bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Integrated Physiological, Cytology and Proteomics Reveals Network of Sugarcane Protoplasts Responses to Enzymolysis
Authors: Zhang Demei , Wang Rui , xiao Jiming , Zhu Shuifang , Li Xinzhu , Han Shijian , Li Zhigang , Zhao Yang , Islam Shohag Md. Jahidul , He Zhenli , Li Suli 
Published: October 2022

AbstractThe protoplast experimental system has been becoming a powerful tool for functional genomics and cell fusion breeding. However, the physiology and molecular mechanism during enzymolysis is not completely understood and has become a major obstacle to protoplast regeneration. Our study used physiological, cytology, iTRAQ (Isobaric Tags for Relative and Absolute Quantification) -based proteomic and RT-PCR analyses to compare the young leaves of sugarcane (ROC22) and protoplasts of more than 90% viability. We found that oxidation product MDA content increased in the protoplasts after enzymolysis and several antioxidant enzymes such as POD, CAT, APX, and O2- content significantly decreased. The cytology results showed that after enzymolysis, the cell membranes were perforated to different degrees, the nuclear activity was weakened, the nucleolus structure was not obvious, and the microtubules depolymerized and formed many short rod-like structures in protoplasts. The proteomic results showed that 1,477 differential proteins were down-regulated and 810 were up-regulated after enzymolysis of sugarcane young leaves. The GO terms, KEGG and KOG enrichment analysis revealed that differentially abundant proteins were mainly involved in bioenergetic metabolism, cellular processes, osmotic stress, and redox homeostasis of protoplasts, which would allow protein biosynthesis or / degradation. The RT-PCR analysis revealed the expression of osmotic stress resistance genes such as DREB, WRKY, MAPK4, and NAC were up-regulated. Meanwhile, the expression of key regeneration genes such as CyclinD3, CyclinA, CyclinB, Cdc2, PSK, CESA and GAUT were significantly down-regulated in the protoplasts. Hierarchical clustering, identification of redox proteins and oxidation products showed that these proteins were involved in dynamic networks in response to oxidative stress after enzymolysis. We used a variety of methods to figure out how young sugarcane leaves react to enzymes.
A complex containing RhoBTB3-SHIP164-Vps26B promotes the biogenesis of early endosome buds at Golgi-endosome contacts
Authors: Wang Jingru , Chu Qingzhu , Chang Weiping , Deng Lin , Ji Wei-Ke 
Published: October 2022

AbstractEarly endosomes (EEs) are central hubs for cargo sorting in vesicular trafficking. Cargoes destined for degradation retain in EEs that are eventually delivered to lysosomes, while recycled cargo destined for the plasma membrane (PM) or to the Golgi are segregated into EE buds, a specialized membrane structure transiently generated on EEs during cargo sorting. Until now, the molecular basis of the membrane expansion during the biogenesis of EE buds is completely elusive. Here, we identify a protein complex containing a Vps13 domain-containing lipid transporter SHIP164, ATPase RhoBTB3 and retromer component Vps26B, promotes the membrane expansion in the biogenesis of EE buds at Golgi-EE contacts. SHIP164 depletion specifically reduces the size and number of EE buds marked by Vps26B and actin, and results in less but enlarged EEs, which can be substantially rescued by wild type SHIP164 other than lipid transfer-defective mutants, suggesting a role of lipid transfer of SHIP164 in the process. SHIP164 and RhoBTB3 interact with enzymes for phospholipid synthesis on motile Golgi vesicles, that frequently contact EEs. Functionally, SHIP164 depletion substantially reduces the trafficking of sphingomyelin to the PM, and impairs cell growth. Together, we propose a lipid transport-dependent route from the Golgi to EEs at the contacts required for EE bud biogenesis.
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface
Authors: Cunningham‐Minnick Michael J. , Roberts H. Patrick , Kane Brian , Milam Joan , King David I. 
Published: October 2022

Abstract

The ecology of the canopy–aerosphere interface within forested ecosystems remains underexplored largely due to the challenges of physically accessing this zone. Sky bridges, towers and other permanent structures are most commonly used to sample the forest canopy–aerosphere interface, but these methods are costly, challenging to replicate, and often alter and degrade the local environment during construction. Thus, there is a clear need for cost‐effective and replicable methods for accessing and passively sampling above the forest canopy.

