bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ipsilateral proximal and shaft femoral fractures treated with bridge-link type combined fixation system
Authors: Kang Liangqi , Liu Hui , Ding Zhenqi , Ding Yiqiang , Hu Wei , Wu Jin 
Published: September 2020

AbstractBackgroundAlthough many treatments for ipsilateral proximal and shaft femoral fractures have been developed, controversy exists regarding their optimal management. The purpose of this retrospective study was to discuss the effectiveness of the bridge-link type combined fixation system (BCFS) and evaluate functional outcomes in treating patients with these complex fractures.Patients and methodsWe retrospectively reviewed 14 cases of ipsilateral proximal and shaft femoral fractures treated from January 2012 to December 2016. All cases were treated by BCFS combined with minimally invasive percutaneous plate osteosynthesis (MIPPO). Clinical and radiographic data were collected during regular post-operative follow-up visits. Functional outcomes were determined according to the Friedman and Wyman scoring system.ResultsThe proximal femoral fractures were emergency diagnoses in 11 cases and delayed diagnoses in 3 cases. The delay time was 5–6 days, with an average of 5.3 days. The mean operation time was 179.6 min (range 135–231 min) with a blood loss volume that ranged from 430 to 535 ml (average 483.6 ml). Follow-up was conducted in 13 cases between 9 and 30 months post-operation, with an average follow-up time of 17.3 months. The proximal femoral fractures were united in 12 cases at the final follow-up. One case had nonunion 13 months after the operation, underwent valgus intertrochanteric osteotomy, and healed 6 months later. The femoral shaft fractures obtained rigid union at the latest follow-up in 12 cases. One case endured nonunion 12 months after the operation. After the revision surgery and iliac bone grafting, the fracture healed 6 months later. Eight of the cases had good functional results, 4 had fair results, and results were poor in 1 case at the final follow-up.ConclusionsThe treatment of ipsilateral proximal femoral and shaft fractures with BCFS in combination with MIPPO demonstrated a high likelihood of union for both fractures and good functional results.
Comment on “The diagnostic value of D-dimer with simplified Geneva score (SGS) pre-test in the diagnosis of pulmonary embolism (PE)”
Authors: Sabour Siamak 
Published: September 2020

AbstractAny decision in clinical practice needs to evaluate both reliability (precision) and validity (accuracy) of a diagnostic test. Without knowledge about the reliability, any judgment would be wrong. In diagnostic accuracy research, it is essential to evaluate the diagnostic added value of a test, since a diagnostic accuracy of a single test might be excellent, however for clinical purposes it can be worthless. Like evaluating discrimination, it would be possible to estimate the diagnostic added value by applying ROC of diagnostic model with and without test results in the model.
Childhood Langerhans cell histiocytosis with severe lung involvement: a nationwide cohort study
Authors: Le Louet Solenne , Barkaoui Mohamed-Aziz , Miron Jean , Galambrun Claire , Aladjidi Nathalie , Chastagner Pascal , Kebaili Kamila , Armari-Alla Corinne , Lambilliotte Anne , Lejeune Julien , Moshous Despina , Della Valle Valeria , Sileo Chiara , Ducou Le Pointe Hubert , Chateil Jean-François , Renolleau Sylvain , Piloquet Jean-Eudes , Portefaix Aurelie , Epaud Ralph , Chiron Raphaël , Bugnet Emmanuelle , Lorillon Gwenaël , Tazi Abdelatif , Emile Jean-François , Donadieu Jean , Héritier Sébastien 
Published: September 2020

