bluuebunny/crossref_metadata_2025 huggingface dataset:
Short- and long-term outcomes in isolated vs. hybrid thoracoscopic ablation in patients with atrial fibrillation: a systematic review and reconstructed individual patient data meta-analysis
Authors: Aerts Luca , Kawczynski Michal J , Bidar Elham , Luermans Justin G L , Chaldoupi Sevasti-Maria , La Meir Mark , Kowalewski Mariusz , Maessen Jos G , Heuts Samuel , Maesen Bart
Published: September 2024

Aims

Both isolated thoracoscopic and hybrid thoracoscopic atrial fibrillation (AF) ablation techniques have demonstrated favourable outcomes in the management of patients with (long-standing) persistent AF, as compared with catheter ablation. However, it is currently unknown whether there is a difference in short- and long-term outcomes when comparing these two minimally invasive surgical AF ablation procedures. Therefore, a systematic review and meta-analysis were performed to investigate these two techniques, with a specific emphasis on long-term freedom from atrial tachyarrhythmias (ATAs).

Methods and results

A systematic search through PubMed, EMBASE, and the Cochrane Library databases was performed. All studies reporting on short-term outcomes were included in the meta-analysis. A pooled analysis of long-term freedom from ATA was performed based on Kaplan–Meier (KM) curve-derived individual patient data. Reconstructed individual time-to-event data were analysed in a multivariable Cox frailty model with adjustments for age, sex, type of AF, duration of AF history, and study variable (frailty term in the frailty Cox model). In total, 53 studies were included in the meta-analysis, encompassing 4950 patients. There were no differences in major short-term outcomes (mortality or stroke) between isolated thoracoscopic and hybrid thoracoscopic ablation. A total of 18 studies reported KM curves for long-term freedom from ATA, comprising 2038 patients. Adjusted analysis revealed that hybrid ablation was significantly associated with greater freedom from ATA [adjusted hazard ratio (aHR) = 0.59, 95% confidence interval (CI): 0.43–0.83, P < 0.001] compared with isolated thoracoscopic ablation. Additionally, older age (aHR = 1.07, 95% CI: 1.03–1.12, P = 0.002) and a higher percentage of male patients (aHR = 1.02, 95% CI: 1.01–1.03, P < 0.001) were significantly associated with lower long-term freedom from ATA recurrence.

Conclusion

Hybrid thoracoscopic AF ablation is associated with a greater long-term freedom from ATA when compared with isolated thoracoscopic ablation, without differences in complications.
The High Prevalence and Complexity of Over-the-Counter Medication Misuse in Older Adults
Authors: Chladek Jason S , Gilson Aaron M , Stone Jamie A , Berbakov Maria E , Watterson Taylor L , Lehnbom Elin C , Hoffins Emily L , Hemesath Katherine A , Moon Jukrin , Welch Lauren L , Walbrandt Pigarelli Denise L , Portillo Edward C , Resendiz Stephanie M , Mai Shiying , Chui Michelle A
Published: September 2024

Background and Objectives

Older adults (≥65 years) are the largest consumers of over-the-counter (OTC) medications and exceptionally vulnerable to the risks of these medications, including adverse drug events (ADEs). However, little is known about how older adults select and use OTCs. This is the first multisite study designed to prospectively quantify the type and intended use of OTCs selected by older adults in community pharmacies where products are purchased.

Research Design and Methods

Older adults (n = 144) were recruited from 10 community pharmacies from a Midwestern health system. Participants were given hypothetical symptoms and asked to select one or more OTCs for self-treatment. They were asked to report how they would use the products at symptom onset and when symptoms persisted or worsened. They also reported their current medication list and health conditions. Participants’ OTC selections were evaluated for 4 types of misuse: drug-age, drug-drug, drug-disease, and drug-label.

Results

Of the 144 participants, 114 (79%) demonstrated at least one type of misuse when describing how they would use their OTC selections at symptom onset. Drug-drug and drug-label misuse had the highest prevalence. Overall, 26 (18%) and 28 (19%) participants showed only drug-drug or drug-label misuse, respectively. Notably, 55 (38%) of participants demonstrated misuse in 2 or more misuse categories. Misuse potential was exacerbated when participants described treating persistent or worsening symptoms.

Discussion and Implications

The results highlight the high prevalence and complexity of OTC misuse in older adults and the need for additional work to improve OTC safety.
Quantifying microbial DNA in metagenomes improves microbial trait estimation
Authors: Eisenhofer Raphael , Alberdi Antton , Woodcroft Ben J
Published: September 2024

Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.
Of Feline Kings and Spying Spirits
Authors: Behrens Paul
Published: September 2024

This article deals with the perspective from which situations of duress under the Statute of the International Criminal Court have to be evaluated, in particular in cases in which (as in Ongwen) strongly individualised circumstances, such as a belief in spirits, have coloured the perception of the alleged threat. It critically analyses objective and subjective approaches, examines their weaknesses, and explores mediating perspectives. In this context, the objective individualised approach emerges as a method which, by focusing on the viewpoint of the social circle of the defendant, avoids the detrimental consequences of the traditional approaches and demonstrates appropriate alignment with the requirement of foreseeability.
Resource selection at fine scale: what drives the decision of a generalist herbivore?
Authors: Boyers Melinda , Parrini Francesca
Published: September 2024

