bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative omics analyses of the ligninolytic Rhodosporidium fluviale LM-2 disclose catabolic pathways for biobased chemical production
Authors: Vilela Nathália , Tomazetto Geizecler , Gonçalves Thiago Augusto , Sodré Victoria , Persinoti Gabriela Felix , Moraes Eduardo Cruz , de Oliveira Arthur Henrique Cavalcante , da Silva Stephanie Nemesio , Fill Taícia Pacheco , Damasio André , Squina Fabio Marcio 
Published: January 2023

Abstract
Background
Lignin is an attractive alternative for producing biobased chemicals. It is the second major component of the plant cell wall and is an abundant natural source of aromatic compounds. Lignin degradation using microbial oxidative enzymes that depolymerize lignin and catabolize aromatic compounds into central metabolic intermediates is a promising strategy for lignin valorization. However, the intrinsic heterogeneity and recalcitrance of lignin severely hinder its biocatalytic conversion. In this context, examining microbial degradation systems can provide a fundamental understanding of the pathways and enzymes that are useful for lignin conversion into biotechnologically relevant compounds.

Results
Lignin-degrading catabolism of a novel Rhodosporidium fluviale strain LM-2 was characterized using multi-omic strategies. This strain was previously isolated from a ligninolytic microbial consortium and presents a set of enzymes related to lignin depolymerization and aromatic compound catabolism. Furthermore, two catabolic routes for producing 4-vinyl guaiacol and vanillin were identified in R. fluviale LM-2.

Conclusions
The multi-omic analysis of R. fluviale LM-2, the first for this species, elucidated a repertoire of genes, transcripts, and secreted proteins involved in lignin degradation. This study expands the understanding of ligninolytic metabolism in a non-conventional yeast, which has the potential for future genetic manipulation. Moreover, this work unveiled critical pathways and enzymes that can be exported to other systems, including model organisms, for lignin valorization.
Walking pace, handgrip strength, age, APOE genotypes, and new-onset dementia: the UK Biobank prospective cohort study
Authors: He Panpan , Zhou Chun , Ye Ziliang , Liu Mengyi , Zhang Yuanyuan , Wu Qimeng , Zhang Yanjun , Yang Sisi , Xiaoqin Gan , Qin Xianhui 
Published: January 2023

Abstract
Background
The independent and additive associations of walking pace and grip strength on dementia risk and the potential modifying effects of age, APOE phenotypes, and other dementia risk factors on the walking pace and dementia relationships demand further clarification. We aimed to investigate the independent and additive relationships of walking pace and handgrip strength on the risk of new-onset dementia and examine the potentially modifying effects of age, APOE phenotypes, lifestyle factors, and family history of dementia in the relationships.

Methods
A total of 495,700 participants from the UK Biobank, who were free of dementia at baseline, were included in this study. Walking pace was self-defined as slow, average, or brisk. Handgrip strength was assessed by dynamometer and was divided into sex-specific quartiles. The APOE genotypes were determined by a combination variant of rs429358 and rs7412. Other dementia risk factors, including education, physical activity, hypertension, depression, diabetes, and family history of dementia, were also collected. The primary outcome was new-onset all-cause dementia.

Results
Over a median follow-up duration of 12.0 years, 3986 (0.8%) participants developed new-onset all-cause dementia. Compared with those with slow walking pace, participants with average (HR, 0.61; 95%CI: 0.55–0.68) or brisk (HR, 0.59; 95%CI: 0.52–0.67) walking pace had a significantly lower risk of new-onset all-cause dementia. Moreover, compared with those with both slow walking pace and lower handgrip strength (the first quartile), the lowest risk of new-onset all-cause dementia was observed in participants with both average or brisk walking pace and higher handgrip strength (the 2–4 quartiles) (HR, 0.45; 95%CI: 0.40–0.52). Notably, the negative relationship between walking pace and the risk of new-onset all-cause dementia was significantly reduced as APOE ε4 dosage increased (APOE ε4 dosages = 0 or 1: brisk vs. slow: HR, 0.55; 95%CI: 0.48–0.63; vs. APOE ε4 dosages = 2: brisk vs. slow: HR, 1.14; 95%CI: 0.77–1.68; P for interaction = 0.001) or age increased (< 58 [median]: brisk vs. slow: HR, 0.27; 95%CI: 0.18–0.41; vs. ≥ 58 years: brisk vs. slow: HR, 0.55; 95%CI: 0.48–0.63; P for interaction = 0.007).