We designed and deployed an inexpensive and lightweight telescopic hanger composed of common materials to sample aerial invertebrates above the forest canopy. Deployment involved climbing into tree crowns and securing our hanger design to vertical branches. We sampled the invertebrate community above forest fragments on the campus of the University of Massachusetts Amherst, USA by suspending blue vane traps from hangers, which were extended to approximately 1 m above the highest terminal bud of the tree, continuously from April through August 2021. We also recorded the microclimate conditions above the canopy at each hanger, including temperature and light intensity.

All hangers and traps remained in place and active throughout the study period. In May, we made minor repairs at two locations where the hangers were attached to the trees and, following an intense weather event in July, observed damage to one hanger that did not affect sampling effort. We include cost breakdowns of design components as well as detailed building instructions.

This tool offers a durable and inexpensive solution for researchers to access and sample the forest canopy–aerosphere interface that has minimal impacts on the environment and is more easily replicated compared to previous methods. Assembly pitfalls and design alterations are discussed based on our experience with the installation and implementation of the tested design, as well as included prototypes.
Pedicled Superficial Circumflex Iliac Artery Perforator (SCIP) flap for perineo‐scrotal reconstruction following Fournier's gangrene
Authors: B Sandeep , Khanna Anmol , Taylor Duncan 
Published: October 2022

AbstractBackgroundFournier's gangrene is a form of necrotising fasciitis involving perineo‐scrotal skin. It is treated with radical debridement, infection control and often leaves a large anatomical defect that is challenging to reconstruct. The anatomical location of the defect leads to faecal contamination, difficulties when mobilizing, and negative psychological impact. Traditional approaches for managing such defects have relied on either healing by secondary intention or skin grafting. There are few reported cases in the literature to cover such defects with a flap.MethodsPedicled Superficial Circumflex Iliac Artery Perforator (SCIP) flap reconstruction was performed in three patients who had perineo‐scrotal defects following debridement for Fournier's gangrene.ResultsAll flaps survived with no significant postoperative complications and good functional and aesthetic outcomes were achieved. The mean age of patient was 52 years and the largest defect measured 22 × 10 cm.ConclusionThe reconstruction of perineo‐scrotal defects is difficult despite a range of reconstructive options. The pedicled SCIP flap offers many advantages over standard techniques. This flap is thin, pliable, and has a consistent anatomy. With continued experience, we feel that this flap could be considered the gold standard of treatment for such defects.
Indwelling stents cause obstruction and induce ureteral injury and fibrosis in a porcine model
Authors: Scotland Kymora B. , Almutairi Khaled , Park Elliya , Wang Lu , Kung Sonia H.Y. , Haegert Anne , Adomat Hans , Bell Robert , LeBihan Stephane , Chew Ben H. , Lange Dirk 
Published: October 2022

ObjectivesTo investigate global changes in ureters at the transcriptional, translational and functional levels, both while stents are indwelling and after removal and recovery, and to study the effects of targeting pathways that play a potential role.MethodsPig ureters were stented for varying amounts of time (48 h, 72 h, 14 days) and the impact on peristalsis, dilatation and hydronephrosis were assessed. RNAseq, proteomic, histological and smooth muscle (SM) function analyses were performed on ureteric and kidney tissues to assess changes induced by stenting and recovery. Pathway analysis was performed using Ingenuity Pathway Analysis software. To study the impact of possible interventions, the effects of erythropoeitin (EPO) and a Gli1 inhibitor were assessed.ResultsStenting triggers massive ureteric dilatation, aperistalsis and moderate hydronephrosis within 48 h. Pathways associated with obstruction, fibrosis and kidney injury were upregulated by stenting. Increased expression of GLI1, clusterin‐α (a kidney injury marker) and collagen 4A2 (a fibrosis marker) was found in stented vs contralateral unstented ureters. EPO did not improve peristalsis or contraction force but did decrease non‐purposeful spasming seen exclusively in stented ureters. Tamsulosin administration increased contractility but not rate of peristalsis in stented ureters.ConclusionsUreters respond to stents similarly to how they respond to an obstruction, that is, with activation of pathways associated with hydronephrosis, fibrosis and kidney injury. This is driven by significant dilatation and associated ureteric SM dysfunction. EPO and tamsulosin induced mild favourable changes in SM physiology, suggesting that targeting specific pathways has potential to address stent‐induced complications.
Japan MG registry: Chronological surveys over 10 years
Authors: Suzuki Shigeaki , Masuda Masayuki , Uzawa Akiyuki , Nagane Yuriko , Konno Shingo , Suzuki Yasushi , Kubota Tomoya , Sugimoto Takamichi , Samukawa Makoto , Watanabe Genya , Ishizuchi Kei , Akamine Hiroyuki , Onishi Yosuke , Yoshizumi Kazuki , Uchi Takafumi , Amino Itaru , Ueta Yuki , Minami Naoya , Kawaguchi Naoki , Kimura Takashi , Takahashi Masanori P. , Murai Hiroyuki , Utsugisawa Kimiaki 
Published: October 2022

