Search

We investigated the impact of assigning specific roles in Process Oriented Guided Inquiry Learning (POGIL) activities versus giving the same group activities without pre-assigned roles. We hoped to show that the group with additional structure would receive tangible benefits: more engagement with partners, greater comprehension of material, heightened content interest, and increased retention. Preliminary results suggest that the proportion of minimally participating students was not statistically significantly different, and neither were the individual assessments. The roled section did have higher scores overall in the course, both in the group activities and also in the final exam; however, the difference was small and not clearly statistically significant. Unexpectedly, disciplinary actions and post course surveys indicate a greater rate of plagiarism on both shared lab reports and individual homework assignments in the free-form group and this may be a factor for instructors to bear in mind when utilizing group activities.

A senior undergraduate course on cryptography for computer science majors that combines the use of conventional materials with Maple worksheets and Mobius modules is in development. The design intent and impact of the Maple-based materials on course conduct is discussed. Pedagogical and practical considerations are discussed along and initial impressions given regarding benefits and difficulties in using the tools.

Hemophagocytic lymphohistiocytosis (HLH) is also known as hemophagocytic syndrome. It is a lethal hematologic condition due to a dysregulated immune response which results in inappropriately activated macrophages damaging host tissues. Based on the etiology, HLH can be primary (genetic) or secondary (acquired). The most common cause of a secondary HLH is an infection. Viral infections are the most common cause of secondary HLH. Among the viral causes of secondary HLH, Epstein-Barr virus is the most common etiologic agent. Cytomegalovirus (CMV) is a common causative pathogen in the immunocompromised host but is rare in an immunocompetent adult. In infection- associated secondary HLH, treatment includes antimicrobial therapy. HLH carries a high mortality and morbidity rate as it is an underdiagnosed clinical condition. Successful early diagnosis allows for adequate time for curative therapy. Treatment for HLH includes chemotherapy, immunomodulators, and a hematopoietic stem-cell transplant. The 2004 diagnostic criteria set by the Histiocyte Society serves as a guide to make an earlier clinical diagnosis. A review of PubMed literature revealed only five reported cases of CMV-induced HLH. We describe the sixth case of CMV pneumonitis-induced HLH and syndrome of inappropriate antidiuretic hormone secretion in a 72-year-old White male. He was treated successfully with oral valganciclovir and corticosteroids.

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity., This project was funded by NIH NHGRI R01HG008742 (E.K.K., B.B., D.P.G., R.S., J.T.-M., J.J., H.J.N., B.P. and J. Armstrong), Swedish Research Council Distinguished Professor Award (K.L.-T., V.D.M., E.M. and J.R.S.M.), Swedish Research Council grant 2018-05973 (K.L.-T.), Knut and Alice Wallenberg Foundation (K.L.-T., V.D.M., E.M. and J.R.S.M.), Uppsala University (K.L.-T., V.D.M., E.M., J.R.S.M., J.J., J. Alfoldi and L.G.), Broad Institute Next10 (L.G.), Gladstone Institutes (K.S.P.), NIH NHGRI 5R01HG002939 (A.F.A.S. and R.H.), NIH NHGRI 5U24HG010136 (A.F.A.S. and R.H.), NIH NHGRI 5R01HG010485 (B.P. and M.D.), NIH NHGRI 2U41HG007234 (B.P., M.D. and J. Armstrong), NIH NIA 5PO1AG047200 (V.N.G.), NIH NIA 1UH2AG064706 (V.N.G.), BFU2017-86471-P MINECO/FEDER, UE (T.M.-B.), Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya GRC 2017 SGR 880 (T.M.-B.), Howard Hughes International Early Career (T.M.-B.), European Research Council Horizon 2020 no. 864203 (T.M.-B.), Obra Social ‘La Caixa’ (T.M.-B.), BBSRC BBS/E/T/000PR9818, BBS/E/T/ 000PR9783 (W.H. and W.N.), BBSRC Core Strategic Programme Grant BB/P016774/1 (W.H., W.N. and F.D.), Sir Henry Dale Fellowship 200517/Z/16/Z jointly funded by the Wellcome Trust and the Royal Society (N.R.C.), FJCI-2016-29558 MICINN (D.J.), Prince Albert II Foundation of Monaco and Canada, Global Genome Initiative, Smithsonian Institution (M.N.), European Research Council Research Grant ERC-2012-StG311000 (E.C.T.), Irish Research Council Laureate Award (E.C.T.), UK Medical Research Council MR/P026028/1 (W.H. and W.N.), National Science Foundation DEB-1457735 (M.S.S.), National Science Foundation DEB-1753760 (W.J.M.), National Science Foundation IOS-2029774 (E.K.K. and D.P.G.), Robert and Rosabel Osborne Endowment (H.A.L. and J.D.), Swedish Research Council, FORMAS 221-2012-1531 (J.R.S.M.), NSF RoL: FELS: EAGER: DEB 1838283 (D.A.R.) and Academy of Finland grant to Center of Excellence in Tumor Genetics Research no. 312042 (T.K. and J.T.).

