bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bird conservation status and cultural values in Indigenous Mexican communities: towards a bioculturally informed conservation policy
Authors: Alcántara-Salinas Graciela , Hunn Eugene S. , Ibáñez-Bravo María Elena , Aldasoro-Maya Elda Miriam , Flores-Hernández Noé , Pérez-Sato Juan Antonio , Real-Luna Natalia , Trujillo Rafael Arturo Muñoz-Márquez , Lope-Alzina Diana , Rivera-Hernández Jaime Ernesto 
Published: December 2022

AbstractBackgroundWe summarize comparative ethnoornithological data for ten Mexican Indigenous communities, an initial step towards a comprehensive archive of the avian diversity conserved within Mexico’s Indigenous territories. We do so by counting highlighted species listed for bird conservation status on widely recognized “red lists” and their cultural value to build biocultural policies in Mexico for their conservation.MethodsIndigenous bird names for each study site were determined to allow calculation of the “Scientific Species Recognition Ratio” (SSRR) for high cultural value birds obtained across communities. This demonstrated patterns of cultural prominence. A matrix of 1275 bird versus seven biocultural values was analysed using a correspondence analysis (InfoStat/L-v2020) to illustrate patterns of concordance between bird conservation status and cultural values.ResultsThis paper contributes to quantitative and qualitative data on the role of ethnoornithology and ethnobiology in biocultural conservation. The areas studied provide refugia for almost 70% of the Mexican avifauna within a fraction of 1% of the national territory, that is 769 bird species recorded for all communities. The global correspondence of regions of biological and linguistic megadiversity is well established, while linguistic diversity is widely accepted as a good proxy for general cultural diversity. Our correspondence analysis explained 81.55% of the variation, indicating a strong relation between cultural importance and bird conservation status. We propose three main categories to establish a bioculturally informed public policy in Mexico for the conservation of what we described as high, medium, and bioculturally prominent bird species all include cultural value in any material or symbolic aspect. High are those species appearing on any threatened list, but also considered in any endemic status, while medium include threatened listed species. The last category included species not necessarily listed on any threat list, but with a wide range of social and cultural uses. We suggest that the concept might be extended to other species of biocultural importance.ConclusionsWe argue that bird conservation policies should be biocultural, that is they should recognize birds of cultural value on a par with bird species “of special interest” because they are most critical for biodiversity conservation. The desire of local people to protect their traditional community lands and livelihoods can be an effective biodiversity conservation strategy, which should be recognized in national biocultural policies.
Is the retromandibular approach a suitable approach to anatomical reduction of unilateral subcondylar fracture? A non-randomized clinical trial
Authors: Mohamed Abdo Ahmed Saleh , Rao Guangxin , Mai Lianxi , Sakran Karim Ahmed , Al-wesabi Saddam Noman , Pan Chaobin , Lin Zhaoyu 
Published: December 2022

AbstractThe aim of this study was to evaluate the efficacy of the retromandibular approach (RMA) to produce three-dimensional (3-D) reduction of the unilateral subcondylar fracture and Temporomandibular Joint (TMJ) functional implication.Methods: A prospective cohort study was designed. Twenty-nine patients with unilateral subcondylar fracture underwent consecutively Open Reduction, and Internal Fixation. The cohorts were divided into two groups; RMA group (n = 16, 55.17%) and submandibular approach SMA group (n = 13, 44.82%). The primary outcome was the anatomical 3-D reduction of the condyle. The secondary outcome was to compare the condyle position and inclination finding with TMJ outcomes. Helkimo Index score was used to evaluate the TMJ outcome at six months postoperatively.Result: There was a significant difference between the mediolateral condylar inclination, condylar medial and vertical positions when RMA compared with SMA groups (P < 0.05). The medial joint space was correlated with the medial condylar position in both groups (P < 0.05). The Helkimo Ai and Di was associated with mediolateral condylar inclination in SMG; however, Helkimo Ai was found to be correlated with the RMA group.Conclusion: The current study demonstrates that the RMA could re-establish the anatomical position of the unilateral subcondylar fracture in patients undergoing ORIF. The clinical outcome of the TMJ with RMA was better than SMA.
A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes
Authors: Marone Marina Püpke , Singh Harmeet Chawla , Pozniak Curtis J. , Mascher Martin 
Published: December 2022

Abstract
Background
As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects.

Results
We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive.

