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Longitudinal cohort studies of HIV and substance use disorders play an important role in understanding these conditions, but high rates of attrition can threaten their integrity and generalizability. This study aimed to identify factors associated with attrition in a 5-year observational cohort study of 469 individuals with and without HIV infection and methamphetamine (MA) dependence. Rates of attrition in our four study groups were approximately 24% in HIV-MA-, 15% in HIV+MA-, 56% in HIV-MA+, and 47% in HIV+MA+ individuals. Predictors of attrition in the overall cohort included history of MA, alcohol, and other substance dependence, learning impairment, reduced cognitive reserve, and independence in activities of daily living (all ps < 0.05), but varied somewhat by clinical group. Of particular note, enrollment in a neuroimaging sub-study was associated with significantly boosted rates of retention in the MA groups. Results from this investigation highlight the complexity of the clinical factors that influence retention in cohort studies of HIV-infected MA users and might guide the development and implementation of targeted retention efforts.

To investigate whether successful host defense against Pneumocystis carinii is dependent on induction of inducible nitric oxide synthase (iNOS) in alveolar macrophages, immunocompetent mice, mice depleted of CD4 lymphocytes with anti-CD4 antibody, and mice with severe combined immunodeficiency (scid) were inoculated intratracheally with P. carinii. Three weeks later, immunocompetent mice had cleared the organisms completely, while CD4 cell-depleted and scid mice were severely infected (scores, 3.6 +/- 0.2 and 2.8 +/- 0.2, respectively). Inflammation scores were significantly higher in CD4 cell-depleted mice (3.4 +/- 0.2) than in scid mice (0.6 +/- 0.2). Minimal iNOS mRNA was detectable in lung tissue from immunocompetent mice; iNOS mRNA was comparable in scid mice and mice inoculated with PBS but was 6-fold higher in CD4 cell-depleted mice. Immunohistochemistry localized iNOS protein to alveolar macrophages in CD4 cell-depleted mice. Thus, iNOS is an unlikely participant in host defense against P. carinii, because enzyme expression does not correlate with either clearance or severity of infection. [ABSTRACT FROM AUTHOR]

Two children are described with anaemia from ileocolic anastomosic ulceration as a late complication of surgery in the newborn period. The anastomosis was revised in each case but in one child there was early recurrence of ulceration. [ABSTRACT FROM AUTHOR]

Human-wildlife interactions are situated within dynamic systems, characterized by social and ecological complexity. Human-wildlife coexistence research, however, typically focuses on one component of these systems in isolation. We inadvertently followed this norm while carrying out semi-structured interviews of livestock-owners in Northern Tanzania. As existing literature highlighted that this area was a hotspot for livestock depredation, our research questions focused on human interactions with carnivores. Interestingly, almost three quarters (72%, n = 72 of 100) of study participants independently raised African elephants (Loxodonta africana) as presenting the greatest impediments to coexistence. By centering our interviews on carnivores, we omitted vital components of this complex system. To counteract the effects of this oversimplification, we changed our intended analytical process after data collection. Instead of conducting a quantitative analysis of rates of livestock depredation and perceptions of risk posed by a suite of sympatric carnivores, we applied a grounded theory approach to assess interactions across multiple dimensions of this complex system. Through this transparent effort to realign our approaches with the complexity of the study system, we highlight the importance of designing research approaches that effectively reflect the complexities inherent to human-wildlife coexistence., (© 2024. The Author(s).)

Connecting chemical properties to various wine characteristics is of great interest to the science of olfaction as well as the wine industry. We explored whether Bordeaux wine chemical identities and vintages (harvest year) can be inferred from a common and affordable chemical analysis, namely, a combination of gas chromatography (GC) and electron ionization mass spectrometry. Using 12 vintages (within the 1990-2007 range) from 7 estates of the Bordeaux region, we report that, remarkably, nonlinear dimensionality reduction techniques applied to raw gas chromatograms recover the geography of the Bordeaux region. Using machine learning, we found that we can not only recover the estate perfectly from gas chromatograms, but also the vintage with up to 50% accuracy. Interestingly, we observed that the entire chromatogram is informative with respect to geographic location and age, thus suggesting that the chemical identity of a wine is not defined by just a few molecules but is distributed over a large chemical spectrum. This study demonstrates the remarkable potential of GC analysis to explore fundamental questions about the origin and age of wine., (© 2023. The Author(s).)

The direct synthesis of dimethyl ether (DME) via CO 2 hydrogenation in a single step was studied using an improved class of bifunctional catalysts in a fixed bed reactor ( T R : 210-270 °C; 40 bar; gas hourly space velocity (GHSV) 19,800 NL kg cat -1 h -1 ; ratio CO 2 /H 2 /N 2 3:9:2). The competitive bifunctional catalysts tested in here consist of a surface-basic copper/zinc oxide/zirconia (CZZ) methanol-producing part and a variable surface-acidic methanol dehydration part and were tested in overall 45 combinations. As dehydration catalysts, zeolites (ferrierite and β-zeolite), alumina, or zirconia were tested alone as well as with a coating of Keggin-type heteropoly acids (HPAs), i.e., silicotungstic or phosphotungstic acid. Two different mixing methods to generate bifunctional catalysts were tested: (i) a single-grain method with intensive intra-particular contact between CZZ and the dehydration catalyst generated by mixing in an agate mortar and (ii) a dual-grain approach relying on physical mixing with low contact. The influence of the catalyst mixing method and HPA loading on catalyst activity and stability was investigated. From these results, a selection of best-performing bifunctional catalysts was investigated in extended measurements (time on stream: 160 h/7 days, T R : 250 and 270 °C; 40 bar; GHSV 19,800 NL kg cat -1 h -1 ; ratio CO 2 /H 2 /N 2 3:9:2). Silicotungstic acid-coated bifunctional catalysts showed the highest resilience toward deactivation caused by single-grain preparation and during catalysis. Overall, HPA-coated catalysts showed higher activity and resilience toward deactivation than uncoated counterparts. Dual-grain preparation showed superior performance over single grain. Furthermore, silicotungstic acid coatings with 1 KU nm -2 (Keggin unit per surface area of carrier) on Al 2 O 3 and ZrO 2 as carrier materials showed competitive high activity and stability in extended 7-day measurements compared to pure CZZ. Therefore, HPA coating is found to be a well-suited addition to the CO 2 -to-DME catalyst toolbox., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

