bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preservation of remnant esophagus during total pharyngolaryngectomy in a patient with previous subtotal esophagectomy: a case report
Authors: Oshikiri Hiroyuki , Okamoto Hiroshi , Taniyama Yusuke , Ishii Ryo , Ohkoshi Akira , Kurosawa Koreyuki , Unno Michiaki , Kamei Takashi 
Published: March 2023

Abstract
Background
With the improved survival rate of patients with esophageal cancer, secondary cancers, including pharyngolaryngeal cancer, have become a problem. Phanryngolaryngeal cancer surgery often requires esophagogastric anastomosis resection in patients with a previous history of subtotal esophagectomy. Owing to adhesions, especially surrounding the esophagogastric anastomosis, caused by the initial surgery, the second surgery might cause postoperative complications.

Case presentation
A 65-year-old man was diagnosed with early stage esophageal squamous cell carcinoma and underwent endoscopic mucosal dissection. However, the histopathological depth of the tumor was pT1b, and additional treatment was required. After administration of the neoadjuvant chemotherapy, he underwent thoracoscopic esophagectomy and retrosternum reconstruction via a gastric tube (pT1N3M0 stage III). Eight months after the first surgery, tumor recurrences were observed at the anastomosis and left cervical lymph node. Definitive chemoradiotherapy was performed for the recurrences, and complete response was achieved. Seven months after chemoradiotherapy, he was diagnosed with hypopharyngeal squamous cell carcinoma in the right piriform fossa (cT2N2bM0 stage IVA), and salvage surgery was chosen as treatment. The surgical findings revealed strong adhesion around the remnant esophagus, which was difficult to dissect from surrounding tissue and was associated with a risk of breaking of the anastomosis. However, indocyanine green fluorescence imaging findings indicated sufficient blood flow to preserve the remnant esophagus, including the anastomosis, even after the interruption of blood flow from the proximal side of the esophagus by total pharyngolaryngectomy. Finally, approximately 4 cm of the remnant esophagus was preserved, and the free jejunum reconstruction with cervical vascular anastomosis was performed. Moreover, the patient was discharged without complications on postoperative day 38. After 10 months of the second surgery, a metastatic lymph node was observed in the right neck. Immune checkpoint inhibitors and chemotherapy were administered, and the patient is alive and under treatment 1.5 years after the second surgery.

Conclusions
Blood supply to the remnant cervical esophagus was thought to be from the gastric conduit over the anastomosis and surrounding capillaries. Thus, the preservation of the remnant esophagus can be considered in total pharyngolaryngectomy even after < 2 years of esophagectomy by blood flow evaluation using indocyanine green fluorescence.
Potato root-associated microbiomes adapt to combined water and nutrient limitation and have a plant genotype-specific role for plant stress mitigation
Authors: Faist Hanna , Trognitz Friederike , Antonielli Livio , Symanczik Sarah , White Philip J. , Sessitsch Angela 
Published: March 2023

Abstract
Background
Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a field experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids, and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure.

Results
The different potato genotypes responded differently to the combined stress and hosted distinct microbiota in the rhizosphere and the root endosphere. Proximity to the root, stress and potato genotype had significant effects on bacteria, whereas fungi were only mildly affected. To address the involvement of microbial functions, we investigated well and poorly performing potato genotypes (Stirling and Desirée, respectively) under stress conditions and executed a metagenome analysis of rhizosphere microbiomes subjected to stress and no stress conditions. Functions like ROS detoxification, aromatic amino acid and terpene metabolism were enriched and in synchrony with the metabolism of stressed plants. In Desirée, Pseudonocardiales had the genetic potential to take up assimilates produced in the fast-growing canopy and to reduce plant stress-sensing by degrading ethylene, but overall yield losses were high. In Stirling, Xanthomonadales had the genetic potential to reduce oxidative stress and to produce biofilms, potentially around roots. Biofilm formation could be involved in drought resilience and nutrient accessibility of Stirling and explain the recorded low yield losses. In the rhizosphere exposed to combined stress, the relative abundance of plasmids was reduced, and the diversity of phages was enriched. Moreover, mobile elements like plasmids and phages were affected by combined stresses in a genotype-specific manner.

