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Biology Direct Oct 2019Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often...
BACKGROUND
Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project participants collected samples from subway surfaces in different cities and performed metagenomic sequencing. Previous studies focused on taxonomic composition of these microbiomes and no explicit functional analysis had been done till now.
RESULTS
As a part of the 2018 CAMDA challenge, we functionally profiled the available ~ 400 subway metagenomes and built predictor for city origin. In cross-validation, our model reached 81% accuracy when only the top-ranked city assignment was considered and 95% accuracy if the second city was taken into account as well. Notably, this performance was only achievable if the similarity of distribution of cities in the training and testing sets was similar. To assure that our methods are applicable without such biased assumptions we balanced our training data to account for all represented cities equally well. After balancing, the performance of our method was slightly lower (76/94%, respectively, for one or two top ranked cities), but still consistently high. Here we attained an added benefit of independence of training set city representation. In testing, our unbalanced model thus reached (an over-estimated) performance of 90/97%, while our balanced model was at a more reliable 63/90% accuracy. While, by definition of our model, we were not able to predict the microbiome origins previously unseen, our balanced model correctly judged them to be NOT-from-training-cities over 80% of the time. Our function-based outlook on microbiomes also allowed us to note similarities between both regionally close and far-away cities. Curiously, we identified the depletion in mycobacterial functions as a signature of cities in New Zealand, while photosynthesis related functions fingerprinted New York, Porto and Tokyo.
CONCLUSIONS
We demonstrated the power of our high-speed function annotation method, mi-faser, by analysing ~ 400 shotgun metagenomes in 2 days, with the results recapitulating functional signals of different city subway microbiomes. We also showed the importance of balanced data in avoiding over-estimated performance. Our results revealed similarities between both geographically close (Ofa and Ilorin) and distant (Boston and Porto, Lisbon and New York) city subway microbiomes. The photosynthesis related functional signatures of NYC were previously unseen in taxonomy studies, highlighting the strength of functional analysis.
Topics: Cities; Metagenome; Microbiota; Railroads
PubMed: 31666099
DOI: 10.1186/s13062-019-0252-y -
Materials Today. Bio Dec 2023Bone regeneration heavily relies on bone marrow mesenchymal stem cells (BMSCs). However, recruiting endogenous BMSCs for in situ bone regeneration remains challenging....
Bone regeneration heavily relies on bone marrow mesenchymal stem cells (BMSCs). However, recruiting endogenous BMSCs for in situ bone regeneration remains challenging. In this study, we developed a novel BMSC-aptamer (BMSC-apt) functionalized hydrogel (BMSC-aptgel) and evaluated its functions in recruiting BMSCs and promoting bone regeneration. The functional hydrogels were synthesized between maleimide-terminated 4-arm polyethylene glycols (PEG) and thiol-flanked PEG crosslinker, allowing rapid in situ gel formation. The aldehyde group-modified BMSC-apt was covalently bonded to a thiol-flanked PEG crosslinker to produce high-density aptamer coverage on the hydrogel surface. In vitro and in vivo studies demonstrated that the BMSC-aptgel significantly increased BMSC recruitment, migration, osteogenic differentiation, and biocompatibility. In vivo fluorescence tomography imaging demonstrated that functionalized hydrogels effectively recruited DiR-labeled BMSCs at the fracture site. Consequently, a mouse femur fracture model significantly enhanced new bone formation and mineralization. The aggregated BMSCs stimulated bone regeneration by balancing osteogenic and osteoclastic activities and reduced the local inflammatory response via paracrine effects. This study's findings suggest that the BMSC-aptgel can be a promising and effective strategy for promoting in situ bone regeneration.
PubMed: 38024846
DOI: 10.1016/j.mtbio.2023.100854 -
International Journal of Environmental... Mar 2020Timely stroke diagnosis and intervention are necessary considering its high prevalence. Previous studies have mainly focused on stroke prediction with balanced data....
