bluuebunny/crossref_metadata_2025_split huggingface dataset:
RegCloser: a robust regression approach to closing genome gaps
Authors: Cao Shenghao , Li Mengtian , Li Lei M. 
Published: June 2023

Abstract
Background
Closing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter.

Results
We propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads.

Conclusions
RegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser. The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.
GBA1 in Parkinson’s disease: variant detection and pathogenicity scoring matters
Authors: Gabbert Carolin , Schaake Susen , Lüth Theresa , Much Christoph , Klein Christine , Aasly Jan O. , Farrer Matthew J. , Trinh Joanne 
Published: June 2023

Abstract
Background
GBA1 variants are the strongest genetic risk factor for Parkinson’s disease (PD). However, the pathogenicity of GBA1 variants concerning PD is still not fully understood. Additionally, the frequency of GBA1 variants varies widely across populations.

Objectives
To evaluate Oxford Nanopore sequencing as a strategy, to determine the frequency of GBA1 variants in Norwegian PD patients and controls, and to review the current literature on newly identified variants that add to pathogenicity determination.

Methods
We included 462 Norwegian PD patients and 367 healthy controls. We sequenced the full-length GBA1 gene on the Oxford Nanopore GridION as an 8.9 kb amplicon. Six analysis pipelines were compared using two aligners (NGMLR, Minimap2) and three variant callers (BCFtools, Clair3, Pepper-Margin-Deepvariant). Confirmation of GBA1 variants was performed by Sanger sequencing and the pathogenicity of variants was evaluated.

Results
We found 95.8% (115/120) true-positive GBA1 variant calls, while 4.2% (5/120) variant calls were false-positive, with the NGMLR/Minimap2-BCFtools pipeline performing best. In total, 13 rare GBA1 variants were detected: two were predicted to be (likely) pathogenic and eleven were of uncertain significance. The odds of carrying one of the two common GBA1 variants, p.L483P or p.N409S, in PD patients were estimated to be 4.11 times the odds of carrying one of these variants in controls (OR = 4.11 [1.39, 12.12]).

Conclusions
In conclusion, we have demonstrated that Oxford long-read Nanopore sequencing, along with the NGMLR/Minimap2-BCFtools pipeline is an effective tool to investigate GBA1 variants. Further studies on the pathogenicity of GBA1 variants are needed to assess their effect on PD.
Multi-environment evaluations across ecological regions reveal climate and soil effects on amides contents in Chinese prickly ash peels (Zanthoxylum bungeanum Maxim.)
Authors: Zheng Tao , Zeng Hai-tao , Sun Bing-yin , Liu Shu-ming 
Published: June 2023

Abstract
Background
Environmental factors difference is the key factor for the difference in the production, transformation and accumulation of effective components in plants. UPLC-MS/MS and multivariate statistical methods were applied to describe the region difference of amides compounds in Chinese prickly ash peels from different regions and their correlation with climatic factors and soil factors.

Results
Amides compounds contents were significantly higher in high altitude areas, with obvious altitude change trend. Two ecotypes were classified based on the amides compounds contents, one was the high altitude-cool type from Qinghai, Gansu, Sichuan and western Shaanxi province, and the other one was low altitude-warm type from eastern Shaanxi, Shanxi, Henan, Hebei and Shandong province. Amides compounds content were negatively correlated with annual mean temperature, max temperature of warmest month, mean temperature of wettest quarter and mean temperature of warmest quarter (P < 0.01). Except for hydroxy-γ-sanshool and ZP-amide A, the residual amides contents were significantly positively correlated with organic carbon, available nitrogen, phosphorus and potassium in soil and negatively correlated with soil bulk density. Low temperature, low precipitation and high organic carbon in soil were conducive to amides accumulation.