AbstractThe primary purpose of the Japanese myasthenia gravis registry (JAMG‐R) has been to research and promote high‐quality medical care for MG patients in Japan. We reviewed the findings of surveys performed by JAMG‐R over an ~10‐y period. The first goal for favorable quality of life (QOL) is a status of minimal manifestations (MM) or better with an oral prednisolone (PSL) dose of 5 mg/d or less (MM‐5 mg). Early and aggressive use of nonoral fast‐acting treatment together with low‐dose oral PSL (the “EFT strategy”) is recommended to reduce disease severity with minimal oral steroid use so that the MM‐5 mg target can be met as soon as possible. We conducted the fourth largest multicenter survey ever in 2021, obtaining detailed clinical information from 1710 consecutive MG patients all over Japan, and compared the 2021 surveys with those from 2012 and 2015. The frequency of patients treated with EFT strategies showed a gradual increase, reaching 39% of the total MG patients in the 2021 survey. The current and maximum dose of PSL and the number of days at high‐dose (>20 mg/d) PSL showed decreases. Survey results indicate that as EFT strategies have spread, the percentage of patients on MM‐5 mg has increased. We again confirmed that MM‐5 mg was associated with favorable QOL in the 2021 survey. Recent data regarding COVID‐19 suggests that it did not seriously impact the MG population in Japan; unfortunately, refractory MG, observed in 21% of patients, is still an unresolved problem.
Does preoperative weight loss in a specialist medical weight management centre influence postoperative weight loss after bariatric surgery?
Authors: Slater Christopher , Santhosh Smrithi H. , Ellison Jodi , Majeed Waseem , Summers Lucinda K. M. , Senapati Siba , Akhtar Khurshid , Ammori Basil J. , New John P. , Syed Akheel A. 
Published: October 2022

SummaryWeight loss of 5%–10% is advised in medical weight management (MWM) programmes prior to bariatric surgery but it remains to be established whether it influences postoperative weight loss outcomes. We studied postoperative percent total weight loss (%TWL) in 168 patients categorized by preoperative referral weight loss <5% or ≥5% in a UK NHS bariatric centre. Eighty‐six (51.2%) patients achieved sustained referral weight loss <5% (Group A) and 82 (48.8%) ≥5% (Group B). Overall postoperative %TWL in Group A compared with Group B was 30.0% versus 28.3% (p = .30) at 12 months and 32.5% versus 29.6% (p = .20) at 24 months. There were no significant differences in postoperative %TWL at 12 and 24 months when categorized by procedure (gastric bypass, n = 106; or sleeve gastrectomy, n = 62), age or sex. Preoperative weight loss during intensive specialist MWM did not influence postoperative weight loss up to 24 months with gastric bypass or sleeve gastrectomy.
Artificial intelligence in pharmacology research and practice
Authors: van der Lee Maaike , Swen Jesse J. 
Published: October 2022

AbstractIn recent years, the use of artificial intelligence (AI) in health care has risen steadily, including a wide range of applications in the field of pharmacology. AI is now used throughout the entire continuum of pharmacology research and clinical practice and from early drug discovery to real‐world datamining. The types of AI models used range from unsupervised clustering of drugs or patients aimed at identifying potential drug compounds or suitable patient populations, to supervised machine learning approaches to improve therapeutic drug monitoring. Additionally, natural language processing is increasingly used to mine electronic health records to obtain real‐world data. In this mini‐review, we discuss the basics of AI followed by an outline of its application in pharmacology research and clinical practice.
Mentalizing in first‐episode psychosis: Correlates with symptomatology and traits of borderline personality disorder
Authors: Archer Michaela , Shnyien Ali , Mansfield Sarah , Draycott Simon 
Published: October 2022