AbstractBackgroundLung involvement in childhood Langerhans cell histiocytosis (LCH) is infrequent and rarely life threatening, but occasionally, severe presentations are observed.MethodsAmong 1482 children (< 15 years) registered in the French LCH registry (1994–2018), 111 (7.4%) had lung involvement. This retrospective study included data for 17 (1.1%) patients that required one or more intensive care unit (ICU) admissions for respiratory failure.ResultsThe median age was 1.3 years at the first ICU hospitalization. Of the 17 patients, 14 presented with lung involvement at the LCH diagnosis, and 7 patients (41%) had concomitant involvement of risk-organ (hematologic, spleen, or liver). Thirty-five ICU hospitalizations were analysed. Among these, 22 (63%) were secondary to a pneumothorax, 5 (14%) were associated with important cystic lesions without pneumothorax, and 8 (23%) included a diffuse micronodular lung infiltration in the context of multisystem disease.First-line vinblastine–corticosteroid combination therapy was administered to 16 patients; 12 patients required a second-line therapy (cladribine:n = 7; etoposide-aracytine:n = 3; targeted therapyn = 2). A total of 6 children (35%) died (repeated pneumothorax:n = 3; diffuse micronodular lung infiltration in the context of multisystem disease:n = 2; following lung transplantation:n = 1). For survivors, the median follow-up after ICU was 11.2 years. Among these, 9 patients remain asymptomatic despite abnormal chest imaging.ConclusionsSevere lung involvement is unusual in childhood LCH, but it is associated with high mortality. Treatment guidelines should be improved for this group of patients: viral infection prophylaxis and early administration of a new LCH therapy, such as targeted therapy.
Retained primary teeth in STAT3 hyper-IgE syndrome: early intervention in childhood is essential
Authors: Meixner Iris , Hagl Beate , Kröner Carolin I. , Spielberger Benedikt D. , Paschos Ekaterini , Dückers Gregor , Niehues Tim , Hesse Ronny , Renner Ellen D. 
Published: September 2020

AbstractBackgroundSTAT3 hyper-IgE syndrome (STAT3-HIES) is a rare primary immunodeficiency that clinically overlaps with atopic dermatitis. In addition to eczema, elevated serum-IgE, and recurrent infections, STAT3-HIES patients suffer from characteristic facies, midline defects, and retained primary teeth. To optimize dental management we assessed the development of dentition and the long-term outcomes of dental treatment in 13 molecularly defined STAT3-HIES patients using questionnaires, radiographs, and dental investigations.ResultsPrimary tooth eruption was unremarkable in all STAT3-HIES patients evaluated. Primary tooth exfoliation and permanent tooth eruption was delayed in 83% of patients due to unresorbed tooth roots. A complex orthodontic treatment was needed for one patient receiving delayed extraction of primary molars and canines. Permanent teeth erupted spontaneously in all patients receiving primary teeth extraction of retained primary teeth during average physiologic exfoliation time.ConclusionsThe association of STAT3-HIES with retained primary teeth is important knowledge for dentists and physicians as timely extraction of retained primary teeth prevents dental complications. To enable spontaneous eruption of permanent teeth in children with STAT3-HIES, we recommend extracting retained primary incisors when the patient is not older than 9 years of age and retained primary canines and molars when the patient is not older than 13 years of age, after having confirmed the presence of the permanent successor teeth by radiograph.
Peroxiredoxin 6 mediates protective function of astrocytes in Aβ proteostasis
Authors: Pankiewicz Joanna E. , Diaz Jenny R. , Martá-Ariza Mitchell , Lizińczyk Anita M. , Franco Leor A. , Sadowski Martin J. 
Published: September 2020

Abstract
Background
Disruption of β-amyloid (Aβ) homeostasis is the initial culprit in Alzheimer’s disease (AD) pathogenesis. Astrocytes respond to emerging Aβ plaques by altering their phenotype and function, yet molecular mechanisms governing astrocytic response and their precise role in countering Aβ deposition remain ill-defined. Peroxiredoxin (PRDX) 6 is an enzymatic protein with independent glutathione peroxidase (Gpx) and phospholipase A2 (PLA2) activities involved in repair of oxidatively damaged cell membrane lipids and cellular signaling. In the CNS, PRDX6 is uniquely expressed by astrocytes and its exact function remains unexplored.

Methods
APPswe/PS1dE9 AD transgenic mice were once crossed to mice overexpressing wild-type Prdx6 allele or to Prdx6 knock out mice. Aβ pathology and associated neuritic degeneration were assessed in mice aged 10 months. Laser scanning confocal microscopy was used to characterize Aβ plaque morphology and activation of plaque-associated astrocytes and microglia. Effect of Prdx6 gene dose on plaque seeding was assessed in mice aged six months.

