bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting the purebred-crossbred genetic correlation from the genetic variance components in the parental lines
Authors: Duenk Pascal , Bijma Piter , Wientjes Yvonne C. J. , Calus Mario P. L. 
Published: February 2021

AbstractBackgroundThe genetic correlation between purebred and crossbred performance ($${r}_{pc}$$rpc) is an important parameter in pig and poultry breeding, because response to selection in crossbred performance depends on the value of$${r}_{pc}$$rpcwhen selection is based on purebred (PB) performance. The value of$${r}_{pc}$$rpccan be substantially lower than 1, which is partly due to differences in allele frequencies between parental lines when non-additive genetic effects are present. This relationship between$${r}_{pc}$$rpcand parental allele frequencies suggests that$${r}_{pc}$$rpccan be expressed as a function of genetic parameters for the trait in the parental lines. In this study, we derived expressions for$${r}_{pc}$$rpcbased on genetic variances within, and the genetic covariance between parental lines. It is important to note that the variance components used in our expressions are not the components that are typically estimated in empirical data. The expressions were derived for a genetic model with additive and dominance effects (D), and additive and epistatic additive-by-additive effects (EAA). We validated our expressions using simulations of purebred parental lines and their crosses, where the parental lines were either selected or not. Finally, using these simulations, we investigated the value of$${r}_{pc}$$rpcfor genetic models with both dominance and epistasis or with other types of epistasis, for which expressions could not be derived.ResultsOur simulations show that when non-additive effects are present,$${r}_{pc}$$rpcdecreases with increasing differences in allele frequencies between the parental lines. Genetic models that involve dominance result in lower values of$${r}_{pc}$$rpcthan genetic models that involve epistasis only. Using information of parental lines only, our expressions provide exact estimates of$${r}_{pc}$$rpcfor models D and EAA, and accurate upper and lower bounds of$${r}_{pc}$$rpcfor two other genetic models.ConclusionThis work lays the foundation to enable estimation of$${r}_{pc}$$rpcfrom information collected in PB parental lines only.
Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Authors: Zondervan Niels A. , Martins dos Santos Vitor A. P. , Suarez-Diez Maria , Saccenti Edoardo 
Published: February 2021

Abstract
Background
Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype.

Results
We compared 235 Staphylococcus and 315 Streptococcus genomes based on their protein domain content. We show the relationships between protein persistence and essentiality by integrating essentiality predictions from two metabolic models and essentiality measurements from six large-scale transposon mutagenesis experiments. We identified clusters of strains within species based on proteins associated to similar biological processes. We built Random Forest classifiers that predicted the zoonotic potential. Furthermore, we identified shared attributes between of Staphylococcus aureus and Streptococcus pyogenes that allow them to cause necrotizing fasciitis.

Conclusions
Differences observed in clustering of strains based on functional groups of proteins correlate with phenotypes such as host tropism, capability to infect multiple hosts and drug resistance. Our method provides a solid basis towards large-scale prediction of phenotypes based on genomic information.
Chloroplast genome variation and phylogenetic relationships of Atractylodes species
Authors: Wang Yiheng , Wang Sheng , Liu Yanlei , Yuan Qingjun , Sun Jiahui , Guo Lanping 
Published: February 2021

Abstract
Background
Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing.

Results
The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus.

Conclusions
Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.
National surveillance of stroke quality of care and outcomes by applying post-stratification survey weights on the Get With The Guidelines-Stroke patient registry
Authors: Ziaeian Boback , Xu Haolin , Matsouaka Roland A. , Xian Ying , Khan Yosef , Schwamm Lee S. , Smith Eric E. , Fonarow Gregg C. 
Published: February 2021

Abstract
Background
The U.S. lacks a stroke surveillance system. This study develops a method to transform an existing registry into a nationally representative database to evaluate acute ischemic stroke care quality.

Methods
Two statistical approaches are used to develop post-stratification weights for the Get With The Guidelines-Stroke registry by anchoring population estimates to the National Inpatient Sample. Post-stratification survey weights are estimated using a raking procedure and Bayesian interpolation methods. Weighting methods are adjusted to limit the dispersion of weights and make reasonable epidemiologic estimates of patient characteristics, quality of hospital care, and clinical outcomes. Standardized differences in national estimates are reported between the two post-stratification methods for anchored and non-anchored patient characteristics to evaluate estimation quality. Primary measures evaluated are patient and hospital characteristics, stroke severity, vital and laboratory measures, disposition, and clinical outcomes at discharge.

Results
A total of 1,388,296 acute ischemic strokes occurred between 2012 and 2014. Raking and Bayesian estimates of clinical data not available in administrative data are estimated within 5 to 10% of margin for expected values. Median weight for the raking method is 1.386 and the weights at the 99th percentile is 6.881 with a maximum weight of 30.775. Median Bayesian weight is 1.329 and the 99th percentile weights is 11.201 with a maximum weight of 515.689.