Spatial patterns in topography and forage distribution significantly influence the movements and choices of large herbivores. However, understanding the foraging strategies of free-grazing herbivores at different temporal and spatial scales remains limited, as different behavioral decisions can apply at different hierarchical levels. This study investigates the fine-scale foraging strategies of the Plains Zebra (Equus quagga) in a South African savanna, with a specific focus on their selection of green vegetation at the plant and feeding patch levels. We used the Normalized Difference Vegetation Index as a proxy for vegetation productivity and quality. Our findings reveal that zebras adapted their foraging strategies according to scale and season. During the late-dry season and early-wet season, selection for greenness was at both the grass tuft and feeding site levels. In contrast, during the mid-dry season, selection was predominantly at the tuft level, focusing solely on greenness. These insights emphasize the importance of conducting multilevel studies when investigating factors influencing foraging decisions. Findings at 1 hierarchical level may not necessarily apply across other levels of investigation, highlighting the need for a nuanced and comprehensive approach to understanding the complex foraging behaviors of animals.
A Defense of the Obligation to Keep Promises to the Dead
Authors: Taylor James Stacey
Published: September 2024

It is widely held that to break a promise that one made to a person who is now dead would be to wrong her. This view undergirds many positions in bioethics, ranging from those that concern who may access a person’s medical records after she has died, to questions concerning organ procurement and posthumous procreation. Ashley Dressel has argued that there is no reason to believe that promissory obligations can be owed to people who are dead. Although her arguments are unsuccessful, others establish that neither of the promissory obligation accounts that she considers (the “Authority Account” and the “harm-based view”) can justify the standard view that directed posthumous promissory obligation is possible. However, this does not mean that the received view that we should keep our promises to the dead is mistaken. First, the theoretical commitments and argumentative strategies of those who endorse the possibility of posthumous promissory obligations preclude them from grounding such on either of these accounts of directed promissory obligation. They are thus already committed to justifying such obligations in other ways. Second, the obligation to keep promises to the dead could be justified on the grounds that not to do so would adversely affect the living.
Why Moral Bioenhancement Cannot Reliably Produce Virtue
Authors: Lebkuecher Gina , Hornewer Marley , Roytman Maya V , Samoska Sydney , Vukov Joseph M
Published: September 2024

Moral bioenhancement presents the possibility of enhancing morally desirable emotions and dispositions. While some scholars have proposed that moral bioenhancement can produce virtue, we argue that within a virtue ethics framework moral bioenhancement cannot reliably produce virtue. Moreover, on a virtue ethics framework, the pursuit of moral bioenhancement carries moral risks. To make this argument, we consider three aspects of virtue—its motivational, rational, and behavioral components. In order to be virtuous, we argue, a person must (i) take pleasure in doing the right thing and have the correct motivational attitudes; (ii) reason correctly about what is called for in a particular ethical dilemma; and (iii) intentionally and continuously practice and cultivate virtues. These dimensions of morality—in short: precisely those emphasized in a virtue ethics framework—cannot be consistently or reliably met using existing moral bioenhancement technology.
Germline testing for veterans with advanced prostate cancer: concerns about service-connected benefits
Authors: Kwon Daniel H , Scheuner Maren T , McPhaul Marissa , Hearst Eliza , Sumra Saffanat , Ursem Carling , Walker Evan , Wang Sunny , Huang Franklin W , Aggarwal Rahul R , Belkora Jeff
Published: September 2024

To better understand veterans’ decisions about germline testing, we conducted a single-site, qualitative study of 32 veterans with advanced prostate cancer. Seven days after oncologist-patient discussions about germline testing, we conducted semistructured interviews with patients to explore their decision-making process using an interview guide. Four of 14 veterans with service-connected disability benefits for prostate cancer declined germline testing for fear of losing benefits because their livelihood depended on these benefits. All 18 veterans without service-connected benefits agreed to testing. Veterans declining germline testing based on this concern can lead to suboptimal cancer care because targeted treatments that could improve their outcomes may go unrecognized. Our findings contributed to new language in the Veterans Benefits Administration Compensation and Pension Manual clarifying that genetic testing showing hereditary predisposition is insufficient to deny service-connected benefits for conditions presumed to be caused by military exposures. Clinicians should communicate this protection when counseling veterans about genetic testing.
Genistein and daidzein induce ferroptosis in MDA-MB-231 cells
Authors: Arzuk Ege , Armağan Güliz
Published: September 2024

Objectives

In recent years, there has been a growing interest in targeting ferroptosis for the treatment and prevention of multiple cancers. This study aimed to assess the contribution of ferroptosis to the antiproliferative effects of genistein (GN) and daidzein (DZ) in breast cancer cell lines.

Methods

MDA-MB-231 and MCF-7 cells were employed as an in vitro model. The antiproliferative effects of GN and DZ were determined by WST-1 assay in the presence of specific inhibitors of different cell death pathways. The mRNA expressions of Gpx4 and Fsp-1, the levels of lipid peroxidation, glutathione (GSH)/glutathione disulfide (GSSG) ratio, and intracellular iron ion content were assessed in GN- or DZ-treated cells.