Following a cancer diagnosis, patients must cope with numerous physical, emotional, and practical challenges. While health information exists to help patients learn how to manage these challenges, health information seeking often declines over time, recalling information is difficult, and limited time with healthcare providers can leave patients feeling uninformed about their illness. We designed MyPath to overcome these information access challenges. The mobile system offers personalized, dynamic, and trusted health information recommendations to help patients learn about and manage their cancer. Through a seven-month deployment study with breast cancer patients, we found that use of the application encouraged proactive health management behaviors, and identified factors that motivated technology adoption and abandonment. We discuss the implications of these results for facilitating use of mHealth tools by a rural patient population and the importance of scaling support to a large range of information needs. We use this work to demonstrate the value of personalized health information systems and to motivate future CSCW research developing personalized support systems for other health situations with complex information access models.

In this paper, we address the question of how to automatically map computational kernels to highly efficient code for a wide range of computing platforms and establish the correctness of the synthesized code. More specifically, we focus on two fundamental problems that software developers are faced with: performance portability across the ever-changing landscape of parallel platforms and correctness guarantees for sophisticated floating-point code. The problem is approached as follows: We develop a formal framework to capture computational algorithms, computing platforms, and program transformations of interest, using a unifying mathematical formalism we call operator language (OL). Then we cast the problem of synthesizing highly optimized computational kernels for a given machine as a strongly constrained optimization problem that is solved by search and a multistage rewriting system. Since all rewrite steps are semantics preserving, our approach establishes equivalence between the kernel specification and the synthesized program. This approach is implemented in the SPIRAL system, and we demonstrate it with a selection of computational kernels from the signal and image processing domain, software-defined radio, and robotic vehicle control. Our target platforms range from mobile devices, desktops, and server multicore processors to large-scale high-performance and supercomputing systems, and we demonstrate performance comparable to expertly hand-tuned code across kernels and platforms.

Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure–activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.

The purpose of this study was to investigate the effectiveness of idle reduction technologies (IRTs) in reducing driver exposure to diesel exhaust, and to study the cost effectiveness of these technologies. IRTs are devices that provide heating and cooling to the cabin of a truck without idling the truck engine. The focus was on diesel-powered IRTs (auxiliary power units and fuel-operated heaters), and their impact on particulate matter (PM2.5) exposure of drivers sleeping or resting in the truck’s cabin. The focus was on diesel-powered IRTs as these devices generate their own emissions, potentially exacerbating in-cab exposure levels. The project involved initial field data collection at truck stops in the states of Georgia, Texas and California. This was followed by laboratory testing in an environmentally controlled test chamber on a sample of trucks, with and without the use of IRTs. The study findings showed that the use of IRTs resulted in a significant reduction of PM2.5 levels in the truck cabin when compared with the baseline scenario of a truck parked with the engine off and the doors and windows closed. Idling the truck engine and running the air conditioning system was also found to reduce in-cabin PM2.5 levels relative to the baseline. The study supports the premise that IRTs reduce driver exposure to diesel exhaust. Additionally, it was found that these devices are cost effective in that they all have payback periods of less than five years, making them viable alternatives to idling the truck engine during long-duration rest periods.

Introduction Ertugliflozin is an oral sodium-glucose cotransporter 2 inhibitor that is being developed to treat type 2 diabetes mellitus (T2DM). This study assessed the efficacy and safety of co-initiation of ertugliflozin and sitagliptin compared with placebo in patients with T2DM inadequately controlled on diet and exercise. Methods In this phase III, randomized, double-blind, multicenter, placebo-controlled 26-week study (NCT02226003), patients with T2DM and glycated hemoglobin (HbA1c) 8.0–10.5% on diet/exercise were randomized 1:1:1 to ertugliflozin 5 mg once daily (QD) and sitagliptin 100 mg QD (E5/S100), ertugliflozin 15 mg QD and sitagliptin 100 mg QD (E15/S100), or placebo. The primary efficacy endpoint was the change from baseline in HbA1c at week 26. Results The mean baseline HbA1c of the randomized patients (n = 291) was 8.9%. At week 26, both ertugliflozin/sitagliptin treatments provided significant reductions from baseline in HbA1c compared with placebo [least squares mean HbA1c change (95% confidence intervals) from baseline was − 0.4% (− 0.7, − 0.2), − 1.6% (− 1.8, − 1.4), and − 1.7% (− 1.9, − 1.5) for placebo, E5/S100, and E15/S100, respectively]. At week 26, 8.3%, 35.7%, and 31.3% of patients receiving placebo, E5/S100, and E15/S100, respectively, had HbA1c

