bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clean room microbiome complexity impacts planetary protection bioburden
Authors: Hendrickson Ryan , Urbaniak Camilla , Minich Jeremiah J. , Aronson Heidi S. , Martino Cameron , Stepanauskas Ramunas , Knight Rob , Venkateswaran Kasthuri 
Published: December 2021

Abstract
Background
The Spacecraft Assembly Facility (SAF) at the NASA’s Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom.

Results
Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter.

Conclusion
This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays.
Systematic review of validated parent-reported questionnaires assessing swallowing dysfunction in otherwise healthy infants and toddlers
Authors: Baqays Abdulsalam , Zenke Julianna , Campbell Sandra , Johannsen Wendy , Rashid Marghalara , Seikaly Hadi , El-Hakim Hamdy 
Published: December 2021

Objectives There has been increasing interest in the management of oropharyngeal swallowing dysfunction (SwD). Its prevalence, particularly in otherwise healthy infants and toddlers (OHITs), is underappreciated. As the standard diagnostic tests are either invasive or scarce, valid parent-reported outcome (PRO) questionnaires could play a pivotal role in the understanding and managing SwD in this group. This article reviewed the literature on PRO questionnaires pertaining to SwD in OHITs. Data source A librarian searched Prospero, Cochrane Library, Embase, Medline, PsycINFO, HaPI, CINAHL, and SCOPUS until February 2021 using the MeSH terms for deglutition and screening methods. Review method Questionnaires that examined disease-specific or eating and feeding concerns or difficulties were excluded. Two reviewers independently identified PRO questionnaires for SwD that were used in OHITs and extracted the author names, publication year, questionnaire name, the studied population, and the reported psychometric assessments. A quality assessment was performed based on consensus-based standards for the selection of health measurement instruments (COSMIN) and updated criteria for good measurement properties. Results Of the 3488 screened articles, we identified only two questionnaires, the pediatric version of the Eating Assessment Tool (PEDI-EAT-10) and the PRO questionnaire for Swallowing Dysfunction in OHITs. The PEDI-EAT-10 authors assessed the validity and reliability on children with cerebral palsy. However, concerns were identified regarding the developmental process and the internal structure validity. The PRO questionnaire for SwD in OHITs meets criteria but has not yet been validated in the population of interest nor its psychometric properties assessed. Conclusion Two instruments were identified. The PED-EAT-10 exhibits methodological flaws, while Edmonton PRO questionnaire for SwD in OHITs awaits construct validation and could fill the current knowledge gap.
Migration routes, behavior and protection status of Eurasian Spoonbills (Platalea leucorodia) wintering in China
Authors: Xi Jire , Deng Xueqin , Zhao Gerelt , Batbayar Nyambayar , Damba Iderbat , Zhao Qingshan , Cui Shoubin , Jiang Chao , Chen Yiwen , Yu Yat-tung , Cao Lei , Fox Anthony David 
Published: December 2021

AbstractBackgroundThe Eurasian Spoonbill (Platalea leucorodia) occurs throughout Eurasia and North and sub-Saharan Africa, with three recognized subspecies and six geographically distributed populations. However, in China, we knew almost nothing about migration routes, habitat use and effectiveness of current site protection measures for this species.MethodsWe deployed Global Positioning System/Global System for Mobile Communications (GPS/GSM) satellite trackers on 29 Eurasian Spoonbills captured in summer in Mongolia and northeastern China, to obtain complete migration routes data from 10 individuals from 19 complete migration episodes.ResultsTracking data showed no geographical overlap during the annual cycle in Eurasian Spoonbills marked in the two main summering areas. Birds marked in the Naoli River Basin in Heilongjiang Province, China, wintered along the Jiangsu coastline in China, while Eurasian Spoonbills from two discrete summering areas (in Inner and western Mongolia) overwintered inland in the Yangtze River floodplain of China. Excluding the single Inner Mongolian bird, spring migration was significantly faster than autumn migration in the other two groups of birds. Eurasian Spoonbills mainly used water, wetland and grassland habitats in summer, but almost exclusively water in winter. Lack of protection of staging sites used by all the birds in spring and poor levels of protection throughout the annual cycle for western Mongolian birds (5–22%) gives considerable cause for concern, although sites used in other time by East Mongolian and Naoli River birds in the rest of their annual life cycle enjoyed good levels of protection (49–95%).ConclusionsThese results revealed previously unknown relationships between summering and wintering areas, migration routes and stopover sites for Eurasian Spoonbills wintering in China, suggesting the existence of discrete biogeographical population units. They also identified winter habitat use of Eurasian Spoonbills in China, confirming open water habitats as being critical throughout the annual cycle, although based on small sample size, gaps in current site safeguard networks for these populations.
Exercise-Based Cardiac Rehabilitation: Secondary Data Analyses of Mortality and Working Capacity in Germany, 2010–2017
Authors: Gabrys Lars , Soff Johannes , Thiel Christian , Schmidt Christian , Swart Enno , Peschke Dirk 
Published: December 2021

