bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization
Authors: Zhao Yan , Dong Luhao , Jiang Conghui , Wang Xueqiang , Xie Jianyin , Rashid Muhammad Abdul Rehman , Liu Yanhe , Li Mengyao , Bu Zhimu , Wang Hongwei , Ma Xin , Sun Silong , Wang Xiaoqian , Bo Cunyao , Zhou Tingting , Kong Lingrang
Published: December 2020

Background

The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes.

Results

Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat.

Conclusions

The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors.
“Having more women humanitarian leaders will help transform the humanitarian system”: challenges and opportunities for women leaders in conflict and humanitarian health
Authors: Patel Preeti , Meagher Kristen , El Achi Nassim , Ekzayez Abdulkarim , Sullivan Richard , Bowsher Gemma
Published: December 2020

Background

It is estimated that over 40% of the half a million humanitarian workers who provide frontline care during emergencies, wars and disasters, are women. Women are at the forefront of improving health for conflict-affected populations through service delivery, education and capacity strengthening, advocacy and research. Women are also disproportionately affected by conflict and humanitarian emergencies. The growing evidence base demonstrating excess female morbidity and mortality reflects the necessity of evaluating the role of women in leadership driving health research, policy and programmatic interventions in conflict-related humanitarian contexts. Despite global commitments to improving gender equality, the issue of women leaders in conflict and humanitarian health has been given little or no attention. The aim of this paper focuses on three domains: importance, barriers and opportunities for women leaders in conflict and humanitarian health. Following thematic analysis of the material collected, we discuss the following themes: barriers of women’s leadership domain at societal level, and organisational level, which is subcategorized into culture and strategy. Building on the available opportunities and initiatives and on inspirational experiences of the limited number of women leaders in this field, recommendations for empowering and supporting women’s leadership in conflict health are presented.

Methods

A desk-based literature review of academic and grey sources was conducted followed by thematic analysis.

Results

There is very limited evidence on women leaders in conflict and humanitarian health. Some data shows that women have leadership skills that help to support more inclusive solutions which are incredibly important in this sector. However, deeply imbedded discrimination against women at the organisational, cultural, social, financial and political levels is exacerbated in conflict which makes it more challenging for women to progress in such settings.

Conclusion

Advocating for women leaders in conflict and health in the humanitarian sector, governmental bodies, academia and the global health community is crucial to increasing effective interventions that adequately address the complexity and diversity of humanitarian crises.
Age at the onset of tobacco smoking in South Africa: a discrete-time survival analysis of the prognostic factors
Authors: Fagbamigbe Adeniyi Francis , Desai Rachana , Sewpaul Ronel , Kandala Ngianga-Bakwin , Sekgala Derrick , Reddy Priscilla
Published: December 2020

Background

While knowledge of onset of smoking tobacco, and associated risk factors can aid the formulation of evidence-based policy and interventions, such information is scarce in South Africa. We assessed age at onset of tobacco smoking in South Africa and identified its risk factors.

Methods

We analysed data of 15,316 respondents aged 15–98 years from the 2012 South African National Health and Nutrition Examination Survey. Descriptive statistics and survival analysis techniques were used alongside weighted percentages.

Results

Overall lifetime prevalence of smoking was 20.5%. Among the 3360 ever-smoked respondents, the overall median age at smoking onset was 18 years (Inter-quartile range (IQR) =5) with 2% starting before age 10 while 60% had smoked before age 20. Likelihood of tobacco smoking was higher among adolescents (<=20 years) and those aged 20–29 years than those aged > = 60 years, thrice higher among males, 29% higher among urban dwellers and thrice higher in Western Cape and Free State than in North West Province. The onset of tobacco smoking was earlier among males, wealthier and “coloured” people from Northern and Eastern Capes.

Conclusion

The onset of tobacco smoking peaked at 15–22 years and varied by province, sex, location, race and other characteristics. The age restrictions on smoking in South Africa has changed over time, coupled with the recent open and electronic advertisement of tobacco, and social media could have influenced the earlier onset of tobacco smoking in South Africa. Stricter regulations on tobacco-related advertisement and sales should be implemented.
Vascular density of optic nerve head in diabetic retinopathy using optical coherence tomography angiography
Authors: Ghassemi Fariba , Berijani Sahar , Roohipoor Ramak , Mohebbi Masoumeh , Babeli Ameneh , Gholizadeh Alireza , Sabour Siamak
Published: December 2020

Purpose

To measure optic nerve head (ONH) blood perfusion using optical coherence tomography angiography (OCTA) at various stages of diabetic retinopathy (DR).

Methods

One hundred seventy six eyes of 94 patients included in this retrospective single-centre cross-sectional study. The subjects were studied in normal, no diabetic retinopathy (NDR), non-proliferative diabetic retinopathy (NPDR) and proliferative retinopathy (PDR) groups. The eyes were subjected to AngioDisc ONH imaging using OCTA for papillary (Disc) and peripapillary (RPC) vascular density (VD) evaluation.

