bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specialized metabolic functions of keystone taxa sustain soil microbiome stability
Authors: Xun Weibing , Liu Yunpeng , Li Wei , Ren Yi , Xiong Wu , Xu Zhihui , Zhang Nan , Miao Youzhi , Shen Qirong , Zhang Ruifu 
Published: January 2021

AbstractBackgroundThe relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing.ResultsWe found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially “nitrogen metabolism” and “phosphonate and phosphinate metabolism,” as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, includingNitrospiraandGemmatimonas, among others.ConclusionsThis study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability.
In situ acoustic analysis of two twentieth-century heritage carillons
Authors: Orr Scott Allan 
Published: February 2021

Abstract
Carillons are a diverse and global form of musical and civic heritage: musical instruments comprised of a series of 23 or more bells, typically hung in a tower-like structure, tuned chromatically and played from a touch-sensitive manual and pedal console using an elaborate mechanical action. Carillon bells have a distinct series of musical overtones which should be accurately tuned to one another and with other bells they sound alongside. Although these overtones have been previously studied ex situ, this study assesses the acoustic characteristics of two early-twentieth century carillons in Toronto, Canada as a combination of structure, bells, and mechanical action. Thus, the instrument and its context are considered holistically, more accurately reflecting the musical sensitivity of a carillonist. Spectral analysis of audio samples of each bell at different musical dynamic levels enabled the analysis of the acoustic qualities of the bells and the mechanical action of the instruments. The tuning of bells in the instruments varied; most importantly, there was a significant difference between the audial intensity of the bell tones produced by the instruments, demonstrating the importance of the mechanical action as part of the ‘carillon system’. This was represented with a resistive power-law model, that represents the sensitivity of intensity to carillonist musical dynamic level. A discussion of the implications for artistic and heritage practice follows. Understanding the in situ physical acoustics of the carillon as a holistic instrument in its context informs performers, arrangers, and composers of how they can best embrace the instrument’s unique qualities to improve artistic pursuits and support the appreciation of carillons as heritage instruments and function as civic voices.
Analytical technique for stability analyses of the rock slope subjected to slide head toppling failure mechanisms considering groundwater and stabilization effects
Authors: Bowa Victor Mwango , Gong Wenping 
Published: February 2021

AbstractThe contributions of the current analytical models on the prediction of the stability of the slope subjected to slide head toppling failure mechanisms, have always focused on the idealized geometry comprising regular blocks dipping into the slope face. Besides, the influence of groundwater and stabilizations from the lowermost block of the slope have been overlooked in the available literature. In this article, the analytical solutions that incorporates the kinematic mechanisms of the jointed rock slope under the influence of groundwater and stabilizing the lowermost block subjected to slide head toppling are derived based on the limit equilibrium. Furthermore, a real slide head toppling failure case history was studied to illustrate the effectiveness of the presented analytical solutions. The investigation results indicate that the presence of groundwater in the jointed rock slope, lowers the distributions of the normal and shear forces thereby inducing slide head toppling. Reinforcing the lowermost block of the slope, enhances the distributions of the normal and shear forces thus improving the stability of the jointed rock slope. The study results depict that the presented analytical solutions can provide an accurate and efficient stability analyses of the jointed rock slope subjected to slide head toppling failure mechanisms considering the presence of groundwater and stabilization effects.
Determining sample size for progression criteria for pragmatic pilot RCTs: the hypothesis test strikes back!
Authors: Lewis M. , Bromley K. , Sutton C. J. , McCray G. , Myers H. L. , Lancaster G. A. 
Published: February 2021

Abstract
Background
The current CONSORT guidelines for reporting pilot trials do not recommend hypothesis testing of clinical outcomes on the basis that a pilot trial is under-powered to detect such differences and this is the aim of the main trial. It states that primary evaluation should focus on descriptive analysis of feasibility/process outcomes (e.g. recruitment, adherence, treatment fidelity). Whilst the argument for not testing clinical outcomes is justifiable, the same does not necessarily apply to feasibility/process outcomes, where differences may be large and detectable with small samples. Moreover, there remains much ambiguity around sample size for pilot trials.

