bluuebunny/crossref_metadata_2025 huggingface dataset:
The genetic landscape of origins of replication in P. falciparum
Authors: Castellano Casilda Muñoz , Lacroix Laurent , Mathis Emilie , Prorok Paulina , Hennion Magali , Lopez-Rubio Jose-Juan , Méchali Marcel , Gomes Ana Rita
Published: December 2023

Various origin mapping approaches have enabled genome-wide identification of origins of replication (ORI) in model organisms, but only a few studies have focused on divergent organisms. By employing three complementary approaches we provide a high-resolution map of ORIs in Plasmodium falciparum, the deadliest human malaria parasite. We profiled the distribution of origin of recognition complex (ORC) binding sites by ChIP-seq of two PfORC subunits and mapped active ORIs using NFS and SNS-seq. We show that ORIs lack sequence specificity but are not randomly distributed, and group in clusters. Licensing is biased towards regions of higher GC content and associated with G-quadruplex forming sequences (G4FS). While strong transcription likely enhances firing, active origins are depleted from transcription start sites. Instead, most accumulate in transcriptionally active gene bodies. Single molecule analysis of nanopore reads containing multiple initiation events, which could have only come from individual nuclei, showed a relationship between the replication fork pace and the distance to the nearest origin. While some similarities were drawn with the canonic eukaryote model, the distribution of ORIs in P. falciparum is likely shaped by unique genomic features such as extreme AT-richness—a product of evolutionary pressure imposed by the parasitic lifestyle.
Using energy to go downhill—a genoprotective role for ATPase activity in DNA topoisomerase II
Authors: Bandak Afif F , Blower Tim R , Nitiss Karin C , Shah Viraj , Nitiss John L , Berger James M
Published: December 2023

Type II topoisomerases effect topological changes in DNA by cutting a single duplex, passing a second duplex through the break, and resealing the broken strand in an ATP-coupled reaction cycle. Curiously, most type II topoisomerases (topos II, IV and VI) catalyze DNA transformations that are energetically favorable, such as the removal of superhelical strain; why ATP is required for such reactions is unknown. Here, using human topoisomerase IIβ (hTOP2β) as a model, we show that the ATPase domains of the enzyme are not required for DNA strand passage, but that their loss elevates the enzyme's propensity for DNA damage. The unstructured C-terminal domains (CTDs) of hTOP2β strongly potentiate strand passage activity in ATPase-less enzymes, as do cleavage-prone mutations that confer hypersensitivity to the chemotherapeutic agent etoposide. The presence of either the CTD or the mutations lead ATPase-less enzymes to promote even greater levels of DNA cleavage in vitro, as well as in vivo. By contrast, aberrant cleavage phenotypes of these topo II variants is significantly repressed when the ATPase domains are present. Our findings are consistent with the proposal that type II topoisomerases acquired ATPase function to maintain high levels of catalytic activity while minimizing inappropriate DNA damage.
Differentiable partition function calculation for RNA
Authors: Matthies Marco C , Krueger Ryan , Torda Andrew E , Ward Max
Published: December 2023

Ribonucleic acid (RNA) is an essential molecule in a wide range of biological functions. In 1990, McCaskill introduced a dynamic programming algorithm for computing the partition function of an RNA sequence. McCaskill’s algorithm is widely used today for understanding the thermodynamic properties of RNA. In this work, we introduce a generalization of McCaskill’s algorithm that is well-defined over continuous inputs. Crucially, this enables us to implement an end-to-end differentiable partition function calculation. The derivative can be computed with respect to the input, or to any other fixed values, such as the parameters of the energy model. This builds a bridge between RNA thermodynamics and the tools of differentiable programming including deep learning as it enables the partition function to be incorporated directly into any end-to-end differentiable pipeline. To demonstrate the effectiveness of our new approach, we tackle the inverse folding problem directly using gradient optimization. We find that using the gradient to optimize the sequence directly is sufficient to arrive at sequences with a high probability of folding into the desired structure. This indicates that the gradients we compute are meaningful.
Microcredit: equilibrium effects
Authors: Bagga Aanchal , Kinnan Cynthia
Published: December 2023

Changes to access to credit can potentially cause changes to the returns to various factors—general equilibrium (GE) effects. This paper considers changes in wages, prices of goods and services, interest rates, and in the returns to forming or maintaining social ties. Such GE effects can lead to positive and/or negative indirect effects on economic agents, including those who are not directly affected by a given credit policy. Thus such effects matter for the average level and distribution of impacts resulting from credit access. In addition, GE effects have implications for research design, in that those who are indirectly affected via GE channels are generally not a valid counterfactual for those who are directly affected.
Automatic estimation of lipid content from in situ images of Arctic copepods using machine learning
Authors: Maps Frédéric , Storożenko Piotr Pasza , Świeżewski Jędrzej , Ayata Sakina-Dorothée
Published: December 2023

