Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in free amino acid, peptide‐N, sugar and pyrazine concentration during cocoa fermentation

The free amino acids, peptide-N, reducing sugars (the flavour precursors in cocoa) and pyrazine profiles of mix hybrid cocoa beans fermented in a rotary drum reactor were monitored over a period of 6 days. As fermentation progressed, the acidic free amino acid concentration decreased significantly (P<0·05) by 15%, whereas total, hydrophobic and other free amino acids increased significantly by 148, 280 and 127%, respectively. In terms of hydrophobic/acidic/other free amino acids ratio, the unfermented cocoa beans contained 30%:18%: 52%, whereas those of fermented beans contained 46%: 6%: 48%. Concentrations of peptide-N and total reducing sugars were significantly (P<0·05) increased by 55 and 208%, respectively during fermentation; however, those of sucrose and total sugars decreased significantly (P<0·05) by 89% and 75%, respectively. The unfermented cocoa beans contained no pyrazine; however during fermentation, the 2-methyl-, 2,5-dimethyl-, 2,6-dimethyl-, 2,3-dimethyl-, trimethyl- and tetramethylpyrazine were formed. The two principle pyrazines were tetramethyl- (2099·30 μg kg−1) and trimethylpyrazine (692·00 μg kg−1).
Comparison of bacterial production in sediments, epiphyton and the pelagic zone of a lowland river

SUMMARY 1. The microbial metabolism of organic matter in rivers has received little study compared with that of small streams. Therefore, we investigated the rate and location of bacterial production in a sixth-order lowland river (Spree, Germany). To estimate the contribution of various habitats (sediments, epiphyton, and the pelagic zone) to total bacterial production, we quantified the contribution of these habitats to areal production by bacteria. 2. Large areas of the river bottom were characterized by loose and shifting sands of relatively homogenous particle size distribution. Aquatic macrophytes grew on 40% of the river bottom. Leaf areas of 2.8 m 2 m )2 river bottom were found in a 6.6 km river stretch. 3. The epiphyton supported a bacterial production of 5‐58 ng C cm )2 h )1 . Bacterial production in the pelagic zone was 0.9‐3.9 l gCL )1 h )1 , and abundance was 4.0‐7.8 · 10 9 cells L )1 . Bacterial production in the uppermost 2 cm of sediments ranged from 1 to 8 l gCc m )3 h )1 , and abundance from 0.84 to 6.7 · 10 9 cells cm )3 . Bacteria were larger and more active in sediments than in the pelagic zone. 4. In spite of relatively low macrophyte abundance, areal production by bacteria in the pelagic zone was only slightly higher than in the epiphyton. Bacterial biomass in the uppermost 2 cm of sediments exceeded pelagic biomass by factors of 6‐22, and sedimentary bacterial production was 17‐35 times higher than in the overlying water column. 5. On a square meter basis, total bacterial production in the Spree was clearly higher than primary productivity. Thus, the lowland river Spree is a heterotrophic system with benthic processes dominating. Therefore, sedimentary and epiphytic bacterial productivity form important components of ecosystem carbon metabolism in rivers and shallow lakes. 6. The sediments are focal sites of microbial degradation of organic carbon in a sandbottomed lowland river. The presence of a lowland river section within a river continuum probably greatly changes the geochemical fluxes within the river network. This implies that current concepts of longitudinal biogeochemical relationships within river systems have to be revised.
Gap structure, disturbance and regeneration in a primeval Picea abies forest

