bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Waiting Room Hypothesis revisited by orchids: were orchid mycorrhizal fungi recruited among root endophytes?
Authors: Selosse Marc-André , Petrolli Rémi , Mujica María Isabel , Laurent Liam , Perez-Lamarque Benoît , Figura Tomáš , Bourceret Amelia , Jacquemyn Hans , Li Taiqiang , Gao Jiangyun , Minasiewicz Julita , Martos Florent 
Published: October 2021

Abstract

Background
As in most land plants, the roots of orchids (Orchidaceae) associate with soil fungi. Recent studies have highlighted the diversity of the fungal partners involved, mostly within Basidiomycotas. The association with a polyphyletic group of fungi collectively called rhizoctonias (Ceratobasidiaceae, Tulasnellaceae and Serendipitaceae) is the most frequent. Yet, several orchid species target other fungal taxa that differ from rhizoctonias by their phylogenetic position and/or ecological traits related to their nutrition out of the orchid roots (e.g. soil saprobic or ectomycorrhizal fungi). We offer an evolutionary framework for these symbiotic associations.

Scope
Our view is based on the ‘Waiting Room Hypothesis’, an evolutionary scenario stating that mycorrhizal fungi of land flora were recruited from ancestors that initially colonized roots as endophytes. Endophytes biotrophically colonize tissues in a diffuse way, contrasting with mycorrhizae by the absence of morphological differentiation and of contribution to the plant’s nutrition. The association with rhizoctonias is probably the ancestral symbiosis that persists in most extant orchids, while during orchid evolution numerous secondary transitions occurred to other fungal taxa. We suggest that both the rhizoctonia partners and the secondarily acquired ones are from fungal taxa that have broad endophytic ability, as exemplified in non-orchid roots. We review evidence that endophytism in non-orchid plants is the current ecology of many rhizoctonias, which suggests that their ancestors may have been endophytic in orchid ancestors. This also applies to the non-rhizoctonia fungi that were secondarily recruited by several orchid lineages as mycorrhizal partners. Indeed, from our review of the published literature, they are often detected, probably as endophytes, in extant rhizoctonia-associated orchids.

Conclusion
The orchid family offers one of the best documented examples of the ‘Waiting Room Hypothesis’: their mycorrhizal symbioses support the idea that extant mycorrhizal fungi have been recruited among endophytic fungi that colonized orchid ancestors.
Heterozygous Tropomodulin 3 mice have improved lung vascularization after chronic hypoxia
Authors: Stobdan Tsering , Jain Pritesh P , Xiong Mingmei , Bafna Vineet , Yuan Jason X-J , Haddad Gabriel G 
Published: October 2021

Abstract
The molecular mechanisms leading to high-altitude pulmonary hypertension (HAPH) remains poorly understood. We previously analyzed the whole genome sequence of Kyrgyz highland population and identified eight genomic intervals having a potential role in HAPH. Tropomodulin 3 gene (TMOD3), which encodes a protein that binds and caps the pointed ends of actin filaments and inhibits cell migration, was one of the top candidates. Here we systematically sought additional evidence to validate the functional role of TMOD3. In-silico analysis reveals that some of the SNPs in HAPH associated genomic intervals were positioned in a regulatory region that could result in alternative splicing of TMOD3. In order to functionally validate the role of TMOD3 in HAPH, we exposed Tmod3−/+ mice to 4 weeks of constant hypoxia, i.e. 10% O2 and analyzed both functional (hemodynamic measurements) and structural (angiography) parameters related to HAPH. The hemodynamic measurements, such as right ventricular systolic pressure, a surrogate measure for pulmonary arterial systolic pressure, and right ventricular contractility (RV- ± dP/dt), increases with hypoxia did not separate between Tmod3−/+ and control mice. Remarkably, there was a significant increase in the number of lung vascular branches and total length of pulmonary vascular branches (P &lt; 0.001) in Tmod3−/+ after 4 weeks of constant hypoxia as compared with controls. Notably, the Tmod3−/+ endothelial cells migration was also significantly higher than that from the wild-type littermates. Our results indicate that, under chronic hypoxia, lower levels of Tmod3 play an important role in the maintenance or neo-vascularization of pulmonary arteries.
Reply to Jansen and Gjerde's (2021) critique of the salmon louse infection model reported in Johnsen et al. (2021)
Authors: Johnsen Ingrid A , Harvey Alison , Næverlid Sævik Pål , Sandvik Anne D , Ugedal Ola , Ådlandsvik Bjørn , Wennevik Vidar , Glover Kevin A , Karlsen Ørjan 
Published: October 2021