During vertebrate infection, obligate intracellular malaria parasites develop within a parasitophorous vacuole, which constitutes the interface between the parasite and its hepatocyte or erythrocyte host cells. To traverse this barrier, Plasmodium spp. utilize a dual-function pore formed by EXP2 for nutrient transport and, in the context of the PTEX translocon, effector protein export across the vacuole membrane. While critical to blood-stage survival, less is known about EXP2/PTEX function in the liver stage, although major differences in the export mechanism are suggested by absence of the PTEX unfoldase HSP101 in the intrahepatic vacuole. Here, we employed the glucosamine-activated glmS ribozyme to study the role of EXP2 during Plasmodium berghei liver-stage development in hepatoma cells. Insertion of the glmS sequence into the exp2 3' untranslated region (UTR) enabled glucosamine-dependent depletion of EXP2 after hepatocyte invasion, allowing separation of EXP2 function during intrahepatic development from a recently reported role in hepatocyte invasion. Postinvasion EXP2 knockdown reduced parasite size and largely abolished expression of the mid- to late-liver-stage marker LISP2. As an orthogonal approach to monitor development, EXP2- glmS parasites and controls were engineered to express nanoluciferase. Activation of glmS after invasion substantially decreased luminescence in hepatoma monolayers and in culture supernatants at later time points corresponding to merosome detachment, which marks the culmination of liver-stage development. Collectively, our findings extend the utility of the glmS ribozyme to study protein function in the liver stage and reveal that EXP2 is important for intrahepatic parasite development, indicating that PTEX components also function at the hepatocyte-parasite interface. IMPORTANCE After the mosquito bite that initiates a Plasmodium infection, parasites first travel to the liver and develop in hepatocytes. This liver stage is asymptomatic but necessary for the parasite to transition to the merozoite form, which infects red blood cells and causes malaria. To take over their host cells, avoid immune defenses, and fuel their growth, these obligately intracellular parasites must import nutrients and export effector proteins across a vacuole membrane in which they reside. In the blood stage, these processes depend on a translocon called PTEX, but it is unclear if PTEX also functions during the liver stage. Here, we adapted the glmS ribozyme to control expression of EXP2, the membrane pore component of PTEX, during the liver stage of the rodent malaria parasite Plasmodium berghei. Our results show that EXP2 is important for intracellular development in the hepatocyte, revealing that PTEX components are also functionally important during liver-stage infection.

Malaria is caused by the parasite Plasmodium falciparum, which contains an essential non-photosynthetic plastid called the apicoplast. A single DNA polymerase, apPOL, is targeted to the apicoplast, where it replicates and repairs the genome. apPOL has no direct orthologs in mammals and is considered a promising drug target for the treatment and/or prevention of malaria. We previously reported screening the Malaria Box to identify MMV666123 as an inhibitor of apPOL. Herein we extend our studies and report structure-activity relationships for MMV666123 and identify key structural motifs necessary for inhibition. Although attempts to crystallize apPOL with the inhibitor were not fruitful, kinetic analysis and crystal structure determinations of WT and mutant apo-enzymes, facilitated model building and provided insights into the putative inhibitor binding site. Our results validate apPOL as an antimalarial target and provide an avenue for the design of high potency, specific inhibitors of apPOL and other A-family DNA polymerases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

Making good decisions requires updating beliefs according to new evidence. This is a dynamical process that is prone to biases: in some cases, beliefs become entrenched and resistant to new evidence (leading to primacy effects), while in other cases, beliefs fade over time and rely primarily on later evidence (leading to recency effects). How and why either type of bias dominates in a given context is an important open question. Here, we study this question in classic perceptual decision-making tasks, where, puzzlingly, previous empirical studies differ in the kinds of biases they observe, ranging from primacy to recency, despite seemingly equivalent tasks. We present a new model, based on hierarchical approximate inference and derived from normative principles, that not only explains both primacy and recency effects in existing studies, but also predicts how the type of bias should depend on the statistics of stimuli in a given task. We verify this prediction in a novel visual discrimination task with human observers, finding that each observer's temporal bias changed as the result of changing the key stimulus statistics identified by our model. The key dynamic that leads to a primacy bias in our model is an overweighting of new sensory information that agrees with the observer's existing belief-a type of 'confirmation bias'. By fitting an extended drift-diffusion model to our data we rule out an alternative explanation for primacy effects due to bounded integration. Taken together, our results resolve a major discrepancy among existing perceptual decision-making studies, and suggest that a key source of bias in human decision-making is approximate hierarchical inference., Competing Interests: The authors have declared that no competing interests exist.

Intraerythrocytic malaria parasites reside within a parasitophorous vacuole membrane (PVM) that closely overlays the parasite plasma membrane. Although the PVM is the site of several transport activities essential to parasite survival, the basis for organisation of this membrane system is unknown. Here, we performed proximity labeling at the PVM with BioID2, which highlighted a group of single-pass integral membrane proteins that constitute a major component of the PVM proteome but whose function remains unclear. We investigated EXP1, the longest known member of this group, by adapting a CRISPR/Cpf1 genome editing system to install the TetR-DOZI-aptamers system for conditional translational control. Importantly, although EXP1 was required for intraerythrocytic development, a previously reported in vitro glutathione S-transferase activity could not account for this essential EXP1 function in vivo. EXP1 knockdown was accompanied by profound changes in vacuole ultrastructure, including apparent increased separation of the PVM from the parasite plasma membrane and formation of abnormal membrane structures. Furthermore, although activity of the Plasmodium translocon of exported proteins was not impacted by depletion of EXP1, the distribution of the translocon pore-forming protein EXP2 but not the HSP101 unfoldase was substantially altered. Collectively, our results reveal a novel PVM defect that indicates a critical role for EXP1 in maintaining proper organisation of EXP2 within the PVM., (© 2020 John Wiley & Sons Ltd.)

