bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative proteomic analysis based on tandem mass tagging (TMT) reveals key proteins related to DNA hydroxymethylation enzyme TET1 for spermatogonia self-renewal
Authors: Liu Lingling , Wang Jin , Tao Xinjie , Wang Kaisheng , Zheng Liming 
Published: October 2022

Abstract
Background
Abnormal spermatogonia (SSCs) can cause spermatogenic disorders such as weak spermatozoa, oligospermia, and azoospermia. DNA hydroxymethylase TET1 hydroxylates the methylation sites of specific genes, enabling the process of DNA demethylation and regulating gene expression. However, the key differential genes affected by the specific action of TET1 and the mechanism of interaction between the differential genes are not clear.
Result
In this study, we applied quantitative proteomics techniques based on Tandem Mass Tags (TMT) to screen the 24h differentially expressed proteins in the TET1 overexpression group (MYC-TET1) and the control group (MYC) to provide a basis for studies such as the regulation of TET1-mediated epigenetic modifications on SSCs. By TMT technique, we identified 5891 proteins, of which 337 were significantly differentially expressed, 76 were up-regulated and 261 were down-regulated. Gene Ontology (GO) enrichment analysis revealed that proteins with significant differential expression such as RARG, RN114, DJC30, and ABHD2 were associated with functions such as sperm-egg recognition, sperm-egg fusion, sperm ejaculation, spermatogenesis and development, and embryonic development. changes in proteins such as GHR, CCNT1, HTRA1, and ANXA3 affected cell viability, gene transcription and translation activities, and important intracellular biological processes in SSCs. intracellular biological processes.
Conclusions
In this study, we obtained differential protein profiles by overexpressing TET1 in SSCs and subsequently by TMT protein sequencing technology, combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis, GO enrichment analysis and protein interaction network map to jointly analyze the epistatic regulatory role of TET1 on SSCs, which provides a scientific basis for further study of spermatogenesis and contributes to the understanding of male reproductive system diseases.
Diagnostic performance of digital PET with a dedicated head and neck protocol for the assessment of cranial arteries inflammation in Giant Cell Arteritis
Authors: DURAND-BAILLOUD Bastien , SAMSON Maxime , BERTAUT Aurelie , THIBAULT Thomas , DROUET Clement , POPOFF Romain , SOUDRY-FAURE Agnès , COCHET Alexandre , BONNOTTE Bernard , ALBERINI Jean Louis 
Published: October 2022

Abstract
Introduction

Giant cell arteritis (GCA) is a frequent granulomatous vasculitis. In the diagnosis of large vessel GCA, FDG-PET/CT imaging has been recommended and its use has steadily increased. The objective of this prospective study was to evaluate the diagnostic performance of digital FDG-PET imaging with a head and neck dedicated protocol, especially to detect cranial arteries involvement, using different visual grading scores, and to assess the inter-reader agreement.

Material and Methods

FDG-PET/CT scans with a 10-min acquisition time on the head and neck were performed in patients suspected of having recent GCA. A score including 20 segments due to the inclusion of cranial segments and a score established only for the cranial segments were compared to the Total Vascular Score (TVS) established on 7 arterial segments. These scores were assessed by two nuclear medicine physicians on a blinded manner and, in case of disagreement, a consensus was established with a third nuclear medicine physician.

Results

GCA diagnosis was retained for 15 of the 52 patients included. Sensitivity and specificity of the 20-segment or the cranial scores were higher than those of TVS (sensitivity and specificity of 80% of 97% for both scores vs 73% and 89% for TVS, respectively). The inter-reader agreement was substantial in the 20-segment score (weighted kappa = 0.68) but better in the cranial segments than other segments.

