Do adolescents use choice to learn about their preferences? Development of value refinement and its associations with depressive symptoms in adolescence.

Independent decision making requires forming stable estimates of one's preferences. We assessed whether adolescents learn about their preferences through choice deliberation and whether depressive symptoms disrupt this process. Adolescents aged 11-18 (N = 214; participated 2021-22; Female: 53.9%; White/Black/Asian/Mixed/Arab or Latin American: 26/21/19/9/8%) rated multiple activities, chose between pairs of activities and re-rated those activities. As expected, overall, participants uprated chosen and downrated unchosen activities (dz = .20). This value refinement through choice was not evident in younger participants but emerged across adolescence. Contrary to our predictions, depressive symptoms were associated with greater value refinement. Despite this, more depressed adolescents reported lower value certainty and choice confidence. The cognitive processes through which choice deliberation shapes preference develop over adolescence, and are disrupted in depression.

Age-related changes in the impact of valence on self-referential processing in female adolescents and young adults.

Adolescence is a period of self-concept development. In the current study, females aged 11-30 years (N = 210) completed two self-referential tasks. In a memory task, participants judged the descriptiveness of words for themselves or a familiar other and their recognition of these words was subsequently measured. In an associative-matching task, participants associated neutral shapes to either themselves or a familiar other and the accuracy of their matching judgements was measured. In the evaluative memory task, participants were more likely to remember self-judged than other-judged words and there was an age-related decrease in the size of this self-reference effect. Negative self-judgements showed a quadratic association with age, peaking around age 19. Participants were more likely to remember positive than negative words and there was an age-related increase in the magnitude of this positivity bias. In the neutral shapes task, there were no age-related changes in the self-reference effect. Overall, adolescent girls showed enhanced processing of self-relevant stimuli when it could be used to inform their self-concept and especially when it was negative.

Association Between Balance Self-efficacy and Walking Ability in Those With New Lower Limb Amputations.

BACKGROUND: A relationship between walking ability and self-efficacy has been demonstrated in various rehabilitation patient populations. In experienced prosthetic ambulators, walking ability is related to self-efficacy of balance, however, this relationship has not been quantified for those with newly acquired lower limb amputations (LLA). OBJECTIVES: To investigate the association between walking performance (objective) and self-reported walking abilities (subjective) on balance self-efficacy in those with LLA. METHODOLOGY: Cross-sectional study of 27 people (17 men; mean age=63.57±9.33) at discharge from inpatient prosthetic rehabilitation for first major unilateral LLA. Individuals completed 6m straight path walking and the L-Test under single- and dual-task conditions. The Prosthesis Evaluation Questionnaire (PEQ) was administered, and the Ambulation subscale provided subjective measures of walking ability. A single PEQ question on satisfaction with walking (16B) was also used as a proxy for subjective walking ability. The Activities-specific Balance Confidence Scale measured balance self-efficacy. Multivariable linear regression was used to evaluate the strength of association between walking ability (objective and subjective) and balance self-efficacy (dependent variable). FINDINGS: Walking velocity on the 6m straight path under single-task (p=0.011) and dual-task conditions (p=0.039), the single-task L-Test (p=0.035) and self-reported satisfaction with walking (p=0.019) were associated with self-efficacy of balance. CONCLUSIONS: Objective measures of walking ability that were independently associated with balance self-efficacy included straight path walking velocity under single and dual-task conditions and the single-task L-Test. Satisfaction with walking was also associated with balance self-efficacy. This highlights the interplay between physical and psychological factors during rehabilitation. More research in the area of self-efficacy and walking ability is needed to establish self-efficacy as a target during prosthetic rehabilitation for those with LLA.

Loss of Neutrophil Homing to the Periodontal Tissues Modulates the Composition and Disease Potential of the Oral Microbiota.

