bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
Authors: Vilperte Vinicius , Lucaciu Calin Rares , Halbwirth Heidi , Boehm Robert , Rattei Thomas , Debener Thomas 
Published: November 2019

Abstract
Background
Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species.

Results
The final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration.

Conclusions
In summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation.
Development of a multi-locus sequence typing system helps reveal the evolution of Cardinium hertigii, a reproductive manipulator symbiont of insects
Authors: Stouthamer Corinne M. , Kelly Suzanne E. , Mann Evelyne , Schmitz-Esser Stephan , Hunter Martha S. 
Published: November 2019

Abstract
Background
Cardinium is an intracellular bacterial symbiont in the phylum Bacteroidetes that is found in many different species of arthropods and some nematodes. This symbiont is known to be able to induce three reproductive manipulation phenotypes, including cytoplasmic incompatibility. Placing individual strains of Cardinium within a larger evolutionary context has been challenging because only two, relatively slowly evolving genes, 16S rRNA gene and Gyrase B, have been used to generate phylogenetic trees, and consequently, the relationship of different strains has been elucidated in only its roughest form.

Results
We developed a Multi Locus Sequence Typing (MLST) system that provides researchers with three new genes in addition to Gyrase B for inferring phylogenies and delineating Cardinium strains. From our Cardinium phylogeny, we confirmed the presence of a new group D, a Cardinium clade that resides in the arachnid order harvestmen (Opiliones). Many Cardinium clades appear to display a high degree of host affinity, while some show evidence of host shifts to phylogenetically distant hosts, likely associated with ecological opportunity. Like the unrelated reproductive manipulator Wolbachia, the Cardinium phylogeny also shows no clear phylogenetic signal associated with particular reproductive manipulations.

Conclusions
The Cardinium phylogeny shows evidence of diversification within particular host lineages, and also of host shifts among trophic levels within parasitoid-host communities. Like Wolbachia, the relatedness of Cardinium strains does not necessarily predict their reproductive phenotypes. Lastly, the genetic tools proposed in this study may help future authors to characterize new strains and add to our understanding of Cardinium evolution.
The increasing menace of dengue in Guangzhou, 2001–2016: the most important epicenter in mainland China
Authors: Zhang Zhoubin , Jing Qinlong , Chen Zongqiu , Li Tiegang , Jiang Liyun , Li Yilan , Luo Lei , Marshall John , Yang Zhicong 
Published: November 2019

Abstract
Background
Dengue is the most prevalent mosquito-borne disease in the world, with China affected seriously in recent years. 65.8% of dengue cases identified in mainland China since 2005 were reported from the city of Guangzhou.

Methods
In this study, we described the incidence rate and distribution of dengue cases using data collected form National Notifiable Infectious Disease Reporting Information System data in Guangzhou for 2001 to 2016. All dengue cases were investigated using standardized questionnaire.

Results
A total of 42,469 dengue cases were reported, with an average annual incidence rate of 20.99 per 100,000 resident population. Over this time period, the incidence rate of indigenous cases increased. Dengue affected areas also expanded sharply geographically from 58.1% of communities affected during 2001–2005 to 96.4% of communities affected in 2011–2016. Overall 95.30% of the overseas imported cases were reported during March and December, while 99.79% of indigenous cases were reported during July and November. All four dengue virus serotypes were identified both in imported cases and indigenous cases. The Aedes albopictus mosquito was the only vector for dengue transmission in the area.

Conclusions
Guangzhou has become the dengue epicenter in mainland China. Control strategies for dengue should be adjusted to the epidemiological characteristics above and intensive study need to be conducted to explore the factors that driving the rapid increase of dengue.
Neurolymphomatosis of the lumbosacral plexus and its branches: case series and literature review
Authors: Bourque Pierre R. , Sampaio Marcos Loreto , Warman-Chardon Jodi , Samaan Sam , Torres Carlos 
Published: November 2019

Abstract
Background
Neurolymphomatosis (NL) is a direct process of invasion of peripheral nerves by lymphoma. It occurs in roughly 5% of patients with lymphoma and represents a particularly difficult diagnostic dilemma when it is the presenting focal manifestation of occult lymphoma.

