bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis of DNA methylation and gene expression identifies genes associated with biological aging in Alzheimer's disease
Authors: Kim Bo‐Hyun , Vasanthakumar Aparna , Li Qingqin S. , Nudelman Kelly N.H. , Risacher Shannon L. , Davis Justin W. , Idler Kenneth , Lee Jong‐Min , Seo Sang Won , Waring Jeffrey F. , Saykin Andrew J. , Nho Kwangsik ,   for the Alzheimer's Disease Neuroimaging Initiative (ADNI)
Published: September 2022

AbstractIntroductionThe acceleration of biological aging is a risk factor for Alzheimer's disease (AD). Here, we performed weighted gene co‐expression network analysis (WGCNA) to identify modules and dysregulated genesinvolved in biological aging in AD.MethodsWe performed WGCNA to identify modules associated with biological clocks and hub genes of the module with the highest module significance. In addition, we performed differential expression analysis and association analysis with AD biomarkers.ResultsWGCNA identified five modules associated with biological clocks, with the module designated as “purple” showing the strongest association. Functional enrichment analysis revealed that the purple module was related to cell migration and death. Ten genes were identified as hub genes in purple modules, of which CX3CR1 was downregulated in AD and low levels of CX3CR1 expression were associated with AD biomarkers.ConclusionNetwork analysis identified genes associated with biological clocks, which suggests the genetic architecture underlying biological aging in AD.Highlights
Examine links between Alzheimer's disease (AD) peripheral transcriptome and biological aging changes.

Weighted gene co‐expression network analysis (WGCNA) found five modules related to biological aging.

Among the hub genes of the module, CX3CR1 was downregulated in AD.

The CX3CR1 expression level was associated with cognitive performance and brain atrophy.
A p‐curve analysis of the emotional Stroop effect among women with eating disorders
Authors: Enouy Sarah , Desrochers Jessica E. , Bossom Isabella R. L. , Tabri Nassim 
Published: September 2022

AbstractObjectiveA recent meta‐review of attentional bias research in eating disorders suggests that meta‐analyses and systematic reviews include many low‐quality and underpowered studies (Stott et al., 2021). As such, we examined whether published research examining the link between attentional bias, using the emotional Stroop task, and eating disorders among women with eating disorders has evidential value (ruling out selective reporting of a statistically significant effect) using a p‐curve analysis. A p‐curve analysis plots statisticall significant p‐values onto a curve from .01 to .05 to examine its distribution. We hypothesized that the p‐curve would be flat, indicating no true effect.MethodThe hypothesis, database search strategy, and data analytic approach were pre‐registered. The inclusion criteria were reports that compared control and eating disorder groups, reported inferential statistics, and that used body shape/weight or general threat target words.ResultsFifty published reports were included in the p‐curve analyses. Unexpectedly, the half and full p‐curves were significantly right‐skewed, indicating evidential value. However, the results were not robust to the exclusion of the seven lowest p‐values and on average, reports were underpowered. There were also 18 reports with null results (they had a p‐value greater than .05), which precluded their inclusion in the p‐curve analyses.DiscussionThe findings suggest that most of the evidence from research examining attentional biases using the emotional Stroop task among women with an eating disorder or with elevated eating disorder symptoms is underpowered and so should be interpreted with considerable caution.Public SignificanceConcerns have been raised about the low quality of research examining attentional biases among women with eating disorders using the emotional Stroop task. In the current research, we observed that the evidential value of primary research reporting differences between women with and without eating disorders was equivocal and had low statistical power. These results can guide researchers towards conducting more rigorous research on attentional biases among people with eating disorders.
Estimating the self‐thinning boundary line for oak mixed forests in central China by using stochastic frontier analysis and a proposed variable density model
Authors: Long Shisheng , Zeng Siqi , Shi Zhenwei , Yang Shengyang 
Published: September 2022

