bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases
Authors: Pires João , Huisman Jana S , Bonhoeffer Sebastian , Van Boeckel Thomas P 
Published: November 2021

Abstract

Background
Next-generation sequencing has considerably increased the number of genomes available in the public domain. However, efforts to use these genomes for surveillance of antimicrobial resistance have thus far been limited and geographically heterogeneous. We inferred global resistance trends in Escherichia coli in food animals using genomes from public databases.

Methods
We retrieved 7632 E. coli genomes from public databases (NCBI, PATRIC and EnteroBase) and screened for antimicrobial resistance genes (ARGs) using ResFinder. Selection bias towards resistance, virulence or specific strains was accounted for by screening BioProject descriptions. Temporal trends for MDR, resistance to antimicrobial classes and ARG prevalence were inferred using generalized linear models for all genomes, including those not subjected to selection bias.

Results
MDR increased by 1.6 times between 1980 and 2018, as genomes carried, on average, ARGs conferring resistance to 2.65 antimicrobials in swine, 2.22 in poultry and 1.58 in bovines. Highest resistance levels were observed for tetracyclines (42.2%–69.1%), penicillins (19.4%–47.5%) and streptomycin (28.6%–56.6%). Resistance trends were consistent after accounting for selection bias, although lower mean absolute resistance estimates were associated with genomes not subjected to selection bias (difference of 3.16%±3.58% across years, hosts and antimicrobial classes). We observed an increase in extended-spectrum cephalosporin ARG blaCMY-2 and a progressive substitution of tetB by tetA. Estimates of resistance prevalence inferred from genomes in the public domain were in good agreement with reports from systematic phenotypic surveillance.

Conclusions
Our analysis illustrates the potential of using the growing volume of genomes in public databases to track AMR trends globally.
Evaluation of abdominal aortic calcification by plain CT predicts anastomotic leakage in laparoscopic surgery for colorectal cancer
Authors: Morita Satoru , Tsuruta Masashi , Okabayashi Koji , Shigeta Kohei , Seishima Ryo , Monno Masayoshi , Itano Osamu , Kitagawa Yuko 
Published: November 2021

Abstract

Background
Anastomotic leakage is one of the most severe and critical complications of laparoscopic surgery for colorectal cancer. However, definitive preoperative predictors of anastomotic leakage remain elusive. With the ageing of society, the number of colorectal cancer patients with arteriosclerotic disease in Japan is increasing. This study was performed to evaluate the correlation between preoperative arteriosclerosis and anastomotic leakage.

Methods
In total, 98 patients undergoing laparoscopic surgery for colorectal cancer with reconstruction using the double-stapling technique without diversion of the stoma were enrolled in the study. Preoperative assessment of arteriosclerotic disease was performed by abdominal computed tomography. The calcification volume percentage of the aorta between the level of the celiac artery root and aortic bifurcation was calculated using ZIOstation2 software, and the relationship between arteriosclerosis and anastomotic leakage was analysed.

Results
Among 98 cases, anastomotic leakage was observed in 16 (16.3%). The median calcification volume percentage (range) was 2.35% (0–40.3%). Age, male sex, hypertension, dissection number, estimated glomerular filtration rate and tumour location were correlated with anastomotic leakage on statistical analysis. Statistical analysis showed that calcification volume percentage was one of the robust risk factors for anastomotic leakage (odds ratio: 1.09, 95% confidence interval: 1.03–1.17, P &lt; 0.01).

