Bodily Remembering: Memory,Place, and Understanding Latino Folk Illnesses among the Amuzgos Indians of Oaxaca,Mexico

This paper takes the theoretical construct of popular nosology of Latino folk illnesses and combines it with Edward Casey’s concept of bodily remembering in order to more fully describe the role of memory and place in the illness experiences of the Amuzgos Indians of Oaxaca, Mexico. I ethnographically describe, across time, the interrelated links among social events, physical symptoms, and illness narratives of Latino folk illness popular nosologies as they are contextualized in their unique, social topographies. This enlarged theoretical perspective implies a smallest unit of meaning that is ethnographically defined, but that will often encompass more than the individual sufferer and more than one illness. The research objective of this study was to understand Amuzgan illness experiences through the narratives of detailed case histories and ethnographic observations that were gathered during 18 months of qualitative research. The data show that Amuzgos experience Latino folk illnesses as bodily rememberings of illness events combined with negative interpersonal interactions. Healing these Latino folk illnesses implies curing bodies, households, social relationships, and living environments.     

TOWARDS A GENERAL THEORY OF GROUP SELECTION

The longstanding debate about the importance of group (multilevel) selection suffers from a lack of formal models that describe explicit selection events at multiple levels. Here, we describe a general class of models for two‐level evolutionary processes which include birth and death events at both levels. The models incorporate the state‐dependent rates at which these events occur. The models come in two closely related forms: (1) a continuous‐time Markov chain, and (2) a partial differential equation (PDE) derived from (1) by taking a limit. We argue that the mathematical structure of this PDE is the same for all models of two‐level population processes, regardless of the kinds of events featured in the model. The mathematical structure of the PDE allows for a simple and unambiguous way to distinguish between individual‐ and group‐level events in any two‐level population model. This distinction, in turn, suggests a new and intuitively appealing way to define group selection in terms of the effects of group‐level events. We illustrate our theory of group selection by applying it to models of the evolution of cooperation and the evolution of simple multicellular organisms, and then demonstrate that this kind of group selection is not mathematically equivalent to individual‐level (kin) selection.     

A SNP streak model for the identification of genetic regions identical-by-descent

The availability of very dense genetic maps is changing in a fundamental way the methods used to identify the genetic basis of both rare and common inherited traits. The ability to directly compare the genomes of two related individuals and quickly identify those regions that are inherited identical-by-descent (IBD) from a recent common ancestor would be of utility in a wide range of genetic mapping methods. Here, we describe a simple method for using dense SNP maps to identify regions of the genome likely to be inherited IBD by family members. This method is based on identifying obligate recombination events and examining the pattern of distribution of such events along the genetic map. Specifically, we use the length of a consecutive set of biallelic markers that have a high probability of having avoided such obligate recombination events. This ;;SNP streak" is derived from subsets of samples within a pedigree and allows us to make statistical inferences about the ancestry of the region(s) containing stretches of markers with these properties. We show that the use of subsets of more than two samples has the advantage of identifying shorter shared subsegments as significant. This mitigates the effects of errors in SNP calls. We provide specific examples of microarray-based SNP data, using a family with a complex pedigree and with a rare form of inherited kidney disease, to illustrate this approach.     

THE SHORT-TERM BEHAVIORAL REACTIONS OF BOTTLENOSE DOLPHINS TO INTERACTIONS WITH BOATS IN DOUBTFUL SOUND, NEW ZEALAND

Doubtful Sound is home to one of the southernmost resident populations of bottlenose dolphins ( Tursiops sp.). This population regularly interacts with scenic cruises. During these interactions, dolphins tend to horizontally and vertically avoid vessels, especially when the behavior of these vessels is intrusive. This study aimed at understanding the behavioral reactions of individuals to these interactions that lead to the disruption of the school's behavioral state. Observing the behavioral events performed by individuals during an interaction can help define the short-term reactions elicited by the boat presence. I recorded the behavioral events performed by all individuals of focal schools. The frequency of occurrence of all events was compared depending on the presence of vessels, their behavior, and the behavioral state of the focal school. Dolphins tended to perform more side flops while interacting with powerboats, a behavior which may be used as a non-vocal communication tool. Moreover, the movement of dolphins became more erratic during interactions with all types of vessels. These effects increased when the boats were more intrusive while interacting. This study shows that the impact of interaction with boats can be minimized if the vessels respect the guidelines in place.     