We investigated patterns of disturbance and recov- ery in Fiby urskog, a primeval spruce (Picea abies) forest, situated south of the border between the Boreo-nemoral and Boreal regions in East-central Sweden. The main types of disturbances are storm damage, fungal infection and insect attacks. The response of the different tree species varied and the mode of tree-fall depended on the different combinations of disturbance agents. The DBH distributions of gap creators and gap-border trees were almost the same. There was a high age diversity (100-240 yr) among the fallen trees. We concluded that all canopy trees (DBH > 20 cm) had the same probability of being felled by storms, irrespective of their age and DBH. According to an estimate along transect lines, gaps made up 31% of the spruce forest area. Individual gap sizes ranged from 9 m2 to 360 m2, but 83% of the gaps were 12.0 m/s; all trees fell in the direction of the wind. However, when we consult the 30-yr record (1959-1989) of the mean hourly wind speed > 12.0 m/s, it is clear that the pattern of storm-directions does not match the pattern of orientation of fallen logs. The present disturbance regime and the predominance of small gaps were more favourable for the regeneration of Picea abies than of light-demanding tree species. In one large, 2900 m2 gap, not crossed by the transects, all the major tree species had established within 7 yr, suggesting that classical succes- sion in the sense of complete species replacement or 'relay floristics' did not occur. Our observations seem rather to fit
Quality of processing tomato (Lycoperscion esculentum) fruit from four bloom dates in relation to optimal harvest timing

Abstract Two related processing tomato (Lycoperscion esculentum (L.)) fruit quality issues were investigated: (1) the difficulty of representative sampling to test quality, given the wide range of fruit age at harvest time; and (2) identifying the best time to harvest for maximum quality. In a Hastings, New Zealand, trial we tagged large samples of opening flowers on each of four dates about a week apart, and at harvest we compared quality of fruit homogenate (puree). There was a distinct pattern of higher quality in the latest‐set (youngest) fruit in terms of total solids, °Brix (soluble solids), titratable acidity, and Bostwick flow (gross viscosity). These data are indirect evidence that fruit would have higher quality if harvested at an earlier stage of maturity than currently practised. Average skin and puree colour were both slightly less red in the fruit from the last bloom date. However, these fruit were much more variable in colour than the earliest‐set (oldest) fruit, raising the concern that fr.
REVIEW ■ : Physical Injury of Neurons: Important Roles for Sodium and Chloride Ions

There is growing evidence that ions other than Ca2+ play important roles in the deterioration of neuronal elements in both gray and white matter after physical injury. This review features information gathered with a tissue culture model of dendrite transection regarding the contributions of Na+ and CI- to ultrastructural damage and neuronal death. This information and the results of other in vitro investigations of physical and ischemic/excitotoxic injuries indicate that elevation of internal Na+ is an early event that may contribute significantly to neuronal injury through effects on Na+-driven transport mechanisms. Proposed deleterious consequences include cytoplasmic acidification, reduced mitochondrial energy production, and elevation of intracellular Ca2+ and extracellular excitatory amino acids to toxic levels. Prevention of Na+ entry into neurons after injury has been found to limit ultrastructural damage, prevent death, and preserve electrophysiological function. Although the role of CI- in neuronal injury is less well defined, there is also evidence that elevation of intracellular CI- contributes to structural damage, particularly to the smooth endoplasmic reticulum. In terventions that limit Na+- and CI--mediated damage to injured neurons may have utility in neurosurgery and as acute phase treatments for nervous system trauma and other pathological states. NEURO SCIENTIST 3:89-101, 1997
Sublittoral soft bottom assemblages within a Marine Protected Area of the northern Alboran Sea