Results

GN and DZ were found to cause ferroptotic cell death in MDA-MB-231, as confirmed by the reversal of viability when cells were pretreated with ferrostatin-1. Furthermore, both phytochemicals induced biochemical markers of ferroptosis, including lipid peroxidation and iron ions levels, and decreased GSH/GSSG levels. The mRNA expression levels of the main anti-ferroptotic genes, Gpx4 and Fsp-1, were diminished by the treatment of both phytochemicals. Surprisingly, ferroptosis did not play a role in GN- or DZ-induced cell death in MCF-7 cells.

Conclusion

Our findings highlight the potential of GN and DZ as ferroptosis inducers in triple-negative breast cancer cells.
Shikonin mitigates cyclophosphamide-induced cardiotoxicity in mice: the role of sirtuin-1, NLRP3 inflammasome, autophagy, and apoptosis
Authors: Alherz Fatemah A , Saleh Asmaa , Alsheikh Mona Y , Borg Hany M , Kabel Ahmed M , Abd Elmaaboud Maaly A
Published: September 2024

Objectives

The aim of this study was to elucidate the protective potential of shikonin (SHK) on cyclophosphamide (CP)-induced cardiotoxicity in Swiss albino mice.

Methods

Mice received SHK in three different doses by oral gavage daily for 14 days and CP at 100 mg/kg, intraperitoneally once on the seventh day. On the 15th day, mice were euthanized, blood collected, and hearts were removed to estimate various biochemical and histopathological parameters.

Key findings

CP significantly increased serum lactate dehydrogenase, creatine kinase-MB, troponin I and NT pro-BNP, and cardiac malondialdehyde and decreased cardiac total antioxidant capacity and Nrf2, whereas increased inflammatory markers in the cardiac tissues. CP also caused hypertrophy and fibrosis in the cardiac tissues via activation of IL6/JAK2/STAT3 while depressed SIRT1 and PI3K/p-Akt pathway with consequent increased apoptosis and dysregulation of autophagy. SHK treatment reversed these changes in a dose-dependent manner and showed a significant protective effect against CP-induced cardiotoxicity via suppressing oxidative stress, inflammation, and apoptosis with modulation of autophagy via induction of SIRT1/PI3K/p-Akt signaling.

Conclusions

Shikonin may be used as an adjuvant to cyclophosphamide in cancer treatment, but further research is needed to investigate its effects on cardiotoxicity in distinct animal cancer models.
Dihydrorhodamine-123 flow cytometry method: time for substantial revision in technical procedure
Authors: Zavvar Mahdi , Zargaran Sina , Baghdadi Hamed , Poopak Peyvand , Poopak Amir Hossein , Nabatchian Fariba , Fatahi Yousef , Khosravipour Gelareh , Poopak Behzad
Published: September 2024

The dihydrorhodamine 123 assay is generally applied to measure the production of intracellular reactive oxygen species in neutrophils using flow cytometry and is considered a diagnostic evaluation for chronic granulomatous disease. In fact, there is a broad range of variables that can directly or indirectly affect test results, either individually or collectively. It is therefore crucial to identify the ideal requirements to achieve reliable results as well as using these requirements to provide standard operating procedures that should be taken into account. Therefore, we focus on aligning optimum results by comparing preanalytical and analytical phases that influence test results, such as the effect of various anticoagulants, transport and maintaining temperature (24°C or 4°C) of samples, test prime run time, appropriate solution concentrations, and effect of incubation temperature (24°C or 37°C) during the test run.
Clinical and hematological profile of patients with pancytopenia at a tertiary medical center in Ethiopia
Authors: Kiya Girum Tesfaye , Dandena Ebissa , Adissu Wondimagegn , Kebede Estifanos
Published: September 2024

Background

Pancytopenia is an important hematological problem encountered in routine clinical practice associated with a multitude of disease states. The possible causes of pancytopenia can be influenced by geography, socioeconomic conditions, and endemic illnesses. Information regarding the underlying clinical conditions and morphologic features of blood cells of pancytopenia is limited and varied across different regions. Thus, this study was designed to assess the peripheral morphologic features of blood cells and the underlying clinical causes of pancytopenia.

Methods

A facility-based cross-sectional study was conducted at the Jimma Medical Center hematology laboratory from June 13 to November 13, 2022. A total of 3 mL of whole blood was collected from each subject for complete blood count analysis and peripheral blood morphology examination. Data on sociodemographic and clinical conditions were collected from medical records using a checklist. The data were analyzed using Statistical Package for the Social Sciences version 26.

Results

A total of 163 patients with pancytopenia were identified within the 5 months. Hyper-reactive malarial splenomegaly was the most prevalent cause (29.4%), followed by megaloblastic anemia (20.2%), chronic liver disease (10.4%), and acute leukemia (8.6%). Anisocytosis was the predominant peripheral blood morphology finding (82.2%), along with microcytosis (49.7%), ovalocytosis (31.3%), and macrocytosis (30.7%). Severe anemia was observed in 57% of cases, whereas the majority (92%) exhibited moderate leukopenia. A significant proportion (42.3%) had a platelet count below 50,000/μL.

