Miracle-dz/UniFAR-FTUs huggingface dataset:
The origins of zooparasitic nematodes

Zooparasitic nematodes are derived from soil nematodes and parasitism apparently originated only after land animals appeared. A major line from soil dwelling rhabditids gave rise to the secernentean parasites, which constitute about 98% of all genera in vertebrates and about 80% of those in invertebrates. A minor line evolved from the predominantly soil-dwelling dorylaimids and gave rise to adenophorean parasites, including mermithoids, trichinelloids, and dioctophymatoids. Nematodes are common in terrestrial invertebrates but rare in aquatic invertebrates (e.g., polychaetes, molluscs, crustaceans). The fauna in terrestrial vertebrates is rich and diversified. In contrast, the fish nematode fauna is limited. Only 17 families of nematodes occur in fishes and only 5 are unique to the fishes. No unique nematode superfamilies occur in fishes. The fish nematode fauna seems closely related to that in terrestrial vertebrates and is evidently derived from it since almost three quarters of the families are shared .
Extraterrestrial Handedness?

Biological systems exhibit molecular handedness: During biosynthesis, predominantly L amino acids rather than D amino acids are incorporated into proteins. The origins of this handedness remain puzzling. In his Perspective, Bada discusses results reported by Cronin and Pizzarello in the same issue (p. 951) showing a slight excess of L amino acids in a well-known extraterrestrial object, the Murchison meteorite. This finding suggests the existence of an enrichment process in cosmochemical environments and could possibly be the source of molecular handedness on Earth.
The frontal shield of the moorhen: sex differences and relationship with body condition

Moorhens Gallinula chloropus have a conspicuous frontal shield, which is used in competitor assessment, and whose size and colour is testosteronedependent in both sexes. During 2 months in winter we examined sex-related differences in size and colour of the red or red-orange shield and the yellow-tipped bill of free-living adult moorhens, as well as their relationship with indices of body condition (body size, tarsi fluctuating asymmetry, fat index, serum lutein carotenoid concentration, and a number of blood parameters). Shield area was greater in males and more red in females. In females, area and colouration intensity of the shield were positively correlated, respectively, to body size and concentration of circulating lutein. In males, area and intensity of red colouration of the shield were positively correlated, respectively, to albumin/globulin ratio and body size, while shield colour saturation was negatively related to the leukocyte index. Our results suggest that shield area and colour of male and female moorhens may provide cues to their opponents for assessment of body size and health status, and therefore of their competitive ability.
Rhipilia penicilloides sp. nov. (Udoteaceae, Chlorophyta) from Fiji

Abstract Rhipilia penicilloides sp. nov. (Udoteaceae, Chlorophyta) is described from the Fiji Islands, South Pacific. Adult thalli are characterized by a penicilloid capitulum of free, dichotomously branched siphons and an elongated corticated stipe arising from a multisiphonous rhizome-like mat or stolon, whereas juvenile stages possess an infundibular capitulum held together by abundant lateral tenaculiferous branch lets. The generic placement of the new species is debatable owing to its close affinities to both the genera Chlorodesmis and Rhipilia, but present evidence favors the latter.
Chromobacterium, Eikenella, Kingella, Neisseria, Simonsiella, and Vitreoscilla Species Comprise a Major Branch of the Beta Group Proteobacteria by 16S Ribosomal Ribonucleic Acid Sequence Comparison: Transfer of Eikenella and Simonsiella to the Family Neisseriaceae (emend.)

The 16S ribosomal ribonucleic acid sequences of the type strain and three other strains of Eikenella corrodens, the type strains of Alcaligenes faecalis, Alcaligenes xylosoxydans subsp. denitrificans, Chromobacterium fluviatile, Chromobacterium violaceum, Kingella denitrificans, Kingella kingae, and Pseudomonas cepacia, and a strain of Vitreoscilla stercoraria were determined by direct sequencing of bacterial ribosomal ribonucleic acid by a modified Sanger method. These sequences were compared with previously published sequences of Neisseria gonorrhoeae and Pseudomonas testosteroni and unpublished sequences of Nitrosolobus sp. , Nitrosomonas europaea, Rhodocyclus gelatinosus, Rhodocyclus purpura, Simonsiella muelleri, and Spirillum volutans. All of the bacteria sequenced in this study were members of the beta group of the class Proteobacteria, formerly called “purple bacteria and their relatives. ” A phylogenetic tree was constructed based upon the sequence homologies. One of the findings of this study is that Eikenella corrodens is related, as indicated by percentage of sequence homology, to the following organisms: Kingella denitrificans (97.7%), Simonsiella muelleri (95.7%), Kingella kingae (96.2%), Neisseria gonorrhoeae (95.1%), Vitreoscilla stercoraria (94.4%), Chromobacterium violaceum (91.7%), and Chromobacterium fluviatile (89.8%). These bacteria constitute a newly recognized branch of the beta group Proteobacteria. The remaining species, including Pseudomonas cepacia, Alcaligenes faecalis, and Alcaligenes xylosoxydans subsp. denitrificans, are members of the major cluster of the beta group Proteobacteria. On the basis of our data we propose that the genera Eikenella and Simonsiella be placed in the family Neisseriaceae.
A controlled deterioration test for Arabidopsis thaliana reveals genetic variation in seed quality

