bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppression of NLR-mediated plant immune detection by bacterial pathogens
Authors: Rufián José S , Rueda-Blanco Javier , Beuzón Carmen R , Ruiz-Albert Javier 
Published: July 2023

Abstract
The plant immune system is constituted of two functionally interdependent branches that provide the plant with an effective defense against microbial pathogens. They can be considered separate since one detects extracellular pathogen-associated molecular patterns by means of receptors on the plant surface, while the other detects pathogen-secreted virulence effectors via intracellular receptors. Plant defense depending on both branches can be effectively suppressed by host-adapted microbial pathogens. In this review we focus on bacterially driven suppression of the latter, known as effector-triggered immunity (ETI) and dependent on diverse NOD-like receptors (NLRs). We examine how some effectors secreted by pathogenic bacteria carrying type III secretion systems can be subject to specific NLR-mediated detection, which can be evaded by the action of additional co-secreted effectors (suppressors), implying that virulence depends on the coordinated action of the whole repertoire of effectors of any given bacterium and their complex epistatic interactions within the plant. We consider how ETI activation can be avoided by using suppressors to directly alter compromised co-secreted effectors, modify plant defense-associated proteins, or occasionally both. We also comment on the potential assembly within the plant cell of multi-protein complexes comprising both bacterial effectors and defense protein targets.
To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes
Authors: Rienstra Juriaan , Hernández-García Jorge , Weijers Dolf 
Published: July 2023

Abstract
Most plant growth and development processes are regulated in one way or another by auxin. The best-studied mechanism by which auxin exerts its regulatory effects is through the nuclear auxin pathway (NAP). In this pathway, Auxin Response Factors (ARFs) are the transcription factors that ultimately determine which genes become auxin regulated by binding to specific DNA sequences. ARFs have primarily been studied in Arabidopsis thaliana, but recent studies in other species have revealed family-wide DNA binding specificities for different ARFs and the minimal functional system of the NAP system, consisting of a duo of competing ARFs of the A and B classes. In this review, we provide an overview of key aspects of ARF DNA binding such as auxin response elements (TGTCNN) and tandem repeat motifs, and consider how structural biology and in vitro studies help us understand ARF DNA preferences. We also highlight some recent aspects related to the regulation of ARF levels inside a cell, which may alter the DNA binding profile of ARFs in different tissues. We finally emphasize the need to study minimal NAP systems to understand fundamental aspects of ARF function, the need to characterize algal ARFs to understand how ARFs evolved, how cutting-edge techniques can increase our understanding of ARFs, and which remaining questions can only be answered by structural biology.
Surgical Treatment of Focal Chondral Lesions of the Knee in the Military Population: Current and Future Therapies
Authors: Tropf Jordan G , Dickens Jonathan F , LeClere Lance E 
Published: July 2023

ABSTRACT

Introduction
Chondral and osteochondral defects of the knee are common injuries in the military population that have a significant impact on readiness. Definitive treatment of these injuries is challenging since cartilage has a limited capacity for self-repair and regeneration. Management is particularly challenging in military patients who maintain a higher level of activity similar to athletes. Existing surgical techniques have variable results and often long recovery times, sparking the development of several new innovative technologies to return service members back to duty more quickly and effectively after cartilage injury. The purpose of this article is to review the current and future surgical treatments for chondral and osteochondral knee lesions and their relevance in managing these injuries in the military.

Methods
In this review article, we describe the current treatments for chondral and osteochondral defects of the knee, reporting on outcomes in military populations. We explore emerging treatment modalities for cartilage defects, reporting innovations, stage of research, and current data. Published results of each treatment option in military populations are reviewed throughout the article.

Results
This review includes 12 treatments for chondral lesions. Of these therapies, four are considered synthetic and the remaining are considered regenerative solutions. Regenerative therapies tend to perform better in younger, healthier populations with robust healing capacity. Success of treatment depends on lesions and patient characteristics. Nearly all modalities currently available in the USA were successful in improving patients from presurgical function in the short (&lt;6 months) term, but the long-term efficacy is still challenged. Upcoming technologies show promising results in clinical and animal studies that may provide alternative options desirable for the military population.

