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The preferred retinal locus (PRL) is the position on the retina to which humans direct stimuli during fixation. In healthy normal eyes, it has been shown to be very stable across time and between different tasks. Previous measurements of the PRL have been made under monocular viewing conditions. The current study examines where the PRLs in the two eyes retinas are when subjects fixate binocularly and whether they shift when the demand for the eyes to converge is changed. Our apparatus allows us to see exactly where binocular stimuli fell on the two retinas during binocular fixation. Thus, our technique bypasses some of the issues involved in measuring binocular alignment with subjective techniques and previous objective techniques that use conventional eye trackers. These results show that PRLs shift slightly but systematically as the demand for convergence increases. The shifts cause under-convergence (also called exo fixation disparity) for near targets. They are not large enough to cause a break in binocular fusion. The fixation disparity we observed with increasing vergence demand is similar to fixation disparity observed in previous reports.

Age-related macular degeneration (AMD) is invariably associated with the chronic accumulation of activated mononuclear phagocytes in the subretinal space. The mononuclear phagocytes are composed of microglial cells but also of monocyte-derived cells, which promote photoreceptor degeneration and choroidal neovascularization. Infiltrating blood monocytes can originate directly from bone marrow, but also from a splenic reservoir, where bone marrow monocytes develop into angiotensin II receptor (ATR1)+ splenic monocytes. The involvement of splenic monocytes in neurodegenerative diseases such as AMD is not well understood. Using acute inflammatory and well-phenotyped AMD models, we demonstrate that angiotensin II mobilizes ATR1+ splenic monocytes, which we show are defined by a transcriptional signature using single-cell RNA sequencing and differ functionally from bone marrow monocytes. Splenic monocytes participate in the chorio-retinal infiltration and their inhibition by ATR1 antagonist and splenectomy reduces the subretinal mononuclear phagocyte accumulation and pathological choroidal neovascularization formation. In aged AMD-risk ApoE2-expressing mice, a chronic AMD model, ATR1 antagonist and splenectomy also inhibit the chronic retinal inflammation and associated cone degeneration that characterizes these mice. Our observation of elevated levels of plasma angiotensin II in AMD patients, suggests that similar events take place in clinical disease and argue for the therapeutic potential of ATR1 antagonists to inhibit splenic monocytes for the treatment of blinding AMD.

Antimicrobial drug resistance poses a global health threat, requiring a deeper understanding of the evolutionary processes that lead to its emergence in pathogens. Complex evolutionary dynamics involve multiple mutations that can result in cooperative or competitive (clonal interference) effects. Candida albicans, a major fungal pathogen, displays high rates of copy number variation (CNV) and loss of heterozygosity (LOH). CNV and LOH events involve large numbers of genes and could synergize during evolutionary adaptation. Understanding the contributions of CNV and LOH to antifungal drug adaptation is challenging, especially in the context of whole-population genome sequencing. Here, we document the sequential evolution of fluconazole tolerance and then resistance in a C. albicans isolate involving an initial CNV on chromosome 4, followed by an LOH on chromosome R that involves KSR1. Similar LOH events involving KSR1, which encodes a reductase in the sphingolipid biosynthesis pathway, were also detected in independently evolved fluconazole resistant isolates. We dissect the specific KSR1 codons that affect fluconazole resistance and tolerance. The combination of the chromosome 4 CNV and KSR1 LOH results in a >500-fold decrease in azole susceptibility relative to the progenitor, illustrating a compelling example of rapid, yet step-wise, interplay between CNV and LOH in drug resistance evolution.

This article reports on our experience in creating Modelica models for systems with thousands of configurations and closed-loop controls. The development of such templates required exploration of class parameterization techniques and data structures for handling large sets of equipment parameters. By describing these issues and the approach taken, we show how the Modelica language can support advanced templating logic. The main limitation we encountered relates to parameter assignment and propagation. The interpretation of parameter attributes at user interface runtime, or the handling of non-trivial constructs involving record classes at compile time is not consistently supported by Modelica tools. This leads to choices that are difficult to make when looking for a generic implementation.

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.

Cold-induced brown adipose tissue (BAT) activation is considered to improve metabolic health. In murine BAT, cold increases the fundamental molecule for mitochondrial function, nicotinamide adenine dinucleotide (NAD+), but limited knowledge of NAD+ metabolism during cold in human BAT metabolism exists. We show that cold increases the serum metabolites of the NAD+ salvage pathway (nicotinamide and 1-methylnicotinamide) in humans. Additionally, individuals with cold-stimulated BAT activation have decreased levels of metabolites from the de novo NAD+ biosynthesis pathway (tryptophan, kynurenine). Serum nicotinamide correlates positively with cold-stimulated BAT activation, whereas tryptophan and kynurenine correlate negatively. Furthermore, the expression of genes involved in NAD+ biosynthesis in BAT is related to markers of metabolic health. Our data indicate that cold increases serum tryptophan conversion to nicotinamide to be further utilized by BAT. We conclude that NAD+ metabolism is activated upon cold in humans and is probably regulated in a coordinated fashion by several tissues.

ObjectivesSmall area analysis is a health services research technique that facilitates geographical comparison of services supply and utilization rates between health service areas (HSAs). HSAs are functionally relevant regions around medical facilities within which most residents undergo treatment. We aimed to identify HSAs for psychiatric outpatient care (HSA-PSY) in Switzerland.MethodsWe used HSAr, a new and automated methodological approach, and comprehensive psychiatric service use data from insurances to identify HSA-PSY based on travel patterns between patients' residences and service sites. Resulting HSA-PSY were compared geographically, demographically and regarding the use of inpatient and outpatient psychiatric services.ResultsWe identified 68 HSA-PSY, which were reviewed and validated by local mental health services experts. The population-based rate of inpatient and outpatient service utilization varied considerably between HSA-PSY. Utilization of inpatient and outpatient services tended to be positively associated across HSA-PSY.ConclusionsWide variation of service use between HSA-PSY can hardly be fully explained by underlying differences in the prevalence or incidence of disorders. Whether other factors such as the amount of services supply did add to the high variation should be addressed in further studies, for which our functional mapping on a small-scale regional level provides a good analytical framework.

Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.

With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.

Decarbonization and resilience to heat waves have recently become high priorities for building and district energy systems. Geothermal coupled district heating and cooling systems that operate a water loop near ground temperature gain increasing adoption to support decarbonization. In these systems, vapor-compression machines, distributed in the energy transfer stations, lift the temperature up or down to the needs of the particular building. In principle, these systems can provide low-power, free cooling from the geothermal bore field during heat waves when electricity is often scarce. However, the performance of such a resilience operation mode and its implication on the energy system configuration and the sizing of the bore field and HVAC equipment is not yet understood. Consequently, we are assessing their resilience, power use and design implications under a scenario of a heat wave on five working days during which chillers are switched off to reduce electrical consumption. Our analysis is based on high-fidelity, coupled dynamic models of district energy, building-side HVAC and actual control logic, with whole building energy simulation used to assess thermal conditions in a 2004 vintage multi-zone office building in Chicago, IL. The results show that relying only on waterside economizer cooling, the indoor thermal conditions can be maintained in a tolerable range for the majority of the building zones with half the electrical energy compared to standard chiller operation. Thermal comfort in the hottest zones can be further improved by oversizing the cooling coil. However, the waterside economizer has significant implications on the system configuration and sizing: The geothermal bore field needs to be sized about 30% larger than the upper limit of the range observed for conventional geothermal systems. Nevertheless, if a central chiller plant is added, the bore field can be downsized to the typical design range. The latter configuration still allows compressor-less cooling during the heat wave with peak power reduced by 60% compared to the standard design and chiller operation.

In U.S. district heating (DH) systems, steam is the most common heat transport medium. Industry demand for new advanced modeling capabilities of complete steam DH systems is increasing; however, the existing models for water/steam thermodynamics are too slow for large system simulations because of computationally expensive algebraic loops that require the solution to nonlinear systems of equations. For practical applications, this work presents a novel split-medium approach that implements numerically efficient liquid water models alongside various water/steam models, breaking costly algebraic loops by decoupling mass and energy balance equations. New component models for steam DH systems are also presented. We implemented the models in the equation based Modelica language and evaluated accuracy and computing speed across multiple scales: from fundamental thermodynamic properties to complete districts featuring 10 to 200 buildings. Compared to district models with the IF97 water/steam model and equipment models from the Modelica Standard Library, the new implementation improves the scaling rate for large districts from cubic to quadratic with negligible compromise to accuracy. For an annual simulation with 180 buildings, this translates to a computing time reduction from 33 to 1–1.5 h. These results are critically important for industry practitioners to simulate steam DH systems at large scales.

ABSTRACT: Asian soybean rust, caused by Phakopsora pachyrhizi, is one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizi’s genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.

BackgroundThe multiplicity, heterogeneity, and dynamic nature of human immunodeficiency virus type-1 (HIV-1) latency mechanisms are reflected in the current lack of functional cure for HIV-1. Accordingly, all classes of latency-reversing agents (LRAs) have been reported to present variable ex vivo potencies. Here, we investigated the molecular mechanisms underlying the potency variability of one LRA: the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC).MethodsWe employed epigenetic interrogation methods (electrophoretic mobility shift assays, chromatin immunoprecipitation, Infinium array) in complementary HIV-1 infection models (latently-infected T-cell line models, primary CD4+ T-cell models and ex vivo cultures of PBMCs from HIV+ individuals). Extracellular staining of cell surface receptors and intracellular metabolic activity were measured in drug-treated cells. HIV-1 expression in reactivation studies was explored by combining the measures of capsid p24Gag protein, green fluorescence protein signal, intracellular and extracellular viral RNA and viral DNA.FindingsWe uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) to the HIV-1 promoter. We showed that UHRF1 redundantly binds to the HIV-1 promoter with different binding modalities where DNA methylation was either non-essential, essential or enhancing UHRF1 binding. We further demonstrated the role of UHRF1 in the epigenetic repression of the latent viral promoter by a concerted control of DNA and histone methylations.InterpretationA better understanding of the molecular mechanisms of HIV-1 latency allows for the development of innovative antiviral strategies. As a proof-of-concept, we showed that pharmacological inhibition of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent viral reactivation from latency. Together, we identify UHRF1 as a novel actor in HIV-1 epigenetic silencing and highlight that it constitutes a new molecular target for HIV-1 cure strategies.FundingFunding was provided by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium), the « Fondation Roi Baudouin », the NEAT (European AIDS Treatment Network) program, the Internationale Brachet Stiftung, ViiV Healthcare, the Télévie, the Walloon Region (« Fonds de Maturation »), « Les Amis des Instituts Pasteur à Bruxelles, asbl », the University of Brussels (Action de Recherche Concertée ULB grant), the Marie Skodowska Curie COFUND action, the European Union's Horizon 2020 research and innovation program under grant agreement No 691119-EU4HIVCURE-H2020-MSCA-RISE-2015, the French Agency for Research on AIDS and Viral Hepatitis (ANRS), the Sidaction and the "Alsace contre le Cancer" Foundation. This work is supported by 1UM1AI164562-01, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases.

