bluuebunny/crossref_metadata_2025_split huggingface dataset:
R-SNARE protein YKT61 mediates root apical meristem cell division via BRASSINOSTEROID-INSENSITIVE1 recycling
Authors: Ma Ting , Tan Jun-Ru , Zhang Yan , Li Sha 
Published: December 2023

AbstractRoot growth is sustained by cell division and differentiation of the root apical meristem (RAM), in which brassinosteroid (BR) signaling mediated via the dynamic targeting of BRASSINOSTEROID-INSENSITIVE1 (BRI1) plays complex roles. BRI1 is constitutively secreted to the plasma membrane (PM), internalized, and recycled or delivered into vacuoles, whose PM abundance is critical for BR signaling. Vesicle–target membrane fusion is regulated by heterotetrameric SNARE complexes. SNARE proteins have been implicated in BRI1 targeting, but how SNAREs affect RAM development is unclear. We report that Arabidopsis (Arabidopsis thaliana) YKT61, an atypical R-SNARE protein, is critical for BR-controlled RAM development through the dynamic targeting of BRI1. Functional loss of YKT61 is lethal for both male and female gametophytes. By using weak mutant alleles of YKT61, ykt61-partially complemented (ykt61-pc), we show that YKT61 knockdown results in a reduction of RAM length due to reduced cell division, similar to that in bri1-116. YKT61 physically interacts with BRI1 and is critical for the dynamic recycling of BRI1 to the PM. We further determine that YKT61 is critical for the dynamic biogenesis of vacuoles, for the maintenance of Golgi morphology, and for endocytosis, which may have a broad effect on development. Endomembrane compartments connected via vesicular machinery, such as SNAREs, influence nuclear-controlled cellular activities such as division and differentiation by affecting the dynamic targeting of membrane proteins, supporting a retro-signaling pathway from the endomembrane system to the nucleus.
Oomycete pathogen pectin acetylesterase targets host lipid transfer protein to reduce salicylic acid signaling
Authors: Situ Junjian , Song Yu , Feng Dinan , Wan Lang , Li Wen , Ning Yue , Huang Weixiong , Li Minhui , Xi Pinggen , Deng Yizhen , Jiang Zide , Kong Guanghui 
Published: December 2023

Abstract
During initial stages of microbial invasion, the extracellular space (apoplast) of plant cells is a vital battleground between plants and pathogens. The oomycete plant pathogens secrete an array of apoplastic carbohydrate active enzymes, which are central molecules for understanding the complex plant–oomycete interactions. Among them, pectin acetylesterase (PAE) plays a critical role in the pathogenesis of plant pathogens including bacteria, fungi, and oomycetes. Here, we demonstrated that Peronophythora litchii (syn. Phytophthora litchii) PlPAE5 suppresses litchi (Litchi chinensis) plant immunity by interacting with litchi lipid transfer protein 1 (LcLTP1). The LcLTP1-binding activity and virulence function of PlPAE5 depend on its PAE domain but not on its PAE activity. The high expression of LcLTP1 enhances plant resistance to oomycete and fungal pathogens, and this disease resistance depends on BRASSINOSTEROID INSENSITIVE 1–associated receptor kinase 1 (BAK1) and Suppressor of BIR1 (SOBIR1) in Nicotiana benthamiana. LcLTP1 activates the plant salicylic acid (SA) signaling pathway, while PlPAE5 subverts the LcLTP1-mediated SA signaling pathway by destabilizing LcLTP1. Conclusively, this study reports a virulence mechanism of oomycete PAE suppressing plant LTP-mediated SA immune signaling and will be instrumental for boosting plant resistance breeding.
Integrative multiomics profiling of passion fruit reveals the genetic basis for fruit color and aroma
Authors: Zheng Yu-Yu , Chen Lin-Hua , Fan Bing-Liang , Xu Zhenni , Wang Qiuxia , Zhao Bo-Yuan , Gao Min , Yuan Min-Hui , Tahir ul Qamar Muhammad , Jiang Yuanyuan , Yang Liu , Wang Lingqiang , Li Weihui , Cai Wenguo , Ma Chongjian , Lu Li , Song Jia-Ming , Chen Ling-Ling 
Published: December 2023

