bluuebunny/crossref_metadata_2025_split huggingface dataset:
A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences
Authors: Nørrevang Anton Frisgaard , Shabala Sergey , Palmgren Michael 
Published: September 2023

Abstract
Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is of interest to identify all members of a given gene family in a genome. In this work, we developed a method for identifying most, if not all, members of a gene family from a raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22. Taken together, the method developed proved useful for identification of P-type ATPase family members in raw genomes that are poorly assembled.
Tracheobronchial diverticulum, a potential risk for diving?
Authors: Qing Long , Wang Yan , Zhang Meng , Pu Qinqin , Cai Wanwan , Pan Yaping , Xia Delin 
Published: September 2023

Abstract
Background: Tracheobronchial diverticulum(TBD) is a cystic lesion outside the lumen of the trachea and bronchus. This is the first report case of a SCUBA(Self Contained Underwater Breathing Apparatus) diver diagnosed with tracheo diverticulum(TD), which is a potential risk to diving. So far no literature or guideline is available on the diving fitness for patients with such a condition.
Case presentation: An asymptomatic 26-year-old male professional diver has a history of SCUBA diving up to depth of 40 m. He did not have any diving-related injuries or symptoms and had no history of smoking, drinking, or other special illnesses except for a COVID-19 infection. A tracheal diverticulum was found by computed tomography(CT), but its communication with the trachea was not clear. Therefore, high-resolution CT and electronic bronchoscopy were used to clarify the situation of diverticulum and identify the diving risk. High-resolution CT showed a possible opening of diverticulum, but this was not seen under electronic bronchoscopy.
Conclusion: Although a potential opening was showed in high-resolution CT, the lack of visual bronchoscopic evidence made it likely to be a dead cavity. As such, there is a higher theoretical risk of barotrauma during decompression, leading to pneumomediastinum, hemorrhage or arterial gas embolism. Take it into consideration, the current clinical consensus is that air-containing tissue should be regarded as relative contraindications to diving. Overall speaking, it is recommended that the diver need to dive carefully and avoid rapid decompression.
Analysis of influencing factors and construction of prediction model for postoperative nausea and vomiting in patients undergoing laparoscopic sleeve gastrectomy: a single-center retrospective cohort study
Authors: Liao Bucheng , Liao Wuhao , Wu Xinhai , Liu Shujuan , Li Yanze , Qin Ruixia , Yin Shuang 
Published: September 2023

Abstract
Background: With the increasing number of bariatric surgeries, the high incidence of postoperative nausea and vomiting (PONV) associated with this surgery has also gradually attracted attention. Among the common bariatric surgery methods, patients undergoing sleeve gastrectomy (SG) have the highest incidence of nausea and vomiting. The mechanism of occurrence of PONV is very complex. This study aims to explore the influencing factors of PONV in patients undergoing laparoscopic sleeve gastrectomy (LSG) and construct a nomogram prediction model based on these factors.
Methods: With the approval of the Ethics Committee, the electronic medical records of patients who underwent LSG from July 2022 to May 2023 were collected retrospectively.
Results: A total of 114 patients with complete medical records who underwent LSG from July 2022 to May 2023 were included in this study. Among them, 46 patients developed PONV, resulting in a PONV incidence rate of 40.4%. Multivariate logistic regression analysis revealed that female gender, the use of inhalation anesthesia, and operation time ≥ 120 minutes were risk factors for PONV in LSG. Additionally, the use of more than two kinds of antiemetic drugs was identified as a protective factor. Based on these factors, a nomogram model was constructed.
Conclusion: PONV in patients undergoing LSG is related to gender, type of anesthesia, duration of surgery, and combination therapy with antiemetic drugs. The nomogram prediction model constructed in this study demonstrates high accuracy and discrimination in predicting the occurrence of PONV in patients undergoing LSG.
Association between Serum Sodium Trajectory and Mortality in Patients with Acute Kidney Injury: A Retrospective Cohort Study
Authors: Huang Shanhe , Li Xiaojing , Chen Baorong , Zhong Yaqi , Li Yuewei , Huang Tucheng 
Published: September 2023

