bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics data of gastric cancer cell lines
Authors: Seo Eun-Hye , Shin Yun-Jae , Kim Hee-Jin , Kim Jeong-Hwan , Kim Yong Sung , Kim Seon-Young 
Published: April 2023

Abstract
Objectives
Gastric cancer (GC) is the fourth most common cancer worldwide, with the highest incidence and mortality regardless of sex. Despite technological advances in diagnosing and treating gastric cancer, GC still has high incidence and mortality rates. Therefore, continuous research is needed to overcome GC. In various studies, cell lines are used to find and verify the cause of specific diseases. Large-scale genomic studies such as ENCODE and Roadmap epigenomic projects provide multiomics data from various organisms and samples. However, few multi-omics data for gastric tissues and cell lines have been generated. Therefore, we performed RNA-seq, Exome-seq, and ChIP-seq with several gastric cell lines to generate a multi-omics data set in gastric cancer.

Data description
Multiomic data, such as RNA-seq, Exome-seq, and ChIP-seq, were produced in gastric cancer and normal cell lines. RNA-seq data were generated from nine GC and one normal gastric cell line, mapped to a human reference genome (hg38) using the STAR alignment tool, and quantified with HTseq. Exome sequence data were produced in nine GC and two normal gastric lines. Sequenced reads were mapped and processed using BWA-MEM and GATK, variants were called by stralka2, and annotation was performed using ANNOVAR. Finally, for the ChIP-seq, nine GC cell lines and four GC cell lines were used in two experimental sets; chip-seq was performed to confirm changes in H3K4me3 and H3K27me3. Data was mapped to human reference hg38 with BWA-MEM, and peak calling and annotation were performed using the Homer tool. Since these data provide multi-omics data for GC cell lines, it will be useful for researchers who use the GC cell lines to study.
Dancing with the patient: a qualitative study of general practitioners’ experiences of managing patients with multimorbidity and common mental health problems
Authors: Kappelin C. , Sandlund C. , Westman J. , Wachtler C. 
Published: April 2023

Abstract
Background
Patients with multimorbidity, having two or more chronic diseases, suffer frequently from undiagnosed common mental health problems and are an increasing challenge in primary care. There is a call to improve care delivery to address all these patients’ needs at the same time. The aim of this study was to identify general practitioners’ experiences of managing patients with multimorbidity and common mental health problems in primary care.

Methods
We conducted five focus group interviews with 28 physicians (3–8 participants in each group) in 5 primary care practices in and outside of Stockholm, Sweden. We used a semi-structured interview guide, and we analysed the data using reflexive thematic analysis. The methodological orientation of the study was inductive, latent constructivism.

Results
We generated two themes from the data: Unmet patient needs and fragmented care send patients and physicians off balance and Dancing with the patient individually and together with others leads to confident and satisfied patients and physicians. The two themes are related as general practitioners expressed a need to shift from disease-specific fragmentation to relational continuity, teamwork, and flexibility to meet the needs of patients with multimorbidity and common mental health problems.

Conclusions
These findings can provide guidance in developing future interventions for patients with multimorbidity and common mental health problems in primary care in general, and in Sweden in particular.
Physical performance and compensation strategies of older adults to maintain physical fitness and well-being during the COVID-19 pandemic in Germany
Authors: Gehle Torben , Lau Sandra , Hackbarth Michel , Zieschang Tania , Koschate Jessica 
Published: April 2023

Abstract
Introduction
During the first wave of the COVID-19 pandemic in March 2020, worldwide restrictions in social life, including the closure of sport facilities, led to a reduction of physical activity and subjective well-being. The aim of this study is to describe physical training habits, and subjective well-being in relation to objective training data from a chip-controlled fitness circuit in the rural area of Oldenburg, Germany.

Materials and methods
Overall, 35 older adults (20 women 71 ± 6 y/o and 15 men, 72 ± 7 y/o), regularly exercising in a chip-controlled fitness circuit before the lockdown in March 2020, were interviewed. The training data from February to August 2020 from six strength and two endurance exercise devices were extracted and compared to data before and up to three months after the lockdown. Additionally, participants’ personal characteristics, physical activities and quality of life before, during, and after the first lockdown were assessed.

