bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutations in CCNB3 affect its location thus causing a multiplicity of phenotypes in human oocytes maturation by aberrant CDK1 activity and APC/C activity at different stages
Authors: Wang Congjing , Chen Meng Xi , Zhang Yuan , Bai Xue , Cao Qiqi , Han Jian , Zhang Nana , Zhao Chun , Ling Xiufeng , Rui Ximan , Guan Yichun , Zhang Junqiang , Huo Ran 
Published: August 2023

Abstract
Background
Oocyte maturation arrest results in female infertility and the genetic etiology of this phenotype remains largely unknown. Previous studies have proven that cyclins play a significant role in the cell cycle both in meiosis and mitosis. Cyclin B3 (CCNB3) is one of the members of the cyclin family and its function in human oocyte maturation is poorly understood.

Methods
118 infertile patients were recruited and WES was performed for 68 independent females that experienced oocyte maturation arrest. Four mutations in CCNB3 were found and effects of these mutations were validated by Sanger sequencing and in vitro functional analyses.

Results
We found these mutations altered the location of cyclin B3 which affected the function of cyclin dependent kinase 1 (CDK1) and led to mouse oocyte arrested at germinal vesicle (GV) stage. And then, low CDK1 activity influenced the degradation of cadherin 1 (CDH1) and the accumulation of cell division cycle 20 (CDC20) which are two types of anaphase-promoting complex/cyclosome (APC/C) activators and act in different stages of the cell cycle. Finally, APC/C activity was downregulated due to insufficient CDC20 level and resulted in oocyte metaphase I (MI) arrest. Moreover, we also found that the addition of PP1 inhibitor Okadic acid and CDK1 inhibitor Roscovitine at corresponding stages during oocyte in vitro maturation (IVM) significantly improved the maturation rates in CCNB3 mutant cRNAs injected oocytes. The above experiments were performed in mouse oocytes.

Conclusion
Here, we report five independent patients in which mutations in CCNB3 may be the cause of oocyte maturation arrest. Our findings shed lights on the critical role of CCNB3 in human oocyte maturation.
Trends in mosquito species distribution modeling: insights for vector surveillance and disease control
Authors: Lippi Catherine A. , Mundis Stephanie J. , Sippy Rachel , Flenniken J. Matthew , Chaudhary Anusha , Hecht Gavriella , Carlson Colin J. , Ryan Sadie J. 
Published: August 2023

AbstractSpecies distribution modeling (SDM) has become an increasingly common approach to explore questions about ecology, geography, outbreak risk, and global change as they relate to infectious disease vectors. Here, we conducted a systematic review of the scientific literature, screening 563 abstracts and identifying 204 studies that used SDMs to produce distribution estimates for mosquito species. While the number of studies employing SDM methods has increased markedly over the past decade, the overwhelming majority used a single method (maximum entropy modeling; MaxEnt) and focused on human infectious disease vectors or their close relatives. The majority of regional models were developed for areas in Africa and Asia, while more localized modeling efforts were most common for North America and Europe. Findings from this study highlight gaps in taxonomic, geographic, and methodological foci of current SDM literature for mosquitoes that can guide future efforts to study the geography of mosquito-borne disease risk.
Graphical Abstract
Diagnostic performance of Strongyloides-specific IgG4 detection in urine for diagnosis of human strongyloidiasis
Authors: Wongphutorn Phattharaphon , Worasith Chanika , Kopolrat Kulthida Y. , Homwong Chutima , Sithithaworn Jiraporn , Eamudomkarn Chatanun , Techasen Anchalee , Tippayawat Patcharaporn , Pitaksakurat Opal , Hongsrichan Nuttanan , Crellen Thomas , Sithithaworn Paiboon 
Published: August 2023

Abstract
Background
Detection of parasite-specific IgG in urine is a sensitive method for diagnosis of strongyloidiasis and gives similar accuracy to serum IgG. However, there are no data concerning detection of IgG subclass in urine. To further explore the utility of diagnosis from urine samples, we evaluated the diagnostic performance of IgG4 in urine compared with parasitological and other immunological methods.

Methods
The urine and sera included proven strongyloidiasis (group 1, n = 93), other parasitic infections (group 2, n = 40) and parasite negatives (group 3, n = 93). The performance of Strongyloides-specific IgG4 in urine for diagnosis of strongyloidiasis using fecal examinations as the reference standard was assessed.

Results
With fecal examination as a gold standard, Strongyloides-specific IgG4 in urine had 91.4% sensitivity and 93.2% specificity while serum IgG4 had 93.6% sensitivity and 91.0% specificity. IgG4 in both urine and serum had almost perfect diagnostic agreements with fecal examination (Cohen's kappa coefficient was > 0.8). Cross-reactivity to Opisthorchis viverrini and Taenia spp. of IgG4 in urine were 7.5% and 12.5% in serum. Concurrent analyses of total IgG in urine and serum showed that the sensitivities (97.9–100%) and specificities (88.7–91.0%) were similar (P > 0.05). The sensitivity for parasitological examination by the formalin-ethyl acetate concentration technique (FECT) was 49.5% and that for agar plate culture technique (APC) it was 92.6%.

