bluuebunny/crossref_metadata_2025 huggingface dataset:
53BP1 mediated recruitment of RASSF1A at ribosomal DNA breaks facilitates local ATM signal amplification
Authors: Tsaridou Stavroula , Velimezi Georgia , Willenbrock Frances , Chatzifrangkeskou Maria , Panagopoulos Andreas , Karamitros Dimitris , Gorgoulis Vassilis , Lygerou Zoi , O’Neill Eric , Pefani Dafni Eleftheria
Published: November 2021

DNA lesions occur across the genome and constitute a threat to cell viability; however, damage at specific genomic loci has a disproportionally greater impact on the overall genome stability. The ribosomal RNA gene repeats (rDNA) are emerging fragile sites due to repetitive nature, clustering and high transcriptional activity. Notably, recent progress in understanding how the rDNA damage response is organized has highlighted the key role of adaptor proteins in the response.

Here we identify that the scaffold and tumor suppressor, RASSF1A is recruited at sites of damage and particularly enriched at rDNA breaks. Employing targeted nucleolar DNA damage, we find that RASSF1A recruitment requires ATM activity and depends on the 53BP1. At sites of damage RASSF1A facilitates local ATM signal establishment and rDNA break repair. RASSF1A silencing, a common epigenetic event during malignant transformation, results in persistent breaks, rDNA copy number alterations and decreased cell viability. Moreover, meta-analysis of a lung adenocarcinoma cohort showed that epigenetic silencing of the scaffold leads in rDNA copy number discrepancies. Overall, we present evidence that RASSF1A acts as a DNA repair factor and offer mechanistic insight in how the nucleolar DNA damage response is organized.
Aspergillus fumigatus ffmA encodes a C2H2-containing transcriptional regulator that modulates azole resistance and is required for normal growth
Authors: Paul Sanjoy , Bowyer Paul , Bromley Michael , Moye-Rowley W. Scott
Published: November 2021

The production of a collection of disruption mutant strains corresponding to a large number of transcription factors from the filamentous fungal pathogen Aspergillus fumigatus has permitted rapid identification of transcriptional regulators involved in a range of different processes. Here we characterize a gene designated ffmA (favors fermentative metabolism) as an C2H2-containing transcription factor that is required for azole drug resistance and normal growth. Loss of ffmA caused cells to exhibit significant defects in growth, either under untreated or azole-challenged conditions. Loss of FfmA caused a reduction in expression of the AbcG1 ATP-binding cassette transporter, previousy shown to contribute to azole resistance. Strikingly, overproduction of the AtrR transcription factor gene restored a wild-type growth phenotype to a ffmAΔ strain. Overexpression of AtrR also suppressed the defect in AbcG1 expression caused by loss of FfmA. Replacement of the ffmA promoter with a doxycycline-repressible promoter restored near normal growth in the absence of doxycycline. Finally, chromatin immunoprecipitation experiments indicated that FfmA bound to its own promoter as well as to the abcG1 promoter. These data imply that FfmA and AtrR interact both with respect to abcG1 expression and also more broadly to regulate hyphal growth.

Importance

Infections associated with azole-resistant forms of the primary human pathogen, Aspergillus fumigatus, are associated with poor outcomes in patient populations. This makes analysis of the mechanisms underlying azole resistance of A. fumigatus a high priority. In this work, we describe characterization of a gene designated ffmA that encodes a sequence-specific transcriptional regulator. We identified ffmA in a screen of a collection of gene disruption mutant strains made in A. fumigatus. Loss of ffmA caused sensitivity to azole drugs and also a large reduction in normal growth. We found that overproduction of the AtrR transcription factor was able to restore growth to ffmA null cells. We provide evidence that FfmA can recognize promoters of genes involved in azole resistance as well as the ffmA promoter itself. Our data indicate that FfmA and AtrR interact to support azole resistance and normal growth.
Activating silent glycolysis bypasses inEscherichia coli
Authors: Iacometti Camillo , Marx Katharina , Hönick Maria , Biletskaia Viktoria , Schulz-Mirbach Helena , Satanowski Ari , Dronsella Beau , Delmas Valérie A. , Berger Anne , Dubois Ivan , Bouzon Madeleine , Döring Volker , Noor Elad , Bar-Even Arren , Lindner Steffen N.
Published: November 2021

All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate inE. coli, we complementarily employedin silicodesign, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal, the other via serine biosynthesis and degradation. Then, we implemented both pathways inE. colistrains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal immediately operated in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary for implementing a functional methylglyoxal pathway. Furthermore, we engineered the ‘serine shunt’ which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection we performed an adaptive laboratory evolution study using an enolase deletion strain. The evolved mutants were shown to use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.
Antagonism of the azoles to olorofim and cross-resistance are governed by linked transcriptional networks in Aspergillus fumigatus
Authors: van Rhijn Norman , Hemmings Sam , Storer Isabelle S. R. , Valero Clara , Alshammri Hajer , Goldman Gustavo H. , Gsaller Fabio , Amich Jorge , Bromley Michael J
Published: November 2021