Background: The iliotibial band (ITB) is used in anterior cruciate ligament (ACL) reconstruction in skeletally immature patients as well as several other orthopedic reconstructions. The purpose of this study is to determine the size of the ITB as an autograft option in ACL reconstruction surgery or other orthopedic soft tissue reconstructions., Methods: Five adult cadavers resulting in nine ITB were used. Thickness and width of the ITB were determined. Using ITB width of 15-60 mm, single and doubled graft sizes were determined using standard surgical graft size technique. Geometric calculations based on average graft thickness were used to mathematically confirm the graft size of the ITB., Results: The ITB is less than 1 mm in thickness in males and females. Cadaveric measurements were less than 1 mm larger than mathematical measurements, in majority of measurements. ITB autograft can be harvested to a maximum 9 mm single-stranded graft or > 12 mm doubled graft. A minimum of 50 mm of ITB width is required to make a 8 mm graft., Conclusions: ITB is a versatile graft that can be used for a graft size up to 9 mm single strand and over 12 mm double strand. A minimum of 50 mm width of ITB is required to obtain a 8 mm-diameter autograft. To ensure appropriate graft size, surgeons should consider harvesting the maximum amount of ITB when performing ACL reconstructions in skeletally immature patients., Clinical Relevance: Surgeons have a quick reference for the width of ITB they should harvest based on the size of graft they require for a successful surgery.

Sensory information is encoded by populations of cortical neurons. Yet, it is unknown how this information is used for even simple perceptual choices such as discriminating orientation. To determine the computation underlying this perceptual choice, we took advantage of the robust visual adaptation in mouse primary visual cortex (V1). We first designed a stimulus paradigm in which we could vary the degree of neuronal adaptation measured in V1 during an orientation discrimination task. We then determined how adaptation affects task performance for mice of both sexes and tested which neuronal computations are most consistent with the behavioral results given the adapted population responses in V1. Despite increasing the reliability of the population representation of orientation among neurons, and improving the ability of a variety of optimal decoders to discriminate target from distractor orientations, adaptation increases animals' behavioral thresholds. Decoding the animals' choice from neuronal activity revealed that this unexpected effect on behavior could be explained by an overreliance of the perceptual choice circuit on target preferring neurons and a failure to appropriately discount the activity of neurons that prefer the distractor. Consistent with this all-positive computation, we find that animals' task performance is susceptible to subtle perturbations of distractor orientation and optogenetic suppression of neuronal activity in V1. This suggests that to solve this task the circuit has adopted a suboptimal and task-specific computation that discards important task-related information. SIGNIFICANCE STATEMENT A major goal in systems neuroscience is to understand how sensory signals are used to guide behavior. This requires determining what information in sensory cortical areas is used, and how it is combined, by downstream perceptual choice circuits. Here we demonstrate that when performing a go/no-go orientation discrimination task, mice suboptimally integrate signals from orientation tuned visual cortical neurons. While they appropriately positively weight target-preferring neurons, they fail to negatively weight distractor-preferring neurons. We propose that this all-positive computation may be adopted because of its simple learning rules and faster processing, and may be a common approach to perceptual decision-making when task conditions allow., (Copyright © 2019 the authors.)

Organophosphorus (OP) nerve agents and pesticides present significant threats to civilian and military populations. OP compounds include the nefarious G and V chemical nerve agents, but more commonly, civilians are exposed to less toxic OP pesticides, resulting in the same negative toxicological effects and thousands of deaths on an annual basis. After decades of research, no new therapeutics have been realized since the mid-1900s. Upon phosphylation of the catalytic serine residue, a process known as inhibition, there is an accumulation of acetylcholine (ACh) in the brain synapses and neuromuscular junctions, leading to a cholinergic crisis and eventually death. Oxime nucleophiles can reactivate select OP-inhibited acetylcholinesterase (AChE). Yet, the fields of reactivation of AChE and butyrylcholinesterase encounter additional challenges as broad-spectrum reactivation of either enzyme is difficult. Additional problems include the ability to cross the blood brain barrier (BBB) and to provide therapy in the central nervous system. Yet another complication arises in a competitive reaction, known as aging, whereby OP-inhibited AChE is converted to an inactive form, which until very recently, had been impossible to reverse to an active, functional form. Evaluations of uncharged oximes and other neutral nucleophiles have been made. Non-oxime reactivators, such as aromatic general bases and Mannich bases, have been developed. The issue of aging, which generates an anionic phosphylated serine residue, has been historically recalcitrant to recovery by any therapeutic approach-that is, until earlier this year. Mannich bases not only serve as reactivators of OP-inhibited AChE, but this class of compounds can also recover activity from the aged form of AChE, a process referred to as resurrection. This review covers the modern efforts to address all of these issues and notes the complexities of therapeutic development along these different lines of research., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Purpose: To determine a simple rule for choosing supplemental allograft size for hybrid anterior cruciate ligament reconstruction using mathematical and cadaveric models., Methods: Mathematical and cadaveric models were used to determine the rule. The mathematical model required application of the geometric Pythagorean theorem to add areas of circles. Cadaveric semitendinosus and gracilis tendons were combined in multiple quadrupled hamstring size combinations and then sized using standard surgical techniques to confirm the mathematical model., Results: Geometric measurement, not simple addition, of graft diameters was required to determine the final graft size. Direct comparison of cadaveric and mathematical models showed close relations. If a final graft size of 7 mm is desired, an added diameter of all grafts of approximately 9.5 mm is needed. If a final graft size of 8 mm is desired, an added diameter of all grafts of approximately 11 mm is needed. If a final graft size of 9 mm is desired, an added diameter of all grafts of approximately 12.5 mm is needed. If a final graft size of 10 mm is desired, an added graft diameter of approximately 14 mm is needed. Cadaveric hamstring measurements were similar to the mathematical model., Conclusions: By use of mathematical and cadaveric models, simple rules for determining the additional size of allograft diameter needed to supplement undersized hamstring autograft were created., Clinical Relevance: With the increasing availability of allograft types and sizes, surgeons currently have no guidelines on the size of allograft that is required to supplement an undersized hamstring autograft. Simple rules were created for determining the amount of allograft supplementation required for undersized hamstrings and are easily applied to clinical situations., (Copyright © 2019 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.)

