bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures
Authors: Liang Linying , Chen Jiawei , Li Yanan , Zhang Haibin 
Published: January 2020

Abstract
Background
Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood.

Results
In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa.

Conclusions
Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.
Volume of tidal gas movement in the nonventilated lung during one-lung ventilation and its relevant factors
Authors: Wei Jionglin , Gao Lei , Sun Fafa , Zhang Mengting , Gu Weidong 
Published: January 2020

AbstractBackgroundThe passive ventilation of nonventilated lung results in tidal gas movement (TGM) and thus affects lung collapse. The present study aimed to measure the volume of TGM and to analyse the relevant factors of the TGM index (TGM/body surface area).MethodsOne hundred eight patients scheduled for elective thoracoscopic surgeries were enrolled. Lung isolation was achieved with a double-lumen endobronchial tube (DLT). The paediatric spirometry sensor was connected to the double-lumen connector of the nonventilated lung to measure the volume of TGM during one-lung ventilation (OLV) in the lateral position. The TGM index was calculated. The multiple linear regression was analysed using the TGM index as the dependent variables. Independent variables were also recorded: 1) age, sex, body mass index (BMI); 2) forced vital capacity (FVC), FEV1/FVC, minute ventilation volume (MVV); 3) dynamic lung compliance (Cdyn) and peak inspiratory pressure (PIP) during dual lung ventilation; 4) the side of OLV; and 5) whether lung puncture for localization of the pulmonary nodule was performed on the day of surgery. The oxygen concentration in the nonventilated lung was measured at 5 min after OLV, and its correlation with the TGM index was analysed.ResultsThe volume of TGM in the nonventilated lung during OLV was 78 [37] mL. The TGM index was 45 [20] mL/m2and was negatively correlated with the oxygen concentration in the nonventilated lung at 5 min after OLV. The multiple linear regression model for the TGM index was deduced as follows: TGM index (mL/m2) = C + 12.770 × a − 3.987 × b-1.237 × c-2.664 × d, where C is a constant 95.621 mL/m2, a is 1 for males and 0 for females, b is 1 for right OLV and 0 for left OLV, c is BMI (kg/m2), and d is PIP (cmH2O).ConclusionsThe TGM index is negatively correlated with the oxygen concentration of the nonventilated lung at 5 min after OLV. Sex, side of OLV, BMI and PIP are independently correlated with the TGM index.Trial registrationThis study was registered at ChiCTR (www.chictr.org.cn, ChiCTR1900024220) on July 1, 2019.
Using research networks to generate trustworthy qualitative public health research findings from multiple contexts
Authors: Nyirenda Lot , Kumar Meghan Bruce , Theobald Sally , Sarker Malabika , Simwinga Musonda , Kumwenda Moses , Johnson Cheryl , Hatzold Karin , Corbett Elizabeth L. , Sibanda Euphemia , Taegtmeyer Miriam 
Published: January 2020

Abstract
Background
Qualitative research networks (QRNs) bring together researchers from diverse contexts working on multi-country studies. The networks may themselves form a consortium or may contribute to a wider research agenda within a consortium with colleagues from other disciplines. The purpose of a QRN is to ensure robust methods and processes that enable comparisons across contexts. Under the Self-Testing Africa (STAR) initiative and the REACHOUT project on community health systems, QRNs were established, bringing together researchers across countries to coordinate multi-country qualitative research and to ensure robust methods and processes allowing comparisons across contexts. QRNs face both practical challenges in facilitating this iterative exchange process across sites and conceptual challenges interpreting findings between contexts. This paper distils key lessons and reflections from both QRN experiences on how to conduct trustworthy qualitative research across different contexts with examples from Bangladesh, Ethiopia, Kenya, Indonesia, Malawi, Mozambique, Zambia and Zimbabwe.

Methods
The process of generating evidence for this paper followed a thematic analysis method: themes initially identified were refined during several rounds of discussions in an iterative process until final themes were agreed upon in a joint learning process.

Results
Four guiding principles emerged from our analysis: a) explicit communication strategies that sustain dialogue and build trust and collective reflexivity; b) translation of contextually embedded concepts; c) setting parameters for contextualizing, and d) supporting empirical and conceptual generalisability. Under each guiding principle, we describe how credibility, dependability, confirmability and transferability can be enhanced and share good practices to be considered by other researchers.