Aspergillosis, in its various manifestations, is a major cause of morbidity and mortality. Very few classes of antifungal drugs have been approved for clinical use to treat these diseases and resistance to the first line therapeutic class, the triazoles, is increasing. A new class of antifungals that target pyrimidine biosynthesis, the orotomides, are currently in development with the first compound in this class, olorofim in late-stage clinical trials. In this study, we identify an antagonistic action of the triazoles on the action of olorofim. We show that this antagonism is the result of an azole induced upregulation of the pyrimidine biosynthesis pathway and regulation. Intriguingly, we show that loss of function in the higher order transcription factor, HapB a member of the heterotrimeric HapB/C/E (CBC) complex or the regulator of nitrogen metabolic genes AreA, leads to cross resistance to both the azoles and olorofim indicating that factors that govern resistance are under common regulatory control. However loss of azole induced antagonism requires decoupling of the pyrimidine biosynthetic pathway in a manner independent of the action of a single transcription factor. Our study provides a first insight into antagonism between the azoles and olorofim through dysregulation of the pyrimidine and ergosterol pathway, showing complex crosstalk between these two pathways.
Essential role for an isoform ofEscherichia colitranslation initiation factor IF2 in repair of two-ended DNA double-strand breaks
Authors: Mallikarjun Jillella , Gowrishankar J
Published: November 2021

InEscherichia coli, three isoforms of the essential translation initiation factor IF2 (IF2-1, IF2-2, and IF2-3) are generated from separate in-frame initiation codons ininfB. The isoforms have earlier been suggested to additionally participate in DNA damage repair and replication restart. It is also known that the proteins RecA and RecBCD are needed for repair of DNA double-strand breaks (DSBs) in E.coli. Here we show that strains lacking IF2-1 are profoundly sensitive to two-ended DSBs in DNA generated by radiomimetic agents phleomycin or bleomycin, or by endonuclease I-SceI. However, these strains remained tolerant to other DSB-generating genotoxic agents or perturbations to whichrecAandrecBCmutants remained sensitive, such as to mitomycin C, type-2 DNA topoisomerase inhibitors, or DSB caused by palindrome cleavage behind a replication fork. Data from genome-wide copy number analyses following I-SceI cleavage at a single chromosomal locus suggested that, in a strain lacking IF2-1, the magnitude of break induced replication through replication restart mechanisms is largely preserved but the extent of DNA resection around the DSB site is reduced. We propose that in absence of IF2-1 it is the annealing of a RecA nucleoprotein filament to its homologous target that is weakened, which in turn leads to a specific failure in assembly ofTer-to-oriCdirected replisomes needed for consummation of two-ended DSB repair.

Importance

Double-strand breaks (DSBs) in DNA are major threats to genome integrity. InEscherichia coli, DSBs are repaired by Rec- and RecBCD-mediated homologous recombination (HR). This study demonstrates a critical role for an isoform (IF2-1) of the translation initiation factor IF2 in the repair of two-ended DSBs inE. coli(that can be generated by ionizing radiation, certain DNA-damaging chemicals, or endonuclease action). It is proposed that IF2-1 acts to facilitate the function of RecA in the annealing between a pair of DNA molecules during HR.
Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing
Authors: Alonge Michael , Lebeigle Ludivine , Kirsche Melanie , Aganezov Sergey , Wang Xingang , Lippman Zachary B. , Schatz Michael C. , Soyk Sebastian
Published: November 2021

Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for automating assembly scaffolding and patching, and we establish chromosome-scale reference genomes for the widely used tomato genotype M82 along with Sweet-100, a rapid-cycling genotype that we developed to accelerate functional genomics and genome editing. This work outlines strategies to rapidly expand genetic systems and genomic resources in other plant species.
Associations and prognostic accuracy of electrolyte imbalances in predicting poor COVID-19 outcome: a systematic review and meta-analysis
Authors: Song Harris Jun Jie Muhammad Danial , Chia Alys Zhi Qin , Tan Benjamin Kye Jyn , Teo Chong Boon , Chua Horng Ruey , Samuel Miny , Kee Adrian
Published: November 2021

Background

Serum electrolyte imbalances are highly prevalent in COVID-19 patients. However, their associations with COVID-19 outcomes are inconsistent, and of unknown prognostic value.

Objectives

To systematically clarify the associations and prognostic accuracy of electrolyte imbalances (sodium, calcium, potassium, magnesium, chloride and phosphate) in predicting poor COVID-19 clinical outcome.

Methods

PubMed, Embase and Cochrane Library were searched. Odds of poor clinical outcome (a composite of mortality, intensive-care unit (ICU) admission, need for respiratory support and acute respiratory distress syndrome) were pooled using mixed-effects models. The associated prognostic sensitivity, positive and negative likelihood ratios (LR+, LR-) and predictive values (PPV, NPV; assuming 25% pre-test probability), and area under the curve (AUC) were computed.

Results

We included 28 observational studies from 953 records with low to moderate risk-of-bias. Hyponatremia (OR=2.08, 95%CI=1.48-2.94, I2=93%, N=8), hypernatremia (OR=4.32, 95%CI=3.17-5.88, I2=45%, N=7) and hypocalcemia (OR=3.31, 95%CI=2.24-4.88, I2=25%, N=6) were associated with poor COVID-19 outcome. These associations remained significant on adjustment for covariates such as demographics and comorbidities. Hypernatremia was 97% specific in predicting poor outcome (LR+ 4.0, PPV=55%, AUC=0.80) despite no differences in CRP and IL-6 levels between hypernatremic and normonatremic patients. Hypocalcemia was 76% sensitive in predicting poor outcome (LR- 0.44, NPV=87%, AUC=0.71). Overall quality of evidence ranged from very low to moderate.