Timely stroke diagnosis and intervention are necessary considering its high prevalence. Previous studies have mainly focused on stroke prediction with balanced data. Thus, this study aimed to develop machine learning models for predicting stroke with imbalanced data in an elderly population in China. Data were obtained from a prospective cohort that included 1131 participants (56 stroke patients and 1075 non-stroke participants) in 2012 and 2014, respectively. Data balancing techniques including random over-sampling (ROS), random under-sampling (RUS), and synthetic minority over-sampling technique (SMOTE) were used to process the imbalanced data in this study. Machine learning methods such as regularized logistic regression (RLR), support vector machine (SVM), and random forest (RF) were used to predict stroke with demographic, lifestyle, and clinical variables. Accuracy, sensitivity, specificity, and areas under the receiver operating characteristic curves (AUCs) were used for performance comparison. The top five variables for stroke prediction were selected for each machine learning method based on the SMOTE-balanced data set. The total prevalence of stroke was high in 2014 (4.95%), with men experiencing much higher prevalence than women (6.76% vs. 3.25%). The three machine learning methods performed poorly in the imbalanced data set with extremely low sensitivity (approximately 0.00) and AUC (approximately 0.50). After using data balancing techniques, the sensitivity and AUC considerably improved with moderate accuracy and specificity, and the maximum values for sensitivity and AUC reached 0.78 (95% CI, 0.73-0.83) for RF and 0.72 (95% CI, 0.71-0.73) for RLR. Using AUCs for RLR, SVM, and RF in the imbalanced data set as references, a significant improvement was observed in the AUCs of all three machine learning methods ( < 0.05) in the balanced data sets. Considering RLR in each data set as a reference, only RF in the imbalanced data set and SVM in the ROS-balanced data set were superior to RLR in terms of AUC. Sex, hypertension, and uric acid were common predictors in all three machine learning methods. Blood glucose level was included in both RLR and RF. Drinking, age and high-sensitivity C-reactive protein level, and low-density lipoprotein cholesterol level were also included in RLR, SVM, and RF, respectively. Our study suggests that machine learning methods with data balancing techniques are effective tools for stroke prediction with imbalanced data.
Topics: Aged; China; Female; Forecasting; Humans; Machine Learning; Male; Prognosis; Prospective Studies; Stroke; Support Vector Machine
PubMed: 32178250
DOI: 10.3390/ijerph17061828 -
Nursing Philosophy : An International... Jul 2022Person-centred care is founded on ethics as a basis for organizing care. In spite of healthcare systems claiming that they have implemented person-centred care, patients... (Review)
Review
Person-centred care is founded on ethics as a basis for organizing care. In spite of healthcare systems claiming that they have implemented person-centred care, patients report less satisfaction with care. These contrasting results require clarification of how to practice person-centred ethics using Paul Ricoeur's 'Little ethics', summarized as: 'aiming for the good life, with and for others in just institutions'. In this ethic Kantian morality is at once subordinate and complementary to Aristotelian ethics because the ethical goal needs to be critically assessed and passed through the examination of the norm in each care situation. This paper presents examples that describes a person-centred care practice that balance a critical review of care activities based on a conviction of aiming for patients' wellbeing. In contrast to patients' experiences of person-centred care in real life, research projects have shown that if the clinical performers comprehend and apply the practice of person-centred ethics, patients report positive outcomes. The implementation of person-centred care therefore demands that stakeholders and managers enables and requires that healthcare staff study ethics in the same way as studying for example pharmacology is required when handling patients' medicines.
Topics: Delivery of Health Care; Humans; Moral Obligations; Morals; Palliative Care; Patient-Centered Care
PubMed: 35213781
DOI: 10.1111/nup.12382 -
BMC Musculoskeletal Disorders Oct 2019Recently, various studies have reported the importance of distinguishing between balanced and unbalanced SL, sustaining the importance of SL reduction in unbalanced...
BACKGROUND
Recently, various studies have reported the importance of distinguishing between balanced and unbalanced SL, sustaining the importance of SL reduction in unbalanced cases. In this study we present our experience in the treatment of isthmic spondylolisthesis in young patients, observing the correlation between SL reduction and sagittal correlation between spine and pelvis.
METHODS
This is a retrospective study of a series of patients treated surgically for isthmic spondylolisthesis. Inclusion criteria were L5-S1 isthmic spondylolisthesis of III° or IV°, pediatric age, clinical and radiographic follow up of at least 1 year. Radiographic evaluation included the following elements: grade and percentage of listhesis (%L), lumbar lordosis (LL), lumbar-sacral angle (LSA), pelvic incidence (PI), sacral slope (SS), pelvic tilt (PT) distinguishing between "balanced" and "unbalanced" patients. Radiographic values were confronted by using Student's t- test, obtaining a statistically significant difference for values inferior to 0,05.
RESULTS
Based on inclusion criteria, 28 patients were selected for our retrospective analysis, 19 female and 9 male. Mean age at surgery was 15,6 years. Mean follow up was 3 years and 3 months (min. 1 year - max 6 years and 7 months). Spondylolisthesis reduction was statistically significant both in balanced and in unbalanced patients, but pelvic incidence values did not improve significantly. We observed fewer mechanical complications in patients treated with interbody support.
CONCLUSION
In our study, differences between pre-op and post-op spinopelvic alignment values were not statistically significant, even though spondylolisthesis reduction was statistically significant in all cases. Our study could be considered an initial attempt to correlate spinopelvic changes to spondylolisthesis reduction in a progressive manner, and possibly in the future, generate threshold values of reduction for ideal spinopelvic alignment in every different patient.