In Arctic marine ecosystems, large planktonic copepods form a crucial hub of matter and energy. Their energy-rich lipid stores play a central role in marine trophic networks and the biological carbon pump. Since the past ~15 years, in situ imaging devices provide images whose resolution allows us to estimate an individual copepod’s lipid sac volume, and this reveals many ecological information inaccessible otherwise. One such device is the Lightframe On-sight Keyspecies Investigation. However, when done manually, weeks of work are needed by trained personnel to obtain such information for only a handful of sampled images. We removed this hurdle by training a machine learning algorithm (a convolutional neural network) to estimate the lipid content of individual Arctic copepods from the in situ images. This algorithm obtains such information at a speed (a few minutes) and a resolution (individuals, over half a meter on the vertical), allowing us to revisit historical datasets of in situ images to better understand the dynamics of lipid production and distribution and to develop efficient monitoring protocols at a moment when marine ecosystems are facing rapid upheavals and increasing threats.
Disclosure of Bank-Specific Information and the Stability of Financial Systems
Authors: Dai Liang , Luo Dan , Yang Ming
Published: December 2023

We find that disclosing bank-specific information reallocates systemic risk, but whether it mitigates systemic bank runs depends on the nature of information disclosed. Disclosure reveals banks’ resilience to adverse shocks and shifts systemic risk from weak to strong banks. Yet, only disclosure of banks’ exposure to systemic risk can mitigate systemic bank runs because it shifts systemic risk from more vulnerable banks to those less vulnerable. Disclosure of banks’ idiosyncratic shortfalls of funds does not differentiate such exposure, rendering the resultant reallocation of systemic risk ineffective in mitigating systemic runs.
Irrigation Targeted to Provoke Ejection of Ascospores of Venturia inaequalis Shortens the Season for Ascospore Release and Results in Less Apple Scab
Authors: Prodorutti Daniele , Bugiani Riccardo , Philion Vincent , Stensvand Arne , Coller Emanuela , Tosi Clelia , Rizzi Claudio , Angeli Gino , Pertot Ilaria
Published: December 2023

Trials were carried out in apple orchards of Emilia-Romagna and Trentino-Alto Adige in northern Italy to investigate the effects of sprinkler irrigation on possible reduction in inoculum and subsequent disease pressure of Venturia inaequalis, the ascomycete causing apple scab. In spring, volumetric spore traps were placed above apple leaf litter containing pseudothecia with ascospores of the fungus. Pseudothecia matured more rapidly in irrigated plots, and 95% of the total number of spores trapped in a season was reached on average 164 degree days (base temperature 0°C) earlier in irrigated compared with nonirrigated plots. On average for seven location/year combinations, more than 50% of the ascospores were trapped following irrigations carried out for 2 h on sunny days before a forecasted rainfall. Subsequently, a much lower number of spores were trapped on rainy days following irrigation. Field trials with scab-susceptible apple cultivars were carried out in the two regions to evaluate the efficacy of sprinkler irrigation on disease. Irrigated and nonirrigated plots were either treated with different fungicide control strategies or not treated. Irrigation significantly reduced the incidence of apple scab at both sites, and the overall number of infected leaves and fruit was reduced by more than 50%. Midday sprinkler irrigation can significantly reduce the inoculum pressure of V. inaequalis in apple orchards. This may be a sustainable management strategy, especially in areas with extended dry periods.
Endoscopic Predictors of Residual Tumor After Total Neoadjuvant Therapy: A Post Hoc Analysis From the Organ Preservation in Rectal Adenocarcinoma Trial
Authors: Williams Hannah , Thompson Hannah M. , Lin Sabrina T. , Verheij Floris S. , Omer Dana M. , Qin Li-Xuan , Garcia-Aguilar Julio ,   On behalf of the OPRA Consortium
Published: December 2023

BACKGROUND:

Restaging endoscopy plays a critical role in selecting locally advanced rectal cancer patients who respond to neoadjuvant therapy for nonoperative management.

OBJECTIVE:

This study evaluated the restaging endoscopic features that best predict the presence of residual tumor in the bowel wall.

DESIGN:

This was a post hoc analysis of a prospective randomized trial.

SETTINGS:

The Organ Preservation in Rectal Adenocarcinoma Trial randomized patients across 18 institutions with stage II/III rectal adenocarcinoma to receive either induction or consolidation total neoadjuvant therapy. Surgeons completed a restaging tumor assessment form, which stratified patients across three tiers of clinical response.

PATIENTS:

Patients enrolled in the Organ Preservation in Rectal Adenocarcinoma Trial with a completed tumor assessment form were included.

MAIN OUTCOME MEASURES:

The main outcome was residual tumor, which was defined as either an incomplete clinical response or local tumor regrowth within two years of restaging. Independent predictors of residual tumor were identified using backwards-selected multivariable logistic regression analysis. Subgroup analyses for complete and near complete clinical responders were performed.

RESULTS:

Surgeons completed restaging forms for 263 patients at a median of 7.7 weeks after neoadjuvant therapy; 128 (48.7%) had residual tumor. On multivariable regression analysis, several characteristics of a near complete response, including ulcer (OR 6.66; 95%CI 2.54-19.9), irregular mucosa (OR 3.66; 95% CI 1.61-8.68) and nodularity (OR 2.96; 95%CI 1.36-6.58) remained independent predictors of residual tumor. A flat scar was associated with lower odds of harboring residual disease (OR 0.32; 95% CI 0.11-0.93) for patients categorized as complete clinical responders.