While equation-based object-oriented modeling language Modelica can evaluate practical energy improvements for district cooling systems, few have adopted Modelica for this type of large-scale thermo-fluid system. Further, to our best knowledge, district cooling modeling studies have yet to include hydraulics in piping networks alongside plant models featuring realistic mechanical systems and controls. These are critical details to include when looking to make energy and control improvements in many physical system installations. To fill these gaps, this study released new open-source district cooling models at the Modelica Buildings Library and leveraged these models for a real-world case study at the University of Colorado Boulder. The site includes six buildings connected to a central chiller plant featuring a waterside economizer. Several energy saving strategies are pursued based on the validated model, including control setpoint optimization, equipment modification, and pump setpoint adjustments. Results indicate that a combination of the studied measures can save the campus annually 84.6 MWh of energy, 8.9% of electricity costs, 58.0 metric tons of carbon dioxide emissions, while the waterside economizer cuts down chillers’ run times by 201 days/year, reducing maintenance costs and extending chiller life.

Accurately modeling the growth process of plants in interaction with their environment is important for predicting their biophysical characteris-tics, referred to as phenotype prediction. Most models are described by dis-crete dynamic systems in general state-space representation with important domain-specific characteristics: First, plant model parameters have usually clear functional meanings and may be of genetic origins, thus necessitating a precise estimation. Second, critical growth variables, specifically biomass production and dynamic allocation to organs, are hidden variables not acces-sible to measure. Finally, the difficulty to assess the local plant environment may imply the introduction of process noises in models. Therefore, a precise understanding of the system’s behavior requires the joint estimation of functional parameters, hidden states, and noise parameters. In this paper we describe how a full Bayesian method of estimation can accurately estimate all these key model variables using Markov chain Monte Carlo (MCMC) tech-niques. In the presence of both process and observation noises, it requires to use adequate particle MCMC (PMCMC) algorithms to efficiently sample the hidden states which, consequently, allows for a precise estimation of all noise parameters involved. Thanks to the Bayesian framework, appropriate choices of prior distributions for the noise parameters have enabled analytical pos-terior distributions and only simple updates are required. Furthermore, this estimation strategy can be easily generalized and adapted to different types of plant growth models, such as organ-scale or compartmental, provided that they are formulated as hidden Markov models. Our estimation method im-proves on those classically used in plant growth modeling in several aspects: First, by building upon a general probabilistic framework the estimation results allow proper statistical analyses. It is useful in prediction, no only for uncertainty and risk analysis (e.g., for crop yield prediction) but also to an-alyze the results of experimental trials, for example, to compare genotypes in breeding. Moreover, the care taken in the estimation of hidden variables opens new perspectives in the understanding of inner growth processes, no-tably the balance and interaction between biomass production and allocation (referred to as source-sink dynamics). Applications of this estimation proce-dure are demonstrated on the GreenLab model for Arabidopsis thaliana and the Log-Normal Allocation and Senescence (LNAS) model for sugar beet, on both synthetic and real data.

The current process for specifying, installing and commissioning building control sequences is largely manual and based on ambiguous natural language specifications. It lacks a formal end-to-end quality control and it has been shown not to deliver high performance sequences at scale. While high-performance HVAC control sequences enable significant reductions in energy consumption, errors in implementing the control logic are common even for less advanced sequences. To improve this situation, we present a digitized building control delivery workflow with formal end-to-end verification, a Control Description Language for the digital specification of building control sequences within this workflow, and software tools that enable digitization of this process. Using the process and tools introduced here, mechanical designers can customize, test and improve these sequences within annual energy simulation, store them in a library for use in other projects, and export them for bidding. Control providers can implement the sequences on existing control product lines through code generation. Commissioning providers can formally verify whether as-installed sequences conform to the digital design specification that was exported by the mechanical designer. Moreover, control product development teams can use the reference implementations of these libraries within their product testing to ensure that their products reproduce the behavior of the reference implementations. This paper presents this process, the language and the supporting software, together with examples of all of the above steps. The presented work has given rise to a new proposed standard, ASHRAE 231P, that will allow digitizing the building control delivery process through the standardization of a control-vendor independent format for exchanging control logic that we pioneered through the here presented work.

The current process for specifying, installing and commissioning building control sequences is largely manual and based on ambiguous natural language specifications. It lacks a formal end-to-end quality control and it has been shown not to deliver high performance sequences at scale. While high-performance HVAC control sequences enable significant reductions in energy consumption, errors in implementing the control logic are common even for less advanced sequences. To improve this situation, we present a digitized building control delivery workflow with formal end-to-end verification, a Control Description Language for the digital specification of building control sequences within this workflow, and software tools that enable digitization of this process. Using the process and tools introduced here, mechanical designers can customize, test and improve these sequences within annual energy simulation, store them in a library for use in other projects, and export them for bidding. Control providers can implement the sequences on existing control product lines through code generation. Commissioning providers can formally verify whether as-installed sequences conform to the digital design specification that was exported by the mechanical designer. Moreover, control product development teams can use the reference implementations of these libraries within their product testing to ensure that their products reproduce the behavior of the reference implementations. This paper presents this process, the language and the supporting software, together with examples of all of the above steps. The presented work has given rise to a new proposed standard, ASHRAE 231P, that will allow digitizing the building control delivery process through the standardization of a control-vendor independent format for exchanging control logic that we pioneered through the here presented work.

Using a survey of French manufacturing firms, we study how firms’ expectations and actions are affected by both aggregate and industry-specific conditions. In response to industry-level shocks that have no aggregate effects, firms’ aggregate expectations respond persistently. This is consistent with “island” models in which firms use the local prices they observe to make inferences about broader aggregate conditions. These patterns are related to observable characteristics of firms and the industries in which they reside. Finally, we extend the analysis to firms’ expectations over their own future price changes and document how these respond to both industry and aggregate variation.

