bluuebunny/crossref_metadata_2025 huggingface dataset:
Mini plant factory development using IoT and cloud system for urban greens cultivation
Authors: Dzaky M A F , Nugroho A P , Prasetyatama Y D , Falah M A F , Sutiarso L , Okayasu T
Published: December 2022

A significant urban population increases with the rising demand for higher food quality and security. Adapting the current food chain system and our eating patterns are needed to make them more sustainable. Plant factories are one approach for making the food chain system more sustainable. However, plant factory systems typically require significant initial capital expenditure. As a result, a mini plant factory, which is more affordable and flexible, will be appropriate in urban areas. The objective of this study was to design, build, and evaluate a mini plant factory system for horticultural crop production. The mini plant factory system comprises a mini cultivation room with three growing shelves equipped with a microclimate sensor, nutrient dosing system, artificial growth light, and ventilation system. Sensors and actuators are integrated with the Agrieye Cloud system for monitoring and control and can autonomously execute data retrieval and actuation. Mini Plant Factory operates by automatically capturing monitoring data every five minutes; if a value exceeds the limit, the actuator control system activates to stabilize that value. The linear regression test yielded the most excellent R2 value of 0.999 for sensor calibration. The validation test was conducted using RMSE (Root Mean Square Error) and MAPE (Mean Absolute Percentage Error). The results show that the lowest RMSE values are 0.133, and the lowest MAPE values are 0.082%. The data logging system’s performance is perfect. The control and scheduling system works well but does not function optimally since there are no interruptions throughout the data gathering process.
Utilizing forest genetic resources in developing a new variety of Acacia hybrid (Acacia mangium × Acacia auriculiformis) to support the sustainable use of plants in Indonesia
Authors: Nirsatmanto A , Sunarti S , Kartikawati N K , Putri A I , Herawan T , Haryjanto L , Wahyuningtyas R S , Santoso P B , Lestari F , Rimbawanto A
Published: December 2022

Tree breeding is a good practice in utilizing forest genetic resources to support the sustainable use of forest trees. However, an adverse relationship among desirable traits often occurred that causes the improvement could not be obtained simultaneously. Interspecies hybridization might then be practiced as an alternative technique by exploiting genetic resources into breeding to produce improved stocks of multiple traits suitable for the end-product targeted. This paper presents lessons learned from a study in developing a new variety of Acacia hybrid as an interspecies crossing between Acacia mangium and Acacia auriculiformis as two species having different superiority in growth, wood properties, adaptability, and disease tolerance. Results of the study revealed that the Acacia hybrid could provide better improvement and outperformed single-species breeding. Commonly adverse correlation on some traits could change to be a positive-moderate correlation. In addition, the morphological characteristics of the Acacia hybrid progenies varied that could be used as a genetic base population for other diverse breeding purposes.
In vitro rumen fermentation characteristics of fermented complete feed based on rice straw with moringa leaves (Moringa oleifera) addition
Authors: Wajizah S , Fhonna F A , Khairi F , Delima M
Published: December 2022

The utilization of rice straw as feed must be supplemented with a higher nutritive quality diet such as moringa leaves, formulated as a fermented complete feed to increase its low digestibility. The purpose of this study was to evaluate in vitro digestibility of fermented complete feed based on rice straw with moringa leaves addition. Complete feed was formulated based on 40% rice straw, mixed with other ingredients, and then fermented with Suplemen Organik Cair (SOC). This study was designed by a completely randomized design (CRD) consisting of 4 treatments, P0 (control without moringa leaves), P1 (addition of 10% moringa leaves), P2 (addition of 20% moringa leaves), and P3 (addition of 30% moringa leaves) with 3 replications in each treatment. Parameters measured in this study were in vitro pH value, dry matter digestibility (IVDMD), organic matter digestibility (IVOMD), total VFA, and methane production. The result indicated that different levels of moringa leave addition into a fermented complete feed based on rice straw had significant effects (P<0,01) on in vitro pH value, IVDMD, IVOMD, and total VFA. However, all treatments did not significantly decrease methane production (P>0,05). It was concluded that the addition of moringa leaves into a fermented complete feed based on rice straw effectively increases rumen fermentation.
A review of climate change studies on paddy agriculture in Indonesia
Authors: Ikhwali M F , Nur S , Darmansyah D , Hamdan A M , Ersa N S , Aida N , Yusra A , Satria A
Published: December 2022

Indonesia is often referred to as an agricultural country as most of its population is working in agricultural sectors. Rice is one of the staple foods of the Indonesian people. The issues concerning the global climate change impose a potential threat on Indonesia’s food security as the rice crop is extremely sensitive to climate change. The IPCC has released climate change scenarios as highlighted in Fifth Assessment Report (AR5) that could contribute positively to projecting the possible condition of future rice farming in Indonesia. Therefore, the goal of this research is to examine how far the Representative Concentration Pathway (RCP) scenarios have been implemented in relevant studies relating the rice farming. By 2021, the RCP scenarios in Indonesia at least have been studied and used in 13 relevant publications. The type of scenario used is mostly dominated by RCP8.5 scenario which is accounted used by 11 publications. Basically, the RCP8.5 is a scenario that projects the climate change with minimal efforts in reducing the emissions and expose the failures to tackle the global warming by 2100. Based on the findings of those research, it is possible to assume that the rice farming in Indonesia is going to face enormous challenges, particularly the potential decline in rice productivity. The emergence of those studies that interrelate the rice farming and climate change definitely will provide the initial footsteps to figure out on how to deal with future weather conditions.
Agricultural waste from crop production as an energy resource
Authors: Andreenko T I , Kiseleva S V , Rafikova Yu Yu
Published: December 2022

