Cell force measurements in 3D microfabricated environments based on compliant cantilevers.

We report the fabrication, functionalization and testing of microdevices for cell culture and cell traction force measurements in three-dimensions (3D). The devices are composed of bent cantilevers patterned with cell-adhesive spots not lying on the same plane, and thus suspending cells in 3D. The cantilevers are soft enough to undergo micrometric deflections when cells pull on them, allowing cell forces to be measured by means of optical microscopy. Since individual cantilevers are mechanically independent of each other, cell traction forces are determined directly from cantilever deflections. This proves the potential of these new devices as a tool for the quantification of cell mechanics in a system with well-defined 3D geometry and mechanical properties.

Moving forward on facilitation research: response to changing environments and effects on the diversity, functioning and evolution of plant communities

Once seen as anomalous, facilitative interactions among plants and their importance for community structure and functioning are now widely recognized. The growing body of modelling, descriptive and experimental studies on facilitation covers a wide variety of terrestrial and aquatic systems throughout the globe. However, the lack of a general body of theory linking facilitation among different types of organisms and biomes and their responses to environmental changes prevents further advances in our knowledge regarding the evolutionary and ecological implications of facilitation in plant communities. Moreover, insights gathered from alternative lines of inquiry may substantially improve our understanding of facilitation, but these have been largely neglected thus far. Despite over 15 years of research and debate on this topic, there is no consensus on the degree to which plant–plant interactions change predictably along environmental gradients (i.e. the stress-gradient hypothesis), and this hinders our ability to predict how plant–plant interactions may affect the response of plant communities to ongoing global environmental change. The existing controversies regarding the response of plant–plant interactions across environmental gradients can be reconciled when clearly considering and determining the species-specificity of the response, the functional or individual stress type, and the scale of interest (pairwise interactions or community-level response). Here, we introduce a theoretical framework to do this, supported by multiple lines of empirical evidence. We also discuss current gaps in our knowledge regarding how plant–plant interactions change along environmental gradients. These include the existence of thresholds in the amount of species-specific stress that a benefactor can alleviate, the linearity or non-linearity of the response of pairwise interactions across distance from the ecological optimum of the beneficiary, and the need to explore further how frequent interactions among multiple species are and how they change across different environments. We review the latest advances in these topics and provide new approaches to fill current gaps in our knowledge. We also apply our theoretical framework to advance our knowledge on the evolutionary aspects of plant facilitation, and the relative importance of facilitation, in comparison with other ecological processes, for maintaining ecosystem structure, functioning and dynamics. We build links between these topics and related fields, such as ecological restoration, woody encroachment, invasion ecology, ecological modelling and biodiversity–ecosystem-functioning relationships. By identifying commonalities and insights from alternative lines of research, we further advance our understanding of facilitation and provide testable hypotheses regarding the role of (positive) biotic interactions in the maintenance of biodiversity and the response of ecological communities to ongoing environmental changes.

Service Level Agreements-Driven Management of Distributed Applications in Cloud Computing Environments

Cloud Computing enables provisioning and distribution of highly scalable services in a reliable, on-demand and sustainable manner. However, objectives of managing enterprise distributed applications in cloud environments under Service Level Agreement (SLA) constraints lead to challenges for maintaining optimal resource control. Furthermore, conflicting objectives in management of cloud infrastructure and distributed applications might lead to violations of SLAs and inefficient use of hardware and software resources. This dissertation focusses on how SLAs can be used as an input to the cloud management system, increasing the efficiency of allocating resources, as well as that of infrastructure scaling. First, we present an extended SLA semantic model for modelling complex service-dependencies in distributed applications, and for enabling automated cloud infrastructure management operations. Second, we describe a multi-objective VM allocation algorithm for optimised resource allocation in infrastructure clouds. Third, we describe a method of discovering relations between the performance indicators of services belonging to distributed applications and then using these relations for building scaling rules that a CMS can use for automated management of VMs. Fourth, we introduce two novel VM-scaling algorithms, which optimally scale systems composed of VMs, based on given SLA performance constraints. All presented research works were implemented and tested using enterprise distributed applications.

