bluuebunny/crossref_metadata_2025_split huggingface dataset:
Description and salient genome characteristics of a putative novel species Methylomonas strain WWC4, isolated from an Indian freshwater ecosystem
Authors: Khatri Kumal , Mohite Jyoti A. , Manvi Shubha , Pardhi Kajal , Rahalkar Monali C. 
Published: April 2023

Abstract
Freshwater wetlands are interesting habitats for methane-oxidizing bacteria or methanotrophs. We isolated a methanotroph, strain WWC4, from the mud of a freshwater creek running close to a beach in the coastal regions of Western India, near Alibag town. Strain WWC4 was a strict methanotroph, thriving only on methane and marginally on methanol. It formed pink to slightly orange-colored round colonies and formed pinkish turbidity or surface pellicle in liquid culture, indicative of the Methylomonas genus. The strain is characterized by thick, short, and motile rods, 2.5-3 µm long and 0.8-1.2 µm wide in size, with a Gram-negative character. Based on the 16S rRNA gene sequence, the culture was classified as a Methylomonas strain, with the nearest type species being Methylomonas koyamae Fw12E-YT showing 97.81% sequence similarity. A comparison of the draft genomes indicated that Methylomonas sp. WWC4 genome showed only 74.45%, 75.72%, and 21.5% similarities of AAI, ANIb, and dDDH values, respectively, with its closest neighbor Methylomonas koyamae Fw12E-YT, indicating its taxonomic novelty at the level of species. The GC content of the genome was 55.9 mol%. The whole-genome shotgun project was deposited at DDBJ/ENA/GenBank, and the accession number is JAATWI01.1. The cell wall lipids indicated a unique fingerprint with 15:1 ω8c (21.09%), 16:0 3OH (15.7%), and 16:1ω5c (12.6%) being the primary fatty acids, dissimilar to any other related Methylomonas species, confirming its taxonomic novelty. The genome was further explored for carotenoid pathways and plant growth promotion genes for its biotechnological potential. Strain WWC4 did not withstand cryopreservation and could not be deposited in two international culture collections. The culture is part of our institutional, WDCM-approved culture collection as MCMB-1474, maintained live. Due to its taxonomical novelty, strain WWC4 is also proposed to be a member of a Candidatus species of the Methylomonas genus and named “Candidatus Methylomonas sedimenticola” strain WWC4.
High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust
Authors: Li Hongna , Luo Jing , Zhang Wenjun , Hua Lei , Li Kun , Wang Jian , Xu Binyang , Yang Chen , Wang Guiping , Rouse Matthew N. , Dubcovsky Jorge , Chen Shisheng 
Published: April 2023

Abstract
Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinse Pgt races. Using a large mapping population (9,522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. Physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant T. monococcum PI 306540. The comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and the discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified only 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and the tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.
Design of Drawing Die for Rear Wheel Cover Outer Panel and Optimization of Wear Process Parameters
Authors: Gong Guoqing , Wang Youmin , Yang Kefan 
Published: April 2023

Abstract
Aiming at the problem of the wear caused by the mutual movement between the convex die and the sheet material in the stamping process, which results in a decrease in the die service life. In the paper, the three-dimensional design of the drawing die for the outer plate of the rear wheel cover was carried out by using UG, the simulation of the die stamping process was carried out by using Deform-3D, the main wear positions of the die were determined, the four process parameters of die clearance, friction coefficient, stamping speed and die hardness were selected as the test factors, the amount of die wear was used as the evaluation index to establish an orthogonal test, the multiple linear regression analysis of the test results was carried out by using SPSS software, and the empirical formula for the surface wear of the drawing die was established. Finally, the BP neural network model between process parameters and wear amount was constructed using MATLAB. The weights and thresholds of the nodes in the implicit layer of the model were optimized by using the whale algorithm to obtain the optimal combination of process parameters with minimum wear amount predicted based on the optimized WOA-BP neural network model. The minimum wear amount of the optimized convex die was 1.02×10-6 mm. The optimal combination of process parameters was friction coefficient 0.12, stamping speed 22mm/s, die hardness 62HRC, and die clearance 0.88mm, which completes the design of the automotive rear wheel cover outer plate drawing die and optimizes its surface wear process parameters.
Postoperative awake prone position in geriatric patients with hip fracture: a protocol for a randomized controlled trial on the efficacy of postoperative prone position in reducing pulmonary complications and improving oxygenation
Authors: Gao Yu-cheng , Shi Liu , Zhang Yuan-wei , Gao Wang , Tian Xie , Cao Mu-min , Li Ying-juan , Chen Hui , Rui Yun-Feng 
Published: April 2023

