bluuebunny/crossref_metadata_2025_split huggingface dataset:
LncExpDB: an expression database of human long non-coding RNAs
Authors: Li Zhao , Liu Lin , Jiang Shuai , Li Qianpeng , Feng Changrui , Du Qiang , Zou Dong , Xiao Jingfa , Zhang Zhang , Ma Lina 
Published: September 2020

AbstractExpression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.
Covering all your bases: incorporating intron signal from RNA-seq data
Authors: Lee Stuart , Zhang Albert Y , Su Shian , Ng Ashley P , Holik Aliaksei Z , Asselin-Labat Marie-Liesse , Ritchie Matthew E , Law Charity W 
Published: September 2020

AbstractRNA-seq datasets can contain millions of intron reads per library that are typically removed from downstream analysis. Only reads overlapping annotated exons are considered to be informative since mature mRNA is assumed to be the major component sequenced, especially for poly(A) RNA libraries. In this study, we show that intron reads are informative, and through exploratory data analysis of read coverage that intron signal is representative of both pre-mRNAs and intron retention. We demonstrate how intron reads can be utilized in differential expression analysis using our index method where a unique set of differentially expressed genes can be detected using intron counts. In exploring read coverage, we also developed the superintronic software that quickly and robustly calculates user-defined summary statistics for exonic and intronic regions. Across multiple datasets, superintronic enabled us to identify several genes with distinctly retained introns that had similar coverage levels to that of neighbouring exons. The work and ideas presented in this paper is the first of its kind to consider multiple biological sources for intron reads through exploratory data analysis, minimizing bias in discovery and interpretation of results. Our findings open up possibilities for further methods development for intron reads and RNA-seq data in general.
Pathological changes in the lungs and lymphatic organs of 12 COVID-19 autopsy cases
Authors: Liu Qian , Shi Yu , Cai Jun , Duan Yaqi , Wang Rongshuai , Zhang Hongyan , Ruan Qiurong , Li Jiansha , Zhao Lei , Ping Yifang , Chen Rong , Ren Liang , Fei Xiaochun , Zhang Heng , Tang Rui , Wang Xi , Luo Tao , Liu Xindong , Huang Xuequan , Liu Zhenhua , Ao Qilin , Ren Yong , Xiong Jing , He Zhicheng , Wu Haibo , Fu Wenjuan , Zhao Pengnan , Chen Xinwei , Qu Guoqiang , Wang Yunyun , Wang Xi , Liu Jia , Xiang Dongfang , Xu Sanpeng , Zhou Xiaowei , Li Qingrui , Ma Jinghong , Li Heng , Zhang Jie , Huang Sizhe , Yao Xiaohong , Zhou Yiwu , Wang Chaofu , Zhang Dingyu , Wang Guoping , Liu Liang , Bian Xiu-Wu 
Published: September 2020

Abstract
Systematic autopsy and comprehensive pathological analyses of COVID-19 decedents should provide insights into the disease characteristics and facilitate the development of novel therapeutics. In this study, we report the autopsy findings from the lungs and lymphatic organs of 12 COVID-19 decedents—findings that evaluated histopathological changes, immune cell signature and inflammatory factor expression in the lungs, spleen and lymph nodes. Here we show that the major pulmonary alterations included diffuse alveolar damage, interstitial fibrosis and exudative inflammation featured with extensive serous and fibrin exudates, macrophage infiltration and abundant production of inflammatory factors (IL-6, IP-10, TNFα and IL-1β). The spleen and hilar lymph nodes contained lesions with tissue structure disruption and immune cell dysregulation, including lymphopenia and macrophage accumulation. These findings provide pathological evidence that links injuries of the lungs and lymphatic organs with the fatal systematic respiratory and immune malfunction in critically ill COVID-19 patients.
Metaplastic carcinoma of breast: a report of two cases
Authors: Yahaya James , Mremi Alex 
Published: September 2020