Conclusion

This study shows the usefulness of grading scores able to highlight involvement of cranial arteries in GCA with a better inter-reader agreement in cranial segments than other segments.
Shadows of very high-frequency oscillations in routine stereoelectroencephalography
Authors: Vasickova Zuzana , Klimes Petr , Cimbalnik Jan , Travnicek Vojtech , Pail Martin , Halamek Josef , Jurak Pavel , Brazdil Milan 
Published: October 2022

Abstract
Very high-frequency oscillations (VHFOs, > 500 Hz) are more specific in localizing the epileptogenic zone (EZ) than high-frequency oscillations (HFOs, < 500 Hz). Unfortunately, VHFOs are not visible in standard clinical stereo-EEG (SEEG) recordings with sampling rates of 1 kHz or lower. Here we show that “shadows” of VHFOs can be found in frequencies below 500 Hz and can help us to identify SEEG channels with a higher probability of increased VHFO rates. Subsequent analysis of Logistic regression models on 141 SEEG channels from thirteen patients shows that VHFO “shadows” provide additional information to gold standard HFO analysis and can potentially help in precise EZ delineation in standard clinical recordings.
Assessment of Fungal spores and spore-like diversity in Environmental Samples by Targeted Lysis
Authors: Ramirez Andrea Corona , Bregnard Danaé , Junier Thomas , Cailleau Guillaume , Dorador Cristina , Bindschedler Saskia , Junier Pilar 
Published: October 2022

Abstract

Resistant cells, such as spores are a vital part of the life cycle of fungi with essential roles in ecology and reproduction. These structures help fungi not only to disperse to other environments but also to survive long periods of time awaiting favorable growth conditions. As a result, fungal spores and resistant cells are part of the microbial seed bank, which is known to influence the microbial community composition, and contribute to the maintenance of diversity. Despite the importance of resistant cells in the life-cycles of fungi, and more largely, of microbial seed banks in the environment, the methods to study the diversity of fungal resistant cells only target spores dispersing in the air, omitting the diversity of these cells elsewhere. In this study, we applied a separation method based on lysis-resistance to enrich fungal spores and resistant cells to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in selected species. The results obtained showed that DNA from fungal spores and from yeast is only obtained after the application of the lysis-resistant enrichment method, while mycelium is always lysed. After validation, we compared the total and fungal seed bank diversity in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from a salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.
Behavior in time of solutions of a Keller--Segel system with flux limitation and source term
Authors: Marras Monica , Vernier-Piro Stella , Yokota Tomomi 
Published: October 2022

Abstract
In this paper we consider radially symmetric solutions of the following parabolic--elliptic cross-diffusion system \begin{equation*} \begin{cases} u_t = \Delta u - \nabla \cdot (u f(|\nabla v|^2 )\nabla v) + g(u), & \\[2mm] 0= \Delta v -m(t)+ u , \quad \int_{\Omega}v \,dx=0, & \\[2mm] u(x,0)= u_0(x), & \end{cases} \end{equation*} in $\Omega \times (0,\infty)$, with $\Omega$ a ball in $\mathbb{R}^N$, $N\geq 3$, under homogeneous Neumann boundary conditions, where $g(u)= \lambda u - \mu u^k$ , $\lambda >0, \ \mu >0$, and $ k >1$, $f(|\nabla v|^2 )= k_f(1+ |\nabla v|^2)^{-\alpha}$, $\alpha>0$, which describes gradient-dependent limitation of cross diffusion fluxes. The function $m(t)$ is the time dependent spatial mean of $u(x,t)$ i.e. $m(t) := \frac 1 {|\Omega|} \int_{\Omega} u(x,t) \,dx$. Under smallness conditions on $\alpha$ and $k$, we prove that the solution $u(x,t)$ blows up in $L^{\infty}$-norm at finite time $T_{max}$ and for some $p>1$ it blows up also in $L^p$-norm. In addition a lower bound of blow-up time is derived. Finally, under largeness conditions on $\alpha$ or $k$, we prove that the solution is global and bounded in time.
Mathematics Subject Classification (2010). Primary 35B44; Secondary 35Q92, 92C17.
Regulation of Whole-Transcriptome Sequencing Expression in COPD after Personalized Precise Exercise Training
Authors: liu panpan , Zhang meilan , Gao Hongchang , Han Shaojun , Liu Jinming , Sun Xingguo , Zhao Lei 
Published: October 2022