Periodontal disease is considered to arise from an imbalance in the interplay between the host and its commensal microbiota, characterized by inflammation, destructive periodontal bone loss, and a dysbiotic oral microbial community. The neutrophil is a key component of defense of the periodontium: defects in their number or efficacy of function predisposes individuals to development of periodontal disease. Paradoxically, neutrophil activity, as part of a deregulated inflammatory response, is considered an important element in the destructive disease process. In this investigation, we examined the role the neutrophil plays in the regulation of the oral microbiota by analysis of the microbiome composition in mice lacking the CXCR2 neutrophil receptor required for recruitment to the periodontal tissues. A breeding protocol was employed that ensured that only the oral microbiota of wild-type (CXCR2+/+) mice was transferred to subsequent generations of wild-type, heterozygote, and homozygote littermates. In the absence of neutrophils, the microbiome undergoes a significant shift in total load and composition compared to when normal levels of neutrophil recruitment into the gingival tissues occur, and this is accompanied by a significant increase in periodontal bone pathology. However, transfer of the oral microbiome of CXCR2-/- mice into germfree CXCR2+/+ mice led to restoration of the microbiome to the wild-type CXCR2+/+ composition and the absence of pathology. These data demonstrate that the composition of the oral microbiome is inherently flexible and is governed to a significant extent by the genetics and resultant phenotype of the host organism.

Impact of expression mode and timing of sample collection, relative to milk ejection, on human milk bacterial DNA profiles.

AIM: To investigate the impact of expression mode: electric breast pump or hand expression, and timing of sample collection: pre- and post-milk ejection on human milk (HM) bacterial DNA profiles. METHODS AND RESULTS: Three HM samples from the same breast were collected from 30 breastfeeding mothers: a pre-milk ejection pump-expressed sample (pre-pump), a post-milk ejection pump-expressed sample (post-pump) and a post-milk ejection hand-expressed sample (post-hand). Full-length 16S rRNA gene sequencing was used to assess milk bacterial DNA profiles. Bacterial profiles did not differ significantly based on mode of expression nor timing of sample collection. No significant differences were detected in the relative abundance of any OTUs based on expression condition (pre-pump/ post-pump and post-pump/post-hand) with univariate linear mixed-effects regression analyses (all P-values > 0·01; α = 0·01). Similarly, no difference in richness was observed between sample types (number of observed OTUs: post-pump/post-hand P = 0·13; pre-pump/post-pump P = 0. 45). CONCLUSION: Bacterial DNA profiles of HM did not differ according to either expression method or timing of sample collection. SIGNIFICANCE AND IMPACT OF THE STUDY: Hand or pump expression can be utilized to collect samples for microbiome studies. This has implications for the design of future HM microbiome studies.

DNA extraction method influences human milk bacterial profiles.

AIMS: To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM). METHODS AND RESULTS: Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0·68 ng µl-1 ) and QM (mean = 0·55 ng µl-1 ). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM. CONCLUSIONS: Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk. SIGNIFICANCE AND IMPACT OF THE STUDY: Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.

Mucosal-associated invariant T (MAIT) cells are activated in the gastrointestinal tissue of patients with combination ipilimumab and nivolumab therapy-related colitis in a pathology distinct from ulcerative colitis.

The aim of this study was to investigate the pathogenesis of combination ipilimumab and nivolumab-associated colitis (IN-COL) by measuring gut-derived and peripheral blood mononuclear cell (GMNC; PBMC) profiles. We studied GMNC and PBMC from patients with IN-COL, IN-treated with no adverse-events (IN-NAE), ulcerative colitis (UC) and healthy volunteers using flow cytometry. In the gastrointestinal-derived cells we found high levels of activated CD8+ T cells and mucosal-associated invariant T (MAIT) cells in IN-COL, changes that were not evident in IN-NAE or UC. UC, but not IN-C, was associated with a high proportion of regulatory T cells (Treg ). We sought to determine if local tissue responses could be measured in peripheral blood. Peripherally, checkpoint inhibition instigated a rise in activated memory CD4+ and CD8+ T cells, regardless of colitis. Low circulating MAIT cells at baseline was associated with IN-COL patients compared with IN-NAE in one of two cohorts. UC, but not IN-COL, was associated with high levels of circulating plasmablasts. In summary, the alterations in T cell subsets measured in IN-COL-affected tissue, characterized by high levels of activated CD8+ T cells and MAIT cells and a low proportion of Treg , reflected a pathology distinct from UC. These tissue changes differed from the periphery, where T cell activation was a widespread on-treatment effect, and circulating MAIT cell count was low but not reliably predictive of colitis.