Results

The mean age of the participants was 56.08 ± 8.87 years and 34 (36.2 percent) were male. With increased DR severity, a statistically significant decrease in peripapillary VD was found. The study showed that only VD of the whole RPC (W-RPC) could be a valid biomarker in the staging assessment. VD of RPC, in all subsections, was considerably different from normal cases in the PDR group. Visual acuity was correlated with whole image ONH VD. The duration of DM, FBS, hyperlipidemia and DME had no effect on the ONH perfusion.

Conclusions

The study showed that only the W-RPC VD could be a reasonable marker in the staging assessment. VDs assessed by OCTA can be useful for assessing and tracking early ONH changes in DR patients.
Botanical description, phytochemistry, traditional uses, and pharmacology of Crataeva nurvala Buch. Ham.: an updated review
Authors: Kumar Dinesh , Sharma Shivangi , Kumar Sunil
Published: December 2020

Background

Crataeva nurvalaBuch. Ham., an important medicinal plant of the Capparidaceae family, is widely distributed in India and tropical and subtropical parts of the world. It has been reported for its folkloric use in various disorders such as blood purifier,breathing problems, fever, metabolic disorders, wound healing, memory loss, and weak immune system.

Results

The present review has focused on the botanical description and ethnomedicinal and traditional uses ofC.nurvalaalong with its reported pharmacological activities. Chief chemical constituents and pharmacological aspects ofC.nurvalahave been deeply explored to unravel the unexplored folklore/ethnomedicinal uses of this plant so that the researchers working on this plant may be able to find new insights to continue further investigation on this plant. The pharmacological aspects like anti-diabetic, anti-inflammatory, anti-nociceptive, anti-diarrheal, anti-fertility, anti-pyretic, and anti-cancer potentials evaluated by various in vitro/in vivo methods on this plant have been reported.

Conclusion

Various traditional uses have been reported that need to be scientifically investigated in depth and several pharmacological activities have been reported for theC.nurvala, but more detailed and mechanism-based studies linked to a particular lead compound need to be targeted in the future. Moreover, this plant has not been completely assessed on the basis of its safety and efficacy on humans. It is expected that this review will compile and improve the existing knowledge on the potential utilization ofC.nurvalain complementary and alternative medicine.
Gambling in Malaysia: an overview
Authors: Rathakrishnan Balan , George Sanju
Published: December 2020

Many forms of gambling are legal and popular in Malaysia. Despite this, in Malaysia, research into gambling is limited and there is no coherent strategy to tackle gambling-related harms. This paper summarises the gambling landscape of Malaysia, law governing gambling and research done so far and gives some recommendations on the way forward.
Single shot echo planar imaging (ssEPI) vs single shot turbo spin echo (ssTSE) DWI of the orbit in patients with ocular melanoma
Authors: Gumeler Ekim , Parlak Safak , Yazici Gozde , Karabulut Erdem , Kiratli Hayyam , Oguz Kader K
Published: December 2020

Objectives:

Diffusion weighted imaging (DWI) has become important for orbital imaging. However, the echoplanar imaging (EPI) DWI has inherent obstacles due to susceptibility to magnetic field inhomogeneities. We conducted a comparative study assessing the image quality of orbits in a patient cohort with uveal melanoma (UM). We hypothesized that single shot turbo spin echo (ssTSE) DWI would have better image quality in terms of less distortion and artifacts and yield better tissue evaluation compared to ssEPI-DWI.

Methods:

ssEPI-DWI and ssTSE-DWI of orbits were obtained from 50 patients with uveal melanoma who were prospectively enrolled in the study. Distortion ratio (DR), signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), diffusion signal properties, and apparent diffusion coefficient (ADC) values were collected and compared between ssEPI-DWI and ssTSE-DWI. Two reviewers evaluated and compared the geometric distortion, susceptibility and ghosting artifacts, resolution, demarcation of ocular mass, and overall quality.

Results:

A higher DR was found in ssEPI-DWI compared to ssTSE-DWI (p < 0.001). SNR and CNR were lower for the temporal lobe cortex (p ≤ 0.004), but higher for melanoma in ssEPI-DWI than ssTSE-DWI (p ≤ 0.037). Geometric distortion and artifacts were more common in ssEPI-DWI (p < 0.001). Resolution (p ≤ 0.013) and overall quality (p < 0.001) were better in ssTSE-DWI. Ocular masses were demarcated better on ssEPI-DWI (p ≤ 0.002). Significant negative correlations between T1 and T2 signal intensities (r = −0.369, p ≤ 0.008) and positive correlations between T2 and both DWI signal intensities (r = 0.686 and p < 0.001 for ssEPI-DWI, r = 0.747 and p < 0.001 for ssTSE-DWI) were revealed.

