bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cellular RNA‐dependent RNA polymerases in plants
Authors: Du Xuan 
Published: August 2024

SummaryRNA‐dependent RNA Polymerases (RdRPs) synthesize double‐stranded RNA (dsRNA) from a single‐stranded RNA (ssRNA) template. In plants, dsRNAs produced by RdRPs can be further processed into small interfering RNA (siRNAs) with different lengths, ranging from 21 to 24 nucleotides (nt). These siRNAs play a pivotal role in various biological processes, including antiviral responses, transposable elements silencing, DNA methylation, and the regulation of plant reproduction and development. Recent research has reported significant progress in uncovering the molecular mechanisms of plant RNA‐DEPENDENT RNA POLYMERASE 2 (RDR2), a representative RdRP involved in the RNA‐directed DNA methylation (RdDM) pathway. These discoveries provide a molecular basis underlying the principles of RdRP function and offer insights into potential advancements in crop breeding and antiviral defense strategies.
Early Radiographic and Clinical Outcomes of Robotic‐arm‐assisted versus Conventional Total Knee Arthroplasty: A Multicenter Randomized Controlled Trial
Authors: Geng Xiao , Zheng Yuhang , Li Yang , Zhao Minwei , Liu Yanqing , Li Zijian , Cai Hong , Zhang Ming , Yan Xinfeng , Sun Zhiwen , Lv Xin , Guo Feng , Li Feng , Tian Hua 
Published: August 2024

ObjectiveA robotic system was recently introduced to improve prosthetic alignment during total knee arthroplasty (TKA). The purpose of this multicenter, prospective, randomized controlled trial (RCT) was to determine whether robotic‐arm‐assisted TKA improves clinical and radiological outcomes when compared to conventional TKA.MethodsOne hundred and thirty patients who underwent primary TKA were enrolled in this prospective, randomized controlled trial, which was conducted at three hospitals. Five patients were lost to follow‐up 6 weeks after surgery. Therefore, 125 participants (63 in the intervention group and 62 in the control group) remained in the final analysis. The primary outcome was the rate at which the mechanical axis of the femur deviated by less than 3° from the mechanical axis of the tibia. This was evaluated by full‐length weight‐bearing X‐rays of the lower limb 6 weeks postoperatively. Secondary outcomes included operation times, 6‐week postoperative functional outcomes evaluated by the American Knee Society score (KSS) and the Western Ontario and McMaster Universities osteoarthritis index (WOMAC), short form‐36 (SF‐36) health survey results, and the occurrence of adverse events (AEs) and serious adverse events (SAEs).ResultsAt 6 weeks postoperatively, we found that the rate of radiographic inliers was significantly higher in the intervention group (78.7% vs 51.6%; p = 0.00; 95% confidence interval, 10.9% to 43.2%). The operation was significantly longer in the intervention group than in the control group (119.5 vs 85.0 min; p = 0.00). There were no significant differences in the 6‐week postoperative functional outcomes, SF‐36, AEs, and SAEs between the two groups. There were no AEs or SAEs that were determined to be “positively related” to the robotic system.ConclusionRobotic‐arm‐assisted TKA is safe and effective, as demonstrated in this trial.
Maintenance Breeding in Pigeonpea [Cajanus cajan (L.) Millspaugh] — An Assessment and Advanced Strategies
Authors: Saxena Kul Bhushan , Saxena Rachit K , Dalvi Vijay A , Choudhary Arbind K , Sultana Rafat 
Published: August 2024

AbstractThe sustainable maintenance breeding of pigeonpea germplasm, genetic stocks, released cultivars, and hybrid parents is a tough job. The prime reason for their genetic contamination is the insect‐aided cross‐pollination. Although various public and private seed agencies are involved in maintenance breeding to produce different grades of pigeonpea seeds, but the limitation of resources and low priority make it difficult to meet the national seed requirements. This manuscript, aside from reviewing the present pigeonpea maintenance breeding methods, their limitations, and accomplishments, also highlights some advanced breeding and genomics approaches to enhance the efficiency of maintenance breeding.
Exogenous melatonin application helps late‐sown durum wheat to cope with waterlogging under Mediterranean environmental conditions
Authors: Quaratiello Giuseppe , Risoli Samuele , Antichi Daniele , Pellegrini Elisa , Nali Cristina , Lorenzini Giacomo , Pampana Silvia , Pisuttu Claudia , Tonelli Mariagrazia , Cotrozzi Lorenzo 
Published: August 2024