The composition and structure of sublittoral faunal assemblages inhabiting soft bottoms (15–72 m depth) within the Marine Protected Area ‘Acantilados y Fondos Marinos de Calahonda-Castell de Ferro’ in southern Spain (North Alboran Sea, Mediterranean) have been studied in relation to sediment and water column variables. Three assemblages were identified and corresponded to mixed bottom, unstable bottom and coastal detritic bottom assemblages, based on Pérès & Picard's (1964) benthic classification. A total of 14,318 individuals were collected and 218 species identified, molluscs being the best represented group (141 species). Species richness displayed significant differences with depth and transect, with the highest values observed in the medium to very fine sand and muddy bottoms with bioclasts located at the shallowest sampling stations. The presence of some rare and poorly known invertebrates that are scarce in other areas of the Mediterranean Sea is remarkable, such as the crustacean decapods Bythocaris cosmetops and Pagurus mbizi, Atlantic species with no records in the Mediterranean Sea, and the bathyal molluscs Poromya granulata and Alvania testae, collected at shallow depths. The spatial distribution of faunal assemblages was mainly related to depth and percentage of gravel and clay according to the canonical correspondence analysis. The geographic location of the area, the heterogeneity of soft bottoms and the presence of upwellings in the area may favour the high biodiversity found in the studied soft bottoms. This study increases the scarce knowledge of the circalittoral fauna of sedimentary habitats of the Alboran Sea, providing a baseline for the management of this interesting SCI and for the EU Marine Strategy Framework Directive.
Lead toxicity and the hypothalamic-pituitary-testicular axis.

Environmental exposure to toxic levels of lead (Pb) occurs in a number of industries with potential adverse effects on the reproductive capacity of exposed men. Clinical and animal studies indicate that abnormalities of spermatogenesis result from toxic lead exposure, but eventual histopathologic alterations involved have not been identified. To explore putative abnormalities in the reproductive gonadotropic axis following lead intoxication, experimental animals when exposed to low levels of lead, 65 days old animals were treated with distilled water containing 0, 0 mg (control), 10 mg lead (Pb)/Kg/day and 15 mg lead (Pb)/Kg/day intraperitoneally for 20 days. At the end of treatment, the animals were sacrificed and the blood collected for luteinizing hormone (LH) and testosterone assays. The testis was processed for histological analysis. The results showed a high serum concentration of LH and testosterone in lead-treated animals compared to controls. Histological examination of testis showed deformities in testicular morphology of lead intoxicated animals with gross damage within the somniferous tubules. A strong correlation was established between LH and testosterone suggesting an alteration in the endocrine components of the gonadotropic axis. Histological examination of pituitary gland showed some degenerative changes in endocrine cells of lead group. Changes in LH and testosterone levels suggest that Pb exposure during the critical time of sexual differentiation induces reproductive axis abnormalities in adulthood. In conclusion, lead has a gonadotoxic effect by decreasing LH and testosterone levels and damaging the testis seminiferous tubules. Catalase activity was significantly reduced in the lead group following 65 days of exposure which possibly indicates that lead might had other mechanisms of action, such as increasing oxidative damage.
Interação de fragmentos florestais com agroecossistemas adjacentes de café e pastagem: respostas das comunidades de formigas (Hymenoptera, Formicidae)

The responses of the ant community to environmental change, from forest fragment to agroecosystems (coffee or pasture) were evaluated in the south of the state of Minas Gerais, Brazil. In this paper we analized the interactions between forest and the two most typical agroecosystem from southest Brazil: sun-growing coffee plantation and introduced pasture. We sampled the ant community from five of each agroecosystems, inside the adjacent forest fragment, and on the edge between them. In each site we removed the litter from fifteen 1m2 plots and extracted the ants using a Winkler extractor. A total of 165 ant species, distributed in 48 genera and 10 subfamilies were recorded. The coffee plantation presented the lowest abundance and estimated species richness. The causes of the changes observed among the areas are discussed.
Role of physical refugia: implications from a mass sponge die-off in a lobster nursery in Florida