In recent years, crop waste has become a promising energy resource in many countries of the world. For Russia, the use of this type of waste for energy purposes is not only an opportunity to provide energy to the population, but also a solution to a number of environmental problems - reducing the risk of forest fires and CO2 emissions. The paper presents the results of an assessment of the energy potential of grain waste within the boundaries of the municipalities of the Rostov region. The gross and technical potential of grain waste (straw), calculated according to the author’s methods, are correlated with the needs of the population of the studied region in thermal energy. The results obtained show a significant amount of technical heat potential for many municipalities of the region. The spatial distribution obtained with the help of geoinformation technologies makes it possible to determine the most promising areas for the use of grain waste for the production of thermal energy. The paper also assessed the prospects for replacing traditional fuels such as coal, diesel fuel, natural gas and fuel oil with energy from straw. The possible environmental effect from the replacement of hydrocarbon fuel for the municipal districts of the Rostov region of the Russian Federation is calculated.
The potential of dewaka banana stems as raw materials for bioethanol
Authors: Suryaningsih N L S , Mursalim  , Laga A , Natsir H
Published: December 2022

Increasing production and consumption of fossil fuels encourage the use of renewable energy. Renewable energy that does not have the potential to disrupt the stability of the availability of other materials is the use of waste. One type of waste that has been researched into bioethanol is banana waste in the form of stems, leaves, skins, and weevil. Dewaka banana is one type of banana that grows in Merauke, has a large enough size so that it has the potential to produce a lot of waste and tastes sour. Dewaka banana production in 2019 was 7,087 tons and produced waste in the form of Dewaka banana stems as much as 28,546.96 tons. The water content of Dewaka banana stems is 93.42%, and taking into account the yield loss of ± 10%, there will be 1,690.55 tons of dry waste. The amount of waste can produce 148,092.27 liters of bioethanol in a year based on the best research results from Roni, et al. Dewaka banana stems can be processed and reused into bioethanol as an alternative energy raw material.
bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data
Authors: Moutsopoulos Ilias , Williams Eleanor C , Mohorianu Irina I
Published: December 2022

Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.
Bayesian semiparametric Markov renewal mixed models for vocalization syntax
Authors: Wu Yutong , Jarvis Erich D , Sarkar Abhra
Published: December 2022

Speech and language play an important role in human vocal communication. Studies have shown that vocal disorders can result from genetic factors. In the absence of high-quality data on humans, mouse vocalization experiments in laboratory settings have been proven useful in providing valuable insights into mammalian vocal development, including especially the impact of certain genetic mutations. Such data sets usually consist of categorical syllable sequences along with continuous intersyllable interval (ISI) times for mice of different genotypes vocalizing under different contexts. ISIs are of particular importance as increased ISIs can be an indication of possible vocal impairment. Statistical methods for properly analyzing ISIs along with the transition probabilities have however been lacking. In this article, we propose a class of novel Markov renewal mixed models that capture the stochastic dynamics of both state transitions and ISI lengths. Specifically, we model the transition dynamics and the ISIs using Dirichlet and gamma mixtures, respectively, allowing the mixture probabilities in both cases to vary flexibly with fixed covariate effects as well as random individual-specific effects. We apply our model to analyze the impact of a mutation in the Foxp2 gene on mouse vocal behavior. We find that genotypes and social contexts significantly affect the length of ISIs but, compared to previous analyses, the influences of genotype and social context on the syllable transition dynamics are weaker.
The role of network topological structure and semantic features in creating verbal aggression
Authors: Abarghouei Nejad Meghdad , Abarghouei Nejad Salman , Memariani Azizollah , Asadpour Masoud , Hatami Javad , Kashani Mohammad Mahdi
Published: December 2022

In this article, we studied the role of the topological structure of semantic networking in creating verbal aggression. It is shown that centralities such as degree, betweenness and closeness play an important role in the activation of verbal aggression in the network. We have also shown that aggressive labelled nodes with spectral clustering in different spectra are often divided into two groups, with the larger group activating more aggressive labelled nodes. In addition, the parameter of eccentric distribution from the origin is introduced to study the dispersion of aggressive nodes around the specific nodes. Hence, studying two networks with different contexts shows that the dispersion of nodes with aggressive labelling around the network’s hub, as the centre of the network with political context, is much more than artistic context. In addition, different clusters of verbal aggression in the political and artistic context have the same pattern of frequency. In addition, we investigated semantic features in creating verbal aggression, showing that non-aggressive words are prone to create verbal aggression as much as aggressive words.
Endocrine functions of the heart: from bench to bedside
Authors: Volpe Massimo , Gallo Giovanna , Rubattu Speranza
Published: December 2022