BackgroundAcute myeloid leukemia (AML) is fatal in elderly patients who are unfit for standard induction chemotherapy. The objective of this study was to evaluate the survival benefit of administering sapacitabine, an oral nucleoside analogue, in alternating cycles with decitabine, a low-intensity therapy, to elderly patients with newly diagnosed AML.MethodsThis randomized, open-label, phase 3 study (SEAMLESS) was conducted at 87 sites in 11 countries. Patients aged ≥70 years who were not candidates for or chose not to receive standard induction chemotherapy were randomized 1:1 to arm A (decitabine in alternating cycles with sapacitabine) received 1-hour intravenous infusions of decitabine 20 mg/m2 once daily for 5 consecutive days every 8 weeks (first cycle and subsequent odd cycles) and sapacitabine 300 mg twice daily on 3 consecutive days per week for 2 weeks every 8 weeks (second cycle and subsequent even cycles) or to control arm C who received 1-hour infusions of decitabine 20 mg/m2 once daily for 5 consecutive days every 4 weeks. Prior hypomethylating agent therapy for preexisting myelodysplastic syndromes or myeloproliferative neoplasms was an exclusion criterion. Randomization was stratified by antecedent myelodysplastic syndromes or myeloproliferative neoplasms, white blood cell count (

BackgroundEndocrine disrupting chemicals (EDCs) contribute to the etiology of metabolic disorders such as obesity, insulin resistance and hepatic dysfunction. Concern is growing about the consequences of perinatal EDC exposure on disease predisposition later in life. Metabolomics are promising approaches for studying long-term consequences of early life EDC exposure. These approaches allow for the identification and characterization of biomarkers of direct or ancestral exposures that could be diagnostic for individual susceptibility to disease and help to understand mechanisms through which EDCs act.ObjectivesWe sought to identify metabolomic fingerprints in mice ancestrally exposed to the model obesogen tributyltin (TBT), to assess whether metabolomics could discriminate potential trans-generational susceptibility to obesity and recognize metabolic pathways modulated by ancestral TBT exposure.MethodsWe used non-targeted 1H NMR metabolomic analyses of plasma and liver samples collected from male and female mice ancestrally exposed to TBT in two independent transgenerational experiments in which F3 and F4 males became obese when challenged with increased dietary fat.ResultsMetabolomics confirmed transgenerational obesogenic effects of environmentally relevant doses of TBT in F3 and F4 males, in two independent studies. Although females never became obese, their specific metabolomic fingerprint evidenced distinct transgenerational effects of TBT in female mice consistent with impaired capacity for liver biotransformation.DiscussionThis study is the first application of metabolomics to unveil the transgenerational effects of EDC exposure. Very early, significant changes in the plasma metabolome were observed in animals ancestrally exposed to TBT. These changes preceded the onset of obesogenic effects elicited by increased dietary fat in the TBT groups, and which ultimately resulted in significant changes in the liver metabolome. Development of metabolomic fingerprints could facilitate the identification of individuals carrying the signature of ancestral obesogen exposure that might increase their susceptibility to other risk factor such as increased dietary fat.

BackgroundEndocrine disrupting chemicals (EDCs) contribute to the etiology of metabolic disorders such as obesity, insulin resistance and hepatic dysfunction. Concern is growing about the consequences of perinatal EDC exposure on disease predisposition later in life. Metabolomics are promising approaches for studying long-term consequences of early life EDC exposure. These approaches allow for the identification and characterization of biomarkers of direct or ancestral exposures that could be diagnostic for individual susceptibility to disease and help to understand mechanisms through which EDCs act.ObjectivesWe sought to identify metabolomic fingerprints in mice ancestrally exposed to the model obesogen tributyltin (TBT), to assess whether metabolomics could discriminate potential trans-generational susceptibility to obesity and recognize metabolic pathways modulated by ancestral TBT exposure.MethodsWe used non-targeted 1H NMR metabolomic analyses of plasma and liver samples collected from male and female mice ancestrally exposed to TBT in two independent transgenerational experiments in which F3 and F4 males became obese when challenged with increased dietary fat.ResultsMetabolomics confirmed transgenerational obesogenic effects of environmentally relevant doses of TBT in F3 and F4 males, in two independent studies. Although females never became obese, their specific metabolomic fingerprint evidenced distinct transgenerational effects of TBT in female mice consistent with impaired capacity for liver biotransformation.DiscussionThis study is the first application of metabolomics to unveil the transgenerational effects of EDC exposure. Very early, significant changes in the plasma metabolome were observed in animals ancestrally exposed to TBT. These changes preceded the onset of obesogenic effects elicited by increased dietary fat in the TBT groups, and which ultimately resulted in significant changes in the liver metabolome. Development of metabolomic fingerprints could facilitate the identification of individuals carrying the signature of ancestral obesogen exposure that might increase their susceptibility to other risk factor such as increased dietary fat.

Cholangiocarcinoma (CCA) results from the malignant transformation of cholangiocytes. Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are chronic diseases in which cholangiocytes are primarily damaged. Although PSC is an inflammatory condition predisposing to CCA, CCA is almost never found in the autoimmune context of PBC. Here, we hypothesized that PBC might favor CCA immunosurveillance. In preclinical murine models of cholangitis challenged with syngeneic CCA, PBC (but not PSC) reduced the frequency of CCA development and delayed tumor growth kinetics. This PBC-related effect appeared specific to CCA as it was not observed against other cancers, including hepatocellular carcinoma. The protective effect of PBC was relying on type 1 and type 2 T cell responses and, to a lesser extent, on B cells. Single-cell TCR/RNA sequencing revealed the existence of TCR clonotypes shared between the liver and CCA tumor of a PBC host. Altogether, these results evidence a mechanistic overlapping between autoimmunity and cancer immunosurveillance in the biliary tract.