AbstractIn Mediterranean countries, late‐sown durum wheat (Triticum turgidum L. subsp. durum) may face waterlogging (WL) at early stages. As mitigation of waterlogging by melatonin (MT) has been poorly explored, we analyzed the effects of exogenous MT foliar application to WL‐stressed durum wheat on its ecophysiological performance, growth and biomass production. Late‐sown plants of a relatively tolerant cultivar (i.e., Emilio‐Lepido) were subjected to two WL durations (i.e., 14 and 35 days of WL; DOW) at tillering, with or without exogenous MT application (i.e., 0 and 100 μM). Prolonged WL reduced shoot biomass (−43%), but the application of MT mitigated this detrimental effect. Waterlogging impaired photosynthesis, reducing leaf CO2 assimilation and chlorophyll content (−61 and − 57%, at 14 and 35 DOW). In control, MT increased the photosynthetic pigments (+48%), whereas it exacerbated the decrease in photosynthesis under both WL conditions (−72%, on average). Conversely, MT reduced WL‐induced oxidative damage in both shoots and roots (−25% hydrogen peroxide production), facilitating osmotic adjustments and mitigating oxidative stress. The accumulation of osmotic regulators in MT + WL plants (+140 and + 42%, in shoots and roots at 35 DOW; respectively) and mineral solutes (+140 and + 104%, on average, in shoots and roots at 14 DOW) likely mitigated WL stress, limiting the impact of oxidative stress and promoting biomass accumulation. Our results highlight the potential of MT as a bioactive compound in mitigating the adverse effects of WL on late‐sown durum wheat and the importance of the complex interactions between physiological responses and environmental stressors.
Pupillometry as a biomarker of postural control: Deep‐learning models reveal side‐specific pupillary responses to increased intensity of balance tasks
Authors: Rosker Jernej , Leskovec Tinka , Tomazin Katja , Majcen Rosker Ziva 
Published: August 2024

AbstractPupillometry has been used in the studies of postural control to assess cognitive load during dual tasks, but its response to increased balance task intensity has not been investigated. Furthermore, it is unknown whether side‐specific changes in pupil diameter occur with more demanding balance tasks providing additional insights into postural control. The two aims of this study were to analyze differences in steady‐state pupil diameter between balance tasks with increased intensity and to determine whether there are side‐specific changes. Forty‐eight healthy subjects performed parallel and left and right one‐legged stances on a force plate with and without foam with right and left pupil diameters measured with a mobile infrared eye‐tracker. Differences between balance tasks in parameters (average pupil diameter of each eye, average of both pupil diameters and the difference between the left and right pupil diameter) were analyzed using a two‐way repeated measures analysis of variance, and deep learning neural network models were used to investigate how pupillometry predicted each balance task. The pupil diameter of the left eye, the average pupil diameter of both eyes and the difference in pupil diameters increased statistically significantly from simpler to more demanding balance tasks, with this being more pronounced for the left eye. The deep learning neural network models revealed side‐specific changes in pupil diameter with more demanding balance tasks. This study confirms pupillary responses to increased intensity of balance task and indicates side‐specific pupil responses that could be related to task‐specific involvement of higher levels of postural control.
Preparing the particular: Kant on the imagination's role in judgment
Authors: Dunn Nicholas 
Published: August 2024

AbstractThat Kant sees the faculties of imagination and judgment as closely related is not controversial. Yet precisely how they relate to each other, especially across his Critical philosophy, is less clear. In this article, I consider the relationship between what Kant calls the “power of imagination” (Einbildungskraft) and the “power of judgment” (Urteilskraft). I argue for the following claim: insofar as the power of judgment is the faculty of thinking particulars under universals, the power of imagination is the faculty of producing and providing particulars for judgment—either to reflect on or to subsume under universals. Such an account reveals that our capacity for imagination is intimately bound up with our capacity to judge.
“You can't really turn it off”: The police “sixth sense” as cultural schema
Authors: Campeau Holly , Keesman Laura D. 
Published: August 2024