Conclusion

Hyponatremia, hypernatremia and hypocalcemia are associated with poor COVID-19 clinical outcome. Hypernatremia is 97% specific for a poor outcome and the association is independent of inflammatory marker levels. Further studies should evaluate if correcting these imbalances help improve clinical outcome.
Wearable technologies in the fashion value ecosystem: a conceptual model
Authors: Serrano Rosiane , Fortunati Larissa , Lacerda Daniel Pacheco
Published: November 2021

Purpose

The fashion sector is complex. It involves multiple actors with distinct and potentially conflicting interests, forming a value ecosystem. Thus, knowing the interested parties and belonging to the fashion sector may be a means to promote technological innovation, such as products with wearables. The purpose of this paper to identify the participants of the fashion ecosystem from the perspective of wearable technologies and develop a conceptual model.

Design/methodology/approach

The present work aims to identify the participants (actors) and develop a conceptual model of the fashion ecosystem from the perspective of wearable technologies. The systematic literature review is the recommended method to qualitatively analyze documents and identify the interested parties (actors) in the fashion sector in order to design the proposed conceptual model.

Findings

From the studies, the conceptual model of the fashion value ecosystem was designed, and the wearable product was considered its core business. The studies identified addressed ecosystems of fashion value in general but not specific to wearable products and their relations with other complementary industries.

Research limitations/implications

The model was designed using secondary data only. Its validation is relevant through interviews with experts.

Originality/value

In terms of relevance, when conducting a systematic literature review, there were no studies that included wearable technologies in the fashion ecosystems discussed and their relations with other industries. The topic of wearables is an emerging subject that needs further research aiming to insert this technology in productive sectors.
Genotyping of intraspecies polymorphisms of Sporothrix globosa using partial sequence of mitochondrial DNA
Authors: Mochizuki Hirokazu , Anzawa Kazushi , Mochizuki Takashi
Published: November 2021

Restriction fragment length polymorphism (RFLP) of mitochondrial DNA (mtDNA) had been used for molecular identification of Sporothrix spp., which is the causative fungi of sporotrichosis and the most prevalent deep‐seated dermatomycosis. Also, mtDNA‐RFLP had been used to investigate the molecular epidemiology of sporotrichosis. While the current standard for molecular diagnosis is performed by sequence analysis of the calmodulin gene (CAL), correspondence between the results from CAL and mtDNA is of diagnostic and epidemiological interest. Here, we investigated the correspondence between CAL and mtDNA used for molecular identification of Sporothrix globosa and S. schenckii, which are two major species. We also investigated and propose molecular markers suitable to describe the epidemiology of S. globosa, which is considered as a species with few intraspecific polymorphisms. Eighty‐seven strains morphologically identified as S. schenckii sensu lato were investigated. They were identified as group A (17 types, 17 strains) or B (14 types, 70 strains) by mtDNA‐RFLP. Partial sequences of CAL, internal transcribed spacer, and spacer between atp9 and cox2 genes of mtDNA of these strains were determined. All group A strains corresponded to S. schenckii, and group B to S. globosa. The sequences of the amplicons targeted on the spacer region in mtDNA of S. globosa ranged 510–515 bp in length and exhibited 10 molecular variations, whereas CAL indicated seven molecular variations. In conclusion, most of the S. schenckii sensu lato strains isolated from Japanese sporotrichosis patients were confirmed as S. globosa, because group B, which comprised the majority of strains, matched perfectly with S. globosa by the CAL sequencing study. We proposed sequence variations in the spacer between atp9 and cox2 genes of mtDNA as a suitable molecular epidemiological marker for S. globosa.
The hidden legacy of megafaunal extinction: Loss of functional diversity and resilience over the Late Quaternary at Hall’s Cave
Authors: Hedberg Carson P. , Lyons S. Kathleen , Smith Felisa A.
Published: November 2021

Aim

Functional traits mediate the interactions of species among themselves and with their environment, providing a link between diversity and ecosystem function. Crucially, the loss of biodiversity can jeopardize the functionality of ecosystems. Much focus is on predicting the impacts of current and future species loss; however, modern ecosystems have undergone biodiversity decline throughout the Late Quaternary, starting with the Pleistocene megafaunal extinctions. Thus, the fossil record offers the opportunity to investigate the long‐term legacy of biodiversity erosion and how this is affecting modern ecosystems in a cumulative manner. We aimed to investigate changes in functional diversity and redundancy of a local mammal community at Hall’s Cave, a site with a continuous record from 21,000 years ago to the present. Additionally, we included several common introduced species in the modern community to test whether they restore some lost ecological function.

Location

Central Texas.

Time period

Late Pleistocene to Present.

Major taxa studied

Mammals.

Methods

We used eight functional traits (mass, diet, arboreality, cursoriality, soil disturbance, group size, activity period and migration habit), which, collectively, describe the ecological role of a species and its influence on ecosystem processes, to construct a multidimensional functional space. The functional richness, range and distribution of the Hall’s Cave community and the degree of functional redundancy were characterized statistically over time.

