Miracle-dz/UniFAR-FTUs huggingface dataset:
Microchip Technology for High-Throughput Cancer Pathology

Novel methodologies for the molecular detection of human cancer have been advanced using microfabricated capillary electrophoresis devices as analytical platforms. These techniques enable direct and quantitative characterization of the unique biomolecular signature inherent to individual cancers and, through reduction of sample usage and analysis time, further the goal of routine genetic screening in the clinical setting.The majority of the work detailed here applies a comparative sequencing technique known as Polymorphism Ratio Sequencing (PRS) to cancer detection with a focus on mutations in the mitochondrial DNA (mtDNA). First, a rigorous optimization of sample processing protocols was undertaken to improve PRS separations on a 96-lane microfabricated sequencing device. A modification of electrokinetic injection conditions has increased capillary success rates to nearly 100%, while the introduction of dynamic coatings and automated data processing has decreased analysis time by 75%. These optimized conditions were validated through a complete mtDNA sequence comparison of two unrelated individuals, uncovering 44 confirmed germline variations, eight of which were undetected in early PRS experiments. Further analysis of paired tumor and blood mtDNA from six individuals with lung and bladder cancer revealed three heteroplasmic somatic variants while uncovering 18 erroneous mutations identified in previous microarray analysis.To establish potential clinical relevance, PRS was independently applied to a mitochondrial D-loop analysis of fourteen bladder cancer patients. A total of 21 somatic variations were identified, with seven patients harboring at least one mutation. Fifteen of these mutations were heteroplasmic, often occurring at low levels or problematic base locations inaccessible to conventional technologies. Where available, matched urine mtDNA was found to contain abundant populations of the mutant genotype, establishing the potential use of bodily fluids for noninvasive screening.Finally, an integrated microdevice capable of PRS extension followed by inline purification and electrophoretic separation is presented. This device makes use of dual on-chip thermal cyclers and orthogonal Sanger extension primers to generate a complete set of PRS fragments prior to oligonucleotide-based capture and injection. Further integration with upstream sample processing steps, including single-cell capture and PCR amplification, is proposed, providing the framework for real-time mutant quantitation in microbiopsies, ultimately enabling full clinical integration.
Increasing the perceived predation risk changes parental care in female but not in male Great Tits Parus major

In birds, little is known about how the presence of predators alters parental food distribution decisions among nestlings. We found that experimentally increasing perceived predation risk changed parental care in female but not in male Great Tits Parus major. Females fed the lightest and average nestlings at similar rates under control conditions when predation risk was not manipulated but ignored the lightest nestling under increased perceived predation risk. Moreover, females reduced the duration of nest visits greatly after encountering a model predator, suggesting that the perception of predators may facilitate brood reduction mechanisms.
Potato (Solanum tuberosum L.) variety development through hybridization: a new era in Bangladesh

Systematic research on potato variety development has been in practice in Bangladesh since 1960, but until 2012, not a single variety was developed in this country through conventional breeding method, mainly due to the short day climatic factors which are not congenial for potato plants to flower. Due to the diversified efforts, TCRC scientists were able to make a breakthrough to overcome the climatic barriers. Flowering was induced in HYV potatoes and produce berries in the year 2000. After hybridization and continuous selection, five hybrid clones were placed in a RYT in 2010-11 from a batch of 502 kg F 1 seedling tubers produced from 45 gram hybrid seeds of 2001-02. Based on the performances of SYT, AYT, RYT and on-farm trials, three varieties were released by the NSB in 2012 as BARI Alu-35, BARI Alu-36, and BARI Alu-37. Their genotype numbers are 4.5W, 4.26R, and 4.40, their mean yields were 38.36, 33.82, and 34.88 t/ha in AYT, 44.01, 41.84, and 40.58 t/ha in RYT, and 38.87, 38.52, and 37.53 t/ha in on-farm trials, respectively. DOI: http://dx.doi. org/10.3329/bjar.v38i4. 19019 Bangladesh J. Agril. Res. 38(4): 637-646, December 2013
Factors influencing habitat shifts of age-0 yellow perch in southwestern Lake Michigan

Abstract Yellow perch Perca flavescens exhibit a consistent early life history across most lakes, with hatching in spring followed by a brief pelagic phase that ends with an ontogenetic shift to benthic habitat. This shift occurs with consistent timing and at consistent sizes in most freshwater systems. In Lake Michigan, however, the pelagic phase is prolonged and age-0 yellow perch undergo the transition to benthic habitat at variable sizes, the reasons for which are unknown. We investigated whether prey resources, diet preferences, and physical environment affected the habitat shift of pelagic, age-0 yellow perch. The shift to nearshore benthic habitat between 1998 and 2005 was strongly correlated with the occurrence of onshore wind events, a surrogate for transport by onshore currents. The timing of this habitat shift was not strongly related to prey resources. Abiotic factors structured the habitat shifts of age-0 yellow perch in Lake Michigan, a pattern atypical of freshwater systems but consistent w.
North Atlantic Oscillation and spring bloom phytoplankton composition in the English Channel