AbstractA suitable self‐thinning model is fundamental to effective density control and management. Using data from 265 plot measurements in oak mixed forests in central China, we demonstrated how to estimate a suitable self‐thinning line for oak mixed forests from three aspects, i.e., self‐thinning models (Reineke's model and the variable density model), statistical methods (quantile regression and stochastic frontier analysis), and the variables affecting stands (topography and stand structure factors). The proposed variable density model, which is based on the quadratic mean diameter and dominant height, exhibited a better goodness of fit and biological relevance than Reineke's model for modeling the self‐thinning line for mixed oak forests. In addition, the normal‐truncated normal stochastic frontier model was superior to quantile regression for modeling the self‐thinning line. The altitude, Simpson index, and dominant height–diameter ratio (/D) also had significant effects on the density of mixed forests. Overall, a variable density self‐thinning model may be constructed using stochastic frontier analysis for oak mixed forests while considering the effects of site quality and stand structure on density. The findings may contribute to a more accurate density management map for mixed forests.
Multiple Doris “kerguelenensis” (Nudibranchia) species span the Antarctic Polar Front
Authors: Maroni Paige J. , Wilson Nerida G. 
Published: September 2022

AbstractDespite strong historical biogeographical links between benthic faunal assemblages of the Magellan region of South America and the Antarctic Peninsula, very few studies have documented contemporary movement and gene flow in or out of the Southern Ocean, especially across the Antarctic Polar Front (APF). In fact, oceanographic barriers such as the APF and Antarctica's long geologic isolation have substantially separated the continents and facilitated the evolution of endemic marine taxa found within the Antarctic region. The Southern Ocean benthic sea slug complex, Doris “kerguelenensis,” are a group of direct‐developing, simultaneous hermaphrodites that lack a dispersive larval stage. To date, there are 59 highly divergent species known within this complex. Here, we provide evidence to show intraspecific genetic connectivity occurs across the APF for multiple species within the D. “kerguelenensis” nudibranch species complex. We addressed questions of genetic connectivity by examining the phylogeographic structure of the three best‐sampled D. “kerguelenensis” species and another three trans‐APF species using the protein coding mtDNA gene, cytochrome oxidase I. We also highlight alternative refugia uses among species with the same life history traits (i.e., benthic and direct developers) and for some species, extremely large distributions are established (e.g., circumpolarity). By improving our sampling of these nudibranchs, we gain better insight into the population structure and connectivity of the Antarctic region. This work also demonstrates how difficult it is to make generalizations across Antarctic marine species, even among ecologically‐similar, closely related species.
How do terrestrial wildlife communities respond to small‐scale Acacia plantations embedded in harvested tropical forest?
Authors: Wong Seth T. , Guharajan Roshan , Petrus Azrie , Jubili Jaffly , Lietz Robin , Abrams Jesse F. , Hon Jason , Alen Lukmann H. , Ting Nicholas T. K. , Wong George T. N. , Tchin Ling T. , Bijack Nelson J. C. , Kramer‐Schadt Stephanie , Wilting Andreas , Sollmann Rahel 
Published: September 2022

AbstractTo offset the declining timber supply by shifting towards more sustainable forestry practices, industrial tree plantations are expanding in tropical production forests. The conversion of natural forests to tree plantation is generally associated with loss of biodiversity and shifts towards more generalist and disturbance tolerant communities, but effects of mixed‐landuse landscapes integrating natural and plantation forests remain little understood. Using camera traps, we surveyed the medium‐to‐large bodied terrestrial wildlife community across two mixed‐landuse forest management areas in Sarawak, Malaysia Borneo which include areas dedicated to logging of natural forests and adjacent planted Acacia forests. We analyzed data from a 25‐wildlife species community using a Bayesian community occupancy model to assess species richness and species‐specific occurrence responses to Acacia plantations at a broad scale, and to remote‐sensed local habitat conditions within the different forest landuse types. All species were estimated to occur in both landuse types, but species‐level percent area occupied and predicted average local species richness were slightly higher in the natural forest management areas compared to licensed planted forest management areas. Similarly, occupancy‐based species diversity profiles and defaunation indices for both a full community and only threatened and endemic species suggested the diversity and occurrence were slightly higher in the natural forest management areas. At the local scale, forest quality was the most prominent predictor of species occurrence. These associations with forest quality varied among species but were predominantly positive. Our results highlight the ability of a mixed‐landuse landscape with small‐scale Acacia plantations embedded in natural forests to retain terrestrial wildlife communities while providing an alternate source of timber. Nonetheless, there was a tendency towards reduced biodiversity in planted forests, which would likely be more pronounced in plantations that are larger or embedded in a less natural matrix.
Uplink transmission with multiuser scheduling in non‐stand‐alone cellular network using virtual MIMO system
Authors: Kukade Shweta , Sutaone Mukul S. , Patil Rajendrakumar 
Published: September 2022