Abstract

Introduction:
Dysnatremia is strongly associated with poor prognosis in acute kidney injury (AKI); however, the impact of sodium trajectories on the prognosis of patients with AKI has not yet been well elucidated. This study aimed to assess the association between sodium trajectories in patients with AKI and mortality at 30-day and 1-year follow-up.
Methods
This retrospective cohort study used data from Medical Information Mart for Intensive Care (MIMIC)-IV database, and patients diagnosed with AKI within 48h after admission were enrolled. Group-based trajectory models (GBTM) were applied to map the developmental course of the serum sodium fluctuations. Kaplan-Meier survival curve was used to compare differences in mortality in AKI patients with distinct serum sodium trajectories. Hazard ratios (HRs) were calculated to determine the association between trajectories and prognosis using Cox proportional hazard models.
Results
A total of 9,314 AKI patients were enrolled. Three distinct sodium trajectories were identified including: (i) stable group (ST, in which the serum sodium levels remained relatively stable, n = 4,935; 53.0%), (ii) descending group (DS, in which the serum sodium levels declined, n = 2,994; 32.15%) and (iii) ascending group (AS, in which the serum sodium levels were elevated, n = 1,383; 14.85%). There was no significant difference in age and gender distribution among the groups. The 30-day mortality rates were 7.9% in ST, 9.5% in DS and 16.6% in AS (p < 0.001). The results of 1-year mortality rates were similar (p < 0.001). In adjusted analysis, patients in the DS (HR = 1.22, 95% confidence interval [CI], 1.04–1.43, p = 0.015) and AS (HR = 1.68, 95% CI, 1.42–2.01, p = 0.013) groups had higher risks of 30-day mortality compared to those in the ST group.
Conclusion
In patients with AKI, the serum sodium trajectories were independently associated with 30-day and 1-year mortality. Association between serum sodium level trajectories and prognosis in patients with AKI deserve further study.
Prediction of Personalized Prognosis in Patients with Acute-on-chronic Liver Failure: A Joint Model for Dynamic Risk Profiling
Authors: Li Xiangyong , Yu Mingxue , Xu Qinyao , Liu Ting , Chong Yutian , wang peipei , Jie Yusheng 
Published: September 2023

Abstract
Background: Short-term mortality is high in patients with acute-on-chronic liver failure (ACLF), defined by the rapid deterioration of underlying chronic liver diseases. Current prediction models cannot estimate dynamic prognosis adequately. This study used both longitudinal and survival data to develop and validate a dynamic prediction model for ACLF.
Methods: Adult patients with ACLF from a retrospective cohort, including 943 patients from 2014 to 2019 at the Third Affiliated Hospital of Sun Yat-sen University, were included. The progression of temporal indices was described using a mixed-effects model, and subject-specific prediction risk models with time-to-event data were constructed using a joint model (JM). The model was validated by testing the data using the area under the curve (AUC) and Brier score.
Results: The AUCs for JM ranged from 0.808 to 0.840 when predicting 28-day mortality and from0.747 to 0.811 when predicting 90-day mortality in patients with ACLF. The linearity of the calibration curves was good, with the Brier scores ranging from 0.083 to 0.205. The performance of the ACLF-JM for 90-day predictions was superior (P < 0.001) to that of the Model for End-Stage Liver Disease score.
Conclusions: It is possible to construct individualized dynamic event prediction models for patients with ACLF by jointly modeling longitudinal data with time-to-event outcomes. This JM provides a potentially valuable evidence-based tool for liver transplantation in clinical practice.
An Empirical Study on the Comprehensive Evaluation and Countermeasures of the Effectiveness of School-Enterprise Cooperation in Vocational Education in China
Authors: Shao Tianshu , Wu Huabin , Lin Mengyan , Xu Xiangdong 
Published: September 2023

