Ward's Hierarchical Clustering Method: Clustering Criterion and Agglomerative Algorithm

The Ward error sum of squares hierarchical clustering method has been very widely used since its first description by Ward in a 1963 publication. It has also been generalized in various ways. However there are different interpretations in the literature and there are different implementations of the Ward agglomerative algorithm in commonly used software systems, including differing expressions of the agglomerative criterion. Our survey work and case studies will be useful for all those involved in developing software for data analysis using Ward's hierarchical clustering method.Comment: 20 pages, 21 citations, 4 figure

In vitro expansion of U87-MG human glioblastoma cells under hypoxic conditions affects glucose metabolism and subsequent in vivo growth

Hypoxia is a characteristic feature of solid tumors leading to the over expression of hypoxia-inducible factor (HIF)-1α protein and therefore to a specific cellular behavior. However, even though the oxygen tension in tumors is low (<5 %), most of the cell lines used in cancer studies are grown under 21 % oxygen tension. This work focuses on the impact of oxygen conditions during in vitro cell culture on glucose metabolism using 1-13C-glucose. Growing U87-MG glioma cells under hypoxic conditions leads to a two- to threefold reduction of labeled glutamine and an accumulation of fructose. However, under both hypoxic and normoxic conditions, glucose is used for de novo synthesis of pyrimidine since the 13C label is found both in the uracil and ribose moieties. Labeling of the ribose ring demonstrates that U87-MG glioma cells use the reversible branch of the non-oxidative pentose phosphate pathway. Interestingly, stereotactic implantation of U87-MG cells grown under normoxia or mild hypoxia within the striatum of nude mice led to differential growth; the cells grown under hypoxia retaining an imprint of the oxygen adaptation as their development is then slowed down

Impact of freshwater on a subarctic coastal ecosystem under seasonal sea ice (southeastern Hudson Bay, Canada) : 3. Feeding success of marine fish larvae

We monitored the feeding success (percent feeding incidence at length and mean feeding ratio at length) of Arctic cod (#Boreogadus saida) and sand lance (#Ammodytes sp. larvae in relation to prey density, light, temperature and potential predator density under the ice cover of southeastern Hudson Bay in the spring of 1988, 1989 and 1990. Both prey density and light limited larval fish feeding. The relationship between feeding success and actual food availability (nauplii density x irradiance) was adequately described by an Ivlev function which explained 64 and 76% of the variance in Arctic cod and sand lance feeding success respectively. By affecting both prey density and irradiance, the thickness of the Great Whale River plume (as defined by the depth of the 25 isohaline) was the main determinant of prey availability. Arctic cod and sand lance larvae stopped feeding when the depth of the 25 isohaline exceeded 9 m. Limitation of feeding success attributable to freshwater inputs occurred exclusively in 1988, the only time when the depth of the 25 isohaline exceeded the 9 m threshold. The close dependence of larval fish feeding success on the timing of the freshet and plume dynamics suggests a direct link between climate and survival of Arctic cod and sand lance larvae. The actual impact of climate fluctuations and/or hydro-electric developments on recruitment will depend on the fraction of the larval dispersal area of the two species that is affected by river plumes. (Résumé d'auteur

Animacy effects on the processing of intransitive verbs:An eye-tracking study

<p>This paper tested an assumption of the gradient model of split intransitivity put forward by Sorace (“Split Intransitivity Hierarchy” (SIH), 2000, 2004), namely that agentivity is a fundamental feature for unergatives but not for unaccusatives. According to this hypothesis, the animacy of the verb’s argument should affect the processing of unergative verbs to a greater extent than unaccusative verbs. By using eye-tracking methodology we monitored the online processing and integration costs of the animacy of the verb’s argument in intransitive verbs. We observed that inanimate subjects caused longer reading times only for unergative verbs, whereas the animacy of the verb’s argument did not influence the pattern of results for unaccusatives. In addition, the unergative verb data directly support the existence of gradient effects on the processing of the subject argument.</p

Atmospheric stilling offsets the benefits from reduced nutrient loading in a large shallow lake