Case presentation
We present 3 examples of invasion of the lumbosacral plexus and its branches. These cases demonstrate a protean clinical picture with regards to the time relationship to the clinical course of lymphoma and the neuroanatomical extent of lumbosacral plexus invasion. We demonstrate the complementary role of different imaging modalities. A review of the literature summarizes 23 reports where lumbosacral plexus invasion was the index manifestation, at the time of first diagnosis or recurrence of lymphoma. This series confirms the strong preponderance of B-cell type (92%). There is a marked predilection for involvement of the sciatic nerve (74%), either focally or in a longitudinally extensive fashion, from the ischium to the popliteal fossa. There can also be restricted and discrete involvement of tibial and fibular branches. In recent years, ultrasound and CT have been given a more limited role, as screening tools or as a guide for biopsy. MRI neurography and PET-CT have become leading diagnostic modalities for diagnosis, staging and assessment of treatment response.

Conclusion
The diagnosis of NL may be challenging, and it was once only reached at autopsy. Improved diagnostic imaging of focal or even asymptomatic disease offers new hope for earlier diagnosis and successful targeted therapy.
Influence of anonymous HIV testing on national HIV surveillance in the Republic of Korea (2000 to 2015): a retrospective analysis
Authors: Kee Mee-Kyung , Yoo Myeongsu , Seong Jaehyung , Choi Ju-Yeon , Han Myung Guk , Lee Joo-Shil , Jee Youngmee , Kim Kisoon , Kim Sung Soon , Kang Chun 
Published: November 2019

Abstract
Background
Owing to the continuous increase in the number of new human immunodeficiency virus (HIV) infection in Korea, public health centers (PHCs) have performed anonymous tests since 1989. No study has examined the patterns of anonymous HIV testing performed at PHCs and the characteristics of HIV infection detected in those tests. We aimed to assess the influence of anonymous HIV testing on Korea’s national HIV surveillance.

Methods
HIV screening test data from 253 PHCs over a 16-year period were classified into 13 groups based on reason for testing. For anonymous HIV test takers (Anonymous), the HIV positivity per 10,000 tests was calculated, as repetitions could not be distinguished. Those with suspected HIV infection voluntarily underwent HIV testing and revealed their identity (Suspected). HIV prevalence was calculated as the number of HIV-positive persons per 10,000 test takers. Analyses were performed using chi-square and Cochran-Armitage trend test with SAS 9.4.

Results
Approximately 400,000 HIV screening tests were performed at PHCs annually, which remained unchanged in the past 10 years. The proportion of anonymous testing increased from < 3.0% before 2014 to 4.8% in 2014 and 6.1% in 2015. While the number of HIV cases increased, the number of anonymous HIV-positive test results per 10,000 tests decreased from 68.8 in 2010 to 41.8 in 2015. The HIV prevalence among the suspected was approximately 20.0 per 10,000 test takers before 2014, which steeply increased to 71.6 in 2015. Those with suspected HIV were predominantly men, aged 20 years, foreigners, and metropolitan city dwellers in the last 6 years. The high prevalence of persons with suspected HIV resulted in a doubling of HIV prevalence at PHCs between 2014 and 2015.