Conclusions
Leveraging existing databases with patient registries to develop post-stratification weights is a reliable approach to estimate acute ischemic stroke epidemiology and monitoring for stroke quality of care nationally. These methods may be applied to other diseases or settings to better monitor population health.
INF2 p.Arg214Cys mutation in a Chinese family with rapidly progressive renal failure and follow-up of renal transplantation: case report and literature review
Authors: Zhao Wenbo , Ma Xinxin , Zhang Xiaohao , Luo Dan , Zhang Jun , Li Ming , Ye Zengchun , Peng Hui 
Published: February 2021

Abstract
Background
Heterozygous mutations in the inverted formin 2 (INF2) gene are related to secondary focal segmental glomerulosclerosis (FSGS), a rare secondary disease associated with rapidly progressive renal failure.

Case presentation
We report a patient with familial autosomal INF2 mutation manifesting nephritic syndromes and elevated serum creatinine levels. Mutational analysis revealed an autosomal dominant (AD) inheritance pattern and a mutation in exon 4 (p.Arg214Cys) of INF2 as the likely cause, which has not been previously described in an Asian family. The patient progressed to end-stage renal disease (ESRD) and received hemodialysis. His mother had undergone renal transplant 3 years earlier, and his grandmother had carried the p.Arg214Cys mutation for more than 80 years without any sign of renal dysfunction.

Conclusions
This is the first report to identify an association between a familial autosomal dominant INF2 p.Arg214Cys mutation and rapidly progressive renal disease in an Asian family. INF2 mutation analysis should not be restricted to individuals without family history of FSGS, rather it should also be performed on individuals for whom drug-based therapies are not effective. In this case, kidney transplant is an effective alternative.
A 10-year bibliometric analysis of osteosarcoma and cure from 2010 to 2019
Authors: Da Wacili , Tao Zhengbo , Meng Yan , Wen Kaicheng , Zhou Siming , Yang Keda , Tao Lin 
Published: February 2021

Abstract
Background
In recent decades, the 5-year survival rate of osteosarcoma remains poor, despite the variety of operations, and exploration of drug therapy has become the key to improvement. This study investigates the contribution of different aspects in osteosarcoma and cure, and predicts research hotspots to benefit future clinical outcomes.

Methods
The Web of Science and PubMed databases were queried to collect all relevant publications related to osteosarcoma and cure from 2009 to 2019. These data were imported into CiteSpace and the Online Analysis Platform of Literature Metrology for bibliometric analysis. Bi-clustering was performed on Bibliographic Item co-occurrence Matrix Builder (BICOMB) and gCLUTO to identify hotspots. Additionally, completed clinical trials on osteosarcoma with results past phase II were collated.

Results
A total of 2258 publications were identified in osteosarcoma and cure from 2009 to 2019. China has the largest number of publications (38.49%), followed by the United States (23.03%) with the greatest impact (centrality = 0.44). The centrality of most institutions is < 0.1, and Central South University and Texas MD Anderson Cancer Center possess the highest average citation rates of 3.25 and 2.87. BMC cancer has the highest average citation rate of 3.26 in 772 journals. Four authors (Picci P, Gorlick R, Bielack SS and Bacci G) made the best contributions. We also identified eight hotspots and collected 41 clinical trials related to drug research on osteosarcoma.

Conclusions
The urgent need exists to strengthen global academic exchanges. Overcoming multidrug resistance in osteosarcoma is the focus of past, present and future investigations. Transformation of the metastasis pattern, microenvironment genetics mechanism, alternative methods of systemic chemotherapy and exploration of traditional Chinese medicine is expected to contribute to a new upsurge of research.
Comparison of irinotecan and oxaliplatin as the first-line therapies for metastatic colorectal cancer: a meta-analysis
Authors: Kawai Sadayuki , Takeshima Nozomi , Hayasaka Yu , Notsu Akifumi , Yamazaki Mutsumi , Kawabata Takanori , Yamazaki Kentaro , Mori Keita , Yasui Hirofumi 
Published: February 2021