Most behaviors such as making tea are not stereotypical but have an obvious structure. However, analytical methods to objectively extract structure from non-stereotyped behaviors are immature. In this study, we analyze the locomotion of fruit flies and show that this non-stereotyped behavior is well-described by a Hierarchical Hidden Markov Model (HHMM). HHMM shows that a fly's locomotion can be decomposed into a few locomotor features, and odors modulate locomotion by altering the time a fly spends performing different locomotor features. Importantly, although all flies in our dataset use the same set of locomotor features, individual flies vary considerably in how often they employ a given locomotor feature, and how this usage is modulated by odor. This variation is so large that the behavior of individual flies is best understood as being grouped into at least three to five distinct clusters, rather than variations around an average fly., Competing Interests: LT, SO, JB, VB No competing interests declared, (© 2019, Tao et al.)

Despite the increasing proportion of women in U.S. medical schools, there are relatively few women in leadership positions, and a number of recent publications have highlighted many factors that could contribute to gender inequity and inequality in medicine. The Association of Pulmonary, Critical Care, and Sleep Division Directors, an organization of Division Directors from across the United States, convened a workshop to review data and obtain input from leaders on the state of gender equity in our field. The workshop identified a number of factors that could contribute to gender inequality and inequity: gender climate (including implicit and perceived biases); disproportionate family responsibilities; lack of women in leadership positions; poor retention of women; and lack of gender equality in compensation. The panel members developed a roadmap of concrete recommendations for societies, leaders, and individuals that should promote gender equity to achieve gender equality and improve retention of women in the field of pulmonary, critical care, and sleep medicine.

Actions are guided by a Bayesian-like interaction between priors based on experience and current sensory evidence. Here we unveil a complete neural implementation of Bayesian-like behavior, including adaptation of a prior. We recorded the spiking of single neurons in the smooth eye-movement region of the frontal eye fields (FEF SEM ), a region that is causally involved in smooth-pursuit eye movements. Monkeys tracked moving targets in contexts that set different priors for target speed. Before the onset of target motion, preparatory activity encodes and adapts in parallel with the behavioral adaptation of the prior. During the initiation of pursuit, FEF SEM output encodes a maximum a posteriori estimate of target speed based on a reliability-weighted combination of the prior and sensory evidence. FEF SEM responses during pursuit are sufficient both to adapt a prior that may be stored in FEF SEM and, through known downstream pathways, to cause Bayesian-like behavior in pursuit.

Real-life decision-making often involves combining multiple probabilistic sources of information under finite time and cognitive resources. To mitigate these pressures, people "satisfice", foregoing a full evaluation of all available evidence to focus on a subset of cues that allow for fast and "good-enough" decisions. Although this form of decision-making likely mediates many of our everyday choices, very little is known about the way in which the neural encoding of cue information changes when we satisfice under time pressure. Here, we combined human functional magnetic resonance imaging (fMRI) with a probabilistic classification task to characterize neural substrates of multi-cue decision-making under low (1500 ms) and high (500 ms) time pressure. Using variational Bayesian inference, we analyzed participants' choices to track and quantify cue usage under each experimental condition, which was then applied to model the fMRI data. Under low time pressure, participants performed near-optimally, appropriately integrating all available cues to guide choices. Both cortical (prefrontal and parietal cortex) and subcortical (hippocampal and striatal) regions encoded individual cue weights, and activity linearly tracked trial-by-trial variations in the amount of evidence and decision uncertainty. Under increased time pressure, participants adaptively shifted to using a satisficing strategy by discounting the least informative cue in their decision process. This strategic change in decision-making was associated with an increased involvement of the dopaminergic midbrain, striatum, thalamus, and cerebellum in representing and integrating cue values. We conclude that satisficing the probabilistic inference process under time pressure leads to a cortical-to-subcortical shift in the neural drivers of decisions., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Experiments that study neural encoding of stimuli at the level of individual neurons typically choose a small set of features present in the world-contrast and luminance for vision, pitch and intensity for sound-and assemble a stimulus set that systematically varies along these dimensions. Subsequent analysis of neural responses to these stimuli typically focuses on regression models, with experimenter-controlled features as predictors and spike counts or firing rates as responses. Unfortunately, this approach requires knowledge in advance about the relevant features coded by a given population of neurons. For domains as complex as social interaction or natural movement, however, the relevant feature space is poorly understood, and an arbitrary a priori choice of features may give rise to confirmation bias. Here, we present a Bayesian model for exploratory data analysis that is capable of automatically identifying the features present in unstructured stimuli based solely on neuronal responses. Our approach is unique within the class of latent state space models of neural activity in that it assumes that firing rates of neurons are sensitive to multiple discrete time-varying features tied to the stimulus, each of which has Markov (or semi-Markov) dynamics. That is, we are modeling neural activity as driven by multiple simultaneous stimulus features rather than intrinsic neural dynamics. We derive a fast variational Bayesian inference algorithm and show that it correctly recovers hidden features in synthetic data, as well as ground-truth stimulus features in a prototypical neural dataset. To demonstrate the utility of the algorithm, we also apply it to cluster neural responses and demonstrate successful recovery of features corresponding to monkeys and faces in the image set.