Heart has a recognized endocrine function as it produces several biologically active substances with hormonal properties. Among these hormones, the natriuretic peptide (NP) system has been extensively characterized and represents a prominent expression of the endocrine function of the heart. Over the years, knowledge about the mechanisms governing their synthesis, secretion, processing, and receptors interaction of NPs has been intensively investigated. Their main physiological endocrine and paracrine effects on cardiovascular and renal systems are mostly mediated through guanylate cyclase-A coupled receptors. The potential role of NPs in the pathophysiology of heart failure and particularly their counterbalancing action opposing the overactivation of renin-angiotensin-aldosterone and sympathetic nervous systems has been described. In addition, NPs are used today as key biomarkers in cardiovascular diseases with both diagnostic and prognostic significance. On these premises, multiple therapeutic strategies based on the biological properties of NPs have been attempted to develop new cardiovascular therapies. Apart from the introduction of the class of angiotensin receptor/neprilysin inhibitors in the current management of heart failure, novel promising molecules, including M-atrial natriuretic peptide (a novel atrial NP-based compound), have been tested for the treatment of human hypertension. The development of new drugs is currently underway, and we are probably only at the dawn of novel NPs-based therapeutic strategies. The present article also provides an updated overview of the regulation of NPs synthesis and secretion by microRNAs and epigenetics as well as interactions of cardiac hormones with other endocrine systems.
Genetic causes of heart failure with preserved ejection fraction: emerging pharmacological treatments
Authors: Olivotto Iacopo , Udelson James E , Pieroni Maurizio , Rapezzi Claudio
Published: December 2022

Heart failure with preserved ejection fraction (HFpEF) is a major driver of cardiac morbidity and mortality in developed countries, due to ageing populations and the increasing prevalence of comorbidities. While heart failure with reduced ejection fraction is dominated by left ventricular impairment, HFpEF results from a complex interplay of cardiac remodelling, peripheral circulation, and concomitant features including age, hypertension, obesity, and diabetes. In an important subset, however, HFpEF is subtended by specific diseases of the myocardium that are genetically determined, have distinct pathophysiology, and are increasingly amenable to targeted, innovative treatments. While each of these conditions is rare, they collectively represent a relevant subset within HFpEF cohorts, and their prompt recognition has major consequences for clinical practice, as access to dedicated, disease-specific treatments may radically change the quality of life and outcome. Furthermore, response to standard heart failure treatment will generally be modest for these individuals, whose inclusion in registries and trials may dilute the perceived efficacy of treatments targeting mainstream HFpEF. Finally, a better understanding of the molecular underpinnings of monogenic myocardial disease may help identify therapeutic targets and develop innovative treatments for selected HFpEF phenotypes of broader epidemiological relevance. The field of genetic cardiomyopathies is undergoing rapid transformation due to recent, groundbreaking advances in drug development, and deserves greater awareness within the heart failure community. The present review addressed existing and developing therapies for genetic causes of HFpEF, including hypertrophic cardiomyopathy, cardiac amyloidosis, and storage diseases, discussing their potential impact on management and their broader implications for our understanding of HFpEF at large.
1-Methylcyclopropene retards pak choi (Brassica rapasubsp. chinensis) yellowing via BcNAC055-, BcMYB44-, and BcOBF1-mediated regulation of the key chlorophyll degrading geneBcNYC1during storage at 20 °C
Authors: Song Liuli , Wang Junping , Yu Haitao , Yu Zhifang
Published: December 2022

The objective of this study was to investigate the molecular regulatory mechanism of 1-methylcyclopropene (1-MCP) treatment on leaf yellowing of pak choi during storage at 20 °C. In the present study, compared with the control and 10 μL/L ethylene-treated pak choi, 5.0 μL/L 1-MCP fumigation alleviated the yellowing process of pak choi as proved by the maintenance of higher levels of colour, chlorophyll content, and appearance. 1-MCP treatment decreased chlorophyll breakdown by downregulating the activity of chlorophyll-degrading enzymes (chlorophyll b reductase (CBR) and pheophytinase (PPH)) and the expression of their related genes (BcNYC1 and BcPPH). The application of 1-MCP also inhibited the transcript abundance of ethylene biosynthesis and signal transduction genes (BcACO, BcEIN3, and BcERF) and reduced ethylene production, thus helping to maintain the green colour of pak choi; however, ethylene treatment exerted the opposite function. Meanwhile, three transcription factors (BcNAC055, BcMYB44, and BcOBF1) were successfully cloned. Experiments performed using yeast one-hybrid assay, dual-luciferase reporter system and in vivo bioluminescence imaging assay, confirmed that BcNAC055, BcMYB44, and BcOBF1 directly bound to the BcNYC1 promoter. 1-MCP inhibited the expression levels of BcNAC055, BcMYB44, BcOBF1, and BcNYC1 during storage, while the application of ethylene activated their expression. In conclusion, 1-MCP downregulated the expression of the key chlorophyll degradation gene BcNYC1 by inhibiting the transcript level of its three positive regulators (BcNAC055, BcMYB44, and BcOBF1) and lowered the activity of chlorophyll-degrading enzyme CBR, thereby helping mitigate chlorophyll breakdown to retard leaf yellowing in pak choi. The results of this work extend our understanding of 1-MCP-delayed yellowing in postharvest pak choi.
Comparing Transgenic Production to Supplementation of ω-3 PUFA Reveals Distinct But Overlapping Mechanisms Underlying Protection Against Metabolic and Hepatic Disorders
Authors: Daniel Noëmie , Le Barz Mélanie , Mitchell Patricia L , Varin Thibault V , Julien Isabelle Bourdeau , Farabos Dominique , Pilon Geneviève , Gauthier Josée , Garofalo Carole , Kang Jing X , Trottier Jocelyn , Barbier Olivier , Roy Denis , Chassaing Benoit , Levy Emile , Raymond Frédéric , Lamaziere Antonin , Flamand Nicolas , Silvestri Cristoforo , Jobin Christian , Di Marzo Vincenzo , Marette André
Published: December 2022

