A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.

Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and found that 3.8% (1,050) of variants, most of which are extremely rare, led to large-effect splice-disrupting variants (SDVs). Importantly, we find that 83% of SDVs are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predict a priori. Our results indicate extant, rare genetic variants can have large functional effects on splicing at appreciable rates, even outside the context of disease, and MFASS enables their empirical assessment at scale.

Stochastic microbiome assembly depends on context.

Observational studies reveal substantial variability in microbiome composition across individuals. Targeted studies in gnotobiotic animals underscore this variability by showing that some bacterial strains colonize deterministically, while others colonize stochastically. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, in this paper we show that for the model organism Drosophila melanogaster, interactions between bacteria can affect the microbiome assembly process, contributing to a baseline level of microbiome variability even among isogenic organisms that are identically reared, housed, and fed. In germ-free flies fed known combinations of bacterial species, we find that some species colonize more frequently than others even when fed at the same high concentration. We develop an ecological technique that infers the presence of interactions between bacterial species based on their colonization odds in different contexts, requiring only presence/absence data from two-species experiments. We use a progressive sequence of probabilistic models, in which the colonization of each bacterial species is treated as an independent stochastic process, to reproduce the empirical distributions of colonization outcomes across experiments. We find that incorporating context-dependent interactions substantially improves the performance of the models. Stochastic, context-dependent microbiome assembly underlies clinical therapies like fecal microbiota transplantation and probiotic administration and should inform the design of synthetic fecal transplants and dosing regimes.

The contributions of social network support and reciprocity to posttraumatic stress symptoms across time among parents and caregivers impacted by the ABC Day Care Center fire in Hermosillo, Mexico.

In 2009, a fire occurred in the ABC Day Care Center in Hermosillo, Mexico, that killed and injured many children who were in attendance that day. This study investigated the association between the posttraumatic stress symptoms (PTSS) of socially connected parents and caregivers whose children were affected by the fire. Parents and caregivers of the children who were in attendance the day of the fire were interviewed 8-11 months and 20-23 months postfire. Linear network autocorrelation modeling was used to test for autocorrelations of the outcome variable count of PTSS within different configurations of the network of caregivers. No significant network effects appeared in models from the first interview period, but effects did appear in the second period, specifically in the three models in which network ties consisted of "receive informational support" (.220), "give and receive emotional support" (.167), and "give and receive both informational and emotional support" (.213). The findings suggest that in these three network configurations, as relationships grew in strength from the first interview to the second, the level of one's own PTSS was more comparable to the level of PTSS of one's social connections. Two theoretical mechanisms that may explain this result are homophily and social influence.

Trends in the relationship between suicide behaviors and obesity among adolescents in the United States from 1999 to 2019.

Previous studies indicate that obesity is a risk factor of suicide behaviors among adolescents. Whether this association has remained consistent during the ongoing obesity epidemic remains unknown. The time trends of the obesity-suicide association were examined using the 1999-2019 biannual Youth Risk Behavior Survey data (n = 161,606). Prevalence odds ratio of suicide behaviors among adolescents with obesity (vs. adolescents with no obesity) for each survey year and time trends using National Cancer Institute Joinpoint regression analysis was calculated. For each year post-baseline, there was a significant increase of prevalence odds ratio of 1.4 (1.2-1.6)-1.6 (1.3-2.0) for suicide ideation, 1.3 (1.1-1.7) -1.7 (1.4-2.0) for plan, and 1.3 (1.0-1.7) -1.9 (1.5-2.4) for an attempt, except for the 2013 survey for attempt (1.19 [0.9-1.6]). Significant positive trends were found from1999 to 2019 for ideation and plan, with biannual %-changes of + 0.92 and + 1.22%, respectively. Adolescents with obesity have consistently higher odds of engaging in suicide behaviors than their peers without obesity since the beginning of the United States obesity epidemic, and this association grew stronger as the obesity epidemic continued.

Using Physiological Markers to Assess Comfort during Neuromuscular Electrical Stimulation Induced Muscle Contraction in a Virtually Guided Environment: Pilot Study for a Path toward Combating ICU-Acquired Weakness.