Functional movements of the GABA type A receptor.

We have performed a parallel tempering crankshaft motion Monte Carlo simulation on a model of the GABA type A receptor with the aim of exploring a wide variety of local conformational space. We develop a novel method to analyse the protein movements in terms of a correlation tensor and use this to explore the gating process, that is, how agonist binding could cause ion channel opening. We find that simulated binding impulses to varying clusters of GABA binding site residues produce channel opening, and that equivalent impulses to single GABA sites produce partial opening.

Horizontal and Vertical Transfer of Oral Microbial Dysbiosis and Periodontal Disease.

One of the hallmark features of destructive periodontal disease, well documented over the last 50 y, is a change to the quantitative and qualitative composition of the associated microbiology. These alterations are now generally viewed as transformational shifts of the microbial populations associated with health leading to the emergence of bacterial species, which are only present in low abundance in health and a proportionate decrease in the abundance of others. The role of this dysbiosis of the health associated microbiota in the development of disease remains controversial: is this altered microbiology the driving agent of disease or merely a consequence of the altered environmental conditions that invariably accompany destructive disease? In this work, we aimed to address this controversy through controlled transmission experiments in the mouse in which a dysbiotic oral microbiome was transferred either horizontally or vertically into healthy recipient mice. The results of these murine studies demonstrate conclusively that natural transfer of the dysbiotic oral microbiome from a periodontally diseased individual into a healthy individual will lead to establishment of the dysbiotic community in the recipient and concomitant transmission of the disease phenotype. The inherent resilience of the dysbiotic microbial community structure in diseased animals was further demonstrated by analysis of the effects of antibiotic therapy on periodontally diseased mice. Although antibiotic treatment led to a reversal of dysbiosis of the oral microbiome, in terms of both microbial load and community structure, dysbiosis of the microbiome was reestablished following cessation of therapy. Collectively, these data suggest that an oral dysbiotic microbial community structure is stable to transfer and can act in a similar manner to a conventional transmissible infectious disease agent with concomitant effects on pathology. These findings have implications to our understanding of the role of microbial dysbiosis in the development and progression of human periodontal disease.

Computing the self-consistent field in Kohn-Sham density functional theory.

A new framework is presented for evaluating the performance of self-consistent field methods in Kohn-Sham density functional theory (DFT). The aims of this work are two-fold. First, we explore the properties of Kohn-Sham DFT as it pertains to the convergence of self-consistent field iterations. Sources of inefficiencies and instabilities are identified, and methods to mitigate these difficulties are discussed. Second, we introduce a framework to assess the relative utility of algorithms in the present context, comprising a representative benchmark suite of over fifty Kohn-Sham simulation inputs, the scf-x n suite. This provides a new tool to develop, evaluate and compare new algorithms in a fair, well-defined and transparent manner.

Detection of group B Streptococcus during antenatal screening in Western Australia: a comparison of culture and molecular methods.

AIM: Global screening strategies for Group B Streptococcus (GBS) include risk- or culture-based methods to guide intrapartum prophylaxis. In Western Australia (WA), antenatal culture-based screening is routine; however, numerous culture methods exist, in addition to molecular methods. We aimed to assess the comparability of research and diagnostic screening approaches. METHODS AND RESULTS: Vaginal and rectal swabs were self-collected by pregnant women (n = 531) from King Edward Memorial Hospital, WA, in parallel to routine screening (35-37 weeks of gestation). Research methods involved culture (Strep B Carrot Broth™ and StrepB CHROMagar™) and molecular methods (real-time PCR) and were compared to routine diagnostic screening (Lim Broth and Granada agar). Overall, GBS detection was comparable between research and diagnostic approaches (3-5% discrepancy, kappa = 0·76). Specificity/sensitivity of Carrot Broth™ was 100%/89%, while that of CHROMagar™ was 73%/100%, respectively. Direct PCR was unable to detect GBS in ~18% of specimens which were culture positive; however, it exhibited 100% specificity. CONCLUSIONS: This clinical evaluation of GBS screening methods provides support for current practice. SIGNIFICANCE AND IMPACT OF THE STUDY: Although CHROM was highly sensitive, further testing is recommended due to a high false-positive rate. Molecular assays are useful for rapid detection; however, low-titre samples may require additional enrichment prior to molecular analysis to improve sensitivity.