We compared endogenous ω-3 PUFA production to supplementation for improving obesity-related metabolic dysfunction. Fat-1 transgenic mice, who endogenously convert exogenous ω-6 to ω-3 PUFA, and wild-type littermates were fed a high-fat diet and a daily dose of either ω-3 or ω-6 PUFA-rich oil for 12 wk. The endogenous ω-3 PUFA production improved glucose intolerance and insulin resistance but not hepatic steatosis. Conversely, ω-3 PUFA supplementation fully prevented hepatic steatosis but failed to improve insulin resistance. Both models increased hepatic levels of ω-3 PUFA-containing 2-monoacylglycerol and N-acylethanolamine congeners, and reduced levels of ω-6 PUFA-derived endocannabinoids with ω-3 PUFA supplementation being more efficacious. Reduced hepatic lipid accumulation associated with the endocannabinoidome metabolites EPEA and DHEA, which was causally demonstrated by lower lipid accumulation in oleic acid-treated hepatic cells treated with these metabolites. While both models induced a significant fecal enrichment of the beneficial Allobaculum genus, mice supplemented with ω-3 PUFA displayed additional changes in the gut microbiota functions with a significant reduction of fecal levels of the proinflammatory molecules lipopolysaccharide and flagellin. Multiple-factor analysis identify that the metabolic improvements induced by ω-3 PUFAs were accompanied by a reduced production of the proinflammatory cytokine TNFα, and that ω-3 PUFA supplementation had a stronger effect on improving the hepatic fatty acid profile than endogenous ω-3 PUFA. While endogenous ω-3 PUFA production preferably improves glucose tolerance and insulin resistance, ω-3 PUFA intake appears to be required to elicit selective changes in hepatic endocannabinoidome signaling that are essential to alleviate high-fat diet-induced hepatic steatosis.
Spatial change in differential stress magnitudes around the source fault before intraplate earthquakes
Authors: Iio Yoshihisa , Matsumoto Satoshi , Yamashita Yusuke , Sakai Shin'ichi , Tomisaka Kazuhide , Sawada Masayo , Iidaka Takashi , Iwasaki Takaya , Kamizono Megumi , Katao Hiroshi , Kato Aitaro , Kurashimo Eiji , Teguri Yoshiko , Tsuda Hiroo , Ueno Takashi
Published: December 2022

How are the sizes of the earthquakes determined? To solve this important problem, we analysed the data from a dense temporary seismic observation network installed in the aftershock area of the 2016 Mw 6.2 Central Tottori earthquake, which occurred in an intraplate region in Japan. We compared the stress field estimated from approximately 10 000 accurate focal mechanisms of aftershocks with the calculated post-earthquake stress field and found that the differential stress before the earthquake was very small near both horizontal edges. These results did not depend significantly on the modeled slip distribution and the orientation of the principal stress before the earthquake. Similar results were obtained for the 2000 Mw 6.7 Western Tottori earthquake, which also occurred in the same intraplate region in Japan. These results suggest that the fault size of large intraplate earthquakes can be determined by the region of small differential stress surrounding future earthquake faults.
Seismic tremor location of 10 large paroxysmal eruptions of Tungurahua volcano, Ecuador
Authors: Palacios Pablo B , Mader Heidy M , Kendall J-Michael , Yepes Hugo A
Published: December 2022

The most recent eruptive period of Tungurahua volcano lasted 17 yr (1999–2016), generating strong eruptive phases with the release of large amounts of seismic and acoustic energies. We have selected 10 large eruptions and located their seismic sources. The location method involves applying a new method for correcting for site effects in the seismic records and identifying, in the frequency domain, the signals from the ground-coupled airwaves and pyroclastic flows. The locations are computed by minimizing the differences of the source energy rates in the [0.4, 2.5] Hz range. The results suggest that the first three eruptions have locations mainly concentrated at the [−1, 2] km depth range (asl), and the locations of the fourth eruption are mainly coincident with depths of a possible reservoir estimated from petrological studies. This fact strongly suggests that this eruption was responsible of changes in the dynamics of Tungurahua, making the volcano prone to produce Vulcanian eruptions.
Citrusβ-carotene hydroxylase 2 (BCH2) participates in xanthophyll synthesis by catalyzing the hydroxylation ofβ-carotene and compensates for BCH1 in citrus carotenoid metabolism
Authors: Zhang Yingzi , Jin Jiajing , Zhu Shenchao , Sun Quan , Zhang Yin , Xie Zongzhou , Ye Junli , Deng Xiuxin
Published: December 2022