ABSTRACT
The pathogenesis of metaplastic breast carcinoma (MBC) is still debatable and it has been hypothesized that MBC develops as a result of transformation of epithelial cells into mesenchymal cells along with formation of a favorable tumor microenvironment. This favorable tumor microenvironment helps the transformed cells to undergo further mutations and clonal expansion. Case 1 was a 42-year old female with a 1-year history of a right breast fungating mass which was histologically confirmed to be matrix-producing type of MBC. Case 2 was a 47-year old female who presented with a recurrent left breast mass. Histologically, the tumor was confirmed to be carcinosarcomatous type of MBC. MBC is a rare, heterogeneous tumor with poor prognosis due to its aggressive behavior. It is more likely to mimic other benign breast conditions, therefore contributing to delay of diagnosis as it was for both of our patients herein presented.
Familial spontaneous pneumothorax and Machado–Joseph disease
Authors: Pelayo Jerald , Rau Naraharisetty , Lo Kevin Bryan , Azmaiparashvili Zurab 
Published: September 2020

ABSTRACT
We report the first known case of a 42-year-old man diagnosed with spinocerebellar ataxia type 3, also known as Machado–Joseph disease (MJD), who presented with recurrent spontaneous pneumothorax. Six other family members affected with MJD died of the same pulmonary complication. To date, there has been no direct genetic linkage between MJD and familial spontaneous pneumothorax. However, the mutated ataxin-3 (ATXN3) gene in MJD and Serpin Family A Member 1 (SERPINA1) gene in hereditary emphysema share the same loci on chromosome 14q32.1, which is suggestive of genetic proclivity of patients with MJD to develop familial pneumothorax. Furthermore, the abnormal ataxin protein encoded by ATXN3 and the patient’s smoking history could have potentiated the dysregulation of the ubiquitin-proteasome system further aggravating his genetic predisposition to develop recurrent pneumothorax. These unexplored areas of inquiry invoke further molecular characterization to give an accent to medical knowledge as well as guide novel therapies in the future.
Internality, transfer, and infinitesimal modeling of infinite processes†
Authors: Bottazzi Emanuele , Katz Mikhail G 
Published: September 2020

ABSTRACTA probability model is underdetermined when there is no rational reason to assign a particular infinitesimal value as the probability of single events. Pruss claims that hyperreal probabilities are underdetermined. The claim is based upon external hyperreal-valued measures. We show that internal hyperfinite measures are not underdetermined. The importance of internality stems from the fact that Robinson’s transfer principle only applies to internal entities. We also evaluate the claim that transferless ordered fields (surreals, Levi-Civita field, Laurent series) may have advantages over hyperreals in probabilistic modeling. We show that probabilities developed over such fields are less expressive than hyperreal probabilities.
Familial associations for rheumatoid autoimmune diseases
Authors: Thomsen Hauke , Li Xinjun , Sundquist Kristina , Sundquist Jan , Försti Asta , Hemminki Kari 
Published: September 2020

AbstractObjectivePrevious studies have shown a familial component in RA and in some other rheumatic autoimmune diseases (RAIDs), but because of the different study designs the risk estimates for familial risks differ extensively. The objective of this study is to identify familial components for RAIDs.MethodsWe collected data on patients diagnosed in Swedish hospitals with RA, AS, PM/DM, SS, SLE and SSc (and scleroderma) and calculated familial standardized incidence ratios (SIRs) for each of these (concordant) and between them (discordant).ResultsThe combined number of RAID patients in the offspring population (for whom SIRs were calculated) was 71 544, and in the whole population the number was 152 714, accounting for 19.8% of all autoimmune diseases in Sweden. AS showed the highest concordant familial risk of 18.42, followed by SLE (14.04), SS (8.63), SSc (4.50), PM/DM (4.03) and RA (3.03). There was no sex difference in SIRs. Risks for AS and SLE were 80.28 and 19.53 for persons whose parents and siblings were affected. Discordant risks were far lower than concordant risks, but they were significant for RA with all the other five RAIDs, for SLE and SSc with four RAIDs, for AS and SS with three RAIDs and for PM/DM with two RAIDs, attesting to extensive polyautoimmunity between RAIDs.ConclusionThe derived familial risks in this nationwide family study on medically diagnosed RAID are compatible with emerging evidence on the polygenic background of these complex diseases. Novel genetic pathways offer new therapeutic targets that alleviate disease onset optimally in high-risk familial patients and others.
CALCULATION OF DOSE CONVERSION FACTORS BASED ON THE RESULTS OF GEOMETRIC MIXTURE MODELS FOR RISK ASSESSMENT OF RADON EXPOSURE
Authors: Zhukovsky Michael , Onishchenko Aleksandra 
Published: September 2020