Conclusions
The current treatment options for cartilage lesions are not entirely satisfactory, usually with long recovery times and mixed results. An ideal therapy would be a single procedure that possesses the ability to enable a quick return to activity and duty, alleviate pain, provide long-term durability, and disrupt the progression of osteoarthritis. Evolving technologies for cartilage lesions are expanding beyond currently available techniques that may revolutionize the future of cartilage repair.
Unravelling the structure of magnetized molecular clouds with SILCC-Zoom: sheets, filaments, and fragmentation
Authors: Ganguly Shashwata , Walch S , Seifried D , Clarke S D , Weis M 
Published: July 2023

ABSTRACT
To what extent magnetic fields affect how molecular clouds (MCs) fragment and create dense structures is an open question. We present a numerical study of cloud fragmentation using the SILCC-Zoom simulations. These simulations follow the self-consistent formation of MCs in a few hundred parsec-sized region of a stratified galactic disc; and include magnetic fields, self-gravity, supernova-driven turbulence, as well as a non-equilibrium chemical network. To discern the role of magnetic fields in the evolution of MCs, we study seven simulated clouds, five with magnetic fields, and two without, with a maximum resolution of 0.1 parsec. Using a dendrogram, we identify hierarchical structures, which form within the clouds. Overall, the magnetized clouds have more mass in a diffuse envelope with a number density between 1 and 100 cm−3. We find that six out of seven clouds are sheet-like on the largest scales, as also found in recent observations, and with filamentary structures embedded within, consistent with the bubble-driven MC formation mechanism. Hydrodynamic simulations tend to produce more sheet-like structures also on smaller scales, while the presence of magnetic fields promotes filament formation. Analysing cloud energetics, we find that magnetic fields are dynamically important for less dense, mostly but not exclusively atomic structures (typically up to ∼100−1000 cm−3), while the denser, potentially star-forming structures are energetically dominated by self-gravity and turbulence. In addition, we compute the magnetic surface term and demonstrate that it is generally confining, and some atomic structures are even magnetically held together. In general, magnetic fields delay the cloud evolution and fragmentation by ∼ 1 Myr.
TESS light curves of cataclysmic variables – III – More superhump systems among old novae and nova-like variables
Authors: Bruch Albert 
Published: July 2023

ABSTRACT
Continuing previous work on the identification and characterization of periodic and non-periodic variations in long and almost uninterrupted high cadence light curves of cataclysmic variables observed by the Transiting Exoplanet Survey Telescope mission, the results on 23 nova-like variables and old novae out of sample of 127 such systems taken from the Ritter & Kolb catalogue are presented. All of them exhibit at least at some epochs either positive or negative (or both) superhumps, and in 19 of them superhumps were detected for the first time. The basic properties of the superhumps such as their periods, their appearance and disappearance, and their waveforms are explored. Together with recent reports in the literature, this elevates the number of known nova-like variables and old novae with superhumps by more than 50 per cent. The previous census of superhumps and the Stolz–Schoembs relation for these stars are updated. Attention is drawn to superhump properties in some stars that behave differently from the average, as well as to positive superhumps in high-mass ratio systems that defy theory. As a by-product, the orbital periods of 13 stars are either improved or newly measured, correcting previously reported erroneous values.
Uncovering Footprints of Natural Selection Through Spectral Analysis of Genomic Summary Statistics
Authors: Arnab Sandipan Paul , Amin Md Ruhul , DeGiorgio Michael 
Published: July 2023