AbstractA variety of concepts in the policing literature denote a so‐called “sixth sense” that police officers claim to possess. “Intuition,” “suspicion,” or “common sense” all specify a tacit knowledge said to heighten an officer's sensitivity to danger and potential suspects. This paper argues this type of knowledge exemplifies the application of “cultural schema” (DiMaggio, 1997): a shared knowledge structure that allows people to respond to environmental stimuli in ways that render their lives more predictable. We combine two case studies—one in Canada, the other in the Netherlands—which include ethnographic field notes and 199 interviews with police officers, to reconsider the police sixth sense in light of theoretical and empirical advances in cultural sociology and cognition research. This paper further discusses the benefit of studying this sixth sense itself as a form of cultural knowledge—that is, as “police culture”—to improve our understanding of cultural resources most or least compatible with emerging police reforms.
Mechanically Induced Deformation of Nuclei in the Tricuspid Valve Interstitial Cells: Experimental Measurements and Multi-scale Computational Simulation
Authors: Pakzadmanesh Mina , Salinas Samuel D. , Thomas Vineet S. , Jennings Turner , DelCiello Hayden , Vargas Ana I. , Clarin Julia , Amini Rouzbeh 
Published: August 2024

Abstract
We examined the mechanical deformation of valve interstitial cells (VICs) in the anterior leaflet of the tricuspid valve and explored the relationship between the extracellular matrix (ECM) structure and cellular mechanics. Fresh porcine hearts were used to prepare specimens, subjected to biaxial tensile testing, and imaged using confocal microscopy with VIC nuclei staining. A multi-scale computational framework was developed to analyze cellular deformation and orientation within the ECM, using nuclear aspect ratio (NAR) as a metric. Experimental results showed that NAR values increased with mechanical loading, from 2.57±0.72 in a traction-free state to 3.4±1.29 at 130 kPa. Model predictions aligned with experimental findings. They also highlighted the significant impact of ECM fiber orientation on VIC nuclei deformation. These results indicate that mechanical forces profoundly influence cellular morphology and, potentially, their function. Further development of models is necessary to understand the complex interplay between the mechanical environment and cellular responses, crucial for identifying how mechanical forces affect tricuspid valve function and malfunction.
Evaluation of a Bayesian hierarchical pharmacokinetic–pharmacodynamic model for predicting parasitological outcomes in Phase 2 studies of new antimalarial drugs
Authors: Tully Meg K. , Dini Saber , Flegg Jennifer A. , McCarthy James S. , Price David J. , Simpson Julie A. 
Published: August 2024

ABSTRACT

The rise of multidrug-resistant malaria requires accelerated development of novel antimalarial drugs. Pharmacokinetic–pharmacodynamic (PK-PD) models relate blood antimalarial drug concentrations with the parasite–time profile to inform dosing regimens. We performed a simulation study to assess the utility of a Bayesian hierarchical mechanistic PK-PD model for predicting parasite–time profiles for a Phase 2 study of a new antimalarial drug, cipargamin. We simulated cipargamin concentration- and malaria parasite-profiles based on a Phase 2 study of eight volunteers who received cipargamin 7 days after inoculation with malaria parasites. The cipargamin profiles were generated from a two-compartment PK model and parasite profiles from a previously published biologically informed PD model. One thousand PK-PD data sets of eight patients were simulated, following the sampling intervals of the Phase 2 study. The mechanistic PK-PD model was incorporated in a Bayesian hierarchical framework, and the parameters were estimated. Population PK model parameters describing absorption, distribution, and clearance were estimated with minimal bias (mean relative bias ranged from 1.7% to 8.4%). The PD model was fitted to the parasitaemia profiles in each simulated data set using the estimated PK parameters. Posterior predictive checks demonstrate that our PK-PD model adequately captures the simulated PD profiles. The bias of the estimated population average PD parameters was low–moderate in magnitude. This simulation study demonstrates the viability of our PK-PD model to predict parasitological outcomes in Phase 2 volunteer infection studies. This work will inform the dose–effect relationship of cipargamin, guiding decisions on dosing regimens to be evaluated in Phase 3 trials.
Critical role of
msgA
in invasive capacity and intracellular survivability of
Salmonella
Authors: Liu Xinqi , Wang Chengzhi , Gai Wenhua , Sun Zhaotong , Fang Lei , Hua Zichun 
Published: August 2024