Audio applications such as mobile phones, hearing aids, true wireless stereo earphones, and Internet of Things devices demand small size, high performance, and reduced cost. Microelectromechanical system (MEMS) capacitive microphones fulfill these requirements with improved reliability and specifications related to sensitivity, signal-to-noise ratio (SNR), distortion, and dynamic range when compared to their electret condenser microphone counterparts. We present the design and modeling of a semiconstrained polysilicon diaphragm with flexible springs that are simply supported under bias voltage with a center and eight peripheral protrusions extending from the backplate. The flexible springs attached to the diaphragm reduce the residual film stress effect more effectively compared to constrained diaphragms. The center and peripheral protrusions from the backplate further increase the effective area, linearity, and sensitivity of the diaphragm when the diaphragm engages with these protrusions under an applied bias voltage. Finite element modeling approaches have been implemented to estimate deflection, compliance, and resonance. We report an 85% increase in the effective area of the diaphragm in this configuration with respect to a constrained diaphragm and a 48% increase with respect to a simply supported diaphragm without the center protrusion. Under the applied bias, the effective area further increases by an additional 15% as compared to the unbiased diaphragm effective area. A lumped element model has been also developed to predict the mechanical and electrical behavior of the microphone. With an applied bias, the microphone has a sensitivity of −38 dB (ref. 1 V/Pa at 1 kHz) and an SNR of 67 dBA measured in a 3.25 mm × 1.9 mm × 0.9 mm package including an analog ASIC.

Introduction This study assessed the safety and efficacy of ertugliflozin (an oral sodium-glucose cotransporter 2 inhibitor) vs. glimepiride in patients with type 2 diabetes mellitus (T2DM) inadequately controlled on metformin. Methods This phase III, double-blind, non-inferiority study (NCT01999218) randomized patients with HbA1c ≥ 7.0% and ≤ 9.0% on stable metformin ≥ 1500 mg/day 1:1:1 to ertugliflozin 15 or 5 mg once-daily (QD), or glimepiride (titrated from 1 mg QD). The primary hypothesis was that ertugliflozin 15 mg was non-inferior to glimepiride on HbA1c (non-inferiority criterion: upper bound of the 95% confidence interval [CI] about the treatment difference Results Mean baseline HbA1c of randomized patients (N = 1326) was 7.8%. Mean and median doses of glimepiride were 3.0 mg/day throughout the study. At week 52, the least squares mean change (95% CI) from baseline in HbA1c was − 0.6% (− 0.7, − 0.5), − 0.6% (− 0.6, − 0.5), and − 0.7% (− 0.8, − 0.7) in the ertugliflozin 15 mg, ertugliflozin 5 mg, and glimepiride groups, respectively. The between-group difference for ertugliflozin 15 mg and glimepiride of 0.1% (− 0.0, 0.2) met the pre-specified non-inferiority criterion. Relative to glimepiride, greater body weight and systolic blood pressure (SBP) reductions were observed with ertugliflozin. The overall incidence of adverse events (AEs) was similar across groups. The incidence of symptomatic hypoglycemia and genital mycotic infection (GMI) were, respectively, lower and higher with ertugliflozin relative to glimepiride. The incidences of urinary tract infection and hypovolemia AEs were not meaningfully different among the groups. Conclusions Ertugliflozin 15 mg was non-inferior to glimepiride in reducing HbA1c when added to metformin in patients with T2DM. Ertugliflozin had an acceptable safety profile and resulted in less hypoglycemia and more GMIs than glimepiride. Clinical Trial Registration Clinicaltrials.gov NCT01999218.

VISUAL ARTS have the potential to enrich both human experience and society by inviting individuals to engage in creative expression. Art exploration should be available to any individual, regardles...

Introduction Ertugliflozin is a sodium-glucose cotransporter 2 inhibitor in development for type 2 diabetes mellitus (T2DM). The safety and efficacy of ertugliflozin were evaluated over 52 weeks in patients with chronic kidney disease (CKD). Methods In this double-blind randomized study (NCT01986855), patients with glycated hemoglobin (A1C) 7.0–10.5% and stage 3 CKD [estimated glomerular filtration rate (eGFR) ≥ 30 to