Results
We show that hemizygous knock in of the overexpressing Prdx6 transgene in APPswe/PS1dE9 AD transgenic mice promotes selective enticement of astrocytes to Aβ plaques and penetration of plaques by astrocytic processes along with increased number and phagocytic activation of periplaque microglia. This effects suppression of nascent plaque seeding and remodeling of mature plaques consequently curtailing brain Aβ load and Aβ-associated neuritic degeneration. Conversely, Prdx6 haplodeficiency attenuates astro- and microglia activation around Aβ plaques promoting Aβ deposition and neuritic degeneration.

Conclusions
We identify here PRDX6 as an important factor regulating response of astrocytes toward Aβ plaques. Demonstration that phagocytic activation of periplaque microglia vary directly with astrocytic PRDX6 expression level implies previously unappreciated astrocyte-guided microglia effect in Aβ proteostasis. Our showing that upregulation of PRDX6 attenuates Aβ pathology may be of therapeutic relevance for AD.
PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis
Authors: Zhang Yuhua , Quick Corbin , Yu Ketian , Barbeira Alvaro ,   The GTEx Consortium, Luca Francesca , Pique-Regi Roger , Kyung Im Hae , Wen Xiaoquan 
Published: September 2020

AbstractWe propose a new computational framework, probabilistic transcriptome-wide association study (PTWAS), to investigate causal relationships between gene expressions and complex traits. PTWAS applies the established principles from instrumental variables analysis and takes advantage of probabilistic eQTL annotations to delineate and tackle the unique challenges arising in TWAS. PTWAS not only confers higher power than the existing methods but also provides novel functionalities to evaluate the causal assumptions and estimate tissue- or cell-type-specific gene-to-trait effects. We illustrate the power of PTWAS by analyzing the eQTL data across 49 tissues from GTEx (v8) and GWAS summary statistics from 114 complex traits.
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
Authors: Gay Nicole R. , Gloudemans Michael , Antonio Margaret L. , Abell Nathan S. , Balliu Brunilda , Park YoSon , Martin Alicia R. , Musharoff Shaila , Rao Abhiram S. , Aguet François , Barbeira Alvaro N. , Bonazzola Rodrigo , Hormozdiari Farhad ,   GTEx Consortium, Ardlie Kristin G. , Brown Christopher D. , Im Hae Kyung , Lappalainen Tuuli , Wen Xiaoquan , Montgomery Stephen B. 
Published: September 2020

Abstract
Background
Population structure among study subjects may confound genetic association studies, and lack of proper correction can lead to spurious findings. The Genotype-Tissue Expression (GTEx) project largely contains individuals of European ancestry, but the v8 release also includes up to 15% of individuals of non-European ancestry. Assessing ancestry-based adjustments in GTEx improves portability of this research across populations and further characterizes the impact of population structure on GWAS colocalization.

Results
Here, we identify a subset of 117 individuals in GTEx (v8) with a high degree of population admixture and estimate genome-wide local ancestry. We perform genome-wide cis-eQTL mapping using admixed samples in seven tissues, adjusted by either global or local ancestry. Consistent with previous work, we observe improved power with local ancestry adjustment. At loci where the two adjustments produce different lead variants, we observe 31 loci (0.02%) where a significant colocalization is called only with one eQTL ancestry adjustment method. Notably, both adjustments produce similar numbers of significant colocalizations within each of two different colocalization methods, COLOC and FINEMAP. Finally, we identify a small subset of eQTL-associated variants highly correlated with local ancestry, providing a resource to enhance functional follow-up.

Conclusions
We provide a local ancestry map for admixed individuals in the GTEx v8 release and describe the impact of ancestry and admixture on gene expression, eQTLs, and GWAS colocalization. While the majority of the results are concordant between local and global ancestry-based adjustments, we identify distinct advantages and disadvantages to each approach.
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction
Authors: Huang Norman , Fan Xiaochen , Zaleta-Rivera Kathia , Nguyen Tri C. , Zhou Jiarong , Luo Yingjun , Gao Jie , Fang Ronnie H. , Yan Zhangming , Chen Zhen Bouman , Zhang Liangfang , Zhong Sheng 
Published: September 2020

Abstract
Background
Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We develop a series of technologies to test for any nuclear-encoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, hereafter called membrane-associated extracellular RNAs (maxRNAs).