Results
The leg score (pre, postJune, postJuly, postAugust: 1207 ± 469 kg, 1248 ± 477 kg, 1254 ± 516 kg, 1283 ± 493 kg; p = 0.137) and endurance scores (ergometer: 0.93 ± 0.35 min− 1 · watt− 1, 0.86 ± 0.31 min− 1 · watt− 1, 0.86 ± 0.31 min− 1 · watt− 1, 0.85 ± 0.28 min− 1 · watt− 1 ; p = 0.442) were not significantly different, in contrast to the rowing score (1426 ± 582 kg, 1558 ± 704 kg, 1630 ± 757 kg, 1680 ± 837 kg; p < 0.001). A significant increase of total energy expenditure (p = 0.026), mainly through gardening, walking, and bike riding was observed. The greatest personal limitation reported, was the loss of social contacts.

Conclusion
The presented data did not show a decrease in training performance, but a slight trend towards an increase. A compensatory increase in regular outdoor activities seems to have a protective effect against a loss of training performance and may have the potential to stabilize subjective well-being during lockdown periods.
Projecting the development of antimicrobial resistance in Neisseria gonorrhoeae from antimicrobial surveillance data: a mathematical modelling study
Authors: Riou Julien , Althaus Christian L. , Allen Hester , Cole Michelle J. , Grad Yonatan H. , Heijne Janneke C. M. , Unemo Magnus , Low Nicola 
Published: April 2023

Abstract
Background
The World Health Organization recommends changing the first-line antimicrobial treatment for gonorrhoea when ≥ 5% of Neisseria gonorrhoeae cases fail treatment or are resistant. Susceptibility to ceftriaxone, the last remaining treatment option has been decreasing in many countries. We used antimicrobial resistance surveillance data and developed mathematical models to project the time to reach the 5% threshold for resistance to first-line antimicrobials used for N. gonorrhoeae.

Methods
We used data from the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP) in England and Wales from 2000–2018 about minimum inhibitory concentrations (MIC) for ciprofloxacin, azithromycin, cefixime and ceftriaxone and antimicrobial treatment in two groups, heterosexual men and women (HMW) and men who have sex with men (MSM). We developed two susceptible-infected-susceptible models to fit these data and produce projections of the proportion of resistance until 2030. The single-step model represents the situation in which a single mutation results in antimicrobial resistance. In the multi-step model, the sequential accumulation of resistance mutations is reflected by changes in the MIC distribution.

Results
The single-step model described resistance to ciprofloxacin well. Both single-step and multi-step models could describe azithromycin and cefixime resistance, with projected resistance levels higher with the multi-step than the single step model. For ceftriaxone, with very few observed cases of full resistance, the multi-step model was needed to describe long-term dynamics of resistance. Extrapolating from the observed upward drift in MIC values, the multi-step model projected ≥ 5% resistance to ceftriaxone could be reached by 2030, based on treatment pressure alone. Ceftriaxone resistance was projected to rise to 13.2% (95% credible interval [CrI]: 0.7–44.8%) among HMW and 19.6% (95%CrI: 2.6–54.4%) among MSM by 2030.

Conclusions
New first-line antimicrobials for gonorrhoea treatment are needed. In the meantime, public health authorities should strengthen surveillance for AMR in N. gonorrhoeae and implement strategies for continued antimicrobial stewardship. Our models show the utility of long-term representative surveillance of gonococcal antimicrobial susceptibility data and can be adapted for use in, and for comparison with, other countries.
The senescence difference between the central and peripheral cornea induced by sutures
Authors: Li Suxia , Wang Ning , Dong Qiaoqiao , Dong Muchen , Qu Mingli , Wang Yao , Shi Weiyun 
Published: April 2023

Abstract
Introduction
Cell senescence plays a regulatory role in tissue fibrosis. Corneal scarring is usually more severe in the central cornea based on clinical observation. In this study, we attempted to explore the senescence difference between the central and peripheral cornea in an in vivo mouse model with suture-induced senescence and in an in vitro model of senescence with hydrogen peroxide (H2O2)-induced rabbit corneal fibroblasts.