Service level agreements-driven management of distributed applications in cloud computing environments

Advancements in cloud computing have enabled the proliferation of distributed applications, which require management and control of multiple services. However, without an efficient mechanism for scaling services in response to changing workload conditions, such as number of connected users, application performance might suffer, leading to violations of Service Level Agreements (SLA) and possible inefficient use of hardware resources. Combining dynamic application requirements with the increased use of virtualised computing resources creates a challenging resource Management context for application and cloud-infrastructure owners. In such complex environments, business entities use SLAs as a means for specifying quantitative and qualitative requirements of services. There are several challenges in running distributed enterprise applications in cloud environments, ranging from the instantiation of service VMs in the correct order using an adequate quantity of computing resources, to adapting the number of running services in response to varying external loads, such as number of users. The application owner is interested in finding the optimum amount of computing and network resources to use for ensuring that the performance requirements of all her/his applications are met. She/he is also interested in appropriately scaling the distributed services so that application performance guarantees are maintained even under dynamic workload conditions. Similarly, the infrastructure Providers are interested in optimally provisioning the virtual resources onto the available physical infrastructure so that her/his operational costs are minimized, while maximizing the performance of tenants’ applications. Motivated by the complexities associated with the management and scaling of distributed applications, while satisfying multiple objectives (related to both consumers and providers of cloud resources), this thesis proposes a cloud resource management platform able to dynamically provision and coordinate the various lifecycle actions on both virtual and physical cloud resources using semantically enriched SLAs. The system focuses on dynamic sizing (scaling) of virtual infrastructures composed of virtual machines (VM) bounded application services. We describe several algorithms for adapting the number of VMs allocated to the distributed application in response to changing workload conditions, based on SLA-defined performance guarantees. We also present a framework for dynamic composition of scaling rules for distributed service, which used benchmark-generated application Monitoring traces. We show how these scaling rules can be combined and included into semantic SLAs for controlling allocation of services. We also provide a detailed description of the multi-objective infrastructure resource allocation problem and various approaches to satisfying this problem. We present a resource management system based on a genetic algorithm, which performs allocation of virtual resources, while considering the optimization of multiple criteria. We prove that our approach significantly outperforms reactive VM-scaling algorithms as well as heuristic-based VM-allocation approaches.

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.

Dual Role of Mesenchymal Stem Cells Allows for Microvascularized Bone Tissue-Like Environments in PEG Hydrogels.

In vitro engineered tissues which recapitulate functional and morphological properties of bone marrow and bone tissue will be desirable to study bone regeneration under fully controlled conditions. Among the key players in the initial phase of bone regeneration are mesenchymal stem cells (MSCs) and endothelial cells (ECs) that are in close contact in many tissues. Additionally, the generation of tissue constructs for in vivo transplantations has included the use of ECs since insufficient vascularization is one of the bottlenecks in (bone) tissue engineering. Here, 3D cocultures of human bone marrow derived MSCs (hBM-MSCs) and human umbilical vein endothelial cells (HUVECs) in synthetic biomimetic poly(ethylene glycol) (PEG)-based matrices are directed toward vascularized bone mimicking tissue constructs. In this environment, bone morphogenetic protein-2 (BMP-2) or fibroblast growth factor-2 (FGF-2) promotes the formation of vascular networks. However, while osteogenic differentiation is achieved with BMP-2, the treatment with FGF-2 suppressed osteogenic differentiation. Thus, this study shows that cocultures of hBM-MSCs and HUVECs in biological inert PEG matrices can be directed toward bone and bone marrow-like 3D tissue constructs.

Analysis of the Heat-Shock Response Displayed by Two Chaetomium Species Originating from Different Thermal Environments

Three features of the heat shock response, reorganization of protein expression, intracellular accumulation of trehalose, and alteration in unsaturation degree of fatty acids were investigated in the thermophilic fungus Chaetomium thermophile and compared to the response displayed by a closely related mesophilic species, C. brasiliense. Thermophilic heat shock response paralleled the mesophilic response in many respects like (i) the temperature difference observed between normothermia and the upper limit of translational activity, (ii) the transient nature of the heat shock response at the level of protein expression including both the induction of heat shock proteins (HSPs) as well as the repression of housekeeping proteins, (iii) the presence of representatives of high-molecular-weight {HSPs} families, (iv) intracellular accumulation of trehalose, and finally (v) modifications in fatty acid composition. On the other hand, a great variability between the two organisms was observed for the proteins expressed during stress, in particular a protein of the {HSP60} family that was only observed in C. thermophile. This peptide was also present constitutively at normal temperature and may thus fulfil thermophilic functions. It is shown that accumulation of trehalose does not play a part in thermophily but is only a stress response. C. thermophile contains less polyunsaturated fatty acids at normal temperature than C. brasiliense, a fact that can be directly related to thermophily. When subjected to heat stress, both organisms tended to accumulate shorter and less unsaturated fatty acids.

School Environments and Behaviors of Students on the Autism Spectrum

This study explores the relationship between the different environments within a school and the stereotyped behaviors of students with autism. The study seeks to identify whether the behaviors of these students are similar or different in the different environments, testing the idea of environment as a stimulus for these behaviors. The study is a naturalistic observational study, and a change in prevalence of these stereotyped behaviors during the duration of the study is not a focus of this study.