The spring phytoplankton composition has been investigated at a 50 m deep station off Plymouth in the English Channel for 6 years (1993–1999). The percentage of diatoms during the spring bloom was significantly correlated with the North Atlantic Oscillation index. A similar relationship between phytoplankton and North Atlantic Oscillation has also been found in a Swedish lake, suggesting a possible link between atmospheric forcing and phytoplankton composition.
Laboratory evaluation of the anticoagulants coumatetralyl and brodifacoum against Rattus argentiventer in Peninsular Malaysia 1

Abstract In laboratory toxicity tests using individually‐caged rice field rats, Rattus argentiventer (Robinson & Klossl, complete mortality occurred when the rats were fed on broken rice/corn oil bait containing 0.0375% coumatetralyl for four days. Equivalent kills were obtained when rats we're fed 0.002% and 0.005% brodifacoum for one day. Both compounds were more toxic than warfarin at 0.025%. Choice tests showed that 0.001% and 0.0005% brodifacoum were as acceptable as 0.025% warfarin, but higher concentrations and 0.005% and 0.0375% coumatetralyl were poorly accepted. The potential advantages of coumatetralyl and brodifacoum over other rodenticides for the control of R. argentiventer in rice fields in Malaysia are discussed.
Does a multi‐plant diet benefit a polyphagous herbivore? A case study with Bemisia tabaci

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a highly polyphagous herbivore. This research was conducted to compare the development of B. tabaci reared in a multi‐plant treatment (polyculture) with those in single‐plant treatments (monocultures). Adult B. tabaci females fed on a mixture of tomato, cabbage, cotton, cucumber, and kidney bean survived longer and laid more eggs than those fed exclusively on one of these plant species. Egg numbers per plant laid in the polyculture treatment were positively correlated with those laid on the same plant species in the monoculture treatments, and egg numbers per plant laid on tomato, cotton, and cucumber in the polyculture were significantly higher than those laid on the same plants in the monocultures. Concentrations of total protein and trehalose in B. tabaci were not significantly different after 7 days of feeding in the respective treatments, but activities of superoxide dismutases (SOD) and alkaline phosphatase (AKP) of B. tabaci in polyculture were lower than those in monoculture. Conversely, activities of trehalase, sucrase, and amylase in B. tabaci kept in polyculture were higher than those of insects from the monoculture. In each of the monoculture treatments, there was a negative correlation between AKP in B. tabaci and oviposition, and also between AKP and amylase. SOD and sucrase activities in B. tabaci were positively correlated with polyphenol oxidase (PPO) and peroxidase (POD) activities in plants. In the plants damaged by whiteflies in the polyculture treatment, activities of SOD in cucumber, PPO in cotton and kidney bean, and POD in tomato and cucumber were lower than those in the monoculture treatments, whereas SOD in cabbage and catalase (CAT) in tomato in the polyculture treatment were higher than those in the monoculture treatments.
Genetic relationships of eight species of pacific tunas (Teleostei:Scombridae) inferred from allozyme analysis

A phylogenetic analysis of eight species of Pacific tunas was made after examining allozyme variation at 23 muscle and liver enzymes encoded by 35 loci. The eight species of tuna were: Thunnus alalunga, albacore; T. obesus, bigeye; T. thynnus orientalis, northern bluefin; T. maccoyii, southern bluefin; T. albacares, yellowfin; Auxis thazard, frigate; Euthynnus affiizii kawakawa; Katsuwonus pelamis, skipjack. All species except the northern bluefin were also examined for variation at three eye-specific loci. The average heterozygosity per locus ranged from 0.038 (frigate) to 0.070 (bigeye). Genetic relationships were examined on the basis of the 35 loci screened in all species. Genetic identities among the five Thunnus species were high, averaging 0.864 and ranging from 0.788 to 0.923. Whereas the albacore appeared to be the most divergent of the Thunnus species (mean identity to other Thunnus species of 0.825, range 0.788-0.452), there was little differentiation between yellowfin, southern bluefin and northern bluefin tunas (mean identity 0.905, range 0.892-0.923), and phylogenetic analyses failed to resolve the branch order among the Thunnus species. The non-Thunnus tunas were quite divergent both from one another and from Thunnus species (mean identity 0.358, range 0.280-0.606). Diagnostic allozyme loci were identified, allowing the discrimination of all species.
Plant Sociology

