bluuebunny/crossref_metadata_2025 huggingface dataset:
Global forests are influenced by the legacies of past inter-annual temperature variability
Authors: Hansen Winslow D , Schwartz Naomi B , Williams A Park , Albrich Katharina , Kueppers Lara M , Rammig Anja , Reyer Christopher P O , Staver A Carla , Seidl Rupert
Published: August 2022

Inter-annual climate variability (hereafter climate variability) is increasing in many forested regions due to climate change. This variability could have larger near-term impacts on forests than decadal shifts in mean climate, but how forests will respond remains poorly resolved, particularly at broad scales. Individual trees, and even forest communities, often have traits and ecological strategies—the legacies of exposure to past variable conditions—that confer tolerance to subsequent climate variability. However, whether local legacies also shape global forest responses is unknown. Our objective was to assess how past and current climate variability influences global forest productivity. We hypothesized that forests exposed to large climate variability in the past would better tolerate current climate variability than forests for which past climate was relatively stable. We used historical (1950–1969) and contemporary (2000–2019) temperature, precipitation, and vapor pressure deficit (VPD) and the remotely sensed enhanced vegetation index (EVI) to quantify how historical and contemporary climate variability relate to patterns of contemporary forest productivity. Consistent with our hypothesis, forests exposed to large temperature variability in the past were more tolerant of contemporary temperature variability than forests where past temperatures were less variable. Forests were 19-fold times less sensitive to contemporary temperature variability where historical inter-annual temperature variability was 0.66 °C (two standard deviations) greater than the global average historical temperature variability. We also found that larger increases in temperature variability between the two study periods often eroded the tolerance conferred by the legacy effects of historical temperature variability. However, the hypothesis was not supported in the case of precipitation and VPD variability, potentially due to physiological tradeoffs inherent in how trees cope with dry conditions. We conclude that the sensitivity of forest productivity to imminent increases in temperature variability may be partially predictable based on the legacies of past conditions.
Use of Personal Protective Equipment Among Healthcare Workers During the First and the Second Wave of the COVID-19 Pandemic
Authors: Cramer Christine , Hansen Karoline Kærgaard , Kinnerup Martin Byskov , Flachs Esben Meulengracht , Vestergaard Jesper Medom , Biering Karin , Nielsen Kent , Würtz Anne Mette , Dalbøge Annett , Würtz Else Toft , Kjærsgaard Mona , Kolstad Henrik Albert , Schlünssen Vivi
Published: August 2022

Introduction

To treat and properly care for COVID-19 patients it is vital to have healthy healthcare workers to ensure the continued function of the healthcare system and to prevent transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to patients, co-workers, and the community. Personal protective equipment (PPE) can prevent healthcare workers from being infected with and transmitting SARS-CoV-2. Experience and training are pivotal to ensure optimal protection. This study aims to examine the use and failure of PPE and compliance with PPE guidelines during the first and the second wave of the COVID-19 pandemic among Danish healthcare workers.

Methods

Healthcare workers from the Central Denmark Region and the Capital Region of Denmark were invited to participate April–June 2020 during the first wave and November 2020–April 2021 during the second wave. Day-by-day, participants reported work procedures, use and failure of PPE, and compliance with PPE guidelines. Register-based information on sex, age, department, and profession was available for all participants.

Results

In total, 21 684 and 10 097 healthcare workers participated during the first and the second wave, respectively. During the first wave, 1.7% used filtering face piece-2 or -3 (FFP2 or FFP3) respirators and 8.2% used face masks [fluid resistant (type IIR) masks, masks with visor (typically type IIR), and other unspecified face masks] during physical contact with patients. During the second wave, the corresponding figures increased to 17.8% and 80.7%. During respiratory procedures, the use of FFP2 or FFP3 respirators increased from 5.6 to 24.3%, and the use of face masks from 14.7 to 77.8%. The no PPE use decreased from 21.3% during the first wave to 0.4% in the second wave, during respiratory procedures. Total PPE failures decreased from 0.7 to 0.4% from the first to second wave. The proportion not complying with PPE guidelines declined from 3.6 to 2.2% during physical contact with patients and from 6.5 to 4.6% during respiratory procedures. PPE failure and non-compliance varied by age, sex and type of department. Frequent reasons for non-compliance were forgetfulness and lack of time, and during the first but not during the second wave, limited availability of PPE.

Conclusion

We found a substantial increase in the use of PPE and a substantial decrease in PPE failures from the first to the second wave of COVID-19 in Denmark. However, there is still a need for continuous focus on compliance in use of PPE among healthcare workers.
Res-Dom: predicting protein domain boundary from sequence using deep residual network and Bi-LSTM
Authors: Wang Lei , Zhong Haolin , Xue Zhidong , Wang Yan
Published: August 2022

Motivation

Protein domains are the basic units of proteins that can fold, function and evolve independently. Protein domain boundary partition plays an important role in protein structure prediction, understanding their biological functions, annotating their evolutionary mechanisms and protein design. Although there are many methods that have been developed to predict domain boundaries from protein sequence over the past two decades, there is still much room for improvement.