Conclusion

Unlike previous studies conducted in other parts of the world, this study showed that hyperreactive malarial splenomegaly was the leading cause of pancytopenia. This emphasizes the necessity of considering this condition as a possible cause for pancytopenia, particularly in malaria-endemic areas. The findings of the hematological profiles and peripheral blood morphology strongly suggest that early identification and prompt management of patients with pancytopenia require collaboration between clinical and laboratory investigations.
Rapid automatic multiple moving objects detection method based on feature extraction from images with non-sidereal tracking
Authors: Wang Lei , Zhang Xiaoming , Bai Chunhai , Xie Haiwen , Li Juan , Ge Jiayi , Wang Jianfeng , Zeng Xianqun , Sun Jiantao , Jiang Xiaojun
Published: September 2024

Optically observing and monitoring moving objects, both natural and artificial, is important to human space security. Non-sidereal tracking can improve the system’s limiting magnitude for moving objects, which benefits the surveillance. However, images with non-sidereal tracking include complex background, as well as objects with different brightness and moving mode, posing a significant challenge for accurate multi-object detection in such images, especially in wide field-of-view telescope images. To achieve a higher detection precision in a higher speed, we proposed a novel object detection method, which combines the source feature extraction and the neural network. First, our method extracts object features from optical images such as centroid, shape, and flux. Then, it conducts a naive labelling based on those features to distinguish moving objects from stars. After balancing the labelled data, we employ it to train a neural network aimed at creating a classification model for point-like and streak-like objects. Ultimately, based on the neural network model’s classification outcomes, moving objects whose motion modes consistent with the tracked objects are detected via track association, while objects with different motion modes are detected using morphological statistics. The validation, based on the space objects images captured in target tracking mode with the 1-m telescope at Nanshan, Xinjiang Astronomical Observatory, demonstrates that our method achieves 94.72 per cent detection accuracy with merely 5.02 per cent false alarm rate, and a processing time of 0.66 s per frame. Consequently, our method can rapidly and accurately detect objects with different motion modes from wide-field images with non-sidereal tracking.
The impact of inter-cycle treatment delays on overall survival in patients with advanced-stage ovarian cancer
Authors: Steventon Luke , Man Kenneth K C , Nicum Shibani , Miller Rowan E , Peleg Hasson Shira , Shah Samixa , Baser Michael , Kipps Emma , Forster Martin D , Almossawi Ofran , Chambers Pinkie
Published: September 2024

Introduction

Chemotherapy forms the cornerstone of systemic treatment for advanced ovarian cancer, extending overall survival; however, drug-related toxicity can lead to treatment delays, potentially diminishing treatment efficacy. This study evaluated the impact of treatment delays on all-cause mortality of patients with ovarian cancer, to better inform decisions on patient management.

Methods

This retrospective, population-based cohort study included 1517 women with advanced-stage ovarian cancer, receiving first-line adjuvant or neoadjuvant chemotherapy in 2014 and 2015. The frequency of inter-cycle delays >7 days was calculated using drug administration dates. Kaplan-Meier estimates were used to compare 2-year overall survival (OS) between patients who were delayed and those treated to schedule. Cox proportional hazards regression was used to investigate the impact of treatment delay on all-cause mortality. Inverse probability of treatment weighting propensity scores were used to adjust for confounding variables.

Results

Delays >7 days occurred in 35.3% of patients. Two-year OS probability was 62.7% in patients who experienced treatment delays >7 days (95% CI, 58.7-66.9) compared to 69.1% in those treated to schedule (95% CI, 66.2-72.0). Delays were not significantly associated with all-cause mortality when adjusted for confounders (HR 1.00 95% CI, 0.83-1.20, P = .9).

Conclusions

Delays to chemotherapy treatment were not significantly associated with worsened survival in patients with advanced-stage ovarian cancer. These results can inform clinical decision making that prioritize toxicity management and quality of life for those treated with chemotherapy.
Pre-existing cardiovascular disease is associated with an increased risk of cardiovascular events during Bruton tyrosine kinase inhibitor therapy
Authors: Fernandez Turizo Maria J , Kim Eunice , Zhang Cancan , Yankama Tuyen , Von Keudell Gottfried , Sermer David J , Mejías-De Jesús Caroline , Asnani Aarti
Published: September 2024

The association between pre-existing cardiovascular disease (CVD) and the development of cardiovascular adverse events (CVAE) during Bruton tyrosine kinase inhibitor (BTKi) therapy is not well established. We compared the rate of CVAE, such as new onset or worsening atrial fibrillation (AF), supraventricular tachycardia, ventricular tachycardia, hypertension, myocardial infarction, and sudden cardiac death, between individuals with and without pre-existing CVD, during BTKi treatment. Secondary objectives were to compare the outcomes of patients treated with first generation BTKi versus second generation BTKi and characterize management decisions. A single-center retrospective review was conducted on patients treated with BTKi from 2013 to 2022 at Beth Israel Deaconess Medical Center. Adjusted logistic regression analyses were performed to evaluate the association between pre-existing CVD and CVAE. In this cohort, 11 out of 54 patients (20.4%) with pre-existing CVD developed CVAE, compared to 11 out of 135 patients (8.1%) without pre-existing CVD [age- and sex-adjusted OR 2.79; 95% CI (1.09, 7.25), P = .03]. Patients with pre-existing CVD had higher odds of developing new or worsening AF [age- and sex-adjusted OR 3.36; 95% CI (1.09, 10.71), P = .03]. Results remained robust after further adjustment of comorbidities, type of BTKi, and baseline medications. These results highlight the need for standardized approaches to prevent and promptly detect CVAE during BTKi treatment, particularly in patients with pre-existing CVD.
Needed but Deplored: Spinners and Singlewomen in Industrial Coventry, c.1490–1525
Authors: Bennett Judith M
Published: September 2024