Conclusion
Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/. The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly.
Estimation of ENPP1 deficiency genetic prevalence using a comprehensive literature review and population databases
Authors: Chunn Lauren M. , Bissonnette Jeffrey , Heinrich Stefanie V. , Mercurio Stephanie A. , Kiel Mark J. , Rutsch Frank , Ferreira Carlos R. 
Published: December 2022

Abstract
Background
ENPP1 Deficiency—caused by biallelic variants in ENPP1—leads to widespread arterial calcification in early life (Generalized Arterial Calcification of Infancy, GACI) or hypophosphatemic rickets in later life (Autosomal Recessive Hypophosphatemic Rickets type 2, ARHR2). A prior study using the Exome Aggregation Consortium (ExAC)—a database of exomes obtained from approximately 60,000 individuals—estimated the genetic prevalence at approximately 1 in 200,000 pregnancies.

Methods
We estimated the genetic prevalence of ENPP1 Deficiency by evaluating allele frequencies from a population database, assuming Hardy–Weinberg equilibrium. This estimate benefitted from a comprehensive literature review using Mastermind (https://mastermind.genomenon.com/), which uncovered additional variants and supporting evidence, a larger population database with approximately 140,000 individuals, and improved interpretation of variants as per current clinical guidelines.

Results
We estimate a genetic prevalence of approximately 1 in 64,000 pregnancies, thus more than tripling the prior estimate. In addition, the carrier frequency of ENPP1 variants was found to be highest in East Asian populations, albeit based on a small sample.

Conclusion
These results indicate that a significant number of patients with ENPP1 Deficiency remain undiagnosed. Efforts to increase disease awareness as well as expand genetic testing, particularly in non-European populations are warranted, especially now that clinical trials for enzyme replacement therapy, which proved successful in animal models, are underway.
p53 regulates expression of nuclear envelope components in cancer cells
Authors: Panatta Emanuele , Butera Alessio , Celardo Ivana , Leist Marcel , Melino Gerry , Amelio Ivano 
Published: December 2022

AbstractNuclear organisation and architecture are essential for the maintenance of genomic integrity as well as for the epigenetic regulations and gene expression. Disruption of lamin B1, major structural and functional member of the nuclear lamina, is observed in human laminopathies and in sporadic cancers, and leads to chromosomal rearrangements and alterations of gene expression. The tumour suppressor p53 has been shown to direct specific transcriptional programmes by regulating lamin A/C, however its relationship with lamin B1 has remained elusive. Here, we show that loss of p53 correlates with increased expression of members belonging to the nuclear pore complex and nuclear lamina and directly regulates transcription of lamin B1. We show that the genomic loci of a fraction of p53-dependent genes physically interact with lamin B1 and Nup210. This observation provides a possible mechanistic explanation for the p53-depedent changes of chromatin accessibility, with the consequent influence of expression and rearrangement of these genomic sites in pancreatic cancer. Overall, these data suggest a potential functional and biochemical regulatory network connecting p53 and nuclear architecture.
Validated HPLC–PDA methodology utilized for simultaneous determination of Etoricoxib and Paracetamol in the presence of Paracetamol toxic impurities
Authors: Abdel Rahman Mona A. , Elghobashy Mohamed R. , Zaazaa Hala E. , Atty Shimaa A. , El-Mosallamy Sally S. 
Published: December 2022

AbstractEtoricoxib (ETO), Paracetamol (PCM), and two toxic impurities for Paracetamol impurity K (4-aminophenol (PAP)) and impurity E (para-hydroxy acetophenone (PHA)) were separated using a simple and selective HPLC method that was tested for the first time. PCM is a commonly used analgesic and antipyretic medication that has recently been incorporated into COVID-19 supportive treatment. Pharmaceuticals containing PCM in combination with other analgesic-antipyretic drugs like ETO help to improve patient compliance. The studied drugs and impurities were separated on a GL Sciences Inertsil ODS-3 (250 × 4.6) mm, 5.0 µm column, and linear gradient elution was performed using 50 mM potassium dihydrogen phosphate adjusted to pH 4.0 with ortho-phosphoric acid and acetonitrile as mobile phase at 2.0 mL/min flow rate at 25 °C and UV detection at 220 nm. The linearity range was 1.5–30.0 µg/mL for ETO and PCM while 0.5–10.0 µg/mL for PAP and PHA, with correlation coefficients (r) for ETO, PCM, PAP, and PHA of 0.9999, 0.9993, 0.9996, and 0.9998, respectively. The proposed method could be used well for routine analysis in quality control laboratory.
Generalized nuclear localization of retroelement transcripts
Authors: Das Simanti , Jones Amanda E. , Abrams John M. 
Published: December 2022

Abstract
Background
LINE-1s, Alus and SVAs are the only retrotransposition competent elements in humans. Their mobilization followed by insertional mutagenesis is often linked to disease. Apart from these rare integration events, accumulation of retrotransposition intermediates in the cytoplasm is potentially pathogenic due to induction of inflammatory response pathways. Although the retrotransposition of LINE-1 and Alu retroelements has been studied in considerable detail, there are mixed observations about the localization of their RNAs.