As an essential horticultural crop, Citrus has carotenoid diversity, which affects its aesthetic and nutritional values. β,β-Xanthophylls are the primary carotenoids accumulated in citrus fruits, and non-heme di-iron carotene hydroxylase (BCH) enzymes are mainly responsible for β,β-xanthophyll synthesis. Previous studies have focused on the hydroxylation of BCH1, but the role of its paralogous gene in citrus, BCH2, remains largely unknown. In this study, we revealed the β-hydroxylation activity of citrus BCH2 (CsBCH2) for the first time through the functional complementation assay using Escherichia coli, although CsBCH2 exhibited a lower activity in hydroxylating β-carotene into β-cryptoxanthin than citrus BCH1 (CsBCH1). Our results showed that overexpression of CsBCH2 in citrus callus increased xanthophyll proportion and plastoglobule size with feedback regulation of carotenogenic gene expression. This study revealed the distinct expression patterns and functional characteristics of two paralogous genes, CsBCH1 and CsBCH2, and illustrated the backup compensatory role of CsBCH2 for CsBCH1 in citrus xanthophyll biosynthesis. The independent function of CsBCH2 and its cooperative function with CsBCH1 in β-cryptoxanthin biosynthesis suggested the potential of CsBCH2 to be employed for expanding the synthetic biology toolkit in carotenoid engineering.
On the robustness to adversarial corruption and to heavy-tailed data of the Stahel–Donoho median of means
Authors: Depersin Jules , Lecué Guillaume
Published: December 2022

We consider median of means (MOM) versions of the Stahel–Donoho outlyingness (SDO) [ 23, 66] and of the Median Absolute Deviation (MAD) [ 30] functions to construct subgaussian estimators of a mean vector under adversarial contamination and heavy-tailed data. We develop a single analysis of the MOM version of the SDO which covers all cases ranging from the Gaussian case to the $L_2$ case. It is based on isomorphic and almost isometric properties of the MOM versions of SDO and MAD. This analysis also covers cases where the mean does not even exist but a location parameter does; in those cases we still recover the same subgaussian rates and the same price for adversarial contamination even though there is not even a first moment. These properties are achieved by the classical SDO median and are therefore the first non-asymptotic statistical bounds on the Stahel–Donoho median complementing the $\sqrt{n}$-consistency [ 58] and asymptotic normality [ 74] of the Stahel–Donoho estimators. We also show that the MOM version of MAD can be used to construct an estimator of the covariance matrix only under the existence of a second moment or of a scatter matrix if a second moment does not exist.
Preparing for Colonoscopy in People with Diabetes: A Review with Suggestions for Clinical Practice
Authors: Chirila Alexandra , Nguyen Mary E , Tinmouth Jill , Halperin Ilana J
Published: December 2022

People with diabetes have an increased risk of adverse events during the peri-colonoscopy period, including hypoglycemia, lactic acidosis, diabetic ketoacidosis and acute kidney injury. This is secondary to inadequate dietary modification, the bowel preparation and antihyperglycemic agent modification. With the availability of many new diabetes agents, endoscopists need updated guidance. This review of current literature provides a practical approach to antihyperglycemic agent modification in the context of colonoscopy preparation, as well as guidelines on dietary changes, the bowel preparation itself and glucose monitoring.
Survival in male breast cancer over the past 3 decades
Authors: Leone José P , Freedman Rachel A , Leone Julieta , Tolaney Sara M , Vallejo Carlos T , Leone Bernardo A , Winer Eric P , Lin Nancy U , Hassett Michael J
Published: December 2022

Background

Breast cancer mortality in women has declined statistically significantly over the past several years. In men, it is unclear whether survival has changed over time. We evaluated changes in breast cancer–specific survival (BCSS) and overall survival (OS) in male breast cancer over the past 3 decades.

Methods

We evaluated men diagnosed with breast cancer between 1988 and 2017, reported in the Surveillance, Epidemiology, and End Results registry. Patients were categorized into 3 groups by year of diagnosis: 1988-1997, 1998-2007, and 2008-2017. BCSS and OS were estimated by Kaplan-Meier, and differences between groups were compared by log-rank test. Multivariable Cox regression evaluated the independent association of year of diagnosis with BCSS and OS. All tests were 2-sided.

Results

We included 8481 men. Overall, BCSS at 5 years was 83.69%, 83.78%, and 84.41% in groups 1988-1997, 1998-2007, and 2008-2017, respectively (P = .86). There was no statistically significant difference in BCSS between the 3 groups within each stage of disease. Among all patients, OS at 5 years was 64.61%, 67.31%, and 69.05% in groups 1988-1997, 1998-2007, and 2008-2017, respectively (P = .01). In adjusted Cox models, each additional year of diagnosis had no statistically significant association with BCSS (hazard ratio = 1.00, 95% confidence interval = 0.99 to 1.01, P = .75), but there was statistically significant improvement in OS (hazard ratio = 0.99, 95% CI = 0.98 to 0.99, P = .009).