Results

In this article, a novel domain boundary prediction tool called Res-Dom was developed, which is based on a deep residual network, bidirectional long short-term memory (Bi-LSTM) and transfer learning. We used deep residual neural networks to extract higher-order residue-related information. In addition, we also used a pre-trained protein language model called ESM to extract sequence embedded features, which can summarize sequence context information more abundantly. To improve the global representation of these deep residual networks, a Bi-LSTM network was also designed to consider long-range interactions between residues. Res-Dom was then tested on an independent test set including 342 proteins and generated correct single-domain and multi-domain classifications with a Matthew’s correlation coefficient of 0.668, which was 17.6% higher than the second-best compared method. For domain boundaries, the normalized domain overlapping score of Res-Dom was 0.849, which was 5% higher than the second-best compared method. Furthermore, Res-Dom required significantly less time than most of the recently developed state-of-the-art domain prediction methods.

Availability and implementation

All source code, datasets and model are available at http://isyslab.info/Res-Dom/.
No means ‘No’: a non-improper modeling approach, with embedded speculative context
Authors: Tiwary Priya , Madhubalan Akshayraj , Gautam Amit
Published: August 2022

Motivation

The medical data are complex in nature as terms that appear in records usually appear in different contexts. Through this article, we investigate various bio model’s embeddings (BioBERT, BioELECTRA and PubMedBERT) on their understanding of ‘negation and speculation context’ wherein we found that these models were unable to differentiate ‘negated context’ versus ‘non-negated context’. To measure the understanding of models, we used cosine similarity scores of negated sentence embeddings versus non-negated sentence embeddings pairs. For improving these models, we introduce a generic super tuning approach to enhance the embeddings on ‘negation and speculation context’ by utilizing a synthesized dataset.

Results

After super-tuning the models, we can see that the model’s embeddings are now understanding negative and speculative contexts much better. Furthermore, we fine-tuned the super-tuned models on various tasks and we found that the model has outperformed the previous models and achieved state-of-the-art on negation, speculation cue and scope detection tasks on BioScope abstracts and Sherlock dataset. We also confirmed that our approach had a very minimal trade-off in the performance of the model in other tasks like natural language inference after super-tuning.

Availability and implementation

The source code, data and the models are available at: https://github.com/comprehend/engg-ai-research/tree/uncertainty-super-tuning.
The potential for treg-enhancing therapies in nervous system pathologies
Authors: Olson Katherine E , Mosley R L , Gendelman Howard E
Published: August 2022

While inflammation may not be the cause of disease, it is well known that it contributes to disease pathogenesis across a multitude of peripheral and central nervous system disorders. Chronic and overactive inflammation due to an effector T-cell-mediated aberrant immune response ultimately leads to tissue damage and neuronal cell death. To counteract peripheral and neuroinflammatory responses, research is being focused on regulatory T cell enhancement as a therapeutic target. Regulatory T cells are an immunosuppressive subpopulation of CD4+ T helper cells essential for maintaining immune homeostasis. The cells play pivotal roles in suppressing immune responses to maintain immune tolerance. In so doing, they control T cell proliferation and pro-inflammatory cytokine production curtailing autoimmunity and inflammation. For nervous system pathologies, Treg are known to affect the onset and tempo of neural injuries. To this end, we review recent findings supporting Treg’s role in disease, as well as serving as a therapeutic agent in multiple sclerosis, myasthenia gravis, Guillain–Barre syndrome, Parkinson’s and Alzheimer’s diseases, and amyotrophic lateral sclerosis. An ever-broader role for Treg in the control of neurologic disease has been shown for traumatic brain injury, stroke, neurotrophic pain, epilepsy, and psychiatric disorders. To such ends, this review serves to examine the role played by Tregs in nervous system diseases with a focus on harnessing their functional therapeutic role(s).
Development and Validation of a Risk Score to Differentiate Viral and Autoimmune Encephalitis in Adults
Authors: Granillo Alejandro , Le Maréchal Marion , Diaz-Arias Luisa , Probasco John , Venkatesan Arun , Hasbun Rodrigo
Published: August 2022

Background

Encephalitis represents a challenging condition to diagnose and treat. To assist physicians in considering autoimmune encephalitis (AE) sooner, we developed and validated a risk score.

Methods

The study was conducted as a retrospective cohort of patients with a diagnosis of definite viral encephalitis (VE) and AE from​​ February 2005 to December 2019. Clinically relevant and statistically significant features between cases of AE and VE were explored in a bivariate logistic regression model and results were used to identify variables for inclusion in the risk score. A multivariable logistic model was used to generate risk score values and predict risk for AE. Results were externally validated.