Methods
Many pilot trials adopt a ‘traffic light’ system for evaluating progression to the main trial determined by a set of criteria set up a priori. We construct a hypothesis testing approach for binary feasibility outcomes focused around this system that tests against being in the RED zone (unacceptable outcome) based on an expectation of being in the GREEN zone (acceptable outcome) and choose the sample size to give high power to reject being in the RED zone if the GREEN zone holds true. Pilot point estimates falling in the RED zone will be statistically non-significant and in the GREEN zone will be significant; the AMBER zone designates potentially acceptable outcome and statistical tests may be significant or non-significant.

Results
For example, in relation to treatment fidelity, if we assume the upper boundary of the RED zone is 50% and the lower boundary of the GREEN zone is 75% (designating unacceptable and acceptable treatment fidelity, respectively), the sample size required for analysis given 90% power and one-sided 5% alpha would be around n = 34 (intervention group alone). Observed treatment fidelity in the range of 0–17 participants (0–50%) will fall into the RED zone and be statistically non-significant, 18–25 (51–74%) fall into AMBER and may or may not be significant and 26–34 (75–100%) fall into GREEN and will be significant indicating acceptable fidelity.

Discussion
In general, several key process outcomes are assessed for progression to a main trial; a composite approach would require appraising the rules of progression across all these outcomes. This methodology provides a formal framework for hypothesis testing and sample size indication around process outcome evaluation for pilot RCTs.
Postprandial effects of macronutrient composition meals on the metabolic responses and arterial stiffness indices of lean and obese male adults: a protocol of a pilot study
Authors: Firouzi Safieh , Rezvani Reza , Pahlavani Naseh , Jarahi Lida , Navashenaq Jamshid Gholizadeh , Ranjbar Golnaz , Malekahmadi Mahsa , Taherzadeh Zhila , Safarian Mohammad 
Published: February 2021

Abstract
Background
Prior studies have shown that meal composition may affect the metabolic responses and arterial stiffness indices, and these responses may be different in lean and obese adults. The primary objective of this study is to determine the feasibility of conducting a trial to compare the effect of three test meals in lean and obese men. Due to the lack of a comprehensive study that concurrently compares metabolic responses and vascular stiffness indices after receiving three different meals in lean and obese men, this pilot study will be conducted with a three-phase parallel design, aiming to investigate the effects of meal composition on the metabolic parameters and arterial stiffness indices of lean and obese adults.

Methods
This pilot, a parallel clinical trial will be performed on 24 male adults aged 18–35 years since January 2021 and will continue until March 2021 who are disease-free and selected based on the inclusion and exclusion criteria at Mashhad University of Medical Sciences, Iran. The subjects will complete three interventions at a 1-week interval, including high carbohydrate (70% carbohydrates, 10% protein, 20% fat), high protein (30% protein, 50% carbohydrates, 20% fat), and high-fat meal (50% fat, 40% carbohydrates, 10% protein). Postprandial effects will be assessed within 360 min after each meal, including the energy expenditure component (resting energy expenditure, thermic effects of feeding, respiratory quotient, and substrate oxidation) and arterial stiffness indices (augmentation index and pulse wave velocity). In addition, blood sampling will be performed to measure glucose, insulin, free fatty acids, and lipid profile.

Discussion
The differences in the postprandial responses can affect the metabolic and vascular parameters due to different meal compositions, thereby providing beneficial data for the establishment of new strategies in terms of nutritional education and metabolic/vascular improvement. Also, the results from this pilot study will inform intervention refinement and efficacy testing of the intervention in a larger randomized controlled trial.