Conclusions
This study aided in site specific exploration of high amides contents yielding samples, enriched the environment factors effects on amides compounds, and provided scientific foundation for the improvement of Chinese prickly ash peels quality and the location of high-quality production areas.
Effect of continuous spinal anesthesia on the hemodynamics of labor analgesia in hypertensive pregnant women: a comparative, randomized clinical trial
Authors: Han Bin , Xu Mingjun 
Published: June 2023

Abstract
Background
To observe the changes in hemodynamic, stress and inflammatory responses during labor and their labor outcomes after continuous spinal anesthesia labor analgesia for hypertensive pregnant women, and to evaluate whether the continuous spinal anesthesia had any advantages compared to continuous epidural analgesia for hypertensive pregnant women and their newborns.

Methods
A total of 160 hypertensive pregnant women were selected and randomly divided into continuous spinal anesthesia analgesia group (CSA group) and continuous epidural analgesia group (EA group). Participant age, height, weight and gestational week were recorded; MAP, VAS score, CO and SVR were recorded after the onset of regular uterine contractions (T0), 10 min after analgesia (T1), 30 min (T2), 60 min (T3), when the uterine opening was complete (T4) and when the fetus was delivered (T5); the duration of the first stage of labor and the second stage of labor were recorded; the number of cases of treatment with oxytocin and antihypertensive therapy, mode of delivery, eclampsia and postpartum hemorrhage were counted; pregnant women Bromage scores were recorded at T2. We also recorded neonatal weight, Apgar scores at 1, 5 and 10 min after birth; arterial blood gas analysis of the umbilical cord was performed in newborns; finally, TNF-α, IL-6, and cortisol in pregnant women venous blood were measured at T0, T5, and 24 h after delivery (T7). The number of successful compressions and the total drug dosage administered by the analgesic pump were recorded for both groups.

Results
The first stage of labor in CSA was longer than EA (P < 0.05); the MAP, VAS and SVR value in CSA were lower than EA group at T1, T3 and T4 (P < 0.05); in contrast, the CO in CSA at T3 and T4 was higher than in EA (P < 0.05). The oxytocin was more often used whereas the antihypertensive drugs were less used in CSA as compared to EA. The level of TNF-α, IL-6, Cor in the CSA at T5 was lower than the EA group (P < 0.05), and the level of TNF-α in the CSA group at T7 was lower than the EA group (P < 0.05).

Conclusion
For pregnant women with hypertension during pregnancy, continuous spinal anesthesia labor analgesia has no significant effect on the final mode of delivery, but shows precise analgesic effect and stabilizes circulatory system, it is recommended to perform continuous spinal anesthesia early in labor for hypertensive pregnant women, which can effectively reduce the stress reaction.

Trial registration
ChiCTR-INR-17012659.
Date of registration: 13/09/2017.
Rationale and design of the Birkebeiner Ageing Study – a prospective cohort study of older endurance athletes
Authors: Myrstad Marius , Johansen Kristoffer Robin , Sørensen Eivind , Ranhoff Anette Hylen 
Published: June 2023

Abstract
Background
While regular physical activity is associated with reduced mortality and morbidity in general populations, health outcomes and functional capacity related to upholding strenuous endurance exercise beyond the age of 65 years are only sparsely studied. The aim of this study is to assess associations of prolonged strenuous endurance sport practice with ageing, functional decline, morbidity and longevity among older recreational endurance athletes, during long-term follow-up.

Methods
Prospective cohort study of older recreational endurance athletes in Norway. All skiers aged 65 years and older who participated in a long-distance endurance competition, the annual 54-km Birkebeiner cross-country ski race in 2009 or 2010, were invited. The participants answered an extensive baseline questionnaire about lifestyle habits, including leisure-time physical activity and endurance sport participation, diseases, medication use and physical and mental health, with follow-up questionnaires planned every fifth year until 2029. New participants may be invited with the aim to increase the study size. Endpoints such as all-cause and disease-specific mortality, incidence and cumulative prevalence of diseases, use of medication, physical and mental health and functional decline will be assessed subsequently.
Out of 658 invited skiers (51 women), 551(84%) completed the baseline questionnaire and were included in the study. The mean age was 68.8 years (median 68, range 65- 90). At baseline, the participants had completed the Birkebeiner race for an average of 16.6 years and reported an average of 33.4 years of regular endurance exercise, with one out of five reporting at least 50 years of exercise. In all, 479 (90%) reported that they were still practicing leisure-time physical activity of moderate or vigorous intensity at least twice weekly. The prevalence of cardiovascular risk factors and diseases was low.