Topics: Adolescent; Child; Female; Follow-Up Studies; Humans; Lumbar Vertebrae; Male; Pelvic Bones; Postural Balance; Retrospective Studies; Sacrum; Spondylolisthesis
PubMed: 31664969
DOI: 10.1186/s12891-019-2865-9 -
Sensors (Basel, Switzerland) Jan 2021Total knee arthroplasty (TKA) surgery with manual instruments provides a quantitatively balanced knee in approximately 50% of cases. This study examined the effect of...
Total knee arthroplasty (TKA) surgery with manual instruments provides a quantitatively balanced knee in approximately 50% of cases. This study examined the effect of combining robotics technology with real-time intra-operative sensor feedback on the number of quantitatively balanced cases in a consecutive series of 200 robotic-assisted primary TKAs. The robotics platform was used to plan the implant component position using correctable poses in extension and a manual, centrally pivoting the balancer in flexion, prior to committing to the femoral cuts. During the initial trialing, the quantitative state of balance was assessed using an instrumented tibial tray that measured the intra-articular loads in the medial and lateral compartments. These sensor readings informed a number of surgical corrections, including bone recuts, soft-tissue corrections, and cement adjustments. During initial trialing, a quantitatively balanced knee was achieved in only 65% of cases. After performing the relevant soft-tissue corrections, bone recuts, and cement adjustments, 87% of cases ended balanced through the range of motion. Meanwhile, this resulted in a wide range of coronal alignment conditions, ranging from 6° valgus to 9° varus. It is therefore concluded that gaps derived from robotics navigation are not indicative for a quantitatively balanced knee, which was only consistently achieved when combining the robotics platform with real-time feedback from intra-operative load sensors.
Topics: Aged; Arthroplasty, Replacement, Knee; Female; Humans; Knee; Knee Joint; Male; Osteoarthritis, Knee; Range of Motion, Articular
PubMed: 33451019
DOI: 10.3390/s21020535 -
Personality & Social Psychology Bulletin Dec 2023What does it mean to be in solitude? Researchers building this nascent field are learning much about the potential affordances of solitude, but lack an agreed-upon...
What does it mean to be in solitude? Researchers building this nascent field are learning much about the potential affordances of solitude, but lack an agreed-upon definition or set of definitions. Arriving at that meaning is crucial to forming a solid foundation for studies that use both naturalistic and laboratory designs to explore outcomes of solitude. This study identified themes from semi-structured interviews with adults aged 19 to 80 from diverse backgrounds. We concluded that solitude is a state in which the dominant relationship is with the self. If not physically alone, people in solitude are mentally distanced from others and away from active technology-mediated interactions. Complete solitude involves both physical separation and inner focus, but solitude is best defined through a taxonomy that recognizes physical separation and internal focus as independent, sufficient characteristics. An internal focus benefits from (but is not defined by) balancing solitude with social time, quiet, and choice.
Topics: Adult; Humans; Young Adult; Middle Aged; Aged; Aged, 80 and over; Psychological Distance
PubMed: 36062325
DOI: 10.1177/01461672221115941 -
Animal : An International Journal of... Nov 2022Feeding diets with an unbalanced amino acid (AA) profile can reduce the postprandial AA utilization for protein synthesis. Growing pigs use dietary AA mainly for protein...
Feeding diets with an unbalanced amino acid (AA) profile can reduce the postprandial AA utilization for protein synthesis. Growing pigs use dietary AA mainly for protein accretion, whereas non-lactating and non-pregnant adult pigs use AA mainly for maintenance. The requirement for AA for growth is much larger than that for maintenance and growing pigs may therefore be more affected by a diet with an unbalanced AA profile than adult pigs. This study aimed to compare the postprandial plasma AA and metabolite concentrations of adult and growing pigs after feeding a diet with either an unbalanced (UNB) or a balanced AA profile (BAL). The postprandial plasma concentrations of AA were used to study the influence of AA balance on postprandial AA metabolism. Extensively hydrolysed feathers (EHF) were used as an AA source. Both BAL and UNB contained EHF supplemented with L-Ala, L-Asp, L-Glu, Gly, and L-Trp while BAL was also supplemented with L-His, L-Ile, L-Lys, L-Met, and L-Tyr. Four growing and four male adult pigs were fitted with a jugular catheter and received each diet as a meal test thrice. The meal test consisted of giving a small meal after an overnight fast followed by serial blood collection for 360 min. A non-linear regression model was used to describe the postprandial plasma AA kinetics. Plasma kinetics of adult and growing pigs fed BAL resulted in a higher area under the curve (AUC) for the AA that were used to balance the diet. For the other AA, feeding BAL resulted in lower AUC, suggesting faster metabolic utilization of AA for protein synthesis. The apparent quantity of dietary AA appearing in the plasma after feeding was lower in adult pigs, suggesting higher first-pass AA utilization in the intestine and liver. For adult and growing pigs, balancing the AA profile of the diet resulted in faster overall metabolic utilization of AA as seen in the generally lower AUC of BAL compared to UNB.