Conclusions
Walking pace was inversely associated with new-onset dementia in the general population, especially in younger participants and those with lower APOE ε4 dosage. Participants with both faster walking pace and higher handgrip strength had the lowest risk of dementia, suggesting that maintaining both high handgrip strength and fast walking pace may be a more comprehensive strategy for preventing dementia risk.
Knockout of secretin ameliorates biliary and liver phenotypes during alcohol-induced hepatotoxicity
Authors: Kyritsi Konstantina , Wu Nan , Zhou Tianhao , Carpino Guido , Baiocchi Leonardo , Kennedy Lindsey , Chen Lixian , Ceci Ludovica , Meyer Alison Ann , Barupala Nipuni , Franchitto Antonio , Onori Paolo , Ekser Burcin , Gaudio Eugenio , Wu Chaodong , Marakovits Corinn , Chakraborty Sanjukta , Francis Heather , Glaser Shannon , Alpini Gianfranco 
Published: January 2023

Abstract
Background
Alcohol-related liver disease (ALD) is characterized by ductular reaction (DR), liver inflammation, steatosis, fibrosis, and cirrhosis. The secretin (Sct)/secretin receptor (SR) axis (expressed only by cholangiocytes) regulates liver phenotypes in cholestasis. We evaluated the role of Sct signaling on ALD phenotypes.

Methods
We used male wild-type and Sct−/− mice fed a control diet (CD) or ethanol (EtOH) for 8 wk. Changes in liver phenotypes were measured in mice, female/male healthy controls, and patients with alcoholic cirrhosis. Since Cyp4a10 and Cyp4a11/22 regulate EtOH liver metabolism, we measured their expression in mouse/human liver. We evaluated: (i) the immunoreactivity of the lipogenesis enzyme elongation of very-long-chain fatty acids 1 (Elovl, mainly expressed by hepatocytes) in mouse/human liver sections by immunostaining; (ii) the expression of miR-125b (that is downregulated in cholestasis by Sct) in mouse liver by qPCR; and (iii) total bile acid (BA) levels in mouse liver by enzymatic assay, and the mRNA expression of genes regulating BA synthesis (cholesterol 7a-hydroxylase, Cyp27a1, 12a-hydroxylase, Cyp8b1, and oxysterol 7a-hydroxylase, Cyp7b11) and transport (bile salt export pump, Bsep, Na+-taurocholate cotransporting polypeptide, NTCP, and the organic solute transporter alpha (OSTa) in mouse liver by qPCR.

Results
In EtOH-fed WT mice there was increased biliary and liver damage compared to control mice, but decreased miR-125b expression, phenotypes that were blunted in EtOH-fed Sct−/− mice. The expression of Cyp4a10 increased in cholangiocytes and hepatocytes from EtOH-fed WT compared to control mice but decreased in EtOH-fed Sct−/− mice. There was increased immunoreactivity of Cyp4a11/22 in patients with alcoholic cirrhosis compared to controls. The expression of miR-125b decreased in EtOH-fed WT mice but returned at normal values in EtOH-fed Sct−/− mice. Elovl1 immunoreactivity increased in patients with alcoholic cirrhosis compared to controls. There was no difference in BA levels between WT mice fed CD or EtOH; BA levels decreased in EtOH-fed Sct−/− compared to EtOH-fed WT mice. There was increased expression of Cyp27a1, Cyp8b1, Cyp7b1, Bsep, NTCP and Osta in total liver from EtOH-fed WT compared to control mice, which decreased in EtOH-fed Sct−/− compared to EtOH-fed WT mice.

Conclusions
Targeting Sct/SR signaling may be important for modulating ALD phenotypes.
Autoregressive graph Volterra models and applications
Authors: Yang Qiuling , Coutino Mario , Leus Geert , Giannakis Georgios B. 
Published: January 2023

AbstractGraph-based learning and estimation are fundamental problems in various applications involving power, social, and brain networks, to name a few. While learning pair-wise interactions in network data is a well-studied problem, discovering higher-order interactions among subsets of nodes is still not yet fully explored. To this end, encompassing and leveraging (non)linear structural equation models as well as vector autoregressions, this paper proposes autoregressive graph Volterra models (AGVMs) that can capture not only the connectivity between nodes but also higher-order interactions presented in the networked data. The proposed overarching model inherits the identifiability and expressibility of the Volterra series. Furthermore, two tailored algorithms based on the proposed AGVM are put forth for topology identification and link prediction in distribution grids and social networks, respectively. Real-data experiments on different real-world collaboration networks highlight the impact of higher-order interactions in our approach, yielding discernible differences relative to existing methods.
A reconfigurable and compact subpipelined architecture for AES encryption and decryption
Authors: Li Ke , Li Hua , Mund Graeme 
Published: January 2023

