bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny, diversification, and biogeography of a hemiclonal hybrid system of native Australian freshwater fishes (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris)
Authors: Thacker Christine E. , Shelley James J. , McCraney W. Tyler , Adams Mark , Hammer Michael P. , Unmack Peter J. 
Published: March 2022

Abstract
Background
Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones.

Results
Hypseleotris cyprinoides, a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris, one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray–Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones.

Conclusions
The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit.
Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction
Authors: Li Bowen , Karthikeyan Adhimoolam , Wang Liqun , Yin Jinlong , Jin Tongtong , Liu Hui , Li Kai , Gai Junyi , Zhi Haijian 
Published: March 2022

Abstract
Background
Soybean mosaic virus (SMV) is one of the most devastating pathogens of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21–24 nucleotides) which are endogenously produced by the plant host as part of a general gene expression regulatory mechanisms, but also play roles in regulating plant defense against pathogens. However, miRNA-mediated plant response to SMV in soybean is not as well documented.

Result
In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1 × Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs profile changes during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. The expression patterns of several miRNAs were validated by quantitative real-time PCR. We also validated the miRNA-target gene interaction by agrobacterium-mediated transient expression in Nicotiana benthamiana.

Conclusion
We have identified a large number of miRNAs and their target genes and also functional annotations. We found that multiple miRNAs were differentially expressed in the two lines and targeted a series of NBS-LRR resistance genes. It is worth mentioning that many of these genes exist in the previous fine-mapping interval of the resistance gene locus. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.
Septic patients without obvious signs of infection at baseline are more likely to die in the ICU
Authors: Campanelli Francesco , Soudry-Faure Agnès , Avondo Aurélie , Roudaut Jean-Baptiste , Quenot Jean-Pierre , Ray Patrick , Charles Pierre-Emmanuel 
Published: March 2022

Abstract
Objective
Early identification of sepsis is mandatory. However, clinical presentation is sometimes misleading given the lack of infection signs. The objective of the study was to evaluate the impact on the 28-day mortality of the so-called “vague” presentation of sepsis.

Design
Single centre retrospective observational study.

Setting
One teaching hospital Intensive Care Unit.

Subjects
All the patients who presented at the Emergency Department (ED) and were thereafter admitted to the Intensive Care Unit (ICU) with a final diagnosis of sepsis were included in this retrospective observational three-year study. They were classified as having exhibited either “vague” or explicit presentation at the ED according to previously suggested criteria. Baseline characteristics, infection main features and sepsis management were compared. The impact of a vague presentation on 28-day mortality was then evaluated.

Interventions
None.

Measurements and main results
Among the 348 included patients, 103 (29.6%) had a vague sepsis presentation. Underlying chronic diseases were more likely in those patients [e.g., peripheral arterial occlusive disease: adjusted odd ratio (aOR) = 2.01, (1.08–3.77) 95% confidence interval (CI); p = 0.028], but organ failure was less likely at the ED [SOFA score value: 4.7 (3.2) vs. 5.2 (3.1), p = 0.09]. In contrast, 28-day mortality was higher in the vague presentation group (40.8% vs. 26.9%, p = 0.011), along with longer time-to-diagnosis [18 (31) vs. 4 (11) h, p < 0.001], time-to-antibiotics [20 (32) vs. 7 (12) h, p < 0.001] and time to ICU admission [71 (159) vs. 24 (69) h, p < 0.001]. Whatever, such a vague presentation independently predicted 28-day mortality [aOR = 2.14 (1.24–3.68) 95% CI; p = 0.006].

Conclusions
Almost one third of septic patient requiring ICU had a vague presentation at the ED. Despite an apparent lower level of severity when initially assessed, those patients had an increased risk of mortality that could not be fully explained by delayed diagnosis and management of sepsis.
Incidence and survival in oral and pharyngeal cancers in Finland and Sweden through half century
Authors: Koskinen Anni I. , Hemminki Otto , Försti Asta , Hemminki Kari 
Published: March 2022