Topics: Swine; Male; Animals; Amino Acids; Animal Feed; Diet; Dietary Supplements; Postprandial Period; Animal Nutritional Physiological Phenomena; Ileum
PubMed: 36368265
DOI: 10.1016/j.animal.2022.100663 -
Giornale Italiano Di Nefrologia :... Dec 2023Although Randomized clinical trials (RCT) represent the gold standard to compare two or more treatments, the impact of observational studies cannot be ignored.... (Review)
Review
Although Randomized clinical trials (RCT) represent the gold standard to compare two or more treatments, the impact of observational studies cannot be ignored. Obviously, these latter are performed on unbalanced sample, and differences among the compared groups could be detected. These differences could have an impact on the estimated association between our allocation and our outcome. To avoid it, some methods should be applied in the analysis of observational cohort. Propensity score (PS) can be considered as a value which sums up and balances the known variables. It aims to adjust or balance the probability of receiving a specific allocation group, and could be used to match, stratify, weight, and perform a covariate adjustment. PS is calculated with a logistic regression, using allocation groups as the outcome. Thanks to PS, we compute the probability of being allocated to one group and we can match patients obtaining two balanced groups. It avoids computing analysis in unbalanced groups. We compared low protein diet (LPD) and the Mediterranean diet in CKD patients and analysed them using the PS methods. Nutritional therapy is fundamental for the prevention, progression and treatment of Chronic Kidney Disease (CKD) and its complications. An individualized, stepwise approach is essential to guarantee high adherence to nutritional patterns and to reach therapeutic goals. The best dietary regimen is still a matter of discussion. In our example, unbalanced analysis showed a significant renal function preservation in LPD, but this correlation was denied after the PS analysis. In conclusion, although unmatched analysis showed differences between the two diets, after propensity analysis no differences were detected. If RCT cannot be performed, balancing the PS score allows to balance the sample and avoids biased results.
Topics: Humans; Diet, Protein-Restricted; Propensity Score; Diet, Mediterranean; Renal Insufficiency, Chronic
PubMed: 38156537
DOI: No ID Found -
BMC Medical Research Methodology Dec 2019The Multiphase Optimization Strategy (MOST) is designed to maximize the impact of clinical healthcare interventions, which are typically multicomponent and increasingly...
BACKGROUND
The Multiphase Optimization Strategy (MOST) is designed to maximize the impact of clinical healthcare interventions, which are typically multicomponent and increasingly complex. MOST often relies on factorial experiments to identify which components of an intervention are most effective, efficient, and scalable. When assigning participants to conditions in factorial experiments, researchers must be careful to select the assignment procedure that will result in balanced sample sizes and equivalence of covariates across conditions while maintaining unpredictability.
METHODS
In the context of a MOST optimization trial with a 2x2x2x2 factorial design, we used computer simulation to empirically test five subject allocation procedures: simple randomization, stratified randomization with permuted blocks, maximum tolerated imbalance (MTI), minimal sufficient balance (MSB), and minimization. We compared these methods across the 16 study cells with respect to sample size balance, equivalence on key covariates, and unpredictability. Leveraging an existing dataset to compare these procedures, we conducted 250 computerized simulations using bootstrap samples of 304 participants.
RESULTS
Simple randomization, the most unpredictable procedure, generated poor sample balance and equivalence of covariates across the 16 study cells. Stratified randomization with permuted blocks performed well on stratified variables but resulted in poor equivalence on other covariates and poor balance. MTI, MSB, and minimization had higher complexity and cost. MTI resulted in balance close to pre-specified thresholds and a higher degree of unpredictability, but poor equivalence of covariates. MSB had 19.7% deterministic allocations, poor sample balance and improved equivalence on only a few covariates. Minimization was most successful in achieving balanced sample sizes and equivalence across a large number of covariates, but resulted in 34% deterministic allocations. Small differences in proportion of correct guesses were found across the procedures.
CONCLUSIONS
Based on the computer simulation results and priorities within the study context, minimization with a random element was selected for the planned research study. Minimization with a random element, as well as computer simulation to make an informed randomization procedure choice, are utilized infrequently in randomized experiments but represent important technical advances that researchers implementing multi-arm and factorial studies should consider.
Topics: Algorithms; Computer Simulation; Humans; Randomized Controlled Trials as Topic; Research Design
PubMed: 31842765
DOI: 10.1186/s12874-019-0883-9