Conclusions
Calcification of the abdominal aorta may be a promising predictor of AL after laparoscopic surgery for colorectal cancer reconstruction using the double-stapling technique.
Biological and internal dosimetry for radiation medicine: current status and future perspectives
Authors: Sudprasert Wanwisa , Belyakov Oleg V , Tashiro Satoshi 
Published: November 2021

Abstract
The International Atomic Energy Agency (IAEA) and Hiroshima International Council for Health Care of the Radiation-Exposed (HICARE) jointly organized two relevant workshops in Hiroshima, Japan, i.e. a Training Meeting ‘Biodosimetry in the 21st century’ (BIODOSE-21) on 10–14 June 2013 and a Workshop on ‘Biological and internal dosimetry: recent advance and clinical applications’ which took place between 17 and 21 February 2020. The main objective of the first meeting was to develop the ability of biodosimetry laboratories to use mature and novel techniques in biological dosimetry for the estimation of radiation doses received by individuals and populations. This meeting had a special focus on the Asia-Pacific region and was connected with the then on-going IAEA Coordinated Research Project (CRP) E35008 ‘Strengthening of “Biological dosimetry” in IAEA Member States: Improvement of current techniques and intensification of collaboration and networking among the different institutes’ (2012–17). The meeting was attended by 25 participants, which included 11 lecturers. The 14 trainees for this meeting came from India, Indonesia, Japan, Malaysia, Philippines, Republic of Korea, Singapore, Thailand and Vietnam. During the meeting 13 lectures by HICARE and IAEA invited lecturers were delivered besides eight research reports presented by the IAEA CRP E35008 network centers from the Asia-Pacific region. Two laboratory exercises were also undertaken, one each at Hiroshima University and the Radiation Effects Research Foundation (RERF). The second training workshop aimed to discuss with the participants the use of mature and novel techniques in biological and internal dosimetry for the estimation of radiation effects by accidental, environmental and medical exposures. The workshop was attended by 19 participants from Indonesia, Jordan, Oman, Philippines, Singapore, Syrian Arab Republic, Thailand, UAE, USA and Yemen. The main outcome of both meetings was a review of the state-of-the-art of biodosimetry and internal dosimetry and their future perspectives in medical management. This report highlights the learning outcome of two meetings for the benefit of all stake-holders in the field of biological and internal dosimetry.
Evidence for evolution and selection of drought-resistant genes based on high-throughput resequencing in weedy rice
Authors: Han Bing , Cui Di , Ma Xiaoding , Cao Guilan , Zhang Hui , Koh Hee Jong , Han Longzhi 
Published: November 2021

Abstract
Weedy rice (Oryza sativa f. spontanea) is a relative of cultivated rice that propagates in paddy fields and has strong drought resistance. In this study, we used 501 rice accessions to reveal the selection mechanism of drought resistance in weedy rice through a combination of selection analysis, genome-wide association studies, gene knockout and overexpression analysis, and Ca2+ and K+ ion flux assays. The results showed that the weedy rice species investigated have gene introgression with cultivated rice, which is consistent with the hypothesis that weedy rice originated from de-domestication of cultivated rice. Regions related to tolerance have particularly diversified during de-domestication and three drought-tolerance genes were identified. Of these, Os01g0800500 was also identified using an assay of the degree of leaf withering under drought, and it was named as PAPH1, encoding a PAP family protein. The drought-resistance capacity of PAPH1-knockout lines was much lower than that of the wild type, while that of overexpression lines was much higher. Concentrations of Ca2+ and K+ were lower in the knockout lines and higher in the overexpression lines compared with those of the wild type, suggesting that PAPH1 plays important roles in coping with drought stress. Our study therefore provides new insights into the genetic mechanisms underlying adaptive tolerance to drought in wild rice and highlights potential new resistance genes for future breeding programs in cultivated rice.
The Arabidopsis HDZIP class II transcription factor ABA INSENSITIVE TO GROWTH 1 functions in leaf development
Authors: Preciado Jesus , Begcy Kevin , Liu Tie 
Published: November 2021