Abstract
Introduction Postoperative pulmonary complications (PPCs) are prevalence in geriatric patients with hip fractures. Low oxygen level is one of the most important risk factors for PPCs. Prone position has been proven efficacy in improving oxygenation and delaying the progress of pulmonary diseases especially in patients with acute respiratory distress syndrome induced by multiple etiologies. The application of awake prone position (APP) has also attracted widespread attention in recent years. A randomized controlled trial (RCT) will be carried out to measure the effect of postoperative APP in a population of geriatric patients undergoing hip fracture surgery.
Methods This is a RCT. Patients older than 65 years old admitted through the emergency room and diagnosed with an intertrochanteric or femoral neck fracture will be eligible for enrollment and randomized to control group with routine postoperative management of orthopedics or APP group with additional prone position for the first three consecutive postoperative days (PODs). Patients receiving conservative treatment will not be eligible for enrollment. We will record the difference in patient’s room-air-breathing arterial partial pressure of oxygen (PaO2) values between the 4th POD (POD 4) and emergency visits, morbidity of PPCs, mortality and ICU stays during hospitalization, length of hospitalization. The rates of PPCs, readmissions and mortality will be followed up for 90 PODs.
Discussion
We describe the protocol for a single-center RCT that will evaluate the efficacy of postoperative APP treatment in reducing pulmonary complications and improving oxygenation in geriatric patients with hip fracture.
Ethics and dissemination: This protocol was approved by the independent ethics committee (IEC) for Clinical Research of Zhongda Hospital, Affiliated to Southeast University and is registered on Chinese Clinical Trial Registry. The findings of the trial will be disseminated through peer-reviewed journals.
Ethics approval number: 2021ZDSYLL203-P01
Trial registration: ChiCTR, ChiCTR2100049311. Registered on 29 July 2021, https://www.chictr.org.cn/listbycreater.aspx
Trial status: Recruiting. Recruitment is expected to be completed in December 2024.
The effectiveness of walking exercise on the bowel preparation before colonoscopy: A single blind randomized clinical trial study
Authors: Rezamand Gholamreza , Joukar Farahnaz , Amini-Salehi Ehsan , Delam Hamed , Samadi Alireza , Mavadati Sara , Hassanipour Soheil , Mansour-Ghanaei Fariborz 
Published: April 2023

Abstract
Background and aim: Bowel preparation is a crucial factor affecting the diagnostic accuracy of colonoscopy, and few randomized control trials evaluated enhancement in bowel preparation. In this study, we aimed to evaluate the effectiveness of walking exercises on bowel preparation before colonoscopy procedure.
Methods: The present study is a single-blind randomized control trial, including 262 patients undergoing colonoscopy procedure. Patients were randomly divided into two groups of intervention (n=131) and control (n=131). Individuals in the intervention group were supposed to consume certain liquids and foods, bisacodyl pills, poly ethylene glycol powder and walk before their colonoscopy day based on a predefined plan. Individuals in the control group were supposed to consume the same regimen as the intervention group but were not told to do walking exercises. On the colonoscopy day, both groups were estimated regarding the number of footsteps taken by a foot counter. An experienced gastroenterologist compared the two groups regarding the Boston Bowel Preparation Scale (BBPS).
Results: The number of taken footsteps in the two groups was significantly different (P<0.001). Although there was no significant difference between the intervention and control groups regarding mean BBPS (6.26±1.9 vs 6.29±1.9, P =0.416), individuals with more than 6900 steps had significantly higher BBPS compared to individuals with less than 6900 footsteps (6.62±1.8 vs 5.92±1.9, P = 0.003). In univariate analysis, BBPS was significantly associated with age below 50 (OR: 2.45, 95%CI: 1.30-4.61, P=0.006) and smoking (OR: 0.41, 95%CI: 0.17-0.94, P=0.043). In multivariate analysis, the relationship between BBPS with age below 50 and smoking remained significant (OR: 2.50, 95%CI: 1.30-4.70, P=0.005 and OR: 0.38, 95%CI: 0.16-0.93, P=0.034, respectively).
Conclusion: Although walking exercise as an intervention before colonoscopy was not significantly associated with BBPS, the higher number of footsteps taken was found to enhance bowel preparation. Also, older people and smokers seem to have fewer benefits from walking exercises for bowel preparation before the colonoscopy procedure.
Trial registration: ISRCTN32724024 (Registration date:22/08/2018).
Changes of Inflammatory Factors in Patients with Small Airway Dysfunction
Authors: Sun Jiaolin , Cheng Xue , Lin Lv , Ji Wenwen , Cui Chen , Zhu Meijun , Yang Lan , Shi Zhihong 
Published: April 2023