Re: "Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community" (2018) 6:87, https://doi.org/10.1186/s40168-018-0475-7.

A recent publication by Lim et al. 2018 (Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community) strongly concluded that the microbiome of amniotic fluid primarily originates from reagent contamination. However, upon closer inspection of the methods used and data presented in this study, in particular the supplementary data, such conclusions do not appear to be supported by the results. We outline such methodological/data interpretation concerns and invite the authors to discuss these.

Characterization of the bacterial microbiome in first-pass meconium using propidium monoazide (PMA) to exclude nonviable bacterial DNA.

Numerous studies have reported bacterial DNA in first-pass meconium samples, suggesting that the human gut microbiome is seeded prior to birth. However, these studies have not been able to discriminate between DNA from living bacterial cells, DNA from dead bacterial cells or cell-free DNA. Here we have used propidium monoazide (PMA) together with 16S rRNA gene sequencing to determine whether there are intact bacterial cells in the fetal gut. DNA was extracted from first-pass meconium (n = 5) and subjected to 16S rRNA gene sequencing with/without PMA treatment. All meconium samples, regardless of PMA treatment, contained detectable levels of bacterial DNA; however, treatment with PMA prior to DNA extraction decreased the DNA yield by approximately 20%. PMA-treated meconium samples did not differ significantly from untreated samples in terms of observed number of OTUs (P = 0·945); although they did differ taxonomically, with around one quarter of OTUs identified in untreated samples only, suggesting that they have originated from cell-free/nonviable DNA. The mean Sørensen coefficient for treated vs untreated samples was 0·527. Our findings suggest that the fetal gut is seeded with intact bacterial cells prior to birth. This is an important finding, as exposure to live bacteria during gestation might have a significant impact on the developing fetus. SIGNIFICANCE AND IMPACT OF THE STUDY: DNA-based microbiome studies performed using 16S rRNA gene sequencing are limited by their inability to discriminate between live bacterial cells, dead bacterial cells and cell-free DNA. Here we use propidium monoazide (PMA) to exclude nonviable bacteria from microbiome analysis of first-pass meconium samples and thereby reveal that the majority of the purported fetal gut microbiome is from intact bacterial cells. This work demonstrates the importance of excluding nonviable bacteria when analysing the microbial community in low-biomass samples such as meconium.

Targeted management of influenza A/B outbreaks incorporating the cobas® Influenza A/B & RSV into the virology laboratory.

During the 2017/18 influenza season, the authors' virology laboratory implemented the cobas® Influenza A/B & RSV (Roche Molecular Diagnostics, Pleasanton, CA, USA) for influenza outbreak management in two scenarios: initial outbreak investigation or at outbreak conclusion to avoid prolonged measures. Twenty-seven investigations were conducted, including declaration of 11 influenza A/B outbreaks. Thirty percent of investigations would have missed the standard batched daily laboratory-developed respiratory polymerase chain reaction (PCR), and delayed outbreak confirmation until the following day. The average reduction in turnaround time for influenza A/B testing was 10.2 h. A rapid molecular PCR in specific outbreak scenarios improved timely management of influenza outbreaks.

Identification and removal of contaminating microbial DNA from PCR reagents: impact on low-biomass microbiome analyses.