Results

A total of 1310 patients were screened. Of the 279 enrolled, 36 patients met criteria for definite AE and 88 criteria for definite VE. Patients with AE compared with VE were more likely to have a subacute to chronic presentation (odds ratio [OR] = 22.36; 95% confidence interval [CI], 2.05–243.7), Charlson comorbidity index <2 (OR = 6.62; 95% CI, 1.05–41.4), psychiatric and/or memory complaints (OR = 203.0; 95% CI, 7.57–5445), and absence of robust inflammation in the cerebrospinal fluid defined as <50 white blood cells/µL and protein <50 mg/dL (OR = 0.06; 95% CI, .005–0.50). Using these 4 variables, patients were classified into 3 risk categories for AE: low (0–1), intermediate (2–3), and high (4). Results were externally validated and the performance of the score achieved an area under the curve of 0.918 (95% CI, .871–.966).

Discussion

This risk score allows clinicians to estimate the probability of AE in patients presenting with encephalitis and may assist with earlier diagnosis and treatment.
Comprehensive analysis of 124 transcriptomes from 31 tissues in developing, juvenile, and adult Japanese Black cattle
Authors: Arishima Taichi , Wakaguri Hiroyuki , Nakashima Ryotaro , Sakakihara Seigo , Kawashima Keisuke , Sugimoto Yoshikazu , Suzuki Yutaka , Sasaki Shinji
Published: August 2022

Omic analyses of economically important animals, including Japanese Black cattle, are currently underway worldwide. In particular, tissue and developmental stage-specific transcriptome characterization is essential for understanding the molecular mechanisms underlying the phenotypic expression of genetic disorders and economic traits. Here, we conducted a comprehensive analysis of 124 transcriptomes across 31 major tissues from fetuses, juvenile calves, and adult Japanese Black cattle using short-read sequencing. We found that genes exhibiting high tissue-specific expression tended to increase after 60 days from fertilization and significantly reflected tissue-relevant biology. Based on gene expression variation and inflection points during development, we categorized gene expression patterns as stable, increased, decreased, temporary, or complex in each tissue. We also analysed the expression profiles of causative genes (e.g. SLC12A1, ANXA10, and MYH6) for genetic disorders in cattle, revealing disease-relevant expression patterns. In addition, to directly analyse the structure of full-length transcripts without transcript reconstruction, we performed RNA sequencing analysis of 22 tissues using long-read sequencing and identified 232 novel non-RefSeq isoforms. Collectively, our comprehensive transcriptomic analysis can serve as an important resource for the biological and functional interpretation of gene expression and enable the mechanistic interpretation of genetic disorders and economic traits in Japanese Black cattle.
Reimbursement practices for use of digital devices in atrial fibrillation and other arrhythmias: a European Heart Rhythm Association survey
Authors: Boriani Giuseppe , Svennberg Emma , Guerra Federico , Linz Dominik , Casado-Arroyo Ruben , Malaczynska-Rajpold Katarzyna , Duncker David , Boveda Serge , Merino Josè Luis , Leclercq Christophe
Published: August 2022

Since digital devices are increasingly used in cardiology for assessing cardiac rhythm and detecting arrhythmias, especially atrial fibrillation (AF), our aim was to evaluate the expectations and opinions of healthcare professionals in Europe on reimbursement policies for the use of digital devices (including wearables) in AF and other arrhythmias. An anonymous survey was proposed through announcements on the European Heart Rhythm Association website, social media channels, and mail newsletter. Two hundred and seventeen healthcare professionals participated in the survey: 32.7%, reported regular use of digital devices, 45.2% reported that they sometimes use these tools, 18.6% that they do not use but would like to. Only a minority (3.5%) reported a lack of trust in digital devices. The survey highlighted a general propensity to provide medical consultation for suspected AF or other arrhythmias detected by a consumer-initiated use of digital devices, even if time constraints and reimbursement availability emerged as important elements. More than 85% of respondents agreed that reimbursement should be applied for clinical use of digital devices, also in different settings such as post-stroke, post-cardioversion, post-ablation, and in patients with palpitations or syncope. Finally, 73.6% of respondents confirmed a lack of reimbursement fees in their country for physicians’ consultations (tracings interpretation) related to digital devices. Digital devices, including wearables, are increasingly and widely used for assessing cardiac rhythm and detecting AF, but a definition of reimbursement policies for physicians’ consultations is needed.
A simple force balance model of subduction initiation
Authors: Li Yida , Gurnis Michael
Published: August 2022

The initiation and development of subduction zones are associated with substantial stress changes both within plates and at plate boundaries. We formulate a simple analytical model based on the force balance equation of a subduction zone, and validate it with numerical calculations of highly non-linear, coupled thermomechanical system. With two kinds of boundary conditions with either fixed velocity or fixed force in the far-field, we quantitatively analyse the role of each component in the force balance equation, including slab pull, interplate friction, plate bending and basal traction, on the kinematics and stress state of a subducting plate. Based on the numerical and analytical models, we discuss the evolution of plate curvature, the role of plastic yielding and elasticity, and how different factors affect the timing of subduction initiation. We demonstrate with the presence of plastic yielding for a plate of thickness, H, that the bending force is proportional to H2, instead of H3 as previously thought. Although elasticity increases the force required to start nucleating subduction it does not substantially change the total work required to initiate a subduction zone when the yielding stress is small. The analytical model provides an excellent fit to the total work and time to initiate subduction and the force and velocity as a function of convergence and time. Plate convergence and weakening rate during nucleation are the dominant factors influencing the force balance of the plate, and 200 km of plate convergence is typically required to bring a nascent subduction zone into a self-sustaining state. The closed-form solution now provides a framework to better interpret even more complex, time-dependent systems in three dimensions.
Presidential Influence and Public Opinion During Crises: The Case of COVID-19 in Brazil
Authors: Batista Pereira Frederico , Nunes Felipe
Published: August 2022

