bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Associated with Patients’ Connection to Referred Social Needs Resources at a Federally Qualified Health Center
Authors: Lian Tyler , Kutzer Kate , Gautam Diwas , Eisenson Howard , Crowder Jane C. , Esmaili Emily , Sandhu Sahil , Trachtman Lawrence , Prvu Bettger Janet , Drake Connor 
Published: June 2021

Introduction: In an effort to improve health outcomes and promote health equity, healthcare systems have increasingly begun to screen patients for unmet social needs and refer them to relevant social services and community-based organizations. This study aimed to identify factors associated with the successful connection (ie, services started) to social needs resources, as well as factors associated with an attempt to connect as a secondary, intermediate outcome. Methods: This retrospective cohort study included patients who had been screened, referred, and subsequently reached for follow-up navigation from March 2019 to December 2020, as part of a social needs intervention at a federally qualified health center (FQHC). Measures included demographic and social needs covariates collected during screening, as well as resource-related covariates that characterized the referred resources, including service domain (area of need addressed), service site (integration relative to the FQHC), and access modality (means of accessing services). Results: Of the 501 patients in the analytic sample, 32.7% had started services with 1 or more of their referred resources within 4 weeks of the initial referral, and 63.3% had at least attempted to contact 1 referred resource, whether or not they were able to start services. Receiving a referral to resources that patients could access via phone call or drop-in visit, as opposed to resources that required additional appointments or applications prior to accessing services, was associated with increased odds (aOR 1.95, 95% CI 1.05, 3.61) of connection success, after adjusting for age, sex, race, ethnicity, education, number of social needs, and resource-related characteristics. This study did not find statistically significant associations between connection attempt and any variable included in adjusted analyses. Conclusion: These findings suggest that referral pathways may influence the success of patients’ connection to social needs resources, highlighting opportunities for more accessible solutions to addressing patients’ unmet social needs.
An Exploratory Qualitative Study of Computer Screening to Support Decision-Making about Use of Palliative Care Registers in Primary Care: GP Think Aloud and Patient and Carer Interviews
Authors: Hubbard Gill , Broadfoot Kirsten , Carolan Clare , van Woerden Hugo C. 
Published: June 2021

Objectives: This study aimed to understand factors that influence general practitioner (GP) use of automated computer screening to identify patients for the palliative care register (PCR) and the experiences of palliative care and this emerging technology from patients’ and carers’ perspectives. Methods: A computer screening program electronically searches primary care records in routine clinical practice to identify patients with advanced illness who are not already on a PCR. Five GPs were asked to “think aloud” about adding patients identified by computer screening to the PCR. Key informant interviews with 6 patients on the PCR and 4 carers about their experiences of palliative care while on the PCR and their views of this technology. Data were analyzed thematically. Results and Conclusions: Using computer screening, 29% additional patients were added by GPs to the PCR. GP decision-making for the PCR was informed by clinical factors such as: if being treated with curative intent; having stable or unstable disease; end-stage disease, frailty; the likelihood of dying within the next 12 months; and psychosocial factors such as, age, personality, patient preference and social support. Six (60%) patients/carers did not know that they/their relative was on the PCR. From a patient/carer perspective, having a non-curative illness was not in and of itself sufficient reason for being on the PCR; other factors such as, unstable disease and avoiding pain and suffering were equally if not more, important. Patients and carers considered that computer screening should support but not replace, GP decision-making about the PCR. Computer screening merits ongoing development as a tool to aid clinical decision-making around entry to a PCR, but should not be used as a sole criterion. Care need, irrespective of diagnosis, disease trajectory or prognosis, should determine care.
Hyperintense acute reperfusion marker associated with hemorrhagic transformation in the WAKE-UP trial
Authors: Wouters Anke , Scheldeman Lauranne , Dupont Patrick , Cheng Bastian , Ebinger Martin , Jensen Märit , Endres Matthias , Gerloff Christian , Muir Keith W , Nighoghossian Norbert , Pedraza Salvador , Simonsen Claus Z , Boutitie Florent , Thijs Vincent , Thomalla Götz , Fiebach Jochen , Lemmens Robin 
Published: June 2021