Abstract
Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation, and comparison of PPF (P. edulis Sims) and YPF (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina, and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, 1 million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma, and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways, and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoid metabolites accumulated more in PPF. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases. Our findings revealed that certain TPS homologs in both YPF and PPF varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the 2 passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.
OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia
Authors: Nouwen Nico , Pervent Marjorie , El M’Chirgui Franck , Tellier Frédérique , Rios Maëlle , Horta Araújo Natasha , Klopp Christophe , Gressent Frédéric , Arrighi Jean-François 
Published: December 2023

Abstract
Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accommodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signaling pathway that activates 2 coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing intercellular infection and lateral root base nodulation remains elusive. Here, we show that Aeschynomene evenia OROSOMUCOID PROTEIN 1 (AeORM1), a key regulator of sphingolipid biosynthesis, is required for nodule formation. Using A. evenia orm1 mutants, we demonstrate that alterations in AeORM1 function trigger numerous early aborted nodules, defense-like reactions, and shorter lateral roots. Accordingly, AeORM1 is expressed during lateral root initiation and elongation, including at lateral root bases where nodule primordium form in the presence of symbiotic bradyrhizobia. Sphingolipidomics revealed that mutations in AeORM1 lead to sphingolipid overaccumulation in roots relative to the wild type, particularly for very long-chain fatty acid-containing ceramides. Taken together, our findings reveal that AeORM1-regulated sphingolipid homeostasis is essential for rhizobial infection and nodule organogenesis, as well as for lateral root development in A. evenia.
Decellularized extracellular matrix-based composite scaffolds for tissue engineering and regenerative medicine
Authors: Xu Peiyao , Kankala Ranjith Kumar , Wang Shibin , Chen Aizheng 
Published: December 2023

Abstract
Despite the considerable advancements in fabricating polymeric-based scaffolds for tissue engineering, the clinical transformation of these scaffolds remained a big challenge because of the difficulty of simulating native organs/tissues’ microenvironment. As a kind of natural tissue-derived biomaterials, decellularized extracellular matrix (dECM)-based scaffolds have gained attention due to their unique biomimetic properties, providing a specific microenvironment suitable for promoting cell proliferation, migration, attachment and regulating differentiation. The medical applications of dECM-based scaffolds have addressed critical challenges, including poor mechanical strength and insufficient stability. For promoting the reconstruction of damaged tissues or organs, different types of dECM-based composite platforms have been designed to mimic tissue microenvironment, including by integrating with natural polymer or/and syntenic polymer or adding bioactive factors. In this review, we summarized the research progress of dECM-based composite scaffolds in regenerative medicine, highlighting the critical challenges and future perspectives related to the medical application of these composite materials.
Turmeric (Curcuma longa): an alternative to antibiotics in poultry nutrition
Authors: Aderemi Foluke Abimbola , Alabi Olufemi Mobolaji 
Published: December 2023

Abstract
Turmeric, a common spice in many countries has been used for centuries in traditional medicine for its antimicrobial properties. Recent research has shown that turmeric can be a viable alternative to antibiotics in poultry production. Antibiotic overuse in poultry has led to the development of antibiotic-resistant bacteria, which poses a threat to both animal and human health. Turmeric contains curcumin, a compound that has been shown to have antimicrobial activity against a wide range of bacteria, including those resistant to antibiotics. In addition, turmeric has anti-inflammatory and immunomodulatory properties, which can help boost the immune system of poultry and reduce the need for antibiotics. Studies have shown that turmeric can improve growth performance, and gut health, and reduce the incidence of disease in poultry. Therefore, the use of turmeric as an alternative to antibiotics in poultry production has the potential to not only improve animal health and welfare but also contribute to the fight against antibiotic resistance. This review aims to provide an overview of the recent knowledge on the use of these plant extracts in poultry feeds as feed additives and their effects on poultry performance.
Safety of dietary nitrate supplementation by calcium nitrate for finishing pigs as measured by methemoglobin and serum and tissue nitrate levels
Authors: Sheppard Amy M , van de Ligt Jennifer L G , Pillai Padmakumar , Crincoli Christine M , Faris Richard J , McGhee Molly L , Frederick Brent R 
Published: December 2023

