bluuebunny/crossref_metadata_2025_split huggingface dataset:
Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes
Authors: Ikemoto Ko , Fujimoto Hinano , Fujimoto Akihiro 
Published: December 2022

Abstract
Background:
Long-read sequencing technologies have the potential to overcome the limitations of short reads and provide a comprehensive picture of the human genome. However, it remains hard to characterize repetitive sequences by reconstructing genomic structures at high resolution solely from long reads. Here, we developed a localized assembly method (LoMA) that constructs highly accurate consensus sequences (CSs) from long reads.
Methods:
We first developed LoMA, by combining minimap2, MAFFT, and our algorithm, which classifies diploid haplotypes based on structural variants and constructs CSs. Using this tool, we analyzed two human samples (NA18943 and NA19240) sequenced with the Oxford Nanopore sequencer. We defined target regions in each genome based on mapping patterns and then constructed a high-quality catalog of the human insertion solely from the long-read data.
Results:
The assessment of LoMA showed high accuracy of CSs (error rate < 0.3%) compared with raw data (error rate > 8%) and superiority to the previous study. The genome-wide analysis of NA18943 and NA19240 identified 5,516 and 6,542 insertions (≥ 100 bp) respectively. Most insertions (~ 80%) were derived from the tandem repeat and transposable elements. We also detected processed pseudogenes, insertions in transposable elements, and long insertions (> 10 kbp). Further, our analysis suggested that short tandem duplications were association with gene expression and transposons.
Conclusions:
Our analysis showed that LoMA constructs high-quality sequences from long reads with substantial errors. This study revealed the true structures of insertions with high accuracy and inferred mechanisms for the insertions. Our approach contributes to the future human genome studies. LoMA is available at our GitHub page: https://github.com/kolikem/loma.
DyHNet: Learning Dynamic Heterogeneous Network Representations
Authors: Nguyen Hoang , Rad Radin Hamidi , Zarrinkalam Fattane , Bagheri Ebrahim 
Published: December 2022

Abstract
Many real-world networks, such as social networks, contain structuralheterogeneity and experience temporal evolution. However, while therehas been growing literature on network representation learning, only afew have addressed the need to learn representations for dynamic hetero-geneous networks. The objective of our work in this paper is to introduce DyHNet, which learns representations for such networks and distinguishesitself from the state-of-the-art by systematically capturing (1) local nodesemantics, (2) global network semantics, and (3) longer-range temporalassociations between network snapshots when learning network repre-sentations. Through experiments on four real-world datasets, we demon-strate that our proposed method is able to show consistently better andmore robust performance compared to the state-of-the-art techniques.
Relationship between efficacy and common metabolic parameters in first- treatment drug-naïve patients with early non-response schizophrenia: a retrospective study
Authors: Zhu Junhong , Wu Jiajia , Liu Xuebing , Ma Jun 
Published: December 2022

Abstract
Background
Comorbid metabolic disorders in patients with schizophrenia are very common. Patients with schizophrenia who respond to therapy early are often strongly predictive of better treatment outcomes. However, the differences in short-term metabolic markers between early responders and early non-responders in schizophrenia are unclear.
Methods
143 first-treatment drug-naïve schizophrenia patients were included in this study and were given a single antipsychotic medication for 6 weeks after admission. After 2 weeks, the sample was divided into an early response group and an early non-response group based on psychopathological changes. For the study endpoints, we depicted the change curves of psychopathology in both subgroups and compared the differences between the two groups in terms of remission rates and multiple metabolic parameters.
Results
The early non-response had 73 cases (51.05%) in the 2nd week. In the 6th week, the remission rate was significantly higher in the early response group than in the early non-response group (30,42.86% vs. 8,10.96%); the body weight, body mass index, blood creatinine, blood uric acid, total cholesterol, triglyceride, low-density lipoprotein, fasting blood glucose, and prolactin of the enrolled samples were significantly increased, and high-density lipoprotein was significantly decreased. ANOVAs revealed a significant effect of treatment time on abdominal circumference, blood uric acid, total cholesterol, triglyceride, high-density lipoprotein, low-density lipoprotein, fasting blood glucose and prolactin, and a significant negative effect of early non-response to treatment on abdominal circumference, blood creatinine, triglyceride, fasting blood glucose.
Conclusion
Schizophrenia patients with early non-response had lower rates of short-term remission and more extensive and severe abnormal metabolic indicators. In clinical practice, patients with early non-response should be given a targeted management strategy, antipsychotic drugs should be switched on time, and active and effective interventions for their metabolic disorders should be given.
Improving the retention campaign effectiveness using customer value index concept and decision tree analytics: a case study of Magenta Bank
Authors: Yus'an Ubaydillah , Wasesa Meditya 
Published: December 2022