Abstract
To estimate salmon lice-induced mortality of wild salmon post-smolts, a model system was developed by Johnsen et al. to support management strategies. To ensure realistic model estimates, lice-infestation values from the model were calibrated against empirical observations on wild post-smolts captured by trawling. These fish were genetically assigned to their rivers of origin. A critique by Jansen and Gjerde claims that the model developed by Johnsen et al. systematically overestimates lice induced mortality of post-smolts. Here, we illustrate how the analysis performed by Jansen and Gjerde is based upon two datasets that mismatch temporally and spatially. In addition, their analysis does not take uneven catch between the rivers into account. Due to this, we argue that the analysis in the criticism is not well founded. We also take the opportunity to present in more detail the observational dataset available for the model calibration, its limitations and the potential impacts on the model estimates. Additional validation with new data demonstrates that the model does not provide systematically biased results. Finally, we argue that the discrepancy between the modelled and observed lice levels in our system is not evidence of its shortcomings, but rather, represents an example of how model estimates can provide valuable supplementary information to empirical observations.
Do in-hospital outcomes of isolated coronary artery bypass grafting vary between male and female octogenarians?
Authors: Attia Rizwan Q , Katumalla Eve , Cyclewala Shabnam , Rochon Melissa , Marczin Nandor , Raja Shahzad G 
Published: October 2021

Abstract

OBJECTIVES
Female gender and advanced age are regarded as independent risk factors for adverse outcomes after isolated coronary artery bypass grafting (CABG). There is paucity of evidence comparing outcomes of CABG between male and female octogenarians. We aimed to analyse in-hospital outcomes of isolated CABG in this cohort.

METHODS
All octogenarians that underwent isolated CABG, from January 2000 to October 2017, were included. A retrospective analysis of a prospectively collected cardiac surgery database (PATS; Dendrite Clinical Systems, Oxford, UK) was performed. A propensity score was generated for each patient from a multivariable logistic regression model based on 25 pre-treatment covariates. A total of 156 matching pairs were derived.

RESULTS
Five hundred and sixty-seven octogenarians underwent isolated CABG. This included 156 females (mean age 82.1 [SD: 0.9]) and 411 males (mean age 82.4 [SD: 2.1 years]). More males were current smokers (P = 0.002) with renal impairment (P = 0.041), chronic obstructive pulmonary disease (P = 0.048), history of cerebrovascular accident (P = 0.039) and peripheral vascular disease (P = 0.027) while more females had New York Heart Association class 4 (P = 0.02), left ventricular ejection fraction 30–49% (P = 0.038) and left ventricular ejection fraction &lt;30% (P = 0.049). On-pump, CABG was performed in 140 males and 52 females (P = 0.921). There was no difference in in-hospital mortality (5.4% vs 6.4%; P = 0.840), stroke (0.9% vs 1.3%; P = 0.689), need for renal replacement therapy (17.0% vs 13.5%; P = 0.732), pulmonary complications (9.5% vs 8.3%; P = 0.746) and sternal wound infection (2.7% vs 2.6%; P = 0.882). The outcomes were comparable for the propensity-matched cohorts.

CONCLUSIONS
No gender difference in outcomes was seen in octogenarians undergoing isolated CABG.
Diversity detected in commensals at host and farm level reveals implications for national antimicrobial resistance surveillance programmes
Authors: Laird Tanya J. , Jordan David , Lee Zheng Zhou , O’Dea Mark , Stegger Marc , Truswell Alec , Sahibzada Shafi , Abraham Rebecca , Abraham Sam 
Published: October 2021

Abstract

Background
A key component to control of antimicrobial resistance (AMR) is the surveillance of food animals. Currently, national programmes test only limited isolates per animal species per year, an approach tacitly assuming that heterogeneity of AMR across animal populations is negligible. If the latter assumption is incorrect then the risk to humans from AMR in the food chain is underestimated.

Objectives
To demonstrate the extent of phenotypic and genetic heterogeneity of Escherichia coli in swine to assess the need for improved protocols for AMR surveillance in food animals.

Methods
Eight E. coli isolates were obtained from each of 10 pigs on each of 10 farms. For these 800 isolates, AMR profiles (MIC estimates for six drugs) and PCR-based fingerprinting analysis were performed and used to select a subset (n = 151) for WGS.

Results
Heterogeneity in the phenotypic AMR traits of E. coli was observed in 89% of pigs, with 58% of pigs harbouring three or more distinct phenotypes. Similarly, 94% of pigs harboured two or more distinct PCR-fingerprinting profiles. Farm-level heterogeneity was detected, with ciprofloxacin resistance detected in only 60% of pigs from a single farm. Furthermore, 58 STs were identified, with the dominant STs being ST10, ST101, ST542 and ST641.