Can presidential messages influence public opinion? The scholarship shows that common features in developed democracies such as fragmented audiences and partisan reasoning tend to limit the persuasive effects of the bully pulpit. In this article, we argue that the effectiveness of the presidential rhetoric is context dependent. Presidents will be the most likely to persuade public opinion when they seek to break consensus by using messages that activate defection among their supporters. To examine this framework, we focus on the setting of the COVID-19 pandemic in Brazil, where the outbreak was initially a valence issue, but quickly it became a divisive matter among the public. We use a survey experiment conducted days before the President Bolsonaro’s national televised address to show that cueing subjects with one of his earlier denialist remarks about the outbreak polarized opinions. We then use Bayesian change-point models to demonstrate how his major televised speeches affected daily trends in online searches related to the pandemic during the first and the most crucial weeks of the outbreak. The findings shed light on the circumstances in which presidential influence can not only be most powerful, but also most harmful.
Can Exceptionalism Withstand Crises? An Evaluation of the Arctic Council's Response to Climate Change and Russia's War on Ukraine
Authors: Gricius Gabriella , Fitz Erin B
Published: August 2022

For almost three decades, the Arctic Council has been considered exceptional in its approach to domestic, environmental, and geopolitical issues. Russia's 2022 war on Ukraine and the subsequent pause of the Arctic Council, however, give cause to question whether the Arctic Council remains exceptional in the face of actual crises. We explore this question in two ways: as an endogenous crisis, we provide a systematic literature review of publications on Arctic Council climate change governance. As an exogenous crisis, we explore the Arctic Council's pause given the Russia–Ukraine war. Taken together, our findings suggest that while the Arctic Council has the potential for exceptionalism, it lacks the capacity to substantively respond to crises. In turn, our study provides further evidence to suggest that even idealized institutions may not truly offer unique methods for withstanding environmental and geopolitical challenges; furthermore, it highlights the precariousness of intergovernmental institutions considered broadly.
Aspartic proteases modulate programmed cell death and secondary cell wall synthesis during wood formation in poplar
Authors: Cao Shenquan , Guo Mengjie , Cheng Jiyao , Cheng Hao , Liu Xiaomeng , Ji Huanhuan , Liu Guanjun , Cheng Yuxiang , Yang Chuanping
Published: August 2022

Programmed cell death (PCD) is essential for wood development in trees. However, the determination of crucial factors involved in xylem PCD of wood development is still lacking. Here, two Populus trichocarpa typical aspartic protease (AP) genes, AP17 and AP45, modulate xylem maturation, especially fibre PCD, during wood formation. AP17 and AP45 were dominantly expressed in the fibres of secondary xylem, as suggested by GUS expression in APpro::GUS transgenic plants. Cas9/gRNA-induced AP17 or AP45 mutants delayed secondary xylem fibre PCD, and ap17ap45 double mutants showed more serious defects. Conversely, AP17 overexpression caused premature PCD in secondary xylem fibres, indicating a positive modulation in wood fibre PCD. Loss of AP17 and AP45 did not alter wood fibre wall thickness, whereas the ap17ap45 mutants showed a low lignin content in wood. However, AP17 overexpression led to a significant decrease in wood fibre wall thickness and lignin content, revealing the involvement in secondary cell wall synthesis during wood formation. In addition, the ap17ap45 mutant and AP17 overexpression plants resulted in a significant increase in saccharification yield in wood. Overall, AP17 and AP45 are crucial modulators in xylem maturation during wood development, providing potential candidate genes for engineering lignocellulosic wood for biofuel utilization.
A machine-learning classifier for LOFAR radio galaxy cross-matching techniques
Authors: Alegre Lara , Sabater Jose , Best Philip , Mostert Rafaël I J , Williams Wendy L , Gürkan Gülay , Hardcastle Martin J , Kondapally Rohit , Shimwell Tim W , Smith Daniel J B
Published: August 2022