Soil carbon flux following pulse precipitation events in the shortgrass steppe

Pulses of water availability characterize semiarid and arid ecosystems. Most precipitation events in these ecosystems are small (≤10 mm), but can stimulate carbon flux. The large proportion of carbon stored belowground and small carbon inputs create the potential for these small precipitation events to have large effects on carbon cycling. Land-use change can modify these effects through alteration of the biota and soil resources. The goal of our research was to determine how small precipitation events (2, 5, and 10 mm) affected the dynamics of soil carbon flux and water loss in previously cultivated Conservation Reserve Program (CRP) fields and undisturbed shortgrass steppe. Total carbon loss and duration of elevated carbon flux increased as event size increased in all field types. Time since cultivation increased in importance for carbon flux as event size increased. A comparison of water loss rates to carbon flux suggests that water is limiting to carbon flux for the smallest events, but is less limiting for events above 5 mm. We also describe how water availability interacts with temperature in controlling carbon flux rate. We conclude that small precipitation events have the potential for large short-term losses of carbon in the shortgrass steppe.     

Integrons: mobilizable platforms that promote genetic diversity in bacteria

Integrons facilitate the capture of potentially adaptive exogenous genetic material by their host genomes. It is now clear that integrons are not limited to the clinical contexts in which they were originally discovered because approximately 10% of bacterial genomes that have been partially or completely sequenced harbour this genetic element. This wealth of sequence information has revealed that integrons are not only much more phylogenetically diverse than previously thought but also more mobilizable, with many integrons having been subjected to frequent lateral gene transfer throughout their evolutionary history. This indicates that the genetic characteristics that make integrons such efficient vectors for the spread of antibiotic resistance genes have been associated with these elements since their earliest origins. Here, we give an overview of the structural and phylogenetic diversity of integrons and describe evolutionary events that have contributed to the success of these genetic elements.     

Implications of an Absolute Simultaneity Theory for Cosmology and Universe Acceleration

An alternate Lorentz transformation, Absolute Lorentz Transformation (ALT), has similar kinematics to special relativity yet maintains absolute simultaneity in the context of a preferred reference frame. In this study, it is shown that ALT is compatible with current experiments to test Lorentz invariance only if the proposed preferred reference frame is locally equivalent to the Earth-centered non-rotating inertial reference frame, with the inference that in an ALT framework, preferred reference frames are associated with centers of gravitational mass. Applying this theoretical framework to cosmological data produces a scenario of universal time contraction in the past. In this scenario, past time contraction would be associated with increased levels of blueshifted light emissions from cosmological objects when viewed from our current perspective. The observation that distant Type Ia supernovae are dimmer than predicted by linear Hubble expansion currently provides the most direct evidence for an accelerating universe. Adjusting for the effects of time contraction on a redshift–distance modulus diagram produces a linear distribution of supernovae over the full redshift spectrum that is consistent with a non-accelerating universe.     

Coincident Gene Conversion during Mitosis in Saccharomyces

During mitosis, gene conversion events at the TRP5 locus on chromosome VII are coupled with conversion events at LEU1 , a locus 18 cM away, 1200 times more frequently than would be expected for two independent acts of recombination. Such coincident conversion events that occur over relatively long distances could be due to several mechanisms. We discuss these possibilities and describe an experiment that indicates that a portion of coincident events is due to extensive heteroduplexes. The phenomenon of coincident gene conversion is discussed in relation to our earlier evidence that spontaneous recombination between homologues occurs prereplicationally in mitosis.     

Multistate modeling and structure selection for multitype recurrent events and terminal event data

In cardiovascular disease studies, a large number of risk factors are measured but it often remains unknown whether all of them are relevant variables and whether the impact of these variables is changing with time or remains constant. In addition, more than one kind of cardiovascular disease events can be observed in the same patient and events of different types are possibly correlated. It is expected that different kinds of events are associated with different covariates and the forms of covariate effects also vary between event types. To tackle these problems, we proposed a multistate modeling framework for the joint analysis of multitype recurrent events and terminal event. Model structure selection is performed to identify covariates with time-varying coefficients, time-independent coefficients, and null effects. This helps in understanding the disease process as it can detect relevant covariates and identify the temporal dynamics of the covariate effects. It also provides a more parsimonious model to achieve better risk prediction. The performance of the proposed model and selection method is evaluated in numerical studies and illustrated on a real dataset from the Atherosclerosis Risk in Communities study.     