Introduction Hyperintense acute reperfusion marker (HARM) is an indicator of early disruption of the blood-brain-barrier. Our aim was to investigate the incidence of HARM in patients with a diffusion weighted imaging (DWI) - fluid attenuated inversion recovery (FLAIR) mismatch and determine the association between this marker and hemorrhagic complications as well as clinical outcome. Patients and Methods We included patients from the Efficacy and Safety of MRI-Based Thrombolysis in Wake-Up Stroke (WAKE-UP) trial who underwent baseline perfusion weighted imaging (PWI). HARM was defined as a hyperintense signal in the cerebrospinal fluid space on FLAIR imaging at 24 h after baseline imaging. We compared baseline characteristics in patients with and without HARM and investigated the association between HARM and any hemorrhagic transformation (HT) and parenchymal hematoma (PH) in a multivariate logistic regression. We also explored HARM as an independent predictor of poor outcome, defined as a modified Rankin Scale of 3–6 at 90 days. Results HARM was present in 14 of 223 (6%) patients with a DWI-FLAIR mismatch and baseline characteristics were similar in patients with vs without HARM. HARM showed an independent relationship with any HT (OR 6.67; 95%CI 1.72–26.58) and any PH (OR 6.92; 95%CI 1.34–29.49). The rate of HARM was similar in patients with good and poor outcome (5%, p = 0.90). Conclusion In the WAKE-UP trial, the incidence of HARM was only 6% at 24 h. An association was present between HARM and hemorrhagic complications, but no relationship with functional outcome was observed.
Geographical variations and associated factors of defaulting from immunization among children aged 12 to 23 months in Ethiopia: using spatial and multilevel analysis of 2016 Ethiopian Demographic and Health Survey
Authors: Awol Mukemil , Alemu Zewdie Aderaw , Moges Nurilign Abebe , Jemal Kemal 
Published: June 2021

Abstract
Background
In Ethiopia, despite the considerable improvement in immunization coverage, the burden of defaulting from immunization among children is still high with marked variation among regions. However, the geographical variation and contextual factors of defaulting from immunization were poorly understood. Hence, this study aimed to identify the spatial pattern and associated factors of defaulting from immunization.

Methods
An in-depth analysis of the 2016 Ethiopian Demographic and Health Survey (EDHS 2016) data was used. A total of 1638 children nested in 552 enumeration areas (EAs) were included in the analysis. Global Moran’s I statistic and Bernoulli purely spatial scan statistics were employed to identify geographical patterns and detect spatial clusters of defaulting immunization, respectively. Multilevel logistic regression models were fitted to identify factors associated with defaulting immunization. A p value < 0.05 was used to identify significantly associated factors with defaulting of child immunization.

Results
A spatial heterogeneity of defaulting from immunization was observed (Global Moran’s I = 0.386379, p value < 0.001), and four significant SaTScan clusters of areas with high defaulting from immunization were detected. The most likely primary SaTScan cluster was seen in the Somali region, and secondary clusters were detected in (Afar, South Nation Nationality of people (SNNP), Oromiya, Amhara, and Gambella) regions. In the final model of the multilevel analysis, individual and community level factors accounted for 56.4% of the variance in the odds of defaulting immunization. Children from mothers who had no formal education (AOR = 4.23; 95% CI: 117, 15.78), and children living in Afar, Oromiya, Somali, SNNP, Gambella, and Harari regions had higher odds of having defaulted immunization from community level.

Conclusions
A clustered pattern of areas with high default of immunization was observed in Ethiopia. Both the individual and community-level characteristics were statistically significant factors of defaulting immunization. Therefore, the Federal Ethiopian Ministry of Health should prioritize the areas with defaulting of immunization and consider the identified factors for immunization interventions.
Predicting biological pathways of chemical compounds with a profile-inspired approach
Authors: Lopez-Ibañez Javier , Pazos Florencio , Chagoyen Monica 
Published: June 2021

Abstract
Background
Assignment of chemical compounds to biological pathways is a crucial step to understand the relationship between the chemical repertory of an organism and its biology. Protein sequence profiles are very successful in capturing the main structural and functional features of a protein family, and can be used to assign new members to it based on matching of their sequences against these profiles. In this work, we extend this idea to chemical compounds, constructing a profile-inspired model for a set of related metabolites (those in the same biological pathway), based on a fragment-based vectorial representation of their chemical structures.

Results
We use this representation to predict the biological pathway of a chemical compound with good overall accuracy (AUC 0.74–0.90 depending on the database tested), and analyzed some factors that affect performance. The approach, which is compared with equivalent methods, can in addition detect those molecular fragments characteristic of a pathway.

Conclusions
The method is available as a graphical interactive web server http://csbg.cnb.csic.es/iFragMent.
Complex II subunit SDHD is critical for cell growth and metabolism, which can be partially restored with a synthetic ubiquinone analog
Authors: Bandara Aloka B. , Drake Joshua C. , Brown David A. 
Published: June 2021

Abstract
Background
Succinate dehydrogenase (Complex II) plays a dual role in respiration by catalyzing the oxidation of succinate to fumarate in the mitochondrial Krebs cycle and transferring electrons from succinate to ubiquinone in the mitochondrial electron transport chain (ETC). Mutations in Complex II are associated with a number of pathologies. SDHD, one of the four subunits of Complex II, serves by anchoring the complex to the inner-membrane and transferring electrons from the complex to ubiquinone. Thus, modeling SDHD dysfunction could be a valuable tool for understanding its importance in metabolism and developing novel therapeutics, however no suitable models exist.