New-generation radio telescopes like LOFAR are conducting extensive sky surveys, detecting millions of sources. To maximize the scientific value of these surveys, radio source components must be properly associated into physical sources before being cross-matched with their optical/infrared counterparts. In this paper, we use machine learning to identify those radio sources for which either source association is required or statistical cross-matching to optical/infrared catalogues is unreliable. We train a binary classifier using manual annotations from the LOFAR Two-metre Sky Survey (LoTSS). We find that, compared to a classification model based on just the radio source parameters, the addition of features of the nearest-neighbour radio sources, the potential optical host galaxy, and the radio source composition in terms of Gaussian components, all improve model performance. Our best model, a gradient boosting classifier, achieves an accuracy of 95 per cent on a balanced data set and 96 per cent on the whole (unbalanced) sample after optimizing the classification threshold. Unsurprisingly, the classifier performs best on small, unresolved radio sources, reaching almost 99 per cent accuracy for sources smaller than 15 arcsec, but still achieves 70 per cent accuracy on resolved sources. It flags 68 per cent more sources than required as needing visual inspection, but this is still fewer than the manually developed decision tree used in LoTSS, while also having a lower rate of wrongly accepted sources for statistical analysis. The results have an immediate practical application for cross-matching the next LoTSS data releases and can be generalized to other radio surveys.
The impact of Covid-19 on research into work and health
Authors: Parsons V , Wainwright E , Karanika-Murray M , Muiry G , Demou E
Published: August 2022

Background

The global coronavirus (Covid-19) pandemic created a profound disruption to the delivery of planned scientific research with unknown immediate and potentially longer-term impacts.

Aims

We explored researchers’ experiences of the impact of the pandemic on the continued development and delivery of research into work and health, and on research infrastructure in this field.

Methods

A cross-sectional study.

Results

Thirty-three questionnaires were completed, representing a response rate of 15%. Sixty-one per cent of respondents were female, the majority (78%) had over 11 years of research experience and 76% worked mainly in academia. Most respondents (88%) were able to progress with research during the pandemic. A small proportion (4%) had studies paused or suspended due to the pandemic, while a larger proportion (19%) had research staff redeployed to assist with other studies or furloughed. Respondents described a range of emerging practical and logistical issues for research into work and health during the pandemic. Some benefited from increased opportunities to collaborate on new multidisciplinary studies, opportunities to engage participants in work and health research, and more flexible and inclusive work practices. Others experienced challenges that had an adverse impact, such as hampering research delivery (e.g. barriers to participant screening and intervention delivery), poor (home) working environments, reduced team cohesion and isolation. A range of future priorities for research was highlighted.

Conclusions

We describe lessons learned and opportunities that can be used to support or further research activities in the field of work and health research in the future.
Occupation and 20-year hearing decline: findings from The HUNT Study
Authors: Molaug I , Engdahl B , Degerud E , Mehlum I S , Aarhus L
Published: August 2022

Background

Studies show that certain occupations are associated with an increased risk of hearing loss. However, many studies are cross-sectional, and the few longitudinal studies are mostly small or focus on only one occupation.

Aims

We aimed to quantify the long-term hearing decline among workers in different occupations and assess whether the change differs between the occupations.

Methods

The study population was 4525 adults who participated in two population-based health studies in Norway, HUNT2 1996–1998 and HUNT4 2017–2019. Linear regression models assessed the association between occupations (clerks as reference) and 20-year hearing decline (hearing thresholds at 3–6 kHz, averaged over both ears) from HUNT2 to HUNT4. Models were adjusted for age, sex, recurrent ear infections, smoking and ear pathology.

Results

Among the participants (40% men), the mean age at HUNT2 was 31.2 ± 5.4 years (range 20–39) and the average 20-year hearing decline was 11.3 ± 9.8 dB. Occupations that were associated with larger hearing decline included other craft and related trades workers (3.9 dB, 95% confidence interval [CI] 0.2–7.7) and building frame and related trades workers (3.4 dB, 95% CI 1.3–5.4). Among occupations with larger hearing decline, a higher proportion of the workers reported exposure to noise.

Conclusions

This large longitudinal study shows a larger long-term hearing decline among building frame workers and craft and related trades workers. Differences between occupations were modest, which may indicate successful preventive measures in Norway during the last two decades.
Medium-chain triglyceride production in Nannochloropsis via a fatty acid chain length discriminating mechanism
Authors: Xin Yi , Wang Qintao , Shen Chen , Hu Chunxiu , Shi Xianzhe , Lv Nana , Du Xuefeng , Xu Guowang , Xu Jian
Published: August 2022

Depending on their fatty acid (FA) chain length, triacylglycerols (TAGs) have distinct applications; thus, a feedstock with a genetically designed chain length is desirable to maximize process efficiency and product versatility. Here, ex vivo, in vitro, and in vivo profiling of the large set of type-2 diacylglycerol acyltransferases (NoDGAT2s) in the industrial oleaginous microalga Nannochloropsis oceanica revealed two endoplasmic reticulum-localized enzymes that can assemble medium-chain FAs (MCFAs) with 8–12 carbons into TAGs. Specifically, NoDGAT2D serves as a generalist that assembles C8-C18 FAs into TAG, whereas NoDGAT2H is a specialist that incorporates only MCFAs into TAG. Based on such specialization, stacking of NoDGAT2D with MCFA- or diacylglycerol-supplying enzymes or regulators, including rationally engineering Cuphea palustris acyl carrier protein thioesterase, Cocos nucifera lysophosphatidic acid acyltransferase, and Arabidopsis thaliana WRINKLED1, elevated the medium-chain triacylglycerol (MCT) share in total TAG 66-fold and MCT productivity 64.8-fold at the peak phase of oil production. Such functional specialization of NoDGAT2s in the chain length of substrates and products reveals a dimension of control in the cellular TAG profile, which can be exploited for producing designer oils in microalgae.
PtoWRKY40 interacts with PtoPHR1-LIKE3 while regulating the phosphate starvation response in poplar
Authors: Chen Ningning , Tong Shaofei , Yang Jian , Qin Jiajia , Wang Weiwei , Chen Kai , Shi Wensen , Li Jiacong , Liu Jianquan , Jiang Yuanzhong
Published: August 2022

