bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competition-based screening helps to secure the evolutionary stability of a defensive microbiome
Authors: Worsley Sarah F. , Innocent Tabitha M. , Holmes Neil A. , Al-Bassam Mahmoud M. , Schiøtt Morten , Wilkinson Barrie , Murrell J. Colin , Boomsma Jacobus J. , Yu Douglas W. , Hutchings Matthew I. 
Published: September 2021

Abstract
Background
The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia, which contributes to the control of Escovopsis fungus garden disease, is never compromised by the secondary acquisition of other bacterial strains. Game theory suggests that competition-based screening can allow the selective recruitment of antibiotic-producing bacteria from the environment, by providing abundant resources to foment interference competition between bacterial species and by using Pseudonocardia to bias the outcome of competition in favour of antibiotic producers.

Results
Here, we use RNA-stable isotope probing (RNA-SIP) to confirm that Acromyrmex ants can maintain a range of microbial symbionts on their cuticle by supplying public resources. We then used RNA sequencing, bioassays, and competition experiments to show that vertically transmitted Pseudonocardia strains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately biassing the bacterial competition to allow the selective establishment of secondary antibiotic-producing strains while excluding non-antibiotic-producing strains that would parasitise the symbiosis.

Conclusions
Our findings are consistent with the hypothesis that competition-based screening is a plausible mechanism for maintaining the integrity of the co-adapted mutualism between the leaf-cutting ant farming symbiosis and its defensive microbiome. Our results have broader implications for explaining the stability of other complex symbioses involving horizontal acquisition.
Beam orientation optimization for coherent X-ray scattering from distributed deep targets
Authors: Breedlove Sophya , Badano Aldo 
Published: September 2021

Abstract
Background
Amyloid deposits in the temporal and frontal lobes in patients with Alzheimer’s disease make them potential targets to aid in early diagnosis. Recently, spectral small-angle X-ray scattering techniques have been proposed for interrogating deep targets such as amyloid plaques.

Results
We describe an optimization approach for the orientation of beams for deep target characterization. The model predicts the main features of scattering profiles from targets with varying shape, size and location. We found that increasing target size introduced additional smearing due to location uncertainty, and incidence angle affected the scattering profile by altering the path length or effective target size. For temporal and frontal lobe targets, beam effectiveness varied up to 2 orders of magnitude.

Conclusions
Beam orientation optimization might allow for patient-specific optimal paths for improved signal characterization.
Support mechanisms for research generation and application for postgraduate students in four universities in Uganda
Authors: Obuku E. A. , Apunyo R. , Mbabazi G. , Mafigiri D. K. , Karamagi C. , Sengooba F. , Lavis J. N. , Sewankambo N. K. 
Published: September 2021

Abstract
Background
A large proportion of postgraduate students the world over complete a research thesis in partial fulfilment of their degree requirements. This study identified and evaluated support mechanisms for research generation and utilization for masters’ students in health institutions of higher learning in Uganda.

Methods
This was a self-administered cross-sectional survey using a modified self-assessment tool for research institutes (m-SATORI). Postgraduate students were randomly selected from four medical or public health Ugandan universities at Makerere, Mbarara, Nkozi and Mukono and asked to circle the most appropriate response on a Likert scale from 1, where the “situation was unfavourable and/or there was a need for an intervention”, to 5, where the “situation was good or needed no intervention”. These questions were asked under four domains: the research question; knowledge production, knowledge transfer and promoting use of evidence. Mean scores of individual questions and aggregate means under the four domains were computed and then compared to identify areas of strengths and gaps that required action.

Results
Most of the respondents returned their questionnaires, 185 of 258 (71.7%), and only 79 of these (42.7%) had their theses submitted for examination. The majority of the respondents were male (57.3%), married or cohabiting (58.4%), and were medical doctors (71.9%) from Makerere University (50.3%). The domain proposal development for postgraduate research project had the highest mean score of 3.53 out of the maximum 5. Three of the four domains scored below the mid-level domain score of 3, that is, the situation is neither favourable nor unfavourable. Areas requiring substantial improvements included priority-setting during research question identification, which had the lowest mean score of 2.12. This was followed by promoting use of postgraduate research products, tying at mean scores of 2.28 each. The domain knowledge transfer of postgraduate research products had an above-average mean score of 2.75.