AbstractBackgroundCancers of the oral cavity and pharynx encompass a heterogeneous group of cancers for which known risk factors include smoking, alcohol consumption and human papilloma virus (HPV) infection but their influence is site-specific with HPV mainly influencing oropharyngeal cancer. Their incidence and survival rates are not well known over extended periods of time.Patients/methodsData were obtained for Finnish (FI) and Swedish (SE) patients from the Nordcan database recently updated through 2019. Age-adjusted incidence trends (FI from 1953, SE from 1960) and relative survival rates for years 1970 through 2019 were calculated.ResultsWe observed a prominent increase in oral and oropharyngeal cancers in FI and SE men and women but the trend for oral cancer was interrupted for SE men in 1985 and possibly also for FI and SE women in 2015. The trend changes in male and female oral cancer was confirmed in data for Denmark and Norway. Relative survival for these cancers has improved overall but they differed for one cluster of oral, oropharyngeal and nasopharyngeal cancers with 60–70% 5-year survival in the last period and hypopharyngeal cancer with 25% male survival. In all these cancers, survival for old patients was unfavorable.Discussion/conclusionWe hypothesize that reduction in smoking prevalence helped to stop the increase in oral cancer especially in men. As the prevalence of smoking is decreasing, HPV is becoming a dominant risk factor, particularly for the increasing oropharyngeal cancer. Prevention needs to emphasize sexual hygiene and HPV vaccination.
Soft infrastructure: the critical community-level resources reportedly needed for program success
Authors: Kavanagh Shane A , Hawe Penelope , Shiell Alan , Mallman Mark , Garvey Kate 
Published: March 2022

Abstract
Background
The mechanisms typically used to fund health promotion in communities, either as part of an effort to scale-up programs or to support the design of local activities, often pay insufficient attention to the foundational means of enhancing well-being. Only recently have researchers begun to critically ‘unpack’ how funding processes connect with and activate local community capacities.

Methods
We conducted a thematic analysis of 33 interviews with policy and program administrators in public health and local community workers and volunteers. We invited them to expound on their understandings of resources - specifically, what needs to be in place to make funded programs successful and/or what do communities draw on to make funded programs effective.

Results
Policy and program administrators reflected mostly on the importance of traditional resources, such as adequate funding and staffing. Community-based participants often went further to describe psychological and sociological resources – the “soft infrastructure” which included trust and hope. Both groups emphasised the importance of building networks and relationships at multiple levels. Community workers also provided examples of how resources grow and improve in value in combination with other processes or through pathways of resource use or resource distribution. So, resources like information/knowledge are made more valuable when relayed locally. Physical amenities (e.g., meeting spaces, kitchens) have an instrumental role, but also act powerfully as a symbolic resource for identity. Participants reported that funding processes can damage the resources required for community health improvement. Funding instability undermines capacity. The ongoing threat of funding removal was described by one administrator as community “bullying”.

Conclusions
Processes of health promotion funding, and even standard processes of program scale-up and readiness assessment, risk underestimating the range of resources that are fundamental for community health improvement, particularly among disadvantaged communities. Funders should design ways to resource communities so that there is constant attention to and coaching of critically important diverse processes of resource growth, independent of program-specific funds.
Associations between serum biomarkers of cartilage metabolism and serum hyaluronic acid, with risk factors, pain categories, and disease severity in knee osteoarthritis: a pilot study
Authors: Papaneophytou Christos , Alabajos-Cea Ana , Viosca-Herrero Enrique , Calvis Carme , Costa Marta , Christodoulides Andreas E. , Kroushovski Alexander , Lapithis Alkis , Lapithi Vaia Maligianni , Papayiannis Ioannis , Christou Andreas , Messeguer Ramon , Giannaki Christoforos , Felekkis Kyriacos 
Published: March 2022

Abstract
Background
Specific serum biomarkers of cartilage metabolism such as cartilage oligomeric matrix protein (sCOMP) and procollagen type II C-terminal propeptide (sPIICP) as well as hyaluronan (sHA), a biomarker of synovitis, have been implicated in the pathophysiology of knee osteoarthritis (OA). However, the associations of these biomarkers with the severity of the disease and OA risk factors, including age and obesity remain inconclusive. This analysis examines the associations between these serum biomarkers and the radiographic severity of OA and knee pain, as wells as obesity, the age and gender of the participants, and other OA risk factors.

Methods
From 44 patients with early knee OA and 130 patients with late knee OA we analyzed the radiographic severity of the disease using the Kellgren and Lawrence (KL) grading system. Moreover, 38 overweight healthy individuals were used as a control group. Specific information was collected from all participants during their recruitment. The levels of the three serum biomarkers were quantified using commercially available ELISA kits. Serum biomarkers were analyzed for associations with the average KL scores and pain in both knees, as well as with specific OA risk factors.