As part of a global phenomenon, a 30% decrease in average wind speed since 1996 in southern Estonia together with more frequent easterly winds resulted in 47% decrease in bottom shear stress in the large (270 km2), shallow (mean depth 2.8 m), and eutrophic Lake Võrtsjärv. Following a peak in eutrophication pressure in the 1970s–80s, the concentrations of total nutrients were declining. Nonmetric Multidimensional Scaling (NMDS) ordination of a 54-year phytoplankton community composition time-series (1964–2017) revealed three distinct periods with breaking points coinciding with changes in wind and/or water level. Contrary to expectations, we detected no decrease in optically active substances that could be related to wind stilling, whereas phytoplankton biomass showed an increasing trend despite reduced nutrient levels. Here we show how opening of the “light niche,” caused by declining amount of suspended sediments, was capitalized and filled by the light-limited phytoplankton community. We suggest that wind stilling is another global factor, complementary to climate warming that counteracts eutrophication mitigation in lakes and may provide a challenge to assessment of the lake ecological status.Main financial support for EMU: European Union’s Horizon 2020 research and innovation programme Under the Marie Skłodowska-Curie Action, Innovative Training Networks, European Joint Doctorates.Project name, acronym and grant number: Management of climatic extreme events in lakes and reservoirs for the protection of ecosystem services, MANTEL, grant agreement No 722518.Publication date and, if applicable, length of embargo period: Published as Early View on 07.10.2019, no embargo period.Main financial support for EMU: European Union’s Horizon 2020 research and innovation programme Under the Marie Skłodowska-Curie Action, Innovative Training Networks, European Joint Doctorate

Environmental constraint of intraguild predation: Inorganic turbidity modulates omnivory in fairy shrimps

Omnivory is widespread in food webs, with an important stabilising effect. The strength of omnivorous trophic interactions may change considerably with changes in the local environment. Shallow temporary waters are often characterised by high levels of inorganic turbidity that may directly limit the food uptake of filter-feeding organisms, but there is little evidence on how it might affect omnivorous species. Anostracans are key species of temporary waters and recent evidence suggests that these organisms are omnivorous consumers of both phyto- and zooplankton. Using Branchinecta orientalis as a model species, our aim was to test how turbidity affects the feeding of an omnivorous anostracan. To do this, we used short-term feeding experiments and stable isotope analyses, with animals collected from soda pans in eastern Austria. In the feeding experiments, algae and zooplankton were offered as food either separately or in combination. The prey type treatments were crossed with turbidity levels in a factorial design. There was a pronounced decrease in the ingested algal biomass with increasing turbidity. Conversely, ingestion rates on zooplankton were less affected by turbidity. Stable isotope analyses from field material supported our experimental results by showing a positive relationship of the trophic position of anostracans and the trophic niche of the communities with turbidity. Our results show that turbidity modulates the intraguild trophic relationship between anostracans and their prey by shifting the diet of anostracans from more herbivorous in transparent to more carnivorous in turbid waters. Thus, inorganic turbidity might also have a community-shaping role in plankton communities of temporary waters through altering trophic relationships

Revisiting the university front

dc.subject: Postdemocracy / Public function of the university / Governance / Knowledge society / research university / Managerialism / Academic audit / Quality contro

Human Galectins Induce Conversion of Dermal Fibroblasts into Myofibroblasts and Production of Extracellular Matrix: Potential Application in Tissue Engineering and Wound Repair

Members of the galectin family of endogenous lectins are potent adhesion/growth-regulatory effectors. Their multi-functionality opens possibilities for their use in bioapplications. We studied whether human galectins induce the conversion of human dermal fibroblasts into myofibroblasts (MFBs) and the production of a bioactive extracellular matrix scaffold is suitable for cell culture. Testing a panel of galectins of all three subgroups, including natural and engineered variants, we detected activity for the proto-type galectin-1 and galectin-7, the chimera-type galectin-3 and the tandem-repeat-type galectin-4. The activity of galectin-1 required the integrity of the carbohydrate recognition domain. It was independent of the presence of TGF-beta 1, but it yielded an additive effect. The resulting MFBs, relevant, for example, for tumor progression, generated a matrix scaffold rich in fibronectin and galectin-1 that supported keratinocyte culture without feeder cells. Of note, keratinocytes cultured on this substratum presented a stem-like cell phenotype with small size and keratin-19 expression. In vivo in rats, galectin-1 had a positive effect on skin wound closure 21 days after surgery. In conclusion, we describe the differential potential of certain human galectins to induce the conversion of dermal fibroblasts into MFBs and the generation of a bioactive cell culture substratum. Copyright (C) 2011 S. Karger AG, Base