We assessed the feasibility of implementing a virtually guided Neuromuscular Electrical Stimulation (NMES) protocol over the tibialis anterior (TA) muscle while collecting heart rate (HR), Numeric Pain Rating Scale (NPRS), and quality of contraction (QoC) data. We investigated if HR, NPRS, and QoC differ ON and OFF the TA motor point and explored potential relationships between heart rate variability (HRV) and the NPRS. Twelve healthy adults participated in this cross-sectional study. Three NMES trials were delivered ON and OFF the TA motor point. HR, QoC, and NPRS data were collected. There was no significant difference in HRV ON and OFF the motor point (p > 0.05). The NPRS was significantly greater OFF the motor point (p < 0.05). The QoC was significantly different between motor point configurations (p < 0.05). There was no correlation between the NPRS and HRV (p > 0.05, r = -0.129). We recommend non-electrical methods of measuring muscle activity for future studies. The NPRS and QoC can be administered virtually. Time-domain HRV measures could increase the validity of the protocol. The variables should be explored further virtually to enhance the protocol before eventual ICU studies.

Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

SciPy 1.0: fundamental algorithms for scientific computing in Python.

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

The effects of feeding dried browse leaves on rumen ammonia levels, methanogens and protozoa amplification of sheep in the Coastal Savannah of Ghana.

Tanniferous browse leaves are reported to inhibit methanogens and protozoa activity in the rumen, thus contributing to a reduction of methane emission. This study evaluated the influence of feeding dried browse leaves to sheep on rumen ammonia concentration, the base pair at which protozoa and methanogens were amplified and double stranded DNA concentration (dsDNA) from rumen fluid and faeces. The eight treatments were urea treated rice straw, Albizzia lebbek (AL), Moringa oleifera (MO), Millettia thonningii (MT), AL + MO, AL + MT, AL + MO + MT and MO + MT. After feeding 32 ram lambs for 3 months, one ram lamb on each of the eight experimental diets was randomly selected and slaughtered to obtain rumen fluid. Genomic DNAs were extracted from methanogen and protozoa strains obtained from rumen liquor and from faecal matter of sheep. Rumen ammonia was determined using spectrophotometer. Methanogens and protozoa from rumen fluid and faeces were amplified at 1100 base pair, 200-1100 base pair, 320-1100 base pair and 200-750 base pair respectively. Rumen ammonia concentration, dsDNA from rumen fluid and faeces ranged from 14.51 to 23.01 mg/dl, 65 to 900 µg/ml and 100 to 950 µg/g respectively. The rumen ammonia concentration met the requirements for efficient growth of microbes. The presence of methanogens and protozoa in the rumen fluid and in the faeces indicated that dried browse diets were able to inhibit the growth of both protozoa and methanogens in the rumen by eliminating them, and thus, were excreted in the faeces. Hence, feeding of dried browse leaves can contribute to lower methane emission.

Perspectives of Patients and Providers in Using Shared Decision Making in Psychiatry.

There is increased interest over the last decade in the use of Shared Decision Making with individuals with serious mental illness to improve engagement in treatment and clinical outcomes. We conducted semi-structured qualitative interviews with 15 individuals with serious mental illness treated in an outpatient transitional care clinic serving people immediately after discharge from a psychiatric hospitalization. Parallel interviews were conducted with a variety of clinical providers (n = 9). Using latent thematic analysis, six themes were identified including: (1) Differences in the Use of SDM, (2) Consideration of Past Experiences, (3) Decisional Power Preferences, (4) Use of SDM in Psychiatry Versus Other Areas of Medicine, (5) Dignity and Disengagement, and (6) External Forces Impacting SDM. Implications for clinical practice and research using a shared decision-making approach within this treatment setting are further discussed.

Intraperitoneal bladder rupture in a young child with vascular Ehlers-Danlos syndrome.

In this report, we present the case of a 3-year-old child with vascular Ehlers-Danlos syndrome (vEDS) previously known as Ehlers-Danlos syndrome type IV. After experiencing a minor traumatic injury to the abdomen, consisting of falling over a bathroom stool on the way to the restroom with a full bladder, the child developed acute abdominal pain. He was found to have an intraperitoneal bladder rupture that was successfully repaired with management techniques tailored to his known diagnosis of vEDS. While tissue fragility and internal organ rupture occurring with minor trauma are known complications of vEDS, this is the first case in the literature of a bladder rupture in a child with vEDS with a confirmed variant in the COL3A1 gene, to our knowledge. This case broadens the clinical presentation of vEDS, demonstrates that children can have life-threatening organ rupture at a young age, and may alert providers to consider this diagnosis when a child presents with bladder rupture.

Aging-induced fragility of the immune system.