The URBANopt project has successfully leveraged OpenStudio/EnergyPlus to model buildings and electrical systems at an urban scale; however, URBANopt has lacked the ability to model district thermal energy systems until recently. This paper will present the modeling infrastructure that was developed specifically for the analysis of district heating and cooling systems, and how it is integrated into the existing URBANopt framework. The paper also discusses the development of new models added to the Modelica Buildings Library to model various district energy system components including loads, energy transfer stations (ETS), distribution networks, and central plants. The paper describes how different building loads can be modeled including time series, TEASER reduced-order models, or Spawn of EnergyPlus models. URBANopt District Energy Systems allows the user to switch between the various configurations.

Best practice control sequences are often not implemented correctly, or are not implemented at all, in large commercial buildings. This typically leads to 10-30 percent energy waste, along with reduced occupant productivity and unnecessary equipment wear. The current process of designing and implementing such control sequences is a manual process that starts with designers who often don’t have adequate training, then requires controls programmers to interpret and program a verbose written sequence. This process has been shown to fail to deliver high performance control sequences at scale. The Open Building Control project digitizes the current control delivery process. The project is developing tools for system designers to select control sequences, assess their energy performance and load flexibility potential using whole building simulation, specify the sequence for implementation using machine-to-machine translation by a control provider and formally testing the as-installed sequences by a commissioning agent. The project developed tools for each stage of this delivery process. The key innovation of the project is the development of the Control Description Language, a language that allows such a digitized control delivery process with end-to-end verification. Libraries of control sequences have been implemented using the Control Description Language, and their performance has been demonstrated using whole building energy simulation. An automated translation of such sequences to a commercial control product line has been conducted using a prototype translator. Tools for formal verification of as-installed control sequences relative to their specification have been developed and demonstrated. The American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE) started the process of forming a committee to make this language an ASHRAE/ANSI Standard. This new standard will complement existing and emerging ASHRAE standards for building communication and semantic modeling by providing a standard for expressing the control logic - the actual brain of the building. We expect this language and the process it enables to be an important contribution to the deployment of high performance building control sequences at scale because it allows taming the complexity of the control delivery process, which is continually increasing due to the need for higher performance and increased load flexibility to meet goals for net zero energy and increased renewable integration.

Spawn is the latest whole-building energy simulation engine developed by the US Department of Energy, NationalLabs and industry. Whereas EnergyPlus was designedas a successor to DOE-2, Spawn is not a direct successor of–nor is it intended as an imminent replacement for–EnergyPlus. Instead, Spawn reuses parts of EnergyPluswhile supporting new use cases in HVAC and controls.Spawn is intended to provide several capabilities that significantly advance beyond EnergyPlus. It is intended tosupport the evaluation of novel HVAC and district energy systems in a more physically realistic way. Critically, it can model control in a physically realistic way,using portable specifications that can be compiled for execution on control platforms. Spawn is also intended tosupport co-simulation in an intrinsic way to enable integration with third-party models.This paper describes the software architecture of Spawnfrom model authoring to compilation and simulation. Itexplains how Spawn reuses the envelope and daylightingmodules of EnergyPlus and couples them to HVAC andcontrol models from the Modelica Buildings Library using the Functional Mockup Interface (FMI) standard. Itpresents a number of examples that: i) validate Spawn’scoupled simulation approach by comparing its results tothose of EnergyPlus, ii) illustrate the Spawn methodologyfor modeling and simulating HVAC systems, and iii) evaluate the performance of Spawn’s Quantized State System(QSS) time integration algorithms

The lack of available table-top extreme ultraviolet (XUV) sources with high enough fluxes and coherence properties has limited the availability of nonlinear XUV and x-ray spectroscopies to free-electron lasers (FELs). Here, we demonstrate second harmonic generation (SHG) on a table-top XUV source by observing SHG near the Ti M2,3 edge with a high-harmonic seeded soft x-ray laser. Furthermore, this experiment represents the first SHG experiment in the XUV. First-principles electronic structure calculations suggest the surface specificity and separate the observed signal into its resonant and nonresonant contributions. The realization of XUV-SHG on a table-top source opens up more accessible opportunities for the study of element-specific dynamics in multicomponent systems where surface, interfacial, and bulk-phase asymmetries play a driving role.

The lack of available table-top extreme ultraviolet (XUV) sources with high enough fluxes and coherence properties has limited the availability of nonlinear XUV and x-ray spectroscopies to free-electron lasers (FELs). Here, we demonstrate second harmonic generation (SHG) on a table-top XUV source by observing SHG near the Ti M2,3 edge with a high-harmonic seeded soft x-ray laser. Furthermore, this experiment represents the first SHG experiment in the XUV. First-principles electronic structure calculations suggest the surface specificity and separate the observed signal into its resonant and nonresonant contributions. The realization of XUV-SHG on a table-top source opens up more accessible opportunities for the study of element-specific dynamics in multicomponent systems where surface, interfacial, and bulk-phase asymmetries play a driving role.