Late medieval Coventry attracted so many in-migrating singlewomen that it might have seemed a city of women — for every ten women, only seven men. Some of these peasants-turned-townswomen supported themselves as labourers, domestic servants or prostitutes, but it was the demand for their industrial labour as spinners of cloth-yarn and cap-yarn that drew most women to the city. Coventry’s merchants and masters, who needed spinners’ work but deplored women’s autonomy, tried with considerable success to push these spinners into supervised living within the city’s established households. The experiences of Coventry’s singlewoman-spinners show that ‘maidservants’ were sometimes industrial workers; that singlewomen were corralled into ‘little commonwealths’ well before Protestantism; and that ‘girl power’ was more about economic growth than the empowerment of women.
Virtual reality training for radiation safety in cardiac catheterization laboratories - an integrated study
Authors: Fujiwara Asahi , Fujimoto Sota , Ishikawa Ren , Tanaka Aoi
Published: September 2024

The advent of fluoroscopically guided cardiology procedures has greatly improved patient outcomes but has also increased occupational radiation exposure for healthcare professionals, leading to adverse health effects such as radiation-induced cataracts, alopecia, and cancer. This emphasizes the need for effective radiation safety training. Traditional training methods, often based on passive learning, fail to simulate the dynamic catheterization laboratory environment adequately. Virtual Reality (VR) offers a promising alternative by providing immersive, interactive experiences that mimic real-world scenarios without the risks of actual radiation exposure. Our study aims to assess the effectiveness of VR-based radiation safety training compared to traditional methods. We conducted a prospective cohort study involving 48 healthcare professionals in a catheterization lab setting. Participants underwent a 1-hour self-directed VR training session using Virtual Medical Coaching’s RadSafe VR software, which simulates real-world clinical scenarios. Pre- and post-intervention radiation dose levels were measured using personal dosimeters at the eye, chest, and pelvis. Knowledge and skills were assessed through tests, and feedback was gathered through surveys and interviews. Statistical analysis revealed significant reductions in radiation exposure across all professional groups after VR training. For cardiologists, the eye dose dropped by 21.88% (from 2.88 mSv to 2.25 mSv), the chest dose decreased by 21.65% (from 4.11 mSv to 3.22 mSv), and the pelvis dose went down by 21.84% (from 2.06 mSv to 1.61 mSv). Perioperative nurses experienced similar reductions, with eye doses decreasing by 14.74% (from 1.56 mSv to 1.33 mSv), chest doses by 26.92% (from 2.6 mSv to 1.9 mSv), and pelvis doses by 26.92% (from 1.3 mSv to 0.95 mSv). Radiographers saw their eye doses reduced by 18.95% (from 0.95 mSv to 0.77 mSv), chest doses by 42.11% (from 1.9 mSv to 1.1 mSv), and pelvis doses by 27.63% (from 0.76 mSv to 0.55 mSv).Participants reported enhanced engagement, improved understanding of radiation safety, and a preference for VR over traditional methods. A cost analysis also demonstrated the economic advantages of VR training, with significant savings in staff time and rental costs compared to traditional methods. Our findings suggest that VR is a highly effective and cost-efficient training tool for radiation safety in healthcare, offering significant benefits over traditional training approaches.
Local neighborhood affects stem rehydration under drought: evidence from mixtures of European beech with two different conifers
Authors: Hackmann Christina A , Sennhenn-Reulen Holger , Mund Martina , Ammer Christian
Published: September 2024

Mixed-species forests are, for multiple reasons, promising options for forest management in Central Europe. However, the extent to which interspecific competition affects tree hydrological processes is not clear. High-resolution dendrometers capture subdaily variations in stem diameter; they can simultaneously monitor stem growth (irreversible changes in diameter) and water status (reversible changes) of individual trees. Using the information on water status, we aimed to assess potential effects of tree species mixture, expressed as local neighborhood identity, on night-time rehydration and water stress. We deployed 112 sensors in pure and mixed forest stands of European beech, Norway spruce and Douglas fir on four sites in the northwestern Germany, measuring stem diameter in 10-min intervals for a period of four years (2019–2022). In a mixture distribution model, we used environmental variables, namely soil matric potential, atmospheric vapor pressure deficit, temperature, precipitation and neighborhood identity to explain night-time rehydration, measured as the daily minimum tree water deficit (TWDmin). TWDmin was used as a daily indicator of water stress and the daily occurrence of sufficient water supply, allowing for stem growth (potential growth). We found that species and neighborhood identity affected night-time rehydration, but the impacts varied depending on soil water availability. While there was no effect at high water availability, increasing drought revealed species-specific patterns. Beech improved night-time rehydration in mixture with Douglas fir, but not in mixture with spruce. Douglas fir, however, only improved rehydration at a smaller share of beech in the neighborhood, while beech dominance tended to reverse this effect. Spruce was adversely affected when mixed with beech. At species level and under dry conditions, we found that night-time rehydration was reduced in all species, but beech had a greater capacity to rehydrate under high to moderate soil water availability than the conifers, even under high atmospheric water demand. Our study gives new insights into neighborhood effects on tree water status and highlights the importance of species-specific characteristics for tree-water relations in mixed-species forests. It shows that drought stress of European beech can be reduced by admixing Douglas fir, which may point towards a strategy to adapt beech stands to climate change.
Contrasting survival strategies for seedlings of two northern conifer species to extreme droughts and floods
Authors: Schulz Katlyn A , Barry Alexandra M , Kenefic Laura S , Wason Jay W
Published: September 2024