Abstract
School-enterprise cooperation is a crucial strategy in China's vocational education and a vital aspect of vocational education reform. Conducting a comprehensive empirical study and evaluation of the effectiveness of school-enterprise cooperation in China's vocational education can enhance the quality and efficiency of such cooperation. Nevertheless, current evaluations of school-enterprise cooperation are predominantly theoretical, and there is a scarcity of systematic indicators and empirical research methods. To address this gap, the author adopts scientific, systematic, goal-oriented, and operational principles and utilizes stakeholder theory and system contract theory as the theoretical basis and framework. The author constructs three primary indicators, namely,participation, return, and potential, and several secondary indicators from the viewpoints of cooperation objectives, process, and results of vocational education school-enterprise cooperation for both schools and enterprises using factor analysis and the fuzzy comprehensive evaluation method. This evaluation offers precise empirical verification and a theoretical and practical reference for the high-quality practice of school-enterprise cooperation in China's vocational education.
Children Benefit from Gestures to Understand Degraded Speech but to a Lesser Extent than Adults
Authors: Sekine Kazuki , Özyürek Aslı 
Published: September 2023

Abstract
The present study investigated to what extent children, compared to adults, benefit from gestures to disambiguate degraded speech by manipulating speech signals and manual modality. Dutch-speaking adults (N = 20) and 6- and 7-year-old children (N = 15) were presented with a series of video clips in which an actor produced a Dutch action verb with or without an accompanying iconic gesture. Participants were then asked to repeat what they had heard. The speech signal was either clear or altered into 4- or 8-band noise-vocoded speech. Children had more difficulty than adults in disambiguating degraded speech in the speech-only condition. However, when presented with both speech and gestures, children reached a comparable level of accuracy to that of adults in the degraded-speech-only condition. Furthermore, for adults, the enhancement of gestures was greater in the 4-band condition than in the 8-band condition, whereas children showed the opposite pattern.Gestures help children to disambiguate degraded speech, but children need more phonological information than adults to benefit from use of gestures. Children’s multimodal language integration needs to further develop to adapt flexibly to challenging situations such as noisy contexts.
The impact of ageing on SARS-CoV-2 and human coronavirus reactive antibodies after COVID-19 vaccination or infection
Authors: Zhou Fan , Vahokoski Juha , Langeland Nina , Cox Rebecca 
Published: September 2023

Abstract
The endemic human coronavirus (HCoV) circulates worldwide yet remain understudied and unmitigated. The observation of elevated levels of HCoV reactive antibodies in COVID-19 patients highlights the urgent necessity of better understanding of HCoV specific immunity. Here, we characterized in-depth the de novo SARS-CoV-2 specific antibody responses and the boosting of HCoV-reactive antibodies after SARS-CoV-2 vaccination and infection in individuals up to 98 years old. The first two vaccine doses elicited potent SARS-CoV-2 spike binding antibodies in individuals up to 80 years old. The third dose largely boosted the previously low S2 domain binding and neutralizing antibodies in elderly 80–90 years old, but less so in those above 90 years. The endemic betacoronavirus (HKU1 and OC43) reactive antibodies were boosted in all vaccinees, although to a lesser extent in those above 80 years old. COVID-19 patients had potent elevation of alpha- and betacoronavirus (229E, NL63, HKU1 and OC43) reactive antibodies. In both patients and vaccinees, S2 domain specific antibody increases correlated with SARS-CoV-2 neutralizing and HCoV-reactive antibody responses in all ages, indicating S2 domain as a candidate for future universal coronavirus vaccine design.
The structure and diversity of denitrifying bacteria mediated by suspended particulate matter in aquaculture water bodies in Higher place pond
Authors: chunyi kuang , sun wei , Mingken Wei , Chunyu Xia , Changxiu Li 
Published: September 2023