Abstract
This study aims to improve retention campaign take up rate as well as justifying the marketing cost to maintain campaign effectiveness that leads into company profitability in Magenta bank. Because In fact, not all customers are good customers, not all customers require massive marketing investment. Retention campaign become major issue since competition of digital banking industry in Indonesia has increasing during Pandemic COVID-19. There is so many new digital banking emerges in this period as they see an opportunity during activity limitation. Some other investment product is also emerging, giving higher interest rate compared to Magenta Deposito. Other thinks that make the condition worsen is buying power of Indonesian is dramatically declining during pandemic COVID-19. This condition will make the retention strategy more difficult due to very tight competition. To see how existing condition of Magenta Bank customer, researcher used Customer Value Index (CVI) to calculate the cost component and income component for each customer. This method is not only measuring customer value, but also create customer segmentation. For example, premium segment is more likely use Magenta as a saving account while other segment uses for transaction. This analysis also indicates a different critical stage of customer retention between each acquisition channel that must be anticipated by Magenta. Using CVI Analysis combined with several portfolio parameter such as MOB, Acquisition channel, and Funding balance tier, the retention campaign strategy can be improved by creating different approach using segmentation based on customer behavior. Researcher used Machine learning analytic approach to create segmentation with Scikit Learn Module to produce decision tree. the predictive result of this model will ensure that the marketing effort is cost-effective by investing more marketing budget on High CVI Customers that has a potential return for Magenta Bank and invest less marketing budget on Zero or Negative CVI Customers.
Tumor-targeted AIE polymeric micelles mediated immunogenic sonodynamic therapy inhibits cancer growth and metastasis
Authors: Deng Kai , Yu Yifeng , Zhao Yong , Li Jia-Mi , Li Kun-Heng , Zhao Hong-Yang , Wu Meng , Huang Shiwen 
Published: December 2022

Abstract
Background: Aggregation-induced emission luminogens (AIEgens) exhibit potent sonosensitivity in nanocarriers compared with conventional organic sonosensitizers owing to the strong fluorescence emission in the aggregated state. However, premature drug leakage and ineffective tumor targeting of current AIE nanosonosensitizers critically restrict their clinical application.
Results: Here, an AIEgens-based sonosensitizer (AIE/Biotin-M) with excellent sonosensitivity was developed by assembling salicylaldazine-based amphiphilic polymers (AIE-1) and 4T1 tumor-targeting amphiphilic polymers (DSPE-PEG-Biotin) for the effective delivery of salicylaldazine to 4T1 tumor tissues, aiming to mediate immunogenic SDT. In vitro, AIE/Biotin-M were highly stable and generated plentiful singlet oxygen (1O2) under ultrasound (US) irradiation. After AIE/Biotin-M targeted accumulation in tumor, upon US irradiation, the generation of 1O2 not only leaded cancer cells death, but also elicited systemically immune response through causing immunogenic cell death (ICD) of cancer cells. In addition to mediate SDT, AIE/Biotin-M could chelate and reduce Fe3+, Cu2+ and Zn2+ by salicylaldazine for inhibiting neovascularization in tumor tissues. Ultimately, AIE/Biotin-M systemically inhibited tumor growth and metastasis upon US irradiation.
Conclusions: This study presents a facile approach to the development of AIE nanosonosensitizers for cancer SDT.
Transformative potential of conservation actions
Authors: Arponen Anni , Salomaa Anna 
Published: December 2022