The trend of ecological thought in Europe has always differed somewhat from that which is at the time in vogue in America. It is peculiarly important, therefore, that American ecologists keep as close an understanding as possible of what is going on across the water. For this purpose the little volume by BRAUN-BLANQUET' is most admirable. His citation of literature is extensive, and extends right up to the date of publication. The very active Scandinavian and Russian ecologists are freely quoted, and much American research is reviewed. The book is a detailed summary of research methods, in fact, together with a critical evaluation of each proposal, and much sound philosophizing. The introductory page points out the difference between studies of the individual organism and studies of communities. Choosing for this volume the second viewpoint, plant sociology is defined as the study of all the phenomena that have to do with the life of plants in social units. Section I discusses commensalism very briefly, and competition at length. Section II, the remainder of the book, presents in order the five principal problems of plant sociology: (i) organization or structure of communities; (2) synecologv, the relation of communities to one another and to the rest of the environment; (3) syngenetics, the origin and decline of plant communities; (4) synchorology, the occurrence and distribution of communities; (5) classification of communities (systematics). The first topic (organization) stands today at the focus of phytosociologic activities. The structure of the community "is the indispensable foundation for an unbiased treatment" of all the related problems. And it is this section that is most needed in American thought and practice. A difficulty arises in finding English equivalents for the terms Assoziation, Einzelbestand, Subassoziation, Fazies, Assoziationsfragment, Siedlung, Vegetationsfleck, Verein, Synusie, and Formation. It is indeed apparent that formation, association, society, as proposed by CLEMENTS and by LIVINGSTON and SHREVE, do not exactly correspond with the categories used by European botanists. It is to be hoped that a clear definition of terms may be decided upon at the forthcoming Cambridge conference. The characteristics of a community are considered under the following heads:
Dynamics of an Increasing Lake Trout Population in Lake Pend Oreille, Idaho

Abstract To quantify movement and abundance of lake trout Salvelinus namaycush in Lake Pend Oreille, Idaho, large trap nets were fished during two periods (30 September 2003–31 March 2004 and 10 September–15 December 2005) and gill nets were fished from 12 February to 6 April 2006. Trap-net catch rates and recapture rates of previously marked lake trout suggested that sampling locations along the eastern shore were associated with either lake trout foraging or spawning aggregations in both years. Abundance of mostly mature lake trout that were vulnerable to trap-netting in autumn increased from 6,000 in 2003 to 11,000 in 2005, whereas total abundance of immature and mature lake trout increased from 12,000 in 2003 (based on trap-net size selectivity) to 36,000 in 2005 (based on gill-net recaptures). The increase in abundance of all immature and mature lake trout estimated by mark–recapture in 1999, 2003, and 2005 was well described by an exponential growth model (intrinsic rate of population change r = 0.4.
Competition for Space, Disturbance, and the Structure of a Benthic Stream Community

Interspecific competition for space limits the distribution and abundance of many ben- thic insects on stones in a western Montana stream. The sessile caddisfly larva Leucotrichia pictipes is territorial and aggressively eliminates conspecifics and other species from its foraging territories. Territoriality produces an intraspecific pattern of regular spacing and negative spatial associations between Leucotrichia and several other sessile insects: Parargyractis confusalis, Rheotanytarsus sp. and Eukiefferiella sp. Experimental removals of Leucotrichia resulted in higher densities of other sessile species and several mobile insects, including Baetis, Glossosoma, and Simulium. These insects show broad microhabitat overlap with Leucotrichia; competition with Leucotrichia limits their dis- tributions and abundances within otherwise suitable microhabitats. Leucotrichia is the only species that monopolizes large areas of space. Physical disturbances interrupt the formation of competitive monopolies by Leucotrichia. During seasonal reduced flows, Leucotrichia is eliminated from stones and boulders in shallow water. Greater densities of a short-lived sessile species with multiple annual generations occupy this ephemeral spatial resource. On permanently submerged stones, Leucotrichia competitively affects a large part of the benthic fauna. On small stones that overturn with higher frequencies during flooding, Leucotrichia densities are reduced and species' abundances are highly equitable. Large, more stable substrates with greater densities of Leucotrichia are characterized by lower species evenness.
Superoxide dismutase and catalase activities in apple fruit during ripening and post‐harvest and with special reference to ethylene

Oxidative stress is involved in many biological systems, among which are fruit ripening and senescence. Free radicals play an important role in senescence and ageing processes. Plants have evolved antioxidative strategies in which superoxide dismutase (SOD, EC 1.15.1.1) and catalase (CAT, EC 1.11.1.6) are the most efficient antioxidant enzymes, influencing patterns of fruit ripening. Variations in total SOD and CAT activities were determined at regular intervals during ripening and senescence in on-tree and cold-stored apple fruits of the cultivars Fuji and Golden Delicious. In all fruits, internal ethylene concentration was also measured. The results suggest that the onset of ripening, signalled by ethylene burst, is closely related to SOD and CAT activities. In on-tree fruits the climacteric peak in ethylene was associated with the peaks of SOD and CAT activity in both cultivars. Quite different results were obtained in cold-stored fruits: Ethylene concentration increased in both cultivars during the storage. CAT activity doubled in both cultivars. SOD activity decreased in Golden Delicious and peaked in Fuji.
Some population characteristics of the Lion Panthera Leo in the Kalahari Gemsbok National Park