Obsessive-compulsive disorder is a severe psychiatric disorder linked to abnormalities in glutamate signaling and the cortico-striatal circuit. We sequenced coding and regulatory elements for 608 genes potentially involved in obsessive-compulsive disorder in human, dog, and mouse. Using a new method that prioritizes likely functional variants, we compared 592 cases to 560 controls and found four strongly associated genes, validated in a larger cohort. NRXN1 and HTR2A are enriched for coding variants altering postsynaptic protein-binding domains. CTTNBP2 (synapse maintenance) and REEP3 (vesicle trafficking) are enriched for regulatory variants, of which at least six (35%) alter transcription factor-DNA binding in neuroblastoma cells. NRXN1 achieves genome-wide significance (p = 6.37 × 10−11) when we include 33,370 population-matched controls. Our findings suggest synaptic adhesion as a key component in compulsive behaviors, and show that targeted sequencing plus functional annotation can identify potentially causative variants, even when genomic data are limited., Nature Communications, 8, ISSN:2041-1723

Background Adolescents with brain injury (BI) often experience impairment in participation, which is an important predictor of outcomes. Objective Describe the Social Participation and Navigation (SPAN) program, and report participant feedback and preliminary outcomes. Method Four adolescents and four coaches participated. SPAN included a mobile app, online didactic information, and peer coaching. Adolescents met weekly with coaches via video-conference, developed participation goals, and plans to achieve goals. Social and behavioral functioning before and after was assessed, and feedback about SPAN was collected. Results SPAN was well received. Participants used the app to define and achieve goals. Medium to large effect sizes were found on adolescent self-reported measures, with negligible effects on parent-report measures. Positive and critical feedback is described. Conclusions Findings support the usability of SPAN, which has the potential to improve social participation of adolescents with a history of TBI through an innovative use of technology and peer coaching.

Positron spectroscopy can identify defects deep within metals and semiconductors with a resolution better than a single atomic lattice site. This article discusses the basic principles and implementation of positron annihilation spectroscopy and a key development that makes it more a more useful tool for semiconductor applications.

Cyberphysical systems (CPSs), ranging from critical infrastructures such as power plants, to modern (semi) autonomous vehicles, are systems that use software to control physical processes. CPSs are made up of many different computational components. Each component runs its own piece of software that implements its control algorithms, based on its model of the environment. Every component then interacts with other components through the signals and values it sends out. Collectively, these components, and the code they run, drive the complex behaviors modern society has come to expect and rely on. Due to these intricate interactions between components, managing the hundreds to millions of lines of software to ensure that the system, as a whole, performs as desired can often be unwieldy.

Aims To conduct a phase III study to evaluate the efficacy and safety of ertugliflozin monotherapy in people with type 2 diabetes. Materials and methods This was a 52-week, double-blind, multicentre, randomized, parallel-group study with a 26-week, placebo-controlled treatment period (phase A), followed by a 26-week active-controlled treatment period (phase B) in 461 men and women, aged ≥18 years with inadequate glycaemic control (glycated haemoglobin [HbA1c] concentration 7.0% to 10.5% [53-91 mmol/mol], inclusive) despite diet and exercise. Results from phase A are reported in the present paper. The primary endpoint was the change in HbA1c from baseline to week 26. Results At week 26, the placebo-adjusted least squares mean HbA1c changes from baseline were −0.99% and −1.16% for the ertugliflozin 5 and 15 mg doses, respectively ( P

Discusses important skills and goals to address issues facing youth and communities, foster leadership training, and develop outreach to improve the lives of people.

Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We show that Cactus is capable of scaling to hundreds of genomes and beyond by describing results from an alignment of over 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment yet created. Further, we show improvements in orthology resolution leading to downstream improvements in annotation.

Osteosarcoma (OS) is a rare, metastatic, human adolescent cancer that also occurs in pet dogs. To define the genomic underpinnings of canine OS, we performed multi-platform analysis of OS tumors from 59 dogs, including whole genome sequencing (n = 24) and whole exome sequencing (WES; n = 13) of primary tumors and matched normal tissue, WES (n = 10) of matched primary/metastatic/normal samples and RNA sequencing (n = 54) of primary tumors. We found that canine OS recapitulates features of human OS including low point mutation burden (median 1.98 per Mb) with a trend towards higher burden in metastases, high structural complexity, frequent TP53 (71%), PI3K pathway (37%), and MAPK pathway mutations (17%), and low expression of immune-associated genes. We also identified novel features of canine OS including putatively inactivating somatic SETD2 (42%) and DMD (50%) aberrations. These findings set the stage for understanding OS development in dogs and humans, and establish genomic contexts for future comparative analyses., Heather Gardner et al. report the genomic landscape of canine osteosarcoma, finding recurrent mutations in the histone methyltransferase gene SETD2 and in DMD, the gene encoding dystrophin. The results support the study of naturally-occurring osteosarcoma in dogs for understanding both human disease mechanisms and canine-specific alterations to identify new treatments.

Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th–20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.