Abstract5G architecture allows the use of new radio alongside long‐term evolution‐A (LTE‐Advanced) and enables cellular mobile networks to handle extraordinarily high traffic volume data. The major challenge in current uplink data transmission systems is making resource blocks (RBs) available in a continuous form and assigning them to active users in an optimum manner to improve the system's spectral efficiency. The best N‐subset (BNS) minimization technique is suggested to identify the best of the best continuous chunks of RBs from the existing system bandwidth, followed by a modified recursive maximum expansion (RME) algorithm to assign RBs to users in the most optimal manner. The algorithm together is referred to as a multiuser uplink scheduler BNSRME algorithm. A constraint utility maximization problem is formulated to allocate RBs to UEs in the most optimized manner. Utility matrix is then converted into a weighted sum‐rate maximization problem allowing weights to be updated adaptively based on marginal utility values. In addition, a threshold limit is considered based on the signal‐to‐noise ratio in the BNSRME‐TH algorithm, which satisfies multiusers in terms of assigned resources and improves system performance, spectral efficiency, and throughput. This MU scheduling strategy is used in the 5G uplink non‐stand‐alone cellular network. The findings exhibit that the proposed multiuser algorithm increases system spectral efficiency by 31.65% in comparison with the existing opportunistic algorithms. It has been observed that the performance of the system is further increased by using the MU‐MIMO framework.
Fatty liver disease reverses the obesity paradox in chronic kidney disease stages 3–5: A follow‐up study of NHANES III
Authors: Huang Jiaofeng , Zhang Min , Wu Yinlian , Wang Mingfang , Zhu Yueyong , Lin Su 
Published: September 2022

Abstract
High body mass index (BMI) has been associated with better survival in patients with end‐stage kidney disease. Individuals with fatty liver disease (FLD) have a higher risk of chronic kidney disease. It remains unclear whether the survival benefit of high BMI in patients with chronic kidney disease is present when there is concomitant FLD. This study used the data set from the Third American National Health and Nutrition Examination Survey and the corresponding survival data. The Cox proportional hazards model was used to evaluate the effect of BMI on mortality. A total of 12,445 participants were included. The prevalence of FLD was 39.8%. The median follow‐up time (with interquartile range) was 22.8 (20.8–24.8) years. During this period, 3749 (30.1%, 14.4 of 1000 person‐year) deaths were observed. Among these, 1169 (31.2%) died within the first 10 years. The Cox regression analysis showed that the BMI level was not associated with 25‐year mortality in patients with decreased glomerular filtration rate (GFR < 60 ml/min/1.73 m2), but 10‐year mortality was significantly lower in patients with BMI ≥ 25 kg/m2 than in those with BMI < 25 kg/m2 (p = 0.049). Multivariate analysis showed BMI ≥ 25 kg/m2 was an independent protective factor for 10‐year mortality (hazard ratio [HR] 0.691, 95% confidence interval [CI] 0.559–0.856; p = 0.001). This protective effect of higher BMI was lost in patients with FLD (HR 0.884, 95% CI 0.585–1.335; p = 0.557) but persisted in the non‐FLD group (HR 0.625, 95% CI 0.479–0.816; p = 0.001). The survival benefit of overweight/obesity for patients with decreased GFR, which was attenuated by the presence of FLD, only existed in the first decade.
Stereoselective Syntheses of Masked β‐Amino Acid Containing Phthalides
Authors: Serusi Lorenzo , Zebrowski Paul , Schörgenhumer Johannes , Massa Antonio , Waser Mario 
Published: September 2022

AbstractWe herein report a protocol for the asymmetric aldol‐initiated cascade addition of isoxazolidin‐5‐ones to ortho‐cyanobenzaldehydes by using Takemoto’s bifunctional organocatalyst. This approach allows for the synthesis of various novel β2,2‐amino acid‐phthalide conjugates with good enantio‐ and diastereoselectivities in reasonable yields and the further ring‐opening of these compounds to acyclic carboxylic acid derivatives was demonstrated too.
Comprehensive analysis of fifteen hub genes to identify a promising diagnostic model, regulated networks, and immune cell infiltration in acute kidney injury
Authors: Sun Tao , Cao Ying , Huang Tiancha , Sang Yiwen , Dai Yibei , Tao Zhihua 
Published: September 2022