Abstract
Background
Chronic obstructive pulmonary disease (COPD) is one of the world’s leading causes of death and a major chronic respiratory disease. Aerobic exercise, the cornerstone of pulmonary rehabilitation, improves prognosis of COPD patients; however, few studies have comprehensively examined the changes in RNA transcript levels and the crosstalk between various transcripts in this context. This study identified the expression of RNA transcripts in COPD patients who engaged in aerobic exercise training for 12 weeks, and further constructions of the possible RNAs networks were made.
Methods
Peripheral blood samples for all four COPD patients who benefited from 12 weeks of PR were collected pre- and post- aerobic exercises and evaluated for the expression of mRNA, miRNA, lncRNA, and circRNA with high-throughput RNA sequencing followed by GEO date validation. In addition, enrichment analyses were conducted on different expressed mRNAs. LncRNA-mRNA and circRNA-mRNA coexpression networks, as well as lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA competing expression networks (ceRNAs) in COPD were constructed.
Results
We identified and analyzed the differentially expressed mRNAs and noncoding RNAs in the peripheral blood of COPD patients’ post-exercise. Eighty-six mRNAs, 570 lncRNAs, 8 miRNAs, and 2087 circRNAs were differentially expressed. Direct function enrichment analysis and Gene Set Variation Analysis showed that differentially expressed RNAs(DE-RNAs) correlated with several critical biological processes such as chemotaxis, DNA replication, anti-infection humoral response, oxidative phosphorylation, and immunometabolism, which might affect the progression of COPD. Some DE-RNAs were validated by Geo databases, and the results were highly correlated with RNA sequencing. We constructed ceRNA networks of DE-RNAs in COPD.
Conclusions
The systematic understanding of the impact of aerobic exercise on COPD was achieved using transcriptomic profiling. This research offers a number of potential candidates for clarifying the regulatory mechanisms that exercise has on COPD, which could ultimately help in understanding the pathophysiology of COPD.
Calcium phosphate ion clusters improve the mechanical properties and bonding strength of demineralized dentine
Authors: Yuan Ding , Yan Lumiao , Chen Ruitian , Chen Zhuo , Tang Ruikang , Chen Zhi 
Published: October 2022

Abstract
Objective

In this laboratory study, the rapid biomimetic remineralization potential of calcium phosphate ion clusters (CPICs) on the interface between demineralized dentin and resin composite was investigated.

Methods

Dentin disks 1 mm thick were prepared from extracted non-carious human third molars. After acid etching, a 5 µm thick demineralized layer was obtained, sprayed with 1 mg/mL CPICs for 5 min and stored in m-SOF for 48 h. Scanning electron microscopy (SEM) was used to observe the ultrastructure of remineralized dentin treated by CPICs, and the phase transformation of the newly formed remineralized layer was determined by X-ray diffraction (XRD). A nanoindentation test was performed to evaluate the elastic modulus and microhardness of demineralized dentin. The inhibitory effect of CPICs on the activity of dentin matrix metalloproteinase was determined. Energy dispersive X-ray spectroscopy (EDS) and microcomputed tomography (micro-CT) was used to observe the bonding interface defects between the resin composite and demineralized dentin. Microtensile bond strength and failure models of bonding interface were also analyzed.

Results

SEM illustrated a remineralized layer of approximately 2 µm on the surface of the demineralized dentin, and the tubules of the dentin were uniformly sealed. The elastic modulus and microhardness were boosted and like those of sound dentin. In addition, have an inhibitory ability against MMP. The integrity of the bonding interface and long-term bonding strength were enhanced. CPICs transformed the failure mode into cohesive failure in the composite

Conclusion

CPICs greatly improved the mechanical and bonding properties of the demineralized dentine.

Clinical Relevance

CPICs have been shown to significantly improve the mechanical and bonding properties of demineralized dentin, which provides a new clinical treatment strategy for the demineralized dentin retained by selective caries removal technology in deep caries treatment.
A Decomposition-based Evolutionary Multi-objective Optimization Method for Solving Constrained Optimization Problems with Imbalanced Objectives or Constraints
Authors: Fan Zhun , Wang Liu , Wang Zhaojun , Xu Biao , Li Wenji 
Published: October 2022