Results
Via CRISPR/Cas9, we mutated SDHD in HEK293 cells and investigated the in vitro role of SDHD in metabolism. Compared to the parent HEK293, the knockout mutant HEK293ΔSDHD produced significantly less number of cells in culture. The mutant cells predictably had suppressed Complex II-mediated mitochondrial respiration, but also Complex I-mediated respiration. SDHD mutation also adversely affected glycolytic capacity and ATP synthesis. Mutant cells were more apoptotic and susceptible to necrosis. Treatment with the mitochondrial therapeutic idebenone partially improved oxygen consumption and growth of mutant cells.

Conclusions
Overall, our results suggest that SDHD is vital for growth and metabolism of mammalian cells, and that respiratory and growth defects can be partially restored with treatment of a ubiquinone analog. This is the first report to use CRISPR/Cas9 approach to construct a knockout SDHD cell line and evaluate the efficacy of an established mitochondrial therapeutic candidate to improve bioenergetic capacity.
kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing
Authors: Lin Xue , Hua Yingying , Gu Shuanglin , Lv Li , Li Xingyu , Chen Pin , Dai Peng , Hu Yunyun , Liu Anna , Li Jian 
Published: June 2021

Abstract
Background
Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations “violent storm”, which is just what the Greek word “kataegis” means.

Results
There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package “kataegis” to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions.

Conclusions
The kataegis package is available on Bionconductor/Github (https://github.com/flosalbizziae/kataegis), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.
Comprehensive identification and expression analysis of B-Box genes in cotton
Authors: Feng Zhen , Li Mengyu , Li Yi , Yang Xu , Wei Hengling , Fu Xiaokang , Ma Liang , Lu Jianhua , Wang Hantao , Yu Shuxun 
Published: June 2021

Abstract
Background
B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton.

Results
In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures showed that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. The qRT-PCR results showed that there were significant differences in GhBBX genes in leaves and shoot apexes between early-maturing materials and late-maturing materials at most periods. Yeast two-hybrid results showed that GhBBX5/GhBBX23 and GhBBX8/GhBBX26 might interact with GhFT. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in abiotic stress and phytohormone response.

Conclusions
Our comprehensive analysis of BBX in G. hirsutum provided a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.
Dietary phytochemical index associated with cardiovascular risk factor in patients with type 1 diabetes mellitus
Authors: Delshad Aghdam Saeideh , Siassi Fereydoun , Nasli Esfahani Ensieh , Qorbani Mostafa , Rajab Asadollah , Sajjadpour Zahra , Bashiri Anahita , Aghayan Maryam , Sotoudeh Gity 
Published: June 2021

Abstract
Background
Dietary phytochemical index (DPI) is useful and inexpensive method to identify the role of phytochemicals on cardiovascular disease (CVD) risk factors. This study aimed to assess the relationship between DPI and CVD risk factors in patients with type1 diabetes mellitus.

Methods

A total of 261 participants aged 18–35 years with T1DM were enrolled in this cross-sectional study to assess the relationship between DPI and CVD risk factors. Anthropometric measurements, blood lipids, glucose, and antioxidant level were measured. Food intakes were determined using a food frequency questionnaire to calculate DPI. Logistic regression was used.

Results
The mean age of participants was 25 years. After adjustment for potential confounders, participants in the highest tertile of DPI had 88 % lower chance of hyperglycemia (P for trend = 0.020), 81 % lower chance of low high-density lipoprotein cholesterol (HDL-C) (P for trend = 0.030) and 98 % lower chance of high low-density lipoprotein cholesterol to HDL-C ratio (P for tend = 0.040). There were no relationships between DPI and other CVD risk factors.

Conclusions
Although higher intake of phytochemical-rich foods had a beneficial effect on some risk factors of CVD, more studies more studies are warranted to corroborate the present findings.
Alterations in MicroRNA gene expression profile in liver transplant patients with hepatocellular carcinoma
Authors: Afshari Afsoon , Yaghobi Ramin , Karimi Mohammad Hossein , Mowla Javad 
Published: June 2021

Abstract
Background
Hepatocellular carcinoma (HCC) can lead to liver failure which renders to liver transplant. miRNAs might be detected as biomarkers in subclinical stage of several hepatobiliary disorders like HCC. Therefore, in the present study, alterations in miRNAs as biomarkers were detected in LT patients with HCC.