Conclusion:

With less geometric distortion and susceptibility artifacts, better resolution, and overall quality, ssTSE-DWI can serve as an alternative to ssEPI-DWI for orbital DWI.

Advances in knowledge:

ssTSE-DWI can be a better alternative of diffusion imaging of orbits with less susceptibility artifact and geometric distortion compared to ssEPI-DWI.
Prediction of lymph node metastases using pre-treatment PET radiomics of the primary tumour in esophageal adenocarcinoma: an external validation study
Authors: Zhang Chong , Shi Zhenwei , Kalendralis Petros , Whybra Phil , Parkinson Craig , Berbee Maaike , Spezi Emiliano , Roberts Ashley , Christian Adam , Lewis Wyn , Crosby Tom , Dekker Andre , Wee Leonard , Foley Kieran G
Published: December 2020

Objectives:

To improve clinical lymph node staging (cN-stage) in oesophageal adenocarcinoma by developing and externally validating three prediction models; one with clinical variables only, one with positron emission tomography (PET) radiomics only, and a combined clinical and radiomics model.

Methods:

Consecutive patients with fluorodeoxyglucose (FDG) avid tumours treated with neoadjuvant therapy between 2010 and 2016 in two international centres (n = 130 and n = 60, respectively) were included. Four clinical variables (age, gender, clinical T-stage and tumour regression grade) and PET radiomics from the primary tumour were used for model development. Diagnostic accuracy, area under curve (AUC), discrimination and calibration were calculated for each model. The prognostic significance was also assessed.

Results:

The incidence of lymph node metastases was 58% in both cohorts. The areas under the curve of the clinical, radiomics and combined models were 0.79, 0.69 and 0.82 in the developmental cohort, and 0.65, 0.63 and 0.69 in the external validation cohort, with good calibration demonstrated. The area under the curve of current cN-stage in development and validation cohorts was 0.60 and 0.66, respectively. For overall survival, the combined clinical and radiomics model achieved the best discrimination performance in the external validation cohort (X2 = 6.08, df = 1, p = 0.01).

Conclusion:

Accurate diagnosis of lymph node metastases is crucial for prognosis and guiding treatment decisions. Despite finding improved predictive performance in the development cohort, the models using PET radiomics derived from the primary tumour were not fully replicated in an external validation cohort.

Advances in knowledge:

This international study attempted to externally validate a new prediction model for lymph node metastases using PET radiomics. A model combining clinical variables and PET radiomics improved discrimination of lymph node metastases, but these results were not externally replicated.
An asymptomatic detachment of the appendix evolved to giant abscess and complete colliquative necrosis: pivotal role of computed tomography in patient management
Authors: Di Vincenzo Anna Olga , Parmeggiani Anna , Casavola Mario , Leonardo Stefano , Golfieri Rita
Published: December 2020

Acute appendicitis (AA) is one of the most common causes of acute abdominal pain and it generally affects young males in the second or third decade of their life. Due to its often insidious presentations, the diagnosis is challenging and, if delayed, can lead to life-threatening complications. This report describes a rare case of an almost asymptomatic complicated appendicitis caused by an appendicolith followed by spontaneous detachment of the vermiform appendix and its complete colliquative necrosis with abscess formation. Thus far this is the first case of spontaneous appendix avulsion in an adult where the appendix is entirely colliquated into an abscess.
Διερευνώντας την προοπτική της αειφορίας στο σύγχρονο πανεπιστήμιο
Authors: Κάτσενου Χριστίνα , Φλογαΐτη Ευγενία
Published: December 2020

Η παρούσα ερευνητική εργασία επιδίωξε να διερευνήσει τις δυνατότητες ανάπτυξης ενός πανεπιστημιακού τμήματος ως εκπαιδευτικού οργανισμού που κινείται στην κατεύθυνση της  Εκπαίδευσης για την Αειφόρο Ανάπτυξη (ΕΑΑ). Η έρευνα εφαρμόστηκε στο Τμήμα ... του Πανεπιστημίου ... Η διεξαγωγή της έρευνας συντονίστηκε από πέντε φοιτητικές ομάδες που μελετούσαν συγκεκριμένες προβληματικές καταστάσεις εντός του πανεπιστημιακού κτιρίου και προωθούσαν λύσεις στην κατεύθυνση της EAA. Η Έρευνα Δράσης ήταν η ερευνητική μέθοδος που επιλέχθηκε για την οργάνωση της ερευνητικής διαδικασίας. Η ανάλυση των ερευνητικών δεδομένων έδειξε ότι οι παγιωμένες αντιλήψεις, η γραφειοκρατική κουλτούρα και οι πολύπλοκες οργανωτικές και διοικητικές δομές λειτουργούσαν ανασταλτικά στην προσπάθεια αναμόρφωσης του πανεπιστημίου.
Alleviative effects of Fara-darmani Consciousness Field on Triticum aestivum L. under salinity stress
Authors: Torabi Sara , Taheri Mohammad Ali , Semsarha Farid
Published: December 2020