Abstract
In recent years, many effective constrained multi-objective evolutionary algorithms (CMOEAs) have been proposed and successfully applied to address constrained multi-objective optimization problems (CMOPs). Nevertheless, few CMOEAs have fully explored CMOPs with imbalanced objectives or constraints. In this study, we propose a hybrid algorithm called M2M-IEpsilon to handle CMOPs with such characteristics, which combines an improved epsilon constraint-handling method (IEpsilon) with a multi-objective to multi-objective (M2M) decomposition strategy. The M2M decomposition mechanism divides a population into a set of sub-populations, which strengthens the diversity of the population. The IEpsilon constraint-handling method enables individuals with small constraint violation values to survive to the next generation, thus leading to a search for promising regions. In addition, a series of imbalanced CMOPs, named IM-CMOPs, is designed to verify the performance of the proposed M2M-IEpsilon algorithm. The comprehensive experimental results indicate that the proposed method can solve such imbalanced CMOPs well and perform significantly better than the other eight new or classical CMOEAs. Finally, we used the proposed M2M-IEpsilon to optimize the wellbore trajectory problem, and it achieved good results compared with previously developed algorithms.
Altered Norepinephrine Transmission after Spatial Learning Impairs Sleep-Mediated Memory Consolidation in rats
Authors: Duran Ernesto , Pandinelli Martina , Logothetis Nikos , Eschenko Oxana 
Published: October 2022

Abstract

The therapeutic use of noradrenergic drugs makes the evaluation of their effects on cognition of high priority. Norepinephrine (NE) is an important neuromodulator for a variety of cognitive processes, including memory. The NE transmission fluctuates with the behavioral state and influences associated neural activity. Here, we addressed the role of NE during a post-learning period in the sleep-mediated mechanisms of memory consolidation. We treated adult male rats with clonidine (0.05 mg/kg, i.p.), propranolol (10 mg/kg, i.p.), or saline after each of seven daily learning sessions on an 8-arm radial maze. We monitored the prefrontal EEG and population activity in the hippocampus for 2h after the drug administration. Both drugs made spatial learning less efficient and dramatically reduced the occurrence of hippocampal ripples at least for 2h post-injection. Clonidine made the sleep onset faster while prolonging quiet wakefulness. Propranolol increased active wakefulness at the expense of NREM sleep. Clonidine reduced the occurrence of slow oscillations (SO) and sleep spindles during NREM sleep and altered the temporal coupling between SO and sleep spindles. Thus, pharmacological alteration of NE transmission produced a suboptimal brain state for memory consolidation. Our results suggest that the post-learning NE contributes to the efficiency of ripple-associated memory trace replay and hippocampal-cortical communication underlying memory consolidation.
Identification and validation of a ten Cuproptosis-related lncRNA prognostic signature for Stomach Adenocarcinoma
Authors: Ma Qi , Hui Yuan , Yang Bin-Feng , Li Jing-Xian , Ma Da-You , Huang Bang-Rong 
Published: October 2022