Conclusions
Phenotypic and genotypic heterogeneity of AMR traits in bacteria from animal populations are real phenomena posing a barrier to correct interpretation of data from AMR surveillance. Evolution towards a more in-depth sampling model is needed to account for heterogeneity and increase the reliability of inferences.
Clinical and pathological analysis of companion diagnostic testing of microsatellite instability-high for pembrolizumab in gynaecologic malignancy
Authors: Takeda Takashi , Tsuji Kosuke , Kobayashi Yusuke , Banno Kouji , Aoki Daisuke 
Published: October 2021

Abstract

Background
Microsatellite instability-high is a known biomarker for anti-PD-1/PD-L1 immune checkpoint therapy. It is also a known tumour feature of Lynch syndrome, detected most frequently in endometrial cancer. However, it remains unclear how microsatellite instability testing is carried out in the clinical field.

Methods
Ninety-nine patients with gynaecological malignant tumours who underwent microsatellite instability testing as a companion diagnosis for pembrolizumab and 16 patients who previously underwent microsatellite instability testing as a screening for Lynch syndrome were recruited. Clinical information, microsatellite instability status, outcomes, genetic assessments and information about cancer tissue were retrospectively analysed.

Results
Ninety-nine patients had 101 gynaecologic malignant tumours including 26 endometrial, 38 ovarian and 28 cervical cancers, 9 with other tumours including 2 synchronous endometrial and ovarian cancers. All tissue samples were successfully tested, even though some were ≥10-year-old samples. Three cases (3.0%, 3/99) showed microsatellite instability-high; all cases were endometrial cancers with one case of synchronous endometrial and ovarian cancer [11.5% (3/26) in endometrial cancer, 2.6% (1/38) in ovarian cancer], and there was no microsatellite instability-high in cervical and other cancers. One of the endometrial cancer patients received pembrolizumab treatment, but finally died of cancer. Two other cases underwent genetic testing; both were diagnosed as Lynch syndrome. Six cases (37.5%) showed microsatellite instability-high in screening for Lynch syndrome.

Conclusions
Microsatellite instability-high was less commonly detected as a companion diagnosis for pembrolizumab in unselected gynaecologic patients. Genetic counselling should be always provided along with treatment selection.
Śaṅkaran Monism and the Limits of Thought
Authors: Gasparri Luca 
Published: October 2021

Abstract
A growing movement in contemporary philosophy of mind is looking back on Indian thought to gain new insights into the problem of consciousness. This paper weighs the prospects of thinking about mentality through the lenses of Śaṅkaran Advaita Vedānta. To start, I outline micropsychist and cosmopsychist accounts of consciousness, introduce Śaṅkaran monism, and describe a potential reason of attraction of the framework over micropsychist and cosmopsychist alternatives. I then show that the eliminativist commitments of the view threaten to yield a self-defeating account of ordinary experience, and that Advaitins took the accommodation of the issue to be beyond the reach of rational inquiry. Finally, I discuss how the analytical debate over Śaṅkaran monism might proceed based on these premises.
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data
Authors: Jhong Jhih-Hua , Yao Lantian , Pang Yuxuan , Li Zhongyan , Chung Chia-Ru , Wang Rulan , Li Shangfu , Li Wenshuo , Luo Mengqi , Ma Renfei , Huang Yuqi , Zhu Xiaoning , Zhang Jiahong , Feng Hexiang , Cheng Qifan , Wang Chunxuan , Xi Kun , Wu Li-Ching , Chang Tzu-Hao , Horng Jorng-Tzong , Zhu Lizhe , Chiang Ying-Chih , Wang Zhuo , Lee Tzong-Yi 
Published: October 2021

AbstractThe last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of &gt;4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.
Knowledge and Adoption of Complex Agricultural Technologies: Evidence from an Extension Experiment
Authors: Hörner Denise , Bouguen Adrien , Frölich Markus , Wollni Meike 
Published: October 2021

Abstract
In most of Sub-Saharan Africa, agricultural extension models have become more decentralized and participatory and thus rely on effective farmer-to-farmer learning, while increasingly including nontraditional forms of education. At the same time, agricultural technologies become more complex and are now often promoted as integrated packages, which are likely to increase the complexity of the diffusion process. Based on a randomized controlled trial, this study assesses the effects of “farmer-to-farmer” extension and a video intervention on adoption of a complex technology package among 2,382 smallholders in Ethiopia. Both extension-only and extension combined with video increase adoption and knowledge of the package, especially of its more complex components; on average, however, the video intervention has no additional effect on adoption. Knowledge and the number of adopted practices also increase among farmers not actively participating in extension activities, which suggests information diffusion. For this group, the additional video intervention has a reinforcing effect, and particularly fosters adoption of the integrated package.
Defining and Describing Terminal Ulcers in Adults at End of Life: An Integrative Review
Authors: Latimer Sharon , Walker Rachel M. , Ray-Barruel Gillian , Shaw Joanie , Mackrell Kristyn , Hunt Tracey , Gillespie Brigid M. 
Published: October 2021

ABSTRACT

OBJECTIVE
The authors identify and synthesize the published primary literature on unavoidable skin breakdown and end-of-life wounds known as terminal ulcers.