Abstract
The results of the geometric mixture model by Tomasek (2011, 2013) were applied for the calculation of radiation risk at radon exposure at the assessment of dose conversion factors (DCF; mSv/WLM) from radon exposure to the effective dose-by-dose conversion convention approach for cohorts with different smoking status. It is shown that the use of a geometric mixture model results in a better agreement between DCF values for men and women.
Impact of Preoperative Opioid Use on Postoperative Patient-reported Outcomes in Lumbar Spine Surgery Patients
Authors: Weiner Joseph A. , Snavely Joseph E. , Johnson Daniel J. , Hsu Wellington K. , Patel Alpesh A. 
Published: September 2020

Study Design:
This was a retrospective cohort study.

Objective:
Investigate the impact of preoperative opioid use on postoperative Patient-Reported Outcomes Measurement Information System (PROMIS) physical function (PF) and pain interference (PI) scores in patients undergoing elective spine surgery.

Background Data:
The PROMIS has demonstrated reliability and validity in conditions such as lumbar stenosis, disc herniation, and cervical spondylosis. Although previous studies have identified the negative impact of preoperative opioid use on legacy patient-reported outcome measures following lumbar spine surgery, no study to date has utilized PROMIS computer adaptive tests.

Methods:
Consecutive patients who underwent lumbar spine surgery at a single institution between 2014 and 2016 completed PROMIS PF and PI scores at baseline preoperatively and at 3, 12, and 24 months postoperatively. Preoperative opioid use was defined as >1 month before surgery. Univariate and linear mixed model multivariate analysis was performed to evaluate for correlation of preoperative opioid use, as well as patient risk factors, with postoperative PROMIS PI and PF scores at each time point.

Results:
Ninety-one patients met inclusion criteria with PROMIS scores at every time point. A total of 36 (39.6%) patients self-reported taking opioids at the time of surgery. Mean duration of opioid use among opioid users was 6.5±7.4 months. Patients taking preoperative opioids had significantly less improvement at all time points out to 24 months. At 24 months, patients in the nonopioid group had mean PI improvement of −13.0±14.2 versus −4.9±15.4 in the opioid group (P=0.014). The mean postoperative improvement in the opioid group did not achieve minimally clinically important difference (MCID) of 8 at any time point.

Conclusions:
Patients who do not use opioids preoperatively show significant postsurgical improvement in PI scores compared with patients who use preoperative opioids. Mean improvement in PROMIS PI scores failed to meet an MCID of 8 in opioid users, whereas mean improvement exceeded this MCID in opioid naive patients. The results of this study help elucidate the deleterious impact of opioids, allowing surgeons to better set patient expectations.

Level of Evidence:
Level III.
Comparison of Hasner valvulotomy outcomes in pediatric and adult patients: does age matter?
Authors: Sun Hua , Ding Jing-Wen , Li Dong-Mei , Wang Ning-Li 
Published: September 2020

Abstract

Background
Hasner valve incision has been recently introduced as a new treatment for ophthalmic patients with epiphora symptoms. The aim of this study was to examine whether surgical outcomes of Hasner valve incision for inferior nasolacrimal duct obstruction were different between pediatric and adult patients.