Abstract
Transformative change can help achieve the 2050 vision of biodiversity, but concrete ways to achieve it are only being discovered. To contribute to the understanding of the practical options for concrete action to foster, accelerate and maintain the transformative change, we assessed the leverage potential of existing conservation actions using the Meadows’ Leverage points framework. We took the actions from the Conservation Actions Classification by the Conservation Measures Partnership. The outcome is a scheme that evaluates at which leverage points, from simple parameters to paradigms, the different conservation actions have potential to make an impact, and thus impact systemic change. We found that all conservation actions have potential to leverage systemic transformative change, with varying coverage of the leverage points. All leverage points were addressed by several actions. The scheme could be used both as an interim tool for evaluating transformative potential in different broad datasets, but also help with planning of new conservation policies, interventions and projects. We hope our work could be a first step toward standardization and broader adoption of assessing leverage in conservation research and practice, achieving broader socio-ecological system leverage with conservation tools.
Anti-diabetic effects of low iodine levels in beta-TC-6 cells and mature 3T3-L1 adipocytes depend on Akt phosphorylation and GLUT-4, although higher doses induce caspase-3 and oxidative stress
Authors: Arely Resendiz-Jiménez , Cristian Arbez-Evangelista , Oscar López-Franco , Cuellar-Rufino Sergio , Rocío Coutino-Rodríguez , Helguera Arroyo 
Published: December 2022

Abstract
In epidemiological clinical reports iodine excess has been associated with diabetes mellitus type 2 and higher blood glucose. The relationship between iodine, pancreas, adipose tissue and glucose transport is unclear. The goal of this study was analyzing the effect of iodine concentrations (as lugol solution) on glucose transport, insulin secretion and cytotoxic effects in mature 3T3-L1 adipocytes and beta-TC-6 cells. The mature adipocytes and Beta-TC-6 cells were treated with 1 to 1000 µM of lugol (molecular iodine dissolved in potassium iodide) for 30 minutes to 24 hours, glucose uptake was measured with the fluorescent analog 2-NBDG, insulin receptor, Akt protein, P-Akt (ser-473) and GLUT4 were measured by immunoblot in mature adipocytes and insulin secretion, cytotoxic MTT assay, oxidative stress and caspase-3 activation were measurement by colorimetric methods. Higher doses of lugol significantly promotes cell growth inhibition, induces oxidative stress and caspase-3 activation on adipocytes and Beta-TC-6 cells. Low levels of lugol significantly induces insulin secretion in Beta-TC-6 cells and increases glucose transport in mature adipocytes. The insulin secretion decrease with higher doses of lugol. Lugol treatment increases GLUT4 protein expression and induce serine-473 phosphorylation of Akt (P-Akt) in mature 3T3-L1 adipocytes Hence, it appears that low iodine concentrations might regulate glucose metabolism, though higher doses have cytotoxic effects in adipocytes and pancreatic cells via oxidative stress.
Unraveling the Patterns and Pathways of Local Recurrence of Nasopharyngeal Carcinoma: Evidence for Individualized Clinical Target Volume Delineation
Authors: Ou Xiaomin , Yan Wenbin , Huang Yangle , He Xiayun , Ying Hongmei , Lu Xueguan , Zhu Hui , Wu Bin , Wang Jiazhou , Hu Chaosu 
Published: December 2022

Abstract
Backgrounds: Despite publication of international guidelines, there are notable controversial points of clinical target volume (CTV) delineation in nasopharyngeal carcinoma (NPC). Recently, scholars proposed a novel way of delineation of CTV in NPC -- individualization of CTV delineation based on T classification and spread patterns, which yielded excellent long-term local control with limited late toxicities. The aim of this study was to clarify the anatomic patterns and pathways of local recurrence of NPC and provide a clinical reference for the delineation of CTV.
Methods: A total of 869 patients with non-metastatic NPC were treated with intensity-modulated radiation therapy (IMRT) at our institution between 2009 and 2010. Among the 57 cases of local/locoregional recurrence, 52 cases with traceable radiotherapy plans and magnetic resonance imaging at the time of the first diagnosis of recurrence were included. Anatomical structures and gross tumor volume of local recurrence were contoured. The incidence of relapse of each anatomic structure, route of local recurrence, and their correlation were analyzed.
Results: Locally advanced disease had a significantly increased risk of recurrence in the posterior nasal cavityand a trend towards higher risk of recurrence in the clivus, lateral pterygoid muscle, and hypoglossal canal. Based on the incidence of local recurrence, we constructed a high-risk map for the early and locally advanced stages. Given the higher incidence of relapses in locally advanced disease, these structures were strongly recommended to be encompassed by the CTV of T3-4 diseases, including posterior ethmoid sinus, lateral pterygoid muscle, hypoglossal canal, inferior orbital fissure, and cavernous sinus. Local recurrences were classified into five routes, where anterior extension accounted for the majority (30.8%), and caudal tumor extension pathway had the lowest incidence (5.8%). There was a significant correlation between the local recurrences of neural foramina and neighboring anatomical structures along each pathway. All cases relapsed at unilateral cavernous sinus, most at the same side of primary tumor.
Conclusions: Local recurrence of NPC varied according to T classification, followed a stepwise pattern, spread via neural foramina, and recurred at ipsilateral cavernous sinus. This provides meaningful clinical evidence for delineation of CTV, especially individualized delineation.
An analysis of the learning styles and attitudes of foreign students in a post-baccalaureate medical education program
Authors: Hsu Hsiang-Chin , Sung Tzu-Ching 
Published: December 2022