Background: The Fara-darmani Consciousness Field was founded by Mohammad Ali Taheri. It is a novel field and is described similarly to the field of gravity, or the electromagnetic field. This field is neither matter nor energy, and therefore does not possess a quantity. Even though there is no direct scientific evidence for the Consciousness Field, it is possible to investigate its effects on objects through controlled experiments. The aim of the present work was to study the alleviative effects of the Fara-darmani Consciousness Field on common wheatTriticum aestivum L. var Star under salt stress.

Methods: Plants were grown under 0 mM NaCl (control) and 150 mM NaCl with or without the influence of Fara-darmani Consciousness Field for 3 weeks. Chlorophyll, hydrogen peroxide (H2O2), malondialdehyde (MDA) content and activity of antioxidant enzymes such as superoxide dismutase (SOD),polyphenol oxidase (PPO), and peroxidase (POX) were measured in all groups of plants.

Results: In the salt-treated plants under the influence of the Fara-darmani Consciousness Field, the contents of total chlorophyll, as well as a and b chlorophyll forms, were elevated compared with the salt-treated plants without Fara-darmani CF (34.8%, 17.8%, and 169% respectively). Additionally, Fara-darmani increased H2O2(57%) and the activity of SOD and PPO by 220% and 168%, respectively, under salinity compared with the salt-treated plants without Fara-darmani CF. MDA content and activity of peroxidase were decreased by 12.5% and 34%, respectively.

Conclusion: These results suggest the Fara-darmani Consciousness Field as a qualitative intervention strategy to withstand salt stress in plants, by increasing the contents of chlorophyll, antioxidant enzyme activities, and decreasing MDA content under salinity.
Biocuration - mapping resources and needs
Authors: Holinski Alexandra , Burke Melissa L. , Morgan Sarah L. , McQuilton Peter , Palagi Patricia M.
Published: December 2020

Background: Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers. Therefore, the ELIXIR Training Platform launched an Implementation Study in order to i) identify communities of biocurators, ii) map the type of curation work being done, iii) assess biocuration training, and iv) draw a picture of biocuration career development.

Methods: To achieve the goals of the study, we carried out a global survey on the nature of biocuration work, the tools and resources that are used, training that has been received and additional training needs. To examine these topics in more detail we ran workshop-based discussions at ISB Biocuration Conference 2019 and the ELIXIR All Hands Meeting 2019. We also had guided conversations with selected people from the EMBL-European Bioinformatics Institute.

Results: The study illustrates that biocurators have diverse job titles, are highly skilled, perform a variety of activities and use a wide range of tools and resources. The study emphasises the need for training in programming and coding skills, but also highlights the difficulties curators face in terms of career development and community building.

Conclusion: Biocurators themselves, as well as organisations like ELIXIR, GOBLET and ISB must work together towards structural change to overcome these difficulties. In this article we discuss recommendations to ensure that biocuration as a role is visible and valued, thereby helping biocurators to proceed with their career.
Who needs a flu vaccination in 2020?
Authors: Duncan Debbie
Published: December 2020

Influenza is a contagious respiratory illness caused by a number of specific viruses. These vary each year and the vaccinations we use reflect this. Most people recover from fever and other symptoms within a week without any features of complicated influenza. There are specific groups of people who are more susceptible to influenza and its resulting complications. Vaccination is the key to reducing risk and this should be promoted in general practice particularly for the ‘at risk groups'. It is more important than ever this year due to the COVID-19 pandemic and the impact this could have on NHS services if we also have a bad influenza season.
Medical Image of the Month: Superior Vena Cava Syndrome
Authors:   University of Arizona, Tucson, AZ USA, Borchart Matthew , Yu Daniel , Nandi Indrajit
Published: December 2020

No abstract available. Article truncated after 150 words. History A 74-year- old man with a history of diastolic heart failure, chronic kidney disease (CKD), and chronic lymphocytic leukemia (CLL) presented with a complaint of dyspnea. He has had several hospitalizations in the last year for heart failure exacerbation and his home bumetanide was recently increased from twice to three times daily due to persistently increasing weight. His CLL was diagnosed two years prior and treatment was stopped three months ago due to side effects. In the emergency department he reported three weeks of worsening dyspnea especially when lying flat, as well as increased swelling in his legs, abdomen, arms, and face. His weight was up to 277lbs from 238lbs the month before. His diuretics were transitioned to IV, but over the next few days he remained clinically volume overloaded. A noncontrast chest CT was obtained to help evaluate his ongoing respiratory distress (Figure 1). It demonstrated innumerable lymph …
The Latin American Movement for Reconceptualisation and radical social work (1960–80): possible similarities
Authors: dos Santos Cláudia Mônica , Eiras Alexandra A. Leite T. Seabra , Defilippo Antoniana Dias , Yazbek Maria Carmelita
Published: December 2020