The adaptive and innate branches of the vertebrate immune system work in close collaboration to protect organisms from harmful pathogens. As an organism ages its immune system undergoes immunosenescence, characterized by declined performance or malfunction in either immune branch, which can lead to disease and death. In this study we develop a mathematical framework of coupled innate and adaptive immune responses, namely the integrated immune branch (IIB) model. This model describes dynamics of immune components in both branches, uses a shape-space representation to encode pathogen-specific immune memory, and exhibits three steady states - health, septic death, and chronic inflammation - qualitatively similar to clinically-observed immune outcomes. In this model, the immune system (initialized in the health state) is subjected to a sequence of pathogen encounters, and we use the number of prior pathogen encounters as a proxy for the "age" of the immune system. We find that repeated pathogen encounters may trigger a fragility in which any encounter with a novel pathogen will cause the system to irreversibly switch from health to chronic inflammation. This transition is consistent with the onset of "inflammaging", a condition observed in aged individuals who experience chronic low-grade inflammation even in the absence of pathogens. The IIB model predicts that the onset of chronic inflammation strongly depends on the history of encountered pathogens; the timing of onset differs drastically when the same set of infections occurs in a different order. Lastly, the coupling between the innate and adaptive immune branches generates a trade-off between rapid pathogen clearance and a delayed onset of immunosenescence. Overall, by considering the complex feedback between immune compartments, our work suggests potential mechanisms for immunosenescence and provides a theoretical framework at the system level and on the scale of an organism's lifetime to account for clinical observations.

Microbiome interactions shape host fitness.

Gut bacteria can affect key aspects of host fitness, such as development, fecundity, and lifespan, while the host, in turn, shapes the gut microbiome. However, it is unclear to what extent individual species versus community interactions within the microbiome are linked to host fitness. Here, we combinatorially dissect the natural microbiome of Drosophila melanogaster and reveal that interactions between bacteria shape host fitness through life history tradeoffs. Empirically, we made germ-free flies colonized with each possible combination of the five core species of fly gut bacteria. We measured the resulting bacterial community abundances and fly fitness traits, including development, reproduction, and lifespan. The fly gut promoted bacterial diversity, which, in turn, accelerated development, reproduction, and aging: Flies that reproduced more died sooner. From these measurements, we calculated the impact of bacterial interactions on fly fitness by adapting the mathematics of genetic epistasis to the microbiome. Development and fecundity converged with higher diversity, suggesting minimal dependence on interactions. However, host lifespan and microbiome abundances were highly dependent on interactions between bacterial species. Higher-order interactions (involving three, four, and five species) occurred in 13-44% of possible cases depending on the trait, with the same interactions affecting multiple traits, a reflection of the life history tradeoff. Overall, we found these interactions were frequently context-dependent and often had the same magnitude as individual species themselves, indicating that the interactions can be as important as the individual species in gut microbiomes.

Being Ostracized Versus Out of the Loop: Redundant or Unique Predictors of Variance in Workplace Outcomes?

Based on the existing research, being excluded from information (i.e., being out of the loop) produces similar consequences as being ignored or excluded from activities. Consequently, one might wonder whether it is necessary to measure or study different types of exclusion in the workplace context, rather than just assessing a single type of exclusion. The current research investigated the associations between two types of workplace exclusion (i.e., being ostracized and being left out of the loop) and various workplace outcomes, with the purpose of determining whether these different types of exclusion predict unique or redundant variance in these workplace outcomes. In Study 1, we obtained better model fit when we assigned items measuring out-of-the-loop experiences at work to a different factor than items assessing experiences with ostracism at work. In Study 2, we observed that measuring employees' experiences with being out of the loop predicted unique variance in workplace outcomes (e.g., job satisfaction), above and beyond experiences with ostracism at work. Relative weight analyses suggested that both ostracism and out-of-the-loop experiences were equally important predictors of these outcomes. Together, these studies indicate that being ostracized and being left out of the loop may be distinct exclusion experiences and better predictions about workplace outcomes can be made by assessing both types of exclusion. On a practical level, measuring different types of exclusion may prove useful, because organizations may need to implement different interventions for addressing distinct types of exclusion.

Diffuse optical spectroscopic imaging reveals distinct early breast tumor hemodynamic responses to metronomic and maximum tolerated dose regimens.