Abstract
Natural selection leaves a spatial pattern along the genome, with a haplotype distribution distortion near the selected locus that fades with distance. Evaluating the spatial signal of a population-genetic summary statistic across the genome allows for patterns of natural selection to be distinguished from neutrality. Considering the genomic spatial distribution of multiple summary statistics is expected to aid in uncovering subtle signatures of selection. In recent years, numerous methods have been devised that consider genomic spatial distributions across summary statistics, utilizing both classical machine learning and deep learning architectures. However, better predictions may be attainable by improving the way in which features are extracted from these summary statistics. We apply wavelet transform, multitaper spectral analysis, and S-transform to summary statistic arrays to achieve this goal. Each analysis method converts one-dimensional summary statistic arrays to two-dimensional images of spectral analysis, allowing simultaneous temporal and spectral assessment. We feed these images into convolutional neural networks and consider combining models using ensemble stacking. Our modeling framework achieves high accuracy and power across a diverse set of evolutionary settings, including population size changes and test sets of varying sweep strength, softness, and timing. A scan of central European whole-genome sequences recapitulated well-established sweep candidates and predicted novel cancer-associated genes as sweeps with high support. Given that this modeling framework is also robust to missing genomic segments, we believe that it will represent a welcome addition to the population-genomic toolkit for learning about adaptive processes from genomic data.
Effects of dietary interventions on cardiovascular outcomes: a network meta-analysis
Authors: Doundoulakis Ioannis , Farmakis Ioannis T , Theodoridis Xenophon , Konstantelos Antonis , Christoglou Maria , Kotzakioulafi Evangelia , Chrysoula Lydia , Siargkas Antonis , Karligkiotis Apostolos , Kyprianou Georgia , Mastromanoli Eleni , Soulaidopoulos Stergios , Zafeiropoulos Stefanos , Antza Christina , Tsiachris Dimitris , Chourdakis Michail 
Published: July 2023

Abstract

Context
Next to a large body of epidemiological observational studies showing that the Mediterranean diet (MD) is an important lifestyle determinant of cardiovascular risk, there is less relevant evidence from well-conducted randomized controlled trials (RCTs) with hard cardiovascular outcomes.

Objective
The objective of the study was to identify the most effective dietary intervention for reducing cardiovascular morbidity and mortality.

Data Sources
A systematic approach following PRISMA network meta-analyses reporting guidelines was applied to a search of electronic databases (MEDLINE, Cochrane Central Register of Controlled Trials, and Embase) without language restrictions, supplemented by scanning through bibliographies of studies and meetings’ abstract material. Inclusion criteria were RCTs conducted in an adult population, investigating the effects of different type of diets or dietary patterns on all-cause mortality and cardiovascular outcomes of interest.

Data Extraction
Data extraction for each study was conducted by 2 independent reviewers.

Data Analysis
A frequentist network meta-analysis using a random-effects model was conducted. Death from any cardiovascular cause was defined as the primary outcome. A total of 17 trials incorporating 83 280 participants were included in the systematic review. Twelve articles (n = 80 550 participants) contributed to the network meta-analysis for the primary outcome. When compared with the control diet, only the MD showed a reduction in cardiovascular deaths (risk ratio = 0.59; 95% confidence interval, 0.42–0.82). Additionally, MD was the sole dietary strategy that decreased the risk of major cardiovascular events, myocardial infarction, angina, and all-cause mortality.

Conclusions
MD may play a protective role against cardiovascular disease and death for primary and also secondary prevention.

Systematic Review Registration
Center for Open Science, https://doi.org/10.17605/OSF.IO/5KX83
DNA metabarcoding reveals rangewide variation in aquatic diet of a riparian avian insectivore, the Prothonotary Warbler
Authors: Rogers Samantha L , Verrelli Brian C , Bukaveckas Paul A , Ames Elizabeth M , Youtz Joseph , Boves Than J , Johnson Erik I , Tonra Christopher M , Bulluck Lesley P 
Published: July 2023