Acetylcholinesterase (AChE) is an essential enzyme that can be targeted by organophosphorus (OP) compounds, including nerve agents. Following exposure to OPs, AChE becomes phosphylated (inhibited) and undergoes a subsequent aging process where the OP-AChE adduct is dealkylated. The aged AChE is unable to hydrolyze acetylcholine, resulting in accumulation of the neurotransmitter in the central nervous system (CNS) and elsewhere. Current therapeutics are only capable of reactivating inhibited AChE. There are no known therapeutic agents to reverse the aging process or treat aged AChE. Quinone methides (QMs) have been shown to alkylate phosphates under physiological conditions. In this study, a small library of novel quinone methide precursors (QMPs) has been synthesized and examined as potential alkylating agents against model nucleophiles, including a model phosphonate. Computational studies have been performed to evaluate the affinity of QMPs for the aged AChE active site, and preliminary testing with electric eel AChE has been performed.

Medical professional societies exist to foster collaboration, guide career development, and provide continuing medical education opportunities. Maintenance of certification is a process by which physicians complete formal educational activities approved by certifying organizations. The American Thoracic Society (ATS) established an innovative maintenance of certification program in 2012 as a means to formalize and expand continuing medical education offerings. This program is unique as it includes explicit opportunities for collaboration and career development in addition to providing continuing medical education and maintenance of certification credit to society members. In describing the development of this program referred to as the "Core Curriculum," the authors highlight the ATS process for content design, stages of curriculum development, and outcomes data with an eye toward assisting other societies that seek to program similar content. The curriculum development process described is generalizable and positively influences individual practitioners and professional societies in general, and as a result, provides a useful model for other professional societies to follow.

Significant advances in culture-independent methods have expanded our knowledge about the diversity of the lung microbial environment. Complex microorganisms and microbial communities can now be identified in the distal airways in a variety of respiratory diseases, including cystic fibrosis (CF) and the posttransplantation lung. Although there are significant methodologic concerns about sampling the lung microbiome, several studies have now shown that the microbiome of the lower respiratory tract is distinct from the upper airway. CF is a disease characterized by chronic airway infections that lead to significant morbidity and mortality. Traditional culture-dependent methods have identified a select group of pathogens that cause exacerbations in CF, but studies using bacterial 16S rRNA gene-based microarrays have shown that the CF microbiome is an intricate and dynamic bacterial ecosystem, which influences both host immune health and disease pathogenesis. These microbial communities can shift with external influences, including antibiotic exposure. In addition, there have been a number of studies suggesting a link between the gut microbiome and respiratory health in CF. Compared with CF, there is significantly less knowledge about the microbiome of the transplanted lung. Risk factors for bronchiolitis obliterans syndrome, one of the leading causes of death, include microbial infections. Lung transplant patients have a unique lung microbiome that is different than the pretransplanted microbiome and changes with time. Understanding the host-pathogen interactions in these diseases may suggest targeted therapies and improve long-term survival in these patients., (Published by Elsevier Inc.)

Much of our real-life decision making is bounded by uncertain information, limitations in cognitive resources, and a lack of time to allocate to the decision process. It is thought that humans overcome these limitations through satisficing, fast but "good-enough" heuristic decision making that prioritizes some sources of information (cues) while ignoring others. However, the decision-making strategies we adopt under uncertainty and time pressure, for example during emergencies that demand split-second choices, are presently unknown. To characterize these decision strategies quantitatively, the present study examined how people solve a novel multicue probabilistic classification task under varying time pressure, by tracking shifts in decision strategies using variational Bayesian inference. We found that under low time pressure, participants correctly weighted and integrated all available cues to arrive at near-optimal decisions. With increasingly demanding, subsecond time pressures, however, participants systematically discounted a subset of the cue information by dropping the least informative cue(s) from their decision making process. Thus, the human cognitive apparatus copes with uncertainty and severe time pressure by adopting a "drop-the-worst" cue decision making strategy that minimizes cognitive time and effort investment while preserving the consideration of the most diagnostic cue information, thus maintaining "good-enough" accuracy. This advance in our understanding of satisficing strategies could form the basis of predicting human choices in high time pressure scenarios. (PsycINFO Database Record, ((c) 2016 APA, all rights reserved).)

Rationale: Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear., Objectives: We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects., Methods: Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38)., Measurements and Main Results: Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects., Conclusions: The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.

Intravenous (i.v.) tissue-type plasminogen activator (tPA) is the only approved noninvasive therapy for acute ischemic stroke (AIS). However, after tPA treatment, the outcome of patients with different subtypes of stroke according to their vascular risk factors remains to be elucidated. We aim to explore the relationship between the outcome and different risk factors in patients with different subtype of acute strokes treated with i.v. tPA. Records of patients in this cohort were reviewed. Data collected and analysed included the demographics, vascular risk factors, baseline National Institutes of Health Stroke Scale (NIHSS) scores, 90-day modified Rankin Scores (mRS), and subtypes of stroke. By using the 90-day mRS, patients were dichotomized into favorable versus unfavorable outcome in each subtype of stroke. We identified the vascular risk factors that are likely associated with the poor outcome in each subtype. Among 570 AIS patients received i.v. tPA, 217 were in the large artery atherosclerosis (LAA) group, 146 in the small vessel occlusion (SVO) group, and 140 in the cardioaortic embolism (CE) group. Lower NIHSS score on admission was related to favorable outcome in patients in all subtypes. Patients with history of dyslipidemia were likely on statin treatment before their admission and hence less likely to have elevated cholesterol level on admission. Therefore, there was a possible paradoxical effect on the outcome in patients with LAA and SVO subtypes of strokes. SVO patients with history of diabetes had higher risk of unfavorable outcome. SVO patients had favorable outcome if their time from onset to treatment was short. In conclusion, the outcome of patients treated with i.v. tPA may be related to different vascular risk factors associated with different subtypes of stroke.

