bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model
Authors: Liu Jiaqi , Wang Jiayin , Xiao Xiao , Lai Xin , Dai Daocheng , Zhang Xuanping , Zhu Xiaoyan , Zhao Zhongmeng , Wang Juan , Li Zhimin 
Published: November 2020

Abstract
Background
The emergence of the third generation sequencing technology, featuring longer read lengths, has demonstrated great advancement compared to the next generation sequencing technology and greatly promoted the biological research. However, the third generation sequencing data has a high level of the sequencing error rates, which inevitably affects the downstream analysis. Although the issue of sequencing error has been improving these years, large amounts of data were produced at high sequencing errors, and huge waste will be caused if they are discarded. Thus, the error correction for the third generation sequencing data is especially important. The existing error correction methods have poor performances at heterozygous sites, which are ubiquitous in diploid and polyploidy organisms. Therefore, it is a lack of error correction algorithms for the heterozygous loci, especially at low coverages.

Results
In this article, we propose a error correction method, named QIHC. QIHC is a hybrid correction method, which needs both the next generation and third generation sequencing data. QIHC greatly enhances the sensitivity of identifying the heterozygous sites from sequencing errors, which leads to a high accuracy on error correction. To achieve this, QIHC established a set of probabilistic models based on Bayesian classifier, to estimate the heterozygosity of a site and makes a judgment by calculating the posterior probabilities. The proposed method is consisted of three modules, which respectively generates a pseudo reference sequence, obtains the read alignments, estimates the heterozygosity the sites and corrects the read harboring them. The last module is the core module of QIHC, which is designed to fit for the calculations of multiple cases at a heterozygous site. The other two modules enable the reads mapping to the pseudo reference sequence which somehow overcomes the inefficiency of multiple mappings that adopt by the existing error correction methods.

Conclusions
To verify the performance of our method, we selected Canu and Jabba to compare with QIHC in several aspects. As a hybrid correction method, we first conducted a groups of experiments under different coverages of the next-generation sequencing data. QIHC is far ahead of Jabba on accuracy. Meanwhile, we varied the coverages of the third generation sequencing data and compared performances again among Canu, Jabba and QIHC. QIHC outperforms the other two methods on accuracy of both correcting the sequencing errors and identifying the heterozygous sites, especially at low coverage. We carried out a comparison analysis between Canu and QIHC on the different error rates of the third generation sequencing data. QIHC still performs better. Therefore, QIHC is superior to the existing error correction methods when heterozygous sites exist.
The role of CXCR3 and its ligands expression in Brucellar spondylitis
Authors: Hu Xin , Shang Xiaoqian , Wang Liang , Fan Jiahui , Wang Yue , Lv Jie , Nazierhan Shaxika , Wang Hao , Wang Jing , Ma Xiumin 
Published: November 2020

Abstract
Aim
Brucellar spondylitis (BS) is one of the most serious complications of brucellosis. CXCR3 is closely related to the severity of disease infection. This research aimed to study the degree of BS inflammatory damage through analyzing the expression levels of CXCR3 and its ligands (CXCL9 and CXCL10) in patients with BS.

Methods
A total of 29 BS patients and 15 healthy controls were enrolled. Real-Time PCR was used to detect the mRNA expression levels of IFN-γ, CXCR3, CXCL9 and CXCL10 in peripheral blood mononuclear cells (PBMCs) of BS patients and healthy controls. Hematoxylin-Eosin staining was used to show the pathological changes in BS lesion tissues. Immunohistochemistry staining was used to show the protein expression levels of Brucella-Ab, IFN-γ, CXCR3, CXCL9 and CXCL10 in BS lesion tissues. At the same time, ELISA was used to detect the serum levels of IFN-γ, CXCL9 CXCL10 and autoantibodies against CXCR3 in patients with BS.

Results
In lesion tissue of BS patients, it showed necrosis of cartilage, acute or chronic inflammatory infiltration. Brucella-Ab protein was abundantly expressed in close lesion tissue. And the protein expression levels of IFN-γ, CXCR3 and CXCL10 were highly expressed in close lesion tissue and serum of BS patients. At the same time, the mRNA expression levels of IFN-γ, CXCR3 and CXCL10 in PBMCs of BS patients were significantly higher than those in controls.

