Polynomial Size Analysis of First-Order Shapely Functions

We present a size-aware type system for first-order shapely function definitions. Here, a function definition is called shapely when the size of the result is determined exactly by a polynomial in the sizes of the arguments. Examples of shapely function definitions may be implementations of matrix multiplication and the Cartesian product of two lists. The type system is proved to be sound w.r.t. the operational semantics of the language. The type checking problem is shown to be undecidable in general. We define a natural syntactic restriction such that the type checking becomes decidable, even though size polynomials are not necessarily linear or monotonic. Furthermore, we have shown that the type-inference problem is at least semi-decidable (under this restriction). We have implemented a procedure that combines run-time testing and type-checking to automatically obtain size dependencies. It terminates on total typable function definitions.Comment: 35 pages, 1 figur

Cyanotoxins and cyanobacteria cell accumulations in drinking water treatment plants with a low risk of bloom formation at the source

Toxic cyanobacteria have been shown to accumulate in drinking water treatment plants that are susceptible to algal blooms. However, the risk for plants that do not experience algal blooms, but that receive a low influx of cells, is not well known. This study determined the extent of cell accumulation and presence of cyanotoxins across the treatment trains of four plants in the Great Lakes region. Samples were collected for microscopic enumeration and enzyme-linked immunosorbent assay (ELISA) measurements for microcystins, anatoxin-a, saxitoxin, cylindrospermopsin, and beta-methylamino-L-alanine (BMAA). Low cell influxes (under 1000 cells/mL) resulted in significant cell accumulations (over 1 x 10(5) cells/mL) in clarifier sludge and filter backwash samples. Microcystins peaked at 7.2 microg/L in one clarifier sludge sample, exceeding the raw water concentration by a factor of 12. Anatoxin-a was detected in the finished drinking water of one plant at 0.6 microg/L. BMAA may have been detected in three finished water samples, though inconsistencies among the BMAA ELISAs call these results into question. In summary, the results show that plants receiving a low influx of cells can be at risk of toxic cyanobacterial accumulation, and therefore, the absence of a bloom at the source does not indicate the absence of risk

Impact of UV-H₂O₂ advanced oxidation and aging processes on GAC capacity for the removal of cyanobacterial taste and odor compounds

ABSTRACT: Cyanobacteria and their taste and odor (T&O) compounds are a growing concern in water sources globally. Geosmin and 2-methylisoborneol (MIB) are the most commonly detected T&O compounds associated with cyanobacterial presence in drinking water sources. The use of ultraviolet and hydrogen peroxide (H₂O₂) as an advanced oxidation treatment for T&O control is an emerging technology. However, residual H₂O₂ (>80% of the initial dose) has to be removed from water prior final disinfection. Recently, granular activated carbon (GAC) is used to remove H₂O₂ residual. The objective of this study is to assess the impact of H₂O₂ quenching and aging processes on GAC capacity for the removal of geosmin and MIB. Pilot columns with different types of GAC and presence/absence of H₂O₂ have been used for this study. H₂O₂ removal for the operational period of 6 months has no significant impact on GAC capacity to remove the geosmin and MIB from water

Modeling the efficiency of UV at 254 nm for disinfecting the different layers within N95 respirators

The study presented a Monte Carlo simulation of light transport in eight commonly used filtered facepiece respirators (FFRs) to assess the efficacy of UV at 254 nm for the inactivation of SARS-CoV-2. The results showed different fluence rates across the thickness of the eight different FFRs, implying that some FFR models may be more treatable than others, with the following order being (from most to least treatable): models 1512, 9105s, 1805, 9210, 1870+, 8210, 8110s and 1860, for single side illumination. The model predictions did not coincide well with some previously reported experimental data on virus inactivation when applied to FFR surfaces. The simulations predicted that FFRs should experience higher log reductions (>>6-log) than those observed experimentally (often limited to ~5-log). Possible explanations are virus shielding by aggregation or soiling, and a lack of the Monte Carlo simulations considering near-field scattering effects that can create small, localized regions of low UV photon probability on the surface of the fiber material. If the latter is the main cause in limiting practical UV viral decontamination, improvement might be achieved by exposing the FFR to UV isotropically from all directions, such as by varying the UV source to the FFR surface angle during treatment

Aberrant lipid metabolism disrupts calcium homeostasis causing liver endoplasmic reticulum stress in obesity.

The endoplasmic reticulum (ER) is the main site of protein and lipid synthesis, membrane biogenesis, xenobiotic detoxification and cellular calcium storage, and perturbation of ER homeostasis leads to stress and the activation of the unfolded protein response. Chronic activation of ER stress has been shown to have an important role in the development of insulin resistance and diabetes in obesity. However, the mechanisms that lead to chronic ER stress in a metabolic context in general, and in obesity in particular, are not understood. Here we comparatively examined the proteomic and lipidomic landscape of hepatic ER purified from lean and obese mice to explore the mechanisms of chronic ER stress in obesity. We found suppression of protein but stimulation of lipid synthesis in the obese ER without significant alterations in chaperone content. Alterations in ER fatty acid and lipid composition result in the inhibition of sarco/endoplasmic reticulum calcium ATPase (SERCA) activity and ER stress. Correcting the obesity-induced alteration of ER phospholipid composition or hepatic Serca overexpression in vivo both reduced chronic ER stress and improved glucose homeostasis. Hence, we established that abnormal lipid and calcium metabolism are important contributors to hepatic ER stress in obesity

Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers

Background: Genomic gains and losses are a result of genomic instability in many types of cancers. BRCA1- and BRCA2-mutated breast cancers are associated with increased amounts of chromosomal aberrations, presumably due their functions in genome repair. Some of these genomic aberrations may harbor genes whose absence or overexpression may give rise to cellular growth advantage. So far, it has not been easy to identify the driver genes underlying gains and losses. A powerful approach to identify these driver genes could be a cross-species comparison of array comparative genomic hybridization (aCGH) data from cognate mouse and human tumors. Orthologous regions of mouse and human tumors that are commonly gained or lost might represent essential genomic regions selected for gain or loss during tumor development. Methods: To identify genomic regions that are associated with BRCA1- and BRCA2-mutated breast cancers we compared aCGH data from 130 mouse Brca1?/?;p53?/?, Brca2?/?;p53?/? and p53?/? mammary tumor groups with 103 human BRCA1-mutated, BRCA2-mutated and non-hereditary breast cancers. Results: Our genome-wide cross-species analysis yielded a complete collection of loci and genes that are commonly gained or lost in mouse and human breast cancer. Principal common CNAs were the well known MYCassociated gain and RB1/INTS6-associated loss that occurred in all mouse and human tumor groups, and the AURKA-associated gain occurred in BRCA2-related tumors from both species. However, there were also important differences between tumor profiles of both species, such as the prominent gain on chromosome 10 in mouse Brca2?/?;p53?/? tumors and the PIK3CA associated 3q gain in human BRCA1-mutated tumors, which occurred in tumors from one species but not in tumors from the other species. This disparity in recurrent aberrations in mouse and human tumors might be due to differences in tumor cell type or genomic organization between both species. Conclusions: The selection of the oncogenome during mouse and human breast tumor development is markedly different, apart from the MYC gain and RB1-associated loss. These differences should be kept in mind when using mouse models for preclinical studies.MediamaticsElectrical Engineering, Mathematics and Computer Scienc

Ubiquitin Fold Modifier 1 (UFM1) and Its Target UFBP1 Protect Pancreatic Beta Cells from ER Stress-Induced Apoptosis

UFM1 is a member of the ubiquitin like protein family. While the enzymatic cascade of UFM1 conjugation has been elucidated in recent years, the biological function remains largely unknown. In this report we demonstrate that the recently identified C20orf116 [1], which we name UFM1-binding protein 1 containing a PCI domain (UFBP1), andCDK5RAP3 interact with UFM1. Components of the UFM1 conjugation pathway (UFM1, UFBP1, UFL1 and CDK5RAP3) are highly expressed in pancreatic islets of Langerhans and some other secretory tissues. Co-localization of UFM1 with UFBP1 in the endoplasmic reticulum (ER)depends on UFBP1. We demonstrate that ER stress, which is common in secretory cells, induces expression of Ufm1, Ufbp1 and Ufl1 in the beta-cell line INS-1E.siRNA-mediated Ufm1 or Ufbp1knockdown enhances apoptosis upon ER stress.Silencing the E3 enzyme UFL1, results in similar outcomes, suggesting that UFM1-UFBP1 conjugation is required to prevent ER stress-induced apoptosis. Together, our data suggest that UFM1-UFBP1participate in preventing ER stress-induced apoptosis in protein secretory cells

Understanding 'non-genetic' inheritance : insights from molecular-evolutionary crosstalk

The idea for this paper was initially proposed by I.A.-K. and was further developed by all authors in a workshop generously funded by grant No 789240 from the European Research Council (ERC) to F.J.W. S.E.S. acknowledges support from Wesleyan University and The John Templeton Foundation.Understanding the evolutionary and ecological roles of 'non-genetic' inheritance (NGI) is daunting due to the complexity and diversity of epigenetic mechanisms. We draw on insights from molecular and evolutionary biology perspectives to identify three general features of 'non-genetic' inheritance systems: (i) they are functionally interdependent with, rather than separate from, DNA sequence; (ii) precise mechanisms vary phylogenetically and operationally; and (iii) epigenetic elements are probabilistic, interactive regulatory factors and not deterministic 'epialleles' with defined genomic locations and effects. We discuss each of these features and offer recommendations for future empirical and theoretical research that implements a unifying inherited gene regulation (IGR) approach to studies of 'non-genetic' inheritance.Publisher PDFPeer reviewe

Machine learning uncovers the most robust self-report predictors of relationship quality across 43 longitudinal couples studies

Given the powerful implications of relationship quality for health and well-being, a central mission of relationship science is explaining why some romantic relationships thrive more than others. This large-scale project used machine learning (i.e., Random Forests) to 1) quantify the extent to which relationship quality is predictable and 2) identify which constructs reliably predict relationship quality. Across 43 dyadic longitudinal datasets from 29 laboratories, the top relationship-specific predictors of relationship quality were perceived-partner commitment, appreciation, sexual satisfaction, perceived-partner satisfaction, and conflict. The top individual-difference predictors were life satisfaction, negative affect, depression, attachment avoidance, and attachment anxiety. Overall, relationship-specific variables predicted up to 45% of variance at baseline, and up to 18% of variance at the end of each study. Individual differences also performed well (21% and 12%, respectively). Actor-reported variables (i.e., own relationship-specific and individual-difference variables) predicted two to four times more variance than partner-reported variables (i.e., the partner’s ratings on those variables). Importantly, individual differences and partner reports had no predictive effects beyond actor-reported relationship-specific variables alone. These findings imply that the sum of all individual differences and partner experiences exert their influence on relationship quality via a person’s own relationship-specific experiences, and effects due to moderation by individual differences and moderation by partner-reports may be quite small. Finally, relationship-quality change (i.e., increases or decreases in relationship quality over the course of a study) was largely unpredictable from any combination of self-report variables. This collective effort should guide future models of relationships