Results
We develop a technique called Surface-seq to selectively sequence maxRNAs and validate two Surface-seq identified maxRNAs by RNA fluorescence in situ hybridization. To test for cell-type specificity of maxRNA, we use antisense oligos to hybridize to single-stranded transcripts exposed on the surface of human peripheral blood mononuclear cells (PBMCs). Combining this strategy with imaging flow cytometry, single-cell RNA sequencing, and maxRNA sequencing, we identify monocytes as the major type of maxRNA+ PBMCs and prioritize 11 candidate maxRNAs for functional tests. Extracellular application of antisense oligos of FNDC3B and CTSS transcripts inhibits monocyte adhesion to vascular endothelial cells.

Conclusions
Collectively, these data highlight maxRNAs as functional components of the cell surface, suggesting an expanded role for RNA in cell-cell and cell-environment interactions.
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Authors: Jin Jian-Jun , Yu Wen-Bin , Yang Jun-Bo , Song Yu , dePamphilis Claude W. , Yi Ting-Shuang , Li De-Zhu 
Published: September 2020

AbstractGetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Authors: Saary Paul , Mitchell Alex L. , Finn Robert D. 
Published: September 2020

AbstractMicrobial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.
Metalign: efficient alignment-based metagenomic profiling via containment min hash
Authors: LaPierre Nathan , Alser Mohammed , Eskin Eleazar , Koslicki David , Mangul Serghei 
Published: September 2020

AbstractMetagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, we present a novel method, Metalign, that performs efficient and accurate alignment-based metagenomic profiling. We use a novel containment min hash approach to pre-filter the reference database prior to alignment and then process both uniquely aligned and multi-aligned reads to produce accurate abundance estimates. In performance evaluations on both real and simulated datasets, Metalign is the only method evaluated that maintained high performance and competitive running time across all datasets.
Effect of acupuncture on women with poor ovarian response: a study protocol for a multicenter randomized controlled trial
Authors: Xu Huanfang , Zheng Chensi , He Liyun , Su Tongsheng , Wang Huidan , Li Yu , Zhao Cui , Zhang Cuilian , Bai Yang , Tong Guoqing , Chen Li , Zhao Fang , Yang Huisheng , Hao Mingzhao , Yin Yaqian , Yang Li , Fang Yigong , Liu Baoyan 
Published: September 2020

AbstractBackgroundPoor ovarian response (POR), a manifestation of low ovarian reserve and ovarian aging, leads to a significant reduction in the pregnancy rate after in vitro fertilization-embryo transfer. Acupuncture has increasingly been used to improve the ovarian reserve. The purpose of this study will be to evaluate the effect of acupuncture on increasing the number of retrieved oocytes after controlled ovarian hyperstimulation in women with POR.MethodsThis will be a multicenter randomized controlled trial. A total of 140 women with POR will be randomly assigned to receive acupuncture or nontreatment for 12 weeks before controlled ovarian hyperstimulation. The primary outcome will be the number of retrieved oocytes. The secondary outcomes will be antral follicle counts, serum levels of anti-Müllerian hormone, basal serum levels of follicle stimulating hormone, luteinizing hormone and estradiol levels, scores from the self-rating anxiety scale, fertilization rates, cleavage rates, available embryo rates, and high-quality embryo rates. The safety of acupuncture will also be assessed.DiscussionThe results of this trial will help to determine the effectiveness of acupuncture in the treatment of POR. This may provide a new treatment option for patients with POR and their physicians.Trial registrationAMCTR-IPR-18000198. Registered on 10 August 2018.
Investigations on the occurrence of tapeworm infections in German horse populations with comparison of different antibody detection methods based on saliva and serum samples
Authors: Jürgenschellert Laura , Krücken Jürgen , Austin Corrine J. , Lightbody Kirsty L. , Bousquet Eric , von Samson-Himmelstjerna Georg 
Published: September 2020

Abstract
Background
Effective and sustainable worm control in horses would benefit from detailed information about the current regional occurrence of tapeworms. Different diagnostic methods are currently available to detect Anoplocephala spp. infections in horses. However, the format as well as the sensitivity and specificity of the methods vary considerably.