Several ecotypes (Landsberg erecta, Enkheim, Cape Verde islands and C24) and mutants (abal-1, abi3-7, gal-1 and tt4-1) of Arabidopsis thaliana L. were subjected to a variety of seed quality tests to assess genetic variation. The wild type (Landsberg erecta) and two mutants (abi3-7, tt4-1) gave close to 100% germination at 25°C whilst other genotypes and mutants showed varying degrees of dormancy. A controlled deterioration assay was developed to compare genotypes with regard to their storability. Equilibration of the seeds at 85% relative humidity and subsequent hermetic storage at 40°C was more discriminatory in identifying differences in storability than was equilibration at 75% relative humidity followed by storage at 40 or 50°C. With longer deterioration treatments, germination was reduced and average germination time and frequency of abnormal seedlings increased. This test revealed clear differences in seed stress tolerance amongst genotypes. Additional differences in seed quality were observed in germination tests performed at sub-optimal conditions, such as low temperatures (10 and 15°C) or under osmotic stress (-0.25 MPa and -0.50 MPa). The observed differences in seed quality and the assays developed can be used to identify genes involved in different aspects of seed quality.
Impact of ambient temperature and age on dietary lysine and energy in turkey production

The commercial turkey market changed during the last two or three decades from predominantly whole turkey to mostly further processed products as consumer demand for breast meat and convenience increased in most western countries. Turkey operations focus on selection in breeding, management, and feeding programs to obtain a high breast meat yield. Main factors that affect breast meat yield are age, weight, sex, strain, genetic selection, and nutrition. The degree of influence by these factors on breast meat yield is highly dependent upon environmental conditions, especially ambient temperatures. This review deals with the response of commercial male turkeys on dietary lysine to energy ratios in moderate and hot climate conditions. A range dietary lysine to energy ratios have been determined to be optimal during each successive four-week period after hatch: 1.12 to 1.65, 1.10 to 1.36, 0.76 to 1.15, 0.64 to 0.81, and 0.53 to 0.86 g dietary lysine per MJ of ME, respectively). These optimum ranges in lysine to energy ratios are partly due to the continuous changes in genetic potential for growth and environmental effects on feed intake. Commercial male turkeys weighed about 18.5 kg at 140 days of age with a feed: gain ratio of 2.6 in 2001, as compared to about 8.0 kg at 220 days of age with a feed: gain ratio of 3.0 in 1966. Moreover, there is clear evidence in scientific literature that feed intake, and thus protein intake is negatively affected by short or long periods of heat stress in moderate and hot climates, respectively. Although some research included ambient temperature as a treatment variable in nutritional requirement studies with turkeys, most have been conducted at moderate temperatures. Feeding turkeys to minimize the adverse effects of heat stress is a big challenge for the modern turkey industry. More research is needed to better understand the relationship between dietary energy and lysine at different climatic conditions.
ANTIOXIDANT PROPERTIES OF ETHANOLIC AND METHANOLIC EXTRACTS FROM MONASCUS-FERMENTED SOYBEANS

Soybeans are very common foods in oriental countries used as a meat substitute. Monascusspecies possess functional components and have been used on traditional fermented food. Solid-state fermentation of the soybean substrate by Monascus species is a new area of investigation. In the present study, methanolic extracts from three samples exhibited better antioxidant activity in the conjugated diene method, reducing power, scavenging ability on 1,1-diphenyl-2-picrylhydrazyl radicals and chelating ability on ferrous ions. Monascus species inoculated onto the soybean substrate contributed higher reducing power, scavenging and chelating abilities and higher amounts of phenol components than uninoculated soybean product. Overall, Monascus-fermented soybeans showed better antioxidant properties and can be developed as a new dietary supplement and functional food. PRACTICAL APPLICATION Soybeans and soy products are rich in isoflavones and are very common foods used as a meat substitute in oriental countries. Fungus Monascus has been used as a traditional fermented food and its metabolic products are also utilized as food pigments or biological agents in oriental countries for centuries. Many reporters showed that soy isoflavone aglycones and Monascus spp. metabolite exhibited physiological activities. In addition, previous studies showed a fermentation process using microorganisms to inoculate onto a nonsoluble material that can produce chemicals and enzymes. Therefore, the ethanolic and methanolic extracts from Monascus-fermented soybeans were evaluated for antioxidant properties, and the information obtained would be more valuable than that from soybeans to develop new functional foods.
Cytotoxic Activities of Salvia. of the Labiatae Family