Fecal coliform contamination in child day care environments in Houston, Texas

Outbreaks of diarrhea are common among children in day care centers (DCC). Enteropathogens associated with these outbreaks are spread by the fecal-oral route through contaminated hands or environmental objects. This prospective study was undertaken to determine the prevalence of fecal coliform (FC) contamination in the DCC environment. Ten rooms in 6 DCC housing 121 children $<$2 years of age were studied for 13 weeks. Inanimate objects (1275), toy balls (724), and hands (954) were cultured 1-3 times per week. FC contamination was common during each week of study and was significantly (p $<$ 0.05) greater for objects, toy balls, and hands of children in toddler compared to infant rooms. In 5 rooms in which clothes were worn over diapers, there was a significantly lower prevalence of FC of toy balls (p $<$ 0.005), inanimate objects (p $<$ 0.05), and hands of children (p $<$ 0.001) and caregivers (p $<$ 0.05) when compared to rooms in which overclothes were not worn. Occurrence of diarrhea was significantly associated with increased contamination of caregivers' and children's hands. Using plasmid analysis of trimethoprim (TMP)-resistant Escherichia coli, stool and environmental isolates from individual DCC rooms had the same plasmid patterns, which were unique to each center. In summary, FC of environmental isolates and hands of children and caregivers in DCC is common; toy balls can serve as sentinels of contamination; FC can be significantly decreased by use of clothes worn over diapers; and plasmid analysis of E. coli strains showed the same patterns from stool and environmental isolates. ^

THE MEASUREMENT OF HUMANISTIC AND DEHUMANISTIC BEHAVIORS IN HOSPITAL NURSING ENVIRONMENTS

The purpose of this investigation was to develop a reliable scale to measure the social environment of hospital nursing units according to the degree of humanistic and dehumanistic behaviors as perceived by nursing staff in hospitals. The study was based on a conceptual model proposed by Jan Howard, a sociologist. After reviewing the literature relevant to personalization of care, analyzing interviews with patients in various settings, and studying biological, psychological, and sociological frames of reference, Howard proposed the following necessary conditions for humanized health care. They were the dimensions of Irreplaceability, Holistic Selves, Freedom of Action, Status Equality, Shared Decision Making and Responsibility, Empathy, and Positive Affect.^ It was proposed that a scale composed of behaviors which reflected Howard's dimensions be developed within the framework of the social environment of nursing care units in hospitals. Nursing units were chosen because hospitals are traditionally organized around nursing care units and because patients spend the majority of their time in hospitals interacting with various levels of nursing personnel.^ Approximately 180 behaviors describing both patient and nursing staff behaviors which occur on nursing units were developed. Behaviors which were believed to be humanistic as well as dehumanistic were included. The items were classified under the dimensions of Howard's model by a purposively selected sample of 42 nurses representing a broad range of education, experience, and clinical areas. Those items with a high degree of agreement, at least 50%, were placed in the questionnaire. The questionnaire consisted of 169 items including six items from the Marlowe Crowne Social Desirability Scale (Short Form).^ The questionnaire, the Social Environment Scale, was distributed to the entire 7 to 3 shift nursing staff (603) of four hospitals including a public county specialty hospital, a public county general and acute hospital, a large university affiliated hospital with all services, and a small general community hospital. Staff were asked to report on a Likert type scale how often the listed behaviors occurred on their units. Three hundred and sixteen respondents (52% of the population) participated in the study.^ An item analysis was done in which each item was examined in relationship to its correlation to its own dimension total and to the totals of the other dimensions. As a result of this analysis, three dimensions, Positive Affect, Irreplaceability, and Freedom of Action were deleted from the scale. The final scale consisted of 70 items with 26 in Shared Decision Making and Responsibility, 25 in Holistic Selves, 12 in Status Equality, and seven in Empathy. The alpha coefficient was over .800 for all scales except Empathy which was .597.^ An analysis of variance by hospital was performed on the means of each dimension of the scale. There was a statistically significant difference between hospitals with a trend for the public hospitals to score lower on the scale than the university or community hospitals. That the scale scores should be lower in crowded, understaffed public hospitals was not unexpected and reflected that the scale had some discriminating ability. These differences were still observed after adjusting for the effect of Social Desirability.^ In summary, there is preliminary evidence based on this exploratory investigation that a reliable scale based on at least four dimensions from Howard's model could be developed to measure the concept of humanistic health care in hospital settings. ^