Variable selection in penalized model-based clustering via regularization on grouped parameters

Summary .   Penalized model-based clustering has been proposed for high-dimensional but small sample-sized data, such as arising from genomic studies; in particular, it can be used for variable selection. A new regularization scheme is proposed to group together multiple parameters of the same variable across clusters, which is shown both analytically and numerically to be more effective than the conventional L ₁ penalty for variable selection. In addition, we develop a strategy to combine this grouping scheme with grouping structured variables. Simulation studies and applications to microarray gene expression data for cancer subtype discovery demonstrate the advantage of the new proposal over several existing approaches.     

Assessing mortality changes from size‐frequency curves

The relationship between the instantaneous mortality rate ( Z ) and the instantaneous change in length‐frequency distribution of organisms per unit of animal size (μ _L ) takes the following form: Z  = μ _L k ( L _∞ −  L ) +  k , where k and L _∞ are coefficients of the von Bertalanffy equation, and L is organism size (length). Z and μ_L change coherently when they are measured for a specific size or age class. Therefore, observations of μ _L can provide information on the relative changes in mortality. This is useful when no precise information about animal growth is available and growth curve is assumed to be invariable. This method was tested on a heavily exploited population of St Peter's fish (mango tilapia) Sarotherodon galilaeus in Lake Kinneret, Israel, where large fluctuations in the size structure of the catch have occurred over the past few years. Analysis of the changes in the length‐frequency distributions showed that the changes in μ _L over multiple years estimated for fully exploited fish reflected the respective changes in Z .     

Selectivity of diamond, square and hexagonal mesh codends for Atlantic horse mackerel Trachurus trachurus, European hake Merluccius merluccius, and greater forkbeard Phycis blennoides in the eastern Mediterranean

Knowledge on selectivity is considered essential for an adequate management of the trawl fishery. This paper compares the selectivity of conventionally used codends of 44 mm diamond mesh, 40 mm square, and hexagonal mesh for Atlantic horse mackerel, European hake and greater forkbeard in the eastern Mediterranean. Data were collected using the covered codend method and analyzed using the logistic equation with the maximum likelihood method. Mean selection curves were analyzed and compared using the between-haul variations model. The mean L ₅₀ v alues of diamond, square and hexagonal mesh codends are 14.7, 15.9 and 17.1 cm total length (TL) for horse mackerel, 10.4, 14.4 and 11.0 cm TL for hake and 12.2, 15.8 and 12.7 cm TL for greater forkbeard, respectively. For horse mackerel, the differences among the codends are statistically significant (P   <   0.05); however, the L ₅₀ values for all three meshes are higher than the minimum landing size (13 cm TL). For hake and greater forkbeard, the L ₅₀ value for the square mesh codend is significantly different from the values for diamond and hexagonal meshes (P   <   0.01), whereas there is no significant difference between diamond and hexagonal meshes (P   >   0.05). Regardless of the mesh shape, L ₅₀ values were substantially lower than the minimum landing size or size at first maturity for hake and greater forkbeard. To enable more effective solutions, research on species-selective trawls is required for the Mediterranean demersal trawl fishery.     

Borrelia burgdorferi BBB07 interaction with integrin alpha3beta1 stimulates production of pro-inflammatory mediators in primary human chondrocytes

Borrelia burgdorferi , the causative agent of Lyme disease, activates multiple signalling pathways leading to induction of pro-inflammatory mediators at sites of inflammation. Binding of B. burgdorferi to integrin α₃β₁ on human chondrocytes activates signalling leading to release of several pro-inflammatory mediators, but the B. burgdorferi protein that binds integrin α₃β₁ and elicits this response has remained unknown. A search of the B. burgdorferi genome for a canonical integrin binding motif, the RGD (Arg–Gly–Asp) tripeptide, revealed several candidate ligands for integrins. In this study we show that one of these candidates, BBB07, binds to integrin α₃β₁ and inhibits attachment of intact B. burgdorferi to the same integrin. BBB07 is expressed during murine infection as demonstrated by recognition by infected mouse sera. Recombinant purified BBB07 induces pro-inflammatory mediators in primary human chondrocyte cells by interaction with integrin α₃β₁. This interaction is specific, as P66, another integrin ligand of B. burgdorferi , does not activate signalling through α₃β₁. In summary, we have identified a B. burgdorferi protein, BBB07, that interacts with integrin α₃β₁ and stimulates production of pro-inflammatory mediators in primary human chondrocyte cells.     