AbstractBackgroundExercise-based cardiac rehabilitation is safe and implemented in international cardiac rehabilitation guidelines. Evidence for long-term health effects is scarce and rare for health care service research.ObjectiveThe aim of this study is to evaluate the effectiveness of exercise-based phase III cardiac rehabilitation programs in improving mortality and working capacity outcomes.MethodsThe present analyses used claims data of the German pension fund from 2010 to 2017. Overall, 54,163 patients with coronary heart disease (ICD10 I20.–I25.) were included and followed up for exercise-based cardiac rehabilitation participation (mean 4.3 ± 1.9 years). All patients were categorized according to participation duration (long: ≥ 90 days, short: < 90 days, no). The effectiveness of exercise-based rehabilitation was analyzed by calculating adjusted hazard ratios for mortality and reduced working capacity in relation to program participation.ResultsOf all the cardiac patients, 57.6% received medical recommendations for exercise-based phase III rehabilitation, and 16.8% participated in this rehabilitation. In total, 1776 (3.3%) patients died during the study period, and 3050 (5.5%) received reduced earning capacity pensions. Mortality risk was nearly doubled for those who did not participate in exercise-based cardiac rehabilitation compared to those who participated for a long duration (HR 1.97, 95% CI 1.60–2.43) and 44% higher compared to a short participation (HR 1.44, 95% CI 1.03–2.01). Furthermore, the risk of reduced working capacity was higher for those who did not participate compared to those who participated for a short duration (HR 1.24, 95% CI 1.00–1.54).ConclusionExercise-based phase III cardiac rehabilitation is independently associated with reduced mortality and reduced loss in working capacity. Strong efforts should be made to increase participation rates to improve cardiac patients care.
Development and evaluation of a virtual patient-centered outcomes research training program for the cystic fibrosis community
Authors: Godfrey Emily M. , Thayer Erin K. , Mentch Laura , Kazmerski Traci M. , Brown Georgia , Pam Molly , Al Achkar Morhaf 
Published: December 2021

AbstractBackgroundPatient-centered outcomes research (PCOR) emphasizes patient-generated research priorities and outcomes, and engages patients throughout every stage of the research process. In the cystic fibrosis (CF) community, patients frequently provide input into research studies, but rarely are integrated onto research teams. Therefore, we developed and evaluated a virtual pilot PCOR training program to build PCOR capacity in the CF community (patients, caregivers, researchers, nonprofit stakeholders and providers). We aimed to show changes among participants’ perceived PCOR knowledge (a.k.a PCOR knowledge), confidence in engaging stakeholders, and post-training session satisfaction.MethodsGuided by a prior CF community educational needs assessment, our researcher and patient-partner team co-developed a four-part virtual online training program. We structured the program towards two learner groups: patients/caregivers and researchers/providers. We evaluated participants’ PCOR knowledge, confidence in engaging stakeholders, and session satisfaction by administering 5-point Likert participant surveys. We tested for significant differences between median ratings pre- and post-training.ResultsA total of 28 patients/caregivers, and 31 researchers/providers participated. For both learner groups, we found the training resulted in significantly higher PCOR knowledge scores regarding “levels of engagement” (p = .008). For the patient/caregiver group, training significantly increased their PCOR knowledge about the barriers/enablers to doing PCOR (p = .017), effective PCOR team elements (p = .039), active participation (p = .012), and identifying solutions for successful PCOR teams (p = .021). For the researcher/healthcare provider group, training significantly increased participants’ ability to describe PCOR core principles (p = .016), identify patient-partners (p = .039), formulate research from patient-driven priorities (p = .039), and describe engagement in research grants (p = .006). No learner group had significant changes in their confidence score. Most participants were either “satisfied” or “very satisfied” with the training program.ConclusionsOverall, our virtual pilot PCOR training program was well received by patients, caregivers, researchers and providers in the CF community. Participants significantly improved their perceived knowledge with core PCOR learning items.Trial registrationRetrospectively registered at clinicaltrials.gov (NCT04999865).
The mutual benefits of patient and public involvement in research: an example from a feasibility study (MoTaStim-Foot)
Authors: Aries Alison M. , Bailey Paul , Hunter Susan M. 
Published: December 2021