LIMITATIONS:

Limitations of this study include analysis of endoscopic features at a single time point and ambiguities in tumor assessment form response criteria.

CONCLUSIONS:

Patients with ulcer, nodularity or irregular mucosa on restaging endoscopy have higher odds of residual tumor. Recognizing these features’ negative prognostic implications will help surgeons better select candidates for nonoperative management and suggests that patients with high-risk characteristics would benefit from close interval surveillance.
A grounded theory of how people process their cancer experiences through a mindfulness-based expressive arts group
Authors: Rieger Kendra L. , Hack Thomas F. , Duff Miriam A. , Campbell-Enns Heather J. , West Christina H.
Published: December 2023

Background:

Given the distress associated with cancer experiences, there is a growing interest in mindfulness-based expressive arts interventions (MBAIs) for promoting patients' well-being. Our research objective was to develop a theoretical understanding of how patients with cancer experience, use, and draw meaning from an MBAI.

Methods:

We used a constructivist grounded theory research design and gathered narrative descriptions of participants' (N = 32) MBAI experiences through semistructured interviews and field notes. Participants brought the artwork they had created in the group, facilitating art elicitation. Data were analyzed with grounded theory methods.

Results:

Participants described how the dynamic interplay of mindfulness, the arts, group sharing, and bearing witness facilitated the processing and sharing of hidden thoughts, experiences, and emotions. The group facilitated several unique meaning-making processes, including re-envisioning personal identity within disruption and loss, creating a fitting container for the exploration of diverse emotions, revisiting difficult experiences within the sensitivity of art, and visualizing hope and healing. This process resulted in important learnings and benefits for living in the here and now: relational connections, facing cancer through artistic play, discovering intuition and personal resources, learning an emotional language and a new mindset to move forward, understanding what one needs to heal, and fostering gratitude and hope.

Conclusions:

MBAIs allowed for a multimodal form of meaning making which facilitated coping, adjustment, and living well with cancer. These findings will enable practitioners to design and implement more effective health services and inform future research about this therapeutically promising approach to psychosocial oncology care.
Interventions to Promote Safety Culture in Cancer Care: A Systematic Review
Authors: Le Dan , Lim Charles H. , Fazelzad Rouhi , Morley Lyndon , Bissonnette Jean-Pierre , Powis Melanie , Krzyzanowska Monika K.
Published: December 2023

Objectives

There is limited guidance on how to effectively promote safety culture in health care settings. We performed a systematic review to identify interventions to promote safety culture, specifically in oncology settings.

Methods

Medical Subject Headings and text words for “safety culture” and “cancer care” were combined to conduct structured searches of MEDLINE, EMBASE, CDSR, CINAHL, Cochrane CENTRAL, PsycINFO, Scopus, and Web of Science for peer-reviewed articles published from 1999 to 2021. To be included, articles had to evaluate a safety culture intervention in an oncology setting using a randomized or nonrandomized, pre-post (controlled or uncontrolled), interrupted time series, or repeated-measures study design. The review followed PRISMA guidelines; quality of included citations was assessed using the ROBINS-I risk of bias tool.

Results

Eighteen articles meeting the inclusion criteria were retained, reporting on interventions in radiation (14 of 18), medical (3 of 18), or general oncology (1 of 18) settings. Articles most commonly addressed incident learning systems (7 of 18), lean initiatives (4 of 18), or quality improvement programs (3 of 18). Although 72% of studies reported improvement in safety culture, there was substantial heterogeneity in the evaluation approach; rates of reporting of adverse events (9 of 18) or Agency for Healthcare Research and Quality Safety Culture survey results (9 of 18) were the most commonly used metrics. Most of the studies had moderate (28%) or severe (67%) risk of bias.

Conclusions

Despite a growing evidence base describing interventions to promote safety culture in cancer care, definitive recommendations were difficult to make because of heterogeneity in study designs and outcomes. Implementation of incident learning systems seems to hold most promise.
Using Manganese Enhanced Magnetic Resonance Imaging (MEMRI) to Assess Calcium Dependent Activity in Vestibular Pathways Following Linear Acceleration
Authors: Naqvi Danial , Braun Rod D. , Muca Antonela , Hali Mirabela , Holt Avril Genene
Published: December 2023