Best practice control sequences are often not implemented correctly, or are not implemented at all, in large commercial buildings. This typically leads to 10-30 percent energy waste, along with reduced occupant productivity and unnecessary equipment wear. The current process of designing and implementing such control sequences is a manual process that starts with designers who often don’t have adequate training, then requires controls programmers to interpret and program a verbose written sequence. This process has been shown to fail to deliver high performance control sequences at scale. The Open Building Control project digitizes the current control delivery process. The project is developing tools for system designers to select control sequences, assess their energy performance and load flexibility potential using whole building simulation, specify the sequence for implementation using machine-to-machine translation by a control provider and formally testing the as-installed sequences by a commissioning agent. The project developed tools for each stage of this delivery process. The key innovation of the project is the development of the Control Description Language, a language that allows such a digitized control delivery process with end-to-end verification. Libraries of control sequences have been implemented using the Control Description Language, and their performance has been demonstrated using whole building energy simulation. An automated translation of such sequences to a commercial control product line has been conducted using a prototype translator. Tools for formal verification of as-installed control sequences relative to their specification have been developed and demonstrated. The American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE) started the process of forming a committee to make this language an ASHRAE/ANSI Standard. This new standard will complement existing and emerging ASHRAE standards for building communication and semantic modeling by providing a standard for expressing the control logic - the actual brain of the building. We expect this language and the process it enables to be an important contribution to the deployment of high performance building control sequences at scale because it allows taming the complexity of the control delivery process, which is continually increasing due to the need for higher performance and increased load flexibility to meet goals for net zero energy and increased renewable integration.

Using a survey of French manufacturing firms, we study how firms’ expectations and actions are affected by both aggregate and industry-specific conditions. In response to industry-level shocks that have no aggregate effects, firms’ aggregate expectations respond persistently. This is consistent with “island” models in which firms use the local prices they observe to make inferences about broader aggregate conditions. These patterns are related to observable characteristics of firms and the industries in which they reside. Finally, we extend the analysis to firms’ expectations over their own future price changes and document how these respond to both industry and aggregate variation.

Understanding the behaviour of matter under conditions of extreme temperature, pressure, density and electromagnetic fields has profound effects on our understanding of cosmologic objects and the formation of the universe. Lacking direct access to such objects, our interpretation of observed data mainly relies on theoretical models. However, such models, which need to encompass nuclear physics, atomic physics and plasma physics over a huge dynamic range in the dimensions of energy and time, can only provide reliable information if we can benchmark them to experiments under well-defined laboratory conditions. Due to the plethora of effects occurring in this kind of highly excited matter, characterizing isolated dynamics or obtaining direct insight remains challenging. High-density plasmas are turbulent and opaque for radiation below the plasma frequency and allow only near-surface insight into ionization processes with visible wavelengths. Here, the output of a high-harmonic seeded laser-plasma amplifier using eight-fold ionized krypton as the gain medium operating at a 32.8 nm wavelength is ptychographically imaged. A complex-valued wavefront is observed in the extreme ultraviolet (XUV) beam with high resolution. Ab initio spatio-temporal Maxwell-Bloch simulations show excellent agreement with the experimental observations, revealing overionization of krypton in the plasma channel due to nonlinear laser-plasma interactions, successfully validating this four-dimensional multiscale model. This constitutes the first experimental observation of the laser ion abundance reshaping a laser-plasma amplifier. The presented approach shows the possibility of directly modelling light-plasma interactions in extreme conditions, such as those present during the early times of the universe, with direct experimental verification.

BACKGROUND: Grafting is widely used in horticulture and rootstocks are known to modify scion growth and adaptation to soil conditions. However, the role of scion genotype in regulating rootstock development and functioning has remained largely unexplored. In this study, reciprocal grafts of two grapevine genotypes were produced as well as the corresponding homo-graft controls. These plants were subjected to a low phosphate (LP) treatment and transcriptome profiling by RNA sequencing was done on root samples collected 27 h after the onset of the LP treatment. RESULTS: A set of transcripts responsive to the LP treatment in all scion/rootstock combinations was identified. Gene expression patterns associated with genetic variation in response to LP were identified by comparing the response of the two homo-grafts. In addition, the scion was shown to modify root transcriptome responses to LP in a rootstock dependent manner. A weighted gene co-expression network analysis identified modules of correlated genes; the analysis of the association of these modules with the phosphate treatment, and the scion and rootstock genotype identified potential hub genes. CONCLUSIONS: This study provides insights into the response of grafted grapevine to phosphate supply and identifies potential shoot-to-root signals that could vary between different grapevine genotypes.

Intense lasers can accelerate protons in sufficient numbers and energy that the resulting beam can heat materials to exotic warm (10 s of eV temperature) states. Here we show with experimental data that a laser-driven proton beam focused onto a target heated it in a localized spot with size strongly dependent upon material and as small as 35 μm radius. Simulations indicate that cold stopping power values cannot model the intense proton beam transport in solid targets well enough to match the large differences observed. In the experiment a 74 J, 670 fs laser drove a focusing proton beam that transported through different thicknesses of solid Mylar, Al, Cu or Au, eventually heating a rear, thin, Au witness layer. The XUV emission seen from the rear of the Au indicated a clear dependence of proton beam transport upon atomic number, Z, of the transport layer: a larger and brighter emission spot was measured after proton transport through the lower Z foils even with equal mass density for supposed equivalent proton stopping range. Beam transport dynamics pertaining to the observed heated spot were investigated numerically with a particle-in-cell (PIC) code. In simulations protons moving through an Al transport layer result in higher Au temperature responsible for higher Au radiant emittance compared to a Cu transport case. The inferred finding that proton stopping varies with temperature in different materials, considerably changing the beam heating profile, can guide applications seeking to controllably heat targets with intense proton beams.

BackgroundA remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity.ResultsWe obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages.ConclusionsOverall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.