Methods
Male Balb/c mice (6–8 weeks) received sutures in the central, superior, inferior, nasal, and temporal cornea. The sutures were removed on the 14th day. Corneal neovascularization was observed under a slit lamp microscope with a digital camera. The fibroblasts isolated from the central and peripheral rabbit cornea were induced with H2O2 to establish the senescence model in vitro. Senescence was evaluated with SA-β-gal staining and gene expression analysis of p21, p27, and p53.

Results
Senescent cells accumulated in the corneal stroma from the third day to the 14th day after the operation and peaked on the 14th day. More senescent keratocytes were observed in the peripheral cornea of the mouse model. In vitro, the peripheral corneal fibroblasts were more prone to senescence due to H2O2. The polymerase chain reaction results showed that the senescence-related genes p21, p27, and p53 were highly expressed in the peripheral corneal fibroblasts compared with the central corneal fibroblasts.

Conclusions
Senescent fibroblasts can limit tissue fibrosis; hence, the senescence difference between the central and peripheral cornea may contribute to the difference in scarring.
Differential diagnosis of precocious puberty in girls during the COVID-19 pandemic: a pilot study
Authors: Sun Huihui , Qian Yi , Wan Naijun , Liu Lili 
Published: April 2023

Abstract
Background
To investigate the differential diagnosis of girls aged 6 to 8 years with idiopathic premature thelarche (IPT) and central precocious puberty (CPP) during the COVID-19 pandemic. We explored predicted adult height (PAH) discrepancy to guide appropriate diagnosis and treatment.

Methods
From January 2020 to December 2021, Chinese girls aged 6 to 8 years with precocious puberty were recruited. They were divided into IPT and CPP groups. Clinical characteristics, including height, weight, body mass index (BMI), basal luteinizing hormone (LH), oestradiol, uterine length and volume, follicle numbers (d > 4 mm) and bone age (BA) were recorded. We analysed differential diagnosis and PAH discrepancy in both groups. Binary logistic regression analysis was used to explore risk factors for CPP, and receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic value of related indexes.

Results
Sixty patients, including 40 girls with IPT and 20 girls with CPP, were recruited. The prevalence of overweight and obesity in the entire cohort was 25% (15/60) and was significantly higher in IPT than CPP, 32.5% (13/40) vs. 10% (2/20), respectively (P=0.045). There were significant differences in LH, uterine volume, follicle numbers and BA (P<0.05). The impaired PAH of IPT and CPP was 0.01 ± 1.19 SD and 0.62 ± 0.94 SD with significant differences (P=0.047). Logistic regression analysis showed that LH and follicle numbers were independent risk factors for CPP. The ROC curve showed that the area under the curve (AUC) of LH and follicle numbers were 0.823 and 0.697. The sensitivity and specificity of LH with a cut off of 0.285 IU/L were 78.9% and 77.8%. The sensitivity and specificity of follicle numbers with a cut off of 3.5 were 89.5% and 52.8%.

Conclusion
The prevalence of overweight and obesity in 6- to 8-year-old girls with precocious puberty was high. Auxological data should not be used in the differential diagnosis of IPT and CPP. Basal LH above 0.285 IU/L and follicle numbers greater than 4 were important features suggestive of CPP. PAH was impaired in individuals with CPP, but it was not impaired in individuals with IPT.
Hypnotic prescription trends and patterns for the treatment of insomnia in Japan: analysis of a nationwide Japanese claims database
Authors: Okuda Shoki , Qureshi Zaina P. , Yanagida Yukiko , Ito Chie , Homma Yuji , Tokita Shigeru 
Published: April 2023

Abstract
Background
There is limited consensus regarding the optimal treatment of insomnia. The recent introduction of orexin receptor antagonists (ORA) has increased the available treatment options. However, the prescribing patterns of hypnotics in Japan have not been comprehensively assessed. We performed analyses of a claims database to investigate the real-world use of hypnotics for treating insomnia in Japan.