Plants usually suffer from phosphorus starvation because of the low inorganic phosphate (Pi) status of most soils. To cope with this, plants have evolved an adaptive phosphate starvation response (PSR) which involves both developmental and metabolic changes regulated mainly by PHOSPHATE STARVATION RESPONSE1 (PHR1) and its homologs. Here, we elucidated how perennial woody plants, such as poplars (Populus spp.), respond to low-Pi stress. We first performed RNA-seq analysis of low-Pi-treated poplars and identified PtoWRKY40 is rapidly downregulated and protein degraded after stress. Overexpressing and knocking-down PtoWRKY40 downregulated and upregulated the expression of Pi starvation signaling genes, respectively, such as PHOSPHATE TRANSPORTER1 (PHT1)-type genes and PURPLE ACID PHOSPHATASE genes. PtoWRKY40 bound to the W box in the promoter of several PtoPHT1s and repressed their expression. Moreover, PtoWRKY40 interacted with PtoPHR1-LIKE3 (PtoPHL3), a PHR1 homolog in poplar, to inhibit the latter binding to the P1BS element and thus reduced PtoPHT1s’ transcription under Pi-sufficient conditions. However, Pi deficiency decreased PtoWRKY40 abundance and therefore released its inhibition on PHT1s. In conclusion, we have uncovered a PSR mechanism mediated by PtoWRKY40 and PtoPHL3 which regulates Pi content in poplars, deepening our understanding of how poplars adapt to diverse Pi conditions and regulate appropriate responses to maintain Pi homeostasis.
Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing
Authors: Deng Longhui , Meile Christof , Fiskal Annika , Bölsterli Damian , Han Xingguo , Gajendra Niroshan , Dubois Nathalie , Bernasconi Stefano M , Lever Mark A
Published: August 2022

Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer.
Longitudinal global transcriptomic profiling of preclinical systemic sclerosis reveals molecular changes associated with disease progression
Authors: Bellocchi Chiara , Beretta Lorenzo , Wang Xuan , Lyons Marka A , Marchini Maurizio , Lorini Maurizio , Carbonelli Vincenzo , Montano Nicola , Assassi Shervin
Published: August 2022

Objective

To investigate peripheral blood cell (PBCs) global gene expression profile of SSc at its preclinical stage (PreSSc) and to characterize the molecular changes associated with progression to a definite disease over time.

Material and methods

Clinical data and PBCs of 33 participants with PreSSc and 16 healthy controls (HCs) were collected at baseline and follow-up (mean 4.2 years). Global gene expression profiling was conducted by RNA sequencing and a modular analysis was performed.

Results

Comparison of baseline PreSSc to HCs revealed 2889 differentially expressed genes. Interferon signalling was the only activated pathway among top over-represented pathways. Moreover, 10 modules were significantly decreased in PreSSc samples (related to lymphoid lineage, cytotoxic/NK cell, and erythropoiesis) in comparison to HCs. At follow-up, 14 subjects (42.4%) presented signs of progression (evolving PreSSc) and 19 remained in stable preclinical stage (stable PreSSc). Progression was not associated with baseline clinical features or baseline PBC transcript modules. At follow-up stable PreSSc normalized their down-regulated cytotoxic/NK cell and protein synthesis modules while evolving PreSSc kept a down-regulation of cytotoxic/NK cell and protein synthesis modules. Transcript level changes of follow-up vs baseline in stable PreSSc vs evolving PreSSc showed 549 differentially expressed transcripts (336 up and 213 down) with upregulation of the EIF2 Signalling pathway.

Conclusions

Participants with PreSSc had a distinct gene expression profile indicating that molecular differences at a transcriptomic level are already present in the preclinical stages of SSc. Furthermore, a reduced NK signature in PBCs was related to SSc progression over time.
From Secrecy to Public Containment: The Role of Hybrid Spaces in the Governance of Nuclear Crises in France
Authors: Arnhold Valerie
Published: August 2022