AbstractAimTo explore the associations between mentalizing, positive and negative symptoms of psychosis, and traits of borderline personality disorder, in a sample of patients with first‐episode psychosis, and in a non‐clinical sample.MethodsA quantitative cross‐sectional design was employed. Thirty‐two adults with first‐episode psychosis and 148 non‐clinical participants were assessed using the reflective functioning questionnaire. The questionnaire measures two dimensions of mentalizing, certainty and uncertainty about mental states. Traits of borderline personality disorder and symptoms of psychosis were measured using the self‐report version of the Zanarini rating scale, the Community Assessment of Psychotic Experiences, and the Green et al., paranoid thought scale.ResultsPatients with first‐episode psychosis reported increased mentalizing impairments, characterized as hypomentalizing tendencies, compared to the non‐clinical group. Regression analysis showed significant associations between higher scores on the uncertainty about mental states scale and negative symptoms of psychosis in both groups. No associations were found between mentalizing impairments and traits of borderline personality disorder in the clinical sample, although associations were found in the non‐clinical sample.ConclusionsThe present findings suggests that impairments in mentalizing may be associated with negative symptoms of psychosis across both clinical and non‐clinical samples. Mentalizing impairments was found to be associated with traits of borderline personality disorder, but this finding was only confirmed in the non‐clinical sample. Mentalizing should therefore be considered in the early assessment and treatment of patients experiencing difficulties with negative symptoms of psychosis.
Towards a heuristic understanding of the storage effect
Authors: Johnson Evan C. , Hastings Alan 
Published: October 2022

AbstractThe storage effect is a general explanation for coexistence in a variable environment. Unfortunately, the storage effect is poorly understood, in part because the generality of the storage effect precludes an interpretation that is simultaneously simple, intuitive and correct. Here, we explicate the storage effect by dividing one of its key conditions—covariance between environment and competition—into two pieces, namely that there must be a strong causal relationship between environment and competition, and that the effects of the environment do not change too quickly. This finer‐grained definition can explain a number of previous results, including (1) that the storage effect promotes annual plant coexistence when the germination rate fluctuates, but not when the seed yield fluctuates, (2) that the storage effect is more likely to be induced by resource competition than the apparent competition, and (3) why the storage effect arises readily in models with either stage structure or environmental autocorrelation. Additionally, our expanded definition suggests two novel mechanisms by which the temporal storage effect can arise—transgenerational plasticity and causal chains of environmental variables—thus suggesting that the storage effect is a more common phenomenon than previously thought.
Fatigue failure modes of rib‐to‐deck joints under the multiaxial stress states caused by various wheel loading characteristics
Authors: Zhu Yiyao , Deng Caiyan , Gong Baoming , Li Siyuan , Guo Baichen , Wang Dongpo , Liang Hang 
Published: October 2022

AbstractOrthotropic steel bridge decks (OSBDs) are characterized by overall structural asymmetries and severe local stress concentrations; meanwhile, complicated service loadings always cause relevant rib‐to‐3deck (RD) welded joints in multiaxial stress states. Under such circumstances, a full‐scale OSBD model was established. Six loading cases were applied, and the multiaxial fatigue deviation was calculated to represent the multiaxial stress state of the bridge deck. Based on the effective traction structural stress method, the most unfavorable loading case for the failure mode of the RD joint under a multiaxial stress state was analyzed, and the failure mode transition in the process of wheel load movement was discussed. The results indicated that the fatigue failure mode of the RD joint was determined by the transverse loading locations. In‐between‐rib loading can cause the initiation of toe‐rib cracks. Cracks are prone to occur under over‐rib loading and riding‐rib loading, and the arrangement of diaphragms can increase the risk that the fatigue crack originates from the weld root.
Experimental and theoretical investigation on mechanical behaviors of TB991 weld sealant under cyclic loading
Authors: Zhang Jun , Zhang Meng Jie , Zhang Xin , Wang Zhuang Zhuang 
Published: October 2022