Trial registration
Iranian Registry of Clinical Trials; code: IRCT20190818044552N1; registered on August 26, 2019
Ethical considerations for engaging frail and seriously ill patients as partners in research: sub-analysis of a systematic review
Authors: Ludwig Claire , Graham Ian D. , Lavoie Josee , Gifford Wendy , Stacey Dawn 
Published: January 2021

Abstract
Background
The commitment to engage patients as partners in research has been described as a political, moral and ethical imperative. Researchers feel ill-equipped to deal with potential ethical implications of engaging patients as partners. The aim of this study is to identify the ethical considerations related to engaging frail and seriously ill (FSI) patients as partners in research.

Methods
We conducted a sub-analysis of a prior systematic review of 30 studies that engaged FSI patients as partners in research. Studies were included if they reported ethical considerations associated with partnering. We performed deductive content analysis, data were categorized according to Beauchamp and Childress’ Principles of Biomedical Ethics (2019): autonomy, non-maleficence, beneficence, and justice.

Results
Twenty-five studies were included. Common ethical considerations reported in relation to the principles were: autonomy – promoting desired level of involvement, addressing relational and intellectual power, facilitating knowledge and understanding of research; non-maleficence – protection from financial burden, physical and emotional suffering; beneficence – putting things right for others, showing value-added, and supporting patient-partners; and, justice – achieving appropriate representation, mutual respect for contributions, and distributing risks and benefits.

Conclusions
When partnering with FSI patients, research teams need to establish shared values and ensure processes are in place to identify and address ethical issues. Researchers and patients should work together to clarify the intent and outcomes of the partnership, actively address power differentials, recognize and minimize the potential for unintended harm, and strive to maximize the benefits of partnership.

Systematic review registration
The protocol for the original systematic review has been registered with the International Prospective Register of Systematic Reviews PROSPERO (CRD42019127994).
Immune cell labelling and tracking: implications for adoptive cell transfer therapies
Authors: Galli Filippo , Varani Michela , Lauri Chiara , Silveri Guido Gentiloni , Onofrio Livia , Signore Alberto 
Published: February 2021

Abstract
Background
The understanding of the role of different immune cell subsets that infiltrate tumors can help researchers in developing new targeted immunotherapies to reactivate or reprogram them against cancer. In addition to conventional drugs, new cell-based therapies, like adoptive cell transfer, proved to be successful in humans. Indeed, after the approval of anti-CD19 CAR-T cell therapy, researchers are trying to extend this approach to other cancer or cell types.

Main body
This review focuses on the different approaches to non-invasively monitor the biodistribution, trafficking and fate of immune therapeutic cells, evaluating their efficacy at preclinical and clinical stages. PubMed and Scopus databases were searched for published articles on the imaging of cell tracking in humans and preclinical models.

Conclusion
Labelling specific immune cell subtypes with specific radiopharmaceuticals, contrast agents or optical probes can elucidate new biological mechanisms or predict therapeutic outcome of adoptive cell transfer therapies. To date, no technique is considered the gold standard to image immune cells in adoptive cell transfer therapies.
Unstimulated whole salivary flow in Sjögren’s Syndrome: systematic literature review and meta-analysis
Authors: Martínez-Ceballos María Alejandra , Aguilera Natalia , Garzón-González Kenny Carolina , Cajamarca-Baron Jairo , Alzate-Granados Juan Pablo , Rojas-Villarraga Adriana 
Published: February 2021

Abstract
Background
Sjögren’s Syndrome compromises the exocrine function, producing xerostomia and xerophthalmia. It can appear as an isolated condition or associated with other autoimmune diseases (polyautoimmunity). The Unstimulated Salivary Flow rate (UWSF) is used to quantify saliva production. There is no objective evidence to differentiate the values in patients with Sjögren’s versus healthy people or patients with non-Sjögren’s sicca. The objective of the present review was to evaluate the UWSF in patients with Sjögren’s syndrome in comparison to controls (healthy and non-Sjögren’s sicca patients).