Discussion
This prospective study of a cohort of recreational athletes exposed to prolonged and strenuous endurance exercise, could complement population-based studies by providing data on associations between life-long endurance sport participation, aging, functional decline and health outcomes during long-term follow-up.
Sociodemographic and clinical predictors for COVID-19 preventive measures compliance among pregnant women in Saudi Arabia: a multicenter study
Authors: Ghamri Ranya A. , Ghamri Kholoud A. 
Published: June 2023

Abstract
Objective
To assess the levels of adherence among pregnant women to the basic COVID-19 preventive measures, and to analyze the effect of risk perception and sociodemographic and clinical factors on adherence.

Method
A multicenter, cross-sectional study was conducted at the obstetrics clinics of 50 primary care centers selected using a multistage sampling method. An online-administered, structured questionnaire was used to collect self-reported levels of adherence to four basic preventive measures against COVID-19, along with perceived COVID-19 severity, infectiousness, and harmfulness to the baby, besides sociodemographic and clinical data including obstetrical and other medical history.

Results
A total of 2460 pregnant women were included with a mean (SD) age of 30.21 (6.11) years. Levels of self-reported compliance were highest for hand hygiene (95.7%), followed by social distancing (92.3%), masking (90.0%), and avoidance of contact with a COVID-19 infected person (70.3%). Perceived COVID-19 severity and infectiousness, and harmfulness to the baby were observed in 89.2%, 70.7%, and 85.0% of the participants, respectively, and were variably associated with compliance to preventive measures. Analysis of sociodemographic factors highlighted the significance of education and economic status in determining adherence to preventive measures, which represents a potential inequity in the risk of COVID-19 infection.

Conclusion
This study highlights the importance of patients’ education to enable functional perception of COVID-19 that promotes self-efficacy, besides investigating the specific social determinants of health to tackle inequalities in terms of prevention efficiency and the subsequent health outcomes.
Reducing the number of unnecessary biopsies for mammographic BI-RADS 4 lesions through a deep transfer learning method
Authors: Meng Mingzhu , Li Hong , Zhang Ming , He Guangyuan , Wang Long , Shen Dong 
Published: June 2023

Abstract
Background
In clinical practice, reducing unnecessary biopsies for mammographic BI-RADS 4 lesions is crucial. The objective of this study was to explore the potential value of deep transfer learning (DTL) based on the different fine-tuning strategies for Inception V3 to reduce the number of unnecessary biopsies that residents need to perform for mammographic BI-RADS 4 lesions.

Methods
A total of 1980 patients with breast lesions were included, including 1473 benign lesions (185 women with bilateral breast lesions), and 692 malignant lesions collected and confirmed by clinical pathology or biopsy. The breast mammography images were randomly divided into three subsets, a training set, testing set, and validation set 1, at a ratio of 8:1:1. We constructed a DTL model for the classification of breast lesions based on Inception V3 and attempted to improve its performance with 11 fine-tuning strategies. The mammography images from 362 patients with pathologically confirmed BI-RADS 4 breast lesions were employed as validation set 2. Two images from each lesion were tested, and trials were categorized as correct if the judgement (≥ 1 image) was correct. We used precision (Pr), recall rate (Rc), F1 score (F1), and the area under the receiver operating characteristic curve (AUROC) as the performance metrics of the DTL model with validation set 2.

Results
The S5 model achieved the best fit for the data. The Pr, Rc, F1 and AUROC of S5 were 0.90, 0.90, 0.90, and 0.86, respectively, for Category 4. The proportions of lesions downgraded by S5 were 90.73%, 84.76%, and 80.19% for categories 4 A, 4B, and 4 C, respectively. The overall proportion of BI-RADS 4 lesions downgraded by S5 was 85.91%. There was no significant difference between the classification results of the S5 model and pathological diagnosis (P = 0.110).