Lowland northern white-cedar (Thuja occidentalis L.) forests are increasingly exposed to extreme droughts and floods that cause tree mortality. However, it is not clear the extent to which these events may differentially affect regeneration of cedar and its increasingly common associate, balsam fir (Abies balsamea (L.) Mill.). To test this, we measured how seedlings of cedar and fir were able to avoid, resist and recover from experimental drought and flood treatments of different lengths (8 to 66 days). Overall, we found that cedar exhibited a strategy of stress resistance and growth recovery (resilience) from moderate drought and flood stress. Fir, on the other hand, appears to be adapted to avoid drought and flood stress and exhibited overall lower growth resilience. In drought treatments, we found evidence of different stomatal behaviors. Cedar used available water quickly and therefore experienced more drought stress than fir, but cedar was able to survive at water potentials > 3 MPa below key hydraulic thresholds. On the other hand, fir employed a more conservative water-use strategy and therefore avoided extremely low water potential. In response to flood treatments, cedar survival was higher and only reached 50% if exposed to 23.1 days of flooding in contrast to only 7.4 days to reach 50% mortality for fir. In both droughts and floods, many stressed cedar were able to maintain partially brown canopies and often survived the stress, albeit with reduced growth, suggesting a strategy of resistance and resilience. In contrast, fir that experienced drought or flood stress had a threshold-type responses and they either had full live canopies with little effect on growth or they died suggesting reliance on a strategy of drought avoidance. Combined with increasingly variable precipitation regimes, seasonal flooding and complex microtopography that can provide safe sites in these forests, these results inform conservation and management of lowland cedar stands.
Genetic Variability and Evolutionary Dynamics of Papaya Ringspot Virus and Papaya Leaf Distortion Mosaic Virus Infecting Feral Papaya in Hainan Island
Authors: Yang Mu-Zhi , Hao Zhi-Gang , Ren Zhen-Tao , Tang Rui , Wu Qing-Hua , Zhou Li-Ying , Hu Yu-Juan , Guo Jing-Yuan , Chen Yi , Guo Yun-Ling , Liu Biao , Liu Lai-Pan , Xue Kun , Jia Rui-Zong
Published: September 2024

Commercialized genetically modified (GM) papaya cultivars have protected papaya from the devastating disease caused by papaya ringspot virus (PRSV). However, papaya leaf distortion mosaic virus (PLDMV), which causes similar infection symptoms but is serologically distinct from PRSV, was found to be a competitive threat to the papaya industry. Our study surveyed the occurrence of PRSV and PLDMV, as well as the transgenic markers of the 35S promoter from cauliflower mosaic virus and the neomycin phosphotransferase II gene in feral papaya plants, which were found frequently growing outside of cultivated papaya fields on Hainan Island. In total, 123 feral papayas, comprising 62 (50.4%) GM plants and 61 (49.6%) non-GM ones, were sampled. Among them, 23 (18.7%) were positive for PRSV, 49 (39.8%) were positive for PLDMV (including five plants co-infected by PRSV and PLDMV), and 56 (45.5%) were free of either virus. In traditional papaya-growing regions, we detected fewer PRSV-infected plants (2 in 33, 6%) than in other regions (21 in 90, 23%). However, overall, whether plants were transgenic or not made no difference to PRSV incidence ( P = 0.230), with 9 PRSV-infected plants among 62 GM papayas and 14 among 61 non-GM papayas. Phylogenetic and genetic differentiation analysis showed a clear correlation between PRSV and PLDMV populations and their geographic origins. Negative selection was estimated for the selected gene regions of both viruses. Notably, PLDMV has deviated from neutral evolution and experienced population expansion, exhibiting increased genetic diversity, and is becoming the predominant threat to papaya in Hainan.
Assessing the Capacity of High-Resolution Commercial Satellite Imagery for Grapevine Downy Mildew Detection and Surveillance in New York State
Authors: Kanaley Kathleen , Combs David B. , Paul Angela , Jiang Yu , Bates Terry , Gold Kaitlin M.
Published: September 2024

