IceDust: Incremental and Eventual Computation of Derived Values in Persistent Object Graphs

Derived values are values calculated from base values. They can be expressed in object-oriented languages by means of getters calculating the derived value, and in relational or logic databases by means of (materialized) views. However, switching to a different calculation strategy (for example caching) in object-oriented programming requires invasive code changes, and the databases limit expressiveness by disallowing recursive aggregation. In this paper, we present IceDust, a data modeling language for expressing derived attribute values without committing to a calculation strategy. IceDust provides three strategies for calculating derived values in persistent object graphs: Calculate-on-Read, Calculate-on-Write, and Calculate-Eventually. We have developed a path-based abstract interpretation that provides static dependency analysis to generate code for these strategies. Benchmarks show that different strategies perform better in different scenarios. In addition we have conducted a case study that suggests that derived value calculations of systems used in practice can be expressed in IceDust

Safe use of proton pump inhibitors in patients with cirrhosis

Contains fulltext : 194399.pdf (publisher's version ) (Open Access

Shrimp aquaculture as a vehicle for Climate Compatible Development in Sri Lanka. The case of Puttalam Lagoon

At present, aquaculture of black tiger shrimp (Penaeus monodon) in the Puttalam district of Sri Lanka is unsustainable with more than 90% of the former shrimp ponds laying abandoned as a result of shrimp disease and improper management. Between 1992-1998, over 50% of the mangrove cover was removed in order to establish shrimp aquaculture. This severely affected the functioning of coastal ecosystems, reducing their provision of useful services and increasing coastal vulnerability to climate change. Changes in the hydrology and polluted residual matter make the soil unsuitable for other agricultural purposes without costly restoration. The root of the problem was inappropriate management and a focus on short term economic gains. Despite this previous failure, the national development plan, Mahinda Chinthana, now promotes aquaculture as an avenue for development. This will only be possible if aquaculture is regulated in a sustainable and well-managed manner, and does not increase local vulnerability to climate change effects. The current paper discusses the possible costs and benefits in applying the concept of Climate Compatible Development (CCD) to shrimp aquaculture in Puttalam, Sri Lanka. It suggests how the sector can support mitigation of Green House Gas (GHG) emissions and adaptation to climate change effects, whilst stimulating development that will also benefit rural societies. Mechanisms that could enable this change include subsidies, insurance and bank loans which will also facilitate investment by foreign private enterprises and subsequent export. The development of a specific aquaculture policy and master plan would facilitate the process further

Amphisbaena angustifrons (Amphisbaenidae) in the Sierras de Tandilia, Buenos Aires, Argentina