Results
We undertook a comprehensive and unbiased approach to analyze retroelement RNA localization using common cell lines and publicly available datasets containing RNA-sequencing data from subcellular fractions. Using our customized analytic pipeline, we compared localization patterns of RNAs transcribed from retroelements and single-copy protein coding genes. Our results demonstrate a generalized characteristic pattern of retroelement RNA nuclear localization that is conserved across retroelement classes as well as evolutionarily young and ancient elements. Preferential nuclear enrichment of retroelement transcripts was consistently observed in cell lines, in vivo and across species. Moreover, retroelement RNA localization patterns were dynamic and subject to change during development, as seen in zebrafish embryos.

Conclusion
The pronounced nuclear localization of transcripts arising from ancient as well as de novo transcribed retroelements suggests that these transcripts are retained in the nucleus as opposed to being re-imported to the nucleus or degraded in the cytoplasm. This raises the possibility that there is adaptive value associated with this localization pattern to the host, the retroelements or possibly both.
SLC22A3 methylation-mediated gene silencing predicts adverse prognosis in acute myeloid leukemia
Authors: Gu Yu , Xu Zi-jun , Zhou Jing-dong , Wen Xiang-mei , Jin Ye , Yuan Qian , Xia Pei-hui , Feng Yuan , Yang Lei , Lin Jiang , Qian Jun 
Published: December 2022

Abstract
Background
We screened out several hypermethylated solute carrier (SLC) family genes in acute myeloid leukemia by reduced representation bisulfite sequencing. SLC22A3 encodes an organic cation transport protein, which is critical for drug transportation and cellular detoxification. SLC22A3 is significantly downregulated and associated with tumor progression and worse prognosis in a variety of solid tumors. However, there are no data available regarding the role of SLC22 in AML. This study aimed to explore the regulatory mechanism of DNA methylation on SLC22A3 expression, as well as its clinical significance in AML prognosis.

Results
SLC22A3 was identified as the sole prognosis-associated gene among SLCs based on TCGA and Beat AML databases. Bone marrow mononuclear cells (BMMNCs) from AML, MDS patients, and healthy donors were enrolled in this study. SLC22A3 methylation was significantly increased in AML compared with controls and MDS patients; meanwhile, the expression level of SLC22A3 was decreased. SLC22A3 hypermethylation presented an obvious association with some specific clinical characteristics and affected the survival time of AML patients as an independent risk indicator. SLC22A3 expression changed regularly as the disease complete remissions and relapses. Demethylation drug 5-aza-2′-deoxycytidine (DAC) activated transcription and increased mRNA expression of SLC22A3 in leukemia cell lines and AML fresh BMMNCs. Knockdown of SLC22A3 in leukemia cells enhanced cell proliferation and suppressed cell apoptosis. Data from public programs were used for auxiliary screening of probable molecular mechanisms of SLC22A3 in the antileukemia effect.

Conclusions
Our results showed that increased methylation and decreased expression of SLC22A3 may be indicators of poor prognosis in AML. Methylation-silenced SLC22A3 expression may have potential guiding significance on antileukemia effect of DAC.
Epigenetic silencing of JAM3 promotes esophageal cancer development by activating Wnt signaling
Authors: Yang Weili , Guo Chao , Herman James G. , Zhu Cheng , Lv Honghui , Su Xiaomo , Zhang Lirong , Zhang Meiying , Guo Mingzhou 
Published: December 2022