How do some large-scale adverse events receive major media coverage and become crises for public actors while others are treated as routine events? This article reinvestigates this question based on a case study of the media treatment in France of the Chernobyl and Fukushima nuclear accidents. Drawing on an original set of media data and an ethnographic study, the article shows how both accidents were subject to forms of opacity that limit their effects on nuclear institutions: Chernobyl has been treated through secrecy that leads to contestation of nuclear institutions, whereas Fukushima has been characterized by “public containment,” relying on extensive publication but low-priority and uncontroversial narratives that do not reflect the stakes of a given policy field. This paper explains the role of Fukushima in France through institutional transformations that public actors engaged in following Chernobyl to reestablish the credibility of public information sources and to monitor public debates over nuclear accidents by developing “hybrid” spaces, located at the interface of organizational frontstages and backstages. This case shows how responding to transparency demands may sometimes create new forms of opacity by reducing the epistemic quality of public debates while containing political crises.
Photosensitizer to the Rescue: In Planta and Field Application of Photodynamic Inactivation Against Plant-Pathogenic Bacteria
Authors: Islam Md Tariqul , Ng Kenneth , Fefer Michael , Liu Jun , Uddin Wakar , Ckurshumova Wenzi , Rosa Cristina
Published: August 2022

Control of plant pathogens using chemical and synthetic pesticides raises a major safety concern for humans and the environment. Despite the ongoing exploration of sustainable alternative methods, management practices for pathogens, especially bacteria, have remained almost unchanged over decades, whereby long-term uses of copper and antibiotics has led to widespread bacterial resistance in the field. Antimicrobial photodynamic inactivation (aPDI) of bacteria is emerging as an alternative strategy to combat resistant plant pathogens. aPDI utilizes light-sensitive molecules (photosensitizers) that, upon illumination, produce reactive oxygen species able to kill pathogens. Here, we explore the potential of an anionic semisynthetic water-soluble derivative of chlorophyl (sodium magnesium chlorophyllin [Mg-chl]) as an antibacterial agent in planta, by simulating processes naturally occurring in the field. Mg-chl in combination with Na2EDTA (cell-wall-permeabilizing agent) was able to effectively inhibit Pseudomonas syringae pv. tomato DC3000 in vitro and in planta in both tomato and Nicotiana benthamiana. Notably, Mg-chl in combination with Na2EDTA and the common surfactant Morwet D-400 significantly reduced Xanthomonas hortorum pv. gardneri and X. fragarie, respectively, in a commercial greenhouse trial against bacterial spot disease in tomato and in field experiments against angular leaf spot disease in strawberry.
Prostate cancer screening: Continued controversies and novel biomarker advancements
Authors: Tidd-Johnson Atiyah , Sebastian Sneha Annie , Co Edzel Lorraine , Afaq Munaza , Kochhar Hansini , Sheikh Mona , Mago Arpit , Poudel Sujan , Fernandez John A. , Rodriguez Ivan D. , Razdan Sanjay
Published: August 2022

Prostate cancer (PCa) screening remains one of the most controversial topics in clinical and public health. Despite being the second most common cancer in men worldwide, recommendations for screening using prostate-specific antigen (PSA) are unclear. Early detection and the resulting postscreening treatment lead to overdiagnosis and overtreatment of otherwise indolent cases. In addition, several unwanted harms are associated with PCa screening process. This literature review focuses on the limitations of PSA-specific PCa screening, reasons behind the screening controversy, and the novel biomarkers and advanced innovative methodologies that improve the limitations of traditional screening using PSA. With the verdict of whether or not to screen not yet unanimous, we hope to aid in resolution of the long-standing debate.
Giftedness and Neurodevelopmental Disorders in Children and Adolescents: A Systematic Review
Authors: Kontakou Afroditi , Dimitriou Georgia , Panagouli Eleni , Thomaidis Loretta , Psaltopoulou Theodora , Sergentanis Theodoros N. , Tsitsika Artemis
Published: August 2022

Objective:

Throughout the years, several myths have arisen suggesting that children diagnosed with neurodevelopmental disorders possess unusually high abilities in specific domains, depending on the disorder. On the other hand, special skills and talents in children with neurodevelopmental disorders are most commonly overshadowed by their difficulties and overlooked. The purpose of this systematic review is to examine the association between giftedness and neurodevelopmental disorders.

Methods:

The related articles published in PubMed, Google Scholar, PsycINFO, and Embase up to December 31, 2020, as well as their reference lists, were reviewed systematically.

Results:

A total of 6069 studies were scanned, and 32 of them (9904 subjects) were deemed eligible for this systematic review. Studies have supported associations between autism spectrum disorders and music ability. Contradictory results have been published regarding associations between giftedness, attention-deficit/hyperactivity disorder, and specific learning disorders. Diagnostic methods seemed to modify associations between giftedness and neurodevelopmental disorders.

Conclusion:

The dearth of the available evidence is prominent. More research is needed to investigate the field of dual exceptionality. Longitudinal studies are needed, addressing methodological challenges pertaining to variability in the definition of giftedness.
Posttraumatic Stress Symptoms and the Quality of Maternal-Child Interactions in Mothers of Preterm Infants
Authors: Elansary Mei , Zuckerman Barry , Patts Gregory , Antonio Jocelyn , Mayes Linda C. , Silverstein Michael
Published: August 2022

Objective:

The purpose of this study was to examine associations between maternal trauma exposure, posttraumatic stress symptoms, and directly observed maternal-child interactions among a diverse cohort of mother-preterm infant dyads at 12-month corrected age.