AbstractAES has been used in many applications to provide the data confidentiality. A new 32-bit reconfigurable and compact architecture for AES encryption and decryption is presented and implemented in non-BRAM FPG in this paper. It can be reconfigured for the options of different key sizes which is very flexible for the users to apply AES for various application environments. The proposed design employs a single-round architecture and subpipeling to minimize the hardware cost. The fully composite field GF((24)2)-based encryption/decryption and keyschedule lead to the lower hardware complexity and efficient subpipelining for 32-bit data path. In addition, a new subpipelined on-the-fly keyschedule over composite field GF((24)2) is proposed for all standard key sizes (128-, 192-, 256-bit) which generates the roundkeys simultaneously and efficiently. This feature is very useful and efficient when the main key has been changed since AES is a symmetric-key cryptography and the session key usually changes frequently. The proposed reconfigurable and compact design has higher throughput and lower hardware cost. It achieves throughputs of 375Mbits/s with 128-bit key, 318Mbits/s with 192-bit key and 275Mbits/s with 256-bit key on VIRTEX XC4VSX25-12, and the total number of slices is 1766. The proposed reconfigurable and compact AES architecture can be efficiently applied in computing-restricted environments such as wireless and embedded devices.
Breast cancer heterogeneity and its implication in personalized precision therapy
Authors: Guo Liantao , Kong Deguang , Liu Jianhua , Zhan Ling , Luo Lan , Zheng Weijie , Zheng Qingyuan , Chen Chuang , Sun Shengrong 
Published: January 2023

AbstractBreast cancer heterogeneity determines cancer progression, treatment effects, and prognosis. However, the precise mechanism for this heterogeneity remains unknown owing to its complexity. Here, we summarize the origins of breast cancer heterogeneity and its influence on disease progression, recurrence, and therapeutic resistance. We review the possible mechanisms of heterogeneity and the research methods used to analyze it. We also highlight the importance of cell interactions for the origins of breast cancer heterogeneity, which can be further categorized into cooperative and competitive interactions. Finally, we provide new insights into precise individual treatments based on heterogeneity.
Alpha-B-Crystallin overexpression is sufficient to promote tumorigenesis and metastasis in mice
Authors: Rashidieh Behnam , Bain Amanda Louise , Tria Simon Manuel , Sharma Sowmya , Stewart Cameron Allan , Simmons Jacinta Ley , Apaja Pirjo M. , Duijf Pascal H. G. , Finnie John , Khanna Kum Kum 
Published: January 2023

Abstract
Background
αB-Crystallin is a heat shock chaperone protein which binds to misfolded proteins to prevent their aggregation. It is overexpressed in a wide-variety of cancers. Previous studies using human cancer cell lines and human xenograft models have suggested potential tumor promoter (oncogene) roles for αB-Crystallin in a wide-spectrum of cancers.

Methods
To determine the causal relationship between CRYAB overexpression and cancer, we generated a Cryab overexpression knock-in mouse model and monitor them for development of spontaneous and carcinogen (DMBA)-induced tumorigenesis. In order to investigate the mechanism of malignancies observed in this model multiple techniques were used such as immunohistochemical characterizations of tumors, bioinformatics analysis of publically available human tumor datasets, and generation of mouse embryonic fibroblasts (MEFs) for in vitro assays (clonogenic survival and migration assays and proteome analysis by mass-spectrometry).

Results
This model revealed that constitutive overexpression of Cryab results in the formation of a variety of lethal spontaneous primary and metastatic tumors in mice. In vivo, the overexpression of Cryab correlated with the upregulation of epithelial-to-mesenchymal (EMT) markers, angiogenesis and some oncogenic proteins including Basigin. In vitro, using E1A/Ras transformed MEFs, we observed that the overexpression of Cryab led to the promotion of cell survival via upregulation of Akt signaling and downregulation of pro-apoptotic pathway mediator JNK, with subsequent attenuation of apoptosis as assessed by cleaved caspase-3 and Annexin V staining.