Abstract
Leaf laminar growth and adaxial–abaxial boundary formation are fundamental outcomes of plant development. Boundary and laminar growth coordinate the further patterning and growth of the leaf, directing the differentiation of cell types within the top and bottom domains and promoting initiation of lateral organs along their adaxial or abaxial axis. Leaf adaxial–abaxial polarity specification and laminar outgrowth are regulated by two transcription factors, REVOLUTA (REV) and KANADI (KAN). ABA INSENSITIVE TO GROWTH 1 (ABIG1) encodes a HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP) class II transcription factor and is a direct target of the adaxial–abaxial regulators REV and KAN. To investigate the role of ABIG1 in leaf development and in the establishment of polarity, we examined the phenotypes of both gain-of-function and loss-of-function mutants. Through genetic interaction analysis with REV and KAN mutants, we determined that ABIG1 plays a role in leaf laminar growth as well as in adaxial–abaxial polarity establishment. Genetic and physical interaction assays showed that ABIG1 interacts with the transcriptional TOPLESS corepressor. This study provides new evidence that ABIG1, another HD-ZIP II, facilitates growth through the corepressor TOPLESS.
Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination
Authors: Xu Jingfei , Zhao Lingyun , Peng Sijia , Chu Huiying , Liang Rui , Tian Meng , Connell Philip P , Li Guohui , Chen Chunlai , Wang Hong-Wei 
Published: November 2021

Abstract
Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51–DNA and Dmc1–DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
Aggregation-induced barrier to oxygen—a new AIE mechanism for metal clusters with phosphorescence
Authors: Jin Yan , Peng Qiu-Chen , Li Si , Su Hui-Fang , Luo Peng , Yang Ming , Zhang Xin , Li Kai , Zang Shuang-Quan , Tang Ben Zhong , Mak Thomas C W 
Published: November 2021

ABSTRACTMetal clusters are useful phosphors, but highly luminescent examples are quite rare. Usually, the phosphorescence of metal clusters is hindered by ambient O2 molecules. Transforming this disadvantage into an advantage for meaningful applications of metal clusters presents a formidable challenge. In this work, we used ligand engineering to judiciously prepare colour-tuneable and brightly emitting Cu(I) clusters that are ultrasensitive to O2 upon dispersion in a fluid solution or in a solid matrix. When the O2 scavenger dimethyl sulfoxide (DMSO) was used as the solvent, joint photo- and oxygen-controlled multicolour switches were achieved for the first time for metal cluster-based photopatterning and photo-anticounterfeiting. More importantly, an aggregation-induced barrier to oxygen, a new aggregation-induced emission mechanism for metal clusters, was proposed, providing a new pathway to realizing the intense emission of metal clusters in the aggregated state. These results are expected to promote the application of metal clusters and enrich the luminescence theory of metal cluster aggregates.
After the New Queer Cinema
Authors: Rich B. Ruby 
Published: November 2021

Abstract
This chapter historicizes the work of the New Queer Cinema (NQC), a term coined by the author to describe a group of groundbreaking films that emerged in the late 1980s and early 1990s. It argues that the NQC sensibility fueled subsequent imaginative film and television, from makers as diverse as Ang Lee, Todd Haynes, Silas Howard, and Celine Sciamma. At the heart of the chapter is the conviction that contemporary politics demand a new framework for queer and trans media, namely the idea of intersectionality, demonstrated by makers and artists such as Janelle Monae, Allie Logout, Wu Tsang, The Nest Collective, and the trio of Mika Gustafson, Olivia Kastebring, and Christina Tsiobanelis. Intersectionality enables mutuality, recognition, and alliance in a time of deep division and terror; it asks queer media makers to take transgression beyond personal expressions and identity into collective acts of world making.
The cross-section measurement for the 3H(e, e′K+)nnΛ reaction
Authors: Suzuki K N , Gogami T , Pandey B , Itabashi K , Nagao S , Okuyama K , Nakamura S N , Tang L , Abrams D , Akiyama T , Androic D , Aniol K , Gayoso C Ayerbe , Bane J , Barcus S , Barrow J , Bellini V , Bhatt H , Bhetuwal D , Biswas D , Camsonne A , Castellanos J , Chen J-P , Chen J , Covrig S , Chrisman D , Cruz-Torres R , Das R , Fuchey E , Gnanvo K , Garibaldi F , Gautam T , Gomez J , Gueye P , Hague T J , Hansen O , Henry W , Hauenstein F , Higinbotham D W , Hyde C E , Kaneta M , Keppel C , Kutz T , Lashley-Colthirst N , Li S , Liu H , Mammei J , Markowitz P , McClellan R E , Meddi F , Meekins D , Michaels R , Mihovilovič M , Moyer A , Nguyen D , Nycz M , Owen V , Palatchi C , Park S , Petkovic T , Premathilake S , Reimer P E , Reinhold J , Riordan S , Rodriguez V , Samanta C , Santiesteban S N , Sawatzky B , Širca S , Slifer K , Su T , Tian Y , Toyama Y , Uehara K , Urciuoli G M , Votaw D , Williamson J , Wojtsekhowski B , Wood S A , Yale B , Ye Z , Zhang J , Zheng X 
Published: November 2021