Conclusion
Our study gives new insights into the interconnectedness of root-associated microbiota and plant stress responses in the field. Functional genes in the metagenome, phylogenetic composition and mobile elements play a role in potato stress adaption. In a poor and a well performing potato genotype grown under stress conditions, distinct functional genes pinpoint to a distinct stress sensing, water availability and compounds in the rhizospheres.
POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling
Authors: Burks David J. , Pusadkar Vaidehi , Azad Rajeev K. 
Published: March 2023

AbstractWe present here POSMM (pronounced ‘Possum’), Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. Built on the top of a rapid Markov model based classification algorithm SMM, POSMM reintroduces high sensitivity associated with alignment-free taxonomic classifiers to probe whole genome or metagenome datasets of increasingly prohibitive sizes. Logistic regression models generated and optimized using the Python sklearn library, transform Markov model probabilities to scores suitable for thresholding. Featuring a dynamic database-free approach, models are generated directly from genome fasta files per run, making POSMM a valuable accompaniment to many other programs. By combining POSMM with ultrafast classifiers such as Kraken2, their complementary strengths can be leveraged to produce higher overall accuracy in metagenomic sequence classification than by either as a standalone classifier. POSMM is a user-friendly and highly adaptable tool designed for broad use by the metagenome scientific community.
The selection of copiotrophs may complicate biodiversity-ecosystem functioning relationships in microbial dilution-to-extinction experiments
Authors: Mao Zhendu , Zhao Zifan , Da Jun , Tao Ye , Li Huabing , Zhao Biying , Xing Peng , Wu Qinglong 
Published: March 2023

AbstractThe relationships between biodiversity-ecosystem functioning (BEF) for microbial communities are poorly understood despite the important roles of microbes acting in natural ecosystems. Dilution-to-extinction (DTE), a method to manipulate microbial diversity, helps to fill the knowledge gap of microbial BEF relationships and has recently become more popular with the development of high-throughput sequencing techniques. However, the pattern of community assembly processes in DTE experiments is less explored and blocks our further understanding of BEF relationships in DTE studies. Here, a microcosm study and a meta-analysis of DTE studies were carried out to explore the dominant community assembly processes and their potential effect on exploring BEF relationships. While stochastic processes were dominant at low dilution levels due to the high number of rare species, the deterministic processes became stronger at a higher dilution level because the microbial copiotrophs were selected during the regrowth phase and rare species were lost. From the view of microbial functional performances, specialized functions, commonly carried by rare species, are more likely to be impaired in DTE experiments while the broad functions seem to be less impacted due to the good performance of copiotrophs. Our study indicated that shifts in the prokaryotic community and its assembly processes induced by dilutions result in more complex BEF relationships in DTE experiments. Specialized microbial functions could be better used for defining BEF. Our findings may be helpful for future studies to design, explore, and interpret microbial BEF relationships using DTE.
Optimized menu formulation to enhance nutritional goals: design of a mixed integer programming model for the workers’ food program in Brazil
Authors: Padovan Marina , de Senna Fernando Ribeiro , Kimura Juliana Klein , Nascimento Samara Tortorella , Moretti Antonio Carlos , Capitani Caroline Dário 
Published: March 2023

Abstract
Background
In Brazil, institutional foodservices are required to meet the recommendations of the Workers? Food Program (WFP), a national public policy used to plan collective menus. The current study aimed to propose a mathematical model to generate a one-month menu that meets the nutritional recommendations of the WFP, with low cost and good quality.

Methods
We considered aspects related to the eating habits of the Brazilian population, spacing of repetitions between the dishes, texture combination, and monotonicity of colors of the dishes served. A mixed integer programming model was built to formulate daily menus for an institutional foodservice for one month. The menu consisted of a base dish, a base dish option, salads (2 options), a protein dish, a protein dish option, a side dish, and a dessert.