Conclusions
Qualitative research is often context-specific with tools designed to explore local experiences and understandings. Without efforts to synthesise and systematically share findings, common understandings, experiences and lessons are missed. The logistical and conceptual challenges of qualitative research across multiple partners and contexts must be actively managed, including a shared commitment to continuous ‘joint learning’ by partners. Clarity and agreement on concepts and common methods and timelines at an early stage is critical to ensure alignment and focus in intercountry qualitative research and analysis processes. Building good relationships and trust among network participants enhance the quality of qualitative research findings.
Hepatocellular carcinoma with hilar bile duct tumor thrombus versus hilar Cholangiocarcinoma on enhanced computed tomography: a diagnostic challenge
Authors: Zhou Xiaoqi , Wang Jifei , Tang Mimi , Huang Mengqi , Xu Ling , Peng Zhenpeng , Li Zi-Ping , Feng Shi-Ting 
Published: January 2020

AbstractBackgroundHepatocellular carcinoma (HCC) with hilar bile duct tumor thrombus (HBDTT) often mimic hilar cholangiocarcinoma (hilar CC). The purpose of this study is to analyze the Computed Tomography (CT) characteristics of HCC with HBDTT and to identify imaging features to aid its differentiation from hilar CC on enhanced CT.MethodsWe retrospectively identified 58 cases with pathologically proved HCC with HBDTT between 2011 and 2018. Seventy-seven cases of pathologically proven hilar CCs were selected during the same period. The clinical features and CT findings of the two groups were reviewed and compared.ResultsHCC with HBDTTs are more commonly found in men (87.9% vs 63.6%,p = 0.001) with lower age of onset (49.84 vs 58.61 years;p < 0.001) in comparison to hilar CCs. Positive correlation were identified between HCC with HBDTTs and chronic HBV infection (72.4% vs 11.7%;p <  0.001), increased serum AFP (67.2% vs 1.3%;p <  0.001), CA19–9 level (58.6% vs 85.7%;p <  0.001) and CEA level (3.4% vs 29.9%;p = 0.001), parenchymal lesion with intraductal lesion (100% vs 18.2%;p <  0.001), washout during the portal venous phase (84.5% vs 6.5%;p <  0.001), thickened bile duct wall (8.6% vs 93.5%;p <  0.001), intrahepatic vascular embolus (44.8% vs 7.8%;p <  0.001), splenomegaly (34.5% vs 2.6%,p <  0.001). A scoring system consisting of the five parameters obtained from characteristics mentioned above was trialed. The sensitivity and specificity for diagnosing HCC with HBDTT were 96.39, 100 and 92.5% respectively when the total score was 2 or more.ConclusionsHCC with HBDTTs are often distinguishable from hilar CCs based on washout during portal venous phase without thickened bile duct wall. HBV infection and serum AFP level facilitate the differentiation.
Perioperative intraretinal fluid observed using optical coherence tomography in the epiretinal membrane
Authors: Lee Jae Jung , Jo Yeon Ji , Kwon Han Jo , Lee Seung Min , Park Sung Who , Byon Ik Soo , Lee Ji Eun 
Published: January 2020

Abstract
Background
Postoperative intraretinal fluid (IRF) is reportedly associated with visual outcomes after epiretinal membrane (ERM) surgery. However, preoperative IRF is common, and persistent IRF would have different impact on visual function from postoperative newly developed IRF. Therefore, we aimed to investigate the incidence rate and clinical implications of perioperative IRF in ERM.

Methods
Medical records of patients who underwent vitrectomy for idiopathic ERM between January 2014 and January 2017 were reviewed retrospectively. The incidence of IRF was analyzed using optical coherence tomography preoperatively and 1, 3, and 6 months postoperatively. On the basis of the presence or absence and the time of detection of IRF, patients were divided into three groups, namely preoperative IRF group, New IRF group, and IRF(−) group. Correlations of various parameters including age, sex, baseline visual acuity (VA), central subfield macular thickness, lens status, and surgical factors with IRF, along with the effect of IRF on VA, were evaluated.

Results
This study included 155 eyes from 155 patients. Thirty-six (23.2%) and 49 (31.6%) eyes demonstrated preoperative and newly developed IRF, respectively. Seventy eyes (45.2%), which did not exhibit IRF during the study period, were assigned to the IRF(−) group. At baseline, the IRF(−) group showed a better VA than the other two groups. Postoperatively, VA improved significantly in all three groups. There was no difference in VA between the IRF(−) and new IRF groups at 6 months; however, the preoperative IRF group had significantly lower VA than the other two groups.

Conclusion
IRF associated with ERM was frequently observed preoperatively and postoperatively, but it did not prevent postoperative vision improvement. Preoperative IRF was related to lower postoperative vision improvement.
A systematic review of factors influencing NHS health check uptake: invitation methods, patient characteristics, and the impact of interventions
Authors: Bunten Amanda , Porter Lucy , Gold Natalie , Bogle Vanessa 
Published: January 2020

Abstract
Background
The NHS Health Check (NHSHC) is a risk assessment for those aged 40–74 without a pre-existing condition in England, with the aim of preventing stroke, kidney disease, heart disease, type 2 diabetes and dementia. Uptake has been lower than anticipated. Ensuring that a high percentage of eligible patients receive a NHSHC is key to optimising the clinical and cost effectiveness of the programme. The aim of this systematic review is to highlight interventions and invitation methods that increase the uptake of NHSHCs, and to identify whether the effectiveness of these interact with broader patient and contextual factors.