Methods
A systematic literature review was carried out (PRISMA guidelines). Analytical observational studies of cases and controls, cross-sectional studies, cohort studies and randomized clinical trials (including healthy controls) were considered. The Medline/OVID, Lilacs, Embase, and Cochrane/OVID databases were consulted. MeSH, DeCS, keywords, and Boolean operators were used. The meta-analysis (RevMan 5.2) was done through the random-effects model [mean difference (MD)]. Level and quality of evidence were evaluated by the Oxford Center Levels of Evidence and Joanna Brigs list respectively.

Results
Thirty-two articles were included (20 were case-control studies, 6 were cross-sectional, 2 prospective cohort, 2 retrospective cohort, and 2 studies were abstracts) and 28 were meta-analyzed. The unstimulated whole salivary flow rate in the Sjögren’s group was lower than in controls (healthy and patients with non-Sjögren Sicca syndrome) (MD-0.18 ml/min; 95% CI, − 0.24 to − 0.13; chi2-P-value < 0.00001). Heterogeneity was 97% and there was publication bias (funnel plot). The level of evidence was mostly 3 or 4. The quality of evidence was met (97% of items valued).

Conclusion
For the first time, the unstimulated whole salivary flow rate is found to be lower in patients with Sjögren’s syndrome compared to controls (healthy and non-SS sicca) through a meta-analysis.

Trial registration
PROSPERO CRD42020211325.
Development and rapid evaluation of services to support the physical health of people using psychiatric inpatient units during the COVID-19 pandemic: study protocol
Authors:   IMPHS group, Williams Julie , Fairbairn Elli , McGrath Ray , Clark Amy , Healey Andy , Bakolis Ioannis , Gaughran Fiona , Sadler Euan , Khadjesari Zarnie , Sevdalis Nick 
Published: February 2021

Abstract
Background
People diagnosed with a serious mental illness have worse physical health and lower life expectancy than the general population. Integration of mental and physical health services is seen as one service development that could better support this. This protocol describes the evaluation of the provision of a Virtual Physical Health Clinic (VPHC) and Consultant Connect (CC) services to one UK-based mental health Trust.

Methods
Prospective, formative, pragmatic evaluation using both quantitative and qualitative techniques and driven by implementation science theoretical frameworks. The VPHC and CC are described along with the methodology being used to rapidly evaluate their implementation, effectiveness and potential economic impact in order to inform future roll out. We will assess the implementation process through quantitative data on uptake and reach and through self-reported data to be collected from interviews and the use of validated implementation outcome assessment measures. We will assess implementation strategies using the Expert Recommendations for Implementing Change (ERIC) strategies as a framework. We will assess the health economic impact of both services using established health economic methods including cost comparison scenarios and health service utilisation analyses.

Discussion
Supporting the physical health management of people in psychiatric inpatient units is important in improving the physical health of this population. Integration of mental and physical health can help this to happen effectively. This initiative provides one of the first service evaluation protocols of its kind to be reported in the UK at the time of the COVID-19 pandemic.
iCAT: diagnostic assessment tool of immunological history using high-throughput T-cell receptor sequencing
Authors: Rajeh Ahmad , Wolf Kyle , Schiebout Courtney , Sait Nabeel , Kosfeld Tim , DiPaolo Richard J. , Ahn Tae-Hyuk 
Published: February 2021