Methods:

We conducted a retrospective cohort study. Maternal trauma exposure and posttraumatic stress symptoms were measured using the Modified Posttraumatic Stress Disorder Symptom Scale at baseline and 6 and 12 months. The primary outcome was directly observed maternal-child interactions at 12-month corrected age using the Coding Interactive Behavior Manual. We used linear regression models to estimate the associations between trauma exposure, posttraumatic stress symptoms (and symptom clusters), and observer-rated maternal-child interactions.

Results:

Among the 236 participants, 89 (37.7%) self-reported as Black and 98 (41.5%) as Latina; mean gestational age of the infants was 31.6 weeks (SD 2.6). Mothers with posttraumatic stress symptoms demonstrated greater maternal sensitivity (β = 0.32; 95% confidence interval [CI], 0.06–0.58; standardized effect size = 0.39) and greater dyadic reciprocity (β = 0.39; 95% CI, 0.04–0.73; standardized effect size = 0.36) compared with those not exposed to trauma; however, we did not observe significant differences between trauma-exposed but asymptomatic women and those not exposed to trauma. Across symptom clusters, differences in maternal sensitivity and dyadic reciprocity were most pronounced for mothers with avoidance and re-experiencing symptoms, but not hyperarousal symptoms.

Conclusion:

Maternal posttraumatic stress symptoms seem to be associated with the quality of maternal-child interactions at age 1 year among a cohort of urban, mother-preterm infant dyads. These findings have implications for strength-based intervention development.
Consideration of Social Determinants Risks in Substance Use Disorder Assessment and Treatment Plan Formulation
Authors: Mulhern John Paul
Published: August 2022

Substance use disorders continue to trend as an increasingly pervasive public health problem in the United States. Substance use disorders are recognized as a global health problem by the World Health Organization. It is imperative to explore all opportunities to improve outcomes of substance use disorder treatment. Consideration of social determinant risks in assessment, treatment planning, and treatment implementation is one such opportunity. Social determinant conditions can be conceptualized along a continuum of primary categories. Developing methods to help clinicians understand and incorporate social determinants into assessment and treatment plan formulation processes may help improve outcomes for those who are experiencing one or more substance use disorders. This column includes a proposal for a framework of primary categories of social determinants and offers a definition for each. The categories are identified as basic needs insecurity, past trauma, historical oppression, current/ongoing severe distress and layered/compounded risks. These categories and definitions are developed in the context of practical application for clinical assessment and treatment plan formulation.
Management of Pancreatic Fluid Collections
Authors: Sameera Sohini , Mohammad Tayyaba , Liao Kelvin , Shahid Haroon , Sarkar Avik , Tyberg Amy , Kahaleh Michel
Published: August 2022

Managing pancreatic fluid collections (PFCs) remains a challenge for many clinicians. Recently, significant progress has been made in the therapy of PFCs, including improvements in technology and devices, as well as in the development of minimally invasive endoscopic techniques, many of which are proven less traumatic when compared with surgical options and more efficacious when compared with percutaneous techniques. This review will explore latest developments in the management of PFCs and how they incorporate into the current treatment algorithm.
The anti-inflammatory effects of a Mediterranean diet: a review
Authors: Itsiopoulos Catherine , Mayr Hannah L. , Thomas Colleen J.
Published: August 2022

Purpose of review

Chronic noncommunicable diseases remain the leading cause of morbidity and mortality worldwide and the majority are preventable with a healthy diet and lifestyle, but controversy remains as to the best approach. Greater adherence to a traditional Mediterranean diet has consistently been associated with lower morbidity and mortality from cardiovascular disease, diabetes and many cancers, and lower all-cause mortality. Despite the well known benefits on chronic disease risk there remains some scepticism as to the effects of this dietary pattern across populations outside the Mediterranean and the mechanisms of action of this traditional plant-based dietary pattern.

This narrative review aims to summarize the latest evidence on the health protective effects of a traditional Mediterranean diet on chronic noncommunicable diseases, specifically focussing on the anti-inflammatory effects of this highly published dietary pattern.

Recent findings

Recent high-quality evidence now supports a Mediterranean diet in secondary prevention of cardiovascular disease with impacts on atherosclerosis progression, likely through reduction of systemic inflammation and irrespective of changes in cholesterol or weight. The Mediterranean diet has a low Dietary Inflammatory Index illustrating its anti-inflammatory potential. This dietary pattern beneficially modulates the gut microbiota and immune system, including emerging evidence for efficacy against severe acute respiratory syndrome coronavirus 2 (coronavirus disease 2019). Emerging evidence shows clinicians are not routinely recommending a Mediterranean diet despite well known evidence due to barriers such as lack of training, patient materials and concerns about potential patient adherence.

The physiological mechanisms of action of this healthy diet pattern are becoming better understood to be multisystem and involving the gut. Larger controlled trials investigating mechanistic effects in broader non-Mediterranean populations are warranted. Although reflected in therapeutic guidelines for chronic disease management worldwide there are individual, clinical practice and health system barriers to its implementation that need a multisectoral approach to address.