Inheritance of Anthracnose Resistance in the Common Bean Differential Cultivar G 2333 and Identification of a New Molecular Marker Linked to the Co-42 gene

The inheritance of anthracnose resistance of the common bean ( Phaseolus vulgaris L.) differential cultivar G 2333 to Colletotrichum lindemuthianum races 73 and 89 was studied in crosses with the susceptible cultivar Rudá. The segregation ratios of 15 : 1 in the F₂ and 3 : 1 in the backcrosses to Rudá indicate that for each of the races tested there are two independent resistance loci in G 2333. A random amplified polymorphic DNA (RAPD) molecular marker (OPH18_1200C) linked in resistance to race 73 was identified in a BC₃F_2:3 population derived from crosses between Rudá and G 2333. A RAPD molecular marker OPAS13_950C, previously identified as linked to gene Co-4² , was also amplified in this population. Co-segregation analyses showed that these two markers are located at 5.6 (OPH18_1200C) and 11.2 (OPAS13_950C) cM of the Co-4² gene. These markers were not present in BC₁F_2:3 plants resistant to race 89 indicating that this population carries a different resistance gene. DNA amplification of BC₁F_2:3 plants with RAPD molecular marker OPAB_450C, previously identified as linked to gene Co-5 , indicated that this gene is present in this population.     

Regional differences in length at sexual maturity for female blue whales based on recovered Soviet whaling data

New blue whale ovarian corpora data from illegal Soviet catches in the Southern Hemisphere and northern Indian Ocean were recovered from the original logbooks. Catches north of 52°S were assumed to be pygmy blue whales ( Balaenoptera musculus brevicauda , n = 1,272); those south of 56°S were assumed to be Antarctic (true) blue whales ( B. m. intermedia , n = 153). Three probable Antarctic blue whales north of 52°S were excluded. Lengths at which 50% and 95% of females become sexually mature ( L ₅₀ and L ₉₅) were estimated from a Bayesian logistic model. These estimates are more precise than previous Japanese estimates because Soviet catches below the legal minimum of 70 ft (21.3 m) were 32 times greater. For pygmy blue whales L ₅₀ was 19.2 m (95% interval 19.1–19.3 m) and L ₉₅ was 20.5 m (95% interval 20.4–20.7 m). Antarctic L ₅₀ (23.4 m, 95% interval 22.9–23.9 m) was much longer than L ₅₀ for pygmy blue whale regions (18.4–19.9 m). The median L ₅₀ for the northern Indian Ocean was 0.5–0.6 m shorter than for pygmy blue whales from other regions; although statistically significant, these small length differences provide little support for northern Indian Ocean blue whales being a separate subspecies, B. m. indica .     

NIDA522131, a new radioligand for imaging extrathalamic nicotinic acetylcholine receptors: in vitro and in vivo evaluation