Conclusions

Over the past 3 decades, there has been no statistically significant improvement in BCSS in male breast cancer. Changes in OS over time are consistent with increasing life expectancy. Efforts to improve BCSS in male breast cancer are warranted.
Particle acceleration in shearing flows: the self-generation of turbulent spine-sheath structures in relativistic magnetohydrodynamic jet simulations
Authors: Wang Jie-Shuang , Reville Brian , Mizuno Yosuke , Rieger Frank M , Aharonian Felix A
Published: December 2022

X-ray observations of kiloparsec-scale extragalactic jets favour a synchrotron origin. The short cooling times of the emitting electrons require a distributed acceleration of electrons up to sub-PeV energies. In a previous paper, we found that this can be self-consistently explained by a shear acceleration model, where particles are accelerated to produce power-law spectra, with the spectral index being determined mainly by the velocity profile and turbulence spectrum. In this paper, we perform 3D relativistic magnetohydrodynamic simulations to investigate the formation of a spine-sheath structure and the development of turbulence for a relativistic jet propagating into a static cocoon. We explore different spine velocities and magnetic field profiles, with values being chosen to match typical Fanaroff–Riley type I/II jets. We find that in all cases a sheath is generated on the interface of the spine and the cocoon mainly as a result of the Kelvin–Helmholtz instability. The large-scale velocity profile in the sheath is close to linear. Turbulence develops in both the spine and the sheath, with a turbulent velocity spectrum consistent with Kolmogorov scaling. The implications for shear particle acceleration are explored, with a focus on the particle spectral index.
Improved radius determinations for the transiting brown dwarf population in the era of Gaia and TESS
Authors: Carmichael Theron W
Published: December 2022

I report updates to the substellar mass–radius diagram for 11 transiting brown dwarfs (BDs) and low-mass stars published before the third data release from the Gaia mission (Gaia DR3). I re-analyse these transiting BD systems whose physical parameters were published between 2008 and 2019 and find that when using the parallax measurements from Gaia DR3, seven BDs show significant differences in their radius estimate or an improvement in the radius uncertainty. This has important implications for how these BDs are used to test substellar evolutionary models in the mass–radius diagram. The remaining four BDs show mass–radius estimates that are consistent with their previous pre-Gaia DR3 measurements. The seven BDs that show significant deviation from the original mass–radius measurements are AD 3116b, CoRoT-3b, CoRoT-15b, EPIC 201702477b, Kepler-39b, KOI-205b, and KOI-415b. Of these, AD 3116b is a known member of the Praesepe cluster at an age of 600 Myr. Additionally, some of the previously smallest known transiting BDs, KOI-205b and KOI-415b, are not as small as once thought, leaving the mass–radius region for the very oldest BDs relatively sparse as a result of this work.
Tracer-field cross-correlations with k-nearest neighbour distributions
Authors: Banerjee Arka , Abel Tom
Published: December 2022

In astronomy and cosmology significant effort is devoted to characterizing and understanding spatial cross-correlations between points – e.g galaxy positions, high energy neutrino arrival directions, X-ray and AGN sources, and continuous fields – e.g. weak lensing meiand Cosmic Microwave Background maps. Recently, we introduced the k-nearest neighbour (kNN) formalism to better characterize the clustering of discrete (point) data sets. Here, we extend it to the point – field cross-correlations analysis. It combines kNN measurements of the point data set with measurements of the field smoothed at many scales. The resulting statistics are sensitive to all orders in the joint clustering of the points and the field. We demonstrate that this approach, unlike the 2-pt cross-correlation, can measure the statistical dependence of two data sets even when there are no linear (Gaussian) correlations between them. We further demonstrate that this framework is far more effective than the two point function in detecting cross-correlations when the continuous field is contaminated by high levels of noise. For a particularly high level of noise, the cross-correlation between haloes and the underlying matter field in a cosmological simulation, between 10 h−1 Mpc and 30 h−1 Mpc, is detected at >5σ significance using the technique presented here, when the two-point cross-correlation significance is ∼1σ. Finally, we show that kNN cross-correlations of haloes and the matter field can be well modelled on quasi-linear scales using the Hybrid Effective Field Theory (HEFT) framework, with the same set of bias parameters as are used for 2-pt cross-correlations. The substantial improvement in the statistical power of detecting cross-correlations using this method makes it a promising tool for various cosmological applications.
The interaction between transport-segment DNA and topoisomerase IA—crystal structure of MtbTOP1 in complex with both G- and T-segments
Authors: Ferdous Shomita , Dasgupta Tumpa , Annamalai Thirunavukkarasu , Tan Kemin , Tse-Dinh Yuk-Ching
Published: December 2022