AbstractBackgroundIrinotecan (IRI) and oxaliplatin (Ox) are standard therapeutic agents of the first-line treatments for metastatic colorectal cancer (mCRC). Previous meta-analyses of randomized controlled trials (RCTs) showed that treatment with Ox-based compared with IRI-based regimens was associated with better overall survival (OS). However, these reports did not include trials of molecular targeting agents and did not take methods for the administration of concomitant drugs, such as bolus or continuous infusion of 5-fluorouracil, into account. A systematic literature review was performed to compare the efficacy and toxicity profiles between IRI- and Ox-based regimens as the first-line treatments for mCRC.MethodsThis meta-analysis used data from the Cochrane Central Register of Controlled Trials, PubMed, and SCOPUS. The primary endpoint was OS, and the secondary endpoints were progression-free survival (PFS), objective response rate (ORR), and adverse events (AEs).ResultsNineteen trials involving 4571 patients were included in the analysis. No statistically significant difference was observed between the two groups in terms of OS, PFS, and ORR. There was no significant heterogeneity. Regarding ≥ grade 3 AEs, IRI-based regimens were associated with a high incidence of leukopenia, febrile neutropenia, and diarrhea. Moreover, there was a high incidence of thrombocytopenia and peripheral sensory neuropathy in patients who received Ox-based regimens. In a subgroup analysis, IRI combined with bevacizumab was correlated with a better PFS (HR = 0.90, 95% CI = 0.82–0.98,P = 0.02), but not with OS (pooled HR = 0.91, 95% CI = 0.80–1.03,P = 0.15).ConclusionAlthough the safety profiles of IRI- and Ox-based regimens varied, their efficacy did not significantly differ. The combination of anti-VEGF antibody and IRI was associated with better PFS compared with anti-VEGF antibody and Ox. Both regimens could be used as the first-line treatments for mCRC with consideration of the patients’ condition or toxicity profiles.
Predicting visual acuity in Bietti crystalline dystrophy: evaluation of image parameters
Authors: Huang Chu-Yen , Kang Eugene Yu-Chuan , Yeh Lung-Kun , Wu An-Lun , Liu Pei-Kang , Huang I-Wen , Ryu Joseph , Liu Laura , Wu Wei-Chi , Lai Chi-Chun , Chen Kuan-Jen , Wang Nan-Kai 
Published: February 2021

Abstract
Background
To analyze multiple imaging modalities in patients with Bietti crystalline dystrophy (BCD) and to investigate which factors from these modalities are associated with best corrected visual acuity (BCVA).

Methods
In this retrospective study, 40 eyes from 22 patients with BCD were included and were separated into group 1 (BCVA ≤20/200) and group 2 (BCVA > 20/200). Data including BCVA and characteristic findings from near-infrared reflectance (NIR) imaging, fundus autofluorescence (FAF), and spectral domain-optic coherence tomography (SD-OCT) were analyzed and compared. The outcome measures of multimodal imaging were evaluated for correlation with BCVA.

Results
NIR is a good diagnostic tool for detecting either crystalline or sclerotic vessels in BCD. Patients in group 1 tended to have a thinner choroid (P = 0.047) with ellipsoid zone (EZ) disruption (P = 0.011). Calculation of the area under the curve indicated that EZ disruption detected on SD-OCT could be a good predictor of legal blindness in BCD.

Conclusion
For the diagnosis of BCD, NIR could be a good diagnostic tool. Of the studied imaging modalities, we found that EZ disruption at the fovea were strongly associated with legal blindness, which could be easily assessed by SD-OCT.
Factors affecting final functional outcomes in open‐globe injuries and use of ocular trauma score as a predictive tool in Nepalese population
Authors: Shrestha Saurav M. , Anthony Casey L. , Justin Grant A. , Thapa Madhu , Shrestha Jyoti B. , Khatri Anadi , Hoskin Annette K , Agrawal Rupesh 
Published: February 2021

Abstract
Background
Open globe injury (OGI) is one of the most devastating form of ocular trauma. The aim of the study is to identify the epidemiology and predict visual outcomes in traumatic open globe injuries using ocular trauma score (OTS) and correlate with final visual acuity (VA) at 3 months.

Methods
Patients older than 5 years, presenting to B.P. Koirala Lions Centre for Ophthalmic Studies (BPKLCOS) from March 2016- March 2017 with OGI that met inclusion criteria were evaluated. Patient profile, nature and cause of injury, and time to presentation were recorded. Patients were managed accordingly and followed up to 3 months. An OTS score for each patient was calculated and raw scores were categorized accordingly. The VA after 3 months were compared to the predicted OTS values.

Results
Seventy-three eyes of 72 patients were examined. 76 % were male, and the mean age was 26.17 years (median, 23.5 years). The mean time from injury to presentation was < 6 hours (30 patients, 41 %). Thirty-seven eyes (51 %) had zone I trauma, followed by twenty eyes (27 %) with zone II, and sixteen eyes (22 %) with zone III trauma. Sixty-five patients (90 %) were managed surgically, and fifty (68 %) received intravitreal antibiotics with steroid. When compared, the projected VA as per OTS were able to predict actual final visual outcomes in 60 % of the eyes with OGI of various zones.