Abstract
The small binding energy of the hypertriton leads to predictions of the non-existence of bound hypernuclei for isotriplet three-body systems such as nnΛ. However, invariant mass spectroscopy at GSI has reported events that may be interpreted as the bound nnΛ state. The nnΛ state was sought by missing-mass spectroscopy via the (e, e′K+) reaction at Jefferson Lab’s experimental Hall A. The present experiment has higher sensitivity to the nnΛ-state investigation in terms of better precision by a factor of about three. The analysis shown in this article focuses on the derivation of the reaction cross-section for the 3H(γ*, K+)X reaction. Events that were detected in an acceptance, where a Monte Carlo simulation could reproduce the data well ($|\delta p/p| \lt 4\%$), were analyzed to minimize the systematic uncertainty. No significant structures were observed with the acceptance cuts, and the upper limits of the production cross-section of the nnΛ state were obtained to be 21 and $31 \, \rm {nb} \, \rm {sr}^{-1}$ at the $90\%$ confidence level when theoretical predictions of (−BΛ, Γ) = (0.25, 0.8) MeV and (0.55, 4.7) MeV, respectively, were assumed. The cross-section result provides valuable information for examining the existence of nnΛ.
Legal professional privilege—what do we make of it in jurisdiction Malta? Part 1
Authors: Galea Patrick 
Published: November 2021

Abstract
Malta is a European Union and Commonwealth Member, and among the family of the “mixed” jurisdictions, being a Civil Law jurisdiction with extensive Common Law experience. This article will assess Legal Professional Privilege in the small island state. The historical, domestic and contemporary ECHR/EU sources, along with other areas such as the sometimes-blurred distinction or overlapping between professional secrecy, confidentiality and Privilege and the jurisprudential contribution of the Maltese Courts, are reviewed. The review addresses ethical standards including the recommendations of the Council of European Bars, joint and common-interest Privilege, whether Privilege on legal advice in a foreign jurisdiction can be upheld, the situation of internal counsel and the “Iniquity Exception.” The conclusion is that Malta does not distinguish between legal advice and litigation Privilege but acknowledges and applies one-unitary privilege to encompass both.
Endothelial SIRT1 as a Target for the Prevention of Arterial Aging: Promises and Challenges
Authors: Begum Musammat Kulsuma , Konja Daniels , Singh Sandeep , Chlopicki Stefan , Wang Yu 
Published: November 2021

Abstract:
SIRT1, a member of the sirtuin family of longevity regulators, possesses potent activities preventing vascular aging. The expression and function of SIRT1 in endothelial cells are downregulated with age, in turn causing early vascular aging and predisposing various vascular abnormalities. Overexpression of SIRT1 in the vascular endothelium prevents aging-associated endothelial dysfunction and senescence, thus the development of hypertension and atherosclerosis. Numerous efforts have been directed to increase SIRT1 signaling as a potential strategy for different aging-associated diseases. However, the complex mechanisms underlying the regulation of SIRT1 have posed a significant challenge toward the design of specific and effective therapeutics. This review aimed to provide a summary on the regulation and function of SIRT1 in the vascular endothelium and to discuss the different approaches targeting this molecule for the prevention and treatment of age-related cardiovascular and cerebrovascular diseases.
Saturday Night Myelopathy
Authors: Martin Andrew J. , Garcia Maria C. 
Published: November 2021

Introduction:
Myelopathy is a common condition with a variety of causes, often eluding diagnosis for some time. Prolonged flexion after surgical procedures has been described.