A novel radioligand, 6-chloro-3-((2-( S )-azetidinyl)methoxy)-5-(2-fluoropyridin-4-yl)pyridine (NIDA522131), for imaging extrathalamic nicotinic acetylcholine receptors (nAChRs) was characterized in vitro and in vivo using positron emission tomography. The K_d and T_1/2 of dissociation of NIDA522131 binding measured at 37°C in vitro were 4.9 ± 0.4 pmol/L and 81 ± 5 min, respectively. The patterns of radioactivity distribution in monkey brain in vivo was similar to that of 2-[¹⁸F]fluoro-3-(2( S )-azetidinylmethoxy)pyridine (2FA), a radioligand that has been successfully used in humans, and matched the α₄β₂* nAChRs distribution. Comparison between [¹⁸F]NIDA522131 and 2FA demonstrated better in vivo binding properties of the new radioligand and substantially greater radioactivity accumulation in brain. Consistent with [¹⁸F]NIDA522131 elevated affinity for nAChRs and its increased lipophilicity, both, the total and non-displaceable distribution volumes were substantially higher than those of 2FA. Estimated binding potential values in different brain regions, characterizing the specificity of receptor binding, were 3–4 fold higher for [¹⁸F]NIDA522131 than those of 2FA. Pharmacological evaluation in mice demonstrated a toxicity that was comparable to 2FA and is in agreement with a 2300 fold higher affinity at α₄β₂* versus α₃β₄* nAChRs. These results suggest that [¹⁸F]NIDA522131 is a promising positron emission tomography radioligand for studying extrathalamic nAChR in humans.     

Relationship between opercular girth, maximum girth and total length of fishes caught in gillnets in the estuarine and lower river sections of Shatt al-Arab River (Basrah Province, Iraq)

In fisheries, the two morphological parameters of opercular and maximum girth are related to the effectivity of capture methods in gilled and wedged fish, respectively. The present work investigates the relationship between opercular ( G _ope) and maximum girths ( G _max) to total length ( L _t) for 10 fish species captured from Shatt al-Arab River, Basrah, Iraq. Data were collected October 2005 to December 2006. Cyprinids were the best represented family with six species; engraulids, silurids, heteropneustids and mugilids were each represented by one species. G _ope and G _max were found to increase linearly with total length of all species, all r ² values being greater than 0.73 and statistically significant (P < 0.01). When G _ope and G _max for all species were plotted against total length, two groups were identified ( G 1, G 2), corresponding to general girth-length relationships: (a) G 1 = −0.252 + 0.424 L _t and G 2 = −0.262  +  0.600 L _t for opercular girth and, (b) G 1 = 1.538 + 0.419 L _t and G 2  =  1.538  +  0.696 L _t for maximum girth. These groups correspond to different body shapes of fishes: G 1-round and G 2-compressed. These relationships have implications when using length data and mesh size to determine size selectivity of gill nets.     

Swimming performance, oxygen consumption and excess post-exercise oxygen consumption in adult transgenic and ocean-ranched coho salmon

Routine oxygen consumption ( M o ₂) was 35% higher in 1 day starved and 21% higher in 4 day starved adult transgenic coho salmon Oncorhynchus kisutch relative to end of migration ocean-ranched coho salmon. Critical swimming speed ( U _crit) and M o ₂ at U _crit ( M o _2max) were significantly lower in 4 day starved transgenic coho salmon (1·25 BL s⁻¹; 8·79 mg O₂ kg⁻¹ min⁻¹) compared to ocean-ranched coho salmon (1·60 BL s⁻¹; 9·87 mg O₂ kg⁻¹ min⁻¹). Transgenic fish swam energetically less efficiently than ocean-ranched fish, as indicated by a poorer swimming economy at U _crit ( M o _2max     ). Although M o _2max was lower in transgenic coho salmon, the excess post-exercise oxygen consumption (EPOC) measured during the first 20 min of recovery was significantly larger in transgenic coho salmon (44·1 mg O₂ kg⁻¹) compared with ocean-ranched coho salmon (34·2 mg O₂ kg⁻¹), which had a faster rate of recovery.     