Abstract
Nitrate supplementation has been studied as a beneficial constituent of the human diet, particularly for its effects on vascular health through vasodilation. Recent studies have focused on the benefits of nitrate supplementation in animals, especially in swine. Up to 1,200 mg/kg dietary nitrate supplementation from Ca nitrate was beneficial in farrowing and lactating sows and their offspring, and up to 6,000 mg/kg supplemental nitrate showed no adverse health effects in sows or piglets. Controlled study data evaluating the safety of nitrate supplementation to growing swine of any weight class is scant. Therefore, an experiment was conducted to test the hypothesis that increased inclusion rates of dietary nitrate through the addition of Ca nitrate in diets would not influence concentrations of nitrate or nitrite in serum and tissue, nor blood hemoglobin and methemoglobin. Forty-eight individually housed pigs (initial weight 119.1 ± 5.3 kg) were randomly allotted to four dietary treatments containing 0, 500, 1,000, or 2,000 mg/kg dietary nitrate and fed experimental diets for 28 d. Growth performance was not influenced (P &gt; 0.10) by dietary treatment. The most sensitive safety endpoint, methemoglobin, did not change (P &gt; 0.10) with dietary nitrate exposure up to 2,000 mg/kg. Serum and tissue nitrate and nitrite levels, myoglobin, and hemoglobin were not adversely affected (P &gt; 0.10). Total myoglobin in the loin linearly increased (P &lt; 0.05) with greater dietary nitrate in the diet, which is correlated with the red color of meat. This work established the safety of up to 2,000 mg/kg dietary nitrate from Ca nitrate as an ingredient in food for finishing pigs.
Jumbo quail responses to diets containing raw or heat-treated Marama bean (Tylosema esculentum) meal
Authors: Fatoki Mary F , Kiarie Elijah G , Mnisi Caven M 
Published: December 2023

Abstract
Growth performance, apparent retention (AR) of amino acids (AA), blood, and meat quality parameters were determined in grower Jumbo quail-fed diets containing raw or heat-treated marama bean (Tylosema esculentum) meal (MBM). The experimental diets were formulated to contain 99.98 g/kg of raw (MBMR), cooked (MBMC), autoclaved (MBMA), and toasted MBM (MBMT) in a standard grower diet (CON). A total of 306, 7-d-old Jumbo quail chicks (30.97 ± 1.79 g live weight) were placed in 35 cages (8/9 birds per cage). The five diets were allocated to the cages to give seven replicates per diet. The diets had varied responses (P &lt; 0.05) on AR of lysine, methionine, and threonine, among others. The CON diet promoted the highest (P &lt; 0.05) overall feed intake (FI) followed by MBMC and MBMA, and the lowest overall FI was from MBMR and MBMT. Quail-fed MBMR and MBMT diets had the least (P &lt; 0.05) overall body weight gain and final body weights than those fed with the CON, MBMC, and MBMA diets. Moreover, quail on MBMR diet had the lowest (P &lt; 0.05) overall gain-to-feed ratio (G:F) than those reared on the other diets, whose G:F values were statistically similar (P &gt; 0.05). Similarly, quail on MBMR diet had the highest (P &lt; 0.05) concentration of serum lipase and the heaviest gizzard than quail fed the other diets. However, quail-fed MBMT diet had heavier (P &lt; 0.05) relative proventriculus weight compared to quail-fed other diets. Heavier (P &lt; 0.05) relative spleen weights were observed for the MBMT and MBMR groups compared to the other groups. The CON diet had higher (P &lt; 0.05) hematocrits and 1-h breast meat redness compared to the other diets. However, CON, MBMC, and MBMA diets increased (P &lt; 0.05) 24-h breast meat redness than MBMR and MBMT diets. In conclusion, feeding diets with cooked or autoclaved marama bean meal resulted in an improvement in AA utilization, growth performance, and indices of carcass quality. However, raw and toasted marama beans had negative effects on performance parameters suggesting that optimal thermal treatment is critical for marama bean utilization.
Tristetraprolin regulates the skeletal phenotype and osteoclastogenic potential through monocytic myeloid‐derived suppressor cells
Authors: Zhang Lixia , Kwack Kyu Hwan , Thiyagarajan Ramkumar , Mullaney Kylie K. , Lamb Natalie A. , Bard Jonathan E. , Sohn Jiho , Seldeen Kenneth L. , Arao Yukitomo , Blackshear Perry J. , Abrams Scott I. , Troen Bruce R. , Kirkwood Keith L. 
Published: December 2023