Conclusion
In our research, the expression levels of IFN-γ, CXCR3 and its ligands were significantly higher than those in controls. It suggested that high expression levels of IFN-γ, CXCR3 and its ligands indicated a serious inflammatory damage in patients with BS.
Effect of magnesium supplementation on emergence delirium and postoperative pain in children undergoing strabismus surgery: a prospective randomised controlled study
Authors: Lee Ji-Hyun , Choi Seungeun , Lee Minkyoo , Jang Young-Eun , Kim Eun-Hee , Kim Jin-Tae , Kim Hee-Soo 
Published: November 2020

AbstractBackgroundThe benefits of intraoperative magnesium supplementation have been reported. In this prospective, randomized study, the effects of magnesium supplementation during general anaesthesia on emergence delirium and postoperative pain in children were evaluated.MethodsA total of 66 children aged 2 to 5 years who underwent strabismus surgery were assigned to the magnesium or to the control group. Preoperative anxiety was assessed using the modified Yale Preoperative Anxiety Scale. After anaesthesia induction, the magnesium group received an initial loading dose of 30 mg/kg magnesium sulphate over 10 min and, then, continuous infusion of 10 mg/kg per h until 10 min before the end of the surgery. The control group received an equal volume of normal saline via the same regimen. The Paediatric Anaesthesia Emergence Delirium (PAED) score, pain score, and respiratory events were assessed at the postanaesthetic care unit.ResultsData obtained from 65 children were analyzed. The PAED and pain scores of the two groups did not differ significantly. There were 26 of 33 (78.8%) and 27 of 32 (84.4%) children with emergence delirium in the control and the magnesium groups, respectively (odds ratio 0.69, 95% CI 0.19–2.44;p = 0.561). The preoperative anxiety score was not significantly correlated with the PAED score. The incidence of respiratory events during the emergence period did not differ significantly between the two groups.ConclusionsMagnesium supplementation during anaesthesia had no significant effects on the incidence of emergence delirium or postoperative pain in children undergoing strabismus surgery.Trial registrationClinicalTrials.gov (NCT03132701). Prospectively registered May 8, 2017.
Addition of routine blood biomarkers to TIMI risk score improves predictive performance of 1-year mortality in patients with ST-segment elevation myocardial infarction
Authors: Oh Pyung Chun , Eom Young Sil , Moon Jeonggeun , Jang Ho-Jun , Kim Tae-Hoon , Suh Jon , Kong Min Gyu , Park Sang-Don , Kwon Sung Woo , Suh Soon Yong , Lee Kyounghoon , Han Seung Hwan , Ahn Taehoon , Kang Woong Chol 
Published: November 2020

Abstract
Background
Several biomarkers have been proposed as independent predictors of poor outcomes in ST-segment elevation myocardial infarction (STEMI). We investigated whether adding information obtained from routine blood tests including hypoxic liver injury (HLI), dysglycemia, anemia, and high neutrophil to lymphocyte ratio (NLR) could improve the prognostic performance of the TIMI risk score for the prediction of 1-year mortality.

Methods
A total of 1057 patients with STEMI undergoing primary percutaneous coronary intervention (PCI) between 2007 and 2014 were retrospectively enrolled from 4-regional hospitals. HLI and dysglycemia were defined as serum transaminase > twice the normal upper limit and glucose < 90 or > 250 mg/dL, respectively. The effect of adding biomarkers to the TIMI risk score on its discriminative ability was assessed using c-statistic, net reclassification improvement (NRI), and integrated discrimination improvement (IDI).

Results
The 1-year mortality rate was 7.1%. The best cutoff value of NLR for the prediction of 1-year mortality was 4.3 (sensitivity, 67%; specificity, 65%). HLI (HR 2.019; 95% CI 1.104–3.695), dysglycemia (HR 2.535; 95% CI 1.324–3.923), anemia (HR 2.071; 95% CI 1.093–3.923), and high NLR (HR 3.651; 95% CI 1.927–6.918) were independent predictors of 1-year mortality. When these 4 parameters were added to the TIMI risk score, the c-statistic significantly improved from 0.841 to 0.876 (p < 0.001), and the NRI and IDI were estimated at 0.203 (95% CI 0.130–0.275; p < 0.001) and 0.089 (95% CI 0.060–0.119; p < 0.001), respectively.