Reliable methods for repetitive and longitudinal assessment of central vestibular pathway functionin vivoare rather limited. Manganese-enhanced magnetic resonance imaging (MEMRI) has been used in various sensory systems to evaluate neuronal activity in central pathways, but MEMRI assessment of central vestibular pathways has been minimal. The present study addressed this gap in knowledge by assessing whether Mn2+can be taken up in an activity-dependent manner through voltage-gated calcium channels in the vestibular nuclear complex (VNC) and the vestibulocerebellum (VeCb) of rats with and without mild linear acceleration stimulation.R1 maps were collected prior to, one day after, and two weeks after Mn2+administration in stimulated and non-stimulated rats. Analysis of MRIR1 values showed that one day after Mn2+administration the VNC and VeCb had significantly greaterR1 values that returned to baseline levels after two weeks. Non-stimulated rats had greaterR1 values than stimulated rats. Mid rostro-caudal sections of the VNC had greaterR1 values than rostral and caudal VNC sections.R1 values also indicated that Mn2+was differentially taken up across subdivisions of the VNC and VeCb. These results correlate well with expected patterns of neuronal activity after linear acceleration. MEMRI is a sensitive tool that may be used to evaluate activity patterns in central vestibular nuclei, proving useful for studying underlying mechanisms of central vestibular dysfunction.
Validation of the Faculty Readiness to Teaching Online (FRTO) scale
Authors: Kim Stella Y. , Martin Florence
Published: December 2023

Purpose

The current study examined several aspects of validity evidence for the Faculty Readiness to Teaching Online (FRTO) scale.

Design/methodology/approach

Data were collected from 307 faculty in higher education. Construct validity was evidenced through an exploratory factor analysis and a reliability coefficient. Differential validity was explored using the differential item functioning analysis to explore potential bias in items due to gender and age. In addition, convergent validity was tested by correlating FRTO with years of teaching online, the primary modality of instruction and whether there is required training in online teaching by the institution.

Findings

The findings from validation showed that new factors emerged and also demonstrated differences based on instructors gender and age, as well as based on teaching experience and primary modality of teaching.

Originality/value

The findings confirmed the previous study's results (Martin et al., 2019) and provided some modifications to the instrument. The factor structure did not conform to the original four factors proposed in the instrument; instead, the newly loaded factors were course design and facilitation, course technologies, course expectations and resources and time management. The revised instrument can be presented and discussed at online teaching professional development programs to help faculty understand the core competencies they need to better instruct students.
The relationship between dynamic capabilities and global value chain upgrading: the mediating role of innovation capability
Authors: Wen Yi , Wen Shuhui
Published: December 2023

Purpose

This study examines how dynamic capabilities (DCs) impact global value chain (GVC) upgrading and assesses the mediating role of innovation.

Design/methodology/approach

The study uses a quantitative research method. The data are collected using an online questionnaire administered to respondents working in Chinese automobile manufacturers in China and Laos. The data are analyzed using structural equation modeling (SEM) and related software.

Findings

The results show that DCs and innovation capabilities (ICs) positively affect GVC upgrading and that ICs plays a mediating role between DC and GVC upgrading. Dynamic capabilities evolution (CE) mediates the relationship between DCs, ICs and GVC upgrading. Finally, differences exist in the effects of the three dimensions of DCs on ICs and GVC upgrading.

Practical implications

Focusing on the absorption and transformation of knowledge, enterprises could experience a clear enhancement of IC and CE and be more likely to obtain higher marginal returns. The study provides insights for emerging market firms to gain higher added value in internationalization.

Originality/value

This study demonstrates that different dimensions of DCs have different effects on GVC upgrading. In terms of theory, the impact of IC is considered in terms of the mediating effect of CE on IC. Differences are highlighted concerning the impact of learning capability, integrating and coordinating capability and sensing capability on the mediated relationships.
The effect of window design factors on the cooling load in hospitals wards
Authors: Almhafdy Abdulbasit , Alsehail Abdullah Mohammed
Published: December 2023

Purpose

This paper investigates the optimization of window design factors (WDFs) in hospital buildings, particularly in government hospitals within the arid climate of the Qassim region, with the aim of achieving a better cooling load reduction. Continuous monitoring of the hospital ward section is crucial due to patients' needs, requiring optimal indoor air quality and cooling load.

Design/methodology/approach

The study identifies the optimal conditions for WDF design to mitigate cooling load, including window-to-wall ratio (WWR), window orientation (WO), room size and U-value (thermal properties), effectively reduce energy consumption in terms of sensible cooling load (MWh/m2) and comply with local codes. Data collection involved a smart weather station, while the Integrated Environmental Solution Virtual Environment (IESVE) software facilitated the simulation process.

Findings

Key findings reveal that larger patient rooms were about 40% more energy-efficient than smaller rooms. The northern orientation showed lower energy consumption, and specific WWRs and glazing U-values significantly affected energy loads. In an analysis of U-value changes in energy performance based on the Saudi Building Code (SBC), the presented values did not meet the minimum energy consumption standards. For a valid 40% WWR with a thermal permeability of 2.89, 0.181 MWh/m2 was consumed, while for an invalid 100% WWR with the same permeability but facing the north, 0.156 MWh/m2 was consumed, which is considered an invalid practice. It is vital to follow prescribed standards to ensure energy efficiency and avoid unnecessary costs.

