bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pentosan polysulfate ameliorates fibrosis and inflammation markers in SV40 MES13 cells by suppressing activation of PI3K/AKT pathway via miR-446a-3p
Authors: Xiao Liangxiang , Chen Anqun , Gao Qing , Xu Bo , Guo Xiaodan , Guan Tianjun 
Published: March 2022

Abstract
Background
Renal fibrosis is a common outcome of various renal damage, including diabetic nephropathy (DN), the leading cause of end-stage renal disease. Currently, there are no effective therapies for renal fibrosis. The present study aimed to determine whether pentosan polysulphate sodium (PPS), a FDA approved medication for interstitial cystitis, protects diabetic renal fibrosis.

Methods
Cell viability and apoptosis were evaluated in mouse mesangial cells (SV40-MES13) after incubating with the advanced glycation end products (AGEs), which play important roles in the pathogenesis of DN. Western blot and ELISA were performed to determine the expression of transforming growth factor-beta1 (TGF-β1) and fibronectin (FN), two biomarkers of renal fibrosis, as well as interleukin-6 (IL-6) and tumor necrosis factor alpha (TNFα), two biomarkers of inflammation. The miRNA-mRNA regulatory network involved in the phosphatidylinositol 3-kinase (PI3K)/Ser and Thr Kinase (AKT) signalling was investigated by miRNA deep sequencing and validated by RT-PCR and miRNA transfection.

Results
AGEs significantly inhibited cell proliferation and promoted cell apoptosis, which was associated with the overexpression of TGF-β1, FN, IL-6, and TNFα. PPS almost completely reversed AGEs-induced biomarkers of fibrosis and inflammation, and significantly altered the miRNA expression profile in AGEs-treated cells. Notably, the PI3K/AKT signalling was one of the most significantly enriched pathways targeted by PPS-related differentially expressed miRNAs. PPS significantly up-regulated miR-466a-3p, which was shown to target PIK3CA, and mediated the inhibitory effect of PPS on AGEs-induced activation of PI3K/AKT pathway.

Conclusions
The treatment of PPS protected against AGEs-induced toxicity in SV40 MES13 cells via miR-466a-3p-mediated inhibition of PI3K/AKT pathway.
Evaluation of prenatal central nervous system anomalies: obstetric management, fetal outcomes and chromosome abnormalities
Authors: Tan Ann Gee , Sethi Neha , Sulaiman Sofiah 
Published: March 2022

Abstract
Objective
To study the outcomes of fetuses who were diagnosed with central nervous system (CNS) anomalies during prenatal period and to describe the obstetric management of those pregnancies.

Methods
In this retrospective study, fetuses who were detected to have central nervous system anomalies by prenatal ultrasound from January 2010 to December 2019 were recruited. Data regarding prenatal diagnosis and obstetric outcomes were retrieved from maternal and paediatric records. The prognosis of fetuses who were born alive was classified based on their neurodevelopmental outcome within two years of life.

Results
There were a total of 365 fetuses with CNS anomalies within the 10-year study period, with a mean gestational age of 24.65±7.37 weeks at diagnosis. Ventriculomegaly (23.36%) was the commonest CNS anomalies seen. 198 (54.20%) of these fetuses had associated extra-CNS anomalies, with cardiovascular being the most common system involved. Fetal karyotyping was performed in 111 pregnancies, with chromosomal aberrations detected in 53 (49.07%) cases and culture failure in 3 cases. Majority of the chromosomal abnormalities were Edward syndrome (trisomy 18) and Patau syndrome (trisomy 13). Fetuses with congenital CNS anomalies and abnormal chromosomal karyotyping were more likely to be diagnosed earlier by prenatal ultrasound and tend to have poorer obstetric and neurocognitive prognosis. Prenatally, 86 (23.56%) of the cases were lost to follow up and likely to deliver elsewhere. Among the 279 cases whom their pregnancy outcomes were available, 139 (49.82%) pregnancies resulted in live births, 105 (37.63%) pregnancies were electively terminated, while the remaining 35 (12.54%) pregnancies ended in spontaneous loss. The decision of termination of pregnancy largely depends on mean diagnostic gestational age, presence of chromosomal aberrations and abnormal amniotic fluid volume in those fetuses. Two years after delivery, only 75 (53.96%) children out of 139 live births were still alive, 43 (30.93%) died and 21 (15.11%) cases were lost to follow-up. 32 (23.02%) children with prenatally diagnosed CNS anomalies had normal neurodevelopmental outcome. The presence of multiple CNS anomalies and involvement of extra-CNS anomalies indicated a poorer neurodevelopmental prognosis.