Conclusions
Anonymous and Suspected, which were driven by similar motives, impacted each other. Increase in HIV prevalence among the suspected led to a higher HIV prevalence among all test takers in PHCs and higher proportions of HIV infection nationwide, which could be attributed to the increase in the number of anonymous tests performed in PHCs. HIV positivity among the anonymous and HIV prevalence among the suspected are key indexes of the national HIV surveillance in Korea.
Worse health status, sleeping problems, and anxiety in 16-year-old students are associated with chronic musculoskeletal pain at three-year follow-up
Authors: Malmborg Julia S. , Bremander Ann , Olsson M. Charlotte , Bergman Anna-Carin , Brorsson A. Sofia , Bergman Stefan 
Published: November 2019

Abstract
Background
Chronic musculoskeletal pain is common in adolescents, and it has been shown that adolescents with pain may become young adults with pain. Pain often coincides with psychosomatic symptoms in adults, but little is known about longitudinal associations and predictors of pain in adolescents. The aim was to investigate chronic musculoskeletal pain and its associations with health status, sleeping problems, stress, anxiety, depression, and physical activity in 16-year-old students at baseline, and to identify risk factors using a three-year follow-up.

Methods
This was a longitudinal study of 256 students attending a Swedish upper secondary school. Questionnaires regarding chronic musculoskeletal pain and distribution of pain (mannequin), health status (EQ-5D-3 L), sleeping problems (Uppsala Sleep Inventory), stress symptoms (single-item question), anxiety and depression (Hospital Anxiety and Depression Scale), and physical activity (International Physical Activity Questionnaire) were issued at baseline and follow-up. Student’s t-test and chi2 test were used for descriptive statistics and logistic regression analyses were used to study associations between chronic pain and independent variables.

Results
Fifty-two out of 221 students at baseline (23.5%) and 39 out of 154 students at follow-up (25.3%) were categorized as having chronic musculoskeletal pain. Chronic musculoskeletal pain at follow-up was separately associated with reporting of an EQ-5D value below median (OR 4.06, 95% CI 1.83–9.01), severe sleeping problems (OR 3.63, 95% CI 1.69–7.82), and possible anxiety (OR 4.19, 95% CI 1.74–10.11) or probable anxiety (OR 3.82, 95% CI 1.17–12.48) at baseline. Similar results were found for associations between chronic musculoskeletal pain and independent variables at baseline. In multiple logistic regression analysis, chronic musculoskeletal pain at baseline was a predictor of chronic musculoskeletal pain at follow-up (OR 2.99, 95% CI 1.09–8.24, R2 = 0.240).

Conclusion
Chronic musculoskeletal pain at baseline was the most important predictor for reporting chronic musculoskeletal pain at the three-year follow-up, but a worse health status, severe sleeping problems, and anxiety also predicted persistence or development of chronic musculoskeletal pain over time. Interventions should be introduced early on by the school health services to promote student health.
Comparison of anterior transthoracic debridement and fusion with posterior transpedicular debridement and fusion in the treatment of mid-thoracic spinal tuberculosis in adults
Authors: Li Weiwei , Liu Zheng , Xiao Xiao , Zhang Zhen , Wang Xiyang 
Published: November 2019

Abstract
Background
The surgical procedures for mid-thoracic spinal tuberculosis mainly include anterior transthoracic debridement and fusion and posterior transpedicular debridement and fusion. Until now, the surgical choice is still controversial. This study aims to compare the clinical efficacy of anterior transthoracic debridement and fusion with posterior transpedicular debridement and fusion in the treatment of mid-thoracic (T5–9) spinal tuberculosis in adult patients.

Methods
Eighty-seven cases with mid-thoracic spinal tuberculosis were treated with anterior transthoracic debridement and fusion (Group A, n = 39) and posterior transpedicular debridement and fusion (Group B, n = 48) from January 2007 to June 2014. Parameters including the operation time, blood loss, time of ESR and CRP decreasing to the normal level, time of abscess disappearance, time of bone graft fusion, rate of surgical complications, Visual Analog Scale (VAS) score, kyphosis angle and SF-36 scale were compared between two groups to evaluate their therapeutic effects.