Originality/value

Focus lies in emphasizing the significance of adhering to prescribed standards, such as SBC, to guarantee energy efficiency and prevent unwarranted expenses. Additionally, the authors highlight the crucial role of optimizing glazing properties and allocating the WWR appropriately to achieve energy-efficient building design, accounting for diverse orientations and climatic conditions.
Untangling the threads of conservation: A closer look at restoration and preservation
Authors: Mori Akira S. , Isbell Forest
Published: December 2023

Global goals and targets were recently set for biodiversity conservation in the coming decade. As action plans are now being developed, it is timely and important to carefully consider where and when various strategies for conservation—such as restoration and preservation—will be most effective.

For example, there is widespread support for expanding protected areas (e.g. protecting 30% of lands and waters by 2030) and restoration (e.g. having restoration completed or underway on at least 30% of degraded lands and waters), but also concerns regarding missed opportunities, and even additional degradation of nature, resulting from the ineffective implementation of these strategies.

Here, we emphasize the importance of prioritizing the preservation of relatively intact and pristine areas when identifying protected areas, and of avoiding the common misconception that, if intact nature is degraded or lost, it can simply be restored. Even the best restorations, after many decades of investments and efforts, are only a shadow of the natural systems they are meant to recreate.

Synthesis and applications. Now that the Global Biodiversity Framework has just been set, there is a critical need to recognize their fundamental differences between the types of places that are priorities for preservation, restoration or both to make collective actions for achieving the targets and goals for nature and people.
Exploring physical function and physical activity in axial spondyloarthritis: Beyond clinical remission or low disease activity
Authors: Pei Jin , Zheng Yan , Zhang Kui , Jia Junfeng , Ding Jin , Zheng Zhaohui , Shang Lei , Zhu Ping
Published: December 2023

Objectives

To investigate the crucial roles of physical function (PF) and physical activity (PA) in axial spondyloarthritis (axSpA) patients, as well as their correlation with disease activity (DA), and to explore the influence of general characteristics among them.

Methods

We enrolled axSpA patients from Xijing Hospital, spanning March 2022 to August 2022. Spearman rank correlation coefficients were used to assess correlations between PA (measured by the Global Physical Activity Questionnaire [GPAQ]), PF (measured by the Assessment of Spondyloarthritis international Society Health Index [ASAS‐HI], the Short Form 36‐Item Health Survey [SF‐36], and the Bath Ankylosing Spondylitis Functional Index [BASFI]), DA, and their influencing factors. A Mann–Whitney U‐test and Kruskal–Wallis H‐test were used to compare variables between different patients grouped by sex, human leukocyte antigen B27 (HLA‐B27), hip involvement, and intensity of PA and DA.

Results

Three hundred fifty‐five axSpA patients were included. We observed a moderate to strong correlation between DA and PF in axSpA patients. PA was weakly correlated with DA or PF. DA varied significantly at different PA levels, and patients with low PA levels had poorer PF. Active patients had worse PF, less transport‐related PA, and a higher rate of hip involvement with a worse Harris Hip Score (HHS).

Conclusions

We identified a close relationship between DA, PF, and PA in axSpA patients. Further, gender, HLA‐B27, and hip involvement affected the clinical manifestation of axSpA patients. These findings demonstrate that clinical remission of axSpA patients requires a comprehensive assessment rather than a single remission of DA.
Enabling translational geroscience by broadening the scope of geriatric care
Authors: Ferrucci Luigi , Wilson David M. , Donega Stefano , Montano Monty
Published: December 2023

Geroscience poses that core biological mechanisms of aging contribute to chronic diseases and disabilities in late life and that health span and longevity can be modulated by pharmacological and behavioral interventions. Despite strong evidence from studies in model organisms and great potentials for translation, most geriatricians remain skeptical that geroscience will help them in the day‐by‐day battle with the consequences of aging in their patients. We believe that a closer collaboration between gerontologists and geriatricians is the key to overcome this impasse. There is evidence that trajectories of health with aging are rooted in intrinsic and extrinsic exposures that occur early in life and affect the pace of molecular and cellular damage accumulation with aging, also referred to as the “pace” of biological aging. Tools that measure the pace of aging currently allow for the identification of individuals experiencing accelerated aging and at higher risk of multimorbidity and disability. What we term “Translational Geroscience”, i.e., the merger of fundamental and translational science with clinical practice, is thus poised to extend the action of geriatric care to a life course perspective. By targeting core mechanisms of aging, gerotherapeutics should be effective in treating patients with multimorbidity and disability, phenotypes that are all too common among geriatric patients nowadays. We call for initiatives that enhance the flow of ideas between gerontologists and geriatricians to facilitate the growth of translational geroscience. This approach can widen the scope of geriatric care, including a new role for geroscience in the promotion and operationalization of healthy longevity.
Physical exercise plays a role in rebalancing the bile acids of enterohepatic axis in non‐alcoholic fatty liver disease
Authors: Zhang Minyu , Xiao Biyang , Chen Xiaoqi , Ou Bingming , Wang Songtao
Published: December 2023