Method
A systematic review was conducted according to the PRISMA checklist. Papers were eligible if they explored the impact of at least one of (i) interventions, (ii) invitation methods or (iii) broader factors on NHSHC uptake. Ten databases were searched in January 2016 and seven were searched in March 2018. Nine-hundred-and-forty-five papers were identified, 238 were screened and 64 full texts were assessed for eligibility. Nine studies were included in the review.

Results
The nine studies were all from peer reviewed journals. They included two randomised controlled trials, one observational cohort and six cross-sectional studies. Different invitation methods may be more effective for different groups of patients based on their ethnicity and gender. One intervention to enhance invitation letters effectively increased uptake but another did not. In addition, individual patient characteristics (such as age, gender, ethnicity and risk level) were found to influence uptake. This review also finds that uptake varies significantly by GP practice, which could be due either to unidentified practice-level factors or deprivation.

Conclusions
Further research is needed to assess the effectiveness of different invitation methods for different population groups. Research should examine how existing invitation methods can be enhanced to drive uptake whilst reducing health inequalities.

Trial registration
This systematic review was registered with PROSPERO on 22.02.2016. Registration number CRD42016035626.
Schistosomiasis vaccine development: update on human clinical trials
Authors: Molehin Adebayo J. 
Published: January 2020

AbstractSchistosomiasis causes significant levels of morbidity and mortality in many geographical regions of the world. The disease is caused by infections with parasitic blood flukes known as schistosomes. The control of schistosomiasis over the last several decades has been centered on the mass drug administration (MDA) of praziquantel (PZQ), which is the only drug currently available for treatment. Despite the concerted efforts of MDA programs, the prevalence and transmission of schistosomiasis has remained largely unchecked due to the fact that PZQ is ineffective against juvenile schistosomes, does not prevent re-infection and the emergence of PZQ-resistant parasites. In addition, other measures such as the water, sanitation and hygiene programs and snail intermediate hosts control have had little to no impact. These drawbacks indicate that the current control strategies are severely inadequate at interrupting transmission and therefore, implementation of other control strategies are required. Ideally, an efficient vaccine is what is needed for long term protection thereby eliminating the current efforts of repeated mass drug administration. However, the general consensus in the field is that the integration of a viable vaccine with MDA and other control measures offer the best chance of achieving the goal of schistosomiasis elimination. This review focuses on the present status of schistosomiasis vaccine candidates in different phases of human clinical trials and provide some insight into future vaccine discovery and design.
Estimating spatio-temporal distributions of mosquito breeding pools in irrigated agricultural schemes: a case study at the Bwanje Valley Irrigation Scheme
Authors: Frake April N. , Namaona Willy , Walker Edward D. , Messina Joseph P. 
Published: January 2020

Abstract
Background
The association between irrigation and the proliferation of adult mosquitoes including malaria vectors is well known; however, irrigation schemes are treated as homogenous spatio-temporal units, with little consideration for how larval breeding varies across space and time. The objective of this study was to estimate the spatio-temporal distribution of pools of water facilitating breeding at the Bwanje Valley Irrigation Scheme (BVIS) in Malawi, Africa as a function of environmental and anthropogenic characteristics.

Methods
Irrigation structure and land cover were quantified during the dry and rainy seasons of 2016 and 2017, respectively. These data were combined with soil type, irrigation scheduling, drainage, and maintenance to model suitability for mosquito breeding across the landscape under three scenarios: rainy season, dry season with limited water resources, and a dry season with abundant water resources.

Results
Results demonstrate seasonal, asymmetrical breeding potential and areas of maximum breeding potential as a function of environmental characteristics and anthropogenic influence in each scenario. The highest percentage of suitable area for breeding occurs during the rainy season; however, findings show that it is not merely the amount of water in an irrigated landscape, but the management of water resources that determines the aggregation of water bodies. In each scenario, timing and direction of irrigation along with inefficient drainage render the westernmost portion of BVIS the area of highest breeding opportunity, which expands and contracts seasonally in response to water resource availability and management decisions.