Results

We found that declines in functional diversity were greater than expected given the decrease in species richness, implying that lost taxa contributed higher than average distinct ecological function. Functional distances between the remaining species increased through time, leading to reduced functional redundancy in younger communities. However, recently introduced taxa increased functional diversity to levels similar to those in the Holocene and partly restored the functional space occupied by Late Pleistocene fauna.

Main conclusions

Our local‐scale analysis demonstrates how prolonged biodiversity erosion not only leads to functionally depauperate communities, but, crucially, lowers ecological resilience to future disturbance.
Avoidable healthcare costs of spinning‐induced rhabdomyolysis: a case series
Authors: Saparamadu Amarasinghe Arachchige Don Nalin Samandika , Teo Winnie Z. Y. , Arsad Asrie
Published: November 2021

Spinning‐induced rhabdomyolysis (SIR) is a well documented cause of exertional rhabdomyolysis. We aim to raise awareness and to call for preventive action towards avoidable healthcare costs associated with SIR. To this end, we describe three cases of SIR, associated healthcare costs and possible preventive strategies. We propose that community‐based preventive measures should be considered in addressing the economic consequences of SIR.
Atelectasis and lung recruitment in pediatric anesthesia: An educational review
Authors: Bruins Suze , Sommerfield David , Powers Neil , von Ungern‐Sternberg Britta S.
Published: November 2021

General anesthesia is associated with development of pulmonary atelectasis. Children are more vulnerable to the development and adverse effects of atelectasis. We review the physiology and risk factors for the development of atelectasis in pediatric patients under general anesthesia. We discuss the clinical significance of atelectasis, the use and value of recruitment maneuvers, and other techniques available to minimize lung collapse. This review demonstrates the value of a recruitment maneuver, maintaining positive end‐expiratory pressure (PEEP) until extubation and lowering FiO2 where possible in the daily practice of the pediatric anesthetist.
Seed coat lignification level is crucial in Capsicum spp seed longevity
Authors: Bissoli Gaetano , Bono Mar , Martínez‐Almonacid Irene , Moreno‐Peris Estela , Renard Joan , Espinosa Ana , Naranjo Miguel Ángel , Yenush Lynne , Fita Ana , Serrano Ramón , Rodríguez‐Burruezo Adrián , Bueso Eduardo
Published: November 2021

Capsicum (pepper) is known for its poor seed germination, particularly seed longevity is usually much shorter than other Solanaceae. However, the molecular mechanisms involved are mostly unknown in these species. The present study examines the differences in seed longevity among Capsicum species and varietal types. Feral or less domesticated species, such as Capsicum chinense and particularly Capsicum frutescens, showed higher germination rates than the more domesticated Capsicum annuum after accelerated seed aging treatments. In addition, variability was detected in the expression of genes involved in the response to seed deterioration. The differences observed in ASPG1 expression led us to study the seed protein profile in dry and germinating seeds. Seed storage protein mobilization during germination was faster in seed aging‐resistant genotypes. Similarly, the transcriptional change observed for the orthologous gene of the trans‐species regulator AtHB25 prompted us to study the structure and molecular components of the seed coat in peppers. All the Capsicum pepper accessions analyzed presented very lignified testa and we observed a positive correlation between the amount of lignin and seed viability. Our results provide essential information to explain the poor germination observed in pepper seeds and provide an experimental framework for future improvements in this important character.
Globalisation, economic uncertainty and labour market regulations: Implications for the COVID‐19 crisis
Authors: Fang Jianchun , Gozgor Giray , Nolt James H.
Published: November 2021

This paper empirically analyses the effects of globalisation on labour market regulations. We also interact globalisation measures with economic uncertainty, and they serve as potential determinants of de jure labour market conditions. For this purpose, we consider new innovative globalisation and economic uncertainty indices (the Revisited KOF Globalisation and the World Uncertainty) in a panel dataset of 136 countries from 2000 to 2017. The findings indicate that globalisation promotes labour market flexibility, while economic uncertainty decreases it. We also find that the interaction of globalisation with economic uncertainty positively affects labour market flexibility. The findings are robust to various sensitivity analyses, that is, different estimation procedures and globalisation indicators, including various controls and excluding outliers.
Primary & Secondary Reference Fuel Effects as a Function of Compression Ratio in a CFR Diesel Engine
Authors: Burnett Kevin , Gupta Ashwani , Luning Prak Dianne , Cowart Jim
Published: November 2021

