or correlated disruptions and responds by setting the retail price on delivery, called responsive pricing. The suppliers set their wholesale prices in a Nash game. Academic/practical relevance: Supplier disruption correlation exists for reasons such as product and service designs, geographic proximity, and common tier 2 suppliers. In practice, many retailers are able to set the product price after knowing the delivered quantity. Methodology: We model this problem as a Stackelberg–Nash game with the suppliers as the leaders and the retailer as the follower and obtain its equilibrium explicitly. We perform sensitivity analyses with respect to suppliers’ production costs, reliabilities, and their correlation. Results: We find, surprisingly, that an increase in the reliability of a supplier may, counter to our intuition, hurt it because of the competition between the suppliers selling to a responsive-pricing retailer. Furthermore, in contrast to the literature, we find that under responsive pricing, a high disruption correlation may benefit a supplier that has a cost advantage, and the total order quantity may increase in that correlation because of supplier competition. Managerial implications: This paper has important implications for unreliable suppliers because the way reliability and correlation influence their profits depends on the retailer’s pricing power and the competition intensity between the suppliers. With a responsive-pricing retailer, a supplier may not benefit from higher reliability but may benefit from a higher correlation. This suggests that a low-cost supplier serving a responsive-pricing retailer could add to its decision-making tools a new incentive of creating a positively correlated supply network by building plants in the geographic location of its competitor or sourcing from the same tier 2 supplier to obtain an increased correlation strategically.