Altres ajuts: A comprehensive canine genetics resource including gene and variation annotation (NIH /OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH) NIH/OD/5R24OD018250 ; NCI/5R37CA218570 ; NIMH/R21MH109938 ; NHGRI/1R01HG008742 Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.

Summary We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network. Availability and implementation Source code is available on GitHub at https://github.com/4dn-dcic/tibanna. Supplementary information Supplementary data are available at Bioinformatics online.

In this chapter, I apply a particular interpretation of Wittgenstein’s thought in On Certainty , namely heterogeneous foundationalism, to the area of morality. In doing so, I aim to clarify the nature of moral bedrock and the relations between moral bedrock and situated moral reasoning, reasoning which depends on the foundations for transcendental rather than justificatory support. I argue that seeing moral foundations in this way, and seeing ungrounded doubts as silly and ignorable, is how we resist sceptical regress arguments directed against moral claims.

Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with high fatality and few effective treatment options. It is both rare and heterogenous, making large, well powered genomic studies nearly impossible. In dogs, angiosarcoma is common, with breeds like the golden retriever carrying heritable genetic factors that put them at very high risk. If the clinical similarity of canine and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine angiosarcoma via whole exome sequencing (47 golden retriever angiosarcomas) and RNA sequencing (74 angiosarcomas from multiple breeds). The predominant mutational signature was the age-associated deamination of cytosine to thymine, and somatic coding mutations occurred most frequently in the tumor suppressorTP53(59.6% of cases) as well as two genes in the PI3K pathway: the oncogenePIK3CA(29.8%) and its regulatory subunitPIK3R1(8.5%). We compared the canine data to human data recently released by The Angiosarcoma Project, and found the same genes and many of the same pathways significantly enriched for somatic mutations, most notably protein kinases, glycoproteins, fibronectin Type III domains, EGF-like domains, and cell adhesion proteins such as cadherins. As in human angiosarcoma,CDKN2A/Bwas recurrently deleted andVEGFA, KDR, and KITrecurrently gained. Canine angiosarcoma closely models human angiosarcoma on a genomic level, and is a powerful tool for investigating the pathogenesis of this devastating disease.

Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with few effective treatment options and high patient mortality. It is both rare and heterogenous, making large, well powered genomic studies nearly impossible. Dogs commonly suffer from a similar cancer, called hemangiosarcoma, with breeds like the golden retriever carrying heritable genetic factors that put them at high risk. If the clinical similarity of canine hemangiosarcoma and human angiosarcoma reflects shared genomic etiology, dogs could be a critically needed model for advancing angiosarcoma research. We assessed the genomic landscape of canine hemangiosarcoma via whole exome sequencing (47 golden retriever hemangiosarcomas) and RNA sequencing (74 hemangiosarcomas from multiple breeds). Somatic coding mutations occurred most frequently in the tumor suppressor TP53 (59.6% of cases) as well as two genes in the PI3K pathway: the oncogene PIK3CA (29.8%) and its regulatory subunit PIK3R1 (8.5%). The predominant mutational signature was the age-associated deamination of cytosine to thymine. As reported in human angiosarcoma, CDKN2A/B was recurrently deleted and VEGFA, KDR, and KIT recurrently gained. We compared the canine data to human data recently released by The Angiosarcoma Project, and found many of the same genes and pathways significantly enriched for somatic mutations, particularly in breast and visceral angiosarcomas. Canine hemangiosarcoma closely models the genomic landscape of human angiosarcoma of the breast and viscera, and is a powerful tool for investigating the pathogenesis of this devastating disease.

Data for the incidence of acute kidney injury (AKI) related to intravenous contrast administration in the pediatric trauma population are limited. Obtaining a creatinine value before elective CT scans is a relatively accepted standard of care. We sought to determine whether there was any significant difference in the incidence of AKI between severely injured patients who received IV contrast and those who did not. We reviewed data from the trauma registry at our Level I pediatric trauma center. We limited the patients to severely injured pediatric traumas (15 years old) directly transported from the scene of injury with a creatinine level measured on arrival. Two hundred and eleven patients were included in the study. AKI was defined by the criteria of the AKI Network. We then compared incidence of AKI in those who received a CT scan with IV contrast with those who did not receive IV contrast. The two groups were comparable in age, gender, Glasgow Coma Scale, Injury Severity Score, mean creatinine on arrival, and mean creatinine post-CT scan/arrival. There was no significant difference in AKI between the two. In a subgroup analysis of patients presenting in shock, there was no significant difference in AKI. Our study suggests that IV contrast is not associated with the development of AKI in severely injured pediatric trauma patients. Although obtaining a creatinine value before exposure is ideal, a CT scan with IV contrast in severely injured children should not be delayed to obtain a creatinine value.