Abstract

BackgroundCuproptosis is a recently discovered method of copper-induced cell death that serves an essential part in the progression and spread of stomach adenocarcinoma (STAD). Multiple studies have found that lncRNAs, or long non-coding RNAs, are strongly correlated with the outcome for STAD patients. However, the nature of the connection between cuproptosis and lncRNAs in STAD is still not completely understood. Our study set out to create a predictive hallmark of STAD based on lncRNAs associated with cuproptosis, with the hope that this would allow for more accurate prediction of STAD outcomes.MethodsWe retrieved the transcriptional profile of STAD as well as clinical information from The Cancer Genome Atlas (TCGA). The cuproptosis-related genes (CRGs) were gathered through the highest level of original research and complemented with information from the available literature. We constructed a risk model using co-expression network analysis, Cox regression analysis, and least absolute shrinkage and selection operator (LASSO) analysis to identify lncRNAs associated with cuproptosis, and then validated its performance in a validation set. Survival study, progression-free survival analysis (PFS), receiver operating characteristic (ROC) curve analysis, Cox regression analysis, nomograms, clinicopathological characteristic correlation analysis, and principal components analysis were used to evaluate the signature's prognostic utility. Additionally, ssGSEA algorithms, KEGG, and GO were employed to assess biological functions. The tumor mutational burden (TMB) and tumor immune dysfunction and rejection (TIDE) scores were utilized in order to evaluate the effectiveness of the immunotherapy.ResultsIn order to construct predictive models, nine distinct lncRNAs (AC087521.1, AP003498.2, AC069234.5, LINC01094, AC019080.1, BX890604.1, AC005041.3, DPP4-DT, AL356489.2, AL139147.1) were identified. The Kaplan-Meier and ROC curves, which were applied to both the training and testing sets of the TCGA, provided evidence that the signature contained a sufficient amount of predictive potential. The signature was shown to contain risk indicators that were independent of the other clinical variables, as demonstrated by the findings of a Cox regression and a stratified survival analysis. The ssGSEA study provided additional evidence that predictive variables were highly connected with the immunological condition of STAD patients. Surprisingly, the combination of high risk and high TMB reduced survival time for patients. A worse prognosis for the immune checkpoint blockade response was also suggested by the fact that patients in the high-risk group had higher TIDE scores.ConclusionThe potential clinical uses of the identified risk profiles for the 10 cuproptosis-related lncRNAs include the assessment of the prognosis and molecular profile of STAD patients and the creation of more targeted therapy strategies.
Superficial Surgical Site Infection in Delayed Primary Vs Primary Wound Closure in Complicated Appendicitis
Authors: Akash Akash , Saxena Neeraj 
Published: October 2022

Abstract
1.1 Background
Wound infection is the most common post-op complication encountered after open appendectomy. Various studies comparing risk of superficial surgical site infection (SSI) in primary closure (PC) and delayed primary closure (DPC) of wound has been conducted in the past. But there is no uniform consensus regarding the method of wound closure. So aim of this study was comparison of the two wound closure techniques.
1.2 Material and Methods
This was prospective study which enrolled 50 patients who underwent open appendectomy. Patients’ demographics, characteristics and operative findings were recorded. Those who were elder than 18 years and had appendectomy with a right lower quadrant incision were included. Patients with any comorbidity, morbid obesity and pregnancy were excluded. Patients were randomized to undergo two techniques of wound closure namely PC and DPC. On follow-up at one week and one month, SSI, post-op pain and LOS were compared among two groups. Clinical assessment included a visual analog scale (1-10) for pain.
1.3 Results
In our study incidence of SSI in DPC group was significantly lower when compared to PC group (p value=0.0002) while post-op pain and LOS were not significantly different on comparison between the two groups.
1.4 Conclusion
We concluded that DPC was superior to PC of wound in terms of reduction of incidence of superficial SSI but with respect to post-op pain and LOS the two techniques of wound closure were not different.
Dependence of Climate Sensitivity Estimates on Internal Climate Variability During 1880-2020
Authors: Spencer Roy W. , Christy John R. 
Published: October 2022

Abstract
Observed rates of global-average deep-ocean and surface warming during 1880–2020 are matched with a 1D forcing-feedback model of vertical energy flow departures from assumed energy equilibrium driven by both anthropogenic and natural forcings. The monthly time resolution model ocean has a mixed layer, a second layer to 2,000 m depth, and a third layer extending to the ocean bottom. The model mixed layer temperature is radiatively forced with estimates of anthropogenic, volcanic, and direct solar forcings since 1765, and radiatively and non-radiatively forced with the observed history of El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) activity since 1880. Model adjustable parameters are chosen to match observed sea surface temperature (SST) and deep ocean (0-2000 m) temperature trends during 1960–2020, as well as twenty years of lag regression relationships between sea surface temperature and satellite longwave and shortwave flux anomalies at the top of the atmosphere. The results support the dominant role of anthropogenic greenhouse gas forcing in ocean warming since 1880. Without ENSO and PDO effects, diagnosed climate sensitivity is 1.8 and 2.2 deg. C for two sea surface temperature datasets, respectively. Inclusion of ENSO and PDO improves agreement between model and observations, from 81–92% explained variance, and reduces the diagnosed sensitivity to 1.5 to 1.8 deg. C, depending on the surface temperature dataset. The global warming slowdown during 1998–2012 is also well matched after inclusion of ENSO and PDO effects.