Methods
Fourteen tissue samples composed of 5 rejected and 9 non-rejected ones were used for studying the miRNAs expression pattern using LNA-array probe assay and the result was evaluated by in house SYBR Green Real-time PCR protocols on 30 other tissue samples composed of 10 rejected and 20 non-rejected ones for the selected miRNAs. All samples were collected from liver transplanted patients with HCC.

Results
The study results revealed that in rejected patients compared to non-rejected ones, hsa-miR-3158-5p, -4449, -4511, and -4633-5p were up-regulated and hsa-miR-122-3p, -194-5p, 548as-3p, and -4284 were down-regulated. ROC curve analysis also confirmed that miR194-5p and -548as-3p in up-regulated and also, miR-3158-5p, -4449 in down-regulated microRNAs are significantly important molecules in rejection.

Conclusion
Finally, the tissue levels of specific miRNAs (especially hsa-miR-3158-5p, -4449, -194-5p and -548as-3p) significantly correlated with the development of HCC, which can be present as biomarkers after further completing studies.
Is insulin the preferred treatment in persons with type 2 diabetes and liver cirrhosis?
Authors: Yen Fu-Shun , Lai Jung-Nien , Wei James Cheng-Chung , Chiu Lu-Ting , Hsu Chih-Cheng , Hou Ming-Chih , Hwu Chii-Min 
Published: June 2021

Abstract
Background
Insulin is highly recommended for diabetes management in persons with liver cirrhosis. However, few studies have evaluated its long-term effects in these persons. We conducted this study to compare the risks of mortality, liver-related complications, and cardiovascular events in persons with type 2 diabetes mellitus (T2DM) and compensated liver cirrhosis.

Methods
From January 1, 2000, to December 31, 2012, we selected 2047 insulin users and 4094 propensity score-matched nonusers from Taiwan’s National Health Insurance Research Database. Cox proportional hazard models were used to assess the risks of outcomes.

Results
The mean follow-up time was 5.84 years. The death rate during the follow-up period was 5.28 and 4.07 per 100 person-years for insulin users and nonusers, respectively. In insulin users, the hazard ratios and 95% confidence intervals (CIs) of all-cause mortality, hepatocellular carcinoma, decompensated cirrhosis, hepatic failure, major cardiovascular events, and hypoglycemia were 1.31 (1.18–1.45), 1.18 (1.05–1.34), 1.53 (1.35–1.72), 1.26 (1.42–1.86), 1.41 (1.23–1.62), and 3.33 (2.45–4.53), respectively.

Conclusions
This retrospective cohort study indicated that among persons with T2DM and compensated liver cirrhosis, insulin users were associated with higher risks of death, liver-related complications, cardiovascular events, and hypoglycemia compared with insulin nonusers.
Serum pepsinogen levels in different regions of China and its influencing factors: a multicenter cross-sectional study
Authors: Tong Yuling , Wang Hongguang , Zhao Yi , He Xueqiang , Xu Hongwei , Li Hong , Shuai Ping , Gong Lirong , Wu Hongbo , Xu Hongzhi , Luo Yinhu , Wang Dong , Liu Shizhu , Song Zhenya 
Published: June 2021

AbstractBackgroundThe aim of this study is to investigate the difference of serum pepsinogen (PG) baseline levels in different regions of China and its influencing factors.MethodsFrom October 2016 to October 2018, asymptomatic health checkup people who underwent nasal endoscopy in nine health management centers in different regions of China were collected. Lifestyle questionnaires were conducted, and serum PG and gastroscopy were performed. The differences in PG levels in baseline population (OLGA-0 grade) were studied according to geographical subregions of China. SPSS software was used for statistical analysis.Results1922 patients were included in the final analysis. Compared with the non-atrophy (OLGA-0) group, PGR levels in atrophy group (OLGA-I to IV) were significantly decreased with the atrophy degree (p < 0.05). A total of 1590 baseline people (OLGA-0) were included in the study, including 254 from South China, 574 from East China, 210 from Southwest China, 332 from Northeast China, and 220 from Central/Northern China. There were significant differences in baseline PGI levels among the five regions (p < 0.05). The PGII levels were also different among the five regions, except for Central/Northern versus Southern China. PGR (PGI/PGII ratio) levels in Southern China were higher than other four regions. Further studies were conducted on the related factors that might affect the baseline PG level, which was affected by nationality, dietary habits, smoking,Helicobacter pyloriinfection and other related factors.ConclusionInfluenced by many factors, the baseline PG levels are different in different regions of China. In the follow-up studies of PG cut-off value, different PG cut-off value based on region may be more effective in the screening of gastric cancer and precancerous lesions in China.