This article deals with the protest movements in Latin American, American and British social work from 1960 to 1980, highlighting the historical and theoretical characteristics of the debate of the radical social work movement and of the Latin American Movement for Reconceptualisation within the context of the Marxist legacy. Within the objective of this article is an analysis of the relationship between the European and American social work protest movements and the Latin American Movement for Reconceptualisation, examining, for the delineated period, the overlaps between the regions involved (the UK, the US and Latin America) in a process of accentuated economic interaction at the global level. In other words, the issue of interest to us in this study is whether there was an actual relationship between the European and American social work protest movements and the Latin American Movement for Reconceptualisation, and on what basis it could be described.
Social work, contestatory movements and socio-professional struggles in the Iberian Peninsula in the 1970s
Authors: Matos-Silveira Rosana , Silva Pedro Gabriel , Martins Alcina , Carrara Virgínia Alves , Perelló Miguel Ángel Oliver
Published: December 2020

A Revolution in Portugal and a democratic transition in Spain marked the end of the Iberian dictatorships in the 1970s. In this article, the results from research focused on the repercussions of contestatory movements for the social work profession in Portugal and Spain during that decade are presented. The information gathered from literature and oral sources allows perceiving the changes endured by social work in both countries, its professional disputes and the impact of the Latin American Reconceptualisation Movement. Special attention will be devoted to the influence of this social work movement, considering the specific socio-historical contexts of Portugal and Spain, and its particular professional backgrounds.
Predicting lifetime of optical components with Bayesian inference
Authors: Smalakys Linas , Melninkaitis Andrius
Published: December 2020

Virtually all optical materials degrade over time when they are used in high average power or intensity optical systems. Extrapolation of optical components lifetime is crucial in such applications in order to avoid downtime or project failure. Measurements of the laser-induced damage threshold (LIDT) fatigue are usually done using the so-called S-on-1 test described in the ISO 21254-2 standard. The standard, however, suggests only rudimentary techniques for extrapolating LIDT, which are rarely used in practice, therefore, the goal of this work was to provide a framework for analyzing LIDT fatigue data using well established methods of Bayesian statistics. Numerical S-on-1 experiments (assuming constant fatigue) were performed for cases of online detection, interval detection and offline detection. Appropriate lifetime distributions were determined and used to fit simulated data taking into consideration data censoring. Credible intervals of lifetime predictions were determined using Markov chain Monte Carlo (MCMC) technique and compared with results from multiple experiments. The Bayesian lifetime analysis method was compared with technique described in the ISO 21254-2 standard for cases of low and high defect densities. Finally, the outlined extrapolation technique was applied to extrapolate lifetime of HR dielectric mirror.
Near-UV optical cavities in Ga2O3 nanowires
Authors: Alonso-Orts Manuel , Chilla Gerwin , Hötzel Rudolfo , Nogales Emilio , San Juan José M. , Nó María L. , Eickhoff Martin , Méndez Bianchi
Published: December 2020

In this Letter, we report optical confinement in the near-ultraviolet
(near-UV) range in

G
a

2

O

3

nanowires (NWs) by distributed Bragg
reflector (DBR) nanopatterned cavities. High-contrast DBRs, which act
as the end mirrors of the cavities of the desired length, are designed
and fabricated by focused ion beam etching. The resonant modes of the
cavities are analyzed by micro-photoluminescence measurements,
analytical models, and simulations, which show very good agreement
between each other. Experimental reflectivities up to 50% are obtained
over the 350–410 nm region for the resonances in this wavelength
range. Therefore,

G
a

2

O

3

NW optical cavities are shown as good
candidates for single-material-based near-UV light emitters.
Cross-phase modulational instability of circularly polarized helical Bloch modes carrying optical vortices in a chiral three-core photonic crystal fiber
Authors: Roth Paul , Frosz Michael H. , Weise Linda , Russell Philip St.J. , Wong Gordon K. L.
Published: December 2020

We report the first, to the best of our knowledge, observation of cross-phase modulational instability (XPMI) of circularly polarized helical Bloch modes carrying optical vortices in a twisted photonic crystal fiber with a three-fold symmetric core, formed by spinning the fiber preform during the draw. When the fiber is pumped by a superposition of left-circular polarization (LCP) and right-circular polarization (RCP) modes, a pair of orthogonal circularly polarized sidebands of opposite topological charge is generated. When, on the other hand, a pure LCP (or RCP) mode is launched, the XPMI gain is zero, and no sidebands are seen. This observation has not been seen before in any system and is unique to chiral structures with