Results
The model ensured compliance with the recommendations proposed by the WFP and the provision of healthy and nutritionally balanced meals. The menu generated met the recommendations of the WFP, with an average of 716.97 kcal/meal, including on average 58.28% carbohydrates, 17.89% proteins, and 24.88% total fats/meal.

Conclusion
The model used can help in the menu elaboration dynamics of institutional foodservices, optimizing the work of the nutritionist in charge.
Body mass index in nursing home residents during the first year after admission
Authors: Vossius Corinna , Borda Miguel G. , Lichtwarck Bjørn , Myhre Janne , Sollid May Ingvild Volungholen , Borza Tom , Feiring Ingvild Hjorth , Benth Jūratė Šaltytė , Bergh Sverre 
Published: March 2023

Abstract
Background
Malnutrition - comprising both undernutrition and overweight - has to be addressed in the medical follow-up of older adults due to the negative consequences for the functional state and general health. Still, little is known about the nutritional state of nursing home (NH) residents, especially with respect to weight gain or weight loss after NH admission. Therefore, this study aims to evaluate changes in the body mass index (BMI) during the first year following NH admission, and to explore demographic and clinical characteristics related to BMI changes.

Methods
Data from two prospective studies that recruited participants at NH admission were combined. Demographic and clinical characteristics including the BMI were assessed at baseline and after one year. A linear regression model was estimated to explore the impact of demographic and clinical characteristics on the change in BMI.

Results
The study cohort consisted of 1,044 participants with a mean age of 84.3 years (SD7.6) at baseline; 64.2% were female. At baseline, 33% of the NH residents had severe to moderate undernutrition, while 10% were obese. During the first year of their NH stay, residents with severe to moderate undernutrition had an average increase in BMI of 1.3 kg/m2 (SD 2.2; p < 0.001), while weight changes were either very small or not significant in the other BMI groups. Characteristics related to weight gain were younger age and less agitation.

Conclusion
Malnutrition is a common health challenge at NH admission, with one third of NH residents being moderately to severely underweight and 10% being obese. However, during the first year of NH stay, there was a favourable development for underweight NH residents, as they increased their BMI, and 43.6% changed to a higher weight classification, while we observed no changes in the BMI in residents with obesity. As NH residents are in the last phase of their lives, interventions to prevent malnutrition or overweight should be initiated while still home-dwelling, and then continued in the nursing homes.
Group antenatal care: findings from a pilot randomised controlled trial of REACH Pregnancy Circles
Authors: Sawtell Mary , Wiggins Meg , Wiseman Octavia , Mehay Anita , McCourt Christine , Sweeney Lorna , Hatherall Bethan , Ahmed Tahania , Greenberg Lauren , Hunter Rachael , Hamborg Thomas , Eldridge Sandra , Harden Angela 
Published: March 2023

Abstract

Background

Antenatal care has the potential to impact positively on maternal and child outcomes, but traditional models of care in the UK have been shown to have limitations and particularly for those from deprived populations. Group antenatal care is an alternative model to traditional individual care. It combines conventional aspects of antenatal assessment with group discussion and support. Delivery of group antenatal care has been shown to be successful in various countries; there is now a need for a formal trial in the UK.

Method
An individual randomised controlled trial (RCT) of a model of group care (Pregnancy Circles) delivered in NHS settings serving populations with high levels of deprivation and diversity was conducted in an inner London NHS trust. This was an external pilot study for a potential fully powered RCT with integral economic evaluation. The pilot aimed to explore the feasibility of methods for the full trial. Inclusion criteria included pregnant with a due date in a certain range, 16 + years and living within specified geographic areas. Data were analysed for completeness and usability in a full trial; no hypothesis testing for between-group differences in outcome measures was undertaken. Pre-specified progression criteria corresponding to five feasibility measures were set. Additional aims were to assess the utility of our proposed outcome measures and different data collection routes. A process evaluation utilising interviews and observations was conducted.