ABSTRACT

Salmonella
enterica serovar Typhimurium, which is a common foodborne pathogen, causes both intestinal and systemic infections in hosts.
Salmonella
has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability, which hampers research on virulence of
Salmonella
. The virulence of
Salmonella
is primarily studied through
Salmonella
pathogenicity islands (SPIs). However, there are also genes outside these SPIs that significantly impact virulence. Macrophage survival gene
msgA
is positioned at a region independent of the SPIs and conserved in
Salmonella
. However, there has been limited research on
msgA
to date. This study aims to investigate the virulent function of
msgA
to deepen our understanding of
Salmonella
virulence. Proteomic and RT-qPCR analyses reveal that MsgA influences multiple metabolic pathways and the expression of SPIs. The depletion of
msgA
led to the significantly reduced invasive capacity and intracellular survivability, and thus the decreased virulence of
Salmonella
. In conclusion, our study suggests that MsgA is an important regulator that mainly regulates virulence. Further research into the function of MsgA will enhance the understanding of
Salmonella
pathogenesis and promote the application of
Salmonella
for medical treatment.

IMPORTANCE

Salmonella
enterica serovar Typhimurium is a common foodborne pathogen, it has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability. The virulence of
Salmonella
is primarily studied through its pathogenicity islands. In contrast, virulence genes located outside the
Salmonella
pathogenicity islands (SPIs) have received less attention. Macrophage survival gene (MsgA) is positioned at a region independent of the SPIs and conserved in
Salmonella
. Our research indicates that MsgA is a novel global regulator influencing the metabolic pathways and SPIs. Further research into the function of MsgA will enhance the understanding of
Salmonella
pathogenesis and promote the application of
Salmonella
for medical treatment.
Co-existence of two antibiotic-producing marine bacteria:
Pseudoalteromonas piscicida
reduce gene expression and production of the antibacterial compound, tropodithietic acid, in
Phaeobacter
sp.
Authors: Svendsen Peter Bing , Henriksen Nathalie N. S. E. , Jarmusch Scott A. , Andersen Aaron J. C. , Smith Kirsty , Selsmark Marcus Weichel , Zhang Sheng-Da , Schostag Morten D. , Gram Lone 
Published: August 2024

ABSTRACT

Many bacteria co-exist and produce antibiotics, yet we know little about how they cope and occupy the same niche. The purpose of the present study was to determine if and how two potent antibiotic-producing marine bacteria influence the secondary metabolome of each other. We established an agar- and broth-based system allowing co-existence of a
Phaeobacter
species and
Pseudoalteromonas piscicida
that, respectively, produce tropodithietic acid (TDA) and bromoalterochromides (BACs). Co-culturing of
Phaeobacter
sp. strain A36a-5a on Marine Agar with
P. piscicida
strain B39bio caused a reduction of TDA production in the
Phaeobacter
colony. We constructed a transcriptional gene reporter fusion in the
tdaC
gene in the TDA biosynthetic pathway in
Phaeobacter
and demonstrated that the reduction of TDA by
P. piscicida
was due to the suppression of the TDA biosynthesis. A stable liquid co-cultivation system was developed, and the expression of
tdaC
in
Phaeobacter
was reduced eightfold lower (per cell) in the co-culture compared to the monoculture. Mass spectrometry imaging of co-cultured colonies revealed a reduction of TDA and indicated that BACs diffused into the
Phaeobacter
colony. BACs were purified from
Pseudoalteromonas
; however, when added as pure compounds or a mixture they did not influence TDA production. In co-culture, the metabolome was dominated by
Pseudoalteromonas
features indicating that production of other
Phaeobacter
compounds besides TDA was reduced. In conclusion, co-existence of two antibiotic-producing bacteria may be allowed by one causing reduction in the antagonistic potential of the other. The reduction (here of TDA) was not caused by degradation but by a yet uncharacterized mechanism allowing
Pseudoalteromonas
to reduce expression of the TDA biosynthetic pathway.