Zn(II)- and Cu(II)-induced non-fibrillar aggregates of amyloid-β (1–42) peptide are transformed to amyloid fibrils, both spontaneously and under the influence of metal chelators

Aggregation of amyloid-β (Aβ) peptides is a central phenomenon in Alzheimer's disease. Zn(II) and Cu(II) have profound effects on Aβ aggregation; however, their impact on amyloidogenesis is unclear. Here we show that Zn(II) and Cu(II) inhibit Aβ₄₂ fibrillization and initiate formation of non-fibrillar Aβ₄₂ aggregates, and that the inhibitory effect of Zn(II) (IC₅₀ = 1.8 μmol/L) is three times stronger than that of Cu(II). Medium and high-affinity metal chelators including metallothioneins prevented metal-induced Aβ₄₂ aggregation. Moreover, their addition to preformed aggregates initiated fast Aβ₄₂ fibrillization. Upon prolonged incubation the metal-induced aggregates also transformed spontaneously into fibrils, that appear to represent the most stable state of Aβ₄₂. H13A and H14A mutations in Aβ₄₂ reduced the inhibitory effect of metal ions, whereas an H6A mutation had no significant impact. We suggest that metal binding by H13 and H14 prevents the formation of a cross-β core structure within region 10–23 of the amyloid fibril. Cu(II)-Aβ₄₂ aggregates were neurotoxic to neurons in vitro only in the presence of ascorbate, whereas monomers and Zn(II)-Aβ₄₂ aggregates were non-toxic. Disturbed metal homeostasis in the vicinity of zinc-enriched neurons might pre-dispose formation of metal-induced Aβ aggregates, subsequent fibrillization of which can lead to amyloid formation. The molecular background underlying metal-chelating therapies for Alzheimer's disease is discussed in this light.     

Three parameters comprehensively describe the temperature response of respiratory oxygen reduction

Using an exponential model that relies on Arrhenius kinetics, we explored Type I, Type II and dynamic (e.g. declining Q ₁₀ with increasing temperature) responses of respiration to temperature. Our Arrhenius model provides three parameters: R _REF (the base of the exponential model, nmol g⁻¹ s⁻¹), E ₀ (the overall activation energy of oxygen reduction that dominates its temperature sensitivity, kJ mol⁻¹) and δ (that describes dynamic responses of E ₀ to measurement temperature, 10³ K²). Two parameters, E ₀ and δ , are tightly linked. Increases in overall activation energy at a reference temperature were inversely related to changes in δ . At an E ₀ of ca. 45 kJ mol⁻¹, δ approached zero, and respiratory temperature response was strictly Arrhenius-like. Physiologically, these observations suggest that as contributions of AOX to combined oxygen reduction increase, E ₀( REF ) decreases because of different temperature sensitivities for V _max, and δ increases because of different temperature sensitivities for K _1/2 of AOX and COX. The balance between COX and AOX activity helps regulate plant metabolism by adjusting the demand for ATP to that for reducing power and carbon skeleton intermediates. Our approach enables determination of respiratory capacity in vivo and opens a path to development of process-based models of plant respiration.     

Age, growth and mortality of the Mediterranean amberjack Seriola dumerili (Risso 1810) from the south-eastern Adriatic Sea

The age, growth and mortality of the Mediterranean amberjack Seriola dumerili (Risso 1810) were determined in 298 specimens collected in the south-eastern Adriatic Sea (Donji Molunat Bay) from 17 May to 26 June 1997. The total length ranged from 32.0 to 160.0 cm and weight from 0.5 to 46.5 kg. Ten age classes, ranging from 1° to 10° years were defined by scale readings. Mean total length and weight-at-age data were used to estimate the growth parameters of the von Bertalanffy equation: L _∞=174.6 cm, K =0.190, t ₀=–0.314; W _∞=79.01 kg, K =0.139 and t ₀=–0.746. The length–weight relationship was estimated at: W =0.000123 ×  L ^2.847. The overall sex ratio was 1 : 1.06 in favour of males. Total ( Z ) and natural ( M ) mortality were found to be 0.41 years⁻¹ and 0.30 years^–1, respectively. The exploitation ratio ( E =0.27) indicates that the fishing pressure on the Mediterranean amberjack was low in the investigated region.     