Non‐alcoholic fatty liver disease (NAFLD) is considered as one of the most common diseases of lipid metabolism disorders, which is closely related to bile acids disorders and gut microbiota disorders. Bile acids are synthesized from cholesterol in the liver, and processed by gut microbiota in intestinal tract, and participate in metabolic regulation through the enterohepatic circulation. Bile acids not only promote the consumption and absorption of intestinal fat but also play an important role in biological metabolic signaling network, affecting fat metabolism and glucose metabolism. Studies have demonstrated that exercise plays an important role in regulating the composition and function of bile acid pool in enterohepatic axis, which maintains the homeostasis of the enterohepatic circulation and the health of the host gut microbiota. Exercise has been recommended by several health guidelines as the first‐line intervention for patients with NAFLD. Can exercise alter bile acids through the microbiota in the enterohepatic axis? If so, regulating bile acids through exercise may be a promising treatment strategy for NAFLD. However, the specific mechanisms underlying this potential connection are largely unknown. Therefore, in this review, we tried to review the relationship among NAFLD, physical exercise, bile acids, and gut microbiota through the existing data and literature, highlighting the role of physical exercise in rebalancing bile acid and microbial dysbiosis.
Histone deacetylase inhibitor boosts anticancer potential of fusogenic oncolytic vaccinia virus by enhancing cell–cell fusion
Authors: Nakatake Motomu , Kurosaki Hajime , Nakamura Takafumi
Published: December 2023

Oncolytic viruses have two anticancer functions: direct oncolysis and elicitation of antitumor immunity. We previously developed a novel fusogenic oncolytic vaccinia virus (FUVAC) from a non‐fusogenic vaccinia virus (VV) and, by remodeling the tumor immune microenvironment, we demonstrated that FUVAC induced stronger oncolysis and antitumor immune responses compared with non‐fusogenic VV. These functions depend strongly on cell–cell fusion induction. However, FUVAC tends to have decreased fusion activity in cells with low virus replication efficacy. Therefore, another combination strategy was required to increase cell–cell fusion in these cells. Histone deacetylase (HDAC) inhibitors suppress the host virus defense response and promote viral replication. Therefore, in this study, we selected an HDAC inhibitor, trichostatin A (TSA), as the combination agent for FUVAC to enhance its fusion‐based antitumor potential. TSA was added prior to FUVAC treatment of murine tumor B16‐F10 and CT26 cells. TSA increased the replication of both FUVAC and parental non‐fusogenic VV. Moreover, TSA enhanced cell–cell fusion and FUVAC cytotoxicity in these tumor cells in a dose‐dependent manner. Transcriptome analysis revealed that TSA‐treated tumors showed altered expression of cellular component‐related genes, which may affect fusion tolerance. In a bilateral tumor‐bearing mouse model, combination treatment of TSA and FUVAC significantly prolonged mouse survival compared with either treatment alone or in combination with non‐fusogenic VV. Our findings demonstrate that TSA is a potent enhancer of cell–cell fusion efficacy of FUVAC.
Exploring mechanisms of spatial segregation between body size groups within fish populations under environmental change
Authors: Tao Hsiao‐Hang , Chang Chun‐Wei , Hsieh Chih‐hao
Published: December 2023

Ample evidence has indicated shifts in distribution of fish populations in response to environmental stress. However, most studies focused at the whole population scale. This neglects the spatial dynamics between groups of different body size (body size groups), that fundamentally shapes the spatial structure of a population. Here, we explored the mechanisms that modulate spatial dynamics of body size groups, and applied our analyses to three North Sea fish populations which experienced severe declines in biomass from 1977 to 2019: Atlantic cod Gadus morhua, haddock Melanogrammus aeglefinus and whiting Merlangius merlangius. All three populations exhibited strong declines in the overlapped area between body size groups in winter over 43 years, yet their mechanisms differed. These declines were either due to 1) different magnitudes of contraction of the distribution area of body size groups; and/or 2) different speeds and directions of spatial shift among various body size groups, both increasing spatial segregation within populations. These patterns were either associated with ocean warming, and/or declining population biomass, and such associations often varied according to distinct body size groups. Increasing spatial segregation between size groups of a population likely hampers life‐cycle connectivity and stability to local perturbations. Our analytical approach provides a powerful tool for identifying vulnerable populations under environmental stress and can be generalized to study a variety of size/age structured populations at various ecosystem types.
The experiences of patients, caregivers and donors on transplant journeys in Canada: A convergent parallel mixed methods study
Authors: Fox Danielle E. , Hall Marc , Thibodeau Carrie , Coldwell Kristi , Lauder Lydia , Dewell Sarah L. , Davidson Sandra J.
Published: December 2023

Introduction

The organ donation and transplantation (ODT) system in Canada is complex and can be challenging for individuals to navigate. We thus aimed to illuminate the experiences of individuals on transplant journeys using a patient‐oriented convergent parallel mixed‐methods approach.

Methods

We captured data on adult patients, living donors, and caregivers on transplant journeys across Canada through an online survey (n = 935) and focus groups (n = 21). The survey was comprised of 48 questions about the individuals' experiences with the living donation and transplantation system, which were analyzed descriptively. Qualitative data were analyzed using an inductive conventional content analysis approach.