Sprint and endurance power and ageing: an analysis of master athletic world records

Human physical performance is notably reduced with ageing. Although the effects of ageing are often compounded by disuse, the study of master athletes provides an opportunity for investigating the effects of ageing per se. It is often held that sprinting is more affected than endurance performance. However, past analyses of master athletic world record data have yielded opposite observations. We argue here that our understanding of these data improves by considering how, biomechanically, metabolic power is related to athletic performance. In line with earlier studies, our analysis showed that running speed declines with age in a more pronounced way for endurance events than for sprinting events, confirming former studies. However, when assessing the metabolic power required to achieve the running world records, sprint and endurance events show a relatively uniform decline with age across the different events. This study has reconciled formerly conflicting scientific results and improves our understanding of the ageing process. However, it is unclear as to which are the governing mechanisms that cause the different systems in our body, responsible for sprinting and for endurance performance, to be affected by ageing in a remarkably uniform way.     

Statin therapy for native and peri-interventional coronary heart disease

Atherosclerosis is a slow, complex process involving many different cell types and their interactions producing excessive oxidant stress, increased inflammation, abnormal endothelium-dependent vasodilation, and localized increases in thrombogenic and decreases in fibrinolytic factors. Numerous factors incite these processes, but oxidized LDL particles seem the most essential component of this pathologic cascade. These oxidized particles set up a chain of biochemical events eventually leading to clinical atherosclerotic events. Statins have been shown to reduce such events by 40 to 50% when LDL cholesterol is lowered to less than 80 mg/dL. But in-vitro studies have shown that the provision of mevalonate, not cholesterol, can result in reversal of some of the beneficial effects of statins, suggesting that other mechanisms such as inhibiting the formation of the isoprenoids, farnesyl pyrophosphate and geranylgeranyl pyrophosphate, and thus prenylation of many cell-signaling proteins may be important in the preventive effects of statins. Clinically, these more rapid, non-lipid-altering effects may be more apparent in acute coronary syndromes. Now that we have more LDL-cholesterol lowering agents which lower LDL-cholesterol without blocking HMG CoA reductase, we may be better able to dissect and understand the importance of these non-lipid-altering effects of statins in human disease.     

Genetic Manipulation of Cerebellar Granule Neurons In Vitro and In Vivo to Study Neuronal Morphology and Migration

Developmental events in the brain including neuronal morphogenesis and migration are highly orchestrated processes. In vitro and in vivo analyses allow for an in-depth characterization to identify pathways involved in these events. Cerebellar granule neurons (CGNs) that are derived from the developing cerebellum are an ideal model system that allows for morphological analyses. Here, we describe a method of how to genetically manipulate CGNs and how to study axono- and dendritogenesis of individual neurons. With this method the effects of RNA interference, overexpression or small molecules can be compared to control neurons. In addition, the rodent cerebellar cortex is an easily accessible in vivo system owing to its predominant postnatal development. We also present an in vivo electroporation technique to genetically manipulate the developing cerebella and describe subsequent cerebellar analyses to assess neuronal morphology and migration.     

Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes

Remolding of tRNAs is a well-documented process in mitochondrial genomes that changes the identity of a tRNA. It involves a duplication of a tRNA gene, a mutation that changes the anticodon and the loss of the ancestral tRNA gene. The net effect is a functional tRNA that is more closely related to tRNAs of a different alloacceptor family than to tRNAs with the same anticodon in related species. Beyond being of interest for understanding mitochondrial tRNA function and evolution, tRNA remolding events can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. Therefore, it is important to identify and catalog these events. Here we describe novel methods to detect tRNA remolding in large-scale data sets and apply them to survey tRNA remolding throughout animal evolution. We identify several novel remolding events in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived from ancestral events.     