In 1991 and 1992, cyanobacterial blooms depleted sponges, the primary refuge of juvenile Caribbean spiny lobsters, in ~20% of the nursery in the Florida Keys, USA. Long-term data from the affected middle Keys were used to study the impact of sponge loss, juvenile abundance, recruitment and shelter use. A manipulative experiment (1991–93) involved artificial shelters on 27 ~0.5-h sites. Conditions on 19 sites over the affected ~ 500 km 2 area were compared before and after the blooms. The entire nursery (~10,000 km2) was surveyed to estimate the impact of the disturbance on total juvenile recruitment. Refuge and lobster abundances declined and the pattern of shelter use changed on previously sponge- rich sites without alternative shelter (solution holes, coral heads, cement blocks, etc.). Although sponge loss often locally reduced juvenile abundance, the juvenile lobster population overall declined by ~5%. The availability of alternative, previously underused shelter (solution holes, coral heads, etc.) in the affected region, continued production in the larger unaffected nursery region, and high postlarval supply that fortuitously coincided with sponge loss all offset a stronger effect. However, postlarval supply is unlikely to remain high until the sponges repopulate the middle Keys (10+ years), so a major factor ameliorating the effect of sponge loss on lobster recruitment may disappear.
Role of CrkII in Fcγ Receptor-mediated Phagocytosis*

Phagocytosis of IgG-opsonized pathogens by Fcγ receptors requires extensive remodeling of the actin cytoskeleton, a process regulated by the small GTPase Rac. Vav was thought to be the guanine nucleotide exchange factor responsible for the activation of Rac, but recent evidence indicates that Fcγ receptor-mediated phagocytosis is unaffected in macrophages lacking all three isoforms of Vav. We therefore tested whether another GEF, DOCK180, participates in Fcγ receptor-initiated phagocytosis. DOCK180 associates with the adaptor protein Crk, which mediates recruitment of the GEF to sites of tyrosine phosphorylation. CrkII and DOCK180 were found to accumulate at the phagocytic cup. Knockdown of Crk or DOCK180 in murine macrophages using small interfering RNA inhibited phagocytosis of IgG-opsonized particles. Moreover, transfection of dominant negative CrkII prevented both recruitment of DOCK180 and the activation of Rac at the phagocytic cup. This is the first report of a role for either Crk or DOCK180 in Fcγ receptor-mediated phagocytosis. The Crk-DOCK180 complex is involved in the clearance of apoptotic cells, which unlike the ingestion of IgG-opsonized particles, is an anti-inflammatory process. The finding that CrkII-DOCK180 is also responsible, at least in part, for the effects of Fcγ receptors implies that additional, parallel pathways must account for the associated pro-inflammatory effect.
The structure of the cell wall in lignifield collenchyma of Eryngium sp. (Umbelliferae)

In Eryngium vesiculosum and E. rostratum, the leaf collenchyma is characterized by the development of a lignified secondary wall in the final stages of cell differentiation. The collenchyma wall is rich in pectic substances which are distributed uniformly. In the outer limiting region of the collenchyma wall the microfibril orientation is random and this structure is considered to be the wall formed at cell division. The collenchyma wall consists of six to eight layers in which the microfibrils are alternately transversely and longitudinally oriented. Each layer consists of a number of lamellae of microfibrils. In the secondary lignified wall the cellulose microfibrils are arranged helically, the direction of their orientation making an angle of 40-45° to the cell axis. Excised leaf segments showed greatest elongation in solutions of glucose and 3-indoleacetic acid, when the collenchyma walls were thin, and no elongation occurred in segments in which secondary wall formation had commenced. In radial sections layers of transversely oriented microfibrils could not be seen distant from the lumen although discontinuities in wall texture were apparent. Layers of transversely oriented microfibrils could be seen adjacent to the lumen. It is suggested that reorientation of layers of initially transversely oriented microfibrils takes place during elongation of the cells.
Forest Soil Chemistry and Mesofauna 20 Years After an Amelioration Fertilization