Results
Seventy-four participants were randomised, two more than the a priori target. Three Pregnancy Circles of eight sessions each were run. Interviews were undertaken with ten pregnant participants, seven midwives and four other stakeholders; two observations of intervention sessions were conducted. Progression criteria were met at sufficient levels for all five measures: available recruitment numbers, recruitment rate, intervention uptake and retention and questionnaire completion rates. Outcome measure assessments showed feasibility and sufficient completion rates; the development of an economic evaluation composite measure of a ‘positive healthy birth’ was initiated.

Conclusion
Our pilot findings indicate that a full RCT would be feasible to conduct with a few adjustments related to recruitment processes, language support, accessibility of intervention premises and outcome assessment.

Trial registration
ISRCTN ISRCTN66925258. Retrospectively registered, 03 April 2017.
An intervention to support stroke survivors and their carers in the longer term: results of a cluster randomised controlled feasibility trial (LoTS2Care)
Authors: Forster Anne , Ozer Seline , Brindle Richard , Barnard Lorna , Hardicre Natasha , Crocker Thomas F. , Chenery Marie , Moreau Lauren , Wright Alan , Burton Louisa-Jane , Hartley Suzanne , Hulme Claire , Dawkins Bryony , Holloway Ivana , House Allan , Hewison Jenny , Farrin Amanda ,   on behalf of the LoTS2Care Programme Team, Atkinson Ross , Prashar Arvin , Cornwall Nicola , Clarke David , Meads David , Schmitt Laetitia , Young John , Dickerson Josie , Hawkins Rebecca , McEachan Rosemary , Fay Matthew , McKevitt Christopher , Foy Robbie , Carter Gillian , Richardson Gillian , Roberts Elaine 
Published: March 2023

Abstract

Background
To address the limited provision of longer-term stroke care, we conducted a programme of research (LoTS2Care) to develop and test an intervention to form part of a replicable longer-term care strategy. New Start, a programme of facilitated self-management, was developed to be delivered at 6 months post-stroke by trained facilitators. Here, we report the findings from the final workstream of this programme, which aimed to evaluate the feasibility and acceptability of implementing a future definitive cluster randomised controlled trial of the developed intervention (New Start) to support stroke survivors and their carers in the longer term.

Methods
A feasibility cluster randomised controlled trial was conducted in English and Welsh NHS stroke services. Stroke services (clusters) were randomised on a 1:1 basis to implement New Start or continue with usual care only. Community-dwelling stroke survivors between 4 and 6 months post-stroke were invited to participate in the trial by post. Outcome measures were collected via post at 3, 6 and 9 months after recruitment. Recruitment and follow-up rates, delivery and uptake of the intervention, data collection feasibility (including postal outcome measures of health and disability, mental well-being at 3, 6, and 9 months post-recruitment) and safety were assessed.

Results
Ten stroke services were recruited. A total of 1127 stroke survivors were screened for participation, and 269 were registered (New Start, n = 145; usual care, n = 124). Retention was high with 239 (89%) stroke survivors being available for follow-up at 9 months, and high return rates of postal questionnaires were achieved (80.3% at 9 months). Intervention training was successfully delivered, and New Start was offered to 95.2% of trial participants in the intervention arm. Uptake was variable, however, ranging from 11.8 to 75.0%. There were no safety concerns.

Conclusions
Stroke service recruitment and longer-term stroke survivor postal recruitment and outcome data collection are feasible; however, refinement of intervention targeting and delivery is required prior to undertaking a definitive trial.

Trial registration
ISRCTN38920246. Registered 22 June 2016 (http://www.isrctn.com/ISRCTN38920246).
The Building Emotional Awareness and Mental health (BEAM) program developed with a community partner for mothers of infants: protocol for a feasibility randomized controlled trial
Authors: Joyce Kayla M. , Rioux Charlie , MacKinnon Anna L. , Katz Laurence Y. , Reynolds Kristin , Kelly Lauren E. , Klassen Terry , Afifi Tracie O. , Mushquash Aislin R. , Clement Fiona M. , Chartier Mariette , Xie Elisabeth Bailin , Penner Kailey E. , Hunter Sandra , Berard Lindsay , Tomfohr-Madsen Lianne , Roos Leslie E. 
Published: March 2023