DATA SOURCES
Sources were identified through a systematic search of the Cochrane Library, Medline, ProQuest, EMBASE, CINAHL complete, and PubMed databases.

STUDY SELECTION
The date limiters were set between 1984 and 2020 to locate primary qualitative, quantitative, and/or mixed-methods studies on terminal ulcers.

DATA EXTRACTION
Investigators examined 180 sources and ultimately included four quantitative studies in this review. All were conducted in the US and published between 1989 and 2019. Retrospective chart audits of deceased patients’ medical files were undertaken in three of the studies, and prospective observations were used in the fourth.

DATA SYNTHESIS
Descriptive and inductive content analyses were conducted. Three categories emerged: (1) distinguishing the ulcer development patterns, (2) identifying the ulcer characteristics, and (3) delivering specialized and individualized end-of-life care.

CONCLUSIONS
Limited primary evidence has been published on terminal ulcers. Pressure injuries and terminal ulcers have similar appearances, but their development differs significantly. The lack of a specific terminal ulcer assessment tool and staging system increases the risk of these unavoidable end-of-life wounds being incorrectly assessed and managed as pressure injuries. Further research on terminal ulcers is needed to inform clinical practice and ensure specialized care is delivered to patients who develop these wounds.
Bone in osteoarthritis: imaging and interventions
Authors: Khokhar Kiran , Conaghan Philip G. 
Published: October 2021

Purpose of review
To review the recent literature on bone in osteoarthritis (OA), with a focus on imaging and intervention studies

Recent findings
Most studies focused on knee OA; hip and hand studies were uncommon. Bone shape studies demonstrated that shape changes precede radiographic OA, predict joint replacement, and have demonstrated high responsiveness. Novel quantitative 3D imaging markers (B-score) have better characterized OA severity, including preradiographic OA status. The addition of computerized tomography-derived 3D metrics has improved the prediction of hip joint replacement when compared to radiographs alone.
Recent studies of bisphosphonates for knee OA have reported no benefits on pain or bone marrow lesion (BML) size. A meta-analysis on Vitamin D supplementation in knee OA suggested minimal symptom improvement and no benefits on the structure. Cathepsin K inhibition demonstrated reduction in OA bone change progression, but with no symptom benefit. Studies of injections of bone substitutes into BMLs (subchondroplasty) have generally been small and potential benefits remain unclear.

Summary
Subchondral bone features are associated with pain, incidence and progression of OA. Recent studies have validated quantitative bone shape as a biomarker for OA trials. Trials of bone-targeted OA therapies have been disappointing although cathepsin K inhibition may slow structural progression.
Expression of proto-oncogene c-Myc in patients with urinary bladder transitional cell carcinoma
Authors: Fragkoulis Charalampos , Ntoumas Georgios , Glykas Ioannis , Papadopoulos Georgios , Stathouros Georgios , Kostopoulou Akrivi , Choreftaki Theodosia , Ntoumas Konstantinos 
Published: October 2021

Abstract

Background:
c-Myc is a proto-oncogene located on human chromosome 8. It encodes a transcriptional factor which regulates the expression of approximately 10% to 15% of human genes, playing a crucial role in cell growth, differentiation, cellular metabolism, apoptosis, and cell transformation. The aim of this study is to correlate the expression of c-Myc in patients suffering from urinary bladder transitional cell carcinoma with tumor grade, stage, and lymph node metastases.

Materials and methods:
Formalin-fixed, paraffin-embedded tissue samples were obtained from 54 consecutive patients who underwent transurethral resection of bladder tumor or radical cystectomy (RC) as treatment for urinary bladder transitional cell carcinoma. Immunohistochemistry was performed using c-Myc monoclonal antibody and c-Myc expression was then analyzed for correlation with tumor stage, grade, and lymph node metastases.

Results:
From a total of 54 patients, 42 (77.8%) had c-Myc positive staining and 12 (22.2%) were c-Myc negative. In the c-Myc positive group, 28 patients (66.7%) had low grade tumors and 33 (78.6%) presented with non-muscle-invasive disease (p < 0.05). In the c-Myc negative group, 10 patients (83.3%) had high-grade disease and 8 (66.7%) presented with muscle-invasive disease (p < 0.05). Lymph node metastases were evaluated in 17 patients who underwent RC. Of these, 5 had lymph node metastases, 4 of whom had c-Myc negative staining (p < 0.05).

Conclusions:
In our study, c-Myc negative staining was associated with higher grade and higher stage disease. On the contrary, most c-Myc positive tumors were low grade and non-muscle-invasive disease. In patients who underwent RC, c-Myc negative staining was associated with lymph node metastases.