Conclusions
This study reports that existing research support mechanisms for postgraduate students in Uganda encourage access to supervisors and mentors during proposal development. Postgraduate students’ engagement with research users was limited in priority-setting and knowledge transfer. Since supervisors and mentors views were not captured, future follow-on research could tackle this aspect.
Comprehensive analysis of EMT-related genes and lncRNAs in the prognosis, immunity, and drug treatment of colorectal cancer
Authors: Yang Yang , Feng Mingyang , Bai LiangLiang , Liao Weiting , Zhou Kexun , Zhang Mengxi , Wu Qiuji , Wen Feng , Lei Wanting , Zhang Pengfei , Zhang Nan , Huang Jiaxing , Li Qiu 
Published: September 2021

Abstract
Background
EMT is an important biological process in the mechanism of tumor invasion and metastasis. However, there are still many unknowns about the specific mechanism of EMT in tumor. At present, a comprehensive analysis of EMT-related genes in colorectal cancer (CRC) is still lacking.

Methods
All the data were downloaded from public databases including TCGA database (488 tumor samples and 52 normal samples) as the training set and the GEO database (GSE40967 including 566 tumor samples and 19 normal samples, GSE12945 including 62 tumor samples, GSE17536 including 177 tumor samples, GSE17537 including 55 tumor samples) as the validation sets. One hundred and sixty-six EMT-related genes (EMT-RDGs) were selected from the Molecular Signatures Database. Bioinformatics methods were used to analyze the correlation between EMT-RDGs and CRC prognosis, metastasis, drug efficacy, and immunity.

Results
We finally obtained nine prognostic-related EMT-RDGs (FGF8, NOG, PHLDB2, SIX2, SNAI1, TBX5, TIAM1, TWIST1, TCF15) through differential expression analysis, Unicox and Lasso regression analysis, and then constructed a risk prognosis model. There were significant differences in clinical characteristics, 22 immune cells, and immune functions between the high-risk and low-risk groups and the different states of the nine prognostic-related EMT-RDGs. The methylation level and mutation status of nine prognostic-related EMT-RDGs all affect their regulation of EMT. The Cox proportional hazards regression model was also constructed by the methylation sites of nine prognostic-related EMT-RDGs. In addition, the expression of FGF8, PHLDB2, SIX2, and SNAIL was higher and the expression level of NOG and TWIST1 was lower in the non-metastasis CRC group. Nine prognostic-related EMT-RDGs also affected the drug treatment response of CRC.

Conclusions
Targeting these nine prognostic-related EMT-RDGs can regulate CRC metastasis and immune, which is beneficial for the prognosis of CRC patients, improve drug sensitivity in CRC patients.
Dexamethasone enhances the efficacy of atorvastatin in inhibiting excessively inflammation-induced abnormal angiogenesis by regulating macrophages
Authors: Gong Zhitao , Zhan Daqiang , Nie Meng , Li Xiaochun , Gao Chuang , Liu Xuanhui , Xiang Tangtang , Yuan Jiangyuan , Jiang Weiwei , Huang Jinhao , Quan Wei , Wang Dong , Tian Ye , Yuan Hengjie , Zhang Jianning , Jiang Rongcai 
Published: September 2021

Abstract
Background
We have recently showed that atorvastatin (ATO) combined with low dose of dexamethasone (DEX) was more efficacious in treating patients with chronic subdural haematoma (CSDH) than ATO monotherapy. This study was designed to investigate the underlying mechanisms of the improved efficacy of this combined therapy.

Methods
Mass spectrometry was performed to quantitatively detect drugs in haematoma fluids and serum samples from CSDH patients and also in cultured macrophages after treatment with either ATO alone or in combination with DEX. The differentiation and apoptosis of macrophages were evaluated using flow cytometry. The expression of cytokines, chemokines and angiogenesis-related proteins was evaluated using proteome profile arrays, immunoblots and ELISA, respectively.