-fold rotational symmetry. The polarization state and topological charge of the generated sidebands are measured. By decomposing the helical Bloch modes into their azimuthal harmonics, we are able to deduce the selection rules for the appearance of modulational instability sidebands. We showed that the four waves in the nonlinear mixing process must exhibit the same set of azimuthal harmonic orders.
Trade-offs between cost and accuracy in active case finding for tuberculosis: A dynamic modelling analysis
Authors: Cilloni Lucia , Kranzer Katharina , Stagg Helen R. , Arinaminpathy Nimalan
Published: December 2020

Background

Active case finding (ACF) may be valuable in tuberculosis (TB) control, but questions remain about its optimum implementation in different settings. For example, smear microscopy misses up to half of TB cases, yet is cheap and detects the most infectious TB cases. What, then, is the incremental value of using more sensitive and specific, yet more costly, tests such as Xpert MTB/RIF in ACF in a high-burden setting?

Methods and findings

We constructed a dynamic transmission model of TB, calibrated to be consistent with an urban slum population in India. We applied this model to compare the potential cost and impact of 2 hypothetical approaches following initial symptom screening: (i) ‘moderate accuracy’ testing employing a microscopy-like test (i.e., lower cost but also lower accuracy) for bacteriological confirmation and (ii) ‘high accuracy’ testing employing an Xpert-like test (higher cost but also higher accuracy, while also detecting rifampicin resistance). Results suggest that ACF using a moderate-accuracy test could in fact cost more overall than using a high-accuracy test. Under an illustrative budget of US$20 million in a slum population of 2 million, high-accuracy testing would avert 1.14 (95% credible interval 0.75–1.99, with p = 0.28) cases relative to each case averted by moderate-accuracy testing. Test specificity is a key driver: High-accuracy testing would be significantly more impactful at the 5% significance level, as long as the high-accuracy test has specificity at least 3 percentage points greater than the moderate-accuracy test. Additional factors promoting the impact of high-accuracy testing are that (i) its ability to detect rifampicin resistance can lead to long-term cost savings in second-line treatment and (ii) its higher sensitivity contributes to the overall cases averted by ACF. Amongst the limitations of this study, our cost model has a narrow focus on the commodity costs of testing and treatment; our estimates should not be taken as indicative of the overall cost of ACF. There remains uncertainty about the true specificity of tests such as smear and Xpert-like tests in ACF, relating to the accuracy of the reference standard under such conditions.

Conclusions

Our results suggest that cheaper diagnostics do not necessarily translate to less costly ACF, as any savings from the test cost can be strongly outweighed by factors including false-positive TB treatment, reduced sensitivity, and foregone savings in second-line treatment. In resource-limited settings, it is therefore important to take all of these factors into account when designing cost-effective strategies for ACF.
Spatiotemporal analysis of mycolactone distribution in vivo reveals partial diffusion in the central nervous system
Authors: Colucci-Guyon Emma , Rifflet Aline , Saint-Auret Sarah , da Costa Anaëlle , Boucontet Laurent , Laval Thomas , Prehaud Christophe , Blanchard Nicolas , Levraud Jean-Pierre , Boneca Ivo G. , Demangel Caroline , Guenin-Macé Laure
Published: December 2020

Mycobacterium ulcerans, the causative agent of Buruli ulcer (BU) disease, is unique amongst human pathogens in its capacity to produce a lipid toxin called mycolactone. While previous studies have demonstrated that bacterially-released mycolactone diffuses beyond infection foci, the spatiotemporal distribution of mycolactone remained largely unknown. Here, we used the zebrafish model to provide the first global kinetic analysis of mycolactone’s diffusion in vivo, and multicellular co-culture systems to address the critical question of the toxin’s access to the brain.

Zebrafish larvae were injected with a fluorescent-derivative of mycolactone to visualize the in vivo diffusion of the toxin from the peripheral circulation. A rapid, body-wide distribution of mycolactone was observed, with selective accumulation in tissues near the injection site and brain, together with an important excretion through the gastro-intestinal tract. Our conclusion that mycolactone reached the central nervous system was reinforced by an in cellulo model of human blood brain barrier and a mouse model of M. ulcerans-infection.