Abstract
Background: Small airway dysfunction (SAD) is considered as a precursor of chronic airway diseases (such as COPD, asthma, etc.). As we all known, patients with COPD and asthma both exhibit infiltration of inflammatory factors in the small airways and alveoli. However, few studies have determined whether SAD is associated with airway inflammation and systemic changes in inflammatory factors. To determine whether there are changes in airway inflammation and systemic inflammatory factors in SAD population.
Methods: A total of 870 subjects from Shaanxi Province, China were selected from June 2019, to April, 2021. The airway inflammation of SAD was assessed by detecting exhaled NO in the nose, air duct, small airway, and alveoli. Serum levels of inflammatory cytokines including Th1 cytokines IFN-γ and IL-2, Th2 cytokines IL-4 and IL-6, and Th17 cytokines IL-17 and TNF-α were determined by ELISA.
Results: The values of FeNO200 (small airway) of SAD, Pre-SAD and Post-SAD were all higher than those of the normal group (P=0.012, P=0.04, P=0.037, respectively). CaNO (alveolar) of SAD, Pre-SAD and Post-SAD were all higher than those of the normal group (all P<0.0001). For Post-SAD, IL-4 is higher than normal group (P=0.034). IL-6, IL-17 and TNF-α in SAD, Pre-SAD and Post-SAD were both higher than those in the normal group (all P<0.05).
Conclusion: Patients with SAD have airway inflammation and change of systemic inflammatory factors.
Identification of a conserved glycolytic protein NbGAPDH interacting with NbMnSOD2 in Nosema bobycis
Authors: Wang Ying , Zhang Zhikun , Nian Siji , Xu Jinzhi , Ran Maoshuang , xiang Heng , Pan Guoqing , Zhou Zeyang 
Published: April 2023

Abstract
Two manganese superoxide dismutases, NbMnSOD1 and NbMnSOD2, were characterized previously in microsporidian Nosema bombycis. However, the functional information related to manganese superoxide dismutase in this obligate parasite is still limited. In this study, we further explored the potential proteins interacting with NbMnSOD2 using Co-immunoprecipitation and tandem mass spectrometry (LC-MS/MS) in N. bombycis, and the result indicated that a glyceraldehyde-3-phosphate dehydrogenase (NbGAPDH), which is a conserved glycolytic protein in microsporidia, may interact with NbMnSOD2. As following, we prepared the polyclonal antibody against NbGAPDH, and immunofluorescence analyses (IFA) revealed NbGAPDH colocalized with NbMnSOD2 on the spore wall of N. bombycis. Immuno-electron microscopy (IEM) further demonstrated that NbGAPDH could be detected on the spore wall of mature spores, consisting with the spore wall localization of NbMnSOD2 reported previously. The Co-immunoprecipitation, IFA and IEM results supported that NbGAPDH was a potential protein interacting with NbMnSOD2, suggesting it may display non-glycolytic functions in microsporidian N. bombycis, due to its special subcelluar localization. Moreover, the gene expression of NbGAPDH was detected in BmE cells during 1-4 days post-infection with qRT-PCR, and the result showed that the expression of NbGAPDH was present during 6h to 4 days post-infection, with the highest expression at day 2 post-infection, suggesting NbGAPDH may play essential roles during the development of N. bombycis. This study provides partial useful insights for the function of manganese superoxide dismutase in this obligate parasite.
E2E-BPF microscope: Extended depth-of-field microscopy
using learning-based implementation of binary phase filter and image deconvolution
Authors: Seong Baekcheon , Kim Woovin , Kim Younghun , Lee Jong-Seok , Yoo Jeonghoon , Joo Chulim 
Published: April 2023