Response of plankton communities to whole-lake Ca(OH)2 and CaCO3 additions in eutrophic hardwater lakes

1. The impact of whole-lake lime (slaked lime, Ca(OH)₂, and/or calcite, CaCO₃) addition on plankton communities was evaluated in eutrophic hardwater lakes on the North American Boreal Plain.
2. Two lakes received a single treatment of lime (Ca(OH)₂ at 74 or 107 mg L^–1), two lakes received multiple treatments with Ca(OH)₂ and/or CaCO₃ (5–78 mg L^–1), and four lakes were untreated and served as reference systems.
3. Over the long-term (> 1 year), phytoplankton biomass was reduced in multiple-dose lakes, but not in single-dose lakes. Cyanobacteria typically dominated the algal community in the years before, during and after lime treatment in both single- and multiple-dose lakes.
4. In the single-dose lakes, randomized intervention analysis showed no significant change in the biomass of zooplankton after lime addition.     

Irreversible blockade of sigma-1 receptors by haloperidol and its metabolites in guinea pig brain and SH-SY5Y human neuroblastoma cells

We evaluated the effect of haloperidol (HP) and its metabolites on [³H](+)-pentazocine binding to σ₁ receptors in SH-SY5Y human neuroblastoma cells and guinea pig brain P₁, P₂ and P₃ subcellular fractions. Three days after a single i.p. injection in guinea pigs of HP (but not of other σ₁ antagonists or (−)-sulpiride), [³H](+)-pentazocine binding to brain membranes was markedly decreased. Recovery of σ₁ receptor density to steady state after HP-induced inactivation required more than 30 days. HP-metabolite II (reduced HP, 4-(4-chlorophenyl)-α-(4-fluorophenyl)-4-hydroxy-1-piperidinebutanol), but not HP-metabolite I (4-(4-chlorophenyl)-4-hydroxypiperidine), irreversibly blocked σ₁ receptors in guinea pig brain homogenate and P₂ fraction in vitro . We found similar results in SH-SY5Y cells, which suggests that this process may also take place in humans. HP irreversibly inactivated σ₁ receptors when it was incubated with brain homogenate and SH-SY5Y cells, but not when incubated with P₂ fraction membranes, which suggests that HP is metabolized to inactivate σ₁ receptors. Menadione, an inhibitor of the ketone reductase activity that leads to the production of HP-metabolite II, completely prevented HP-induced inactivation of σ₁ receptors in brain homogenates. These results suggest that HP may irreversibly inactivate σ₁ receptors in guinea pig and human cells, probably after metabolism to reduced HP.     

Age, growth and reproduction of the barrelfish Hyperoglyphe perciformis (Mitchill) in the western North Atlantic

Otoliths ( n = 847) and gonads ( n = 817) were collected from barrelfish Hyperoglyphe perciformis that were captured by commercial fishermen in the waters off South Carolina and Georgia in 1995, 1997 and 2001–2006. Of the otoliths collected, 97% were aged successfully, and specimens sampled ranged from 5 to 85 years, with a median age of 12 years. The von Bertalanffy growth parameters yielded the equation: L_t = 857·8{1 − e^{−0·0985[ t −(−8·95)]}}, where L_t is fork length ( L _F) at time t . Through histological examination, 94% of the gonads assessed were assigned to a sex and reproductive class. Females spawned from September to May with a peak from November to January. Males spawned year round, but had a peak from September to April. The sex ratio (M:F) for this population was 1:1·34. The smallest mature female was 605 mm L _F and the youngest immature female was 697 mm L _F. Estimates of L _F and age at 50% maturity ( L ₅₀ and A ₅₀) for females were 660 mm L _F (95% CI = 633–667 mm L _F) and 6·08 years (95% CI = 3·50–7·27 years), respectively. The youngest mature male was 575 mm L _F and the oldest immature male was 762 mm L _F, and no estimates of L ₅₀ or A ₅₀ were made for males. It was determined that barrelfish exhibit the typical characteristics of long life span, slow growth and high age at maturity seen in other deepwater fishes, and that care should be taken to manage this species accordingly.     