Here we show that mycolactone has a broad but heterogenous profile of distribution in vivo. Our investigations in vitro and in vivo support the view that a fraction of bacterially-produced mycolactone gains access to the central nervous system. The relative persistence of mycolactone in the bloodstream suggests that assays of circulating mycolactone are relevant for BU disease monitoring and treatment optimization.
Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112
Authors: Yang Yan , Dhakal Smit , Chu Chenggen , Wang Shichen , Xue Qingwu , Rudd Jackie C. , Ibrahim Amir M. H. , Jessup Kirk , Baker Jason , Fuentealba Maria Pilar , Devkota Ravindra , Baker Shannon , Johnson Charles D. , Metz Richard , Liu Shuyu
Published: December 2020

Two drought-tolerant wheat cultivars, ‘TAM 111’ and ‘TAM 112’, have been widely grown in the Southern Great Plains of the U.S. and used as parents in many wheat breeding programs worldwide. This study aimed to reveal genetic control of yield and yield components in the two cultivars under both dryland and irrigated conditions. A mapping population containing 124 F5:7 recombinant inbred lines (RILs) was developed from the cross of TAM 112/TAM 111. A set of 5,948 SNPs from the wheat 90K iSelect array and double digest restriction-site associated DNA sequencing was used to construct high-density genetic maps. Data for yield and yield components were obtained from 11 environments. QTL analyses were performed based on 11 individual environments, across all environments, within and across mega-environments. Thirty-six unique consistent QTL regions were distributed on 13 chromosomes including 1A, 1B, 1D, 2A, 2D, 3D, 4B, 4D, 6A, 6B, 6D, 7B, and 7D. Ten unique QTL with pleiotropic effects were identified on four chromosomes and eight were in common with the consistent QTL. These QTL increased dry biomass grain yield by 16.3 g m-2, plot yield by 28.1 g m-2, kernels spike-1 by 0.7, spikes m-2 by 14.8, thousand kernel weight by 0.9 g with favorable alleles from either parent. TAM 112 alleles mainly increased spikes m-2 and thousand kernel weight while TMA 111 alleles increased kernels spike-1, harvest index and grain yield. The saturated genetic map and markers linked to significant QTL from this study will be very useful in developing high throughput genotyping markers for tracking the desirable haplotypes of these important yield-related traits in popular parental cultivars.
A DNA algorithm for the job shop scheduling problem based on the Adleman-Lipton model
Authors: Tian Xiang , Liu Xiyu , Zhang Hongyan , Sun Minghe , Zhao Yuzhen
Published: December 2020

A DNA (DeoxyriboNucleic Acid) algorithm is proposed to solve the job shop scheduling problem. An encoding scheme for the problem is developed and DNA computing operations are proposed for the algorithm. After an initial solution is constructed, all possible solutions are generated. DNA computing operations are then used to find an optimal schedule. The DNA algorithm is proved to have an O(n2) complexity and the length of the final strand of the optimal schedule is within appropriate range. Experiment with 58 benchmark instances show that the proposed DNA algorithm outperforms other comparative heuristics.
COVID-19 healthcare demand projections: Arizona
Authors: Gel Esma S. , Jehn Megan , Lant Timothy , Muldoon Anna R. , Nelson Trisalyn , Ross Heather M.
Published: December 2020

Beginning in March 2020, the United States emerged as the global epicenter for COVID-19 cases with little to guide policy response in the absence of extensive data available for reliable epidemiological modeling in the early phases of the pandemic. In the ensuing weeks, American jurisdictions attempted to manage disease spread on a regional basis using non-pharmaceutical interventions (i.e., social distancing), as uneven disease burden across the expansive geography of the United States exerted different implications for policy management in different regions. While Arizona policymakers relied initially on state-by-state national modeling projections from different groups outside of the state, we sought to create a state-specific model using a mathematical framework that ties disease surveillance with the future burden on Arizona’s healthcare system. Our framework uses a compartmental system dynamics model using a SEIRD framework that accounts for multiple types of disease manifestations for the COVID-19 infection, as well as the observed time delay in epidemiological findings following public policy enactments. We use a compartment initialization logic coupled with a fitting technique to construct projections for key metrics to guide public health policy, including exposures, infections, hospitalizations, and deaths under a variety of social reopening scenarios. Our approach makes use of X-factor fitting and backcasting methods to construct meaningful and reliable models with minimal available data in order to provide timely policy guidance in the early phases of a pandemic.
Effects of unilateral posterior missing-teeth on the temporomandibular joint and the alignment of cervical atlas
Authors: Fang Tsun-Hung , Chiang Meng-Ta , Hsieh Ming-Chun , Kung Ling-Yu , Chiu Kuo-Chou
Published: December 2020