Introduction: It is well known that the efficacy of intravenous (i.v.) tissue plasminogen activator (tPA) is time-dependent when used to treat patients with acute ischemic strokes., Aim: Our study examines the safety issue of giving IV tPA without complete blood count (CBC) resulted., Materials and Methods: This is a retrospective observational study by examining the database from Huashan Hospital in China and OSF/INI Comprehensive Stroke Center in United States. Patient data collected included demographics, occurrence of symptomatic intracranial hemorrhage, door to needle intervals, National Institute of Health Stroke Scale scores on admission, CBC results on admission and follow-up modified Rankin Scale scores. Linear regression and multivariable logistic regression analysis were used to identify factors that would have an impact on door-to-needle intervals., Results: Our study included 120 patients from Huashan Hospital and 123 patients from INI. Among them, 36 in Huashan Hospital and 51 in INI received i.v. tPA prior to their CBC resulted. Normal platelet count was found in 98.8% patients after tPA was given. One patient had thrombocytopenia but no hemorrhagic event. A significantly shorter door to needle interval (DTN) was found in the group without CBC resulted. There was also a difference in treatment interval between the two hospitals. Door to needle intervals had a strong correlation to onset to treatment intervals and NIHSS scores on admission., Conclusion: In patients presented with acute ischemic stroke, the risk of developing hemorrhagic event is low if i.v. tPA is given before CBC has resulted. The door to needle intervals can be significantly reduced.

Rationale: The lung microbiome is spatially heterogeneous in advanced airway diseases, but whether it varies spatially in health is unknown. We postulated that the primary determinant of lung microbiome constitution in health is the balance of immigration and elimination of communities from the upper respiratory tract (URT; "adapted island model of lung biogeography"), rather than differences in regional bacterial growth conditions., Objectives: To determine if the lung microbiome is spatially varied in healthy adults., Methods: Bronchoscopy was performed on 15 healthy subjects. Specimens were sequentially collected in the lingula and right middle lobe (by bronchoalveolar lavage [BAL]), then in the right upper lobe, left upper lobe, and supraglottic space (by protected-specimen brush). Bacterial 16S ribosmal RNA-encoding genes were sequenced using MiSeq (Illumina, San Diego, CA)., Measurements and Main Results: There were no significant differences between specimens collected by BAL and protected-specimen brush. Spatially separated intrapulmonary sites, when compared with each other, did not contain consistently distinct microbiota. On average, intrasubject variation was significantly less than intersubject variation (P = 0.00003). By multiple ecologic parameters (community richness, community composition, intersubject variability, and similarity to source community), right upper lobe microbiota more closely resembled those of the URT than did microbiota from more distal sites. As predicted by the adapted island model, community richness decreased with increasing distance from the source community of the URT (P < 0.05)., Conclusions: In healthy lungs, spatial variation in microbiota within an individual is significantly less than variation across individuals. The lung microbiome in health is more influenced by microbial immigration and elimination (the adapted island model) than by the effects of local growth conditions on bacterial reproduction rates, which are more determinant in advanced lung diseases. BAL of a single lung segment is an acceptable method of sampling the healthy lung microbiome. Clinical trial registered with www.clinicaltrials.gov (NCT02392182).

Unlabelled: No studies have examined the relationships between bacterial communities along sites of the upper aerodigestive tract of an individual subject. Our objective was to perform an intrasubject and intersite analysis to determine the contributions of two upper mucosal sites (mouth and nose) as source communities for the bacterial microbiome of lower sites (lungs and stomach). Oral wash, bronchoalveolar lavage (BAL) fluid, nasal swab, and gastric aspirate samples were collected from 28 healthy subjects. Extensive analysis of controls and serial intrasubject BAL fluid samples demonstrated that sampling of the lungs by bronchoscopy was not confounded by oral microbiome contamination. By quantitative PCR, the oral cavity and stomach contained the highest bacterial signal levels and the nasal cavity and lungs contained much lower levels. Pyrosequencing of 16S rRNA gene amplicon libraries generated from these samples showed that the oral and gastric compartments had the greatest species richness, which was significantly greater in both than the richness measured in the lungs and nasal cavity. The bacterial communities of the lungs were significantly different from those of the mouth, nose, and stomach, while the greatest similarity was between the oral and gastric communities. However, the bacterial communities of healthy lungs shared significant membership with the mouth, but not the nose, and marked subject-subject variation was noted. In summary, microbial immigration from the oral cavity appears to be the significant source of the lung microbiome during health, but unlike the stomach, the lungs exhibit evidence of selective elimination of Prevotella bacteria derived from the upper airways., Importance: We have demonstrated that the bacterial communities of the healthy lung overlapped those found in the mouth but were found at lower concentrations, with lower membership and a different community composition. The nasal microbiome, which was distinct from the oral microbiome, appeared to contribute little to the composition of the lung microbiome in healthy subjects. Our studies of the nasal, oral, lung, and stomach microbiomes within an individual illustrate the microbiological continuity of the aerodigestive tract in healthy adults and provide culture-independent microbiological support for the concept that microaspiration is common in healthy individuals., (Copyright © 2015 Bassis et al.)

Unlabelled: DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples., Importance: Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health., (Copyright © 2015 Venkataraman et al.)

Assessment of graduate medical trainee progress via the accomplishment of competency milestones is an important element of the Next Accreditation System of the Accreditation Council for Graduate Medical Education. This article summarizes the findings of a multisociety working group that was tasked with creating the entrustable professional activities and curricular milestones for fellowship training in pulmonary medicine, critical care medicine, and combined programs. Using the Delphi process, experienced medical educators from the American College of Chest Physicians, American Thoracic Society, Society of Critical Care Medicine, and Association of Pulmonary and Critical Care Medicine Program Directors reached consensus on the detailed curricular content and expected skill set of graduates of these programs. These are now available to trainees and program directors for the purposes of curriculum design, review, and trainee assessment.