BACKGROUND: Breast cancer patients with early-stage disease are increasingly administered neoadjuvant chemotherapy (NAC) to downstage their tumors prior to surgery. In this setting, approximately 31% of patients fail to respond to therapy. This demonstrates the need for techniques capable of providing personalized feedback about treatment response at the earliest stages of therapy to identify patients likely to benefit from changing treatment. Diffuse optical spectroscopic imaging (DOSI) has emerged as a promising functional imaging technique for NAC monitoring. DOSI uses non-ionizing near-infrared light to provide non-invasive measures of absolute concentrations of tissue chromophores such as oxyhemoglobin. In 2011, we reported a new DOSI prognostic marker, oxyhemoglobin flare: a transient increase in oxyhemoglobin capable of discriminating NAC responders within the first day of treatment. In this follow-up study, DOSI was used to confirm the presence of the flare as well as to investigate whether DOSI markers of NAC response are regimen dependent. METHODS: This dual-center study examined 54 breast tumors receiving NAC measured with DOSI before therapy and the first week following chemotherapy administration. Patients were treated with either a standard of care maximum tolerated dose (MTD) regimen or an investigational metronomic (MET) regimen. Changes in tumor chromophores were tracked throughout the first week and compared to pathologic response and treatment regimen at specific days utilizing generalized estimating equations (GEE). RESULTS: Within patients receiving MTD therapy, the oxyhemoglobin flare was confirmed as a prognostic DOSI marker for response appearing as soon as day 1 with post hoc GEE analysis demonstrating a difference of 48.77% between responders and non-responders (p < 0.0001). Flare was not observed in patients receiving MET therapy. Within all responding patients, the specific treatment was a significant predictor of day 1 changes in oxyhemoglobin, showing a difference of 39.45% (p = 0.0010) between patients receiving MTD and MET regimens. CONCLUSIONS: DOSI optical biomarkers are differentially sensitive to MTD and MET regimens at early timepoints suggesting the specific treatment regimen should be considered in future DOSI studies. Additionally, DOSI may help to identify regimen-specific responses in a more personalized manner, potentially providing critical feedback necessary to implement adaptive changes to the treatment strategy.

Risk Factors for Development of Hypocalcemia in Patients With Cancer Treated With Bone-Modifying Agents.

BACKGROUND: This retrospective analysis describes the prevalence of and risk factors associated with the development of hypocalcemia in patients with cancer receiving bone-modifying agents (BMAs) as supportive care. PATIENTS AND METHODS: Patients with cancer treated with an intravenous or subcutaneous BMA, including pamidronate, zoledronic acid, or denosumab, at a tertiary care/safety net hospital in 2005 through 2015 were included in this retrospective review. We reviewed the medical records for predictive clinical and laboratory parameters and for patient outcomes. RESULTS: A total of 835 patients with cancer received at least one dose of a BMA during the specified time frame; 205 patients (25%) developed hypocalcemia of CTCAE grade ≥1 within 8 weeks of BMA initiation, 18 of whom (8.8%) had grade ≥3, and 3 patients died as a result. Multivariate analysis showed that patients with hematologic malignancy (odds ratio [OR], 1.956; P=.025), bone metastases (OR, 2.443; P=.017), inpatient status (OR, 2.592; P<.001), and deficient baseline vitamin D levels (OR, 2.546; P<.023) were more likely to develop hypocalcemia. Hypercalcemia before BMA administration (OR, 0.474; P=.032) was protective. CONCLUSIONS: Certain patient populations, including those with hematologic malignancies and/or bone metastases, warrant closer monitoring of calcium levels while receiving BMAs because of the high rate of hypocalcemia. Low pretreatment vitamin D levels are associated with the development of hypocalcemia. These data support close monitoring of calcium levels in patients with cancer receiving BMAs, in addition to adequate repletion of vitamin D before initiation of BMAs when possible.

Posttraumatic Stress Disorder Symptom Network Structures: A Comparison Between Men and Women.

This study estimated gender differences in the posttraumatic stress disorder (PTSD) symptom network structure (i.e., the unique associations across symptoms) using network analysis in a Latin American sample. Participants were 1,104 adults, taken from epidemiological studies of mental health following natural disasters and accidents in Mexico and Ecuador. Symptoms of DSM-IV PTSD were measured dichotomously with the Spanish version of the Composite International Diagnostic Interview. We estimated the PTSD symptom network of the full sample and in male and female subsamples as well as indices of centrality, the stability and accuracy of the modeled networks, and communities of nodes within each network. The male and female networks were compared statistically using the Network Comparison Test (NCT). Results indicated strength centrality was the only stable centrality measure, with correlation stability (CS) coefficients of .59, .28, and .44 for the full, male, and female networks, respectively. We found the most central symptoms, measured by strength centrality, were loss of interest and flashbacks for men; and concentration impairment, avoiding thoughts/feelings, and physiological reactivity for women. The NCT revealed that the global structure (M = 0.84), p = .704, and global strength (S = 5.04), p = .556, of the male and female networks did not differ significantly. Although some gender differences in the most central symptoms emerged, thus offering some evidence for gender differences pending replication in larger samples, on the whole, our results suggest that once PTSD develops, the way the symptoms are associated does not differ substantially between men and women.