Case Report:
A 20-year-old female presented with acute paraparesis after polysubstance drug intoxication and a period of prolonged neck flexion while unconscious. Imaging demonstrated extensive cervicothoracic central cord signal change, in addition to posterior neck musculature hyperintensity. Additional workup directed to other causes was negative. The patient was diagnosed with flexion myelopathy and was treated with a course of steroids, with marked improvement.

Conclusions:
The clinician should consider the possibility of flexion-related myelopathy particularly in cases of drug intoxication or prolonged unconsciousness. Signal change within cervical musculature may provide additional clues and allow diagnosis in a timely manner.
Prevalence of the need for adaptive seating systems among children with cerebral palsy in Egypt
Authors: Abdallah Mohamed Adel , Abdelaziem Faten , Soliman Mostafa 
Published: November 2021

Background:
An adaptive seating system is a basic rehabilitation need for children and youth with cerebral palsy (CP) as it supports the structure and function of the musculoskeletal system and can positively affect their activities and participation. Despite the importance of adaptive seating systems, there is limited access to such systems in low-income countries.

Objectives:
To determine the percentage of children and youth between 4 and 18 years of age with CP in Egypt whose activity level and sitting ability suggest the need for an adaptive seating system.

Study design:
Observational cross-sectional study.

Methods:
One hundred ninety-three participants were included after fulfilling the criteria of the Surveillance of Cerebral Palsy of Europe. Their level of activity was assessed by a physical therapist using the Gross Motor Function Classification System (GMFCS), and their sitting ability was evaluated using the Level of Sitting Scale (LSS). Participants were considered to require an adaptive seating system if they scored GMFCS level IV or V and LSS level 1–5 concurrently.

Results:
Approximately 44% of the study participants were classified as GMFCS level IV or V and LSS level 1-5, suggesting that they were in need of an adaptive seating system.

Conclusions:
There is a large percentage of children and youth with CP in Egypt who need an adaptive seating system to be integrated into their rehabilitation.
New perspectives on mobile genetic elements: a paradigm shift for managing the antibiotic resistance crisis
Authors: Ghaly Timothy M. , Gillings Michael R. 
Published: November 2021

Mobile genetic elements (MGEs) are primary facilitators in the global spread of antibiotic resistance. Here, we present novel ecological and evolutionary perspectives to understand and manage these elements: as selfish entities that exhibit biological individuality, as pollutants that replicate and as invasive species that thrive under human impact. Importantly, each viewpoint suggests new means to control their activity and spread. When seen as biological individuals, MGEs can be regarded as therapeutic targets in their own right. We highlight promising conjugation-inhibiting compounds that could be administered alongside antibiotic treatment. Viewed as pollutants, sewage treatment methods could be modified to efficiently remove antimicrobials and the resistance genes that they select. Finally, by recognizing the invasive characteristics of MGEs, we might apply strategies developed for the management of invasive species. These include environmental restoration to reduce antimicrobial selection, early detection to help inform appropriate antibiotic usage, and biocontrol strategies that target MGEs, constituting precision antimicrobials. These actions, which embody the One Health approach, target different characteristics of MGEs that are pertinent at the cellular, community, landscape and global levels. The strategies could act on multiple fronts and, together, might provide a more fruitful means to combat the global resistance crisis.
This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
Transposable elements promote the evolution of genome streamlining
Authors: van Dijk Bram , Bertels Frederic , Stolk Lianne , Takeuchi Nobuto , Rainey Paul B. 
Published: November 2021

Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using anin silicomodel describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock–paper–scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.