Results

Most participants were female (70.1%), English speaking (92.6%) and White (87.8%). Participants' experiences were represented across six key themes: holistic person‐centred care, accountable care, collective impact, navigating uncertainty, connection and advocacy. Quantitative and qualitative data were integrated to identify five opportunities to improve the organ donation and transplantation system in Canada: enhancing mental health support, establishing formal peer support programmes, improving continuity of care, improving knowledge acquisition, and expanding resources and support.

Conclusion

It is imperative that the ODT system commits to asking, listening, and learning from individuals on transplant journeys and to provide them opportunities to help improve it.
Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance
Authors: Pogoda Cloe S. , Keepers Kyle G. , Reinert Stephan , Talukder Zahirul I. , Smart Brian C. , Attia Ziv , Corwin Jason A. , Money Kennedy L. , Collier‐zans Erin C. E. , Underwood William , Gulya Thomas J. , Quandt C. Alisha , Kane Nolan C. , Hulke Brent S.
Published: December 2023

Host–microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community‐scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co‐vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human‐altered environments.
Detection of 2‐ethyl‐1‐hexanol and its modulating effect in biofilm of Fusarium oxysporum
Authors: Veiga Flavia Franco , Marcomini Emilli Karine , Salvador Alana , Chiavelli Lucas Ulisses Rovigatti , Barros Isabella Letícia Esteves , de Castro Lidiane Vizioli , Lucca Diego Luis , Ochikubo Larissa Miwa Kikuchi , Baesso Mauro Luciano , Pomini Armando Mateus , Svidzinski Terezinha Inez Estivalet , Negri Melyssa
Published: December 2023

In immunocompetent individuals, Fusarium spp. stands out as the causative agent of onychomycosis, among the non‐dermatophyte molds. Despite evidence indicating that Fusarium oxysporum organizes itself in the form of a biofilm causing onychomycosis, there is little literature on the etiopathogenesis of the biofilm on the nail, specifically the signaling molecules present, known as quorum sensing (QS). Thus, this study detected the presence of a molecule related to QS from the ex vivo biofilm of F. oxysporum on human nail and investigated its effect on preformed biofilm in vitro. The detection and physicochemical characterization of a QS molecule, from the extracellular matrix (ECM), was carried out by Fourier transform infrared (FTIR) spectroscopy with an attenuated total reflectance (ATR) accessory and by headspace gas chromatography coupled to mass spectrometry (GC–MS) analyses. Determination of viable cells, cell activity, total biomass, ECM components and scanning electron microscopy (SEM) were performed to evaluate the influence of the QS molecule on the in vitro biofilm of F. oxysporum. The beginning, in the ex vivo biofilm of F. oxysporum on human nails, the volatile organic compound 2‐ethyl‐1‐hexanol (2EH) was detected as a component of QS. Thereafter in vitro analyses, synthetic 2EH was able to modulate the biofilm by stimulating its filament, increasing total biomass and ECM production in terms of total carbohydrates, but with a reduction in total proteins and nucleic acids. We thus evidence, for the first time, the presence of 2EH in the biofilm of F. oxysporum, developed on the human nail, and the in vitro action of this compound as a QS molecule.
Astragalus roseocephalus, a new species of section Poliothrix from Pakistan
Authors: Khan Amjad , Sultan Amir , Shah Sayed Afzal
Published: December 2023

A new species, Astragalus roseocephalus sp. nov., is described and illustrated. It is known from Islamabad Capital Territory (Margalla hills), Rawalpindi district, Hazara and Kashmir. It belongs to Astragalus section Poliothrix Bunge. Morphologically, it is closely related to Astragalus leucocephalus Benth., but differs in height, presence of connate stipules, opposed to free lateral stipules in A. leucocephalus, stipule shape, leaf length, leaflet size, number, arrangement and shape, peduncle length, corolla colour, size and shape of standard, fruit shape and number of seeds. In addition, anatomy, pollen morphology, distribution and conservation status of the new species are discussed.
Evaluating thermal niche overlap of a predator–prey system: Do spiders choose suboptimal temperatures in pursuit of prey?
Authors: Taucare‐Ríos Andrés , Chia‐Daponte Weixing , Gaete‐Collao Cristofer
Published: December 2023

Ectotherm predators and their prey could potentially respond differently to habitat temperatures. Predators might select higher temperatures to increase their probability of capture while prey could select lower or higher temperatures that may enhance their escape capability. We used a combination of field and laboratory analyses to characterise the thermal niches of predator species and their potential arthropod prey. We studied a predator–prey system in northern Chile using a common desert‐dwelling spider Loxosceles laeta and three potential prey: a tenebrionid beetle Psammetichus costatus (Coleoptera), Pycnoscelus surinamensis (Blattodea) and Porcellio laevis (Isopoda). Results showed that the predator L. laeta selects warmer temperatures (Tp = 27.22 ± 4.87°C) in laboratory and lower temperatures in field conditions (Ts = 20.8 ± 1.59°C), with low temperatures in the morning and high temperatures at night. The three prey species had lower and different preferred temperatures than the predator in laboratory conditions. However, we found a high overlap in the thermal niche between the predator and their prey in field conditions, whereby the predator selected similar temperatures to its prey, one exception being P. laevis that chooses completely different habitat temperatures. This suggests that predators look for their prey in places with low temperatures that are not thermally suitable for them, whereas the prey may use this strategy of selecting low temperatures to evade potential predators.
Weakly supervised semantic segmentation of mobile laser scanning point clouds via category balanced random annotation and deep consistency‐guided self‐distillation mechanism
Authors: Liu Jiacheng , Guan Haiyan , Lei Xiangda , Yu Yongtao
Published: December 2023