Abstract
Several image-based biomedical diagnoses require high-resolution imaging capabilities at large spatial scales. However, conventional microscopes exhibit an inherent trade-off between depth-of-field (DoF) and spatial resolution, and thus require objects to be refocused at each lateral location, which is time-consuming. Here, we present a computational imaging platform, termed E2E-BPF microscope, which enables large-area, high-resolution imaging of large-scale objects without serial refocusing. This method involves a physics-incorporated, deep-learned design of binary phase filter (BPF) and jointly optimized deconvolution neural network, which altogether produces high-resolution, high-contrast images over extended depth ranges. We demonstrate the method through numerical simulations and experiments with fluorescently labeled beads, cells and tissue section, and present high-resolution imaging capability over a 15.5-fold larger DoF than the conventional microscope. Our method provides highly effective and scalable strategy for DoF-extended optical imaging system, and is expected to find numerous applications in rapid image-based diagnosis, optical vision, and metrology.
The effects of the administration sequence and the type of hypnotics on the development of remifentanil-induced chest wall rigidity:A randomized controlled trial
Authors: Oh Yu Jin , Kim Yesull , Lee Chanhong , Kim Dong-Chan , Doo Aram 
Published: April 2023

Abstract
Background
Research on remifentanil-induced chest wall rigidity is limited. Furthermore, its incidence is unknown, and the clinical factors influencing its development remain unclear. This prospective, double-blind, randomized controlled trial aimed to investigate the effects of the administration sequence of hypnotics and remifentanil as well as the type of hypnotic administered on the development of remifentanil-induced chest wall rigidity.
Methods
A total of 125 older patients aged \(\ge\)65 years, who were scheduled to undergo elective surgery under general anesthesia, were enrolled in this study. Participants were randomly assigned to one of four groups; Thio-Remi, Pro-Remi, Remi-Thio, or Remi-Pro. After confirming the loss of consciousness and achieving a target effect-site concentration of 3 ng/mL remifentanil, the development of remifentanil-induced chest wall rigidity was evaluated.
Results
The incidence of chest wall rigidity was significantly higher in the remifentanil-hypnotic group than in the hypnotic-remifentanil (opposite sequence) group (55.0% vs. 21.7%, P < 0.001). Logistic regression analysis revealed that remifentanil-hypnotic administration was a significant predictor of the development of chest wall rigidity (crude odds ratio 4.42, 95% confidence interval 1.99; 9.81, P < 0.001).
Conclusions
Pretreatment with hypnotics potentially reduces the development of chest wall rigidity during the induction of balanced anesthesia with remifentanil in older patients.
Trial registration
This article was registered at WHO International Clinical Trials Registry Platform (Trial number: KCT0006542).
Understanding the role of Reynolds number on self-assembly formation of nanoparticles
Authors: Dai Zhiqi , Yuan Ruoshi , Yuan Ru-Yue , Liu Yan-Jun , Xu Jiang 
Published: April 2023

Abstract
Self-assembly formation of nanoparticles (NPs) is a central theme in nanotechnology that has garnered significant attention in both academia and industry. The size of self-assembled NPs plays crucial role in their physicochemical properties. It has long been known that when macromolecules in a solvent being exposed to an anti-solvent, they can spontaneously form NPs of varying sizes through static diffusion (mixing rate = 0) and dynamic convection (mixing rate > 0). However, the impact of solvent mixing rate on the size of self-assembled NPs remains a mystery. Here, for the first time, we mathematically and experimentally prove that Reynolds number (Re), which quantifies fluid turbulence, is decisive on the self-assembly formation of NPs, by exponentially influencing the way kinetic energy of precursor molecules converting into surface energy of subsequent NPs. We surprisingly find that various self-assembly systems share a very similar critical value of Re about 1,000 ~ 1,200, which predetermines whether self-assembly occurs following a low or high energy dissipation pathway. This new framework further enables us to quantitatively determine energy conversion efficiency of a self-assembly process, measure surface tension of NP in a complex system, and predict NP size at arbitrary Re (including 0), which cannot be achieved in the past due to the limits of technology.
Artificial intelligence for the prevention and prediction of colorectal neoplasms
Authors: Tokutake Kohjiro , Morelos-Gomez Aaron , Hoshi Ken-ichi , Katouda Michio , Tejima Syogo , Endo Morinobu 
Published: April 2023