Abstract Soil chemical properties and soil mesofauna composition were assessed at a forest site in northern Austria, where 20 years earlier an amelioration treatment had been performed. The site had been treated with limestone, a high P slag, and ammonium nitrate to replace the poorly growing pine (Pinus sylvestris) forest with a Norway spruce (Picea abies) stand. This treatment was at that time a common means for the amelioration of nutrient‐poor forest soils with recalcitrant forest floor layers. After treatment, a dense cover of a nitrophilic stinging nettle (Urtica dioica) developed. Most likely, the site had been over‐fertilized, and inadvertently, an experiment with extreme N enrichment had been conducted. The abundance of collembolans increased, and dominance structure shifted from Isotomiella minor, Lipothrix lubbocki, and Isotoma notabilis at fertilizer treatment to Friesea mirabilis, Isotomiella minor, and Sphaeridia pumilis in the control, but the abundance of soil mesofauna generally decreased in the fertilizer treatment. Fertilization reduced the mass of the litter layer from 7.6 to 2.4 kg/m2. The total carbon pool in the soil was reduced due to reduction of the litter layer. However, the content of soil organic matter in the upper mineral soil was significantly increased. A part of the applied and mineralized nitrogen had been lost from the soil, but N retention in the upper mineral soil was still considerable. Soil pH and the base saturation were sustainably increased. Carbon losses upon mineralization of the litter layer were not offset by the increase in C content of the mineral soil. Presently, the C pool in the soil of the fertilized treatment is lower than in the control. However, the overall nutrient enrichment of the soil may facilitate C sequestration in the fertilized site in the future.
Factors determining farmers' decision on highly pathogenic avian influenza vaccination at the small poultry farms in Western Java.

Vaccination of highly pathogenic avian influenza (HPAI) is one of the control measures in poultry farm. There are several factors determining farmer's decision on the implementation of this vaccination. They are the type of poultry, the experience of farmers in the poultry farm, the pattern of poultry farm management, the role of poultry farm on household income, the scale of poultry farm, the mortality rate of poultry, the cost of medication, and the case of HPAI. The analysis result showed that two factors namely type of poultry and the role of poultry farm on household income had significant influence on farmer's decision to implement HPAI vaccination. In fact, the implementation of HPAI vaccination would be more effective in independent farms since the risk of this disease was single-handedly borne by farmers. Apart from that, the implementation of HPAI vaccination would also be more effective in farms that had never been infected by HPAI, particularly layer farms. Overall, HPAI vaccination would be more effectively implemented through supporting biosecurity measures in poultry farms.
Early Endosomal Retention of Murine Cytomegalovirus m06 Protein

Murine cytomegalovirus (MCMV) encodes several genes which products interact with MHC class I molecules (MHC-I) in the secretory pathway to evade antigen presentation. The product of MCMV-m06 gene associates with nascent MHC-I proteins and redirects them into lysosomes for degradation. This report will demonstrate that MCMV-m06 protein is retained in perinuclear early endosomes together with internalized MHC-I molecules. Since we were not able to capture the MCMV-m06 protein on the cell surface, our data suggests that the MCMV-m06 protein is transported from the Golgi into early endosomal intermediates prior to their maturation into multivesicular endosomes and lysosomes. In NIH 3T3 cells with the transfected m06 gene, the endosomal localization of the m06 protein was not observed, suggesting that another MCMV function remodels the route of m06 trafficking from the Golgi towards late endosomes. (doi: 10.5562
Estimating the genic and chromosomal components of reproductive isolation within and between subspecies of the grasshopper Caledia captiva

Previous studies have indicated that the Moreton and Torresian subspecies of the grasshopper Caledia captiva are distinguished by a series of pericentric rearrangements involving 8 of the 12 members of the genome. In addition, they show distinctive allozyme patterns with. The two taxa meet in southeast Queensland where they form a narrow hybrid zone. Experimental hybridization between the taxa reveals that the F2 generation is totally inviable and backcrosses are 53–64% inviable.A major component of inviability is correlated with the redistribution of chiasmata which occurs in F1 heterozygotes and leads to the production of novel recombinant chromosomes. However, the relative contributions of the effects of chromosomal heterozygosity versus those effects because of genic divergence could not be distinguished. The discovery that the metacentric Moreton subspecies represents the northerly limit of a continuous chromosomal cline has resolved this problem. At the southern end of the cline (Lakes Entrance), th.