Thermal stress induces persistently altered coral reef fish assemblages

Ecological communities are reorganizing in response to warming temperatures. For continuous ocean habitats this reorganization is characterized by large‐scale species redistribution, but for tropical discontinuous habitats such as coral reefs, spatial isolation coupled with strong habitat dependence of fish species imply that turnover and local extinctions are more significant mechanisms. In these systems, transient marine heatwaves are causing coral bleaching and profoundly altering habitat structure, yet despite severe bleaching events becoming more frequent and projections indicating annual severe bleaching by the 2050s at most reefs, long‐term effects on the diversity and structure of fish assemblages remain unclear. Using a 23‐year time series spanning a thermal stress event, we describe and model structural changes and recovery trajectories of fish communities after mass bleaching. Communities changed fundamentally, with the new emergent communities dominated by herbivores and persisting for >15 years, a period exceeding realized and projected intervals between thermal stress events on coral reefs. Reefs which shifted to macroalgal states had the lowest species richness and highest compositional dissimilarity, whereas reefs where live coral recovered exceeded prebleaching fish richness, but remained dissimilar to prebleaching compositions. Given realized and projected frequencies of bleaching events, our results show that fish communities historically associated with coral reefs will not re‐establish, requiring substantial adaptation by managers and resource users.     

Posttranslational Modification of p53: Cooperative Integrators of Function

The p53 protein is modified by as many as 50 individual posttranslational modifications. Many of these occur in response to genotoxic or nongenotoxic stresses and show interdependence, such that one or more modifications can nucleate subsequent events. This interdependent nature suggests a pathway that operates through multiple cooperative events as opposed to distinct functions for individual, isolated modifications. This concept, supported by recent investigations, which provide exquisite detail as to how various modifications mediate precise protein–protein interactions in a cooperative manner, may explain why knockin mice expressing p53 proteins substituted at one or just a few sites of modification typically show only subtle effects on p53 function. The present article focuses on recent, exciting progress and develops the idea that the impact of modification on p53 function is achieved through collective and integrated events.     

Estimation of separable direct and indirect effects in continuous time

Many research questions involve time-to-event outcomes that can be prevented from occurring due to competing events. In these settings, we must be careful about the causal interpretation of classical statistical estimands. In particular, estimands on the hazard scale, such as ratios of cause-specific or subdistribution hazards, are fundamentally hard to interpret causally. Estimands on the risk scale, such as contrasts of cumulative incidence functions, do have a clear causal interpretation, but they only capture the total effect of the treatment on the event of interest; that is, effects both through and outside of the competing event. To disentangle causal treatment effects on the event of interest and competing events, the separable direct and indirect effects were recently introduced. Here we provide new results on the estimation of direct and indirect separable effects in continuous time. In particular, we derive the nonparametric influence function in continuous time and use it to construct an estimator that has certain robustness properties. We also propose a simple estimator based on semiparametric models for the two cause-specific hazard functions. We describe the asymptotic properties of these estimators and present results from simulation studies, suggesting that the estimators behave satisfactorily in finite samples. Finally, we reanalyze the prostate cancer trial from Stensrud et al. (2020).     

The Alexander disease-causing glial fibrillary acidic protein mutant, R416W, accumulates into Rosenthal fibers by a pathway that involves filament aggregation and the association of alpha B-crystallin and HSP27

Here, we describe the early events in the disease pathogenesis of Alexander disease. This is a rare and usually fatal neurodegenerative disorder whose pathological hallmark is the abundance of protein aggregates in astrocytes. These aggregates, termed "Rosenthal fibers," contain the protein chaperones alpha B-crystallin and HSP27 as well as glial fibrillary acidic protein (GFAP), an intermediate filament (IF) protein found almost exclusively in astrocytes. Heterozygous, missense GFAP mutations that usually arise spontaneously during spermatogenesis have recently been found in the majority of patients with Alexander disease. In this study, we show that one of the more frequently observed mutations, R416W, significantly perturbs in vitro filament assembly. The filamentous structures formed resemble assembly intermediates but aggregate more strongly. Consistent with the heterozygosity of the mutation, this effect is dominant over wild-type GFAP in coassembly experiments. Transient transfection studies demonstrate that R416W GFAP induces the formation of GFAP-containing cytoplasmic aggregates in a wide range of different cell types, including astrocytes. The aggregates have several important features in common with Rosenthal fibers, including the association of alpha B-crystallin and HSP27. This association occurs simultaneously with the formation of protein aggregates containing R416W GFAP and is also specific, since HSP70 does not partition with them. Monoclonal antibodies specific for R416W GFAP reveal, for the first time for any IF-based disease, the presence of the mutant protein in the characteristic histopathological feature of the disease, namely Rosenthal fibers. Collectively, these data confirm that the effects of the R416W GFAP are dominant, changing the assembly process in a way that encourages aberrant filament-filament interactions that then lead to protein aggregation and chaperone sequestration as early events in Alexander disease.