Methods
A total of 53 eyes of 52 patients who underwent Hasner valve incision in the Beijing Tongren Hospital from October 2016 to November 2019 were retrospectively observed. Patients were divided into two groups, including pediatric group (23 eyes of 22 patients, <18 years old) and adult group (30 eyes of 30 patients, ≥18 years old). Success rate of surgery was determined by both subjective measure (complete resolution of epiphora) and objective measure (lacrimal passage irrigation and tear meniscus height). Fisher exact test was conducted.

Results
By conducting Fisher exact test and comparing complete resolution of epiphora (P = 0.627), lacrimal passage irrigation (P = 0.663), measurement of Tear Meniscus Height (P = 0.561), and appearance of complication (P = 0.339), there was no statistically significant difference of surgical outcomes between pediatric and adult patients (P > 0.05).

Conclusion
Hasner valve incision was effective for both adult and children with inferior nasolacrimal duct obstruction, with no difference in surgical outcomes between the two groups.
Impact of Therapeutic Drug Monitoring on Once-Daily Regimen of Amikacin in Patients With Urinary Tract Infection: A Prospective Observational Study
Authors: Jayakumar Ilanthamizhan , Mathaiyan Jayanthi , Mandal Jharna , Deepanjali Surendran , Sreenivasan Sreerag K. 
Published: September 2020

Background:
Amikacin is a semisynthetic antibiotic used in the treatment of gram-negative bacterial infections and has a narrow therapeutic index. Although therapeutic drug monitoring is recommended for amikacin, it is not routinely performed because of the use of a less toxic once-daily regimen. Only few studies have evaluated the role of therapeutic drug monitoring in patients treated with amikacin. The objective of our study was to find an association between the pharmacokinetic parameters of amikacin and the time required for a clinical cure, creatinine clearance, and frequency of ototoxicity in patients with urinary tract infection treated for 7 or more days.

Methods:
A prospective study was conducted on patients with urinary tract infections who were administered amikacin for 7 or more days. Blood samples were obtained from the patients to measure the maximum drug concentration (Cmax) and trough concentration (Ctrough). Minimum inhibitory concentration (MIC) values were determined for patients with positive urine cultures. Serum creatinine levels were estimated every 3 days. The auditory assessment was performed using pure tone audiometry at baseline and weekly until the patients were discharged. Levels of amikacin were analyzed using a validated liquid chromatography-tandem mass spectrometry method.

Results:
Of 125 patients analyzed, the median time required for a clinical cure was less in the group of patients who achieved a Cmax/MIC ratio ≥8 than it was in those who did not achieve this level [7 versus 8 days (P = 0.02)]. The Ctrough of amikacin was associated with the change in serum creatinine level (P = 0.01) and the incidence of nephrotoxicity (P = 0.004).

Conclusions:
In patients receiving short-term amikacin therapy, Cmax/MIC value can be used to predict the time required for a clinical cure. Ctrough can be used to predict the occurrence of nephrotoxicity in patients receiving amikacin therapy.
Comparison of the Long-term Impact and Clinical Outcomes of Fewer Doses and Standard Doses of Human Papillomavirus Vaccine in the United States: A Database Study
Authors: Rodriguez Ana M. , Zeybek Burak , Vaughn Micah , Westra Jordan , Kaul Sapna , Montealegre Jane R. , Lin Yu-Li , Kuo Yong-Fang 
Published: September 2020

(Abstracted from Cancer 2020;126:1656–1667)
Human papillomavirus (HPV) is the most common sexually transmitted disease in the United States, and persistent infection with 1 of the 12 high-risk genotypes has been causally linked with development of cervical cancer. Several vaccines targeting high-risk genotypes have been developed and implemented.
Hepatitis B Virus Infection in Pregnancy: An Update on Evidence-Based Management
Authors: Sirilert Sirinart , Tongsong Theera 
Published: September 2020

Importance
Vertical hepatitis B virus (HBV) transmission is the important route of chronic HBV infection. Although infant immunoprophylaxis is effective, a significant number of infants still become infected, most are associated with intrauterine infection. New evidences support intrauterine treatment in cases of high risk.