Conclusions
The addition of HLI, dysglycemia, anemia, and high NLR to the TIMI risk score may be useful for very early risk stratification in patients with STEMI receiving primary PCI.
Validation of age-specific survival prediction in pediatric patients with blunt trauma using trauma and injury severity score methodology: a ten-year Nationwide observational study
Authors: Toida Chiaki , Muguruma Takashi , Gakumazawa Masayasu , Shinohara Mafumi , Abe Takeru , Takeuchi Ichiro , Morimura Naoto 
Published: November 2020

Abstract
Background
In-hospital mortality in trauma patients has decreased recently owing to improved trauma injury prevention systems. However, no study has evaluated the validity of the Trauma and Injury Severity Score (TRISS) in pediatric patients by a detailed classification of patients’ age and injury severity in Japan. This retrospective nationwide study evaluated the validity of TRISS in predicting survival in Japanese pediatric patients with blunt trauma by age and injury severity.

Methods
Data were obtained from the Japan Trauma Data Bank during 2009–2018. The outcomes were as follows: (1) patients’ characteristics and mortality by age groups (neonates/infants aged 0 years, preschool children aged 1–5 years, schoolchildren aged 6–11 years, and adolescents aged 12–18 years), (2) validity of survival probability (Ps) assessed using the TRISS methodology by the four age groups and six Ps-interval groups (0.00–0.25, 0.26–0.50, 0.51–0.75, 0.76–0.90, 0.91–0.95, and 0.96–1.00), and (3) the observed/expected survivor ratio by age- and Ps-interval groups. The validity of TRISS was evaluated by the predictive ability of the TRISS method using the receiver operating characteristic (ROC) curves that present the sensitivity, specificity, positive predictive value, negative predictive value, accuracy, area under the receiver operator characteristic curve (AUC) of TRISS.

Results
In all the age categories considered, the AUC for TRISS demonstrated high performance (0.935, 0.981, 0.979, and 0.977). The AUC for TRISS was 0.865, 0.585, 0.614, 0.585, 0.591, and 0.600 in Ps-interval groups (0.96–1.00), (0.91–0.95), (0.76. − 0.90), (0.51–0.75), (0.26–0.50), and (0.00–0.25), respectively. In all the age categories considered, the observed survivors among patients with Ps interval (0.00–0.25) were 1.5 times or more than the expected survivors calculated using the TRISS method.

Conclusions
The TRISS methodology appears to predict survival accurately in Japanese pediatric patients with blunt trauma; however, there were several problems in adopting the TRISS methodology for younger blunt trauma patients with higher injury severity. In the next step, it may be necessary to develop a simple, high-quality prediction model that is more suitable for pediatric trauma patients than the current TRISS model.
Are general practitioners referring patients with low back pain for CTs appropriately according to the guidelines: a retrospective review of 3609 medical records in Newfoundland using routinely collected data
Authors: Logan Gabrielle S. , Dawe Russell Eric , Aubrey-Bassler Kris , Coombs Danielle , Parfrey Patrick , Maher Chris , Etchegary Holly , Hall Amanda 
Published: November 2020

Abstract
Background
CT Imaging is often requested for patients with low back pain (LBP) by their general practitioners. It is currently unknown what reasons are common for these referrals and if CT images are ordered according to guidelines in one province in Canada, which has high rates of CT imaging. The objective of this study is to categorise lumbar spine CT referrals into serious spinal pathology, radicular syndrome, and non-specific LBP and evaluate the appropriateness of CT imaging referrals from general practitioners for patients with LBP.

Methods
A retrospective medical record review of electronic health records was performed in one health region in Newfoundland and Labrador, Canada. Inclusion criteria were lumbar spine CT referrals ordered by general practitioners for adults ≥18 years, and performed between January 1st-December 31st, 2016. Each CT referral was identified from linked databases (Meditech and PACS). To the study authors’ knowledge, guidelines regarding when to refer patients with low back pain for CT imaging had not been actively disseminated to general practitioners or implemented at clinics/hospitals during this time period. Data were manually extracted and categorised into three groups: red flag conditions (judged to be an appropriate referral), radicular syndrome (judged be unclear appropriateness), or nonspecific LBP (determined to be inappropriate).

Results
Three thousand six hundred nine lumbar spine CTs were included from 2016. The mean age of participants was 54.7 (SD 14 years), with females comprising 54.6% of referrals. 1.9% of lumbar CT referrals were missing/unclear, 6.5% of CTs were ordered on a red-flag suspicion, 75.6% for radicular syndromes, and 16.0% for non-specific LBP; only 6.5% of referrals were clearly appropriate. Key information including patient history and clinical exams performed at appointment were often missing from referrals.