The evolutionary history of a gene helps predict its function and relationship to phenotypic traits. Although sequence conservation is commonly used to decipher gene function and assess medical relevance, methods for functional inference from comparative expression data are lacking. Here, we use RNA-seq across seven tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein–Uhlenbeck process, a commonly proposed model of continuous trait evolution. We apply this model to identify expression pathways under neutral, stabilizing, and directional selection. We further demonstrate novel applications of this model to quantify the extent of stabilizing selection on a gene's expression, parameterize the distribution of each gene's optimal expression level, and detect deleterious expression levels in expression data from individual patients. Our work provides a statistical framework for interpreting expression data across species and in disease.

Patients with advanced-stage gastroenteropancreatic neuroendocrine tumors (GEP-NETs) have a poor overall prognosis despite chemotherapy and radiotherapy (e.g., peptide receptor radionuclide therapy (PRRT)). Better treatment options are needed to improve disease regression and patient survival. The purpose of this study was to examine a new treatment strategy by combining PI3K/mTOR dual inhibition and radiotherapy. First, we assessed the efficacy of two PI3K/mTOR dual inhibitors, PF-04691502 and PKI-402, to inhibit pAkt and increase apoptosis in NET cell lines (BON and QGP-1) and patient-derived tumor spheroids as single agents or combined with radiotherapy (XRT). Treatment with PF-04691502 decreased pAkt (Ser473) expression for up to 72 h compared with the control, in contrast, decreased pAkt expression was noted for less than 24 h with PKI-402. Simultaneous treatment with PF-04691502 and XRT did not induce apoptosis in NET cells, however, the addition of PF-04691502 48 h after XRT significantly increased apoptosis compared to PF-04691502 or XRT treatment alone. Our results demonstrate that schedule-dependent administration of a PI3K/mTOR inhibitor, combined with XRT, can enhance cytotoxicity by promoting the radiosensitivity of NET cells. Moreover, our findings suggest that radiotherapy, in combination with timed PI3K/mTOR inhibition, may be a promising therapeutic regimen for patients with GEP-NET.

Background: Peptide receptor radionuclide therapy (PRRT) is a novel radiotherapy approved for gastroenteropancreatic neuroendocrine tumors (GEP-NETs); however, PRRT has a relatively low treatment response rate of 20-30%. We hypothesize that addition of 3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP), a ribonucleotide reductase (RnR) inhibitor that inhibits the rate-limiting enzyme of DNA synthesis and repair, can improve radiotherapy outcomes. The purpose of this study is to determine the therapeutic rationale of RnR-targeted therapy and evaluate 3-AP as a radiosensitizer in treating GEP-NET in vitro and in vivo. Methods: We utilized two human GEP-NET cell lines: BON, a pancreatic carcinoid tumor, and QGP-1, a somatostatinoma. (i) Cells were treated with 3-AP for 96h and cell proliferation assays were performed using a sulforhodamine B (SRB) kit. Next, cells were treated with 3-AP for 24, 48, 72, 96h and cell cycle analyses were performed with Beckman Coulter cell cycle kit and quantified by flow cytometry. Expression of cell cycle arrest markers (i.e., pCdk-1, cyclin D1) was assessed by immunoblotting. (ii) To determine radiosensitivity in vitro, cells were treated with 3-AP for 16h, followed by X-ray radiotherapy (XRT), and incubation in drug-free medium. Cell survival was assessed by colony formation assay and quantified by SRB kit at 14d post-XRT. Apoptosis was measured at 72 and 96h post-XRT, and expression of apoptotic proteins (i.e., cleaved PARP and cleaved CASPASE 3) was examined by immunoblotting. (iii) To determine radiosensitivity in vivo, we randomized 20 nude mice bearing QGP-1 xenografts into four groups: control; 3-AP (10mg/Kg); XRT (2 Gy); and combination (XRT immediately followed by 3-AP); each mouse received 5 consecutive treatments. Results: (i) A dose of 2500nM 3-AP arrested cells before entering G2/M phase, significantly reducing percentage of G2/M cells from 8.4% to 0.5% at 72h. Concurrently, we observed increased expression of checkpoint proteins (pRb, pCdk1, pCdk2, pCdc2) and decreased expression of cell cycle inhibitory proteins (cyclin D1, p21, p27 Kip). (ii) Exposure of QGP-1 and BON cells to 3-AP prior to XRT resulted in a synergistic decrease (i.e., 85% and 90%, respectively) in clonogenicity. Furthermore, the combination of 3-AP and XRT increased apoptosis 5-fold and cleaved PARP expression in BON cells. (iii) A significant decrease in tumor size was noted in mice with XRT alone compared to control (146mm2 vs. 280 mm2, respectively); combination treatment (3-AP + XRT) demonstrated a further 48% decrease in tumor size compared to XRT alone. There was no significant decrease in tumor size with 3-AP treatment alone. Conclusion: 3-AP treatment prior to XRT therapy resulted in significant increase in apoptosis in vitro and decrease in tumor size in vivo, suggesting synergistic cytotoxicity and radiosensitivity. Selective RNR inhibition by 3-AP provides a potent therapeutic strategy as a radiosensitizer and offers a novel approach in treating advanced GEP-NETs. Citation Format: Zeta Chow, Jeremy Johnson, Aman Chauhan, Tadahide Isumi, Lowell Anthony, Courtney M. Townsend, B. Mark Evers, Piotr Rychahou. 3-Aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP): A promising radiochemotherapy for gastroenteropancreatic neuroendocrine tumors [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-014.