Conclusions
Overall, through the generation and characterization of Cryab overexpression model, we provide evidence supporting the role of αB-Crystallin as an oncogene, where its upregulation is sufficient to induce tumors, promote cell survival and inhibit apoptosis.
The effect of positive thinking training on hope and adherence to treatment in hemodialysis patients: a randomized controlled trial
Authors: Sabouri Fatemeh , Rambod Masoume , Khademian Zahra 
Published: January 2023

Abstract
Background
Patients undergoing hemodialysis are exposed to psychological problems, such as despair, which in turn can be a trigger for them to abandon the treatment process. This study aimed to determine the effect of positive thinking training on hope and adherence to treatment in hemodialysis patients.

Methods
This randomized controlled trial was performed on 80 hemodialysis patients referred to two hemodialysis centers in Shiraz, Iran. They were randomly divided into an intervention and a control group. Eight sessions of positive thinking skills training carried out individually on the patients' bedsides. The primary and secondary outcomes were hope and adherence to treatment, respectively. The data were collected using Snyder Hope Questionnaire, End-Stage Renal Disease Adherence Questionnaire, laboratory tests, and weight measurements. Data were analyzed by Chi-square and Paired and Independent T-test using SPSS software version 18.

Results
After the intervention, the mean score of hope was significantly higher in the intervention group (42.1 ± 6.1) than in the control group (38.7 ± 6.5) (p = 0.024). Moreover, after the intervention, the mean score of adherence to treatment was significantly higher in the intervention group (1070.2 ± 80.1) compared to the control group (1018.4 ± 105.3) (p = 0.019). In addition, blood urea nitrogen, phosphate and inter-dialytic weight gain were lower in the intervention group compared to the control group after the intervention.

Conclusions
The findings showed that positive thinking interventions could lead to improvement in hope and adherence to treatment in hemodialysis patients. Positive thinking training could be used in caring of hemodialysis patients to improve their hope and adherence to treatment.
Trial registration RCT Registry: Iranian Registry of Clinical Trials; RCT registration number: IRCT20180915041044N1; Registration date: 19/12/2018.
Sustainable refugee camp design in the Dalhamyie settlement (Bekaa, Lebanon) for climate change context
Authors: Tiwari Pallavi , Al Azzawi Nibal , Amir Lübna 
Published: January 2023

AbstractEmergency shelters are often designed to be of temporary nature but end up adopting a more permanent nature in becoming informal settlements. On one hand, these settlements suffer from the conflicts and environmental pressures. On the other hand, they also bear the inadequacies of services and facilities. This adds to the vulnerability of the refugee population to climatic extremes and environmental extremes along with a low quality of life. The present study aims to identify the pressures both environmental and socio-economic on a refugee camp in the Dalhamyie settlement in Bekaa, Lebanon and design a resilient model which address both internal and external risks. We propose a master plan as a suggested guideline representing a preliminary design umbrella plan that may be updated and altered depending on the population of the community, the site's limitations, and the general availability of resources. To help the local refugees become more resilient and self-sufficient in times of crisis, recommendations are here presented are not strict structural plans but rather a strategic, data-driven collection of actions. With the increasing mental stress that refugees experience, the idea of resilience at all levels is needed to lessen and reinforce the constant environmental, physical, and economic threat that they are subjected to. Residential zoning has been detailed out with respect to the form, structure and assembling of components along with cluster planning within the settlement. Recommendations are not a rigid structural plan but a strategic, data driven set of actions that can be implemented by the local refugee community in order to achieve greater resilience and self-sustainability during crisis situations. Such model is applicable with modifications for other emergency settlements also with varying risk factors. The proposed model addresses the challenges and the multiple risks that the people are exposed to present a framework that can lead to better quality of life in temporary settlements. With more climate refugees, conflict driven refugees and internal refugees, absence of such models was a gap and the authors have tried to build the same through one case study.
IPR treatment and attachments design in clear aligner therapy and risk of open gingival embrasures in adults
Authors: Zhang Yubohan , Wang Xu , Wang Jihong , Gao Jie , Liu Xulin , Jin Zuolin , Ma Yanning 
Published: January 2023

Abstract
Background
The incidence of open gingival embrasures (OGE) in patients after fixed appliance treatment is relatively high, while there are no detailed reports on patients after clear aligner therapy. Also, no clinical studies with large sample size have investigated whether interproximal enamel reduction (IPR) can actually avoid OGE. The purpose of this study was to determine the prevalence of OGE in adults after clear aligner therapy and to investigate the risk of OGE associated with IPR treatment and attachment design, focusing on the amount and distribution in mandibular anterior teeth.