Results
The levels of sCOMP were elevated in patients with severe late OA and knee pain and correlated weakly with OA severity. A weakly correlation of sHA levels and OA severity OA was observed. We demonstrated that only sPIICP levels were markedly decreased in patients with late knee OA suggesting the alterations of cartilage metabolism in this arthritic disease. Moreover, we found that sPIICP has the strongest correlation with obesity and the severity of OA, as well as with the knee pain at rest and during walking regardless of the severity of the disease. ROC analysis showed that the area under the ROC curve (AUC) was 0.980 (95% CI: 0.945–0.995; p < 0.0001), suggesting high diagnostic accuracy of sPIICP. Interestingly, gender and age had also an effect on the levels of sPIICP.

Conclusion
This study revealed the potential of serum PIICP to be used as a biomarker to monitor the progression of knee OA, however, further studies are warranted to elucidate its clinical implication.
Three-dimensional imaging for the localization of related anatomical structures during surgery on the internal auditory canal
Authors: Guo Ying , Li Mengxing , Cheng Kailiang , Li Youqiong , Ma Qingjie 
Published: March 2022

AbstractBackgroundThe Fisch infra-temporal fossa approach (Fisch’s method), first proposed in 1970, is commonly used during internal auditory canal (IAC) surgery with an approach that advances through the middle cranial fossa. This study was designed to address the technical difficulties encountered in recognizing and localizing the arcuate eminence with respect to the superior semicircular canal (SSC).MethodsForty men and 40 women (18–57 years of age) without space-occupying lesions in the petrous part of the temporal bone were selected for the study. In total, 160 samples were obtained from both sides of the temporal bone. The temporal bone in these 160 samples was scanned using computed tomography, and a three-dimensional coordinate system was established to measure the three-dimensional coordinate values of structures adjacent to the arcuate eminence, the SSC, and the IAC.ResultsThe results showed that the shape of the arcuate eminence is highly variable. Approximately 23.12% of samples had no obvious arcuate eminence, which prevented the use of Fisch’s method to localize the SSC. The arcuate eminence was difficult to identify in 37 samples.ConclusionsAnalysis samples showed that the SSC was located in a fan ring centered at the midpoint of the upper edge of the petrous portion of the temporal bone. The arcuate eminence did not correspond directly with the SSC, as the former was located posterolateral to the latter in 85.83% of samples. The angle between the SSC and the IAC ranged from 0° to 60° degrees, as reported previously by Fisch. However, the angle typically ranged from 10–30° in our study.
Salvage robot-assisted radical prostatectomy following focal ablation with irreversible electroporation: feasibility, oncological and functional outcomes
Authors: Blazevski Alexandar , Gondoputro William , Scheltema Matthijs J. , Amin Amer , Geboers Bart , Barreto Daniela , Haynes Anne-Maree , Shnier Ron , Delprado Warick , Agrawal Shikha , Thompson James E. , Stricker Phillip D. 
Published: March 2022

Abstract
Background
To report the feasibility, oncological and functional outcomes of salvage robot-assisted radical prostatectomy (sRARP) for recurrent prostate cancer (PCa) after irreversible electroporation (IRE).

Methods
This was a retrospective analysis of patients who underwent sRARP by a single high-volume surgeon after IRE treatment in our institution. Surgical complications, oncological and functional outcomes were assessed.

Results
15 patients with at least 12 months follow up were identified out of the 234 men who underwent primary IRE between 2013 and 2019. The median [IQR] age was 68 (62–70) years. The median [IQR] time from focal IRE to sRARP was 42 (21–57) months. There were no rectal, bladder or ureteric injuries. The T-stage was pT2 in 9 (60%) patients and pT3a in 6 (40%) patients. Only one (7%) patient had a positive surgical margin. At a median [IQR] follow up of 22 (16–32) months no patient had a biochemical recurrence (PSA > 0.2). All 15 patients were continent (pad-free) by 6 months and 9 (60%) patients had erections sufficient for intercourse with or without PDE5 inhibitors. No predisposing factors were identified for predicting erectile dysfunction after sRARP.

Conclusions
In patients with recurrent or residual significant PCa after focal IRE ablation it is feasible to obtain good functional and oncological outcomes with sRARP. Our results demonstrate that good outcomes can be achieved with sRARP, when respecting close monitoring post-IRE, good patient selection and surgical experience. The limitations of this study are that it is a small series, with short follow up and a lack of standardised quality of life instruments.
Nutrient pattern analysis of mineral based, simple sugar based, and fat based diets and risk of metabolic syndrome: a comparative nutrient panel
Authors: Nikniaz Leila , Mahmudiono Trias , Jasim Saade Abdalkareem , Vajdi Mahdi , Thangavelu Lakshmi , Farhangi Mahdieh Abbasalizad 
Published: March 2022

Abstract
Background
Although there is growing evidence on the association between nutrient patterns and metabolic risk factors, very little is known about the relationship between nutrient patterns and metabolic syndrome (MetS). The aim of this study was to examine the associations of nutrient patterns with MetS among apparently healthy obese adults living in Tabriz, Iran.