AbstractTristetraprolin (TTP; also known as NUP475, GOS24, or TIS11), encoded by Zfp36, is an RNA‐binding protein that regulates target gene expression by promoting mRNA decay and preventing translation. Although previous studies have indicated that TTP deficiency is associated with systemic inflammation and a catabolic‐like skeletal phenotype, the mechanistic underpinnings remain unclear. Here, using both TTP‐deficient (TTPKO) and myeloid‐specific TTPKO (cTTPKO) mice, we reveal that global absence or loss of TTP in the myeloid compartment results in a reduced bone microarchitecture, whereas gain‐of‐function TTP knock‐in (TTPKI) mice exhibit no significant loss of bone microarchitecture. Flow cytometry analysis revealed a significant immunosuppressive immune cell phenotype with increased monocytic myeloid‐derived suppressor cells (M‐MDSCs) in TTPKO and cTTPKO mice, whereas no significant changes were observed in TTPKI mice. Single‐cell transcriptomic analyses of bone marrow myeloid progenitor cell populations indicated a dramatic increase in early MDSC marker genes for both cTTPKO and TTPKO bone marrow populations. Consistent with these phenotypic and transcriptomic data, in vitro osteoclastogenesis analysis of bone marrow M‐MDSCs from cTTPKO and TTPKO displayed enhanced osteoclast differentiation and functional capacity. Focused transcriptomic analyses of differentiated M‐MDSCs showed increased osteoclast‐specific transcription factors and cell fusion gene expression. Finally, functional data showed that M‐MDSCs from TTP loss‐of‐function mice were capable of osteoclastogenesis and bone resorption in a context‐dependent manner. Collectively, these findings indicate that TTP plays a central role in regulating osteoclastogenesis through multiple mechanisms, including induction of M‐MDSCs that appear to regulate skeletal phenotype.
Impact of COVID-19 on total hip arthroplasty: results from California state inpatient database
Authors: Barclay Gabriel J. , Saxena Anshul , Ramamoorthy Venkataraghavan , Roy Mukesh , Appunni Sandeep , Doke Mayur , Ahmed Md Ashfaq , Zhang Zhenwei , Zhang Yanjia , Rubens Muni 
Published: December 2023

Background:
COVID-19 pandemic has significantly affected orthopedic surgery, resulting in postponements and cancellations. The aim of this study is to determine the possible effects of COVID-19 on the number of total hip arthroplasty (THA) hospitalizations and hospital outcomes using a large database.

Methods:
We conducted a retrospective analysis of data gathered and stored in the California State Inpatient Database (SID) during 2019 and 2020. All THA hospitalizations ≥18 yr that occurred in 2019 and 2020 and COVID-19 hospitalizations that occurred in 2020 were used for the analysis. The primary outcomes of the study were trends in THA hospitalizations between 2019 and 2020. Secondary outcomes were mortality, surgical, medical, and other complications, and prolonged length of stay.

Results:
A total of 36,760 and 20,243 THA hospitalizations occurred during 2019 and 2020, respectively. Trends in THA hospitalizations during 2019 and 2020 showed that the rates of these hospitalizations were substantially lower throughout 2020. Logistic regression analysis showed that the odds of mortality (odds ratio [OR], 2.77; 95% CI, 1.38-5.53), surgical complications (OR,1.61; 95% CI, 1.36-1.89), medical complications (OR,1.27; 95% CI, 1.20-1.33), other complications (OR,1.42; 95% CI, 1.19-1.69), and prolonged length of stay (OR,1.10; 95% CI, 1.05-1.16) were significantly higher during 2020.

Conclusions:
Our findings show that during COVID-19 pandemic THA hospitalizations were prioritized based on case severity. By the end of 2020 THA hospitalizations did not steeply decrease in numbers compared to the advent of the pandemic, indicating that orthopedic surgeons and other healthcare professionals functioned optimally even during the COVID-19 pandemic.
Relationship Between Pain and Delirium in Critically Ill Adults
Authors: Wu Ting Ting , Vernooij Lisette M. , Duprey Matthew S. , Zaal Irene J. , Gélinas Céline , Devlin John W. , Slooter Arjen J.C. 
Published: December 2023

OBJECTIVES:
Although opioids are frequently used to treat pain, and are an important risk for ICU delirium, the association between ICU pain itself and delirium remains unclear. We sought to evaluate the relationship between ICU pain and delirium.

DESIGN:
Prospective cohort study.