Primary Reference Fuels (PRFs) and Secondary Reference Fuels (SRFs) in the range of cetane from 30 to 60 were operated in a Waukesha Diesel Cooperative Fuels Research (CFR) engine under operating conditions that emulate the cetane rating test. Due to the large number of test points in this study, the exact ASTM cetane rating protocol was not followed precisely, however these results are representative of cetane characterization testing with very similar equivalence ratio and combustion phasing across a broad range of Ignition Delays (IGDs) that varied as a result of Compression Ratio (CR) changes in the eleven to twenty-two range. Intake air temperature was operated both heated, as in the cetane rating test, as well as at ambient laboratory conditions. Additional research instrumentation was added beyond the standard CFR equipment for advanced combustion analysis. Combustion analysis shows that engine torque and efficiency increase significantly with increases in CR. At longer IGDs representative of the cetane rating test (13 deg IGD), the increase in IGD with reduced cetane number is relatively linear. For all of the fuels tested, IGD steadily monotonically decreases with increased CR significantly by more than a factor of two. Shorter IGDs lead to longer burn durations; fuel effect differences become less important at very high CRs. Associated companion analysis shows that at the time of fuel injection (Start Of Injection – SOI), cylinder pressure roughly doubles over the CRs studied, however, cylinder charge temperature only moderately increases. This effect leads to a doubling in cylinder air charge concentration at the highest CRs showing an important effect on the fast kinetics at high CRs. A common IGD correlation was evaluated showing good agreement except for the high CN fuel. New IGD correlations are also presented.
Adapting an Internal Combustion Engine to Oxy-Fuel Combustion With In-Situ Oxygen Production
Authors: Arnau Francisco , Novella Ricardo , García-Cuevas Luis Miguel , Gutiérrez Fabio
Published: November 2021

In transport applications, reciprocating internal combustion engines still have important advantages in terms of endurance and refueling time and available infrastructure when compared against fuel cell or battery-based powertrains. Although conventional internal combustion engine configurations produce important amounts of greenhouse gases and pollutant emissions, oxyfuel combustion can be used to mitigate to a great extent such emissions, mainly producing NOx-free, CO2 and H2O exhaust gases. However, the oxygen needed for the combustion, which is mixed with flue gases before entering the cylinder, has to be stored in an additional tank, which hinders the adoption of this technology. Fortunately, the latest developments in gas separation membranes are starting to produce extremely-high selectivity and high permeability oxygen-separation membranes. Using the waste heat of the exhaust gases to heat up a mixed ionic-electronic conducting membrane, and feeding it with pressurized air, it is possible to produce all the oxygen needed by the combustion process while keeping the whole system compact. This works presents a design of an oxy-fuel combustion engine with in-situ oxygen production. The numerical simulations show also that this concept keeps a competitive brake specific fuel consumption, while the high concentration of CO2 in the exhaust gases facilitates the introduction of carbon sequestration technologies, leading to potentially carbon-neutral internal combustion engines.
Direct Numerical Simulation of Partial Fuel Stratification Assisted Lean Premixed Combustion for Assessment of Hybrid G-Equation/Well-Stirred Reactor Model
Authors: Xu Chao , Ameen Muhsin , Pal Pinaki , Som Sibendu
Published: November 2021

Partial fuel stratification (PFS) is a promising fuel injection strategy to stabilize lean premixed combustion in spark-ignition (SI) engines. PFS creates a locally stratified mixture by injecting a fraction of the fuel, just before spark timing, into the engine cylinder containing homogeneous lean fuel/air mixture. This locally stratified mixture, when ignited, results in complex flame structure and propagation modes similar to partially premixed flames, and allows for faster and more stable flame propagation than a homogeneous lean mixture. This study focuses on understanding the detailed flame structures associated with PFS-assisted lean premixed combustion. First, a two-dimensional direct numerical simulation (DNS) is performed using detailed fuel chemistry, experimental pressure trace, and realistic initial conditions mapped from a prior engine large-eddy simulation (LES), replicating practical lean SI operating conditions. DNS results suggest that conventional triple flame structures are prevalent during the initial stage of flame kernel growth. Both premixed and non-premixed combustion modes are present with the premixed mode contributing dominantly to the total heat release. Detailed analysis reveals the effects of flame stretch and fuel pyrolysis on the flame displacement speed. Based on the DNS findings, the accuracy of a hybrid G-equation/well-stirred reactor (WSR) combustion model is assessed for PFS-assisted lean operation in the LES context. The G-equation model qualitatively captures the premixed branches of the triple flame, while the WSR model predicts the non-premixed branch of the triple flame. Finally, potential needs for improvements to the hybrid G-equation/WSR modeling approach are discussed.
The Electric Monochord: A Musical Demonstration About Electromagnetic Induction
Authors: Eff-Darwich Antonio
Published: November 2021

In this work, an easy-to-set-up demonstration about electromagnetic induction is presented, where a simple toy electric motor is transformed into a musical instrument. With this creative way to mix physics and music, it is expected to engage and motivate students to learn about the basic concepts of electromagnetism.
Robotic telescope labs for survey-level undergraduates
Authors: Reichart Daniel E.
Published: November 2021

For the past dozen years, the University of North Carolina (UNC) at Chapel Hill has been developing a unique, survey-level astronomy curriculum, primarily for undergraduate students, with the goal of significantly boosting STEM enrollments on a national scale, as well as boosting students’ technical and research skills. Called “Our Place In Space!” (OPIS!), this curriculum leverages Skynet—a global network of ≈20 fully automated, or robotic, professional-grade telescopes located at some of the world’s best observing sites. We have recently received $1.85M from NSF’s IUSE program to expand OPIS! nationwide and $3M from DoD’s NDEP program to integrate a global network of 5-m to 30-m diameter radio telescopes into Skynet, and to develop a follow-up curriculum to OPIS!, called “Astrophotography of the Multi-Wavelength Universe!” or MWU! Both grants come with funding for participating instructors.
What Physics Instructors Might Do to Support Immunosuppressed Students in the Return to In-Person Instruction: Thoughts from one chronically ill and immunosuppressed physicist
Authors: Robertson Amy D.
Published: November 2021