Methods
Pre-treatment and post-treatment intraoral frontal photographs of 225 non-extraction patients were evaluated retrospectively for the occurrence and severity of OGE. The amount of IPR and the number of attachments in the anterior teeth from subjects after screening were recorded according to the first version of clear aligner software (Clincheck, San Jose, USA) and clinical medical documents. Logistic regression analysis was performed to identify the factors contributing to OGE.

Results
The incidence of OGE in non-extraction patients after clear therapy between maxillary and mandibular central incisors was 25.7% and 40.3%, respectively. IPR was not associated with the occurrence of OGE but was associated with severity (P < 0.05). The number of attachments in the anterior teeth or central incisors was significantly related to the incidence of OGE (P < 0.05) but was not associated with severity.

Conclusion
A high rate of OGE occurs after clear aligner therapy. Clinicians should be aware of the application of IPR and the design of attachments during clear aligner therapy.
Comparative proteomics study of mitochondrial electron transport system modulation in SH-SY5Y cells following MPP+ versus 6-OHDA-induced neurodegeneration
Authors: Hyon Ju-Yong , Lee Hea Ji , Yun Sung Ho , Han Eun Hee , Chung Young-Ho 
Published: January 2023

AbstractParkinson’s disease (PD) is the second-most common neurodegenerative disease worldwide. Several studies have investigated PD for decades; however, the exact mechanism of disease development remains unknown. To study PD, SH-SY5Y cells are often treated with 6-hydroxydopamine (6-OHDA) or 1-methyl-4-phenylpyridinium (MPP+) to induce PD. To understand the mechanism of PD pathogenesis, we confirmed protein changes between 6-OHDA- and MPP+-treated SH-SY5Y cells via proteomics analysis using liquid chromatography coupled with tandem mass spectrometry. 6-OHDA-treated SH-SY5Y cells showed increased expression of electron transporter-related proteins compared to that in the control group, along with decreased expression in MPP+-treated SH-SY5Y cells. However, both down- and upregulation of electron transporter-related proteins increased mitochondrial dysfunction and apoptosis. These proteins were confirmed via protein–protein interaction network analysis using IPA and STRING to induce mitochondrial dysfunction and apoptosis. Cell-based experiments using flow cytometry verified that apoptosis and mitochondrial membrane potential were increased in both 6-OHDA- and MPP+-treated SH-SY5Y cells. Our results provide new insights into PD pathogenesis, thereby contributing to the understanding of the mechanisms of PD development.
New insights of minimum requirement on legumes (Fabaceae sp.) daily intake in Malaysia
Authors: Jaafar Mohd Hasni , Ismail Noor Hassim , Ismail Rosnah , Md Isa Zaleha , Mohd Tamil Azmi , Md Yasin Mazapuspavina , Mat Nasir Nafiza , Ab Razak Nurul Hafiza , Zainol Abidin Najihah , Dehghan Mahshid , Yusof Khairul Hazdi 
Published: January 2023

Abstract
Background
Despite their low energy density and high nutrient content, legumes may be under-recognised as a beneficial food for the prevention and management of obesity and related diseases, such as cardiovascular disease (CVD). This study aims to analyse the moderation effect of legume intake on the relationship between BMI and the prevalence of CVD among the Malaysian adult population.

Methods
This study addressed communities of urban and rural Malaysia, including adults aged between 35 and 70 years old at the baseline recruitment. A series of standardised questionnaires were used to assess legume intake, history of comorbidities and socio-demographic information. Resting blood pressure measurements and physical examinations were performed to collect blood pressure and anthropometric data. Bivariate analysis was completed to determine the association between legume intake, socio-demographic characteristics and CVD prevalence. Moderation analysis was used to quantify the moderation effect of minimum daily legume intake on the relationship between BMI and CVD prevalence.

Results
This study found that those who consume less than 3 servings of legumes per day benefit from protective effects against CVD risk (POR = 0.56, 95% CI = 0.37 – 0.85). Moderation analysis of a minimum of three servings/day for the relationship between BMI and CVD prevalence showed significant effects. The group that benefited the most from this effect was those with a BMI in the range of 26 to 34 kg/m2.

Conclusions
This study provides new insights into the recommendation for legume intake according to the relationship between BMI and the prevalence of CVD in Malaysian adults. This study recommends that those with a BMI of 26 to 34 kg/m2 should consume at least 3 servings of legumes per day to reduce the risk of CVD. Further prospective research is warranted to affirm these findings throughout the Malaysian population.