Conclusion
Less than 50% of fetuses with prenatally diagnosed CNS anomalies resulted in live births. Even if they survive till delivery, 36.45% of them passed away within 2 years and 62.79% of children who survived till 2 years old had neurodevelopmental disability.
Suicidal ideation among recently arrived refugees in Germany
Authors: Nesterko Yuriy , Haase Elisa , Schönfelder Antje , Glaesmer Heide 
Published: March 2022

Abstract
Background
Refugees are considered a high-risk population for developing mental health disorders. Yet little research has been conducted on suicidal ideation among refugees resettled in Western high-income countries. In the present hstudy, suicidal ideation and its association with different socio-demographic, flight-related, and mental health-related factors were analyzed in recently arrived refugees in Germany.

Methods
The study was conducted in a reception facility for asylum-seekers in Leipzig, where 564 newly arrived adult residents participated. The questionnaire included socio-demographic and flight-related questions as well as standardized instruments for assessing suicidal ideation (item 9 from PHQ-9), a variety of traumatic experiences (LEC-5), posttraumatic stress disorder (PCL-5), depression (PHQ-8), and somatic symptoms (SSS-8). Multiple logistic regression models were run to predict suicidal ideation in relation to different socio-demographic, flight, and mental health-related factors.

Results
In total, 171 (30.3%) participants who had just or very recently arrived in Germany reported having experienced suicidal ideation within the two weeks prior to being assessed. Those who reported suicidal ideation also reported higher prevalence of somatic symptoms, posttraumatic stress disorder, depression, and experiences of sexual violence, as well as worse self-rated mental and physical health. In addition, there were significant independent associations between suicidal ideation and (1) younger age, (2) longer flight duration, (3) experiences of sexual violence, (4) symptoms of posttraumatic stress disorder, and (5) symptoms of depression.

Conclusions
The results emphasize the association between suicidal ideation and different clinically relevant mental health symptoms among newly arrived refugees in Germany. Special attention should not only be given to refugees suffering from symptoms of poor mental health, but also to those of younger age as well as refugees who have experienced sexual violence, as they might be affected by suicidal ideation whether or not they suffer from other mental health problems.
The effect of the number of hepatic inflow occlusion times on the prognosis of ruptured hepatocellular carcinoma patients after hepatectomy
Authors: Xia Feng , Huang Zhiyuan , Ndhlovu Elijah , Zhang Mingyu , Chen Xiaoping , Zhang Bixiang , Zhu Peng 
Published: March 2022

Abstract
Background and aim
It has been previously reported that inflow occlusion does not affect postoperative outcomes in hepatocellular carcinoma patients. However, for patients with ruptured hepatocellular carcinoma(rHCC), the effect of hepatic inflow occlusion and the number of occlusion times on the prognosis is unknown.

Methods
203 patients with ruptured hepatocellular carcinoma were enrolled in this study. They were first divided into the non-hepatic inflow occlusion (non-HIO) group and the hepatic inflow occlusion (HIO) group. The Kaplan–Meier method was used to compare the recurrence-free survival and overall survival between the two groups. Patients in the HIO group were further divided into one-time HIO and two times HIO groups. KM method was also used to compare the two groups. Finally, independent risk factors affecting RFS and OS were determined by multivariate Cox regression analysis.

Result
In the non-HIO group, 1-,3- and 5-year OS rates were 67.0%, 41.0%, and 22.0%respectively, and RFS rates were 45.0%, 31.0%, and 20.0% respectively; In the one-HIO group, the 1-,3-, and 5-year OS rates were 55.1%, 32.1%, and 19.2% respectively, and RFS rates were 33.3%, 16.7%, and 7.7% respectively; In the two-HIO group, 1-,3-, and 5-year OS rates were 24.0%, 0.0%, and 0.0% respectively, and RFS rates were 8.0%, 0.0%, and 0.0% respectively. By Cox regression analysis, HIO was an independent risk factor for a poor prognosis in rHCC patients.

Conclusion
One time hepatic inflow occlusion did not affect postoperative OS, but negatively affected the RFS of rHCC patients; two times hepatic inflow occlusion negatively affected the postoperative OS and RFS in patients with rHCC.
A simplified Gibson assembly method for site directed mutagenesis by re-use of standard, and entirely complementary, mutagenesis primers
Authors: Olszakier Shunit , Berlin Shai 
Published: March 2022

Abstract
Background
Site-directed mutagenesis (SDM) is a key method in molecular biology; allowing to modify DNA sequences at single base pair resolution. Although many SDM methods have been developed, methods that increase efficiency and versatility of this process remain highly desired.

Method
We present a versatile and simple method to efficiently introduce a variety of mutation schemes using Gibson-assembly but without the need to design uniquely designated Gibson primers. Instead, we explore the re-use of standard SDM primers (completely overlapping in sequence) in combination with regular primers (~ 25 bps long) for amplification of fragments flanking the site of mutagenesis. We further introduce a rapid amplification step of the Gibson-assembled product for analysis and quality control, as well as for ligation, or re-ligation at instances the process fails (avoiding expenditure of added Gibson reaction mixtures).

