bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core issues, case studies, and the need for expanded Legacy African American genomics
Authors: Jackson Fatimah , Clinton Carter , Caldwell Jennifer 
Published: June 2023

Introduction: Genomic studies of Legacy African Americans have a tangled and convoluted history in western science. In this review paper, core issues affecting African American genomic studies are addressed and two case studies, the New York African Burial Ground and the Gullah Geechee peoples, are presented to highlight the current status of genomic research among Africa Americans.Methods: To investigate our target population’s core issues, a metadatabase derived from 22 publicly accessible databases were reviewed, evaluated, and synthesized to identify the core bioethical issues prevalent during the centuries of the African American presence in North America. The sequence of metadatabase development included 5 steps: identification of information, record screening and retention of topic relevant information, identification of eligibility via synthesis for concept identifications, and inclusion of studies used for conceptual summaries and studies used for genetic and genomic summaries. To these data we added our emic perspectives and specific insights from our case studies.Results: Overall, there is a paucity of existing research on underrepresent African American genomic diversity. In every category of genomic testing (i.e., diagnostic, clinical predictive, pharmacogenomic, direct-to-consumer, and tumor testing), African Americans are disproportionately underrepresented compared to European Americans. The first of our case studies is from the New York African Burial Ground Project where genomic studies of grave soil derived aDNA yields insights into the causes of death of 17th and 18th Century African Americans. In the second of our case studies, research among the Gullah Geechee people of the Carolina Lowcountry reveals a connection between genomic studies and health disparities.Discussion: African Americans have historically borne the brunt of the earliest biomedical studies used to generate and refine primitive concepts in genetics. As exploited victims these investigations, African American men, women, and children were subjected to an ethics-free western science. Now that bioethical safeguards have been added, underrepresented and marginalized people who were once the convenient targets of western science, are now excluded from its health-related benefits. Recommendations to enhance the inclusion of African Americans in global genomic databases and clinical trials should include the following: emphasis on the connection of inclusion to advances in precision medicine, emphasis on the relevance of inclusion to fundamental questions in human evolutionary biology, emphasis on the historical relevance of inclusion for Legacy African Americans, emphasis on the ability of inclusion to foster expanded scientific expertise in the target population, ethical engagement with their descendants, and increase the number of science researchers from these communities.
Investigating the causal relationship between ankylosing spondylitis and osteoporosis in the European population: a bidirectional Mendelian randomization study
Authors: Mei Jian , Hu Hongxin , Ding Haiqi , Huang Ying , Zhang Wenming , Chen Xiaoqing , Fang Xinyu 
Published: June 2023

BackgroundAnkylosing Spondylitis (AS) is an inflammatory condition affecting the spine, which may lead to complications such as osteoporosis (OP). Many observational studies have demonstrated a close relationship with strong evidence between OP and AS. The combination of AS and OP is already an indisputable fact, but the exact mechanism of AS complicated with OP is unclear. To better prevent and treat OP in patients with AS, it is necessary to understand the specific mechanism of OP in these patients. In addition, there is a study showing that OP is a risk factor for AS, but the causal relationship between them is not yet clear. Therefore, we conducted a bidirectional Mendelian randomization (MR) analysis to determine whether there is a direct causal effect between AS and OP and to investigate the co-inherited genetic information between the two.MethodsBone mineral density (BMD) was used as a phenotype for OP. The AS dataset was taken from the IGAS consortium and included people of European ancestry (9,069 cases and 13,578 controls). BMD datasets were obtained from the GEFOS consortium, a large GWAS meta-analysis study, and the UK Biobank and were categorized based on site (total body (TB): 56,284 cases; lumbar spine (LS): 28,498 cases; femoral neck (FN): 32,735 cases; forearm (FA): 8,143 cases; and heel: 265,627 cases) and age (0-15: 11,807 cases; 15-30: 4,180 cases; 30-45: 10,062 cases; 45-60: 18,062 cases; and over 60: 22,504 cases).To obtain the casual estimates, the inverse variant weighted (IVW) method was mainly used due to its good statistical power and robustness. The presence of heterogeneity was evaluated using Cochran’s Q test. Pleiotropy was assessed utilizing MR-Egger regression and MR-pleiotropy residual sum and outlier (MR-PRESSO).ResultsGenerally, there were no significant causal associations between genetically predicted AS and decreased BMD levels. The results of MR-Egger regression, Weighted Median, and Weighted Mode methods were consistent with those of the IVW method. However, there was a sign of a connection between genetically elevated BMD levels and a decreased risk of AS (Heel-BMD: OR = 0.879, 95% CI: 0.795-0.971, P = 0.012; Total-BMD: OR = 0.948, 95% CI: 0.907-0.990, P = 0.017; LS-BMD: OR = 0.919, 95% CI: 0.861-0.980, P = 0.010). The results were confirmed to be reliable by sensitivity analysis.ConclusionThis MR study found that the causal association between genetic liability to AS and the risk of OP or lower BMD in the European population was not evident, which highlights the second effect (e.g., mechanical reasons such as limited movement) of AS on OP. However, genetically predicted decreased BMD/OP is a risk factor for AS with a causal relationship, implying that patients with OP should be aware of the potential risk of developing AS. Moreover, OP and AS share similar pathogenesis and pathways.
Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages
Authors: Wilton Joana , de Mendonça Filipa Lopes , Pereira-Castro Isabel , Tellier Michael , Nojima Takayuki , Costa Angela M. , Freitas Jaime , Murphy Shona , Oliveira Maria Jose , Proudfoot Nicholas J. , Moreira Alexandra 
Published: June 2023

IntroductionMacrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3’UTR (3’UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, particularly in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells affect 3’UTR-APA and IPA in primary human macrophages was unclear.MethodsIn this study, we isolated primary human monocytes from healthy donors, differentiated and polarized them into a pro-inflammatory state and performed indirect co-cultures with CRC cells. ChrRNA-Seq and 3’RNA-Seq was performed to quantify gene expression and characterize new 3’UTR-APA and IPA mRNA isoforms.ResultsOur results show that polarization of human macrophages from naïve to a pro-inflammatory state causes a marked increase of proximal polyA site selection in the 3’UTR and IPA events in genes relevant to macrophage functions. Additionally, we found a negative correlation between differential gene expression and IPA during pro-inflammatory polarization of primary human macrophages. As macrophages are abundant immune cells in the CRC microenvironment that either promote or abrogate cancer progression, we investigated how indirect exposure to CRC cells affects macrophage gene expression and 3’UTR-APA and IPA events. Co-culture with CRC cells alters the inflammatory phenotype of macrophages, increases the expression of pro-tumoral genes and induces 3’UTR-APA alterations. Notably, some of these gene expression differences were also found in tumor-associated macrophages of CRC patients, indicating that they are physiologically relevant. Upon macrophage pro-inflammatory polarization, SRSF12 is the pre-mRNA processing gene that is most upregulated. After SRSF12 knockdown in M1 macrophages there is a global downregulation of gene expression, in particular in genes involved in gene expression regulation and in immune responses.DiscussionOur results reveal new 3’UTR-APA and IPA mRNA isoforms produced during pro-inflammatory polarization of primary human macrophages and CRC co-culture that may be used in the future as diagnostic or therapeutic tools. Furthermore, our results highlight a function for SRSF12 in pro-inflammatory macrophages, key cells in the tumor response.
Disparities in brain health comorbidity management in intracerebral hemorrhage
Authors: Mayerhofer Ernst , Zaba Natalie O. , Parodi Livia , Ganbold Alena S. , Biffi Alessandro , Rosand Jonathan , Yechoor Nirupama , Anderson Christopher D. 
Published: June 2023

BackgroundIntracerebral hemorrhage (ICH) disproportionally affects underserved populations, and coincides with risk factors for cardiovascular events and cognitive decline after ICH. We investigated associations between social determinants of health and management of blood pressure (BP), hyperlipidemia, diabetes, obstructive sleep apnea (OSA), and hearing impairment before and after ICH hospitalization.MethodsSurvivors of the Massachusetts General Hospital longitudinal ICH study between 2016 and 2019 who received healthcare at least 6 months after ICH were analyzed. Measurements of BP, LDL and HbA1c and their management in the year surrounding ICH and referrals for sleep studies and audiology up to 6 months after ICH were gathered from electronic health records. The US-wide area deprivation index (ADI) was used as proxy for social determinants of health.ResultsThe study included 234 patients (mean 71 years, 42% female). BP measurements were performed in 109 (47%) before ICH, LDL measurements were performed in 165 (71%), and HbA1c measurements in 154 (66%) patients before or after ICH. 27/59 (46%) with off-target LDL and 3/12 (25%) with off-target HbA1c were managed appropriately. Of those without history of OSA or hearing impairment before ICH, 47/207 (23%) were referred for sleep studies and 16/212 (8%) to audiology. Higher ADI was associated with lower odds of BP, LDL, and HbA1c measurement prior to ICH [OR 0.94 (0.90–0.99), 0.96 (0.93–0.99), and 0.96 (0.93–0.99), respectively, per decile] but not with management during or after hospitalization.ConclusionSocial determinants of health are associated with pre-ICH management of cerebrovascular risk factors. More than 25% of patients were not assessed for hyperlipidemia and diabetes in the year surrounding ICH hospitalization, and less than half of those with off-target values received treatment intensification. Few patients were evaluated for OSA and hearing impairment, both common among ICH survivors. Future trials should evaluate whether using the ICH hospitalization to systematically address co-morbidities can improve long-term outcomes.
Be aware of the sodium intake outside student canteens: development and validation of a sodium food frequency questionnaire in Chinese undergraduates
Authors: Xi Yue , Xiang Caihong , Liang Jiajing , Huo Jiaqi , Yong Cuiting , Zou Hanshuang , Pan Yunfeng , Wu Minchan , Xie Qingqing , Deng Jing , Yang Lina , Chen Jihua , Qi Yufei , Li Ying , Lin Qian 
Published: June 2023