Conclusions
OTS can be an accurate predictive tool for final visual acuity even with a short follow up period of 3 months; with poor presenting visual acuity, delayed presentation, posterior zones of injury, need for intravitreal injections, endophthalmitis, and globe rupture associated with poorer prognosis.
A 15 month experience with a primary care-based telemedicine screening program for diabetic retinopathy
Authors: Benjamin James E. , Sun Justin , Cohen Devin , Matz Joseph , Barbera Angela , Henderer Jeffrey , Cheng Lorrie , Grachevskaya Julia , Shah Rajnikant , Zhang Yi 
Published: February 2021

Abstract
Background
Using telemedicine for diabetic retinal screening is becoming popular especially amongst at-risk urban communities with poor access to care. The goal of the diabetic telemedicine project at Temple University Hospital is to improve cost-effective access to appropriate retinal care to those in need of close monitoring and/or treatment.

Methods
This will be a retrospective review of 15 months of data from March 2016 to May 2017. We will investigate how many patients were screened, how interpretable the photographs were, how often the photographs generated a diagnosis of diabetic retinopathy (DR) based on the screening photo, and how many patients followed-up for an exam in the office, if indicated.

Results
Six-hundred eighty-nine (689) digital retinal screening exams on 1377 eyes of diabetic patients were conducted in Temple’s primary care clinic. The majority of the photographs were read to have no retinopathy (755, 54.8%). Among all of the screening exams, 357 (51.8%) triggered a request for a referral to ophthalmology. Four-hundred forty-nine (449, 32.6%) of the photos were felt to be uninterpretable by the clinician. Referrals were meant to be requested for DR found in one or both eyes, inability to assess presence of retinopathy in one or both eyes, or for suspicion of a different ophthalmic diagnosis. Sixty-seven patients (9.7%) were suspected to have another ophthalmic condition based on other findings in the retinal photographs. Among the 34 patients that were successfully completed a referral visit to Temple ophthalmology, there was good concordance between the level of DR detected by their screening fundus photographs and visit diagnosis.

Conclusions
Although a little more than half of the patients did not have diabetic eye disease, about half needed a referral to ophthalmology. However, only 9.5% of the referral-warranted exams actually received an eye exam. Mere identification of referral-warranted diabetic retinopathy and other ophthalmic conditions is not enough. A successful telemedicine screening program must close the communication gap between screening and diagnosis by reviewer to provide timely follow-up by eye care specialists.
Leaving no one behind? An equity analysis of the HIV care cascade among a cohort of people living with HIV in Manitoba, Canada
Authors: McClarty Leigh M. , Blanchard James F. , Becker Marissa L. 
Published: February 2021

Abstract
Background
Manitoba is a central Canadian province with annual rates of new HIV infections consistently higher than the Canadian average. National surveillance statistics and data from the provincial HIV care program suggest that epidemiological heterogeneity exists across Manitoba. New HIV cases are disproportionately reported among females, Indigenous-identifying individuals, and those with a history of injection drug use. Given the heterogeneity in acquisition, it is of interest to understand whether this translates into inequalities in HIV care across Manitoba.

Methods
A sample of 703 participants from a clinical cohort of people living with HIV in Manitoba, with data current to the end of 2017, was used to conduct cross-sectional, disaggregated analyses of the HIV care cascade to identify heterogeneity in service coverage and clinical outcomes among different groups receiving HIV care in Manitoba. Equiplots are used to identify and visualize inequalities across the cascade. Exploratory multivariable logistic regression models quantify associations between equity variables (age, sex, geography, ethnicity, immigration status, exposure category) and progression along the cascade. Adjusted odds ratios (AOR) and 95% confidence intervals (95%CI) are reported.

Results
Equity analyses highlight inequalities in engagement in and coverage of HIV-related health services among cohort participants. Equiplots illustrate that the proportion of participants in each cascade step is greater for those who are older, white, non-immigrants, and report no history of injection drug use. Compared to those living in Winnipeg, participants in eastern Manitoba have greater odds of achieving virologic suppression (AOR[95%CI] = 3.8[1.3–11.2]). The odds of Indigenous participants being virologically suppressed is half that of white participants (AOR[95%CI] = 0.5[0.3–0.7]), whereas African/Caribbean/Black participants are significantly less likely than white participants to be in care and retained in care (AOR[95%CI] = 0.3[0.2–0.7] and 0.4[0.2–0.9], respectively).

Conclusions
Inequalities exist across the cascade for different groups of Manitobans living with HIV; equiplots are an innovative method for visualizing these inequalities. Alongside future research aiming to understand why inequalities exist across the cascade in Manitoba, our equity analyses can generate hypotheses and provide evidence to inform patient-centred care plans that meet the needs of diverse client subgroups and advocate for policy changes that facilitate more equitable HIV care across the province.