Conclusions
Changes in the geography of breeding potential across irrigated spaces can have profound effects on the distribution of malaria risk for those living in close proximity to irrigated agricultural schemes. The methods presented are generalizable across geographies for estimating spatio-temporal distributions of breeding risk for mosquitoes in irrigated schemes, presenting an opportunity for greater geographically targeted strategies for management.
Treatment of patellar dislocation with arthroscopic medial patellofemoral ligament reconstruction using gracilis tendon autograft and modified double-patellar tunnel technique: minimum 5-year patient-reported outcomes
Authors: Gao Guanying , Liu Ping , Xu Yan 
Published: January 2020

Abstract
Background
The purpose of this study was to retrospectively analyze the clinical outcomes of patients with recurrent patellar dislocation who underwent arthroscopic medial patellofemoral ligament (MPFL) reconstruction using gracilis tendon autograft and a modified double-patellar tunnel method. We hypothesized that our modified method would provide good clinical outcomes.

Methods
Patients who underwent arthroscopic MPFL reconstruction with autograft gracilis tendon and modified double-patellar tunnels technique for recurrent patellar dislocation and were followed up for a minimum of 5 years were identified, and the clinical and follow-up data were retrospectively analyzed. Preoperatively, joint hypermobility was assessed with the Beighton score. The Insall–Salvati ratio, TT–TG distance, and Q angle were measured on radiographic images. Patient-reported outcomes including the Kujala, Lysholm, and Tegner scores were collected preoperatively and postoperatively. Patient satisfaction was assessed at the end of 5 years. Complications and recurrent dislocation occurring after surgery were recorded.

Results
A total of 79 patients (94 knees) were enrolled; of these, 13 (16.5%) were lost to follow-up. The data of 66 patients (80 knees) were available for final analysis. Mean age at surgery was 21.3 ± 7.8 years. Mean follow-up time was 66.1 ± 5.5 months (range, 60–78 months). Postoperative patient-reported outcome was not associated with Beighton score, Insall–Salvati ratio, or TT–TG distance. Q angle was negatively correlated to Kujala scores and Lysholm scores. Severity of trochlear dysplasia was not associated with postoperative patient-reported outcome. The mean Kujala score increased from 69.4 ± 7.9 to 96.1 ± 1.9, the mean Tegner score increased from 3.1 ± 1.3 to 5.9 ± 1.3, and the mean Lysholm score increased from 73.5 ± 14.6 to 95.3 ± 3.4. Two patients experienced recurrent patellar dislocation during follow-up.

Conclusions
MPFL reconstruction using autologous gracilis tendon under arthroscopy appears to be a reliable and safe method for treating recurrent patellar dislocation.

Level of evidence
Level IV.
Comparison of liver MRI R2(FerriScan®) VS liver MRI T2* as a measure of body iron load in a cohort of beta thalassaemia major patients
Authors: Padeniya Padmapani , Siriwardana Shirom , Ediriweera Dileepa , Samarasinghe Nayana , Silva Sasanka , Silva Ishari , Ahamed Nizri , Niriella Madunil , Premawardhena Anuja 
Published: January 2020

AbstractTo compare the similarity of the non-patented T2* and the high cost patented R2 (Ferriscan®) MRI techniques in the measurement of liver iron concentration (LIC) in heavily transfused patients with thalassaemia major in a real- life Sri Lankan hospital setup. We compared LIC measured by MRI, obtained 2 weeks apart, using both T2* and R2 techniques in 15 patients with beta thalassaemia major. They all had a history of > 100 units of blood transfusions life long and also a history of sub optimal chelation. MRI R2 and MRI T2* scan values showed a negative correlation (co-rrelation coefficient = − 0.63, p = 0.01) This correlation was strong in lower LICs and progressively decreased with upper LIC values. Thus a significant discrepancy was observed between median values of two MRI technologies (p = 0.0005) with T2* tending to underestimate iron overload especially in those with very high LIC identified by R2. The lack of concordance of T2* and R2 especially in those with very high reading on R2 suggest the potential errors in interpretations that can occur in “non-expert centres”; which are likely to lead to errors in clinical judgement on the intensity of chelation therapy needed.
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods
Authors: Moore Jill E. , Pratt Henry E. , Purcaro Michael J. , Weng Zhiping 
Published: January 2020

Abstract
Background
Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes.

Results
To facilitate the development of computational methods for predicting target genes, we develop a Benchmark of candidate Enhancer-Gene Interactions (BENGI) by integrating the recently developed Registry of cCREs with experimentally derived genomic interactions. We use BENGI to test several published computational methods for linking enhancers with genes, including signal correlation and the TargetFinder and PEP supervised learning methods. We find that while TargetFinder is the best-performing method, it is only modestly better than a baseline distance method for most benchmark datasets when trained and tested with the same cell type and that TargetFinder often does not outperform the distance method when applied across cell types.

Conclusions
Our results suggest that current computational methods need to be improved and that BENGI presents a useful framework for method development and testing.