As I type, it is late September 2021, and emails are streaming into my inbox about my university’s return to in-person instruction in just a few weeks. I wish I could say I feel excited or relieved or grateful for all of the incredible care that went into planning for this, but I actually just want to scream. Because no matter what we do, we are still in the midst of a global pandemic with variants that are “covered in ultrafast-drying Gorilla super glue” that “make [them] extremely effective in attaching to human cells and gaining entry,” and returning to in-person instruction is not safe. I know this in my gut because I am chronically ill and immunosuppressed, and my survival depends on my careful assessment of risk in this pandemic climate.
Monolayer 1T-NbSe
2
as a 2D-correlated magnetic insulator
Authors: Liu Mengke , Leveillee Joshua , Lu Shuangzan , Yu Jia , Kim Hyunsue , Tian Cheng , Shi Youguo , Lai Keji , Zhang Chendong , Giustino Feliciano , Shih Chih-Kang
Published: November 2021

1T-NbSe
2
is a correlated insulator with localized magnetic moments exhibiting Kondo resonances when exchange-coupled to 2H-NbSe
2
.
R-loops trigger the release of cytoplasmic ssDNAs leading to chronic inflammation upon DNA damage
Authors: Chatzidoukaki Ourania , Stratigi Kalliopi , Goulielmaki Evi , Niotis George , Akalestou-Clocher Alexia , Gkirtzimanaki Katerina , Zafeiropoulos Alexandros , Altmüller Janine , Topalis Pantelis , Garinis George A.
Published: November 2021

R-loops lead to chronic inflammation upon DNA damage.
Supplemental Material: Magma recharge patterns control eruption styles and magnitudes at Popocatépetl volcano (Mexico)
Authors: Mangler Martin , al. et
Published: November 2021

Items S1 (full time scale datasets), (S2) diffusion model details, and S3 (priming durations for eruptions with published time-scale data).
Supplemental Material: Correlative tomography of an exceptionally preserved Jurassic ammonite implies hyponome-propelled swimming
Authors: Cherns Lesley , al. et
Published: November 2021

Details of materials, geological setting, methods, and a movie showing virtual reconstruction of Sigaloceras enodatum.
Extensive extraintestinal manifestations of ulcerative colitis in a patient initially suspected to have disseminated malignancy
Authors: Juul Nikolai , Dahl Stig Søgaard , Chiranth Deepthi Jermaly , Penninga Luit
Published: November 2021

A 44-year-old patient with known ulcerative colitis presented with abdominal pain and an abdominal mass. CT revealed cecal stranding, a mass at the left colonic flexure involving the pancreas and multiple lesions in the lungs, retroperitoneum and liver. The patient had also developed a scalp rash as well as impaired hearing. Biopsies from the abdominal mass and lungs revealed necrotic inflammation, and the clinical suspicion of malignancy could not be ruled out. After further examination, the patient was treated with high-dose steroids, which rapidly reduced the extraintestinal manifestations. Due to a persistent abscess formation at the left colonic flexure and pancreas, the patient was referred to our hospital for a total colectomy. Histology showed acute and chronic inflammation with cryptitis, indicating ulcerative colitis. Our case is a rare presentation of extensive extraintestinal disease in organs such as the lungs and liver, as well as necrotic mass formation at the colon site which mimicked malignancy.
BMJ HCIlaunches partnership programme for patients and carers as authors and peer reviewers
Authors: Lewis Dana , Scott Philip
Published: November 2021

BMJ Health & Care Informatics(BMJHCI) is launching a partnership programme, where patients write articles and serve as peer reviewers on both patient-written and researcher-written articles. This article outlines the programme and describes the importance of public involvement in research and implementation in digital health. We think patients and carers should be funded to participate at this stage of research as well as other stages of research. The quality of peer review can be greatly improved by recruiting patients to peer review and improve readability and understanding of scientific literature and to ensure that research and other articles appropriately include what matters most to patients. Just as real-time communication is two-way communication, both healthcare providers and patients should have a voice in the literature, and involving patients in journals is an important step toward amplifying and supporting the balance of perspectives. Patients are the whole purpose of research and practice in health and care, so this rightly includes their role in the publication and review of health informatics literature as well as the publication of their own perspectives regarding access and delivery of healthcare. Patients and carers can provide valuable insights into research articles, and they can also serve as effective peer reviewers. The BMJHCI is excited to kick off the new partnership programme and encourages all interested patients and carers to apply to participate as authors and/or reviewers.
The QUality of Interhospital Transportation in the Euregion Meuse-Rhine (QUIT-EMR) score: a cross-validation study
Authors: Strauch Ulrich , Florack Micheline C D M , Jansen Jochen , van Bussel Bas C T , Beckers Stefan K , Habers Joachim , Winkens Bjorn , van der Horst Iwan C C , van Mook Walther N K A , Bergmans Dennis C J J
Published: November 2021

Objectives

Interhospital transports of critically ill patients are high-risk medical interventions. Well-established parameters to quantify the quality of transports are currently lacking. We aimed to develop and cross-validate a score for interhospital transports.