Abstract
Background
Drastic increases in the rates of maternal depression and anxiety have been reported since the COVID-19 pandemic began. Most programs aim to improve maternal mental health or parenting skills separately, despite it being more effective to target both concurrently. The Building Emotional Awareness and Mental health (BEAM) program was developed to address this gap. BEAM is a mobile health program aiming to mitigate the impacts of pandemic stress on family well-being. Since many family agencies lack infrastructure and personnel to adequately treat maternal mental health concerns, a partnership will occur with Family Dynamics (a local family agency) to address this unmet need. The study’s objective is to examine the feasibility of the BEAM program when delivered with a community partner to inform a larger randomized controlled trial (RCT).

Methods
A pilot RCT will be conducted with mothers who have depression and/or anxiety with a child 6–18 months old living in Manitoba, Canada. Mothers will be randomized to the 10 weeks of the BEAM program or a standard of care (i.e., MoodMission). Back-end App data (collected via Google Analytics and Firebase) will be used to examine feasibility, engagement, and accessibility of the BEAM program; cost-effectiveness will also be examined. Implementation elements (e.g., maternal depression [Patient Health Questionnaire-9] and anxiety [Generalized Anxiety Disorder-7]) will be piloted to estimate the effect size and variance for future sample size calculations.

Discussion
In partnership with a local family agency, BEAM holds the potential to promote maternal-child health via a cost-effective and an easily accessible program designed to scale. Results will provide insight into the feasibility of the BEAM program and will inform future RCTs.

Trial registration {2a}
This trial was retrospectively registered with ClinicalTrial.gov (NCT05398107) on May 31st, 2022.
Patterns of preschool children’s screen time, parent–child interactions, and cognitive development in early childhood: a pilot study
Authors: Rai Jasmine , Predy Madison , Wiebe Sandra A. , Rinaldi Christina , Zheng Yao , Carson Valerie 
Published: March 2023

AbstractBackgroundThe primary objective of this study was to explore the feasibility of a virtual study protocol for a future longitudinal study, including recruitment, study measures, and procedures. The secondary objective was to examine preliminary hypotheses of associations, including 1) the correlations between total duration and patterns of screen time and cognitive development, and 2) the differences in quality of parent–child interactions for two screen-based tasks and a storybook reading task.MethodsParticipants included 44 children aged 3 years and their parents from Edmonton, Alberta and surrounding areas. Children’s screen time patterns (i.e., type, device, content, context) were parental-reported using a 2-week online daily diary design. Children’s cognitive development (i.e., working memory, inhibitory control, self-control, and language) was measured virtually through a recorded Zoom session. Parent–child interactions during three separate tasks (i.e., video, electronic game, and storybook reading) were also measured virtually through a separate recorded Zoom session (n = 42). The quality of the interactions was determined by the Parent–Child Interaction System (PARCHISY). Descriptive statistics, Intra-class correlations (ICC), Spearman’s Rho correlations, and a one-way repeated measures ANOVA with a post-hoc Bonferroni test were conducted.ResultsAll virtual protocol procedures ran smoothly. Most (70%) participants were recruited from four 1-week directly targeted Facebook ads. High completion rates and high inter-rater reliability in a random sample (Diary: 95% for 13/14 days; Cognitive development: 98% 3/4 tests, ICC > 0.93; Parent–child interactions: 100% for 3 tasks, Weighted Kappa ≥ 0.84) were observed for measures. Across cognitive development outcomes, medium effect sizes were observed for five correlations, with positive correlations observed with certain content (i.e., educational screen time) and negative associations observed for total screen time and certain types (show/movie/video viewing) and contexts (i.e., co-use). Medium and large effect sizes were observed for the differences in parent–child interaction quality between the three tasks.ConclusionsThe virtual study protocol appeared feasible. Preliminary findings suggest it may be important to go beyond total duration and consider type, content, and context when examining the association between screen time and cognitive development. A future longitudinal study using this virtual protocol will be conducted with a larger and more generalizable sample.