Methods
A coprological, serological and questionnaire study was conducted to investigate the prevalence and risk factors of tapeworm infections on 48 horse farms in the region of Berlin and Brandenburg, Germany. In total, faecal samples of 484 horses were analysed using the double centrifugation/combined sedimentation-flotation and mini-FLOTAC. Serum (n = 481) and saliva (n = 365) samples were analysed by ELISAs to determine antibody levels against Anoplocephala spp. 12/13 kDa excretory/secretory (E/S) antigens.

Results
Cestode eggs were detected in 0.6% of faecal samples (farm prevalence 6.3%) without differences between the two methods. In contrast, antibodies against Anoplocephala spp. were detected in 16.2% (farm prevalence 52.1%) and in 29.5% (farm prevalence 75.7%) of the serum and saliva samples, respectively. Both ELISA based methods for detection of tapeworms reported a greater number of infected animals requiring treatment than were positively identified by coproscopy. Logistic regression analysis identified permanent pasture access, large pastures and regular pasture changes and high strongyle egg counts as risk factors for positive serum antibody responses to Anoplocephala spp. while last treatment with praziquantel was protective. Other protective factors were the presence of foals and high numbers of horses on the farm. Daily removal of faeces from the pasture and horse age did not have a significant effect.

Conclusions
The findings of the present serological investigation indicate that tapeworm prevalence in Berlin/Brandenburg horse farms is much higher than would be anticipated by using conventional/coproscopic analyses. Moreover, the majority of tapeworm-positive horses had not received a cestocidal drug at their last treatment. Considering the already known low sensitivity of the coproscopic detection, the equine veterinary diagnostics can be enhanced by the use of antibody detection methods such as the saliva-based ELISA.
High sensitivity of one-step real-time reverse transcription quantitative PCR to detect low virus titers in large mosquito pools
Authors: Tang Zhaoyang , Yamada Hanano , Kraupa Carina , Canic Sumejja , Busquets Núria , Talavera Sandra , Jiolle Davy , Vreysen Marc J. B. , Bouyer Jérémy , Abd-Alla Adly M. M. 
Published: September 2020

Abstract
Background
Mosquitoes are the deadliest animals in the world. Their ability to carry and spread diseases to humans causes millions of deaths every year. Due to the lack of efficient vaccines, the control of mosquito-borne diseases primarily relies on the management of the vector. Traditional control methods are insufficient to control mosquito populations. The sterile insect technique (SIT) is an additional control method that can be combined with other control tactics to suppress specific mosquito populations. The SIT requires the mass-rearing and release of sterile males with the aim to induce sterility in the wild female population. Samples collected from the environment for laboratory colonization, as well as the released males, should be free from mosquito-borne viruses (MBV). Therefore, efficient detection methods with defined detection limits for MBV are required. Although a one-step reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) method was developed to detect arboviruses in human and mosquito samples, its detection limit in mosquito samples has yet to be defined.

Methods
We evaluated the detection sensitivity of one step RT-qPCR for targeted arboviruses in large mosquito pools, using pools of non-infected mosquitoes of various sizes (165, 320 and 1600 mosquitoes) containing one infected mosquito body with defined virus titers of chikungunya virus (CHIKV), usutu virus (USUV), West Nile virus (WNV) and Zika virus (ZIKV).

Results
CHIK, USUV, ZIKV, and WNV virus were detected in all tested pools using the RT-qPCR assay. Moreover, in the largest mosquito pools (1600 mosquitoes), RT-qPCR was able to detect the targeted viruses using different total RNA quantities (10, 1 and 0.1 ng per reaction) as a template. Correlating the virus titer with the total RNA quantity allowed the prediction of the maximum number of mosquitoes per pool in which the RT-qPCR can theoretically detect the virus infection.

Conclusions
Mosquito-borne viruses can be reliably detected by RT-qPCR assay in pools of mosquitoes exceeding 1000 specimens. This will represent an important step to expand pathogen-free colonies for mass-rearing sterile males for programmes that have a SIT component by reducing the time and the manpower needed to conduct this quality control process.