Conclusion
This audit found high proportions of inappropriate or questionable referrals for lumbar spine CT and many were missing information needed to categorise. Further research to understand the drivers of inappropriate imaging and cost to the healthcare system would be beneficial.
Is preoperative anxiety associated with postoperative delirium in older persons undergoing cardiac surgery? Secondary data analysis of a randomized controlled trial
Authors: Milisen Koen , Van Grootven Bastiaan , Hermans Wim , Mouton Karen , Al Tmimi Layth , Rex Steffen , Detroyer Elke 
Published: November 2020

Abstract
Background
Although many studies have reported numerous risk factors for postoperative delirium, data are scarce about preoperative anxiety as a risk factor. The study aimed to investigate the association between preoperative anxiety and postoperative delirium in older patients undergoing cardiac surgery.

Methods
Secondary data analysis of a randomized, observer-blind, controlled trial. A total of 190 patients 65 years or older and admitted to the intensive care unit and cardiac surgery unit of a university hospital scheduled for elective on-pump cardiac surgery were included. State anxiety was measured preoperatively using the Amsterdam Preoperative Anxiety and Information Scale and the Visual Analogue Scale for anxiety. Incidence of delirium was measured during the first 5 postoperative days using the Confusion Assessment Method for Intensive Care Unit (when ventilated), or the 3 Minute Diagnostic Interview for Confusion Assessment Method (when extubated) and by daily chart review.

Results
Preoperative state anxiety was reported by 31% of the patients and 41% had postoperative delirium. A multiple step logistic regression analyses revealed no association between preoperative anxiety and postoperative delirium. Significant risk factors for postoperative delirium were age (OR = 1.10, 95% CI (1.03–1.18)), activities of daily living (0.69, 95% CI (0.50–0.96)), diabetes mellitus (OR = 3.15, 95% CI (1.42–7.00)) and time on cardiopulmonary bypass (OR = 1.01, 95% CI (1.00 to 1.02)).

Conclusions
No relationship could be found between preoperative anxiety and postoperative delirium.
Factors influencing the deterioration from cognitive decline of normal aging to dementia among nursing home residents
Authors: Hayajneh Audai A. , Rababa Mohammad , Alghwiri Alia A. , Masha’al Dina 
Published: November 2020

Abstract
Background
A dearth of differential research exists regarding the determinants of mild cognitive impairment (MCI) and moderate cognitive impairment or dementia among nursing home residents. This study aimed to identify and examine the association between medical factors (number of comorbidities, hospitalization, disability, depression, frailty and quality of life) and moderate cognitive impairment or dementia in nursing homes residents.

Methods
A cross-sectional design was used in this study. Convenience sampling of 182 participants was conducted in nursing homes located in the central part of Jordan. Montreal cognitive assessment (MoCA) was used to screen both MCI and moderate cognitive impairment or dementia. Bivariate analysis, including t-test and ANOVA test, and logistic and linear regression models were used to examine and identify the medical factors associated with moderate cognitive impairment or dementia compared to mild cognitive impairment.

Results
Most nursing home residents had MCI (87.4%) compared to a few with moderate cognitive impairment or dementia. Age (t = − 2.773), number of comorbidities (t = − 4.045), depression (t = − 4.809), frailty (t = − 4.038), and quality of life physical (t = 3.282) and mental component summaries (t = 2.469) were significantly different between the stages of cognitive impairment. Marital status (t = − 4.050, p <  0.001), higher-income (t = 3.755, p <  0.001), recent hospitalization (t = 2.622,p = 0.01), depression (t = − 2.737, p = 0.007), and frailty (t = 2.852, p = 0.005) were significantly associated with mental ability scores among nursing home residents.

Conclusion
The coexistence of comorbidities and depression among nursing home residents with MCI necessitates prompt management by healthcare providers to combat depressive symptoms in order to delay the dementia trajectory among at-risk residents.

Trail registration
ClinicalTrials.gov NCT04589637, October 15,2020, Retrospectively registered.
Changes in tear film osmolarity after 25G+ PPV
Authors: Němčanský J. , Kopecký A. , Mašek P. 
Published: November 2020

Abstract
Background
The aim of our study was to assess changes of tear film osmolarity after micro-incision 25G+ pars plana vitrectomy (PPV) in a prospective study.

Methods
The group consisted of 21 patients (17 women, 4 men) with an average age of 70,52 years [48; 85]. All patients underwent 25G + PPV surgery due to a disorder of the vitreomacular interface (macular hole or epimacular membrane). Only patients who did not use artificial tears before the surgery and who had not been diagnosed with dry eye syndrome at ours or another institution were included in the study. Except cataract surgery, all ocular surface diseases, intraocular diseases, trauma or surgery were exclusion criterias.
Tear film osmolarity was measured in both eyes in every patient before surgery, 10 days after surgery and 30 days after surgery. A paired test was used for statistical evaluation.