Conclusion
The S5 model we proposed here can be used as an effective approach for reducing the number of unnecessary biopsies that residents need to conduct for mammographic BI-RADS 4 lesions and may have other important clinical uses.
Paracentral acute middle maculopathy presenting as a sign of impending central retinal artery occlusion: a case report
Authors: Louie Emily , Tang Anthony , King Benjamin 
Published: June 2023

Abstract
Background
To report a case of paracentral acute middle maculopathy (PAMM) that progressed to central retinal artery occlusion (CRAO) on spectral domain-optical coherence tomography (SD-OCT).

Case Presentation
A 63-year-old male presented with a paracentral scotoma that began several days ago. His past medical history consisted of third-degree atrioventricular heart block requiring a pacemaker. Giant cell arteritis was unlikely given the patient’s labs, demographics and review of systems. SD-OCT revealed a characteristic hyperreflective band in the inner nuclear layer consistent with PAMM in his left eye. Fluorescein angiography was obtained and was unremarkable. Five days later, the patient developed no light perception in the left eye. SD-OCT showed a diffuse inner retinal hyperreflectivity consistent with CRAO.

Conclusion
PAMM can be a harbinger event for complete CRAO. Complete stroke evaluation should be performed to prevent a cerebrovascular event or progression to complete blindness in the involved eye.
The role of parental health beliefs in seeking an eye examination for their child
Authors: Masarwa Dua , Niazov Yulia , Ben Natan Merav , Mostovoy Dina 
Published: June 2023

Abstract
Background
We aimed to explore the role of parental health beliefs in parent seeking of eye examinations for their children, using the Health Belief Model.

Methods
In this quantitative correlational survey study, 100 parents who presented to Barzilai University Medical Center in July 2021 to perform an eye examination to their child completed a questionnaire.

Results
Only 29.6% of the parents knew that a vision screening is performed in first grade, and 10% of the parents were unsure about where to find local eye care for their kids. Moreover, 19% of the parents indicated that they were concerned that their child would be prescribed glasses unnecessarily, and 10% believed that wearing glasses would weaken their child’s eyes. Various parental health beliefs regarding children’s eye examinations were found associated with parent seeking of eye examinations for their child. Thus, perceived susceptibility (r = 0.52, p < 0.01), perceived benefits (r = 0.39, p < 0.01), and perceived barriers (r=-0.31, p < 0.01) are associated with parent seeking of eye examinations for their child. Also, parents’ level of knowledge was associated with seeking eye examinations for their child (r = 0.20, p < 0.01).

Conclusion
Parent perceptions of the child’s susceptibility to vision problems and perceived barriers to seeking eye examinations predicted parents seeking of eye examinations for their child. Interventions aimed at increasing timely eye examinations among children should focus on raising parent awareness of vision problems in childhood, dispelling misconceptions, and providing parents with practical information regarding available services.
Collagen cross-linking as monotherapy in experimentally induced corneal abscess in rabbits
Authors: Saad Zeinab A. , Elnashar Hazem , Negm Sahar , Elsayed Hala A. , Abdallah Mohamed Gaber , Abuamara Tamer M. M. , Abd-Elhay Wagih M. , Elghonemy Hanan M. 
Published: June 2023

Abstract
Background and purpose
Collagen cross-linking (CXL) has evolved as an essential therapeutic approach for corneal infections, allowing for rapidly eliminating the infecting microorganism while reducing inflammation. This study aims to evaluate the efficacy of CXL as a monotherapy for managing infectious keratitis caused by Fusarium solani and Pseudomonas aeruginosa.