The pathogen exposure history of an individual is recorded in their T-cell repertoire and can be accessed through the study of T-cell receptors (TCRs) if the tools to identify them were available. For each T-cell, the TCR loci undergoes genetic rearrangement that creates a unique DNA sequence. In theory these unique sequences can be used as biomarkers for tracking T-cell responses and cataloging immunological history. We developed the immune Cell Analysis Tool (iCAT), an R software package that analyzes TCR sequencing data from exposed (positive) and unexposed (negative) samples to identify TCR sequences statistically associated with positive samples. The presence and absence of associated sequences in samples trains a classifier to diagnose pathogen-specific exposure. We demonstrate the high accuracy of iCAT by testing on three TCR sequencing datasets. First, iCAT successfully diagnosed smallpox vaccinated versus naïve samples in an independent cohort of mice with 95% accuracy. Second, iCAT displayed 100% accuracy classifying naïve and monkeypox vaccinated mice. Finally, we demonstrate the use of iCAT on human samples before and after exposure to SARS-CoV-2, the virus behind the COVID-19 global pandemic. We were able to correctly classify the exposed samples with perfect accuracy. These experimental results show that iCAT capitalizes on the power of TCR sequencing to simplify infection diagnostics. iCAT provides the option of a graphical, user-friendly interface on top of usual R interface allowing it to reach a wider audience.
Interactive SARS-CoV-2 mutation timemaps
Authors: Warren René L. , Birol Inanc 
Published: February 2021

As the year 2020 came to a close, several new strains have been reported of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 mutates and evolves in its human hosts. To get an appreciation for the rapid evolution of the coronavirus, we built interactive scalable vector graphics maps that show daily nucleotide variations in genomes from the six most populated continents compared to that of the initial, ground-zero SARS-CoV-2 isolate sequenced at the beginning of the year. Availability: The tool used to perform the reported mutation analysis results, ntEdit, is available from GitHub. Genome mutation reports are available for download from BCGSC. Mutation time maps are available from https://bcgsc.github.io/SARS2/.
A Nenets vocabulary from the archive of Vladimir Evladov in Salekhard
Authors: Lyublinskaya Marina 
Published: February 2021

The archive of the Salekhard District Museum and Exhibition Complex named after I. S. Šemanovskij hosts a Tundra Nenets word list which was compiled for a practical dictionary by the topographer and land surveyor Vladimir Petrovič Evladov. Evladov collected this material between 1926 and 1935 during three expeditions to the Yamal Peninsula. He also consulted with students of the Institute of Northern Peoples in Leningrad. The material consists of two word lists, a Nenets-Russian and a Russian- Nenets one. The material reflects Tundra Nenets pronunciation and the meaning of lexemes around these years. It is important for studies on the period of language construction in Soviet Russia. We publish here the Nenets-Russian vocabulary in the Unified Northern Alphabet.
Kokkuvõte. Marina Ljublinskaja: Neenetsi sõnastik Vladimir Evladovi arhiivist Salehardis. Salehardi I. S. Šemanovskij nimelises ringkonnamuuseumis ja näitusekompleksis asub tundraneenetsi sõnaloend, mille koostas praktilise sõnastikuna topograaf ja maamõõtja Vladimir Petrovič Evladov, kes kogus selle jaoks materjali oma ekspeditsioonil 1926. ja 1935. aasta vahel. Ka konsulteeris ta Leningradis Põhjarahvaste Instituudi üliõpilastega. Andmestik koosneb kahest sõnaloendist: üks neenetsi-vene suunal ja teine vene-neenetsi suunal. Materjal kajastab tolleaegset tundraneenetsi hääldust ja lekseemide tähendusi ja on oluline uurimaks keelekonstrueerimise perioodi Nõukogude Venemaal. Uurimus sisaldab neenetsi-vene sõnastikku ühtses põhjarahvaste tähestikus.
Аннотация. Марина Люблинская: Ненецкий словарь из архива В. П. Евладова в Салехарде. В архиве музейно-выставочного комплекса в городе Салехарде (ЯНАО) хранятся списки слов на ненецком языке, собранные топографом и землеустроителем В. П. Евладовым. Слова были записаны в 1926–35 годах во время исследовательских экспедиций по Ямалу для составления практического словаря. Между поездками Евладов обсуждал материал с ненецкими студентами института Народов Севера в Ленинграде. Готовилось два словаря – ненецко-русский и русско-ненецкий, которые так и не были изданы. Записи Евладова передают произношение и значене ненецких слов в начале XX века. Также материал значим для изучения периода языкового строительства в Советской России. Ниже публикуется ненецко-русская часть словаря, записанная Единым Северным алфавитом.