BackgroundChinese college students used to eat in student canteens, making dietary consumption outside the cafeterias the main reason for the difference in sodium intake. This study aims to develop and validate a food frequency questionnaire (Sodium-FFQ) targeting dietary sodium intake outside the canteens among undergraduates in China.MethodsThis cross-sectional study included 124 and 81 college students from comprehensive universities in the development and validation stage. A 24 h dietary recall and a food frequency questionnaire were used to develop the Sodium-FFQ. Food items were selected according to the foods that contributed more to the total sodium intake. Test–retest correlation coefficients with an interval of 14 days were employed to evaluate reproducibility. Validity was assessed against a single 24 h urine collection and a 3-day dietary record using correlation coefficients, Bland–Altman analyses, and cross-classification analysis of Kappa coefficients.ResultsThe Sodium-FFQ consists of 12 groups of foods with 48 items. The Spearman correlation coefficient of test–retest on sodium intake was 0.654 (p &lt; 0.05), and that between the Sodium-FFQ, 3 × 24 h dietary record, and 24-h urinary sodium were 0.393 (p &lt; 0.05) and 0.342 (p &lt; 0.05), respectively. The Sodium-FFQ was correlated to 24 h urinary sodium-to-potassium ratio, with a Spearman coefficient of 0.370 (p &lt; 0.05). The classification agreement of the Sodium-FFQ and 24 h urinary sodium was 68.4%, and the Kappa coefficient was 0.371 (p &lt; 0.001).ConclusionThe Sodium-FFQ developed in this study presented an acceptable reproducibility, validity, and classification agreement. It indicates that the Sodium-FFQ could be a potential tool for promoting sodium restriction in college students.
Associations of specific dietary unsaturated fatty acids with risk of overweight/obesity: population-based cohort study
Authors: Chen Weiming , Ao Yang , Lan Xiaochun , Tong Wenzhou , Liu Xiaohui , Zhang Xia , Ye Qiang , Li Yin , Liu Linfen , Ye Hao , Zhuang Pan , Zhang Yu , Zheng Weifang , Jiao Jingjing 
Published: June 2023