Reagent-derived contamination can compromise the integrity of microbiome data, particularly in low microbial biomass samples. This contamination has recently been attributed to the 'kitome' (contamination introduced by the DNA extraction kit), prior to which attention was mostly paid to potential contamination introduced by PCR reagents. In this study, we assessed the proportion to which our DNA extraction kit and PCR master mix introduce contaminating microbial DNA to bacterial microbial profiles generated by 16S rRNA gene sequencing. Utilizing a commercial dsDNase treatment protocol to decontaminate the PCR master mix, we demonstrated that the vast majority of contaminating DNA was derived from the PCR master mix. Importantly, this contamination was almost completely eliminated using the simple dsDNase treatment, resulting in a 99% reduction in contaminating bacterial reads. We suggest that dsDNase treatment of PCR reagents should be explored as a simple and effective way of reducing contamination in low-biomass microbiome studies and producing more robust and reliable data. SIGNIFICANCE AND IMPACT OF THE STUDY: Reagent contamination with microbial DNA is a major problem in microbiome studies of low microbial biomass samples. Levels of such contaminating DNA often outweigh what is present in the sample and heavily confound subsequent data analysis. Previous studies have suggested this contamination is primarily derived from DNA extraction kits. Here, we identified the PCR master mix as the primary source of contamination, and showed that enzymatic removal of the contamination drastically reduced the blank signal and improved precision. Decontamination of PCR master mixes may have the potential to improve the sensitivity and accuracy of low-biomass microbiome studies.

Quality of Life and Mental Health in Older Adults with Obesity and Frailty: Associations with a Weight Loss Intervention.

OBJECTIVE: To examine the bi-directional associations of a weight loss intervention with quality of life and mental health in obese older adults with functional limitations. DESIGN: Combined-group analyses of secondary variables from the MEASUR-UP randomized controlled trial. SETTING: Academic medical center. PARTICIPANTS: Obese community-dwelling men and women (N = 67; age ≥60; BMI ≥30) with functional limitations (Short Physical Performance Battery [SPPB] score of 4-10 out of 12). INTERVENTION: Six-month reduced calorie diet at two protein levels. MEASUREMENTS: Weight, height, body composition, physical function, medical history, and mental health and quality of life assessments (Center for Epidemiologic Studies Depression Scale [CES-D]; Profile of Mood States [POMS], Pittsburgh Sleep Quality Index [PSQI]; Perceived Stress Scale [PSS]; Satisfaction with Life Scale [SWLS]; and Short Form Health Survey [SF-36]) were acquired at 0, 3 and 6 months. RESULTS: Physical composite quality of life (SF-36) improved significantly at 3 months (ß = 6.29, t2,48 = 2.60, p = 0.012) and 6 months (ß = 10.03, t2,48 = 4.83, p < 0.001), as did several domains of physical quality of life. Baseline depression symptoms (CES-D and POMS) were found to predict lower amounts of weight loss; higher baseline sleep latency (PSQI) and anger (POMS) predicted less improvement in physical function (SPPB). CONCLUSION: The significant bi-directional associations found between a weight loss intervention and mental health/quality of life, including substantial improvements in physical quality of life with obesity treatment, indicate the importance of considering mental health and quality of life as part of any weight loss intervention for older adults.

Prediction of GABARAP interaction with the GABA type A receptor.

We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.

Large outbreak of multiple gastrointestinal pathogens associated with fresh curry leaves in North East England, 2013.

A total of 592 people reported gastrointestinal illness following attendance at Street Spice, a food festival held in Newcastle-upon-Tyne, North East England in February/March 2013. Epidemiological, microbiological and environmental investigations were undertaken to identify the source and prevent further cases. Several epidemiological analyses were conducted; a cohort study; a follow-up survey of cases and capture re-capture to estimate the true burden of cases. Indistinguishable isolates of Salmonella Agona phage type 40 were identified in cases and on fresh curry leaves used in one of the accompaniments served at the event. Molecular testing indicated entero-aggregative Escherichia coli and Shigella also contributed to the burden of illness. Analytical studies found strong associations between illness and eating food from a particular stall and with food items including coconut chutney which contained fresh curry leaves. Further investigation of the food supply chain and food preparation techniques identified a lack of clear instruction on the use of fresh uncooked curry leaves in finished dishes and uncertainty about their status as a ready-to-eat product. We describe the investigation of one of the largest outbreaks of food poisoning in England, involving several gastrointestinal pathogens including a strain of Salmonella Agona not previously seen in the UK.