Results
ATO was detected in haematoma fluids and serum samples, whose levels were increased significantly in samples collected from patients treated with both ATO and DEX. ATO was also increased in cultured macrophages treated with ATO and DEX. The numbers of M1-polarized macrophages were higher than the M2 phenotype in the haematoma fluids of patients. Cultured macrophages treated with ATO and DEX had reduced numbers of M1-polarized macrophages, increased numbers of M2-polarized macrophages as compared to monotherapies, and decreased rate of apoptosis induced by high-dose DEX. DEX enhanced the anti-inflammatory and anti-angiogenic activity of ATO by suppressing VEGFA and other inflammatory angiogenic factors. Consistent with the finding, patients responded well to the drug treatments had lower serum levels of VEGFA.

Conclusions
We have shown for the first time that ATO given orally was detected in CSDH haematoma fluids. DEX enhances the anti-inflammatory and anti-angiogenic effects of ATO, primarily by increasing the presence of ATO in haematoma and macrophages and by regulating the functions of macrophages.
Development of genus-specific universal primers for the detection of flaviviruses
Authors: Daidoji Tomo , Morales Vargas Ronald Enrique , Hagiwara Katsuro , Arai Yasuha , Watanabe Yohei , Nishioka Keisuke , Murakoshi Fumi , Garan Kotaro , Sadakane Hiroki , Nakaya Takaaki 
Published: September 2021

Abstract
Background
Flaviviruses are representative arboviruses carried by arthropods and/or vertebrates; these viruses can pose a public health concern in many countries. By contrast, it is known that a novel virus group called insect-specific flaviviruses (ISFs) also infects arthropods, although no such virus has yet been isolated from vertebrates. The characteristics of ISFs, which affect replication of human-pathogenic flaviviruses within co-infected mosquito cells or mosquitoes without affecting the mosquitoes themselves, mean that we should pay attention to both ISFs and human-pathogenic flaviviruses, despite the fact that ISFs appear not to be directly hazardous to human health. To assess the risk of diseases caused by flaviviruses, and to better understand their ecology, it is necessary to know the extent to which flaviviruses are harbored by arthropods.

Methods
We developed a novel universal primer for use in a PCR-based system to detect a broad range of flaviviruses. We then evaluated its performance. The utility of the novel primer pair was evaluated in a PCR assay using artificially synthesized oligonucleotides derived from a template viral genome sequence. The utility of the primer pair was also examined by reverse transcription PCR (RT-PCR) using cDNA templates prepared from virus-infected cells or crude supernatants prepared from virus-containing mosquito homogenates.

Results
The novel primer pair amplified the flavivirus NS5 sequence (artificially synthesized) in all samples tested (six species of flavivirus that can cause infectious diseases in humans, and flaviviruses harbored by insects). In addition, the novel primer pair detected viral genomes in cDNA templates prepared from mosquito cells infected with live flavivirus under different infectious conditions. Finally, the viral genome was detected with high sensitivity in crude supernatants prepared from pooled mosquito homogenates.

Conclusion
This PCR system based on a novel primer pair makes it possible to detect arthropod-borne flaviviruses worldwide (the primer pair even detected viruses belonging to different genetic subgroups). As such, an assay based on this primer pair may help to improve public health and safety, as well as increase our understanding of flavivirus ecology.
Androgen receptor regulates the proliferation of myoblasts under appropriate or excessive stretch through IGF-1 receptor mediated p38 and ERK1/2 pathways
Authors: Fu Shaoting , Lin Xiaojing , Yin Lijun , Wang Xiaohui 
Published: September 2021

Abstract
Background
Androgen receptor (AR) exerts important roles in exercise-induced alterations of muscle mass, in which the proliferation and differentiation of satellite cells or myoblasts are crucial. Our previous study in C2C12 myoblasts demonstrated that 15% (mimic appropriate exercise) and 20% (mimic excessive exercise) stretches promoted and inhibited the proliferation respectively; and AR played a crucial role in 15% stretch-induced pro-proliferation through IGF-1-modulated PI3K/Akt, p38 and ERK1/2 pathways, but AR’s role in stretches-modulated proliferation of general myoblasts, especially 20% stretch, remains unclear, and the mechanisms need to be further clarified.

Methods
Firstly, the discrepancy in proliferation and the above indicators between L6 (without AR) and C2C12 (with AR) myoblasts were compared under 15% or 20% stretch. Then the influences of transfection AR or exogenous IGF-1 treatment on proliferation and these indicators were detected in stretched L6 myoblasts.