AbstractBackgroundPatient and public involvement (PPI) in research has increased steadily over the last two decades and is now both expected and appropriately resourced by many funding bodies, including the National Institute for Health Research (NIHR). However, PPI in research occurs in many different capacities and numerous frameworks exist for reporting or appraising patient involvement activities. The aim of this article is to describe processes involving PPI contributions to an NIHR-funded mixed-methods feasibility study (MoTaStim-Foot). Details of PPI advisors’ input, from initial identification and prioritisation of research ideas, to research delivery and dissemination, are discussed.MethodsExtensive PPI for MoTaStim-Foot is reported, with consideration of Research Design Service (RDS) advice for PPI for research, involving identifying and prioritising: design; grant proposal development; undertaking/managing research; analysing and interpreting; dissemination; implementation; monitoring and evaluation. Two PPI workshops were undertaken; success in meeting UK standards for public involvement was audited against specific success criteria by two researchers, with discussion and consideration regarding how well our PPI achieved inclusive opportunities, working together, support and learning, governance, communications and impact. How PPI can be improved for future trials was also considered. Although the advantages of PPI for researchers were considered, the benefits for PPI advisors were also analysed.ResultsUK standards for public involvement were achieved, along with seven relevant research processes suggested by the RDS. PPI advisor contributions: informed study design; contributed to successful funding; enhanced trial delivery by informing participant information sheets and daily diaries; added value through undertaking note-taker roles in focus groups and helping to analyse focus group transcripts; and assisted in dissemination. However, benefits were mutual with PPI advisors reporting feeling valued and respected, a sense of pride with renewed confidence and purpose in life.ConclusionsImportance and value of PPI, to researchers and patient advisors, have been highlighted, reinforcing the benefits of working in partnership with PPI advisors.Trial registrationISRCTN 13676183; Central Portfolio Management System ID 30449. Registered 02/01/2015,https://www.isrctn.com/ISRCTN13676183.
Urgent-start peritoneal dialysis for end-stage renal disease patients: literature review and worldwide evidence-based practice
Authors: Phongphithakchai Atthaphong , Dandecha Phongsak , Raksasuk Sukit , Srithongkul Thatsaphan 
Published: December 2021

AbstractThe prevalence of end-stage renal disease (ESRD) is on the rise worldwide. Meanwhile, the number of older people requiring dialysis therapy is increasing as a result of this population. We found that starting dialysis in an unplanned manner is a common occurrence, even for patients with nephrology follow-up. Most centers choose hemodialysis with a high rate of central venous catheter use at the time of initiation of dialysis. Current data has found that central venous catheter use is independently associated with increased mortality and high bacteremia rates. Peritoneal dialysis is one option to avoid bacteremia. The International Society for Peritoneal Dialysis guidelines suggests a break-in period of at least two weeks prior to an elective start of peritoneal dialysis, without mentioning urgent-start peritoneal dialysis. For unplanned ESRD patients, it is unrealistic to wait for two weeks before initiating peritoneal dialysis therapy. Urgent-start peritoneal dialysis has been suggested to be a practical approach of prompt initiation of peritoneal dialysis after catheter insertion, which may avoid an increased risk of central venous catheter-related complications, including bacteremia, central venous stenosis, and thrombosis associated with the temporary use of hemodialysis. Peritoneal dialysis is the alternative option, and many studies have presented an interest in urgent-start peritoneal dialysis. Some reports have compared urgent-start hemodialysis to peritoneal dialysis and found that urgent-start peritoneal dialysis is a safe and effective alternative to hemodialysis for an unplanned dialysis patient. This review aims to compare each literature report regarding techniques, prescriptions, outcomes, complications, and costs of urgent-start peritoneal dialysis.
Developing a patient-driven chronic obstructive pulmonary disease (COPD) research agenda in the U.S.
Authors: Gruß Inga , McCreary Gretchen M. , Ivlev Ilya , Houlihan Mary Ellen , Yawn Barbara P. , Pasquale Cara , Clark William , Mularski Richard A. 
Published: December 2021