Each catalytic cycle of type IA topoisomerases has been proposed to comprise multistep reactions. The capture of the transport-segment DNA (T-segment) into the central cavity of the N-terminal toroidal structure is an important action, which is preceded by transient gate-segment (G-segment) cleavage and succeeded by G-segment religation for the relaxation of negatively supercoiled DNA and decatenation of DNA. The T-segment passage in and out of the central cavity requires significant domain–domain rearrangements, including the movement of D3 relative to D1 and D4 for the opening and closing of the gate towards the central cavity. Here we report a direct observation of the interaction of a duplex DNA in the central cavity of a type IA topoisomerase and its associated domain–domain conformational changes in a crystal structure of a Mycobacterium tuberculosis topoisomerase I complex that also has a bound G-segment. The duplex DNA within the central cavity illustrates the non-sequence-specific interplay between the T-segment DNA and the enzyme. The rich structural information revealed from the novel topoisomerase–DNA complex, in combination with targeted mutagenesis studies, provides new insights into the mechanism of the topoisomerase IA catalytic cycle.
Polyribosomes of circular topology are prevalent in mammalian cells
Authors: Baymukhametov Timur N , Lyabin Dmitry N , Chesnokov Yury M , Sorokin Ivan I , Pechnikova Evgeniya V , Vasiliev Alexander L , Afonina Zhanna A
Published: December 2022

Polyribosomes, the groups of ribosomes simultaneously translating a single mRNA molecule, are very common in both, prokaryotic and eukaryotic cells. Even in early EM studies, polyribosomes have been shown to possess various spatial conformations, including a ring-shaped configuration which was considered to be functionally important. However, a recent in situ cryo-ET analysis of predominant regular inter-ribosome contacts did not confirm the abundance of ring-shaped polyribosomes in a cell cytoplasm. To address this discrepancy, here we analyzed the cryo-ET structure of polyribosomes in diluted lysates of HeLa cells. It was shown that the vast majority of the ribosomes were combined into polysomes and were proven to be translationally active. Tomogram analysis revealed that circular polyribosomes are indeed very common in the cytoplasm, but they mostly possess pseudo-regular structures without specific inter-ribosomal contacts. Although the size of polyribosomes varied widely, most circular polysomes were relatively small in size (4–8 ribosomes). Our results confirm the recent data that it is cellular mRNAs with short ORF that most commonly form circular structures providing an enhancement of translation.
High-throughput quantitative binding analysis of DNA aptamers using exonucleases
Authors: Canoura Juan , Alkhamis Obtin , Liu Yingzhu , Willis Connor , Xiao Yi
Published: December 2022

Aptamers are nucleic acid bioreceptors that have been used in various applications including medical diagnostics and as therapeutic agents. Identifying the most optimal aptamer for a particular application is very challenging. Here, we for the first time have developed a high-throughput method for accurately quantifying aptamer binding affinity, specificity, and cross-reactivity via the kinetics of aptamer digestion by exonucleases. We demonstrate the utility of this approach by isolating a set of new aptamers for fentanyl and its analogs, and then characterizing the binding properties of 655 aptamer–ligand pairs using our exonuclease digestion assay and validating the results with gold-standard methodologies. These data were used to select optimal aptamers for the development of new sensors that detect fentanyl and its analogs in different analytical contexts. Our approach dramatically accelerates the aptamer characterization process and streamlines sensor development, and if coupled with robotics, could enable high-throughput quantitative analysis of thousands of aptamer–ligand pairs.
Microbiota-Based Live Biotherapeutic RBX2660 for the Reduction of Recurrent Clostridioides difficile Infection in Older Adults With Underlying Comorbidities
Authors: Tillotson Glenn , Archbald-Pannone Laurie , Johnson Stuart , Ng Samson , Ando Masakazu , Harvey Adam , Bancke Lindy , Feuerstadt Paul
Published: December 2022

Background

Advanced age and underlying comorbidities are associated with greater rates of recurrence in patients with Clostridioides difficile infection (CDI). Reducing the likelihood of recurrence through treatment with an antimicrobial followed by a microbiota replacement therapy can decrease the burden of this infection and improve patient outcomes. We report the efficacy and safety of RBX2660, a microbiota-based live biotherapeutic, in older adults with recurrent CDI, grouped by comorbidities.

Methods

In this post hoc subgroup analysis of the PUNCH CD3 trial, we assessed outcomes in older adults (age ≥65 years) grouped by Charlson Comorbidity Index severity scores at screening (moderate [3–4] and severe [≥5]) and by the presence of underlying cardiac, renal, or gastrointestinal disorders.

Results

RBX2660 treatment success rates in older adults with comorbidities were consistent across subgroups and similar to those in the total RBX2660-treated population. A greater percentage of RBX2660-treated older adults remained free of CDI recurrence through 8 weeks following treatment compared with placebo-treated participants in all but 2 subgroups assessed. Across all subgroups, most treatment-emergent adverse events (TEAEs) were mild or moderate in severity and related to a preexisting condition. None of the serious or life-threatening TEAEs that occurred were related to RBX2660 or its administration. Occurrence of TEAEs did not cluster in any subgroup.