Rosemary extract (RE) is an approved food preservative in the European Union and contains dietary phytochemicals that are beneficial for gastrointestinal health. This study investigated the effects of RE on dextran sodium sulfate (DSS)-induced colitis and also determined the pharmacokinetics of dietary phytochemicals administered to mice via oral gavage. Individual components of rosemary extract were separated and identified by LC–MS/MS. The pharmacokinetics of two major diterpenes from RE, carnosic acid (CA) and carnosol (CL), administered to mice via oral gavage were determined. Then, the effect of RE pre-treatment on the disease activity index (DAI) of DSS-induced colitis in mice was investigated. The study determined that 100 mg/kg RE significantly improved DAI in DSS-induced colitis compared to negative control. Sestrin 2 protein expression, which increased with DSS exposure, was reduced with RE treatment. Intestinal barrier integrity was also shown to improve via fluorescein isothiocyanate (FITC)–dextran administration and Western blot of zonula occludens-1 (ZO-1), a tight junction protein. Rosemary extract was able to improve the DAI of DSS-induced colitis in mice at a daily dose of 100 mg/kg and showed improvement in the intestinal barrier integrity. This study suggests that RE can be an effective preventative agent against IBD.

The complex life cycle of Mycobacterium tuberculosis requires diverse energy mobilization and utilization strategies facilitated by a battery of lipid metabolism enzymes. Among lipid metabolism enzymes, the Lip family of mycobacterial serine hydrolases is essential to lipid scavenging, metabolic cycles, and reactivation from dormancy. On the basis of the homologous rescue strategy for mycobacterial drug targets, we have characterized the three-dimensional structure of full length LipW from Mycobacterium marinum, the first structure of a catalytically active Lip family member. LipW contains a deep, expansive substrate-binding pocket with only a narrow, restrictive active site, suggesting tight substrate selectivity for short, unbranched esters. Structural alignment reinforced this strict substrate selectivity of LipW, as the binding pocket of LipW aligned most closely with the bacterial acyl esterase superfamily. Detailed kinetic analysis of two different LipW homologues confirmed this strict substrate selectivity, as each homologue selected for unbranched propionyl ester substrates, irrespective of the alcohol portion of the ester. Using comprehensive substitutional analysis across the binding pocket, the strict substrate selectivity of LipW for propionyl esters was assigned to a narrow funnel in the acyl-binding pocket capped by a key hydrophobic valine residue. The polar, negatively charged alcohol-binding pocket also contributed to substrate orientation and stabilization of rotameric states in the catalytic serine. Together, the structural, enzymatic, and substitutional analyses of LipW provide a connection between the structure and metabolic properties of a Lip family hydrolase that refines its biological function in active and dormant tuberculosis infection.

Francisella tularensis is the causative agent of the highly, infectious disease, tularemia. Amongst the genes identified as essential to the virulence of F. tularensis was the proposed serine hydrolase FTT0941c. Herein, we purified FTT0941c to homogeneity and then characterized the folded stability, enzymatic activity, and substrate specificity of FTT0941c. Based on phylogenetic analysis, FTT0941c was classified within a divergent Francisella subbranch of the bacterial hormone sensitive lipase (HSL) superfamily, but with the conserved sequence motifs of a bacterial serine hydrolase. FTT0941c showed broad hydrolase activity against diverse libraries of ester substrates, including significant hydrolytic activity across alkyl ester substrates from 2 to 8 carbons in length. Among a diverse library of fluorogenic substrates, FTT0941c preferred α-cyclohexyl ester substrates, matching with the substrate specificity of structural homologues and the broad open architecture of its modeled binding pocket. By substitutional analysis, FTT0941c was confirmed to have a classic catalytic triad of Ser115, His278, and Asp248 and to remain thermally stable even after substitution. Its overall substrate specificity profile, divergent phylogenetic homology, and preliminary pathway analysis suggested potential biological functions for FTT0941c in diverse metabolic degradation pathways in F. tularensis., Highlights • FTT0941c is an unstudied virulence associated hydrolase from F. tularensis (74). • Classified as a bacterial HSL enzyme within a unique subclade of Francisella (85). • Broad substrate specificity for alkyl, unsaturated, tertiary, and cyclic esters (79). • Distinct substrate selectivity for α-cyclohexyl esters (54). • Proposed metabolic role in cyclohexyl and benzoate ester hydrolysis pathways (76).