Conclusion
Our findings showed that specific IgG4 detection in urine yielded similar diagnostic performance to the same biomarkers in serum. This suggests that accurate diagnosis of strongyloidiasis can be performed using urine samples and IgG4 is a valid choice of diagnostic marker. Further assessment is required to assess the utility of urine IgG4 for measuring the response treatment in strongyloidiasis.

Graphical Abstract
Idiopathic omental hemorrhage: a case report and review of the literature
Authors: Rashidi Fatemeh , Samimiat Alireza , Jafarimehrabady Niloofar , Hajebi Reza 
Published: August 2023

Abstract
Background
A spontaneous rupture of an omental vessel can cause severe intraabdominal hemorrhage. We present a case of idiopathic omental hemorrhage caused by a vascular malformation. The literature is systematically reviewed.

Case presentation
A 65-year-old Iranian man was admitted to the emergency department for 10 days with abdominal pain. His medical history was not significant. Fever, vomiting, nausea, or anorexia were not reported. However, he was suffering from diaphoresis and malaise at the time. He did not smoke or drink alcohol. During physical examination, blood pressure was 82/60 mmHg with a temperature of 36.6 °C; heart rate was 96 beats/minute and respiratory rate was 18 breaths per/minute. An abdominal examination revealed mild tenderness in the periumblical. The focused assessment with sonography in trauma examination yielded positive results. The complete blood count showed 14 × 103/mcL of white blood cells and 185 × 103/mcL of platelets. The hemoglobin value was 6.7 g/L at admission. To stabilize the patient’s condition, a unit of packed cell was administered. A double contrast enhancement abdominal computer tomography was performed, which revealed a massive hemoperitoneum. Subsequently, an exploratory laparoscopy was performed to search for the responsible pathology. But it was not successful. The surgical plan was changed to laparotomy. The hemorrhage source was not found during laparotomy. Observation revealed a massive hemoperitoneum originating in the omental vessels. A portion of the omentum located on the greater omentum at the greater curve was removed. Based on the pathological examination of the extracted tissue, vascular malformations were identified. The patient recovered uneventfully and was discharged from the hospital 7 days after surgery. Previous reports assessing idiopathic omental bleeding were systematically reviewed. A total of 14 hits were identified in PubMed and Scopus from 2015 to November 2022 for idiopathic omental bleeding.

Conclusion
Presence of positive focused assessment with sonography in trauma, abdominal pain, imaging evidence of fluid accumulation, and a reduction in hemoglobin levels collectively indicate the likelihood of arteriovenous malformation occurrence. The treatment options include surgical intervention and transcatheter arterial embolization. Surgical intervention is recommended for subjects with hemodynamic instability, persistent hypotension and those whose diagnosis is unconfirmed.
Efficient strategy to isolate exosomes using anti-CD63 antibodies conjugated to gold nanoparticles
Authors: Panwar Dikshita , Shrivastava Deepali , Kumar Arvind , Gupta Lavleen Kumar , Kumar N. S. Sampath , Chintagunta Anjani Devi 
Published: August 2023

AbstractExosomes, a subpopulation of Extracellular vesicles (EVs), are cell-secreted vesicles found in the majority of biological fluids, including breast milk, tears, sweat, blood and, urine. The density and size of these vesicles depend on a variety of factors, including age, gender and the biological condition of the individual. Researchers are now focusing on the selective extraction of exosomes from bodily fluids due to the unique biomolecule composition of exosomes, which is critical for diagnosis, disease, and regeneration. Furthermore, current approaches for exosome isolation have limitations, necessitating the development of a simpler and more effective technique to achieve this goal. In this study, we investigated a quick and effective strategy for isolating exosomes from serum using a bench-top centrifuge. This was accomplished by raising antibodies against exosome surface tetraspanins (CD9, CD63 & CD81) in Leghorn chickens due to their phylogenetic distance from humans and cost-effectiveness for commercial use. In order to separate exosomes from a complex biological fluid, the antibodies were further coupled with gold nanoparticles (AuNPs). The findings were validated using ELISA, spectrophotometry, and transmission electron microscopy (TEM). Using this technique, exosome isolation from serum was achieved rapidly and these were captured by using anti CD63 antibodies bound to AuNPs. To summarize, exosomes were purified from serum using anti-CD63 antibodies conjugated to gold nanoparticles (IgY@AuNPs). Consequently, the approach for exosome isolation from biological fluid could be useful for clinically monitoring the biological state of the patients.
Blind reconfigurable intelligent surface-aided fixed non-orthogonal multiple access for intelligent vehicular networks
Authors: Kumaravelu Vinoth Babu , Selvaprabhu Poongundran , Han Dong Seog , Sarker Md. Abdul Latif , Periyakarupan Gurusamy Sivabalan Velmurugan , Sundarrajan Jayaraman Thiruvengadam , Murugadass Arthi , Evangeline C. Suganthi 
Published: August 2023