Two methods of estimating the number of lions in the Kalahari Gemsbok National Park, Republic of South Africa, are described; the first gives a minimum figure (113) and the second a more realistic one (140). Data are presented on sex and age ratios and pride composition. The factors contributing to the low density are briefly discussed and some management practices in connection with lions trespassing out of the Park are suggested.
The spatial aggregation of organic farming in England and its underlying environmental correlates

Summary 1 Given the current debate on the global food crisis, conservation in Europe is expected to shift from maximizing biodiversity at the expense of yield to conserving biodiversity under food production constraints. Organic farming is potentially of great importance for environmentally sustainable farming. Understanding the distribution of organic farms and the environmental, social and cultural correlates is necessary to predict the way in which this may change over time. 2 We collated data from 30 variables describing the topography, climate, soils, farm size/type, human population characteristics and farm business in the English agricultural landscape. Factor analysis reduced these variables to six orthogonal axes, which describe the suitability of land for arable farming, the degree of ruralization (distance to urban centres and population density), the farm size and type, the soil hydrology and texture, and the amount of woodland (forestry). 3 An analysis of the distribution of organic farms showed that they are spatially aggregated at the regional and neighbourhood scales and that their presence in a 10 × 10-km grid square can be predicted from the farm size/type. 4 Analysis of the concentration of organic farms showed that about a third of the variance in their occurrence across the country can be predicted by a statistical model including the six landscape axes and a term to account for spatial aggregation. 5 Synthesis and applications. Our results show that a combination of environmental variables associated with a lower agricultural potential predisposes farmers to convert to organic farming, which further promotes conversion of farmers in the neighbourhood. Organic farming as a ‘wildlife friendly’ method is more likely to occur in agriculturally less-favoured areas where economic incentives for conversion to organic farming do not need to be high and the loss of production due to conversion will be comparatively small. This suggests that an efficient conservation strategy, which takes the global demand for food into account, would be to promote organic farming as an agri-environment scheme in landscapes that are already rich in organic farms at the expense of those existing high-production landscapes that are not.
Method for determining glucose in plasma, cerebrospinal fluid, and urine by means of p-bromaniline.

This paper describes a rapid, accurate, and cheap micro-method for determining glucose in plasma, cerebrospinal fluid, and urine—well-suited for automation. Its principle is that during heating with acetic acid the glucose is converted to a furfurol forming with p-bromaniline a yellowish colour which at 380 nm has a well-defined absorption maximum. A precision study shows a coefficient of variation of 1.6 on blood levels of glucose around 100 mg/100 ml. The day-to-day reproducibility for a serum sample with a glucose content of 178 mg/100 ml is ±4.5%. The specificity is elucidated 1) by experiments using addition of glucose to whole blood and urine. (The correlation coefficients between the measured amount of glucose and the expected amount are 0.98 and 0.99 respectively.) 2) By comparison of glucose levels in plasma and blood determined by the new method and by the glucose oxidase method. The glucose concentration measured in deproteinized plasma was identical with the plasma glucose concentration measur.
Antioxidant role of ascorbic acid on oxidative stress induced by sub-acute exposure of lead and cypermethrin in erythrocytes of Wistar rats

This study aimed to evaluate the reparative potential of ascorbic acid (AA, 100 mg/kg, orally for 28 days) in sub-acute lead (Pb, 100 ppm in drinking water for 28 days) or cypermethrin (CPM, 50 mg/kg, orally in vehicle for 28 days) poisoning alone and as binary mixture on the basis of oxidative stress parameters in erythrocytes of Wistar rats. Both Pb and CPM produced significant increase in lipid peroxidation along with elevated glutathione-S-transferase and catalase activity individually but not as a binary mixture. Glutathione peroxidase activity was significantly increased but glutathione levels were significantly reduced irrespective of single or co-exposure while the activity of superoxide dismutase and erythrocytic protein content were not significantly affected. Co-exposure led to a comparatively lower level of oxidative stress than that induced by Pb or CPM alone indicating an antagonistic toxicodynamic profile in rat erythrocytes. Co-administration of AA along with Pb and/or CPM significantly restored the oxidative stress parameters to normal values. Overall results indicated that co-exposure induces a lower level of oxidative stress and AA ameliorates Pb- and/or CPM-induced oxidative damage in rat erythrocytes.