Abstract
Suspended particulate matter (SPM) was an important part of aquaculture water and provides an important carrier for denitrification. SPM with different particle sizes were collected in the high place pond in Dianbai District of Maoming City. Phylogenetic diversity, community composition and their relationships with environmental factors were studied by high-throughput sequencing、fluorescence quantitative PCR and statistical analysis. The results showed that Proteobacteria was the dominant phylum of microbial community structure in aquaculture environment. The community of denitrifying bacteria mediated by SPM with different particle sizes was different. Low concentration and nutrient concentration made nitrifying archaea distributed in small particle size SPM. Moreover, the abundance of denitrification functional genes showed a trend of 5μm > 1μm > 0.22μm on SPM in the same site. The pH, DO, COD and TSS were the key factors affecting the niche distribution of denitrifying bacteria on SPM in the high place pond. These findings were crucial for deepening our understanding of the microbiology of nitrogen cycle processes such as denitrification and optimizing wastewater treatment strategies.
Comparison of the gene expression profile of testicular tissue before and after sexual maturity in Qianbei Ma goats
Authors: Chen Jiajing , Chen Xiang , Guo Wei , Tang Weng , Zhang Yuan , Tian Xingzhou , Zou Yue 
Published: September 2023

Abstract
Background:In this work that we took 3-month-old (presexual maturity) and 9-month-old (post-sexual maturity) goats as test subjects and observed the changes in the morphology of testicular tissues through HE staining; detected the serum testosterone,luteinizing hormone,follicle stimulating hormone and anti-Müllerianhormone content; analysedthe mRNA expression profiles of Qianbei Ma goat testes before and after sexual maturity by transcriptomics; and screened for differences in the expression of genes before and after sexual maturity.
Results:The results showed that the area and diameter of spermatogenic tubules were larger at age 9 months than at age 3 months, and the number of spermatocytes, interstitial cells, spermatogonia and secondary spermatocytes in the lumen of the tubules was increased compared with that at age 3 months. The appearance of spermatozoa at age 3 months indicated that puberty had begun in Qianbei goats. The Elasa test for testosterone, luteinizing hormone, follicle stimulating hormone and anti-Müllerian hormone showed that the levels of these hormones in the serum at age 9 months were all extremely significantly higher than those at age 3 months (p<0.01). we performed RNA-seq analysis 490 were found to be differentially expressed genes（DEGs）at the criteria of |log2(foldchange)| > 1 and pvalue＜0.05. of which 233 genes were upregulated and 257 genes were downregulated. Through GO and KEGG enrichment analysis, the candidate genes, PRSS58, ECM1, WFDC8 and LHCGR.
Conclusions:This work that may be involved in the regulation of testicular development and spermatogenesis in Qianbei Ma goats were identified, providing a theoretical basis and data support for later studies on the influence of testicular development and spermatogenesis before and after sexual maturity in Qianbei Ma goats.
Optimizing the Photocatalytic Degradation of 2,4-Dichlorophenoxyacetic Acid Herbicide from Aqueous Solution
Authors: Mehralipour Jamal , Motie Abolfazl , Kermani Majid 
Published: September 2023

Abstract
This study focuses on the synthesis of a g-C3N4/Fe3O4 nanocomposite and optimization of PCP in degrading 2,4-D in water. The g-C3N4 and the g-C3N4/Fe3O4 were synthesized using a two-step direct calcination approach and co-precipitation respectively. The quality assessment of the synthesized nanocomposite was conducted through the utilization of XRD, DRS, FTIR, FE-SEM, EDS, elemental mapping, TEM and VSM analytical techniques. The quadratic model has a high F-value (152.27) and low P-value (0.0001), indicating its suitability for explaining the amplification relationship between response values. The optimum parameters for PCP to decompose 2,4-D were determined to be pH~6.5, catalyst dose~16.5 mg/L, reaction time~55.5 min, and initial 2,4-D concentration~52 mg/L (96.11% degradation efficacy). The data showed strong correlation with first-order kinetics (R2>0.95). The efficiency of the PCP is boosted by the existence of a catalyst and photolysis, which creates multiple pathways for 2,4-D breakdown. The PCP exhibited a capacity to diminish COD and TOC by 75% and 63%, respectively. The reaction time decreases with higher light intensity and 2,4-D removal is complete in 45 minutes at 60 mW/cm2. Methanol greatly affects the PCP's scavenging ability. In contrast, the impact of sodium azide was observed to be the least significant and the OH● is deemed as the principal ROS in the PCP. The results show that PO43- reduces efficiency to 72%. The PCP's ability to remove 2,4-D, COD, and TOC remained consistent even after the sixth cycle. The EE/O, 17.3 KW/h.m3.order was calculated. The intermediate products were 2,4-dichlorophenol, 2,6-dichlorophenol, 4,6-dichlororesorcinol, 2-chlorohydroquinone, and 2-chloro-1,4-benzoquinone.
Interatrial conduction block – the phantom menace for patients with severe COVID 19?
Authors: Zawadzki Jacek , Gajek Jacek , Zawadzki Grzegorz , Kudliński Bartosz 
Published: September 2023