Cervical atlas alignment changes are associated with craniofacial development. Disturbance of craniofacial development may be associated with temporal mandibular joint function. Therefore, we examined the possibility of a correlation between unilateral missing teeth and morphologic changes of the spine and posture. We collected eighty-nine patients (38 men and 51 women) with unilateral posterior missing teeth and twenty patients without previous orthodontic treatment or missing posterior teeth by tracing and analyzing their panoramic and cephalometric film. We measured the angulations of articular eminence, cranio-cervical angle, and the percentage of the occlusal plane passing through the first and second cervical vertebrae with other morphologic geometric data. The angle of articular eminence inclination was higher in the non-missing teeth group than the missing teeth group (46.66° and 42.28°, respectively). The cranio-cervical angle was smaller in the missing posterior teeth group than the non-missing posterior teeth group (99.81° and 103.27°, respectively). The missing teeth group also showed fewer occlusal planes passing through the intersection of the first and second cervical vertebrae compared to the non-missing teeth group (28.9% and 65%, respectively). Individuals with unilateral missing teeth had lower articular eminence inclination, smaller cranio-cervical angle, and a lower percentage of the occlusal plane passing through the intersection of the first and second cervical vertebrae.
A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
Authors: Ekman Lisa , Bagge Elisabeth , Nyman Ann , Persson Waller Karin , Pringle Märit , Segerman Bo
Published: December 2020

Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on theirk-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g.Corynebacterium,Staphylococcus,Brevibacterium luteolum,Trueperella pyogenesandFusobacterium necrophorum.Bifidobacteriumspp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.
Genetic liability in individuals at ultra-high risk of psychosis: A comparison study of 9 psychiatric traits
Authors: Lim Keane , Lam Max , Huang Hailiang , Liu Jianjun , Lee Jimmy
Published: December 2020

Individuals at ultra-high risk (UHR) of psychosis are characterised by the emergence of attenuated psychotic symptoms and deterioration in functioning. In view of the high non-psychotic comorbidity and low rates of transition to psychosis, the specificity of the UHR status has been called into question. This study aims to (i) investigate if the UHR construct is associated with the genetic liability of schizophrenia or other psychiatric conditions; (ii) examine the ability of polygenic risk scores (PRS) to discriminate healthy controls from UHR, remission and conversion status. PRS was calculated for 210 youths (nUHR = 102, nControl = 108) recruited as part of the Longitudinal Youth at Risk Study (LYRIKS) using nine psychiatric traits derived from twelve large-scale psychiatric genome-wide association studies as discovery datasets. PRS was also examined to discriminate UHR-Healthy control status, and healthy controls from UHR remission and conversion status. Result indicated that schizophrenia PRS appears to best index the genetic liability of UHR, while trend level associations were observed for depression and cross-disorder PRS. Schizophrenia PRS discriminated healthy controls from UHR (R2 = 7.9%, p = 2.59 x 10−3, OR = 1.82), healthy controls from non-remitters (R2 = 8.1%, p = 4.90 x 10−4, OR = 1.90), and converters (R2 = 7.6%, p = 1.61 x 10−3, OR = 1.82), with modest predictive ability. A trend gradient increase in schizophrenia PRS was observed across categories. The association between schizophrenia PRS and UHR status supports the hypothesis that the schizophrenia polygenic liability indexes the risk for developing psychosis.
NIRS-based monitoring of kidney graft perfusion
Authors: Maly Stepan , Janousek Libor , Bortel Radoslav , Sebek Jan , Hospodka Jiri , Skapa Jiri , Fronek Jiri
Published: December 2020

Introduction

Acute early vascular complications are rare, but serious complications after kidney transplantation. They often result in graft loss. For this reason, shortening the diagnostic process is crucial. Currently, it is standard procedure to monitor renal graft perfusion using Doppler ultrasound (DU). With respect to acute vascular complications, the main disadvantage of this type of examination is its periodicity. It would be of great benefit if graft blood perfusion could be monitored continuously during the early postoperative period. It appears evident that a well-designed near infrared spectroscopy (NIRS) monitoring system could prove very useful during the early post-transplantation period. Its role in the immediate diagnosis of vascular complications could result in a significant increase in graft salvage, thus improving the patient’s overall quality of life and lowering morbidity and mortality for renal graft recipients. The aim of this study was to design, construct and test such a monitoring system.

Materials and methods

We designed a rough NIRS-based system prototype and prepared a two-stage laboratory experiment based on a laboratory pig model. In the first stage, a total of 10 animals were used to verify and optimize the technical aspects and functionality of the prototype sensor by testing it on the animal kidneys in-vivo. As a result of these tests, a more specific prototype was designed. During the second stage, we prepared a unique laboratory model of a pig kidney autotransplantation and tested the system for long-term functionality on a group of 20 animals. Overall sensitivity and specificity were calculated, and a final prototype was prepared and completed with its own analytic software and chassis.

Results

We designed and constructed a NIRS-based system for kidney graft perfusion monitoring. The measurement system provided reliable performance and 100% sensitivity when detecting acute diminished blood perfusion of the transplanted kidneys in laboratory conditions.

Conclusion

The system appears to be a useful tool for diagnosing diminished blood perfusion of kidney transplants during the early postoperative period. However, further testing is still required. We believe that applying our method in current human transplantation medicine is feasible, and we are confident that our prototype is ready for human testing.