AbstractBackgroundTo document a generalizable process for developing a patient-prioritized chronic obstructive pulmonary disease (COPD) research agenda and to provide an overview of domains that were developed in response to people living with COPD and caregivers’ suggestions for research.MethodsAdults with COPD and caregivers who are members of the COPD Patient-Powered Research Network (PPRN) provided suggestions for COPD-related research through a self-administered, online survey. These responses were analyzed with a content analysis approach: domains for categorizing all survey responses were created, then all responses were categorized independently by a group of researchers, then these categorizations were adjudicated, and finally a density map was created that represented the number of responses in each of the domains.ResultsAt the time of analysis, 6157 adults had fully completed the baseline survey. Survey responses were categorized across seven domains as follows: 22.5% of all responses fell into the domain family/social/community research, 20.8% of all responses fell into the domain well-being, 15% of all responses fell into the domain curative research, 14.6% of all responses fell into the domain biomedical therapies, 10.5% of all responses fell into the domain policy concerns, 6% of all responses fell into the domain holistic therapies and 10.7% of all responses fell into the domain ambiguous comments that could not be translated into concrete research topics.ConclusionUsing qualitative open-ended survey responses from the COPD PPRN registrants, we were able to identify six key domains of research about COPD that are considered most important by patients. These domains differ in content from prior scientist-led efforts to develop priorities for COPD research, demonstrating the ongoing importance of involving patients and their caregivers in determining research priorities. The results suggest the field can more closely align research efforts to patient priorities by considering the identified domains.
Phytochemical competence and pharmacological perspectives of an endangered boon—Costus speciosus (Koen.) Sm.: a comprehensive review
Authors: Sohrab Saima , Mishra Pratibha , Mishra Sanjay Kumar 
Published: December 2021

Abstract
Background
Costus speciosus (Koen) Sm. popularly known as crepe ginger or spiral ginger and insulin plant is a perennial rhizomatous herb contain variable number of medicinally important bioactive phytochemicals having intensive pharmacological effects due to antioxidant, antimicrobial, insecticidal, anticancerous, and antidiabetic properties. This plant is widely distributed throughout India and has tremendous ethnobotanical uses. This review article is the coalescence of the distribution, morphology, phytochemistry, pharmacology, effect, and mode of action of pharmacologically active principles of Costus speciosus.

Main body
The therapeutic potential possessed by the plant is mainly the attribution of the bioactive compounds such as phenolics, steroids, alkaloids, flavonoids, saponins, terpenoids, and tannins, which are found to be present in different parts of the plant. Bioactive constituents like diosgenin, gracillin, dioscin, prosapogenins A and B of dioscin, eremanthin, costunolide, β-sitosterol, β-D-glucoside, β-carotene, α-tocopherol quinine, dihydrophytylplastoquinone, 5α-stigmast-9(11) en3β-ol, tetracosanyl octadecanoate, methyl hexadecanoate, methyl octadecanoate, cycloartenol, cycloartanol, and cycloalaudenol are specifically found in C. speciosus. This review also focuses on the possible mechanisms followed by these bioactive compounds while exhibiting various pharmacological properties. Because of the presence of diosgenin, this plant is given the name “insulin plant.” Diosgenin along with an important sesquiterpene, costunolide, performs significantly high antioxidant, anticancer, and antidiabetic activities. Besides these properties, insecticidal, antifungal, antibacterial, and anthelminthic properties have also been discussed. This plant needs to be given more emphasis as it is exploited at the commercial level by the pharmaceutical industries, conservation status is getting poorer, and it is already in a near-threatened state. Therefore, more systematic and intensive research should be done in a sustainable manner.

Conclusion
Spiral ginger plant shows diverse pharmacological effects due to presence of variety of bioactive phytochemicals, but the compounds like diosgenins, costunolides, eremanthin, and arbusculin are highly specific that exhibit effective antidiabetic, anticancerous, and antioxidative properties through different mechanism. Thus, C. speciosus can be exploited as an economically sustainable source of effective drugs against deadly diseases like diabetes and cancers with less or no side effects, and further research is needed to explore the intricacy of its pharmacological actions with human trials.

Graphical Abstract