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1.
bioRxiv ; 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38585817

ABSTRACT

Mediation analysis has emerged as a versatile tool for answering mechanistic questions in microbiome research because it provides a statistical framework for attributing treatment effects to alternative causal pathways. Using a series of linked regression models, this analysis quantifies how complementary data modalities relate to one another and respond to treatments. Despite these advances, the rigid modeling assumptions of existing software often results in users viewing mediation analysis as a black box, not something that can be inspected, critiqued, and refined. We designed the multimedia R package to make advanced mediation analysis techniques accessible to a wide audience, ensuring that all statistical components are easily interpretable and adaptable to specific problem contexts. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, and bootstrap confidence interval construction. We illustrate the package through two case studies. The first re-analyzes a study of the microbiome and metabolome of Inflammatory Bowel Disease patients, uncovering potential mechanistic interactions between the microbiome and disease-associated metabolites, not found in the original study. The second analyzes new data about the influence of mindfulness practice on the microbiome. The mediation analysis identifies a direct effect between a randomized mindfulness intervention and microbiome composition, highlighting shifts in taxa previously associated with depression that cannot be explained by diet or sleep behaviors alone. A gallery of examples and further documentation can be found at https://go.wisc.edu/830110.

2.
mBio ; 12(1)2021 02 16.
Article in English | MEDLINE | ID: mdl-33593964

ABSTRACT

The world faces two seemingly unrelated challenges-a shortfall in the STEM workforce and increasing antibiotic resistance among bacterial pathogens. We address these two challenges with Tiny Earth, an undergraduate research course that excites students about science and creates a pipeline for antibiotic discovery.


Subject(s)
Anti-Bacterial Agents , Drug Discovery/education , Science/education , Students , Bacteria/drug effects , Drug Discovery/methods , Humans
3.
JPEN J Parenter Enteral Nutr ; 41(1): 15-103, 2017 01.
Article in English | MEDLINE | ID: mdl-27815525

ABSTRACT

Enteral nutrition (EN) is a valuable clinical intervention for patients of all ages in a variety of care settings. Along with its many outcome benefits come the potential for adverse effects. These safety issues are the result of clinical complications and of process-related errors. The latter can occur at any step from patient assessment, prescribing, and order review, to product selection, labeling, and administration. To maximize the benefits of EN while minimizing adverse events requires that a systematic approach of care be in place. This includes open communication, standardization, and incorporation of best practices into the EN process. This document provides recommendations based on the available evidence and expert consensus for safe practices, across each step of the process, for all those involved in caring for patients receiving EN.


Subject(s)
Enteral Nutrition , Food, Formulated , Consensus , Humans , Parenteral Nutrition Solutions/chemistry , Parenteral Nutrition Solutions/standards , Practice Guidelines as Topic
4.
Nutr Clin Pract ; 30(4): 522-9, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26084508

ABSTRACT

Bariatric surgery, an effective treatment for morbid obesity, may result in complications that require nutrition support. Common goals for nutrition support in post-bariatric surgery patients include nutrition repletion, avoiding overfeeding, preserving lean body mass, and promoting wound healing. It is often questioned if continued weight loss can be part of the nutrition goals and if weight loss is safe for patients who become critically ill following bariatric surgery. Recent clinical practice guidelines from both the American Society for Parenteral and Enteral Nutrition (A.S.P.E.N.) and Society of Critical Care Medicine (SCCM) have recommended the use of hypocaloric, high-protein nutrition support in both critically and non-critically ill obese patients. Hypocaloric feedings of 50%-70% of estimated energy requirements based on predictive equations or <14 kcal/kg actual body weight, as well as high-protein feedings of 1.2 g/kg actual weight or 2-2.5 g/kg ideal body weight, are suggested by A.S.P.E.N. in the 2013 clinical guidelines for nutrition support of hospitalized adult patients with obesity. Two small studies in complicated post-bariatric surgery patients requiring nutrition support have shown that the strategy of hypocaloric, high-protein feedings can result in positive outcomes, including positive nitrogen balance, wound healing, weight loss, and successful transition to oral diets. Additional research, including large, randomized studies, is still needed to validate these findings. However, based on a review of available clinical practice guidelines, predictive equations, indirect calorimetry, case studies, and systematic reviews, hypocaloric, high-protein nutrition support appears to at least be equal to eucaloric feedings and may be a useful tool for clinicians to achieve continued weight loss in complicated bariatric surgery patients requiring nutrition support.


Subject(s)
Bariatric Surgery/adverse effects , Caloric Restriction/methods , Dietary Proteins/administration & dosage , Nutritional Support/methods , Obesity, Morbid/diet therapy , Postoperative Complications/diet therapy , Weight Loss , Adult , Critical Illness/therapy , Humans , Nutritional Requirements , Obesity, Morbid/surgery , Treatment Outcome
5.
Nutr Clin Pract ; 29(4): 435-444, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24961877

ABSTRACT

Older adults are becoming a significant percentage of the world's population. A multitude of factors, from the normal aging process to the progression of chronic disease, influence the nutrition needs of this very diverse group of people. Appropriate micronutrient intake is of particular importance but is often suboptimal. Here we review the available data regarding micronutrient needs and the consequences of deficiencies in the ever growing aged population.

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