A decline in fish catches and the size of Oreochromis niloticus in Lake Wamala (Uganda) following human exploitation

The fishery of Lake Wamala has declined since the lake was stocked in 1956 and opened to fishing during the 1960s. Surveys were conducted on the lake during 1975/78 and 1988/92 to investigate the causes of declining fish catches. The lake produced an average of 4000 - 6000 tonnes of fish annually from 1960s through 1970s. Total fish catches decreased from a maximum of 7100 tonnes in 1967 to less than 500 tonnes by 1990s. Catch rates decreased from about 8 kg in the 1960s to less than 1 kg per net per night by 1975. During the 1970s the catch was dominated by Oreochromis niloticus (67%) followed by Clarias gariepinus (17%), and Protopterus aethiopicus (15.1 %). By 1990s the proportion of O. niloticus had decreased to 45.1% while that of P. aethiopicus had increased to 37.6%. These changes seem to have been caused by overfishing resulting from increased fishing effort from the recommended 250 to about 1000 boats and the additional increase in effort through driving fish into the nets by beating water. The maximum size of O. niloticus in the fishery decreased from 32 cm total length in 1975/78 to 22 cm in 1988/92 while the size at first maturity decreased from about 21 cm to 14 cm during the period. This has been concurrent with a shift in the mesh size of gillnet used from 127 mm (5") in 1960s to 64 mm by 1990s. Environmental changes, especially in lake level in 1980, may also have affected the fishery.

Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development.

Exploitation of linguistic ambiguity in Polish and English jokes

English & Polish jokes based on linguistic ambiguity are constrasted. Linguistic ambiguity results from a multiplicity of semantic interpretations motivated by structural pattern. The meanings can be "translated" either by variations of the corresponding minimal strings or by specifying the type & extent of modification needed between the two interpretations. C. F. Hockett's (1972) translatability notion that a joke is linguistic if it cannot readily be translated into other languages without losing its humor is used to interpret some cross-linguistic jokes. It is claimed that additional intralinguistic criteria are needed to classify jokes. By using a syntactic representation, the humor can be explained & compared cross-linguistically. Since the mapping of semantic values onto lexical units is highly language specific, translatability is much less frequent with lexical ambiguity. Similarly, phonological jokes are not usually translatable. Pragmatic ambiguity can be translated on the basis of H. P. Grice's (1975) cooperative principle of conversation that calls for discourse interpretations. If the distinction between linguistic & nonlinguistic jokes is based on translatability, pragmatic jokes must be excluded from the classification. Because of their universality, pragmatic jokes should be included into the linguistic classification by going beyond the translatability criteria & using intralinguistic features to describe them.

Transformation from natural (thermal contraction) to anthropogenic (resource exploitation) depressions in the Krotoszyn-Koźmin-Raszków area (Polish Lowland)

An exceptional concentration of almost identical depressions exist near the small towns of Krotoszyn, Koźmin and Raszków (southern Wielkopolska). Their origin is, however, different from that of the typical post glacial-relief: they are Man-made enlarged thermal-contraction structures that developed at the very end of the Middle Polish (Warthian) glaciation and during the North Polish (Weichselian) glaciation, most probably under periglacial conditions.

The dynamic efficiency costs of common-pool resource exploitation

We conduct the first empirical investigation of common-pool resource users' dynamic and strategic behavior at the micro level using real-world data. Fishermen's strategies in a fully dynamic game account for latent resource dynamics and other players' actions, revealing the profit structure of the fishery. We compare the fishermen's actual and socially optimal exploitation paths under a time-specific vessel allocation policy and find a sizable dynamic externality. Individual fishermen respond to other users by exerting effort above the optimal level early in the season. Congestion is costly instantaneously but is beneficial in the long run because it partially offsets dynamic inefficiencies.

Exploitation of symbolic information in interprocedural dependence analysis

The requirement for a very accurate dependence analysis to underpin software tools to aid the generation of efficient parallel implementations of scalar code is argued. The current status of dependence analysis is shown to be inadequate for the generation of efficient parallel code, causing too many conservative assumptions to be made. This paper summarises the limitations of conventional dependence analysis techniques, and then describes a series of extensions which enable the production of a much more accurate dependence graph. The extensions include analysis of symbolic variables, the development of a symbolic inequality disproof algorithm and its exploitation in a symbolic Banerjee inequality test; the use of inference engine proofs; the exploitation of exact dependence and dependence pre-domination attributes; interprocedural array analysis; conditional variable definition tracing; integer array tracing and division calculations. Analysis case studies on typical numerical code is shown to reduce the total dependencies estimated from conventional analysis by up to 50%. The techniques described in this paper have been embedded within a suite of tools, CAPTools, which combines analysis with user knowledge to produce efficient parallel implementations of numerical mesh based codes.