Conclusions

RBX2660 is efficacious and safe in older adults with recurrent CDI and underlying comorbidities.
Detangling the Structural Neural Correlates Associated with Resting versus Dynamic Phantom Limb Pain Intensity Using a Voxel-based Morphometry Analysis
Authors: Pinto Camila B , Pacheco-Barrios Kevin , Saleh Velez Faddi G , Gunduz Muhammed E , Münger Marionna , Fregni Felipe
Published: December 2022

The management of phantom limb pain (PLP) is still challenging due to a partial understanding of its neurophysiological mechanisms. Structural neuroimaging features are potential biomarkers. However, only a few studies assessed their correlations with clinical severity and treatment response. This study aims to explore the association between brain gray matter volume (GMV) with phantom limb manifestations severity and PLP improvement after neuromodulatory treatments (transcranial direct current stimulation and mirror therapy). Voxel-based morphometry analyses and functional decoding using a reverse inference term-based meta-analytic approach were used. We included 24 lower limb traumatic amputees with moderate to severe PLP. We found that alterations of cortical GMV were correlated with PLP severity but not with other clinical manifestations. Less PLP severity was associated with larger brain clusters GMV in the non-affected prefrontal, insula (non-affected mid-anterior region), and bilateral thalamus. However, only the insula cluster survived adjustments. Moreover, the reverse inference meta-analytic approach revealed that the found insula cluster is highly functionally connected to the contralateral insula and premotor cortices, and the decoded psychological processes related to this cluster were “rating,” “sustained attention,” “impulsivity, ” and “suffering.” Moreover, we found that responders to neuromodulatory treatment have higher GMV in somatosensory areas (total volume of S1 and S2) in the affected hemisphere at baseline, compared to non-responders, even after adjustments.
Effects of providing sensory attractants to suckling pigs during lactation and after weaning on post-weaning growth performance
Authors: Wensley Madie R , Tokach Mike D , Woodworth Jason C , Goodband Robert D , DeRouchey Joel M , Gebhardt Jordan T , McKilligan Denny , Upah Nathan
Published: December 2022

Three experiments were conducted to determine the effect of sensory attractants pre- and post-weaning on the growth performance of pigs after weaning. For each experiment, treatments were arranged as a 2 × 2 × 2 factorial with main effects of pre-weaning application (without or with), post-weaning application (without or with), and body weight category (representing the lightest or heaviest 50% of the population). In Exp. 1, 356 nursery pigs (initially 5.7 kg) were used in a 28-d trial with enrichment cubes used as the sensory attractant. A greater percentage of heavy pigs (P = 0.007) or pigs offered enrichment cubes pre-weaning (P = 0.044) lost BW from weaning to d 3 compared to light pigs or pigs not offered enrichment cubes pre-weaning. From weaning to d 7, a greater percentage of pigs lost weight when not offered cubes post-weaning (P = 0.002) compared to pigs offered cubes post-weaning. In Exp. 2, 355 nursery pigs (initially 5.6 kg) were used in a 29-d trial with a powder used as the sensory attractant. Providing a powder attractant both pre- and post-weaning reduced the percentage of pigs that lost weight from weaning to d 3 as compared with providing a powder either pre- or post-weaning only (interaction, P < 0.05). In Exp. 3, 355 nursery pigs (initially 5.9 kg) were used in a 24-d trial with a liquid spray used as the sensory attractant. A greater percentage of heavy pigs that did not receive liquid attractant lost weight from weaning to d 3, whereas a greater percentage of light pigs lost weight when they received liquid attractant only pre-weaning (three-way interaction; P = 0.016). Across all three experiments, sensory attractant application had limited effects on the growth performance of pigs after weaning; however, varying responses were observed for the percentage of pigs that lost weight in the first 3 to 7 d immediately post-weaning. In summary, environmental enrichment with cubes (Exp. 1) appears to have the greatest effect when applied post-weaning whereas flavor attractants (Exp. 2 and 3) appear to have the greatest effect when applied both pre- and post-weaning.
Periostin increased by mechanical stress upregulates interleukin‐6 expression in the ligamentum flavum
Authors: Yabu Akito , Suzuki Akinobu , Hayashi Kazunori , Hori Yusuke , Terai Hidetomi , Orita Kumi , Habibi Hasibullah , Salimi Hamidullah , Kono Hiroshi , Toyoda Hiromitsu , Maeno Takafumi , Takahashi Shinji , Tamai Koji , Ozaki Tomonori , Iwamae Masayoshi , Ohyama Shoichiro , Imai Yuuki , Nakamura Hiroaki
Published: December 2022

Ligamentum flavum (LF) hypertrophy is a major cause of lumbar spinal canal stenosis. Although mechanical stress is thought to be a major factor involved in LF hypertrophy, the exact mechanism by which it causes hypertrophy has not yet been fully elucidated. Here, changes in gene expression due to long‐term mechanical stress were analyzed using RNA‐seq in a rabbit LF hypertrophy model. In combination with previously reported analysis results, periostin was identified as a molecule whose expression fluctuates due to mechanical stress. The expression and function of periostin were further investigated using human LF tissues and primary LF cell cultures. Periostin was abundantly expressed in human hypertrophied LF tissues, and periostin gene expression was significantly correlated with LF thickness. In vitro, mechanical stress increased gene expressions of periostin, transforming growth factor‐β1, α‐smooth muscle actin, collagen type 1 alpha 1, and interleukin‐6 (IL‐6) in LF cells. Periostin blockade suppressed the mechanical stress‐induced gene expression of IL‐6 while periostin treatment increased IL‐6 gene expression. Our results suggest that periostin is upregulated by mechanical stress and promotes inflammation by upregulating IL‐6 expression, which leads to LF degeneration and hypertrophy. Periostin may be a pivotal molecule for LF hypertrophy and a promising therapeutic target for lumbar spinal stenosis.