Results
(1) Under un-stretched state, the proliferation of L6 was slower than C2C12 cells. Furthermore, AR knockdown in C2C12 myoblasts repressed, while AR overexpression in L6 myoblasts promoted the proliferation. (2) 15% stretch-induced increases in the proliferation and activities of p38 and ERK1/2 were lower in L6 than C2C12 cells; AR overexpression enhanced the proliferation of 15% stretched L6 cells accompanied with the increases of p38 and ERK1/2 activities. (3) 20% stretch-induced anti-proliferation and inhibition of p38 activity were severer in L6 than C2C12 myoblasts; AR overexpression reversed the anti-proliferation of 20% stretch and enhanced p38 activity in L6 myoblasts. (4) In stretched L6 myoblasts, AR overexpression increased IGF-1R level despite no detectable IGF-1; and recombinant IGF-1 increased the proliferation, the level of IGF-1R, and the activities of p38 and ERK1/2 in 15% stretched L6 myoblasts.

Conclusions
The study demonstrated AR's crucial roles in stretches-regulated proliferation of myoblasts, and increased AR fulfilled 15% stretch's pro-proliferation via activating IGF-1R- p38 and ERK1/2 pathways while decreased AR achieved 20% stretch's anti-proliferation via inhibiting IGF-1R- p38 pathway, which is useful to understand in depth the role and mechanisms of AR in appropriate exercise increasing while excessive exercise decreasing muscle mass.
Analysis of risk factors for perioperative hidden blood loss in unilateral biportal endoscopic spine surgery: a retrospective multicenter study
Authors: Wang Haosheng , Wang Kai , Lv Bin , Li Wenle , Fan Tingting , Zhao Jianwu , Kang Mingyang , Dong Rongpeng , Qu Yang 
Published: September 2021

Abstract
Background
Hidden blood loss (HBL) represents an important complication of unilateral biportal endoscopic (UBE) spine surgery. This study aimed to evaluate HBL and its possible risk factors among patients undergoing UBE surgery for lumbar degenerative diseases.

Methods
This multicentric retrospective study was conducted in 3 different medical centers between July 2020 and April 2021. Data of patients who underwent UBE surgery were extracted by electronic medical record system. The patient’s demographic characteristics and blood loss-related parameters were recorded. We calculated the amount of HBL and explored the association between patient’s characteristics and HBL using Pearson or Spearman correlation analysis. Multivariate linear regression analysis was conducted to identify independent risk factors of HBL.

Results
A total of 136 patients (55 females and 81 males, age range 43 to 74 years) were included in this study. A substantial amount of HBL (469.5 ± 195.3 ml, 57.6% of TBL, total blood loss) occurred following UBE surgery. Multiple linear regression analysis indicated that the risk factors of HBL were as follows: age (P = 0.000), number of fusion levels (P = 0.015), American Society of Anesthesiologists (ASA) classification (P = 0.046), surgery time (P = 0.017), patient’s blood volume (PBV, P = 0.026), total blood loss (TBL, P = 0.001), postoperative (i.e., day 2 or 3) hematocrit (Hct, P = 0.034), Hct loss (P = 0.005), and fibrinogen (P = 0.028).

Conclusions
A certain amount of HBL occurs in UBE surgery and cannot be ignored in daily clinical practice. The age, number of fusion levels, ASA classification, surgery time, PBV, TBL, postoperative Hct, Hct loss, and fibrinogen are independent risk factors for HBL.
Epidemiology, classification, treatment, and mortality of adult femoral neck and basicervical fractures: an observational study of 40,049 fractures from the Swedish Fracture Register
Authors: Sundkvist Jonas , Brüggeman Anders , Sayed-Noor Arkan , Möller Michael , Wolf Olof , Mukka Sebastian 
Published: September 2021

Abstract
Background
Although femoral neck fractures (FNFs) are common in orthopedic departments, optimal treatment methods remain in dispute. There are few large nationwide studies, including basicervical FNFs (bFNFs), on epidemiology, treatment, and mortality. This nationwide study aims to describe the epidemiology, fracture classification, current treatment regimens, and mortality of undisplaced and minimally displaced (Garden I–II, uFNF), displaced (Garden III–IV, dFNF) and bFNFs in adults.