BackgroundThe role of specific unsaturated fatty acids (FAs) in the development of overweight/obesity remains unclear in the general population. Here, we aimed to explore the associations of different types of unsaturated FAs with overweight/obesity risk among the Chinese population.MethodsEight thousand seven hundred forty-two subjects free of overweight/obesity at entry in the China Health and Nutrition Survey (CHNS) were followed up until 2015. Dietary unsaturated FAs were assessed by 3-day 24-h recalls with a weighing method in each wave. Cox regression models were used to obtain the hazard ratios (HRs) and 95% confidence intervals (CIs) for overweight/obesity risk associated with unsaturated FAs.ResultsDuring a median follow-up of 7 years, 2,753 subjects (1,350 males and 1,403 females) developed overweight/obesity. Consuming more monounsaturated FAs (MUFAs) was associated with a lower risk of overweight/obesity (highest vs. lowest quartile: HR 0.80, 95% CI 0.67–0.96; P-trend = 0.010). Similar inverse associations were observed for plant-MUFAs (HRQ4vsQ1 0.83, 95% CI: 0.73–0.94; P-trend = 0.003) and animal-MUFAs (HRQ4vsQ1 0.77, 95% CI: 0.64–0.94; P-trend = 0.004), total dietary oleic acid (OA) (HRQ4vsQ1 0.66, 95% CI: 0.55–0.79; P-trend &lt;0.001), plant-OA (HRQ4vsQ1 0.73, 95% CI: 0.64–0.83; P-trend &lt;0.001) and animal-OA (HRQ4vsQ1 0.68, 95% CI: 0.55–0.84; P-trend &lt;0.001). In addition, the intakes of n-3 polyunsaturated FAs (PUFAs) (HRQ4vsQ1 1.24, 95% CI: 1.09–1.42; P-trend = 0.017) and α-linolenic acid (ALA) (HRQ4vsQ1 1.22, 95% CI: 1.07–1.39; P-trend = 0.039) but not marine n-3 PUFAs were positively linked to overweight/obesity risk. Consumption of n-6 PUFAs (HRQ4vsQ1 1.13, 95% CI: 0.99–1.28; P-trend = 0.014) and linoleic acid (LA) (HRQ4vsQ1 1.11, 95% CI: 0.98–1.26; P-trend = 0.020) had marginal and positive relationships with the incidence of overweight/obesity. N-6/n-3 PUFA ratio ranging from 5.7 to 12.6 was related to higher risk of overweight/obesity.ConclusionHigher dietary intake of MUFAs was associated with lower overweight/obesity risk, which was mainly driven by dietary OA from either plant or animal sources. Intakes of ALA, n-6 PUFAs and LA were related to higher risk of overweight/obesity. These results support consuming more MUFAs for maintaining a healthy body weight among the Chinese population.
Association between ultra-processed foods and risk of cancer: a systematic review and meta-analysis
Authors: Lian Ying , Wang Gang-Pu , Chen Guo-Qiang , Chen Hua-Nan , Zhang Guang-Yong 
Published: June 2023

BackgroundDespite increasing evidence that has shown the association of ultra-processed foods (UPFs) with cancer risk, the results remain inconclusive. We, therefore, conducted the meta-analysis to clarify the association by including recently published studies.MethodsA comprehensive search was conducted in PubMed, Embase, and Web of Science to identify all relevant studies from inception to January 2023. To pool data, fixed-effects or random-effects models were used where appropriate. Subgroup analyses, sensitivity analyses, and publication bias tests were performed.ResultsA total of 13 studies (4 cohort studies and 9 case–control studies) were included in the analysis, with a total of 625,738 participants. The highest UPFs consumption was associated with increased risk of colorectal cancer (OR = 1.23, 95% CI: 1.10–1.38), colon cancer (OR = 1.25, 95% CI: 1.14–1.36), and breast cancer (OR = 1.10, 95% CI: 1.00–1.20) but not rectal cancer (OR = 1.18, 95% CI: 0.97–1.43) and prostate cancer (OR = 1.03, 95% CI: 0.93–1.12). In addition, the subgroup analyses showed that a positive association between UPFs consumption and colorectal cancer was observed among men (OR = 1.31, 95% CI: 1.15–1.50), whereas no significant association was observed among women (OR = 1.10, 95% CI: 0.94–1.29).ConclusionThe present meta-analysis suggests that high UPFs consumption is associated with a significantly increased risk of certain site-specific cancers, especially the digestive tract and some hormone-related cancers. However, further rigorously designed prospective and experimental studies are needed to better understand causal pathways.
Exploring the adoption of less restricted criteria for respiratory syncytial virus prophylaxis in late preterm infants: insights from a retrospective analysis
Authors: Mondì Vito , Paolillo Piermichele , Bedetta Manuela , Lucangeli Natalia , Picone Simonetta 
Published: June 2023