Blackbox algorithms for linear algebra problems start with projection of the sequence of powers of a matrix to a sequence of vectors (Lanczos), a sequence of scalars (Wiedemann) or a sequence of smaller matrices (block methods). Such algorithms usually depend on the minimal polynomial of the resulting sequence being that of the given matrix. Here exact formulas are given for the probability that this occurs. They are based on the generalized Jordan normal form (direct sum of companion matrices of the elementary divisors) of the matrix. Sharp bounds follow from this for matrices of unknown elementary divisors. The bounds are valid for all finite field sizes and show that a small blocking factor can give high probability of success for all cardinalities and matrix dimensions., Comment: 19 pages. To be published in the Journal of Symbolic Computation, please cite as "Harrison, G., et al. Probabilistic analysis of Wiedemann's algorithm for minimal polynomial computation. J. Symb. Comput. (2015), http://dx.doi.org/10.1016/j.jsc.2015.06.005"

Federal housing policy reveals an unexpected political cycle of Republican innovation and Democratic appropriation. The political trajectory of rental housing vouchers since their inception reveals a partisan policy cycle. Vouchers were originally proposed as a Republican alternative to Democratic public housing construction and slowly emerged as a viable component of housing policy in the United States. In the mid-1990s, a shift occurred in which Democrats embraced vouchers and Republicans retreated from their innovation. This article suggests a partisanship model of policy making that both challenges and supplements conventional models of the policy process.

We determine the probability, structure dependent, that the block Wiedemann algorithm correctly computes leading invariant factors. This leads to a tight lower bound for the probability, structure independent. We show, using block size slightly larger than $r$, that the leading $r$ invariant factors are computed correctly with high probability over any field. Moreover, an algorithm is provided to compute the probability bound for a given matrix size and thus to select the block size needed to obtain the desired probability. The worst case probability bound is improved, post hoc, by incorporating the partial information about the invariant factors., 17 pages

Introduction. Triple negative breast cancer (TNBC) is very aggressive, has a higher metastatic rate than other breast cancer subtypes, and lacks traditional targetable factors. AMPK-activated protein kinase (AMPK) is an important energy regulator within the cell that also impacts cancer progression. AMPK's catalytic subunit is composed of α1 and α2 isoforms, but little is known about their individual roles in TNBC. The purpose of this study was to establish the specific function of each isoform in TNBC with respect to expression, cell proliferation, cell cycle progression, and metabolism. Methods. (i) Immunohistochemistry, immunofluorescence, and immunoblotting were used to determine the expression and localization of AMPKα1 and AMPKα2 in TNBC PDX samples or cell lines. (ii) To study the role of each isoform individually, TNBC cells were transfected with siRNA to NTC, AMPKα1, or AMPKα2 (50 nM) and were either harvested for immunoblotting or subseeded for cell cycle analysis, proliferation assays, or Seahorse analysis. Results. (i) AMPKα1 expression was localized in the cytoplasm of all 9 TNBC PDX cell lines, whereas AMPKα2 was expressed predominantly in the nucleus in 6 of the 9 of TNBC samples. IF analysis of MDA-MB-231 cells confirmed expression findings in the PDX cell lines with AMPKα1 expression noted in the cytoplasm and AMPKα2 expression in both the cytoplasm and nucleus. (ii) siRNA knockdown of AMPKα1 or AMPKα2 induced G1 cell cycle arrest and decreased proliferation of MDA-MB-231 cells. Moreover, knockdown of AMPKα1 decreased levels of cyclin D1 in MDA-MB-231, MDA-MB-468, and BT-20 cells. siRNA knockdown of AMPKα1, but not AMPKα2, led to decreased basal and compensatory glycolysis in MDA-MB-231 cells. Conclusions. Our findings indicate that both AMPKα1 and AMPKα2 can impact cell cycle progression and proliferation in TNBC; both isoforms promote progression through the cell cycle, thus supporting the proliferative capacity of TNBC. Importantly, AMPKα1 may also affect TNBC proliferation by increasing energy availability through glycolysis. Citation Format: Jeremy Johnson, Piotr Richahou, B. Mark Evers. AMPK alpha1 and AMPK alpha 2 control TNBC proliferation through cell cycle regulation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 93.