We present results from spectroscopic follow-up observations of stars identified in the Kepler field and carried out by teams of the Kepler Follow-up Observation Program. Two samples of stars were observed over 6 yr (2009-2015): 614 standard stars (divided into "platinum" and "gold" categories) selected based on their asteroseismic detections and 2667 host stars of Kepler Objects of Interest (KOIs), most of them planet candidates. Four data analysis pipelines were used to derive stellar parameters for the observed stars. We compare the T eff, log(g), and [Fe/H] values derived for the same stars by different pipelines; from the average of the standard deviations of the differences in these parameter values, we derive error floors of ∼100 K, 0.2 dex, and 0.1 dex for T eff, log(g), and [Fe/H], respectively. Noticeable disagreements are seen mostly at the largest and smallest parameter values (e.g., in the giant star regime). Most of the log(g) values derived from spectra for the platinum stars agree on average within 0.025 dex (but with a spread of 0.1-0.2 dex) with the asteroseismic log(g) values. Compared to the Kepler Input Catalog (KIC), the spectroscopically derived stellar parameters agree within the uncertainties of the KIC but are more precise and thus an important contribution toward deriving more reliable planetary radii.

BACKGROUND:A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity. RESULTS:We obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages. CONCLUSIONS:Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.

Intense lasers can accelerate protons in sufficient numbers and energy that the resulting beam can heat materials to exotic warm (10 s of eV temperature) states. Here we show with experimental data that a laser-driven proton beam focused onto a target heated it in a localized spot with size strongly dependent upon material and as small as 35 μm radius. Simulations indicate that cold stopping power values cannot model the intense proton beam transport in solid targets well enough to match the large differences observed. In the experiment a 74 J, 670 fs laser drove a focusing proton beam that transported through different thicknesses of solid Mylar, Al, Cu or Au, eventually heating a rear, thin, Au witness layer. The XUV emission seen from the rear of the Au indicated a clear dependence of proton beam transport upon atomic number, Z, of the transport layer: a larger and brighter emission spot was measured after proton transport through the lower Z foils even with equal mass density for supposed equivalent proton stopping range. Beam transport dynamics pertaining to the observed heated spot were investigated numerically with a particle-in-cell (PIC) code. In simulations protons moving through an Al transport layer result in higher Au temperature responsible for higher Au radiant emittance compared to a Cu transport case. The inferred finding that proton stopping varies with temperature in different materials, considerably changing the beam heating profile, can guide applications seeking to controllably heat targets with intense proton beams.

The rates of mineral dissolution reactions in porous media are difficult to predict, in part because of a lack of understanding of mineral reactive surface area in natural porous media. Common estimates of mineral reactive surface area used in reactive transport models for porous media are typically ad hoc and often based on average grain size, increased to account for surface roughness or decreased by several orders of magnitude to account for reduced surface reactivity of field as opposed to laboratory samples. In this study, accessible mineral surface areas are determined for a sample from the reservoir formation at the Nagaoka pilot CO2 injection site (Japan) using a multi-scale image analysis based on synchrotron X-ray microCT, SEM QEMSCAN, XRD, SANS, and FIB-SEM. This analysis not only accounts for accessibility of mineral surfaces to macro-pores, but also accessibility through connected micro-pores in smectite, the most abundant clay mineral in this sample. While the imaging analysis reveals that most of the micro- and macro-pores are well connected, some pore regions are unconnected and thus inaccessible to fluid flow and diffusion. To evaluate whether mineral accessible surface area accurately reflects reactive surface area a flow-through core experiment is performed and modeled at the continuum scale. The core experiment is performed under conditions replicating the pilot site and the evolution of effluent solutes in the aqueous phase is tracked. Various reactive surface area models are evaluated for their ability to capture the observed effluent chemistry, beginning with parameter values determined as a best fit to a disaggregated sediment experiment (Beckingham et al., 2016) described previously. Simulations that assume that all mineral surfaces are accessible (as in the disaggregated sediment experiment) over-predict the observed mineral reaction rates, suggesting that a reduction of RSA by a factor of 10–20 is required to match the core flood experimental data. While the fit of the effluent chemistry (and inferred mineral dissolution rates) greatly improve when the pore-accessible mineral surface areas are used, it was also necessary to include highly reactive glass phases to match the experimental observations, in agreement with conclusions from the disaggregated sediment experiment. It is hypothesized here that the 10–20 reduction in reactive surface areas based on the limited pore accessibility of reactive phases in core flood experiment may be reasonable for poorly sorted and cemented sediments like those at the Nagaoka site, although this reflects pore rather than larger scale heterogeneity.

This data article describes serum glycoprotein biomarker discovery and qualification datasets generated using lectin magnetic bead array (LeMBA) - mass spectrometry techniques, "Serum glycoprotein biomarker discovery and qualification pipeline reveals novel diagnostic biomarker candidates for esophageal adenocarcinoma" [1]. Serum samples collected from healthy, metaplastic Barrett׳s esophagus (BE) and esophageal adenocarcinoma (EAC) individuals were profiled for glycoprotein subsets via differential lectin binding. The biomarker discovery proteomics dataset consisting of 20 individual lectin pull-downs for 29 serum samples with a spiked-in internal standard chicken ovalbumin protein has been deposited in the PRIDE partner repository of the ProteomeXchange Consortium with the data set identifier PRIDE: PXD002442. Annotated MS/MS spectra for the peptide identifications can be viewed using MS-Viewer (〈http://prospector2.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msviewer〉) using search key "jn7qafftux". The qualification dataset contained 6-lectin pulldown-coupled multiple reaction monitoring-mass spectrometry (MRM-MS) data for 41 protein candidates, from 60 serum samples. This dataset is available as a supplemental files with the original publication [1].