Grapevine downy mildew (GDM), caused by the oomycete Plasmopara viticola, can cause 100% yield loss and vine death under conducive conditions. High-resolution multispectral satellite platforms offer the opportunity to track rapidly spreading diseases such as GDM over large, heterogeneous fields. Here, we investigated the capacity of PlanetScope (3 m) and SkySat (50 cm) imagery for season-long GDM detection and surveillance. A team of trained scouts rated GDM severity and incidence at a research vineyard in Geneva, New York, from June to August 2020, 2021, and 2022. Satellite imagery acquired within 72 h of scouting was processed to extract single-band reflectance and vegetation indices (VIs). Random forest models trained on spectral bands and VIs from both image datasets could classify areas of high and low GDM incidence and severity with maximum accuracies of 0.85 (SkySat) and 0.92 (PlanetScope). However, we did not observe significant differences between VIs of high and low damage classes until late July to early August. We identified cloud cover, image co-registration, and low spectral resolution as key challenges to operationalizing satellite-based GDM surveillance. This work establishes the capacity of spaceborne multispectral sensors to detect late-stage GDM and outlines steps toward incorporating satellite remote sensing in grapevine disease surveillance systems.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
A Draft Genome Resource for ‘Candidatus Phytoplasma prunorum’, the Agent Associated with European Stone Fruit Yellows Disease
Authors: Fonseca Jose Pedro , Nunziata Schyler , Yasuhara-Bell Jarred , Bertaccini Assunta , Rivera Yazmín , Newberry Eric
Published: September 2024

‘ Candidatus Phytoplasma prunorum’ is associated with European stone fruit yellows disease, affecting wild and cultivated species of Prunus at different degrees of susceptibility, and so far is being mainly restricted to Europe. Here, we report draft genome sequences for ‘ Ca. Phytoplasma prunorum’ strains ESFY1 and LNS1, which represent the first available for this species. Strain ESFY1 is the causal agent of the European stone fruit yellows disease of P. persica in Germany, and LNS1 is the causal agent of leptonecrosis disease of P. salicina in Italy. Their draft genomes consist of 480,123 and 490,930 bases assembled into 28 and 16 contigs, with an average GC content of 21.1 and 20.7%, respectively. Analysis of average nucleotide identity (ANI) values between genomes further supported the delineation of ‘ Ca. P. prunorum’ as a species distinct from ‘ Ca. P. mali’, in agreement with previous phylogenetic data.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Altered cellular metabolic pathway and epithelial cell maturation induced by MYO5B defects are partially reversible by LPAR5 activation
Authors: Momoh Michael , Rathan-Kumar Sudiksha , Burman Andreanna , Brown Monica E , Adeniran Francisca , Ramos Cynthia , Goldenring James R , Roland Joseph T , Kaji Izumi
Published: September 2024

Functional loss of the motor protein, Myosin Vb (MYO5B), induces various defects in intestinal epithelial function and causes a congenital diarrheal disorder, microvillus inclusion disease (MVID). Utilizing the MVID model mice,Vil1-CreERT2;Myo5bflox/flox(MYO5BΔIEC) andVil1-CreERT2;Myo5bflox/G519R(MYO5B(G519R)), we previously reported that functional MYO5B loss disrupts progenitor cell differentiation and enterocyte maturation that result in villus blunting and deadly malabsorption symptoms. In this study, we determined that both absence and a point mutation of MYO5B impair lipid metabolism and alter mitochondrial structure, which may underlie the progenitor cell malfunction observed in MVID intestine. Along with a decrease in fatty acid oxidation, the lipogenesis pathway was enhanced in the MYO5BΔIEC small intestine. Consistent with these observationsin vivo, RNA-sequencing of enteroids generated from two MVID mouse strains showed similar downregulation of energy metabolic enzymes, including mitochondrial oxidative phosphorylation genes. In our previous studies, lysophosphatidic acid (LPA) signaling ameliorates epithelial cell defects in MYO5BΔIEC tissues and enteroids. The present study demonstrates that the highly soluble LPAR5-preferred agonist, Compound-1, improved sodium transporter localization and absorptive function, and tuft cell differentiation in patient-modeled MVID animals that carry independent mutations in MYO5B. Body weight loss in male MYO5B(G519R) mice was ameliorated by Compound-1. These observations suggest that Compound-1 treatment has a trophic effect on intestine with MYO5B functional loss through epithelial cell-autonomous pathways that may improve the differentiation of progenitor cells and the maturation of enterocytes. Targeting LPAR5 may represent an effective therapeutic approach for treatment of MVID symptoms induced by different point mutations in MYO5B.

NEW & NOTEWOTHY

This study demonstrates the importance of MYO5B for cellular lipid metabolism and mitochondria in intestinal epithelial cells, a previously unexplored function of MYO5B. Alterations in cellular metabolism may underlie the progenitor cell malfunction observed in microvillus inclusion disease (MVID). To examine the therapeutic potential of progenitor-targeted treatments, the effects of LPAR5-preferred agonist, Compound-1, was investigated utilizing several MVID model mice and enteroids. Our observations suggests that Compound-1 may provide a therapeutic approach for treating MVID.