Methods
Data were retrieved for outpatients (aged ≥ 20 to < 75 years old) prescribed ≥ 1 hypnotic for a diagnosis of insomnia between April 1st, 2009 and March 31st, 2020, with ≥ 12 months of continuous enrolment in the JMDC Claims Database. Patients were classified as new or long-term users of hypnotics. Long-term use was defined as prescription of the same mechanism of action (MOA) for ≥ 180 days. We analyzed the trends (2010–2019) and patterns (2018–2019) in hypnotics prescriptions.

Results
We analyzed data for 130,177 new and 91,215 long-term users (2010–2019). Most new users were prescribed one MOA per year (97.1%–97.9%). In 2010, GABAA-receptor agonists (benzodiazepines [BZD] or z-drugs) were prescribed to 94.0% of new users. Prescriptions for BZD declined from 54.8% of patients in 2010 to 30.5% in 2019, whereas z-drug prescriptions remained stable (~ 40%). Prescriptions for melatonin receptor agonist increased slightly (3.2% to 6.3%). Prescriptions for ORA increased over this time from 0% to 20.2%. Prescriptions for BZD alone among long-term users decreased steadily from 68.3% in 2010 to 49.7% in 2019. Prescriptions for ORA were lower among long-term users (0% in 2010, 4.3% in 2019) relative to new users. Using data from 2018–2019, multiple (≥ 2) MOAs were prescribed to a higher proportion of long-term (18.2%) than new (2.8%) users. The distribution of MOAs according to psychiatric comorbidities, segmented by age or sex, revealed higher proportions of BZD prescriptions in elderly (new and long-term users) and male (new users) patients in all comorbidity segments.

Conclusion
Prescriptions for hypnotics among new and long-term users in Japan showed distinct patterns and trends. Further understanding of the treatment options for insomnia with accumulating evidence for the risk–benefit balance might be beneficial for physicians prescribing hypnotics in real-world settings.
Mediation effect of insomnia symptoms between positive psychotic like experiences and suicidal ideation among Lebanese young adults
Authors: Farah Nour , Obeid Sahar , Malaeb Diana , Haddad Chadia , Fekih-Romdhane Feten , Hallit Souheil 
Published: April 2023

Abstract
Background
Psychotic symptoms reported by healthy individuals in the general population are referred to as psychotic-like experiences (PLEs) and have been proven to increase the risk of suicidal ideation (SI) in these individuals. As it is well established that PLEs and insomnia share a bidirectional association and also that insomnia is linked to SI, we hypothesized that insomnia may represent a mediator underlying the relationship between PLEs and SI. Our aim was to validate this hypothesis among Lebanese young adults.

Methods
A total of 3103 young adults (mean age 21.73 ± 3.80 years; 63.6% females) recruited from all Lebanese governorates completed a self-administered online questionnaire. PLEs were assessed using the CAPE-42 scale, SI using the Columbia Suicide Rating Scale, and insomnia using the Insomnia Severity Index). We conducted a mediation analysis using SPSS PROCESS v3.4 model 4 with three pathways. Variables that showed a p < 0.25 in the bivariate analysis were entered in the path analysis.

Results
A total of 1378 participants (44.4%) had insomnia; 18.8% had SI; 42.5% reported at least one positive PE ‘nearly always’, and 30.5% reported at least one negative PE with this frequency. The results of the mediation analysis showed that insomnia severity partially mediated the association between positive dimension and SI; higher positive dimension was significantly associated with more insomnia severity, which was, in turn, significantly associated with more SI. Finally, more positive dimension was significantly and directly associated with more SI.

Conclusion
These preliminary findings might encourage the implementation of new preventive measures to reduce SI among PLEs patients. Treating symptoms of insomnia might help reduce the risk of suicide.
Achieving the “Ending the HIV Epidemic in the U.S.” incidence reduction goals among at-risk populations in the South
Authors: Hamilton Deven T. , Hoover Karen W. , Smith Dawn K. , Delaney Kevin P. , Wang Li Yan , Li Jingjing , Hoyte Tamika , Jenness Samuel M. , Goodreau Steven M. 
Published: April 2023

Abstract
Introduction
Antiretroviral medication coverage remains sub-optimal in much of the United States, particularly the Sothern region, and Non-Hispanic Black or African American persons (NHB) continue to be disproportionately impacted by the HIV epidemic. The “Ending the HIV Epidemic in the U.S.” (EHE) initiative seeks to reduce HIV incidence nationally by focusing resources towards the most highly impacted localities and populations. This study evaluates the impact of hypothetical improvements in ART and PrEP coverage to estimate the levels of coverage needed to achieve EHE goals in the South.