Methods
All FNFs, including bFNFs with a registered injury date between 1 April 2012 and 31 December 2020, were included in this observational study from the Swedish Fracture Register (SFR). Data on age, sex, injury mechanism, fracture classification, primary treatment, and seasonal variation were analyzed.

Results
Some 40,049 FNFs were registered in the SFR. The mean age of the patients in the register was 80.3 (SD 11) years and 63.8% (25,567) were female. Of all FNFs, 25.0% (10,033) were uFNFs, 63.4% (25,383) dFNFs, and 11.6% (4,633) bFNFs. Non-surgical treatment was performed in 0.6% (261) of the patients. Internal fixation (IF) (84.7%) was the main treatment for uFNFs and arthroplasty (87.3%) for dFNFs. For bFNFs, IF (43.8%) and hip arthroplasty (45.9%) were performed equally often. Of the 33,105 patients with a 1-year follow-up mortality at 1-year was 20.6% for uFNF, 24.3% for dFNF, and 25.4% for bFNF.

Conclusion
The main treatment of uFNFs is IF with screws or pins. Hip arthroplasty is the predominant treatment for dFNF. bFNF are more common than previously reported and treated with IF or arthroplasty, depending on patient age. These results may help health care providers, researchers and clinicians better understand the panorama of FNFs in Sweden.

Level of Evidence
IV, retrospective cohort study.
The influence of posterior tibial slope on the mid-term clinical effect of medial-pivot knee prosthesis
Authors: Shi Weipeng , Jiang Yaping , Zhao Xuan , Zhang Haining , Wang Yingzhen , Li Tao 
Published: September 2021

Abstract
Objective
To evaluate the effect of posterior tibial slope (PTS) on the mid-term clinical outcome following a medial-pivot (MP) prosthesis.

Method
Two hundred thirty-three patients from The Affiliated Hospital of Qingdao University, who had undergone a total knee arthroplasty (TKA) with MP prosthesis between January 2015 and December 2015, were retrospectively included in this study. They were divided into 3 groups according to postoperative PTS: A ≤ 5°; B 5-7°; and C ≥ 7°. Multiple assessments were made on the patient postoperatively and recorded in the three groups, the measurements of this study included: the range of motion (ROM), knee scoring system (KSS), Western Ontario and McMaster universities osteoarthritis index (WOMAC), posterior condylar offset (PCO), joint line height, and postoperative complications.

Results
The average post-operative ROM for groups B and C were 108° and 110° respectively; this was significantly higher than that of group A (98°, P < 0.001). The WOMAC scores of patients in group C were significantly lower than those in groups A and B (P < 0.05). However, there were no significant differences in KSS, PCO, and joint line height among the 3 groups (P > 0.05). Only 2 cases of postoperative complications occurred in group C, these were ameliorated after operation.

Conclusion
With an increase to PTS, the postoperative ROM can be significantly increased for the patient. However, the knee joint function will not be significantly improved, and the stability of knee joint will not be affected when within the limits of appropriate PTS.
Liberal or conservative oxygen therapy for ventilated patients in the ICU: a meta-analysis of randomized controlled trials
Authors: Liu Lu , Tian Yali 
Published: September 2021

Abstract
Background
The acknowledgment that conservative oxygen therapy (COT) was related to better prognosis in the intensive care unit (ICU) was challenged recently. We conducted an updated meta-analysis aimed to determine whether liberal oxygen therapy (LOT) or COT is associated with better improve clinical outcomes.

Methods
We systematically searched the electronic databases (PubMed, Web of Science and Embase) up to May 2021 for randomized controlled trials (RCTs). The primary outcome was the mortality of the final follow-up time and secondary outcomes were ICU mortality, the ICU length of stay and the number of ventilator-free days.

Results
A total of 7 RCTs were included, with 2166 patients admitted to the ICU. There was no significant difference in the primary outcome between the LOT and COT. Additionally, LOT could not significantly increase ICU mortality and the ICU length of stay compared with COT.

Conclusions
The present study showed that COT was not significantly superior to LOT in clinical outcomes. Therefore, additional high-quality studies with novel designs are required to further elucidate this controversy.