Results
No statistically significant change in osmolarity was found in the operated eyes (p > 0.05). No statistically significant changes in time (p > 0.05) were found when both eyes were compared. There were no postoperative complications or failure to observe the study protocol.

Conclusion
Micro-incision 25G + PPV does not affect the osmolarity of the tear film.
Prospective assessment of plate-haptic rotationally asymmetric multifocal toric intraocular lens with near addition of + 1.5 diopters
Authors: Oshika Tetsuro , Negishi Kazuno , Noda Toru , Arai Hiroyuki , Inamura Mikio , Inoue Yasushi , Miyoshi Teruyuki , Fujita Yoshifumi , Miyata Kazunori , Hasegawa Yumi 
Published: November 2020

Abstract
Background
To prospectively evaluate surgical results following implantation of rotationally asymmetric, plate-haptic, refractive segmented multifocal toric intraocular lenses (IOLs) with near addition of + 1.5 diopters (D) (Lentis Comfort LS-313 MF15T, Oculentis GmbH).

Methods
In 59 eyes of 41 patients, ocular examinations were conducted before and 1 day, 1 week, 1, 3, and 6 months after surgery. Uncorrected (UDVA) and corrected (CDVA) distance visual acuity, uncorrected (UIVA) and distance-corrected (DCIVA) intermediate visual acuity at 70 cm, and uncorrected (UNVA) and distance-corrected (DCNVA) near visual acuity at 30 cm were tested. A defocus curve was drawn, and the degree of disturbing photic phenomena were questioned.

Results
The IOL showed excellent rotational stability; the average absolute rotation was 1.66 ± 1.17 degrees from 1 day 1 to 6 months postoperatively, and 98.1 and 100% of eyes yielded rotation of less than 5 and 10 degrees, respectively. Postoperative distance and intermediate visual acuity were highly satisfactory; UDVA, CDVA, UIVA, and DCIVA were about 20/20, 20/16, 20/25, 20/25, respectively. Near visual acuity was suboptimal; UNVA and DCNVA were at approximately 20/60. The defocus curve analysis showed that 20/25 and 20/40 uncorrected visual acuity was attained at as close as 60 and 40 cm, respectively. Contrast sensitivity was within a normal range, and subjective photic phenomena were minimum.

Conclusions
The refractive segmented, rotationally asymmetric multifocal toric IOLs with + 1.5 D near addition showed superb rotational stability and highly satisfactory distance and intermediate vision. Contrast sensitivity was high and incidence of photic symptoms was very low.

Trial registration
This study was registered at JAPIC Clinical Trials Information, ID: JapicCTI-183,877, https://www.clinicaltrials.jp/cti-user/trial/Search.jsp (February 5, 2018).
Clinical characteristics of dry eye with ocular neuropathic pain features: comparison according to the types of sensitization based on the Ocular Pain Assessment Survey
Authors: Kim Jonghwa , Yoon Hyeon Jeong , You In Cheon , Ko Byung Yi , Yoon Kyung Chul 
Published: November 2020

Abstract
Background
To compare the clinical characteristics of dry eye patients with ocular neuropathic pain features according to the types of sensitization based on the Ocular Pain Assessment Survey (OPAS).

Methods
Cross-sectional study of 33 patients with dry eye and ocular neuropathic pain features. All patients had a comprehensive ophthalmic assessment including detailed history, the intensity and duration of ocular pain, the tear film, ocular surface, and Meibomian gland examination, and OPAS. Patients with < 50% improvement in pain intensity after proparacaine challenge test were assigned to the central-dominant sensitization group (central group) and those with ≥50% improvement were assigned to the peripheral-dominant sensitization group (peripheral group). All variables were compared between the two groups.

Results
No significant differences were observed in age, sex, underlying diseases, history of ocular surgery, duration of ocular pain, tear film, ocular surface and Meibomian gland parameters (all p > 0.05). Ocular pain and non-ocular pain severity and the percentage of time spent thinking about non-ocular pain were significantly higher in the central group than in the peripheral group (all p < 0.05). Central group complained more commonly of a burning sensation than did the peripheral group (p = 0.01).

Conclusions
Patients with central-dominant sensitization may experience more intense ocular and non-ocular pain than the others and burning sensation may be a key symptom in those patients.