Abstract
In a scenario of ongoing changes in the theory and methodology of teaching, student-centered practices are crucial in improving teaching and learning outcomes. This study aimed to evaluate whether the learning styles and attitudes (connected and separate knowing) associated with the curriculum differ among medical students. The research subjects consisted of 43 first- and second-year medical students attending a post-baccalaureate medical education program exclusively for foreign students at comprehensive university in Kaohsiung City, Taiwan. A self-administered Attitudes Toward Thinking and Learning Survey (ATTLS) was used to assess the differences in learning styles and attitudes among grade, gender, and nationality of these post-baccalaureate medical students. The reliability values of Cronbach Alpha coefficients for all items of ATTLS was 0.93. Significant higher connected knowing styles are reported than separate knowing among these medical students. The average score of the connected knowing for first-year students taking the "International Health" course is significantly higher than that of second-year students taking the "Population Health and Sustainable Development" course. There is no difference in the separate knowing between these two curricula. The learning styles and attitudes of students participating in the teaching process showed no difference in grade, gender, and nationality. The evidence that there is a significant interaction effect of grade, gender, and nationality examined in relation to the separate knowing, rather than the connected knowing, suggests that this heterogenicity of learning methodology needs to be considered and integrated into future teaching methods.
Inhibin B -to- Anti-Mullerian Hormone Ratio as noninvasive predictors of positive sperm retrieval in idiopathic non-obstructive azoospermia
Authors: Deng Chenyao , Liu Defeng , Zhao Lianming , Lin Haocheng , Mao Jiaming , Zhang Zhe , Yang Yuzhuo , Zhang Haitao , Xu Huiyu , Hong Kai , Jiang Hui 
Published: December 2022

Abstract
Background
The lack of clinically useful biomarkers for predicting micro-TESE outcomes in males with idiopathic NOA. To find clinically reliable serum reproductive hormone markers to predict the outcome of sperm retrieval in men with idiopathic NOA undergoing micro-TESE.
Methods
We analyzed the clinical data of 168 men with idiopathic NOA treated with micro-TESE. The clinical predictors of a successful sperm retrieval were put to the test using logistic regression analysis. The clinical net benefit was calculated using a decision-curve analysis, and the predictive power of each variable was assessed using the ROC-derived area under the curve.
Result
Between positive group and negative group for sperm retrieval, there was a statistically significant difference in INHB, AMH, and INHB/AMH. AMH, INHB, and INHB/AMH were each independent predictors of successful sperm retrieval, with INHB (OR1.02, p = 0.03), AMH (OR0.85, p = 0.01), INHB/AMH (OR1.08, p < 0.01). The ROC curve determined the optimal cut-off values for serum INHB and INHB/AMH in positive sperm retrieval patients undergoing micro-TESE. 21.51 pg/ml was the cut-off value for INHB. The cut-off value for INHB/AMH was 3.19, which had a 86.3% sensitivity and a 53.8% specificity. Using INHB and INHB/AMH prior to micro-TESE sperm retrieval in idiopathic NOA patients improved the net benefit of positive sperm retrieval, and the net benefit score of INHB/AMH was better than that of INHB, according to decision analysis curves.
Conclusion
Serum INHB have predictive value for sperm retrieval outcomes in idiopathic NOA patients undergoing micro-TESE. Combining INHB and AMH, INHB/AMH seems to be a better predictor.
The Neurotoxic Mechanisms of Graphene Family Nanomaterials at the Cellular Level: A Solution-based Approach Review
Authors: Rafieian-Kopaei Mahmoud , Ghazimoradi Mohammad Mahdi , Azad Farhan Vahdat , Jalali Fatemeh 
Published: December 2022