Results
All patients were followed up for 5–10 years with the mean of 6.2 ± 1.1 years. No significant differences were observed regarding the gender composition ratio, age, course of disease, number of lesion segments, and preoperative indexes of ESR, CRP, VAS score, kyphosis angle and SF-36 scale between the two groups. Besides, no significant differences were observed regarding VAS score, kyphosis angle and SF-36 scale between the two groups in the 5th postoperative year (P > 0.05). However, the operation time (158.2 ± 10.7 min vs. 183.7 ± 14.1 min), blood loss (517.9 ± 76.5 ml vs.714.6 ± 57.4 ml), time of ESR (2.3 ± 1.1 months vs.3.1 ± 1.4 months) and CRP (1.1 ± 0.3 months vs.1.2 ± 0.6 months) decreasing to the normal level, time of abscess disappearance (2.7 ± 1.6 months vs.4.9 ± 1.9 months), and time of bone graft fusion (6.6 ± 0.8 months vs.8.0 ± 9.6 months) in Group A were less than those in Group B (P < 0.05).

Conclusions
Both anterior transthoracic debridement and fusion and posterior transpedicular debridement and fusion have a low risk of surgical complications and provide good quality of life for the patients with mid-thoracic (T5–9) spinal tuberculosis followed up in the mid-term. Moreover, the anterior procedure leads to early resolution of the disease and faster fusion.
Intra-substance steroid injection for full-thickness supraspinatus tendon rupture
Authors: Liu Chung-Ting , Yang Ten-Fang 
Published: November 2019

Abstract
Background
The use of steroid injection for treatment of a full-thickness rotator cuff tear is still controversial. This study aimed to evaluate the effectiveness and safety of this treatment method.

Methods
Twelve patients in Group 1 received an intra-substance injection into rupture area of supraspinatus tendon with Diprospan 1 cc (betamethasone disodium phosphate 2 mg and betamethasone dipropionate 5 mg) and 1% xylocaine 1 cc. Twelve patients in Group 2 received an injection with normal saline 1 cc and 1% xylocaine 1 cc. The rupture size was measured by sonography before the injection, 3 months after the injection, and 6 months after the injection. Shoulder Pain and Disability Index (SPADI) score and Pain Visual Analogue Scale (VAS) score were measured and compared between the two groups before the injection, 1 week after the injection, 3 months after the injection, and 6 months after the injection.

Results
Pain and function improved more in Group 1 than in Group 2. The therapeutic effect lasted for at least 6 months in both groups. The size of the supraspinatus tendon rupture was not increased after injection in either group.

Conclusions
Intra-substance injection into rupture area of supraspinatus tendon with steroid and xylocaine is effective to reduce pain and improve function in patients with full-thickness supraspinatus tendon rupture without increasing the size of the rupture.

Trial registration
Current Controlled Trials ChiCTR1900026376, data of registration: 2019/10/05 retrospectively registered.
Reliability and validity of miniscrews as references in cone-beam computed tomography and intraoral scanner digital models: study on goat heads
Authors: Jiang Yiran , Chen Gui 
Published: November 2019

Abstract
Background
Miniscrews have been used to superimpose three-dimensional (3D) craniofacial images as well as explore stable structures in jaws. Our purpose was to evaluate the reliability and validity of linear and angular measurements made with miniscrews on a 3D cone-beam computed tomography (CBCT) at two voxel sizes and compared to models created by an intraoral scanner (IOS).

Methods
Altogether, 64 miniscrews were placed in 12 goat jaws. The jaws were scanned by CBCT machine at 0.12 mm and 0.3 mm voxels and by the IOS. Linear and angular measurements between miniscrews on CBCT at the two voxel settings and the IOS were compared with actual measurements and with each other.

Results
An intra-and inter-class correlation of 0.961–1.000 were obtained by each method. Linear measurements showed significant overestimations of 0.27 ± 0.24, 0.14 ± 0.22 and 0.15 ± 0.26 mm, and angular measurements showed non-significant differences of 0.11 ± 1.97°, 0.15 ± 2.79° and 0.41 ± 2.34° for the CBCT at 0.12-mm, 0.3-mm voxels and the IOS, respectively. Equal magnification of linear measurements was on homolateral and contralateral sides using CBCT, whereas significantly greater magnification on the homolateral side than on the opposite was observed using the IOS. There was no significant difference with angular measurements between digital CBCT models at two voxels and IOS. In addition, all angular measurements were comparable to actual measurement results.