Methods
Three hundred and forty-seven apparently healthy obese (BMI ≥ 30 kg/m2) adults aged 20–50 years were included in this cross-sectional study. Dietary intake of 38 nutrients was assessed by a validated semi-quantitative food frequency questionnaire (FFQ) of 132 food items. Nutrient patterns were determined using factor analysis. The MetS was defined based on the guidelines of the National Cholesterol Education Program Adult Treatment Panel III (ATP III).

Results
Three major nutrient patterns were extracted: “Mineral based pattern”, “Simple sugar based pattern” and “Fat based pattern”. There was no significant association between nutrient patterns and MetS,
in the crude model even after adjusting for confounders. There was a significant difference between quartiles in the mineral based pattern for free mass (FFM), diastolic blood pressure (DBP), large Waist circumference (WC) and Waist-to-hip ratio (WHR). In the simple sugar based pattern, we observed a significant association for SBP, DBP, and triglyceride (TG) levels. In addition, the fat based pattern was positively associated with BMI, and weight.

Conclusions
We did not observe any significant association of nutrient patterns with the risk of MetS amongst the apparently healthy obese adult's population. Whereas we confirmed the deleterious effect of the simple sugar and fat based patterns on several metabolic risk factors, our findings also showed that the mineral based pattern is related to healthier metabolic factors in an Iranian population. These results should be approved by future studies to recognize any causal relationship between adherence to specific nutrient patterns and MetS.
New technique for detecting cracked teeth and evaluating the crack depth by contrast-enhanced cone beam computed tomography: an in vitro study
Authors: Zhou Jie , Fu Jieni , Xiao Mo , Qiao Feng , Fu Tiantian , Lv Yangyang , Wu Fei , Sun Cuicui , Li Peng , Wu Ligeng 
Published: March 2022

Abstract
Background
Cracked teeth may cause various clinical symptoms depending on the extension depth of the crack and the subsequent bacterial infections. However, techniques to reliably determine the extension depths of cracks in teeth before treatment are lacking. The aim of this study was to develop a new technique based on contrast-enhanced cone beam computed tomography (CBCT) to improve the accuracy of crack depth evaluation in vitro.

Methods
We developed an in vitro artificial simulation model of cracked teeth. Pre-experimental CBCT (pre-CBCT), and micro-computed tomography (micro-CT) were first performed for all cracked teeth (n = 31). Contrast-enhanced CBCT was then performed by infiltrating the crack with ioversol under vacuum conditions. The sensitivities of pre-CBCT and contrast-enhanced CBCT for the diagnosis of cracked teeth were calculated. According to the K-means clusters, crack depths measured by micro-CT were changed into categorical variables. Bland–Altman plot and the intraclass correlation coefficient (ICC) were used to analyze the consistency of the crack depths between the pre-CBCT and contrast-enhanced CBCT, as well as the ICC between the contrast-enhanced CBCT and micro-CT. Receiver operating characteristic (ROC) curves were generated to assess the ability for predicting crack depth in the differential diagnosis using pre-CBCT and contrast-enhanced CBCT. Restricted cubic splines were also used to model the non-linear relationship between the crack depths of contrast-enhanced CBCT and micro-CT.

Results
The sensitivities of pre-CBCT and contrast-enhanced CBCT were 48.4%, and 67.7%, respectively. The ICC value of crack depth as measured by pre-CBCT and contrast-enhanced CBCT was 0.847 (95% confidence interval [CI] 0.380–0.960; P < 0.001). The areas under ROC curves (AUC) of pre-CBCT and contrast-enhanced CBCT were different: the AUC of pre-CBCT was 0.958 (P = 0.000, 95% CI 0.843–1.074), and the AUC of contrast-enhanced CBCT was 0.979 (P = 0.000, 95% CI 0.921–1.037), and the difference was not statistically significant (Z = − 0.707, P = 0.480). The ICC value of crack depth as measured by contrast-enhanced CBCT and micro-CT was 0.753 (95% CI 0.248–0.911; P < 0.001).

Conclusion
Contrast-enhanced CBCT under vacuum conditions with a contrast medium can significantly improve the crack detection rate of cracked teeth; however, it cannot measure the crack depths accurately.