BackgroundPreterm infants born between 33 and 35 weeks of gestational age (wGA) have been considered a “major underserved population” and ineligible to receive palivizumab (PLV), the only drug authorized to date for respiratory syncytial virus (RSV) prophylaxis, by current international guidelines. In Italy, such a vulnerable population is currently eligible for prophylaxis, and, in our region, specific risk factors are taken into consideration (SINLazio score) to target prophylaxis for those at highest risk. Whether the adoption of less or more restrictive eligibility criteria for PLV prophylaxis would translate into differences in bronchiolitis and hospitalization incidence is not known.Materials and methodsA retrospective analysis was conducted in 296 moderate-to-late preterm infants (born between 33 and 35+6 weeks) who were being considered for prophylaxis in two epidemic seasons: 2018–2019 and 2019–2020. The study participants were categorized according to both the SINLazio score and the Blanken risk scoring tool (BRST), which was found to reliably predict RSV-associated hospitalization in preterm infants on the basis of three risk factor variables.ResultsBased on the SINLazio score, approximately 40% of infants (123/296) would meet the criteria to be eligible for PLV prophylaxis. In contrast, none of the analyzed infants would be considered eligible for RSV prophylaxis on the basis of the BRST. A total of 45 (15.2%) bronchiolitis diagnoses were recorded on average at 5 months of age in the overall population. Almost seven out of 10 (84/123) patients exhibiting ≥3 risk factors to be eligible for RSV prophylaxis according to SINLazio criteria would not be receiving PLV if they were categorized on the basis of the BRST. Bronchiolitis occurrence in patients with a SINLazio score ≥3 was approximately 2.2 times more likely than that in patients with a SINLazio score &lt;3. PLV prophylaxis has been associated with a 91% lower risk of requiring a nasal cannula.ConclusionOur work further supports the need for targeting late preterm infants for RSV prophylaxis and calls for an appraisal of the current eligibility criteria for PLV treatment. Therefore, adopting less restrictive criteria may ensure a comprehensive prophylaxis of the eligible subjects, thus sparing them from avoidable short- and long-term consequences of RSV infection.
The impact of CYP2C19 genotype on phenoconversion by concomitant medication
Authors: de Jong Laura M. , Boussallami Soukayna , Sánchez-López Elena , Giera Martin , Tushuizen Maarten E. , Hoekstra Menno , Hawinkels Lukas J. A. C. , Rissmann Robert , Swen Jesse J. , Manson Martijn L. 
Published: June 2023

Introduction: Pharmacogenetics-informed drug prescribing is increasingly applied in clinical practice. Typically, drug metabolizing phenotypes are determined based on genetic test results, whereupon dosage or drugs are adjusted. Drug-drug-interactions (DDIs) caused by concomitant medication can however cause mismatches between predicted and observed phenotypes (phenoconversion). Here we investigated the impact of CYP2C19 genotype on the outcome of CYP2C19-dependent DDIs in human liver microsomes.Methods: Liver samples from 40 patients were included, and genotyped for CYP2C19*2, *3 and *17 variants. S-mephenytoin metabolism in microsomal fractions was used as proxy for CYP2C19 activity, and concordance between genotype-predicted and observed CYP2C19 phenotype was examined. Individual microsomes were subsequently co-exposed to fluvoxamine, voriconazole, omeprazole or pantoprazole to simulate DDIs.Results: Maximal CYP2C19 activity (Vmax) in genotype-predicted intermediate metabolizers (IMs; *1/*2 or *2/*17), rapid metabolizers (RMs; *1/*17) and ultrarapid metabolizers (UMs; *17/*17) was not different from Vmax of predicted normal metabolizers (NMs; *1/*1). Conversely, CYP2C19*2/*2 genotyped-donors exhibited Vmax rates ∼9% of NMs, confirming the genotype-predicted poor metabolizer (PM) phenotype. Categorizing CYP2C19 activity, we found a 40% concordance between genetically-predicted CYP2C19 phenotypes and measured phenotypes, indicating substantial phenoconversion. Eight patients (20%) exhibited CYP2C19 IM/PM phenotypes that were not predicted by their CYP2C19 genotype, of which six could be linked to the presence of diabetes or liver disease. In subsequent DDI experiments, CYP2C19 activity was inhibited by omeprazole (−37% ± 8%), voriconazole (−59% ± 4%) and fluvoxamine (−85% ± 2%), but not by pantoprazole (−2 ± 4%). The strength of CYP2C19 inhibitors remained unaffected by CYP2C19 genotype, as similar percental declines in CYP2C19 activity and comparable metabolism-dependent inhibitory constants (Kinact/KI) of omeprazole were observed between CYP2C19 genotypes. However, the consequences of CYP2C19 inhibitor-mediated phenoconversion were different between CYP2C19 genotypes. In example, voriconazole converted 50% of *1/*1 donors to a IM/PM phenotype, but only 14% of *1/*17 donors. Fluvoxamine converted all donors to phenotypic IMs/PMs, but *1/*17 (14%) were less likely to become PMs than *1/*1 (50%) or *1/*2 and *2/*17 (57%).Conclusion: This study suggests that the differential outcome of CYP2C19-mediated DDIs between genotypes are primarily dictated by basal CYP2C19 activity, that may in part be predicted by CYP2C19 genotype but likely also depends on disease-related factors.