This article describes the curricular milestones and entrustable professional activities for trainees in pulmonary, critical care, or combined fellowship programs. Under the Next Accreditation System of the Accreditation Council for Graduate Medical Education (ACGME), curricular milestones compose the curriculum or learning objectives for training in these fields. Entrustable professional activities represent the outcomes of training, the activities that society and professional peers can expect fellowship graduates to be able to perform unsupervised. These curricular milestones and entrustable professional activities are the products of a consensus process from a multidisciplinary committee of medical educators representing the American College of Chest Physicians (CHEST), the American Thoracic Society, the Society of Critical Care Medicine, and the Association of Pulmonary and Critical Care Medicine Program Directors. After consensus was achieved using the Delphi process, the document was revised with input from the sponsoring societies and program directors. The resulting lists can serve as a roadmap and destination for trainees, program directors, and educators. Together with the reporting milestones, they will help mark trainees' progress in the mastery of the six ACGME core competencies of graduate medical education.

Investigation of the human microbiome has become an important field of research facilitated by advances in sequencing technologies. The lung, which is one of the latest body sites being explored for the characterization of human-associated microbial communities, has a microbiome that is suspected to play a substantial role in health and disease. In this review, we provide an overview of the basics of microbiome studies. Challenges in the study of the lung microbiome are highlighted, and further attention is called to the optimization and standardization of methodologies to explore the role of the lung microbiome in health and disease. We also provide examples of lung microbial communities associated with disease or infection status and discuss the role of fungal species in the lung. Finally, we review studies demonstrating that the environmental microbiome can influence lung health and disease, such as the finding that the diversity of microbial exposure correlates inversely with the development of childhood asthma.

Many chronic pulmonary diseases, including those that are not primarily infectious in etiology, have some aspects of their pathogenesis that are influenced by infectious organisms. Microorganisms may contribute to chronic lung diseases, either directly (i.e., overt infection) or indirectly, via the amplification of inflammatory pathways that are critical to host defense. As techniques for detecting and characterizing microorganisms have advanced, investigations of both infecting and colonizing organisms have yielded new insights into mechanisms of pulmonary disease. In addition, changes in patterns of infection and microbial resistance have important implications for treatment. Examples of these infectious-pulmonary associations, including Haemophilus influenzae infection and chronic obstructive pulmonary disease, nontuberculous mycobacteria and bronchiectasis, and human immunodeficiency virus and obstructive lung disease, are reviewed.

Background: Multiple independent culture-based studies have identified the presence of Pseudomonas aeruginosa in respiratory samples as a positive risk factor for bronchiolitis obliterans syndrome (BOS). Yet, culture-independent microbiological techniques have identified a negative association between Pseudomonas species and BOS. Our objective was to investigate whether there may be a unifying explanation for these apparently dichotomous results., Methods: We performed bronchoscopies with bronchoalveolar lavage (BAL) on lung transplant recipients (46 procedures in 33 patients) and 26 non-transplant control subjects. We analyzed bacterial communities in the BAL fluid using qPCR and pyrosequencing of 16S rRNA gene amplicons and compared the culture-independent data with the clinical metadata and culture results from these subjects., Findings: Route of bronchoscopy (via nose or via mouth) was not associated with changes in BAL microbiota (p = 0.90). Among the subjects with positive Pseudomonas bacterial culture, P. aeruginosa was also identified by culture-independent methods. In contrast, a distinct Pseudomonas species, P. fluorescens, was often identified in asymptomatic transplant subjects by pyrosequencing but not detected via standard bacterial culture. The subject populations harboring these two distinct pseudomonads differed significantly with respect to associated symptoms, BAL neutrophilia, bacterial DNA burden and microbial diversity. Despite notable differences in culturability, a global database search of UM Hospital Clinical Microbiology Laboratory records indicated that P. fluorescens is commonly isolated from respiratory specimens., Interpretation: We have reported for the first time that two prominent and distinct Pseudomonas species (P. fluorescens and P. aeruginosa) exist within the post-transplant lung microbiome, each with unique genomic and microbiologic features and widely divergent clinical associations, including presence during acute infection.

The concepts of activity cliffs and matched molecular pairs (MMP) are recent paradigms for analysis of data sets to identify structural changes that may be used to modify the potency of lead molecules in drug discovery projects. Analysis of MMPs was recently demonstrated as a feasible technique for quantitative structure-activity relationship (QSAR) modeling of prospective compounds. Although within a small data set, the lack of matched pairs, and the lack of knowledge about specific chemical transformations limit prospective applications. Here we present an alternative technique that determines pairwise descriptors for each matched pair and then uses a QSAR model to estimate the activity change associated with a chemical transformation. The descriptors effectively group similar transformations and incorporate information about the transformation and its local environment. Use of a transformation QSAR model allows one to estimate the activity change for novel transformations and therefore returns predictions for a larger fraction of test set compounds. Application of the proposed methodology to four public data sets results in increased model performance over a benchmark random forest and direct application of chemical transformations using QSAR-by-matched molecular pairs analysis (QSAR-by-MMPA).