Shiga toxin-producing Escherichia coli and atypical enteropathogenic Escherichia coli strains isolated from healthy sheep of different populations in São Paulo, Brazil

Aims:  Sheep are important carriers of Shiga toxin-producing Escherichia coli (STEC) in several countries. However, there are a few reports about ovine STEC in American continent.
Methods and Results:  About 86 E. coli strains previously isolated from 172 healthy sheep from different farms were studied. PCR was used for detection of stx ₁, stx ₂, eae, ehxA and saa genes and for the identification of intimin subtypes. Restriction fragment length polymorphism (RFLP)–PCR was performed to investigate the variants of stx ₁ and stx ₂, and the flagellar antigen ( fli C) genes in nonmotile isolates. Five isolates were eae ⁺ and stx ⁻, and belonged to serotypes O128:H2/β-intimin (2), O145:H2/γ, O153:H7/β and O178:H7/ε. Eighty-one STEC isolates were recovered, and the stx genotypes identified were stx _1c stx _2d-O118 (46·9%), stx _1c (27·2%), stx _2d-O118 (23·4%), and stx _1c stx _2dOX3a (2·5%). Pulsed-field gel electrophoresis (PFGE) revealed 27 profiles among 53 STEC and atypical enteropathogenic Escherichia coli (EPEC) isolates.
Conclusions:  This study demonstrated that healthy sheep in São Paulo, Brazil, can be carriers of potential human pathogenic STEC and atypical EPEC.
Significance and Impact of the Study:  As some of the STEC serotypes presently found have been involved with haemolytic uraemic syndrome (HUS) in other countries, the important role of sheep as sources of STEC infection in our settings should not be disregarded.     

Salinity effects on water relations in Lycopersicon esculentum and its wild salt-tolerant relative species L. pennellii

Cultivated tomato Lycopersicon esculentum (L.) Mill. cv. P-73 and its wild salt tolerant relative L. pennellii (Correll) D'Arcy accession PE-47, were grown during spring-summer 1989 under unheated plastic greenhouse conditions. Plants were submitted to two different salt treatments using 0 and 140 mM NaCI irrigation water. In both tomato species, salinity caused a proportionally larger reduction in leaf area than in leaf weight and, in L. esculentum , a proportionally larger decrease in stem weight than in leaf weight. Daily variations in leaf water potential (Ψ₁) were fundamentally due to changes in the evaporative demand of the atmosphere. Reductions in Ψ₁ due to salinity were consistent only in L. esculentum . In all the conditions studied, leaf turgor was maintained. Leaf conductance (g₁)was higher in L. esculentum than in L. pennellii .Salinity induced a clear reduction in g₁ levels in L. esculentum whereas, in L. pennellii , this reduction was noted only in May. In both species the Ψ^o_s (leaf osmotic potential at full turgor) levels were reduced by salinity. The bulk modulus of elasticity (E) and relative water content at turgor loss point (RWC_tlp) were not affected by salinity. The RWC_tlp values in L. pennellii seem to be controlled by E values.     

A comparative study of blood oxygen transport in turbot and sea bass: effect of chronic hypoxia

A comparative study of blood oxygen binding and carrying capacities of turbot Scophthalmus maximus and sea bass Dicentrarchus labrax , two fish species differing in their demand for oxygen, was carried out under three levels of chronic hypoxia ( P o ₂ = 93, 65 and 40 mmHg) for 40 days. Blood O₂ affinity in normoxia was moderately high in both species ( P ₅₀ was c . 12–13 mmHg at pH 7·7). The Bohr factor was significantly lower in turbot (−0·52) than in sea bass (−0·85). In both species, blood O₂ affinity was not significantly affected by oxygen depletion whatever its level and duration. In turbot, however, P ₅₀ appeared to slightly decrease at the two more severe levels of hypoxia. In both species, blood O₂ carrying capacity was not affected by hypoxia and remained twice as high in sea bass than in turbot.