AbstractBackgroundThe role of JAM3 in different tumors is controversial. The epigenetic regulation and the mechanism of JAM3 remain to be elucidated in human esophageal cancer (EC).MethodsEleven EC cell lines, 49 cases of esophageal intraepithelial neoplasia (EIN) and 760 cases of primary EC samples were employed. Methylation-specific polymerase chain reaction, immunohistochemistry, MTT, western blot and xenograft mouse models were applied in this study.ResultsThe inverse association between RNA expression and promoter region methylation of JAM3 was found by analyzing 185 cases of EC samples extracted from the TCGA database (p < 0.05). JAM3 was highly expressed in KYSE450, KYSE520, TE1 and YES2 cells, low level expressed in KYSE70 cells and unexpressed in KYSE30, KYSE150, KYSE410, KYSE510, TE13 and BIC1 cells. JAM3 was unmethylated in KYSE450, KYSE520, TE1 and YES2 cells, partial methylated in KYSE70 cells and completely methylated in KYSE30, KYSE150, KYSE410, KYSE510, TE13 and BIC1 cells. The expression of JAM3 is correlated with methylation status. The levels of JAM3 were unchanged in KYSE450, KYSE520, TE1 and YES2 cells, increased in KYSE70 cells and restored expression in KYSE30, KYSE150, KYSE410, KYSE510, TE13 and BIC1 cells after 5-aza-2′-deoxycytidine treatment, suggesting that the expression of JAM3 is regulated by promoter region methylation. JAM3 was methylated in 26.5% (13/49) of EIN and 51.1% (388/760) of primary EC, and methylation of JAM3 was associated significantly with tumor differentiation and family history (allp < 0.05). Methylation of JAM3 is an independent prognostic factor of poor 5-year overall survival (p < 0.05). JAM3 suppresses cell proliferation, colony formation, migration and invasion and induces G1/S arrest and apoptosis in EC. Further study demonstrated that JAM3 suppressed EC cells and xenograft tumor growth by inhibiting Wnt/β-catenin signaling.ConclusionJAM3 is frequently methylated in human EC, and the expression of JAM3 is regulated by promoter region methylation. JAM3 methylation is an early detection and prognostic marker of EC. JAM3 suppresses EC growth both in vitro and in vivo by inhibiting Wnt signaling.
Systematic identification and characterization of repeat sequences in African swine fever virus genomes
Authors: Zhu Zhaozhong , Ge Shengqiang , Cai Zena , Wu Yifan , Lu Congyu , Zhang Zheng , Fu Ping , Mao Longfei , Wu Xiaodong , Peng Yousong 
Published: December 2022

AbstractAfrican swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5’ end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution.
An enhanced beamspace channel estimation algorithm for wideband millimeter-wave massive MIMO systems
Authors: Liu Yang , Song Kaipeng , Luo Yi , Han Ding , Zhang Yinghui , Jin Minglu 
Published: December 2022

AbstractAccurate beamspace channel estimation is critical in wideband millimeter-wave (mmWave) massive multiple-input multiple-output (MIMO) communication systems. However, the beam squint effect caused by the increase in bandwidth and array dimension can bring additional challenges to the wideband channel estimation. In this study, we propose a wideband channel estimation scheme based on compressed sensing to solve the beam squint effect in broadband mmWave massive MIMO systems. First, the channel estimation problem is transformed into a beamspace direction estimation problem by exploiting the special frequency-dependent sparse structure of a broadband beamspace channel. Then, we propose a beam-band function-based orthogonal matching pursuit algorithm, in which a beam-band function is constructed and used to capture the power of each path component to estimate the spatial direction. In addition, the support of each path component at different sub-carriers is estimated to reduce the influence of the beam squint effect. Moreover, the support is estimated adaptively to improve the estimation accuracy further. Simulation results demonstrate that the proposed scheme reduces the pilot overhead under the beam squint effect and improve the estimation accuracy significantly.
Artificial intelligence for channel estimation in multicarrier systems for B5G/6G communications: a survey
Authors: Vilas Boas Evandro C. , e Silva Jefferson D. S. , de Figueiredo Felipe A. P. , Mendes Luciano L. , de Souza Rausley A. A. 
Published: December 2022

AbstractMulticarrier modulation allows for deploying wideband systems resilient to multipath fading channels, impulsive noise, and intersymbol interference compared to single-carrier systems. Despite this, multicarrier signals suffer from different types of distortion, including channel noise sources and long- and short-term fading. Consequently, the receiver must estimate the channel features and compensate it for data recovery based on channel estimation techniques, such as non-blind, blind, and semi-blind approaches. These techniques are model-based and designed with accurate mathematical channel models encompassing their features. Nevertheless, complex environments challenge accurate mathematical channel estimation modeling, which might neither be accurate nor correspond to reality. This impairment decreases the system performance due to the channel estimation accuracy loss. Fortunately, (AI) algorithms can learn the relationship among different system variables using a model-driven or model-free approach. Thereby, AI algorithms are used for channel estimation by exploiting its complexity without unrealistic assumptions, following a better performance than conventional techniques under the same channel. Hence, this paper comprehensively surveys AI-based channel estimation for multicarrier systems. First, we provide essential background on conventional channel estimation techniques in the context of multicarrier systems. Second, the AI-aided channel estimation strategies are investigated using the following approaches: classical learning, neural networks, and reinforcement learning. Lastly, we discuss current challenges and point out future research directions based on recent findings.