El género Amphisbaena comprende 102 especies, de las cuales 9 están presentes en la Argentina (Abdala et al., 2012; Montero, 2016; Uetz et al., 2023). En la provincia de Buenos Aires existen 3 especies: Amphisbaena angustifrons, Amphisbaena darwinii y Amphisbaena kingii (Montero, 1997, 2016).Las sierras de Tandilia se encuentran ubicadas en el centro de la provincia de Buenos Aires, cubriendo alrededor de 12,000 km2 de superficie (Fig. 1; Dalla Salda et al., 2006). En este sistema serrano solo se han registrado dos especies de Amphisbaenidae: Amphisbaena darwinii y Amphisbaena kingii (Vera et al., 2021). Tettamanti & Vera (2022) mencionan la probable presencia de Amphisbaena angustifrons en casi toda la provincia de Buenos Aires, incluyendo además las sierras de Tandilia (Fig. 1). Sin embargo, estos autores no mencionan localidades concretas ni material de referencia para dicho sistema serrano. En el presente trabajo, se confirma la presencia de Amphisbaena angustifrons en el sistema serrano de Tandilia sobre la base de ejemplares observados en el campo.Se colectaron dos ejemplares de anfisbénidos que fueron depositados en la Colección Herpetológica del Museo de La Plata (MLP R.). Los ejemplares, en ambos casos, presentaron las siguientes características diagnósticas, verificadas por Ricardo Montero: aspecto robusto; cuello marcado; ausencia de anillo autotómico caudal evidente; presencia de 4 escamas supralabiales; escamas uniformemente pigmentadas. El día 22 de septiembre de 2022 se halló un ejemplar de Amphisbaena angustifrons (Fig. 2, MLP R. 6838) bajo una piedra, en un ambiente de pastizal serrano, en la Reserva Natural Privada Paititi, localidad de Sierra de los Padres, Partido de General Pueyrredón, Buenos Aires (37.91098°S, 57.833258°O, WGS 84). Posteriormente, el 27 de octubre de 2022 se halló otro ejemplar (Fig. 3, MLP R. 6849) bajo piedra, en ambiente serrano, en la Reserva Natural Boca de la Sierra, Localidad de Pablo Acosta, Partido de Azul, Buenos Aires (37.054055°S, 59.732745°O; WGS 84).El registro más austral de esta especie que figura en Montero (1997; mencionada ahí como Amphisbaena a. angustrifrons) es la localidad de Claromecó. Sin embargo, Montero (2012) cuestiona la identificación de estos ejemplares y sugiere que pueden ser formas híbridas entre Amphisbaena angustifrons y A. plumbea, por lo que pone en duda la real identificación de los ejemplares de Claromecó (MACN 3388; 34372). Entonces, el límite austral de los ejemplares confirmados de Amphisbaena angustifrons (sensu Montero, 2012) parecía estar marcado por el paralelo 37, entre las localidades de Bonifacio al oeste (Gans, 1965) y Punta Médanos al este (Kacoliris et al., 2006). Los registros aquí presentados extienden la distribución confirmada de Amphisbaena angustifrons en casi un grado de latitud, a 157 km al sur de Punta Médanos. Además, representan hasta la fecha, los únicos registros en zonas serranas dentro de la provincia de Buenos Aires, y añaden una especie más a la lista de reptiles publicada por Vera et al. (2021) para el sistema serrano de Tandilia.Fil: Vera, David Gustavo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Di Pietro, Diego Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Rolón, Melisa Celia Jazmin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Harkes, M.. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Kacoliris, Federico Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Berkunsky, Igor. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Instituto Multidisciplinario de Ecosistemas y Desarrollo Sustentable; Argentin

Safe use of proton pump inhibitors in patients with cirrhosis

Aims: Proton pump inhibitors (PPIs) belong to the most frequently used drugs, also in patients with cirrhosis. PPIs are extensively metabolized by the liver, but practice guidance on prescribing in cirrhosis is lacking. We aim to develop practical guidance on the safe use of PPIs in patients with cirrhosis. Methods: A systematic literature search identified studies on the safety (i.e. adverse events) and pharmacokinetics of PPIs in cirrhotic patients. This evidence and data from the product information was reviewed by an expert panel who classified drugs as safe; no additional risks known; additional risks known; unsafe; or unknown. Guidance was aimed at the oral use of PPIs and categorized by the severity of cirrhosis, using the Child–Turcotte–Pugh (CTP) classification. Results: A total of 69 studies were included. Esomeprazole, omeprazole and rabeprazole were classified as having ‘no additional risks known’. A reduction in maximum dose of omeprazole and rabeprazole is recommended for CTP A and B patients. For patients with CTP C cirrhosis, the only PPI advised is esomeprazole at a maximum dosage of 20 mg per day. Pantoprazole and lansoprazole were classified as unsafe because of 4- to 8-fold increased exposure. The use of PPIs in cirrhotic patients has been associated with the development of infections and hepatic encephalopathy and should be carefully considered. Conclusions: We suggest using esomeprazole, omeprazole or rabeprazole in patients with CTP A or B cirrhosis and only esomeprazole in patients with CTP C. Pharmacokinetic changes are also important to consider when prescribing PPIs to vulnerable, cirrhotic patients

IHC-based Ki67 as response biomarker to tamoxifen in breast cancer window trials enrolling premenopausal women