Objective
The aim of this study was to review the current evidences and recommendations for management of HBV infection in pregnancy.

Evidence Acquisition
Original research articles, review articles, and guidelines were reviewed.

Results
The management can be summarized as follows: (1) all pregnant women should be screened for hepatitis B surface antigen (HBsAg) and antibody to HBsAg. High-risk HBsAg-negative pregnant women without immunity should be vaccinated during pregnancy. (2) HBsAg-positive pregnant women should undergo further workup for liver status and indicative factors for immunoprophylaxis failure. (3) Pregnant women should be treated with HBV DNA levels greater than 200,000 IU/mL or 6 log copies/mL. (4) Antiviral drug should be started around 28 to 32 weeks. The first-line drug is tenofovir disoproxil fumarate. (5) Delivery route should be chosen based only on obstetric indications. (6) Breastfeeding is not contraindicated because it does not increase the risk of transmission in neonates with HBV vaccine and immunoglobulin administration. (7) Neonates born to HBsAg-positive mothers should receive HBV vaccine and immunoglobulin after birth as soon as possible. (8) Follow-up of the mothers and neonates is important. Beware of hepatitis flare after birth and after antiretroviral drug discontinuation; alanine transaminase assessment every 1 to 3 months until 6 months is suggested. Also, the schedule of infant vaccination and follow-up of serologic testing at 9 to 12 months old is needed.

Target Audience
Obstetricians and gynecologists, family physicians

Learning Objectives
After the completion of this review, the learners should be better able to summarize updated knowledge of infant immunoprophylaxis failure; outline how to manage pregnancy with HBV infection, both antepartum and postpartum period; and describe advantages and disadvantages of the commonly used antiviral drugs.
Are Simulation Learning Objectives Educationally Sound? A Single-Center Cross-Sectional Study
Authors: Hui Madeleine , Mansoor Muqtasid , Sibbald Matthew 
Published: September 2020

Introduction
Accreditation standards of simulation stress the importance of educationally sound learning objectives. We aimed to assess whether learning objectives adhered to theoretical frameworks outlined by accreditation standards, lending themselves to maximal learning outcomes.

Methods
A retrospective study was conducted at the Centre for Simulation-Based Learning at McMaster University. Raters coded 848 faculty-designed learning objectives from 722 sessions based on Bloom's Taxonomy, SMART (Specific, Measurable, Attainable, Realistic, and Timely) criteria, and the presence of inappropriate verbs. Learning objective categorization was compared with student evaluations.

Results
Using Bloom's Taxonomy, learning objectives were mostly focused on application 53%, followed by smaller percentages focused on knowledge 21.4% and comprehension 12.2%. Few learning objectives focused on higher levels of analysis 7.2%, synthesis 2.3%, and evaluation 3.7%. By SMART criteria, learning objectives were 49.6% specific, 60.8% measurable, 88.8% attainable, 85.0% realistic, and 9.1% timely. Approximately 1 in 5 objectives used inappropriate verbs. No correlations were observed between categorization by Bloom's Taxonomy or inappropriate verbs to student ratings. However, those containing attainable and timely goals were associated with lower levels of perceived achievement by students.

Conclusions
There was a disconnect between simulation accreditation standards and current practices at McMaster University's simulation center. Most objectives were classified at lower stages of Bloom's Taxonomy. The majority followed SMART guidelines, with the exception of specificity and mention of time frames. A minority of learning objectives contained inappropriate verbs. Given the costs associated with simulation-based education, educators should focus simulation learning objectives on higher levels of Bloom's Taxonomy and include references to time frames.