IMPORTANCE
The drug potential of antimicrobial secondary metabolites has been the main driver of research into these compounds. However, in recent years, their natural role in microbial systems and microbiomes has become important to determine the assembly and development of microbiomes. Herein, we demonstrate that two potent antibiotic-producing bacteria can co-exist, and one mechanism allowing the co-existence is the specific reduction of antibiotic production in one bacterium by the other. Understanding the molecular mechanisms in complex interactions provides insights for applied uses, such as when developing TDA-producing bacteria for use as biocontrol in aquaculture.
Contributions of
Hanseniaspora
species to Pinot Noir microbial terroir in Oregon’s Willamette Valley wine region
Authors: Snyder Tess , Osborne James , Curtin Chris 
Published: August 2024

ABSTRACT

The apiculate yeast genus
Hanseniaspora
has appeared frequently in enological research for more than 100 years, mostly focused upon the species
H. uvarum
due to its notable capacity to cause spoilage. Recently, there has been increased research into the potential benefits of other
Hanseniaspora
species, such as
H. vineae,
in producing more complex wines. Furthermore, large-scale DNA sequencing-based (metabarcoding) vineyard ecology studies have suggested that
Hanseniaspora
species may not be evenly distributed. To address potential differences across geographical areas in Oregon, we sampled extensively from 12 vineyards within the Willamette Valley American Viticultural Area (AVA), across 2 sub-AVAs (Eola-Amity Hills and Yamhill-Carlton). Metabarcoding was then used to assess the contribution of
Hanseniaspora
to the grape berry fungal community and the impact of wine processing on diversity. While 6 of the 23 recognized
Hanseniaspora
species were present on Pinot Noir grapes in the Willamette Valley AVA, differences between vineyards were driven by the abundance of
H. uvarum
. Significant positive correlations between the amount of
H. uvarum
present in must and at cold soak, and then cold soak to early ferment were observed. While intuitive, it is worth noting that no prior studies have observed this across such a large number of grape samples from different vineyards. Our results provide clear evidence that the abundance of
H. uvarum
on grapes may be an important predictor of potential impacts on wine quality, particularly if performing cold soak, which acts as an enrichment step.

IMPORTANCE

Hanseniaspora
yeasts are frequently found in uninoculated wine fermentations, and depending upon the species present, their contributions to the wine may be positive or negative. We found that in Oregon’s Willamette Valley, the most common species of
Hanseniaspora
in Pinot Noir vineyards was the known spoilage organism,
H. uvarum
. This species was one of the strongest contributors to differences in fungal communities between different vineyards and was enriched during typical Pinot Noir processing. These results support
Hanseniaspora
as an integral and functional component of vineyard “microbial terroir” within Oregon.
The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies
Authors: Etlin Sofia , Rose Julianna , Bielski Luca , Walter Claire , Kleinman Ashley S. , Mason Christopher E. 
Published: August 2024

SUMMARY
The human microbiota encompasses the diverse communities of microorganisms that reside in, on, and around various parts of the human body, such as the skin, nasal passages, and gastrointestinal tract. Although research is ongoing, it is well established that the microbiota exert a substantial influence on the body through the production and modification of metabolites and small molecules. Disruptions in the composition of the microbiota—dysbiosis—have also been linked to various negative health outcomes. As humans embark upon longer-duration space missions, it is important to understand how the conditions of space travel impact the microbiota and, consequently, astronaut health. This article will first characterize the main taxa of the human gut microbiota and their associated metabolites, before discussing potential dysbiosis and negative health consequences. It will also detail the microbial changes observed in astronauts during spaceflight, focusing on gut microbiota composition and pathogenic virulence and survival. Analysis will then turn to how astronaut health may be protected from adverse microbial changes via diet, exercise, and antibiotics before concluding with a discussion of the microbiota of spacecraft and microbial culturing methods in space. The implications of this review are critical, particularly with NASA’s ongoing implementation of the Moon to Mars Architecture, which will include weeks or months of living in space and new habitats.