Window studies are gaining traction to assess (molecular) changes in short timeframes. Decreased tumor cell positivity for the proliferation marker Ki67 is often used as a proxy for treatment response. Immunohistochemistry (IHC)-based Ki67 on tissue from neo-adjuvant trials was previously reported to be predictive for long-term response to endocrine therapy for breast cancer in postmenopausal women, but none of these trials enrolled premenopausal women. Nonetheless, the marker is being used on this subpopulation. We compared pathologist assessed IHC-based Ki67 in samples from pre- and postmenopausal women in a neo-adjuvant, endocrine therapy focused trial (NCT00738777), randomized between tamoxifen, anastrozole, or fulvestrant. These results were compared with (1) IHC-based Ki67 scoring by AI, (2) mitotic figures, (3) mRNA-based Ki67, (4) five independent gene expression signatures capturing proliferation, and (5) blood levels for tamoxifen and its metabolites as well as estradiol. Upon tamoxifen, IHC-based Ki67 levels were decreased in both pre- and postmenopausal breast cancer patients, which was confirmed using mRNA-based cell proliferation markers. The magnitude of decrease of Ki67 IHC was smaller in pre- versus postmenopausal women. We found a direct relationship between post-treatment estradiol levels and the magnitude of the Ki67 decrease in tumors. These data suggest IHC-based Ki67 may be an appropriate biomarker for tamoxifen response in premenopausal breast cancer patients, but anti-proliferative effect size depends on estradiol levels.</p

Anti-Epithelial Cell Adhesion Molecule Antibodies and the Detection of Circulating Normal-Like Breast Tumor Cells

Identification of specific subtypes of circulating tumor cells in peripheral blood of cancer patients can provide information about the biology of metastasis and improve patient management. However, to be effective, the method used to identify circulating tumor cells must detect all tumor cell types. We investigated whether the five subtypes of human breast cancer cells that have been defined by global gene expression profiling—normal-like, basal, HER2-positive, and luminal A and B—were identified by CellSearch, a US Food and Drug Administration–approved test that uses antibodies against the cell surface–expressed epithelial cell adhesion molecule (EpCAM) to isolate circulating tumor cells. We used global gene expression profiling to determine the subtypes of a well-defined panel of 34 human breast cancer cell lines (15 luminal, nine normal-like, five basal-like, and five Her2-positive). We mixed 50-150 cells from 10 of these cell lines with 7.5 mL of blood from a single healthy human donor, and the mixtures were subjected to the CellSearch test to isolate the breast cancer cells. We found that the CellSearch isolation method, which uses EpCAM on the surface of circulating tumor cells for cell isolation, did not recognize, in particular, normal-like breast cancer cells, which in general have aggressive features. New tests that include antibodies that specifically recognize normal-like breast tumor cells but not cells of hematopoietic origin are needed

Rock fracture grouting with microbially induced carbonate precipitation

Microbially induced carbonate precipitation has been proposed for soil stabilization, soil strengthening and permeability reduction as an alternative to traditional cement and chemical grouts. In this paper we evaluate the grouting of fine aperture rock fractures with calcium carbonate, precipitated through urea hydrolysis, by the bacteria Sporosarcina pasteurii. Calcium carbonate was precipitated within a small-scale and a near field-scale (3.1 m2) artificial fracture consisting of a rough rock lower surfaces and clear polycarbonate upper surfaces. The spatial distribution of the calcium carbonate precipitation was imaged using time-lapse photography and the influence on flow pathways revealed from tracer transport imaging. In the large-scale experiment, hydraulic aperture was reduced from 276 μm to 22 μm, corresponding to a transmissivity reduction of 1.71x10-5 m2/s to 8.75x10-9 m2/s, over a period of 12 days under constantly flowing conditions. With a modified injection strategy a similar three orders of magnitude reduction in transmissivity was achieved over a period of three days. Calcium carbonate precipitated over the entire artificial fracture with strong adhesion to both upper and lower surfaces and precipitation was controlled to prevent clogging of the injection well by manipulating the injection fluid velocity. These experiments demonstrate that microbially induced carbonate precipitation can successfully be used to grout a fracture under constantly flowing conditions and may be a viable alternative to cement based grouts when a high level of hydraulic sealing is required and chemical grouts when a more durable grout is required