Abstract
Riparian avian insectivores not only depend on terrestrial insect prey but also benefit from the inclusion of aquatic prey during critical life-history periods. Diets identified herein show that Prothonotary Warbler (Protonotaria citrea) nestlings were provisioned with aquatic prey throughout the breeding season across their range, but with variation in prey frequency of occurrence and taxonomy. Anthropogenic activity and climate change may impact the trophic link especially between aquatic and riparian habitats by altering the presence, abundance, and timing of prey availability. Thus, we used DNA metabarcoding of fecal samples to quantify the frequency of occurrence of nestling diet items at 9 sites across their breeding range that differed in expected aquatic prey consumption. We analyzed spatial and temporal differences in the occurrence and multivariate diet assemblages of each prey source. Lepidoptera was the predominant terrestrial prey occurring in diets across space and time, whereas emergent aquatic insects and freshwater mollusks in aquatic diet exhibited greater variation. The frequency of emergent aquatic prey occurrence in nestling diets ranged from 61% to 100% across sites and was greater for early-season nestlings. The seasonal decrease in aquatic prey consumption indicates a potential temporal shift in the nutritional landscape from aquatic to terrestrial prey sources and a possible nutritional phenological mismatch for early nestlings as climate change advances the timing of insect emergence. Our findings also suggest that Prothonotary Warblers respond to environmental variability by consuming alternative prey and argue for future research investigating the extent to which shifting diets have nutritional consequences for riparian nestlings.
Local food availability and nonbreeding carry-over effects affect breeding propensity and success of a tundra-nesting predator, the Long-tailed Jaeger
Authors: Seyer Yannick , Gauthier Gilles , Bêty Joël , Therrien Jean-François , Legagneux Pierre , Lecomte Nicolas 
Published: July 2023

AbstractReproduction of long-distance migrants can be affected by local conditions on the breeding grounds as well as those encountered during the nonbreeding season through carry-over effects. We show that this is true in Long-tailed Jaegers (Stercorarius longicaudus) because individuals that spent less time flying at sea during winter had a high breeding propensity and a reduced pre-laying interval, but breeding propensity and nesting success were also positively associated with food abundance at the breeding site. This seabird switches from a marine to a terrestrial lifestyle to breed in summer in the Arctic, where it primarily feeds on lemmings. We monitored jaeger reproduction and lemming densities on Bylot Island in the Canadian Arctic for 16 years, and we used geolocator to study annual movements. We assessed whether movement parameters (travel distance, migration duration, phenology, and number of flying bouts inferred by saltwater immersions) during the nonbreeding season affected the breeding propensity, phenology, and success of individuals. We also examined whether cyclic lemming fluctuations influenced Long-tailed Jaeger reproduction and whether nesting success affected the phenology of their outbound migration. We found that increased time spent flying during winter and early arrival at the breeding site reduced breeding propensity. Moreover, spending less time flying during winter shortened the pre-laying period, and advancing laying date increased nesting success. Birds may thus face a trade-off to minimize the relative costs associated with arriving too early and breeding too late. Local food availability had a strong effect on reproduction because breeding propensity and nesting success increased sharply with lemming abundance. Failed breeders advanced their outbound migration by 10 days on average compared to successful ones, but migration duration was similar. Therefore, the unpredictability of the highly seasonal Arctic environment, especially fluctuating food abundance, appears to be a strong driver of reproduction that can modulate the strength of carry-over effects.
“Restoring That Faith in My Shoulder”: A Qualitative Investigation of How and Why Exercise Therapy Influenced the Clinical Outcomes of Individuals With Rotator Cuff–Related Shoulder Pain
Authors: Powell Jared K , Costa Nathalia , Schram Ben , Hing Wayne , Lewis Jeremy 
Published: July 2023

Abstract

Objective
Rotator cuff–related shoulder pain (RCRSP) is the most common form of shoulder pain. Exercise therapy is a first-line recommended treatment for RCRSP. However, the causal mechanisms underpinning the benefits of exercise for RCRSP are not well understood. Moreover, how individuals with lived experience of RCRSP believe exercise helped or did not help them is unknown. This study aimed to gain insights into how individuals with RCRSP believe exercise influenced their shoulder pain and identify the clinical conditions that promoted or inhibited their beliefs.

Methods
This qualitative study was underpinned by a critical realist approach to thematic analysis. Participants were recruited using hybrid purposive and convenience sampling techniques. Each participant attended an online semi-structured interview. The data were coded by 2 members of the research team (J.K.P. and N.C.) and verified by a third (B.S.). Recruitment continued until theoretical sufficiency was achieved. Participants reviewed and validated preliminary causal explanations.