Setting

An expert panel developed a score for interhospital transport by a Mobile Intensive Care Unit (MICU), the QUality of Interhospital Transportation in the Euregion Meuse-Rhine (QUIT-EMR) score. The QUIT-EMR score is an overall sum score that includes component scores of monitoring and intervention variables of the neurological (proxy for airway patency), respiratory and circulatory organ systems, ranging from −12 to +12. A score of 0 or higher defines an adequate transport. The QUIT-EMR score was tested to help to quantify the quality of transport.

Participants

One hundred adult patients were randomly included and the transport charts were independently reviewed and classified as adequate or inadequate by four transport experts (ie, anaesthetists/intensivists).

Outcome measures

Subsequently, the level of agreement between the QUIT-EMR score and expert classification was calculated using Gwet’s AC1.

Results

From April 2012 to May 2014, a total of 100 MICU transports were studied. The median (IQR) QUIT-EMR score was 1 (0–2). Experts classified six transports as inadequate. The percentage agreement between the QUIT-EMR score and experts’ classification for adequate/inadequate transport ranged from 84% to 92% (Gwet’s AC10.81–0.91). The interobserver agreement between experts was 87% to 94% (Gwet’s AC10.89–0.98).

Conclusion

The QUIT-EMR score is a novel validated tool to score MICU transportation adequacy in future studies contributing to quality control and improvement.

Trial registration number

NTR 4937.
Prestroke physical activity and outcomes after intracerebral haemorrhage in comparison to ischaemic stroke: protocol for a matched cohort study (part of PAPSIGOT)
Authors: Viktorisson Adam , Buvarp Dongni , Sunnerhagen Katharina S
Published: November 2021

Introduction

Piling evidence suggests that a higher level of prestroke physical activity can decrease stroke severity, and reduce the risk of poststroke mortality. However, prior studies have only included ischaemic stroke cases, or a majority of such. We aim to investigate how premorbid physical activity influences admission stroke severity and poststroke mortality in patients with intracerebral haemorrhage, compared with ischaemic stroke. A prespecified analysis plan counteract some inherent biases in observational studies, and promotes transparency.

Methods and analysis

This is a statistical analysis protocol for a matched cohort study, including all adult patients with intracerebral haemorrhage, and matched ischaemic stroke controls, treated at Sahlgrenska University Hospital in Sweden between 1 November 2014 and 30 June 2019. All patients have been identified in the Väststroke register, and the data file has been sent for merging with national registries. The follow-up of time for survival will be approximately 2–7 years. The sample size calculation indicates that a minimum of 628 patients with intracerebral haemorrhage is needed for power of 80% at an alpha level of 0.01. Multiple imputation by chained equations will be used to handle missing data. The entire cohort of patients with intracerebral haemorrhage will be matched with consecutive ischaemic stroke controls (1:3 ratio) using nearest neighbour propensity score matching. The association between prestroke physical activity and admission stroke severity will be evaluated using multivariable ordinal regression models, and risk for all-cause mortality will be analysed using multivariable Cox proportional-hazards models. Potential confounders include age, ethnicity, income, educational level, comorbidity, medical treatments, alcohol-related disorders, drug abuse and smoking.

Ethics

Data collection for the Physical Activity Pre-Stroke In GOThenburg project was approved by the Regional Ethical Board on 4 May 2016. An additional application was approved by the National Ethical Review Authority on 7 July 2021.
Critical social framework on the determinants of primary healthcare access and utilisation
Authors: Hamiduzzaman Mohammad , De-Bellis Anita , Abigail Wendy , Fletcher Amber
Published: November 2021

This paper aims to contextualise ‘healthcare access and utilisation’ within its wider social circumstances, including structural factors that shape primary healthcare for marginalised groups. Mainstream theories often neglect complexities among the broader social, institutional and cultural milieus that shape primary healthcare utilisation in reality. A blended critical social framework is presented to highlight the recognition and emancipatory intents surrounding person, family, healthcare practice and society. Using the theoretical contributions of Habermas and Honneth, the framework focuses on power relationships, misrecognition/recognition strategies, as well as disempowerment/empowerment dynamics. To enable causal and structural analysis, we draw on the depth ontology of critical realism. The framework is then applied to the case of rural elderly women’s primary healthcare use in Bangladesh. Drawing on the literature, this article illustrates how a blended critical social perspective reveals the overlapping and complex determinants that affect primary healthcare utilisation, before concluding with the importance of situating healthcare access in sociocultural structures.
Feebly-interacting particles: FIPs 2020 workshop report
Authors: Agrawal P. , Bauer M. , Beacham J. , Berlin A. , Boyarsky A. , Cebrian S. , Cid-Vidal X. , d’Enterria D. , De Roeck A. , Drewes M. , Echenard B. , Giannotti M. , Giudice G. F. , Gninenko S. , Gori S. , Goudzovski E. , Heeck J. , Hernandez P. , Hostert M. , Irastorza I. G. , Izmaylov A. , Jaeckel J. , Kahlhoefer F. , Knapen S. , Krnjaic G. , Lanfranchi G. , Monroe J. , Outschoorn V. I. Martinez , Lopez-Pavon J. , Pascoli S. , Pospelov M. , Redigolo D. , Ringwald A. , Ruchayskiy O. , Ruderman J. , Russell H. , Salfeld-Nebgen J. , Schuster P. , Shaposhnikov M. , Shchutska L. , Shelton J. , Soreq Y. , Stadnik Y. , Swallow J. , Tobioka K. , Tsai Y.-D.
Published: November 2021