Materials and methods
Forty-eight white New Zealand rabbits weighing approximately 1.5–2 KG were included. The cornea of one eye of each rabbit was inoculated with either Fusarium solani or Pseudomonas aeruginosa. Group A served as a control and was subdivided into two subgroups, A1 and A2; each subgroup consisted of 8 eyes and was injected with either Fusarium solani or Pseudomonas aeruginosa, respectively. Group B (16 eyes) was inoculated with Fusarium solani, while group C (16 eyes) were inoculated with Pseudomonas aeruginosa. All animals in Group B and C received CXL treatment one week after inoculation of the organisms and after corneal abscess formation was confirmed. At the same time, animals in Group A were left untreated.

Results
There was a statistically significant reduction in the number of colony-forming units (CFU) in Group B following CXL. No growth existed in any samples at the end of the 4th week. There was a statistically significant difference in the number of CFU between group B and the control group (p < 0.001). In group C, there was a statistically significant reduction in the CFU at the end of the first week after CXL. However, there was regrowth in all samples afterward. All 16 models in Group C showed uncountable and extensive growth during the subsequent follow-ups. There was no statistically significant difference between the number of CFU in Group C and the control group. Histopathology showed lesser corneal melting in CXL-treated Pseudomonas aeruginosa.

Conclusions
Collagen cross-linking is promising monotherapy and alternative treatment in managing infective keratitis caused by Fusarium solani but is less effective in Pseudomonas aeruginosa as monotherapy.
The quality of mental health care for people with bipolar disorders in the Italian mental health system: the QUADIM project
Authors: D’Avanzo Barbara , Barbato Angelo , Monzio Compagnoni Matteo , Caggiu Giulia , Allevi Liliana , Carle Flavia , Di Fiandra Teresa , Ferrara Lucia , Gaddini Andrea , Sanza Michele , Saponaro Alessio , Scondotto Salvatore , Tozzi Valeria D , Giordani Cristina , Corrao Giovanni , Lora Antonio 
Published: June 2023

Abstract
Background
The assessment of the quality of care pathways delivered to people with severe mental disorders in a community-based system remains uncommon, especially using healthcare utilization databases. The aim of the study was to evaluate the quality of care provided to people with bipolar disorders taken-in-care by mental health services of four Italian areas (Lombardy, Emilia-Romagna, Lazio, province of Palermo).

Methods
Thirty-six quality indicators were implemented to assess quality of mental health care for patients with bipolar disorders, according to three dimensions (accessibility and appropriateness, continuity, and safety). Data were retrieved from healthcare utilization (HCU) databases, which contain data on mental health treatments, hospital admissions, outpatient interventions, laboratory tests and drug prescriptions.

Results
29,242 prevalent and 752 incident cases taken-in-care by regional mental health services with a diagnosis of bipolar disorder in 2015 were identified. Age-standardized treated prevalence rate was 16.2 (per 10,000 adult residents) and treated incidence rate 1.3. In the year of evaluation, 97% of prevalent cases had ≥ 1 outpatient/day-care contacts and 88% had ≥ 1 psychiatric visits. The median of outpatient/day-care contacts was 9.3 interventions per-year. Psychoeducation was provided to 3.5% of patients and psychotherapy to 11.5%, with low intensity. 63% prevalent cases were treated with antipsychotics, 71.5% with mood stabilizers, 46.6% with antidepressants. Appropriate laboratory tests were conducted in less than one-third of prevalent patients with a prescription of antipsychotics; three quarters of those with a prescription of lithium. Lower proportions were observed for incident patients. In prevalent patients, the Standardized Mortality Ratio was 1.35 (95% CI: 1.26–1.44): 1.18 (1.07–1.29) in females, 1.60 (1.45–1.77) in males. Heterogeneity across areas was considerable in both cohorts.

Conclusions
We found a meaningful treatment gap in bipolar disorders in Italian mental health services, suggesting that the fact they are entirely community-based does not assure sufficient coverage by itself. Continuity of contacts was sufficient, but intensity of care was low, suggesting the risk of suboptimal treatment and low effectiveness. Care pathways were monitored and evaluated using administrative healthcare databases, adding evidence that such data may contribute to assess the quality of clinical pathways in mental health.