Abstract:The graphene family nanomaterials (GFNs) have been recognized to have potential applications in biomedicine, especially in the rag nostic, drug delivery and neuroimaging. Multiple studies have examined the neurotoxicity of GFNs to assay their toxic effects on organisms and ecosystems. In this article, we reviewed the different neurotoxicity effects of GFNs at intracellular levels, including nucleus-related effects and cytosolic mechanisms, as well as extracellular levels, including effects on enzyme activity, oxidative stress, behavior, neurotransmitters, and central nervous system (CNS). Furthermore, for the sake of the solution, we discussed the reducing ways of graphene toxicity. A schematic description is shown in Fig. (1).
LINC00665: A Promising Biomarker in Gastrointestinal Tumors
Authors: Yuan Mengping , Gu Yuyang , Chen Jiawen , Jiang Yibin , Qian Jing , Cao Shuguang 
Published: December 2022

Abstract:
An increasing volume of studies has reported that long non-codingRNAs
(lncRNAs) are involved in the carcinogenesis of many different cancers. Especially in
gastrointestinal tumors, lncRNAs are found to participate in various physiological and
pathological processes. LncRNAs can regulate gene expression at multiple levels,
including transcriptional, post-transcription, translational, and post-translational levels.
Long intergenic non-protein coding RNA 665(LINC00665), a novel cancer-related
lncRNA, is frequently dysregulated in multiple gastrointestinal tumors, including gastric
and colorectal cancers, hepatocellular carcinoma, and so on. In this review, we
analyzed the expression and prognostic value of LINC00665 in human gastrointestinal
tumors, systematically summarized the current literature about the clinical significance
of this lncRNA, and explored the regulatory mechanisms of LINC00665 as a competing
endogenous RNA (ceRNA) in tumor progression. Consequently, we concluded
that LINC00665 might act as a prognostic biomarker and a potential target for gastrointestinal
tumor diagnosis and treatment.
Triplication of Synaptojanin 1 in Alzheimer’s Disease Pathology in Down
Syndrome
Authors: Hwang Jr. Robert , Dang Lam-Ha , Chen Jacinda , Lee Joseph H. , Marquer Catherine 
Published: December 2022

Abstract:
Down Syndrome (DS), caused by triplication of human chromosome 21 (Hsa21) is the most
common form of intellectual disability worldwide. Recent progress in healthcare has resulted in a dramatic
increase in the lifespan of individuals with DS. Unfortunately, most will develop Alzheimer’s
disease like dementia (DS-AD) as they age. Understanding similarities and differences between DSAD
and the other forms of the disease – i.e., late-onset AD (LOAD) and autosomal dominant AD
(ADAD) – will provide important clues for the treatment of DS-AD. In addition to the APP gene that
codes the precursor of the main component of amyloid plaques found in the brain of AD patients, other
genes on Hsa21 are likely to contribute to disease initiation and progression. This review focuses on
SYNJ1, coding the phosphoinositide phosphatase synaptojanin 1 (SYNJ1). First, we highlight the function
of SYNJ1 in the brain. We then summarize the involvement of SYNJ1 in the different forms of
AD at the genetic, transcriptomic, proteomic and neuropathology levels in humans. We further examine
whether results in humans correlate with what has been described in murine and cellular models of
the disease and report possible mechanistic links between SYNJ1 and the progression of the disease.
Finally, we propose a set of questions that would further strengthen and clarify the role of SYNJ1 in
the different forms of AD.
A Multifaceted Scaffold for Building Bioactive Compounds: Phenothiazine
Authors: Upadhyay Prabhat Kumar , Pathak Shilpi , Mishra Raghav , Kumar Rajesh , Jain Ankit 
Published: December 2022

Abstract:
In the growing field of heterocyclic compounds, phenothiazine and the associated nucleus
are among the most significant potential scaffolds with excellent pharmacological activities.
The knowledge of chemistry, synthetic routes, and various physicochemical parameters of these
compounds draws particular attention to create a chemical library. Related compounds synthesized
by various routes have diverse pharmacological functions. The exhaustive search of phenothiazine
literature helps the medicinal chemists who develop the molecules for designing new drugs. A
broad view of the synthetic routes has been outlined in this study. This paper includes the chemistry,
physiochemical properties, and various biological activities of phenothiazine and related compounds.