Background: Cigarette smoke (CS) is the major etiologic factor of chronic obstructive pulmonary disease (COPD). CS-exposed mice develop emphysema and mild pulmonary inflammation but no airway obstruction, which is also a prominent feature of COPD. Therefore, CS may interact with other factors, particularly respiratory infections, in the pathogenesis of airway remodeling in COPD., Methods: C57BL/6 mice were exposed to CS for 2 h a day, 5 days a week for 8 weeks. Mice were also exposed to heat-killed non-typeable H. influenzae (HK-NTHi) on days 7 and 21. One day after the last exposure to CS, mice were sacrificed and lung inflammation and mechanics, emphysematous changes, and goblet cell metaplasia were assessed. Mice exposed to CS or HK-NTHi alone or room air served as controls. To determine the susceptibility to viral infections, we also challenged these mice with rhinovirus (RV)., Results: Unlike mice exposed to CS or HK-NTHi alone, animals exposed to CS/HK-NTHi developed emphysema, lung inflammation and goblet cell metaplasia in both large and small airways. CS/HK-NTHi-exposed mice also expressed increased levels of mucin genes and cytokines compared to mice in other groups. CS/HK-NTHi-exposed mice infected with RV demonstrated increased viral persistence, sustained neutrophilia, and further increments in mucin gene and chemokine expression compared to other groups., Conclusions: These findings indicate that in addition to CS, bacteria may also contribute to development of COPD, particularly changes in airways. Mice exposed to CS/HK-NTHi are also more susceptible to subsequent viral infection than mice exposed to either CS or HK-NTHi alone.

The lungs of healthy humans have traditionally been considered to be sterile when examined by culture-based techniques. However, molecular identification techniques are now being used to explore the lung microbiome in ways that mirror study of other body sites and organ systems. Familiarity with population definitions and indices of diversity will lead to better understanding of the literature now coming to publication. Differences in methodology and sampling may contribute significantly to experimental variability, and the field has not coalesced around standard ways to present data or to perform statistical comparisons. This emerging and exciting field of investigation is leading to new ways of thinking about the lung and about lung disease.

Categorization is a cornerstone of perception and cognition. Computationally, categorization amounts to applying decision boundaries in the space of stimulus features. We designed a visual categorization task in which optimal performance requires observers to incorporate trial-to-trial knowledge of the level of sensory uncertainty when setting their decision boundaries. We found that humans and monkeys did adjust their decision boundaries from trial to trial as the level of sensory noise varied, with some subjects performing near optimally. We constructed a neural network that implements uncertainty-based, near-optimal adjustment of decision boundaries. Divisive normalization emerges automatically as a key neural operation in this network. Our results offer an integrated computational and mechanistic framework for categorization under uncertainty.

There is strong behavioral and physiological evidence that the brain both represents probability distributions and performs probabilistic inference. Computational neuroscientists have started to shed light on how these probabilistic representations and computations might be implemented in neural circuits. One particularly appealing aspect of these theories is their generality: they can be used to model a wide range of tasks, from sensory processing to high-level cognition. To date, however, these theories have only been applied to very simple tasks. Here we discuss the challenges that will emerge as researchers start focusing their efforts on real-life computations, with a focus on probabilistic learning, structural learning and approximate inference.

The broad variety of pulmonary infections encountered in human immunodeficiency virus (HIV)-infected individuals demonstrates that the host defense network is impaired. An improved understanding of these events in the lung can lead to specific interventions aimed at restoration of deficient function. This review summarizes the pulmonary host defense deficits in HIV-infected individuals, focusing on lymphocytes, alveolar macrophages, and neutrophils., (Published by Elsevier Inc.)

Rationale: Results from 16S rDNA-encoding gene sequence-based, culture-independent techniques have led to conflicting conclusions about the composition of the lower respiratory tract microbiome., Objectives: To compare the microbiome of the upper and lower respiratory tract in healthy HIV-uninfected nonsmokers and smokers in a multicenter cohort., Methods: Participants were nonsmokers and smokers without significant comorbidities. Oral washes and bronchoscopic alveolar lavages were collected in a standardized manner. Sequence analysis of bacterial 16S rRNA-encoding genes was performed, and the neutral model in community ecology was used to identify bacteria that were the most plausible members of a lung microbiome., Measurements and Main Results: Sixty-four participants were enrolled. Most bacteria identified in the lung were also in the mouth, but specific bacteria such as Enterobacteriaceae, Haemophilus, Methylobacterium, and Ralstonia species were disproportionally represented in the lungs compared with values predicted by the neutral model. Tropheryma was also in the lung, but not the mouth. Mouth communities differed between nonsmokers and smokers in species such as Porphyromonas, Neisseria, and Gemella, but lung bacterial populations did not., Conclusions: This study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear in significantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.

Rationale: Lung infections caused by opportunistic or virulent pathogens are a principal cause of morbidity and mortality in HIV infection. It is unknown whether HIV infection leads to changes in basal lung microflora, which may contribute to chronic pulmonary complications that increasingly are being recognized in individuals infected with HIV., Objectives: To determine whether the immunodeficiency associated with HIV infection resulted in alteration of the lung microbiota., Methods: We used 16S ribosomal RNA targeted pyrosequencing and shotgun metagenomic sequencing to analyze bacterial gene sequences in bronchoalveolar lavage (BAL) and mouths of 82 HIV-positive and 77 HIV-negative subjects., Measurements and Main Results: Sequences representing Tropheryma whipplei, the etiologic agent of Whipple's disease, were significantly more frequent in BAL of HIV-positive compared with HIV-negative individuals. T. whipplei dominated the community (>50% of sequence reads) in 11 HIV-positive subjects, but only 1 HIV-negative individual (13.4 versus 1.3%; P = 0.0018). In 30 HIV-positive individuals sampled longitudinally, antiretroviral therapy resulted in a significantly reduced relative abundance of T. whipplei in the lung. Shotgun metagenomic sequencing was performed on eight BAL samples dominated by T. whipplei 16S ribosomal RNA. Whole genome assembly of pooled reads showed that uncultured lung-derived T. whipplei had similar gene content to two isolates obtained from subjects with Whipple's disease., Conclusions: Asymptomatic subjects with HIV infection have unexpected colonization of the lung by T. whipplei, which is reduced by effective antiretroviral therapy and merits further study for a potential pathogenic role in chronic pulmonary complications of HIV infection.