AbstractIn intelligent vehicular networks, vehicles should be able to communicate with their surroundings while traveling. This results in more efficient, safer, and comfortable driving experiences, as well as new commercial prospects in a variety of industries. Connected vehicles and autonomous vehicles expect 100% reliable connectivity without any compromise in quality. However, due to challenges such as difficult channel terrains in urban scenarios and dead zones, the reliability of current vehicle-to-infrastructure (V2I) and vehicle-to-vehicle communication systems cannot be guaranteed. The performance of vehicular networks can be considerably enhanced with reconfigurable intelligent surfaces (RIS). Non-orthogonal multiple access (NOMA) allows for massive connectivity with the surroundings. In vehicular networks, the RIS-assisted NOMA can ensure regulated channel gains, better coverage, throughput, and energy efficiency. In this work, a blind RIS-assisted fixed NOMA (FNOMA) system is proposed for a downlink V2I scenario. The closed-form analytical outage probability and throughput expressions are derived by considering RIS as an intelligent reflector and as a roadside unit. It is observed that the analytical and Monte Carlo simulation results are closely related. In simulations, it has been discovered that RIS-assisted FNOMA outperforms the traditional NOMA variants in terms of outage and throughput. Even without precise channel knowledge, blind RIS transmission outperforms traditional NOMA variants due to huge array gain. The increase in the number of reflective elements also results in a significant improvement in signal-to-noise ratio gains.
RETRACTED ARTICLE: Hybrid extreme learning machine-based approach for IDS in smart Ad Hoc networks
Authors: Liu Bijian 
Published: August 2023

AbstractIn recent years, intrusion detection systems (IDSs) have increasingly come to be regarded as a significant method due to their potential to develop into a key component that is necessary for the safety of computer networks. This work focuses on the usage of extreme learning machines, which are also known as ELMs, with the purpose of spotting prospective intrusions and assaults. The proposed method combines the self-adaptive differential evolution method for optimising network input weights and hidden node biases and multi-node probabilistic approach with the extreme learning machine for deriving network output weights. This body of work presents an innovative method of learning that can be put into practice in order to determine whether or not an incursion has taken place in the system that is the focus of the investigation that is being carried out by this body of work. A hybrid extreme learning machine is used in the execution of this strategy. When there is one thousand times more traffic on a network, the ability of regular IDS systems to detect malicious network intrusions is lowered by a factor of one hundred. This is because there are less opportunities to detect the intrusions. This is due to the fact that there are less probabilities to identify potential dangers. This paper lays the groundwork for a novel methodology for identifying malicious network breaches. The findings of the simulation demonstrated that putting into practice the approach that was proposed resulted in an improvement in the accuracy of the scenario's classification while it was being investigated. The implementation of the method seems to have produced the desired results.
MFGAD-INT: in-band network telemetry data-driven anomaly detection using multi-feature fusion graph deep learning
Authors: Duan Yunfeng , Li Chenxu , Bai Guotao , Chen Guo , Zhou Fanqin , Chen Jiaxing , Gao Zehua , Zhang Chun 
Published: August 2023

AbstractAs the cloud services market grows, cloud management tools that detect network anomalies in a non-intrusive manner are critical to improve users’ experience of cloud services. However, some network anomalies, such as Microburst, in cloud systems are very discreet. Network monitoring methods, e.g., SNMP, Ping, are of coarse temporal granularity or low-dimension metrics, have difficulty to identify such anomalies quickly and accurately. Network telemetry is able to collect rich network metrics with fine temporal granularity, which can provide deep insight into network anomalies. However, the rich features in the telemetry data are insufficient exploited in existing research. This paper proposes a Multi-feature Fusion Graph Deep learning approach driven by the In-band Network Telemetry, shorted as MFGAD-INT, to efficiently extract and process the spatial-temporal correlation information in telemetry data and effectively identify the anomalies. The experimental results show that the accuracy performance of the proposed method improves about 10.56% compared to the anomaly detection method without network telemetry and about 9.73% compared to the network telemetry-based method.
Linking soil organic carbon mineralization to soil physicochemical properties and bacterial alpha diversity at different depths following land use changes
Authors: Guo Jing , Xiong Wulai , Qiu Jian , Wang Guibin 
Published: August 2023