SETTING:
A 32-bed academic medical-surgical ICU.

PATIENTS:
Critically ill adults (n = 4,064) admitted greater than or equal to 24 hours without a condition hampering delirium assessment.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Daily mental status was classified as arousable without delirium, delirium, or unarousable. Pain was assessed six times daily in arousable patients using a 0–10 Numeric Rating Scale (NRS) or the Critical Care Pain Observation Tool (CPOT); daily peak pain score was categorized as no (NRS = 0/CPOT = 0), mild (NRS = 1–3/CPOT = 1–2), moderate (NRS = 4–6/CPOT = 3–4), or severe (NRS = 7–10/CPOT = 5–8) pain. To address missingness, a Multiple Imputation by Chained Equations approach that used available daily pain severity and 19 pain predictors was used to generate 25 complete datasets. Using a first-order Markov model with a multinomial logistic regression analysis, that controlled for 11 baseline/daily delirium risk factors and considered the competing risks of unarousability and ICU discharge/death, the association between peak daily pain and next-day delirium in each complete dataset was evaluated.

RESULTS:
Among 14,013 ICU days (contributed by 4,064 adults), delirium occurred on 2,749 (19.6%). After pain severity imputation on 1,818 ICU days, mild, moderate, and severe pain were detected on 2,712 (34.1%), 1,682 (21.1%), and 894 (11.2%) of the no-delirium days, respectively, and 992 (36.1%), 513 (18.6%), and 27 (10.1%) of delirium days (p = 0.01). The presence of any pain (mild, moderate, or severe) was not associated with a transition from awake without delirium to delirium (aOR 0.96; 95% CI, 0.76–1.21). This association was similar when days with only mild, moderate, or severe pain were considered. All results were stable after controlling for daily opioid dose.

CONCLUSIONS:
After controlling for multiple delirium risk factors, including daily opioid use, pain may not be a risk factor for delirium in the ICU. Future prospective research is required.
Correlation Between Sleep Continuity and Patient-Reported Sleep Quality in Conscious Critically Ill Patients at High Risk of Reintubation: A Pilot Study
Authors: Van Camp Eloïse , Rault Christophe , Heraud Quentin , Frat Jean-Pierre , Balbous Anais , Thille Arnaud W. , Fernagut Pierre-Olivier , Drouot Xavier 
Published: December 2023

OBJECTIVES:
It is well-established that sleep quality of ICU patients is poor, with sleep being highly fragmented by multiple awakenings. These sleep disruptions are associated with poor outcomes such as prolonged weaning duration from mechanical ventilation. Polysomnography can measure sleep continuity, a parameter associated positively with outcomes in patients treated with noninvasive ventilation, but polysomnography is not routinely available in all ICUs, and simple means to assess sleep quality are needed. The Richards-Campbell sleep questionnaire (RCSQ) assesses sleep quality in ICU patients but is difficult to administrate in patients who are not fully awake, and a simpler sleep numeric rating scale (sleep-NRS) has been proposed as an alternative. We here investigated the relationships between sleep continuity and patients-reported sleep quality.

DESIGN:
Single-center retrospective study.

SETTING:
Medical ICU of Poitiers University Hospital.

PATIENTS:
Seventy-two patients were extubated from mechanical ventilation and at high risk of reintubation.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
We analyzed 52 previously recorded polysomnographies in nonsedated and conscious ICU patients. Sleep was recorded the night after extubation. Sleep continuity was measured using an automated scoring algorithm from one electroencephalogram (EEG) channel of the polysomnography. Patient-reported sleep quality was assessed using RCSQ and sleep-NRS. Sleep continuity could be calculated on 45 polysomnographies (age: 68 [58–77], median [25th–75th]) RCSQ (62 [48–72]) and sleep-NRS (6.0 [5.0–7.0]) were obtained in 21 patients and 34 patients, respectively. Our results show a significant correlation between sleep continuity and sleep-NRS (p = 0.0037; ρ = 0.4844; n = 34) but not with RCSQ score (p = 0.6732; ρ = 0.1005; n = 20).

CONCLUSION:
Sleep continuity correlates with patient-reported sleep quality assessed using sleep-NRS and may capture the refreshing part of sleep. Sleep-NRS can be easily administered in ICU patients. Sleep continuity and sleep-NRS are simple tools that may prove useful to evaluate sleep quality in ICU patients.