Results
We first demonstrate that standard SDM primers can be used with the Gibson assembly method and, despite the need for extensive digestion of the DNA past the entire primer sequence, the reaction is attainable within as short as 15 min. We also find that the amount of the assembled Gibson product is too low to be visualized on standard agarose gel. Our added amplification step (by use of the same short primers initially employed) remedies this limitation and allows to resolve whether the desired Gibson-assembled product has been obtained on agarose gel or by sequencing of amplicons. It also provides large amounts of amplicons for subsequent ligations, bypassing the need to re-employ Gibson mixtures. Lastly, we find that our method can easily accommodate SDM primers with degenerate sequences.

Conclusion
We employ our alternative approach to delete, replace, insert, and degenerate sequences within target DNA sequences, specifically DNA sequences that proved very resistant to mutagenesis by multiple other SDM methods (standard and commercial). Importantly, our approach involves the re-use of SDM primers from our primer-inventory. Our scheme thereby reduces the need (and time and money) to design and order new custom Gibson-primers. Together, we provide a simple and versatile protocol that spans only 4 days (including the added amplification step), requires minimal primer sets and provides very high yields and success rates (> 98%).
Being fast or cautious? Sociocultural conditions influencing the sexual pathways of Black females in the United States
Authors: Crooks Natasha , King Barbara , Tluczek Audrey 
Published: March 2022

Abstract
Background
Black females in the United States face unique sociocultural conditions that impact their sexual development and increase their risk for sexually transmitted infections (STI), including but not limited to chlamydia, gonorrhea, and HIV. Research has not adequately explained how sociocultural conditions contribute to this increased risk. The purpose of our investigation was to explore the sociocultural conditions that influence Black cisgender females risk for STI.

Methods
This grounded theory study involved in-depth audio-recorded interviews with 20, primarily heterosexual, Black females ages 19–62.

Results
Findings informed a conceptual model that builds on previous theory about the sexual development of Black females and explains how sociocultural conditions impact two, participant identified, sexual pathways: Fast and Cautious. Movement on these sexual pathways was not always a linear trajectory; some participants shifted between pathways as their sociocultural contexts changed (i.e., sexual assault, STI, and level of protection). The Fast sexual pathway often led to greater STI risk.

Conclusions
This model may inform future research designed to prevent STI/HIV and promote the sexual health of Black females across the life course.
The public impact of academic and print media portrayals of TMS: shining a spotlight on discrepancies in the literature
Authors: Scheper Abigail , Rosenfeld Cynthia , Dubljević Veljko 
Published: March 2022

Abstract
Background
Transcranial magnetic stimulation (TMS) is an FDA approved treatment for major depression, migraine, obsessive compulsive disorder, and smoking addiction. TMS has gained popular media support, but media coverage and commercial reporting of TMS services may be contributing to the landscape of ethical issues.

Methods
We explore the differences between the academic and print media literature portrayals of TMS to evaluate their ethical impact for the public. We performed a comprehensive literature review using PubMed and NexisUni databases to evaluate the literature available on TMS from 2014 to 2019. Our sample consisted of 1632 academic articles and 468 print media articles for a total of 2100 articles. We then coded each article for seven specific top-level codes: (1) type of source, (2) year of publication, (3) purpose of TMS application, (4) age of subjects, (5) population, (6) overall tone, and (7) specification of TMS parameters. We also made some additional notes of the TMS parameters where specified and the breakdown of mental health applications.

Results
Our results indicated several discrepancies between the academic and the print media reporting about TMS technology, particularly with regards to tone and specificity. Namely, the academic sample was largely neutral and specific about the parameters under which TMS was being applied, while the print media sample was heavily optimistic and presented the application of TMS with far less specificity. There was some convergence between the two samples, such as the focus of both on therapy as the predominant TMS application.

Conclusions
We call upon the academic community to increase scrutiny of TMS services in order to ensure that people’s knowledge of health technologies is not unduly influenced by sensational claims and a general lack of adequate information.
Fat mass and obesity–associated protein promotes liver steatosis by targeting PPARα
Authors: Wei Xiaohui , Zhang Jielei , Tang Min , Wang Xuejiao , Fan Nengguang , Peng Yongde 
Published: March 2022

Abstract
Background
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. The fat mass and obesity–associated protein (FTO) has been shown to be involved in obesity; however, its role in NAFLD and the underlying molecular mechanisms remain largely unknown.

Methods
FTO expression was first examined in the livers of patients with NAFLD and animal and cellular models of NAFLD by real-time PCR and Western blotting. Next, its role in lipid accumulation in hepatocytes was assessed both in vitro and in vivo via gene overexpression and knockdown studies.