AbstractThe mechanical behaviors of TB991 weld sealant under cyclic loading conditions were experimentally investigated. The evolution of relaxation stress, cyclic softening, and dissipated energy was evaluated with the effect of strain amplitude and mean strain. The experimental results showed that the stress–strain response curves of the first loading‐unloading and cyclic loading‐unloading were significantly different. The phenomenon of stress relaxation and cyclic softening occurred under cyclic strain loading conditions. Furthermore, the relaxation stress and dissipated energy decreased rapidly during the initial cyclic loading and then steadily decreased with the increase of cycle number, while the cyclic softening increased rapidly at first and then steadily. Besides, a viscoelastic constitutive model was proposed which can describe the different shapes of stress–strain curve between the initial loading‐unloading and the cyclic loading‐unloading and also considers the cyclic stress relaxation and cyclic softening of the materials under cyclic loading condition. Comparisons between the numerical results and the experimental data demonstrated that the proposed model can better describe the mechanical behavior of TB991 weld sealant under cyclic loading conditions.
Moderate salinity improves the availability of soil P by regulating P‐cycling microbial communities in coastal wetlands
Authors: Hu Minjie , Le Yixun , Sardans Jordi , Yan Ruibing , Zhong Yi , Sun Dongyao , Tong Chuan , Peñuelas Josep 
Published: October 2022

AbstractAccelerated sea‐level rise is expected to cause the salinization of freshwater wetlands, but the responses to salinity of the availability of soil phosphorus (P) and of microbial genes involved in the cycling of P remain unexplored. We conducted a field experiment to investigate the effects of salinity on P cycling by soil microbial communities and their regulatory roles on P availability in coastal freshwater and brackish wetlands. Salinity was positively correlated with P availability, with higher concentrations of labile P but lower concentrations of moderately labile P in the brackish wetland. The diversity and richness of microbial communities involved in P cycling were higher in the brackish wetland than the freshwater wetland. Salinity substantially altered the composition of the P‐cycling microbial community, in which those of the brackish wetland were separated from those of the freshwater wetland. Metagenomic sequence analysis indicated that functional genes involved in the solubilization of inorganic P and the subsequent transport and regulation of P were more abundant in coastal soils. The relative abundances of most of the target genes differed between the wetlands, with higher abundances of P‐solubilization (gcd and ppa) and ‐mineralization (phoD, phy, and ugpQ) genes and lower abundances of P‐transport genes (pstB, ugpA, ugpB, ugpE, and pit) in the brackish wetland. A significant positive correlation between the concentration of labile P and the abundances of the target genes suggested that salinity may, at least in part, improve P availability by regulating the P‐cycling microbial community. Our results suggest that the P‐cycling microbial community abundance and P availability respond positively to moderate increases in salinity by promoting the microbial solubilization and mineralization of soil P. Changes in microbial communities and microbially mediated P cycling may represent microbial strategies to adapt to moderate salinity levels, which in turn control soil function and nutrient balance.
Unbiased prediction of off‐target sites in genome‐edited rice using SITE‐Seq analysis on a web‐based platform
Authors: Narushima Jumpei , Kimata Shinya , Shiwa Yuh , Gondo Takahiro , Akimoto Satoshi , Soga Keisuke , Yoshiba Satoko , Nakamura Kosuke , Shibata Norihito , Kondo Kazunari 
Published: October 2022

AbstractGenome‐editing using the CRISPR‐Cas9 system has the potential to substantially accelerate crop breeding. Since off‐target editing is one of problems, a reliable method for comprehensively detecting off‐target sites is needed. A number of in silico methods based on homology to on‐target sequence have been developed, however the prediction without false negative is still under discussion. In this study, we performed a SITE‐Seq analysis to predict potential off‐target sites. SITE‐Seq analysis is a comprehensive method that can detect double‐strand breaks in vitro. Furthermore, we developed a systematic method using SITE‐Seq in combination with web‐based Galaxy system (Galaxy for Cut Site Detection), which can perform reproducible analyses without command line operations. We conducted a SITE‐Seq analysis of a rice genome targeted by OsFH15 gRNA‐Cas9 as a model, and found 41 candidate off‐target sites in the annotated regions. Detailed amplicon‐sequencing revealed mutations at one off‐target site in actual genome‐edited rice. Since this off‐target site has an uncommon protospacer adjacent motif, it is difficult to predict using in silico methods alone. Therefore, we propose a novel off‐target assessment scheme for genome‐edited crops that combines the prediction of off‐target candidates by SITE‐Seq and in silico programs and the validation of off‐target sites by amplicon‐sequencing.