Physical and Cognitive Load Effects Due to a Powered Lower-Body Exoskeleton.

OBJECTIVE: The aim of this study is to determine the effects of a powered exoskeleton on measures of physical and cognitive performance. BACKGROUND: US warfighters carry heavy equipment into battle, and exoskeletons may reduce that burden. While exoskeletons are currently evaluated for their effects on physical performance, their cognitive effects are not currently considered. METHOD: Twelve military members participated in a simulated patrol task under three conditions: wearing a powered exoskeleton (PWR), an unpowered exoskeleton (UNP), and without wearing an exoskeleton (OFF). While following a confederate over obstacles at a constant pace, participants performed additional audio and visual tasks. Dependent measures included visual misses, visual reaction time, audio misses, audio reaction time, incremental lag time, and NASA-TLX scores. RESULTS: The variability in the follow-task lag time was lowest with OFF and highest with UNP, highlighting reduced ability to maintain pace with the exoskeleton. Visual reaction time was significantly slower with PWR compared to OFF for 5 of 12 subjects. The NASA-TLX overall workload scores were lower for OFF compared to PWR and UNP. CONCLUSION: Efforts to understand individual variability are warranted such that exoskeleton designs can be used for a wider set of the population. While not all subjects had measurable differences in the selected performance tasks, the perception of increased workload was present across subjects. It remains to be determined what difference in reaction time would be operationally relevant for task-specific settings. APPLICATION: Findings draw attention to the need to consider "cognitive fit" and subject differences in the design and implementation of exoskeletons.

Destroying God's Temple? Physical Inactivity, Poor Diet, Obesity, and Other "Sin" Behaviors.

On average, our participants (N = 112), who self-proclaimed to be Christians, believed that physically inactive lifestyles, unhealthy eating, overeating, and being obese destroy the body, God's temple. However, these beliefs were less definitive, than those of other common "sin" behaviors, such as drug use, smoking, and excessive drinking of alcohol. In addition, destroying the body with physical inactivity or poor diet was not necessarily viewed as sinful. Subsequently, these beliefs did not relate to self-reported physical activity, dietary behavior, or body mass index. It is possible that inactivity, poor dietary habits, and obesity are not internalized into the spiritual perspective as destroying the body, God's temple, in the same way as other "sin" behaviors.

In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations.

In this paper we study antibiotic-induced C. difficile infection (CDI), caused by the toxin-producing C. difficile (CD), and implement clinically-inspired simulated treatments in a computational framework that synthesizes a generalized Lotka-Volterra (gLV) model with SIR modeling techniques. The gLV model uses parameters derived from an experimental mouse model, in which the mice are administered antibiotics and subsequently dosed with CD. We numerically identify which of the experimentally measured initial conditions are vulnerable to CD colonization, then formalize the notion of CD susceptibility analytically. We simulate fecal transplantation, a clinically successful treatment for CDI, and discover that both the transplant timing and transplant donor are relevant to the the efficacy of the treatment, a result which has clinical implications. We incorporate two nongeneric yet dangerous attributes of CD into the gLV model, sporulation and antibiotic-resistant mutation, and for each identify relevant SIR techniques that describe the desired attribute. Finally, we rely on the results of our framework to analyze an experimental study of fecal transplants in mice, and are able to explain observed experimental results, validate our simulated results, and suggest model-motivated experiments.

Integrating Journalism Into Health Promotion: Creating and Disseminating Community Narratives.

Media coverage of mental health and other social issues often relies on episodic narratives that suggest individualistic causes and solutions, while reinforcing negative stereotypes. Community narratives can provide empowering alternatives, serving as media advocacy tools used to shape the policy debate on a social issue. This article provides health promotion researchers and practitioners with guidance on how to develop and disseminate community narratives to broaden awareness of social issues and build support for particular programs and policy solutions. To exemplify the community narrative development process and highlight important considerations, this article examines a narrative from a mental health consumer-run organization. In the narrative, people with mental health problems help one another while operating a nonprofit organization, thereby countering stigmatizing media portrayals of people with mental illness as dangerous and incompetent. The community narrative frame supports the use of consumer-run organizations, which are not well-known and receive little funding despite evidence of effectiveness. The article concludes by reviewing challenges to disseminating community narratives, such as creating a product of interest to media outlets, and potential solutions, such as engaging media representatives through community health partnerships and using social media to draw attention to the narratives.