Results
FTO expression was obviously elevated in the livers of mice and humans with hepatic steatosis, probably due to its decreased ubiquitination. FTO overexpression in HepG2 cells induced triglyceride accumulation, whereas FTO knockdown exerted an opposing effect. Consistent with the findings of in vitro studies, adeno-associated viruses 8 (AAV8)-mediated FTO overexpression in the liver promoted hepatic steatosis in C57BL/6J mice. Mechanistically, FTO inhibited the mRNA of peroxisome proliferator-activated receptor α (PPARα) in hepatocytes. Activation of PPARα by its agonist GW7647 reversed lipid accumulation in hepatocytes induced by FTO overexpression.

Conclusions
Overall, FTO expression is increased in NAFLD, and it promotes hepatic steatosis by targeting PPARα.
Molecular identification and safety assessment of Bacillus strains isolated from Burkinabe traditional condiment “soumbala”
Authors: Dabiré Yérobessor , Somda Namwin Siourimè , Somda Marius K. , Mogmenga Iliassou , Traoré Abdoulaye K. , Ezeogu Lewis I. , Traoré Alfred S. , Ugwuanyi Jerry O. , Dicko Mamoudou H. 
Published: March 2022

Abstract
Purpose
Alkaline-fermented foods (AFFs) play an essential role in the diet of millions of Africans particularly in the fight against hidden hunger. Among AFFs, soumbala is a very popular condiment in Burkina Faso, available and affordable, rich in macronutrients (proteins, lipids, carbohydrates, essential amino acids, and fatty acids), micronutriments (minerals, B group vitamins), and fibers. Bacillus spp. are known to be the predominant microbial species in AFFs and thus have elicited enhanced interest as starter cultures or probiotics. However, few data exist on identification and safety attributes of relevant Bacillus species from African AFFs, particularly from Burkinabe soumbala.

Methods
This study aimed to genotypically characterize 20 Bacillus strains previously isolated from soumbala, using PCR and sequencing of the 16S rRNA genes, and to evaluate their safety attributes.

Results
Phylogenetic analysis revealed that the strains were most closely related by decreasing numbers to B. cereus, B. subtilis, Bacillus sp., B. tropicus, B. toyonensis, B. nealsonii, B. amyloliquefaciens, Brevibacillus parabrevis, and B. altitudinis. Among the isolates, 10 were β-hemolytic and 6 were γ-hemolytic while 4 were of indeterminate hemolysis. The 6 γ-hemolytic (presumptively non-pathogenic) strains were susceptible to all tested antibiotics except bacitracin. Strains F20, and F21 were the most sensitive to imipenem (38.04 ± 1.73 mm and 38.80 ± 1.57 mm, respectively) while strain B54 showed the weakest sensitivity to bacitracin (11.00 ± 0.63 mm) with high significant differences (p < 0.0001).

Conclusion
The findings highlight identification and safety quality of Bacillus strains which could be further characterized as probiotic-starter cultures for high-quality soumbala production.
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data
Authors: Kaliyaperumal Rajaram , Wilkinson Mark D. , Moreno Pablo Alarcón , Benis Nirupama , Cornet Ronald , dos Santos Vieira Bruna , Dumontier Michel , Bernabé César Henrique , Jacobsen Annika , Le Cornec Clémence M. A. , Godoy Mario Prieto , Queralt-Rosinach Núria , Schultze Kool Leo J. , Swertz Morris A. , van Damme Philip , van der Velde K. Joeri , Lalout Nawel , Zhang Shuxin , Roos Marco 
Published: March 2022

Abstract
Background
The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles.

Results
Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR.

Conclusions
Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.
Effects of sustainable agricultural practices on farm income and food security in northern Ghana
Authors: Setsoafia Edinam Dope , Ma Wanglin , Renwick Alan 
Published: March 2022

AbstractThe adoption of sustainable agricultural practices (SAPs) has been recommended by many experts and international institutions to address food security and climate change problems. Global support for the Sustainable Development Goals has focused attention on efforts to up-scale the adoption of SAPs in developing countries where growth in populations and incomes compromises the resilience of natural resources. This study investigates the factors affecting smallholder farmers’ decisions to adopt SAPs (improved seed, fertilizer, and soil and water conservation) and the impacts of the adoption on farm income and food security, using data collected from Ghana. Food security is captured by the reduced coping strategy index and household dietary diversity. The multinomial endogenous switching regression model is utilized to address selection bias issues. Results show that farmers’ decisions to adopt SAPs are influenced by the social demographics of the households, plot-level characteristics, extension services and locations. Adopting all three SAPs has larger positive impacts on farm income and food security than adopting single or two SAPs. Our findings advocate for policies that enhance the quality of extension service and strengthen farmer-based organizations for the wider dissemination of adequate SAP information. Farmers should be encouraged to adopt SAPs as a comprehensive package for increasing farm income and ensuring food security.