With the establishment and maturation of the experimental programs searching for new physics with sizeable couplings at the LHC, there is an increasing interest in the broader particle and astrophysics community for exploring the physics of light and feebly-interacting particles as a paradigm complementary to a New Physics sector at the TeV scale and beyond. FIPs 2020 has been the first workshop fully dedicated to the physics of feebly-interacting particles and was held virtually from 31 August to 4 September 2020. The workshop has gathered together experts from collider, beam dump, fixed target experiments, as well as from astrophysics, axions/ALPs searches, current/future neutrino experiments, and dark matter direct detection communities to discuss progress in experimental searches and underlying theory models for FIPs physics, and to enhance the cross-fertilisation across different fields. FIPs 2020 has been complemented by the topical workshop “Physics Beyond Colliders meets theory”, held at CERN from 7 June to 9 June 2020. This document presents the summary of the talks presented at the workshops and the outcome of the subsequent discussions held immediately after. It aims to provide a clear picture of this blooming field and proposes a few recommendations for the next round of experimental results.
Retrieving the Missing Data From Incomplete Soft Set, Incomplete Fuzzy Soft Set and Incomplete Intuitionistic Fuzzy Soft Set
Authors: Srivastava Julee , Maddheshiya Sudhir
Published: November 2021

Dealing with an incomplete information has been a major issue in the theory of soft sets. In this paper, we have presented an approach to deal with incomplete soft set, incomplete fuzzy soft set and incomplete intuitionistic fuzzy soft set. For this purpose, we have introduced the notion of distance between two objects (parameters) which will be used to compute the degree of interdependence between them. This approach will use the full information of known data and the relationships between them. Data filling converts an incomplete soft set into a complete one which makes the soft sets applicable not only to decision making but also to other fields.
Time-Dependent Evolution Study of Ar/N2 Plasma-Activated Cu Surface for Enabling Two-Step Cu-Cu Direct Bonding in a Non-Vacuum Environment
Authors: Hu Liangxing , Goh Simon Chun Kiat , Tao Jing , Lim Yu Dian , Zhao Peng , Lim Michael Joo Zhong , Salim Teddy , Velayutham Uvarajan M , Tan Chuan Seng
Published: November 2021

In this paper, a two-step copper-copper direct bonding process in a non-vacuum environment is reported. Time-dependent evolution of argon/nitrogen plasma-activated copper surface is carefully studied. A multitude of surface characterizations are performed to investigate the evolution of the copper surface, with and without argon/nitrogen plasma treatment, when it is exposed to the cleanroom ambient for a period of time. The results reveal that a thin layer of copper nitride is formed upon argon/nitrogen plasma activation on copper surface. It is hypothesized that the nitride layer could dampen surface oxidation. This allows the surface to remain in an “activated” state for up to 6 h. Afterwards, the activated dies are physically bonded at room temperature in cleanroom ambient. Thereafter, the bonded dies are annealed at 300 °C for varying duration, which results in an improvement of the bond strength by a factor of 70∼140 times. A sample bonded after plasma activation and 2-h cleanroom ambient exposure demonstrates the largest shear strength (∼5 MPa). The degradation of copper nitride layer at elevated temperature could aid in maintaining a localized inert environment for the initial diffusion of copper atoms across the interface. This novel bonding technique would be useful for high-throughput three-dimensional wafer bonding and heterogeneous packaging in semiconductor manufacturing.
Novel Negative Capacitance and Conductance in All Temperatures and Voltages of Au/CNTs/n-Si/Al at Low and High Frequencies
Authors: Ashery A. , Gad S. A. , Gaballah A. E. H. , Turky G. M.
Published: November 2021

The structure of carbon nanotube CNTs functioning as p-type material deposited over n-type silicon to produce heterojunction of Au/CNTs/n-Si/Al is presented in this study. This work explored the capacitance and conductance at various frequencies, temperatures, and voltages, the novelty here is that negative capacitance and conductance were observed at high frequencies in all temperatures and voltages, whereas capacitance appeared at both high and low frequencies, such as (2 × 107,1× 107,1 × 102,10) Hz. At high-frequency f = 2 × 107 Hz, the capacitance raises while the conductance decreases; at all temperatures and voltages, the capacitance and conductance exhibit the same behavior at particular frequencies such as 1 × 106,1 × 105,1 × 104,1 × 103 Hz, however their behavior differs at 2 × 107,1 × 107, 1 × 102 and 10 Hz. Investigating the reverse square capacitance with voltage yielded the energy Fermi (Ef), density surface of states (Nss), depletion width (Wd), barrier height, series resistance, and donor concentration (Nd).
Global Existence of Solution for the Fisher Equation via Faedo–Galerkin’s Method
Authors: Hamrouni Ahmed , Choucha Abdelbaki , Alharbi Asma , Idris Sahar Ahmed
Published: November 2021

In this study, we consider the Fisher equation in bounded domains. By Faedo–Galerkin’s method and with a homogeneous Dirichlet conditions, the existence of a global solution is proved.