Graphic Abstract
An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model
Authors: Waddell Peter J. , Bouckaert Remco
Published: September 2024

The combination of atimereversible Markov process with a “hidden” mixture ofgamma distributed relative site rates plusinvariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes). However, these models assume a homogeneous and stationary distribution of nucleotide (character or base) frequencies. Here, we explore the potential benefits and pitfalls of allowing each rate category (rate class) of a 4gi mixture model to have its own base frequencies. This is achieved by starting each of the five rate classes, at the tree’sroot, with its own free choice of nucleotidefrequencies to create a 4gi5rf model or a 5rf model in shorthand.

We assess the practical identifiability of this approach with a BEAST 2 implementation, aiming to determine if it can accurately estimate credibility intervals and expected values for a wide range of plausible parameter values. Practical identifiability, as distinguished from mathematical identifiability, gauges the model’s ability to identify parameters in real-world scenarios, as opposed to theoretically with infinite data.

One of the most common types of phylogenetic data is mitochondrial DNA (mtDNA) protein coding sequence. It is often assumed current models analyse robustly such data and that higher likelihood/posterior probability models do better. However, this abstract shows that vertebrate mtDNA remains a very difficult type of data to fully model, and that dramatically higher likelihoods do not mean a model is measurably more accurate with respect to recovering key parameters of biological interest (e.g., monophyletic groups, their support and their ages). The 4gi5rf model considerably improves marginal likelihoods and seems to reverse some apparent errors exacerbated by the 4gi model, while introducing others. Problems appear to be linked to non-stationary DNA repair processes that alter the mutation/substitution spectra across lineages and time. We also show such problems are not unique to mtDNA and are encountered in analysing nuclear sequences. Non-stationarity of DNA repair processes mutation/substitution spectra thus pose an active challenge to obtaining reliable inferences of relationships and divergence times near the root of placental mammals, for example.

An open source implementation is available under the LGPL 3.0 license in the beastbooster package for BEAST 2, available fromhttps://github.com/rbouckaert/beastbooster.
Mapping HIV-1 RNA Structure, Homodimers, Long-Range Interactions and persistent domains by HiCapR
Authors: Zhang Yan , Han Jingwan , Xie Dejian , Shen Wenlong , Li Ping , Lau Jian You , Li Jingyun , Li Lin , Kudla Grzegorz , Zhao Zhihu
Published: September 2024

Human Immunodeficiency Virus (HIV) persists as a leading global health issue. A significant gap in knowledge exists in our understanding of long-range interactions within the HIV-1 RNA genome. To bridge this gap, we introduce HiCapR, incorporating a psoralen crosslinking RNA proximity ligation and post-library hybridization for capturing HIV RNA-RNA interactions.

Leveraging HiCapR, we confirm the presence of stem structures in the key regions, such as the 5’-untranslated region(5’-UTR) and Rev Response Element (RRE) stems, and dimer sites in 5’-UTR region, which is responsible for HIV packaging. Importantly, we reveal multiple previously unknown homodimers along the HIV genome, which may have important implications for viral RNA splicing and packaging processes. Also, we uncover a wealth of unprecedented long-range interactions, particularly within the 5’-UTR of infected cells.

Intriguingly, our findings indicate a pronounced reduction in long-range RNA-RNA interactions, signifying a transition from a state of abundant interactions, hence a relative loose state within infected cells to a condensed structure within virions. Concurrently, we have demonstrated the presence of stable genomic domains within virions that are instrumental in the dimerization process. These domains are preserved throughout the packaging process.

Our findings shed light on the functional significance of RNA organization, including stable and persistent genomic domains, homodimerization, and long-range RNA-RNA interactions, in the splicing, packaging as well as assembly of HIV.

Highlights

HiCapR is a new proximity ligation method for mapping RNA structures and homodimers in the HIV genome with sufficient reliability and efficiency.

Multiple homodimers were discovered along the genome, with potential implications for splicing and packaging processes.

Long-range RNA-RNA interactions are abundant in infected cells but significantly reduced in virions.

Stable genomic domains encluding homodimer sites are persistent in virions and are involved in dimerization.
A statistical-based method for the construction and analysis of gene network: application to bacteria
Authors: Zhang Zhiyuan , Chen Guozhong , Li Erguang
Published: September 2024

Bacteria play a crucial role in environmental conservation, human health, and medicine. Whether in the gut or the soil, bacterial genomes are rich repositories of resources, such as exploring potential drugs and biopesticides. However, our ability to develop new therapies and deepen our understanding of the bacterial world is hindered by the largely unknown functions of bacterial genes. In this study, we proposed a method of gene network construction and analysis based on a Gaussian Graphical Model (GGM) and random sampling strategy to infer direct interactions at the genomic level in bacteria. UsingVibrio choleraeandStaphylococcus aureusas examples, we integrated partial correlation-based gene co-expression data with gene regulatory and essentiality information extracted from public databases to construct more comprehensive gene networks. Networks built upon bacterial different phenotypes, such as biofilm formation, flagellar assembly, and stress response, demonstrate the effectiveness of this method in deciphering unknown gene functions, uncovering new phenotype-associated factors, and identifying their corresponding interactions, thus providing new targets for experimental validation by researchers. Additionally, we extended this method to 14 bacteria, including 13 pathogens, supporting the investigation of gene functions and pathways at the genomic level in these bacteria. More importantly, for other species, this method of gene network construction can be easily implemented, provided that sufficient transcriptome sequencing samples are available.