Scene understanding of mobile laser scanning (MLS) point clouds is vital in autonomous driving and virtual reality. Most existing semantic segmentation methods rely on a large number of accurately labelled points, which is time‐consuming and labour‐intensive. To cope with this issue, this paper explores a weakly supervised learning (WSL) framework for MLS data. Specifically, a category balanced random annotation (CBRA) strategy is employed to obtain balanced labels and enhance model performance. Next, based on KPConv‐Net as a backbone network, a WSL semantic segmentation framework is developed for MLS point clouds via a deep consistency‐guided self‐distillation (DCS) mechanism. The DCS mechanism consists of a deep consistency‐guided self‐distillation branch and an entropy regularisation branch. The self‐distillation branch is designed by constructing an auxiliary network to maintain the consistency of predicted distributions between the auxiliary network and the original network, while the entropy regularisation branch is designed to increase the confidence of the network predicted results. The proposed WSL framework was evaluated on the WHU‐MLS, NPM3D and Toronto3D datasets. By using only 0.1% labelled points, the proposed WSL framework achieved a competitive performance in MLS point cloud semantic segmentation with the mean Intersection over Union (mIoU) scores of 60.08%, 72.0% and 67.42% on the three datasets, respectively.
Geographic distribution, host preference and phylogenetic relationships among Pyricularia species inciting millet and rice blast disease in India
Authors: Palanna K. B. , Vinaykumar H. D. , Koti Prasanna S. , Jeevan B. , Rajashekara H. , Raveendra H. R. , Patro T. S. S. K. , Ramesh G. V. , Mudalagiriyappa  , Rawat Laxmi , Netam Prahlad , Ekka Savita , Rajesha G. , Das I. K. , Chandranayaka S. , Nagaraja T. E. , Satyavathi C. Tara
Published: December 2023

Blast disease causes significant damage to millets (pearl millet, finger millet and foxtail millet) and rice in India. This study investigates strains of Pyricularia, the causal agent of blast disease, in rice and millets in India in terms of their diversity, host preferences and phylogeny. One hundred and thirty‐six Pyricularia isolates causing rice and millet blast were collected from 46 locations in India. They displayed morphological diversity irrespective of host or location. All Pyricularia isolates were separated into two major clusters by a multilocus sequence‐based phylogenetic tree, which also demonstrated that most isolates are grouped according to their host associations. In contrast, a few finger millet isolates were found to be grouped with foxtail millet isolates. We explored how Pyricularia isolates behaved when exposed to rice and millets. Finger millet isolates were shown to be pathogenic on a wide variety of millets, whereas rice isolates were only found to infect rice and wheat. The majority of the blast isolates of millets were shown to be pathogenic on common weed species of the millet ecosystem, such as Echinochloa crusgalli, Eleusina indica and Erogrotis gagantica. Our findings emphasize the importance of pathogen surveillance in both cultivated crops and weed hosts, as well as the possible risk of blast fungus infection in Indian millets due to host expansion. Blast disease control programmes in India will be greatly enhanced by the knowledge gained in this study on the diversity and host association of Pyricularia strains.
Regulating for trust: Can law establish trust in artificial intelligence?
Authors: Tamò‐Larrieux Aurelia , Guitton Clement , Mayer Simon , Lutz Christoph
Published: December 2023

The current political and regulatory discourse frequently references the term “trustworthy artificial intelligence (AI).” In Europe, the attempts to ensure trustworthy AI started already with the High‐Level Expert Group Ethics Guidelines for Trustworthy AI and have now merged into the regulatory discourse on the EU AI Act. Around the globe, policymakers are actively pursuing initiatives—as the US Executive Order on Safe, Secure, and Trustworthy AI, or the Bletchley Declaration on AI showcase—based on the premise that the right regulatory strategy can shape trust in AI. To analyze the validity of this premise, we propose to consider the broader literature on trust in automation. On this basis, we constructed a framework to analyze 16 factors that impact trust in AI and automation more broadly. We analyze the interplay between these factors and disentangle them to determine the impact regulation can have on each. The article thus provides policymakers and legal scholars with a foundation to gauge different regulatory strategies, notably by differentiating between those strategies where regulation is more likely to also influence trust on AI (e.g., regulating the types of tasks that AI may fulfill) and those where its influence on trust is more limited (e.g., measures that increase awareness of complacency and automation biases). Our analysis underscores the critical role of nuanced regulation in shaping the human‐automation relationship and offers a targeted approach to policymakers to debate how to streamline regulatory efforts for future AI governance.