Conclusions
Miniscrews in CBCT and IOS are reliable and clinical valid when used as a reference measuring tooth movement. However, when miniscrews are involved in high precision measurement in CBCT or IOS image, systematic error should be taken into consideration. When comparing CBCT images, using the same voxel size is recommended for miniscrew related measurements to reduce error.
Fetal Down syndrome screening models for developing countries; Part I: Performance of Maternal Serum Screening
Authors: Wanapirak Chanane , Piyamongkol Wirawit , Sirichotiyakul Supatra , Tongprasert Fuanglada , Srisupundit Kasemsri , Luewan Suchaya , Traisrisilp Kuntharee , Jatavan Phudit , Tongsong Theera 
Published: November 2019

Abstract
Background
To identify the performance of fetal Down syndrome (DS) screening for developing countries.

Methods
A prospective study on MSS (maternal serum screening) with complete follow-ups (n = 41,924) was conducted in 32 network hospitals in the northern part of Thailand. Various models of MSS were tested for performance.

Results
MSS based on Caucasian reference range resulted in very high false positive rate (FPR; 13%) in our country, compared to the rate of 7.8% with our own (Thai) reference range, whereas the detection rate was comparable. As individual screening, C-S (contingent first trimester screening including PAPP-A, and free beta-hCG, classified as a) high risk [> 1:30], indicated for invasive diagnosis; b) intermediate risk [1:30–1500], indicated for STS; and c) low risk [< 1:1500], need no further tests.) was the most effective model (sensitivity 84.9%, FPR 7.7%) but nearly one-third needed the second trimester test (STS) because of intermediate results. Additionally, about one-third had their first visits in the second trimester and had no chance of FTS (first trimester screening). C-S plus STS had a sensitivity of 82.4% and FPR 8.1% whereas independent first and second trimester screening model (I-S) gave the sensitivity of 78.4% and FPR of 7.5% but was much more convenient and practical.

Conclusion
C-S plus STS was the most effective models while I-S model was also effective and may be better for developing countries because of its simplicity and feasibility.
Facilitators and barriers of patient-centered care at the organizational-level: a study of three district hospitals in the central region of Ghana
Authors: Nkrumah Jacqueline , Abekah-Nkrumah Gordon 
Published: November 2019

Abstract
Background
Improving patient experience of care has gained enormous attention from policy makers and providers of healthcare services in Ghana. In spite of the supposed support for patient-centered care as the means for improving patient experience of care, scientific evidence point to poor patient experience of care in Ghana. Moreover, there seem to be little evidence on organizational-level factors that facilitate or hamper patient-centered care. In this study we assess organizational-level factors that facilitate or impede patient-centered care in three district hospitals in the Central Region of Ghana.

Methods
The study was exploratory research that used qualitative methods to collect data from seven senior managers and 3 junior managers in three district hospitals in the Central Region of Ghana. Data were collected with the aid of an interview guide and a checklist. Data were analyzed using content analysis.

Results
Two main Organizational-level factors were identified, namely, facilitators and barriers of patient-centered care. Facilitators to patient-centered care included: 1) Leadership commitment. 2) Leadership support. 3) Training and education for patient-centered care. Patient-centered care barriers identified in the hospitals were: 1) Leadership conceptualization of patient-centered care. 2) Lack of goals and sufficient activities for patient-centered care. 3) Communication related challenges.4) Ownership type. 5) Degree of centralization. 6) Financial constraints.

Conclusion
Organizational-level factors that promoted patient-centered care were fairly present in the hospitals. Yet, several other factors negatively affected patient-centered care in the hospitals. A suitable patient-focused intervention is recommended for implementation at the health system and institutional-levels to improve patient-centered care. Hospitals managers should develop suitable goals and activities to stimulate patient-centered care with the full participation of hospital employees and patients and families.