Methods
We developed a stochastic, agent-based network model of 500,000 individuals to simulate the HIV epidemic and hypothetical improvements in ART and PrEP coverage.

Results
New infections declined by 78.6% at 90%/40% ART/PrEP and 94.3% at 100%/50% ART/PrEP. Declines in annual incidence rates surpassed 75% by 2025 with 90%/40% ART/PrEP and 90% by 2030 with 100%/50% ART/PrEP coverage. Increased ART coverage among NHB MSM was associated with a linear decline in incidence among all MSM. Declines in incidence among Hispanic/Latino and White/Other MSM were similar regardless of which MSM race group increased their ART coverage, while the benefit to NHB MSM was greatest when their own ART coverage increased. The incidence rate among NHB women declined by over a third when either NHB heterosexual men or NHB MSM increased their ART use respectively. Increased use of PrEP was associated with a decline in incidence for the groups using PrEP. MSM experienced the largest absolute declines in incidence with increasing PrEP coverage, followed by NHB women.

Conclusions
Our analysis indicates that it is possible to reach EHE goals. The largest reductions in HIV incidence can be achieved by increasing ART coverage among MSM and all race groups benefit regardless of differences in ART initiation by race. Improving ART coverage to > 90% should be prioritized with a particular emphasis on reaching NHB MSM. Such a focus will reduce the largest number of incident cases, reduce racial HIV incidence disparities among both MSM and women, and reduce racial health disparities among persons with HIV. NHB women should also be prioritized for PrEP outreach.
Geographic disparities and temporal changes of COVID-19 incidence risks in North Dakota, United States
Authors: Deb Nath Nirmalendu , Khan Md Marufuzzaman , Schmidt Matthew , Njau Grace , Odoi Agricola 
Published: April 2023

Abstract
Background
COVID-19 is an important public health concern due to its high morbidity, mortality and socioeconomic impact. Its burden varies by geographic location affecting some communities more than others. Identifying these disparities is important for guiding health planning and service provision. Therefore, this study investigated geographical disparities and temporal changes of the percentage of positive COVID-19 tests and COVID-19 incidence risk in North Dakota.

Methods
COVID-19 retrospective data on total number of tests and confirmed cases reported in North Dakota from March 2020 to September 2021 were obtained from the North Dakota COVID-19 Dashboard and Department of Health, respectively. Monthly incidence risks of the disease were calculated and reported as number of cases per 100,000 persons. To adjust for geographic autocorrelation and the small number problem, Spatial Empirical Bayesian (SEB) smoothing was performed using queen spatial weights. Identification of high-risk geographic clusters of percentages of positive tests and COVID-19 incidence risks were accomplished using Tango’s flexible spatial scan statistic. ArcGIS was used to display and visiualize the geographic distribution of percentages of positive tests, COVID-19 incidence risks, and high-risk clusters.

Results
County-level percentages of positive tests and SEB incidence risks varied by geographic location ranging from 0.11% to 13.67% and 122 to 16,443 cases per 100,000 persons, respectively. Clusters of high percentages of positive tests were consistently detected in the western part of the state. High incidence risks were identified in the central and south-western parts of the state, where significant high-risk spatial clusters were reported. Additionally, two peaks (August 2020-December 2020 and August 2021-September 2021) and two non-peak periods of COVID-19 incidence risk (March 2020-July 2020 and January 2021-July 2021) were observed.

Conclusion
Geographic disparities in COVID incidence risks exist in North Dakota with high-risk clusters being identified in the rural central and southwest parts of the state. These findings are useful for guiding intervention strategies by identifying high risk communities so that resources for disease control can be better allocated to communities in need based on empirical evidence. Future studies will investigate predictors of the identified disparities so as to guide planning, disease control and health policy.