AbstractBackgroundAcute kidney injury is a common clinical problem with no sensitive and specific diagnostic biomarkers and definitive treatments. The underlying molecular mechanisms of acute kidney injury are unclear. Therefore, it is pivotal to explore the underlying mechanisms and screen for novel diagnostic biomarkers, and therapeutic targets.MethodsThe present study identified 15 hub genes by WGCNA analysis. LASSO‐based logistic regression analysis was used to select key features and construct a diagnostic model of AKI. In addition, GO and KEGG analyses were performed and TF‐mRNA and miRNA‐mRNA network analysis and immune infiltration analysis of hub genes were performed to reveal the underlying mechanisms of AKI.ResultsA diagnostic model was constructed by LASSO‐based logistic regression analysis and was validated by RT‐qPCR based on 15 hub genes. GO and KEGG analyses revealed DEGs were enriched in oxidation–reduction process, cell adhesion, proliferation, migration, and metabolic process. The enriched TFs were BRD2, EP300, ETS1, MYC, SPI1, and ZNF263. The enriched miRNAs were miR‐181c‐5p, miR‐218‐5p, miR‐485‐5p, miR‐532‐5p and miR‐6884‐5p. The immune infiltration analysis showed that Macrophages M2 was decreasing significantly revealing a protective factor for further AKI treatment.ConclusionsThe present study identified 15 hub genes based on WGCNA. Development and validation of a potentially diagnostic model based on 15 hub genes. In addition, exploring the interaction between transcriptional factors and 15 hub genes, and miRNA‐mRNA relationship pairs. Furthermore, immune infiltration analysis was performed by analyzing gene expression profiles of AKI. Our study provides some basis for further experimental studies.
Molecular mechanisms, physiological roles, and therapeutic implications of ion fluxes in bone cells: Emphasis on the cation‐Cl− cotransporters
Authors: Garneau Alexandre P. , Slimani Samira , Haydock Ludwig , Nsimba‐Batomene Thy‐René , Préfontaine Florence C.M. , Lavoie Mathilde M. , Tremblay Laurence E. , Fiola Marie‐Jeanne , Mac‐Way Fabrice , Isenring Paul 
Published: September 2022

AbstractBone turnover diseases are exceptionally prevalent in human and come with a high burden on physical health. While these diseases are associated with a variety of risk factors and causes, they are all characterized by common denominators, that is, abnormalities in the function or number of osteoblasts, osteoclasts, and/or osteocytes. As such, much effort has been deployed in the recent years to understand the signaling mechanisms of bone cell proliferation and differentiation with the objectives of exploiting the intermediates involved as therapeutic preys. Ion transport systems at the external and in the intracellular membranes of osteoblasts and osteoclasts also play an important role in bone turnover by coordinating the movement of Ca2+, PO42−, and H+ ions in and out of the osseous matrix. Even if they sustain the terminal steps of osteoformation and osteoresorption, they have been the object of very little attention in the last several years. Members of the cation‐Cl− cotransporter (CCC) family are among the systems at work as they are expressed in bone cells, are known to affect the activity of Ca2+‐, PO42−‐, and H+‐dependent transport systems and have been linked to bone mass density variation in human. In this review, the roles played by the CCCs in bone remodeling will be discussed in light of recent developments and their potential relevance in the treatment of skeletal disorders.
Orientation‐based edge‐colorings and linear arboricity of multigraphs
Authors: Wdowinski Ronen 
Published: September 2022

AbstractThe Goldberg–Seymour Conjecture for ‐colorings states that the ‐chromatic index of a loopless multigraph is essentially determined by either a weighted maximum degree or a weighted maximum density parameter. We introduce an oriented version of ‐colorings, where now each color class of the edge‐coloring is required to be orientable in such a way that every vertex has indegree and outdegree at most some specified values and . We prove that the associated ‐oriented chromatic index satisfies a Goldberg–Seymour formula. We then present simple applications of this result to variations of ‐colorings. In particular, we show that the Linear Arboricity Conjecture holds for ‐degenerate loopless multigraphs when the maximum degree is at least , improving a recent bound by Chen, Hao, and Yu for simple graphs. Finally, we demonstrate that the ‐oriented chromatic index is always equal to its list coloring analogue.
A model‐based estimate of nitrate leaching in Germany for GHG reporting
Authors: Eysholdt Max , Kunkel Ralf , Rösemann Claus , Wendland Frank , Wolters Tim , Zinnbauer Maximilian , Fuß Roland 
Published: September 2022