Abstract
Background
Colonoscopy is a useful as a cancer screening test. However, in countries with limited medical resources, there are restrictions on the widespread use of endoscopy. Non-invasive screening methods to determine whether a patient requires a colonoscopy are thus desired. Here, we investigated whether artificial intelligence (AI) can predict colorectal neoplasia.
Methods
We used data from physical exams and blood analyses to determine the incidence of colorectal polyp. However, these features exhibit highly overlapping classes. The use of a kernel density estimator (KDE)-based transformation improved the separability of both classes.
Results
Along with an adequate polyp size threshold, the optimal machine learning (ML) models' performance provided 0.37 and 0.39 Matthews correlation coefficient (MCC) for the datasets of men and women, respectively. The models exhibit a higher discrimination than fecal occult blood test with 0.047 and 0.074 MCC for men and women, respectively.
Conclusion
The ML model can be chosen according to the desired polyp size discrimination threshold, may suggest further colorectal screening, and possible adenoma size. The KDE feature transformation could serve to score each biomarker and background factors (healthy lifestyles) to suggest measures to be taken against colorectal adenoma growth. All the information that the AI model provides can lower the workload for healthcare providers and be implemented in health care systems with scarce resources. Furthermore, risk stratification may help us to optimize the efficiency of resources for screening colonoscopy.
Network-level mechanisms underlying effects of transcranial direct current stimulation (tDCS) on visuomotor learning impairments in schizophrenia.
Authors: Javitt Daniel , Sehatpour Pejman , Kreither Johanna , Lopez-Calderon Javier , Shastry Adithya , De-Baun Heloise , Martinez Antigona 
Published: April 2023

Abstract
Motor learning is a fundamental skill to our daily lives. Dysfunction in motor performance in schizophrenia (Sz) is associated with poor social and functional outcomes, but nevertheless remains understudied relative to other neurocognitive domains. Moreover, transcranial direct current stimulation (tDCS) can influence underlying brain function in Sz and may be especially useful in enhancing local cortical plasticity, but underlying neural mechanisms remain incompletely understood. Here, we evaluated performance of Sz individuals on the Serial Reaction Time Task (SRTT), which has been extensively used in prior tDCS research, in combination with concurrent tDCS and EEG source localization first to evaluate the integrity of visuomotor learning in Sz relative to other cognitive domains and second to investigate underlying neural mechanisms. Twenty-seven individuals with Sz and 21 healthy controls (HC) performed the SRTT task as they received sham or active tDCS and simultaneous EEG recording. Measures of motor, neuropsychological and global functioning were also assessed. Impaired SRTT performance correlated significantly with deficits in motor performance, working memory, and global functioning. Time-frequency (“Beamformer”) EEG source localization showed beta-band coherence across supplementary-motor, primary-motor and visual cortex regions, with reduced visuomotor coherence in Sz relative to HC. Cathodal tDCS targeting both visual and motor regions resulted in significant modulation in coherence particularly across the motor-visual nodes of the network accompanied by significant improvement in motor learning in both controls and patients. Overall, these findings demonstrate the utility of the SRTT to study mechanisms of visuomotor impairment in Sz and demonstrate significant tDCS effects on both learning and connectivity when applied over either visual or motor regions. The findings support continued study of dysfunctional dorsal-stream visual connectivity and motor plasticity as components of cognitive impairment in Sz, of local tDCS administration for enhancement of plasticity, and of source-space EEG-based biomarkers for evaluation of underlying neural mechanisms.