Abstract
Background
Anthropogenic land use changes (LUCs) impart intensifying impacts on soil organic carbon (SOC) turnover, leading to uncertainty concerning SOC mineralization patterns and determining whether soils act as “source” or “sink” in the global carbon budget. Therefore, understanding the SOC mineralization characteristics of different LUC patterns and their potential influencing factors is crucial. An indoor incubation experiment was conducted to study the SOC mineralization patterns and their relevance to soil physicochemical properties, soil enzyme activity, SOC fractions, and bacterial alpha diversity. The soils were collected from two layers of five typical LUC patterns in Yellow Sea Forest Park, including four that were converted from wheat–corn rotation systems [a gingko plantation (G), a metasequoia plantation (M), a gingko–wheat–corn agroforestry system (GW), and a gingko–metasequoia system (GM)] and a traditional wheat–corn system (W).

Results
LUCs had significant and diverse impacts on the SOC content and SOC fraction contents and on soil enzyme activity. The cumulative SOC mineralization was significantly higher in the M systen than in the W and GW systems at 0–20 cm depth and higher in the G system than in the GW system at 20–40 cm depth after 60-day incubation. The mineralization ratio was highest in the W system and lowest in the GW system. The soil pH and bulk density had a significant negative correlation with the cumulative SOC mineralization, while the soil bacterial Shannon index had a significant positive correlation with cumulative SOC mineralization. Multiple stepwise linear regression analysis showed that the SOC mineralization potential was dominantly explained by the bacterial Shannon index and operational taxonomic units (OTUs). The GW system had lower potentially mineralizable SOC and higher SOC stability. Additionally, the incubation time and cumulative SOC mineralization were well fitted by the first-order kinetic equation.

Conclusions
LUCs significantly changed SOC mineralization characteristics and the results highlighted the important roles of the bacterial community in soil carbon cycling, which contributes to the fundamental understanding of SOC turnover regulation.
The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses
Authors: Zhai Xichuan , Castro-Mejía Josué L. , Gobbi Alex , Aslampaloglou Antonios , Kot Witold , Nielsen Dennis S. , Deng Ling 
Published: August 2023

Abstract
Background
There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing.

Results
We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4 °C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100 days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100 days. Prolonged storage time (500 days) at – 80 °C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as “uncharacterised”. Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction.

Conclusion
Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4 °C for the isolation of viruses and at – 80 °C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing.
Multi-omics reveal microbial determinants impacting the treatment outcome of antidepressants in major depressive disorder
Authors: Wang Yaping , Zhou Jingjing , Ye Junbin , Sun Zuoli , He Yi , Zhao Yingxin , Ren Siyu , Zhang Guofu , Liu Min , Zheng Peng , Wang Gang , Yang Jian 
Published: August 2023

Abstract
Background
There is a growing body of evidence suggesting that disturbance of the gut-brain axis may be one of the potential causes of major depressive disorder (MDD). However, the effects of antidepressants on the gut microbiota, and the role of gut microbiota in influencing antidepressant efficacy are still not fully understood.

Results
To address this knowledge gap, a multi-omics study was undertaken involving 110 MDD patients treated with escitalopram (ESC) for a period of 12 weeks. This study was conducted within a cohort and compared to a reference group of 166 healthy individuals. It was found that ESC ameliorated abnormal blood metabolism by upregulating MDD-depleted amino acids and downregulating MDD-enriched fatty acids. On the other hand, the use of ESC showed a relatively weak inhibitory effect on the gut microbiota, leading to a reduction in microbial richness and functions. Machine learning-based multi-omics integrative analysis revealed that gut microbiota contributed to the changes in plasma metabolites and was associated with several amino acids such as tryptophan and its gut microbiota-derived metabolite, indole-3-propionic acid (I3PA). Notably, a significant correlation was observed between the baseline microbial richness and clinical remission at week 12. Compared to non-remitters, individuals who achieved remission had a higher baseline microbial richness, a lower dysbiosis score, and a more complex and well-organized community structure and bacterial networks within their microbiota. These findings indicate a more resilient microbiota community in remitters. Furthermore, we also demonstrated that it was not the composition of the gut microbiota itself, but rather the presence of sporulation genes at baseline that could predict the likelihood of clinical remission following ESC treatment. The predictive model based on these genes revealed an area under the curve (AUC) performance metric of 0.71.

Conclusion
This study provides valuable insights into the role of the gut microbiota in the mechanism of ESC treatment efficacy for patients with MDD. The findings represent a significant advancement in understanding the intricate relationship among antidepressants, gut microbiota, and the blood metabolome. Additionally, this study offers a microbiota-centered perspective that can potentially improve antidepressant efficacy in clinical practice. By shedding light on the interplay between these factors, this research contributes to our broader understanding of the complex mechanisms underlying the treatment of MDD and opens new avenues for optimizing therapeutic approaches.