AbstractBackgroundConversion of leached and runoff nitrate (NO3–) from agricultural land into emissions of the greenhouse gas (GHG) nitrous oxide (N2O) by denitrification in water bodies has to be reported in national GHG inventories. The global IPCC default methodology for estimating these indirect N2O emissions assumes that a fixed fraction of nitrogen (N) inputs (Fracleach) is lost through leaching and runoff. However, this method does not consider all relevant country‐specific conditions that may influence NO3– leaching.AimsThe aim of this study was to apply a model‐based approach for estimating indirect N2O emissions through NO3– leaching and runoff from agricultural soils for use in Germany's national GHG inventory.MethodsHigh‐resolution spatial data and a comprehensive model system (RAUMIS‐mGROWA‐DENUZ) were used to derive regionally differentiated and temporarily dynamic Fracleach values from N surplus and hydrogeological conditions. These were then used to estimate indirect N2O emissions in accordance with the IPCC methodology.ResultsThe nationwide average of the new implied Fracleach values was 0.099 kg N (kg N input)−1 in 2019. The new estimate of indirect N2O emissions was 10.4 Gg N2O in 1990 and 5.7 Gg N2O in 2019, which are 27 and 52% less than the calculation based on the 2006 IPCC Tier 1 methodology.ConclusionsThe model‐based method for estimating Fracleach incorporates relevant factors that influence NO3– leaching and runoff and considers site‐specific, spatially varying conditions and differences in the agrarian structure. The use of N surplus as the model driver allows annual changes in cropping conditions and the effects of N‐regulating policies and mitigation measures to be represented.
Treatment of Nevus of Ota in Black patients with the 1064 nm QS or picosecond laser and nonablative fractional photothermolysis
Authors: Kubicki Shelby L. , Guo Emily L. , Richmond Heather , Friedman Paul M. 
Published: September 2022

AbstractObjectivesNevus of Ota is a benign melanocytic lesion that presents as a unilateral blue gray to brown facial patch favoring the distribution of the first two branches of the trigeminal nerve. Incidence is highest in Asian and Black populations, however, the overwhelming majority of studies are limited to diagnosis and treatment in Asian patients. We herein present 10 Black patients with Fitzpatrick skin types (FST) V and VI who underwent laser treatment for Nevus of Ota.MethodsWe performed a retrospective review of Black patients presenting with Nevus of Ota. Race was self‐designated by all patients and documented in the medical record at the time of initial consultation. Primary outcomes were based on improvement using before and after photographs which were graded by three independent board‐certified dermatologists using a 5‐point visual analog scale.ResultsTen FST V or VI patients with an age range of 9 months to 45 years were treated for Nevus of Ota. All patients were treated with the 1064 nm Q‐switched neodymium doped yttrium aluminum garnet (QS Nd:YAG) and on average received 4.7 treatments at 2–10 month intervals. Fluence ranged from 1.8 to 2.3 J/cm2, and total pulse count ranged from 510.9 to 776.6. 2/10 patients were additionally treated with 1550 nm nonablative fractional resurfacing (NAFR), and 1/10 patients underwent combination therapy with both NAFR and 1064 nm picosecond laser therapy. Overall, patients saw a mean improvement of 51%–75% at follow‐up 5–254 weeks (mean 51.5 weeks) after treatment. Three patients experienced mild guttate hypopigmentation in treated areas. No other long‐term adverse events were encountered.Conclusion1064 nm QS Nd:YAG laser therapy is a safe and efficacious treatment for Nevus of Ota in patients with FST V and VI. When patient improvement plateaus, combining therapy with 1550 nm NAFR or transitioning to 1064 nm picosecond laser may be of benefit. Patients should be counseled on the risk of guttate hypopigmentation. This is the largest case series to date of Black patients with Nevus of Ota, highlighting the need for further investigation to determine optimal device settings and treatment parameters for this population.