Intensity-modulated radiation therapy (IMRT) currently plays an important role in radiotherapy, but its treatment plan quality can vary significantly among institutions and planners. Treatment plan quality control (QC) is a necessary component for individual clinics to ensure that patients receive treatments with high therapeutic gain ratios. The voxel-weighting factor-based plan re-optimization mechanism has been proved able to explore a larger Pareto surface (solution domain) and therefore increase the possibility of finding an optimal treatment plan. In this study, we incorporated additional modules into an in-house developed voxel weighting factor-based re-optimization algorithm, which was enhanced as a highly automated and accurate IMRT plan QC tool (TPS-QC tool). After importing an under-assessment plan, the TPS-QC tool was able to generate a QC report within 2 minutes. This QC report contains the plan quality determination as well as information supporting the determination. Finally, the IMRT plan quality can be controlled by approving quality-passed plans and replacing quality-failed plans using the TPS-QC tool. The feasibility and accuracy of the proposed TPS-QC tool were evaluated using 25 clinically approved cervical cancer patient IMRT plans and 5 manually created poor-quality IMRT plans. The results showed high consistency between the QC report quality determinations and the actual plan quality. In the 25 clinically approved cases that the TPS-QC tool identified as passed, a greater difference could be observed for dosimetric endpoints for organs at risk (OAR) than for planning target volume (PTV), implying that better dose sparing could be achieved in OAR than in PTV. In addition, the dose-volume histogram (DVH) curves of the TPS-QC tool re-optimized plans satisfied the dosimetric criteria more frequently than did the under-assessment plans. In addition, the criteria for unsatisfied dosimetric endpoints in the 5 poor-quality plans could typically be satisfied when the TPS-QC tool generated re-optimized plans without sacrificing other dosimetric endpoints. In addition to its feasibility and accuracy, the proposed TPS-QC tool is also user-friendly and easy to operate, both of which are necessary characteristics for clinical use.

Intensity-modulated radiation therapy (IMRT) currently plays an important role in radiotherapy, but its treatment plan quality can vary significantly among institutions and planners. Treatment plan quality control (QC) is a necessary component for individual clinics to ensure that patients receive treatments with high therapeutic gain ratios. The voxel-weighting factor-based plan re-optimization mechanism has been proved able to explore a larger Pareto surface (solution domain) and therefore increase the possibility of finding an optimal treatment plan. In this study, we incorporated additional modules into an in-house developed voxel weighting factor-based re-optimization algorithm, which was enhanced as a highly automated and accurate IMRT plan QC tool (TPS-QC tool). After importing an under-assessment plan, the TPS-QC tool was able to generate a QC report within 2 minutes. This QC report contains the plan quality determination as well as information supporting the determination. Finally, the IMRT plan quality can be controlled by approving quality-passed plans and replacing quality-failed plans using the TPS-QC tool. The feasibility and accuracy of the proposed TPS-QC tool were evaluated using 25 clinically approved cervical cancer patient IMRT plans and 5 manually created poor-quality IMRT plans. The results showed high consistency between the QC report quality determinations and the actual plan quality. In the 25 clinically approved cases that the TPS-QC tool identified as passed, a greater difference could be observed for dosimetric endpoints for organs at risk (OAR) than for planning target volume (PTV), implying that better dose sparing could be achieved in OAR than in PTV. In addition, the dose-volume histogram (DVH) curves of the TPS-QC tool re-optimized plans satisfied the dosimetric criteria more frequently than did the under-assessment plans. In addition, the criteria for unsatisfied dosimetric endpoints in the 5 poor-quality plans could typically be satisfied when the TPS-QC tool generated re-optimized plans without sacrificing other dosimetric endpoints. In addition to its feasibility and accuracy, the proposed TPS-QC tool is also user-friendly and easy to operate, both of which are necessary characteristics for clinical use.

In 2013, the California Legislature passed Senate Bill 4 (SB 4), setting the framework for regulation of well stimulation technologies in California, including hydraulic fracturing. SB 4 also requires the California Natural Resources Agency to conduct an independent scientific study of well stimulation technologies in California to assess current and potential future practices, including the likelihood that well stimulation technologies could enable extensive new petroleum production in the state, evaluate the impacts of well stimulation technologies and the gaps in data that preclude this understanding, identify risks associated with current practices, and identify alternative practices which might limit these risks.The study is issued in three volumes. This document, Volume I, provides the factual basis describing well stimulation technologies, how and where operators deploy these technologies for oil and gas production in California, and where they might enable production in the future. Volume II discusses how well stimulation affects water, the atmosphere, seismic activity, wildlife and vegetation, traffic, light and noise levels; it will also explore human health hazards, and identify data gaps and alternative practices. Volume III presents case studies to assess environmental issues and qualitative

To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database. Considering both cell types, a large number of transcripts showed significant variation across the inbred strains, with 22% of the transcriptome varying by 2-fold or more. These included 119 loci with apparent complete loss of function, where the corresponding transcript was not expressed in some of the strains, representing a useful resource of "natural knockouts." We identified 1222 cis-expression quantitative trait loci (cis-eQTL) that control some of this variation. Most (60%) cis-eQTLs were shared between T cells and neutrophils, but a significant portion uniquely impacted one of the cell types, suggesting cell type-specific regulatory mechanisms. Using a conditional regression algorithm, we predicted regulatory interactions between transcription factors and potential targets, and we demonstrated that these predictions overlap with regulatory interactions inferred from transcriptional changes during immunocyte differentiation. Finally, comparison of these and parallel data from CD4(+) T cells of healthy humans demonstrated intriguing similarities in variability of a gene's expression: the most variable genes tended to be the same in both species, and there was an overlap in genes subject to strong cis-acting genetic variants. We speculate that this "conservation of variation" reflects a differential constraint on intraspecies variation in expression levels of different genes, either through lower pressure for some genes, or by favoring variability for others.