Results
Three causal explanations were consistently expressed by 11 participants to explain the benefits of exercise therapy: (1) shoulder strength; (2) changes to psychoemotional status; and (3) exercise has widespread health effects. However, the activation of these causal mechanisms depended on (1) the presence of a strong therapeutic relationship; (2) the provision of a structured and tailored exercise program; and (3) experiencing timely clinical progress.

Conclusion
Participants believed exercise improved their shoulder pain through associated health benefits, improved shoulder strength, and psychoemotional variables. Whether an exercise program was able to cause a clinical improvement for an individual with RCRSP was contingent on clinical contextual features. Thus, the clinical context that an exercise program is delivered within may be just as important as the exercise program itself.

Impact
Exercise is a recommended first-line intervention to manage RCRSP. The results of this study suggest that a positive experience and outcome with exercise for RCRSP is contingent on several clinical contextual features, such as a strong therapeutic relationship. The clinical context that an exercise program is prescribed and delivered within should be considered by clinicians.
The problem of ‘shadow species’ as illustrated with the taxonomic hotchpotch Cyphoderia ampulla (Rhizaria: Cyphoderiidae)
Authors: Soler-Zamora Carmen , Useros Fernando , González-Miguéns Rubén , Gómez-Rodríguez Pablo , Lara Enrique 
Published: July 2023

Abstract
Accurate species delimitation based on an integrative approach is indispensable for biodiversity evaluation. Accordingly, species that were formerly only described morphologically often need to be split into several evolutionary independent units. However, taxonomic actions often lag behind, even when the required data are already available. As a result, invalid species names are carried over the years, with negative implications on ecology, biogeography, and conservation; we designate these entities as ‘shadow species’. This is particularly common in protists, due to the lack of specialized taxonomists and the difficulties of working with microscopic organisms. Here, we resolve the case of the testate amoeba shadow species Cyphoderia ampulla (Rhizaria: Cercozoa: Euglyphida: Cyphoderiidae), a known polyphyletic taxon. Purposely, we integrated the current ecological, genetic, and morphological data on the family Cyphoderiidae with its described evolutionary history. Subsequently, we took the required taxonomic actions to resolve the taxonomy of the family, erecting four new genera (Psammoderia gen nov., Knarr gen. nov., Ichthyosquama gen. nov., and Oleiformis gen. nov.), emending Cyphoderia and describing four new species (Ichthyosquama sanabriensis sp. nov., Ichthyosquama catoirensis sp. nov., Ichthyosquama loricaria sp. nov., and Oleiformis carmelae sp. nov.). Finally, we discuss the extension and relevance of the ‘shadow species’ issue in eukaryotic taxa, and differentiate it from species complex concept.
Fusarium Species Recovered from Postharvest Hemp Materials from Kentucky Fields
Authors: Szarka D. , Smith H. S. , Dixon E. , Munir M. , Rahnama M. , Gauthier N. A. 
Published: July 2023

As hemp becomes established as a commodity in the United States, continued cultivation demands a greater understanding of the pathogens that affect the consumable portions, such as flowers and grain. Four Fusarium spp. have been confirmed to cause Fusarium head blight on hemp in Kentucky. Several Fusarium species, including F. graminearum, that are known to produce mycotoxins have been confirmed pathogenic on hemp. Fusarium mycotoxins are regulated in grains used for human and animal consumption. Determining which Fusarium species infect hemp is the first step to producing safe material. Although field disease is under investigation, there have been no studies regarding stored hemp. Harvested and stored floral material for production of cannabidiol (CBD) were collected from seven Kentucky producers from 2019 and 2020 harvests. The material was screened using a Fusarium-selective medium and DNA sequencing. At least 12 different species were isolated, most from the Incarnatum-equiseti species complex (75.6%). Species from the Sambucinum (16.3%), Oxysporum (0.8%), Fujikuroi (5.7%), and Solani (1.6%) species complexes were also identified. Additional research is essential to determine whether these Fusarium species are pathogenic or saprophytic and whether they can produce toxins dangerous for humans and animals. Such information is crucial to determine how to store hemp, manage infected material, and promote successful production of hemp products.