Abstract
SARS-CoV-2 is responsible for a worldwide pandemic, which has caused nearly 7 million of deaths. The effective treatment of COVID-19 is dependent on multipular risk factors, which are still under clinical research. The presence of interatrial block (IAB) could have an influence on the pulmonary circulation which can contribute to the severity of the disease. Our aim was to prove the IAB results in atrial asynchronous contraction which may contribute to the hemodynamic disorders or higher pressure in pulmonary circulation, and worse prognosis in COVID 19. The study included 50 patients (25F, 26M), aged 69,5+/-13,1 years, under hospitalization due to COVID 19. The study groups were divided dependent on the P wave morphology. 6 patients with AF were excluded from the study. All qualified patients required oxygen therapy (at least HFNO) and pharmacological treatment against SARS-CoV-2 related pneumonia. The clinical data included assessment of lungs lesions (CT scan), the lowest measured pO2/fiO2, and the comorbidities. The P wave was measured at 200mm/s, x265. The ECHO included EF, assessment of mitral regurgitation, LA strain, LA volume, the parameters of PVs regurgitation flow. We found that the normal P wave morphology was connected to the higher survival rate (p=0.019) while the full Bachmann bundle block (A-IAB) presented the opposite tendency (p=0,037). LV EF was another relevant variable in this regard (p=0.006). Among statistically relevant comorbidities we can enumerate HF (p=0.033) and arterial hypertension (p=0.006) from which suffered all patients who died in our research group. Interestingly, PACS and LA strain conduit did not correlate with survival. Similarly, the parameters of PVs reverse flow didn’t reveal the correlation with survival. Concluding, the presence of IAB (especially in the form of A-IAB), results in asynchronous LA contraction, which may constitute a risk factor in the course of COVID-19.
In vivo femtosecond laser nanosurgery of cell wall enables patch-clamp on filamentous fungi
Authors: Pajić Tanja , Stevanović Katarina , Todorović Nataša , Krmpot Aleksandar , Živić Miroslav , Savić-Šević Svetlana , Lević Steva , Stanić Marina , Pantelić Dejan , Jelenković Brana , Rabasović Mihailo 
Published: September 2023

Abstract
Studying the membrane physiology of filamentous fungi is key to understanding their interactions with the environment and crucial for developing new therapeutic strategies for disease-causing pathogens. However, their plasma membrane has been inaccessible for micron sized patch-clamp pipette for pA currents recordings due to the rigid chitinous cell wall. We report here the first femtosecond IR laser nanosurgery of the cell wall of filamentous fungi, enabling patch-clamp measurements on protoplasts released from hyphae. A reproducible and highly precise (diffraction limited, sub-micron resolution) method for obtaining viable released protoplasts was developed. Protoplast release from the nanosurgery-generated incisions in cell wall was achieved from different regions of the hyphae. Plasma membrane of obtained protoplasts formed tight and high-resistance (GΩ) contacts with the recording pipette. The entire nanosurgical procedure followed by patch-clamp technique can be completed in less than 1 hour. Compared to previous studies using heterologously expressed channels, this technique provides the opportunity to identify new ionic currents and to study the properties of ion channels in protoplasts of filamentous fungi in their native environment.