ABSTRACT Eight crude extracts of five Salvia. species were evaluated for cytotoxic activities against brine shrimps and four human cancer cell lines [human colon adenocarcinoma (HCA), HepG2, MCF-7, and human pancreatic carcinoma (HPC) along with a normal mouse cell line (areolar cells)] as a control. In the brine shrimp lethality test, all samples, except S. fruticosa. L. (Sifnos collection) and S. verbenaca. L. (Zante collection), were found to be highly active with ED50 values less than 300 μg/ml. In the case of human cancer cell lines, S. fruticosa. , collected from Kalymnos and Crete, were active against HCA cells with LC50 = 60.4 and 40.1 μg/ml respectively. Interestingly, only one sample, S. fruticosa. collected from Kalymnos, was active against HepG2 cells with LC50 = 68.1 μg/ml. In the case of MCF-7 cells, S. fruticosa. collected from three different locations (Kalymnos, Rhodos, and Crete) showed similar activity with LC50 = 43.1, 41.1, and 42.3 µg/ml, respectively. All S. fruticosa. samples were found to be cytotoxic toward a normal mouse cell line when tested at 0.1 mg/ml. All the other samples had LC50 values greater than 75 µg/ml,and were considered to be inactive.
A Therapeutic Targeting Identification from Microarray Data and Quantitative Network Analysis

Personalized therapy is “the right drug for the right patient at the right time”. Here we reported a case of personalized therapy using gene expression signature (GES) related drug discovery to treat a patient with drug-resistant metastases from breast-tumor. Methods: After mRNA obtained from metastatic liver tissue was performed by microarray, GES of genomic profiles were uncovered by bioinformatics tool and targeting drugs related with GES were mined by drug-bank. Several targeting-drugs approved by FDA were selected to treat the patient. Results: 1198 genes were uncovered for the higher expression by two-fold to compare normal liver specimens in which 10 of mined genes were identified as set-1 GES for metastasis and 16 of genes were uncovered as set-2 directly for primary breast tumor. Drug-bank platform were used to discover drugs for target set-1/2 genes. Eventually, medropxyoprogesterone (MPA) targeting set-I gene and doxorubicin targeting set-2 gene were selected for the patient because the two drugs have already been approved by FDA. After doxorubicin and MPA were administered, patient's metastatic-tumor showed complete response. Conclusions: We not only analyze genomic expression profiles but also discover sensitive compounds for drug-resistant tumor. We successfully select drugs approved by FDA to treat the patient.
Impact of Peptides on the Recognition of HLA Class I Molecules by Human HLA Antibodies

MHC class I molecules expressed on cell surfaces are composed of H chain, β2-microglobulin and any of a vast array of peptides. The role of peptide in the recognition of HLA class I by serum HLA Abs is unknown. In this study, the solid-phase assay of a series (n = 11) of HLA-A2-reactive, pregnancy-induced, human mAbs on a panel (n = 12) of recombinant monomeric HLA-A2 molecules, each containing a single peptide, revealed peptide selectivity of the mAbs. The flow cytometry membrane staining intensities on the HLA-A2-transduced cell line K562, caused by these mAbs, correlated with the number of monomer species detected by the mAbs. Flow cytometry staining on HLA-A2-bearing cell lines of a variety of lineages was indicative of tissue selectivity of these HLA-A2 mAbs. This tissue selectivity suggests that the deleterious effect on allografts is confined to alloantibodies recognizing only HLA class I loaded with peptides that are derived from tissue-specific and household proteins. Since Abs that are only reactive with HLA loaded with irrelevant peptides are expected to be harmless toward allografts, the practice of HLA Ab determination on lymphocyte-derived HLA deserves reconsideration.
Nutrient and algal responses to winterkilled fish-derived nutrient subsidies in eutrophic lakes

Abstract Fishes inhabiting shallow, glacial lakes of the Prairie Pothole Region in the United States and Canada periodically experience hypoxia in severe winters that can lead to extensive fish mortality resulting in high biomasses of dead fish. However, the role of carcass-derived nutrient subsidies in shallow, eutrophic lakes translocated to pelagic primary producers is not well documented. This study quantified the influence of winterkill events on nutrient contributions from decaying fish carcasses of common carp (Cyprinus carpio) and the phytoplankton response among pre- and postwinterkill years and compared seasonal patterns of nutrient limitation and phytoplankton community composition between winterkill and nonwinterkill lakes. We found that fish carcasses contributed an estimated 2.5–4.3 kg/ha of total (Kjeldahl) nitrogen (N) and 0.3–0.5 kg/ha of total phosphorus (P) to lakes that experienced winterkill conditions. Nutrient bioassays showed that winterkill lakes were primarily N limited, congruent with the low N:P ratios produced by fish carcasses corrected for the disproportionate release of N and P (8.6). Nutrient subsidies translocated from decomposed fish to pelagic primary producers seemed to have little immediate influence on the seasonal phytoplankton community composition, but total N and subsequent chlorophyll-a increased the year following the winterkill event. Cyanobacteria density varied seasonally but was higher in winterkill lakes, presumably due to the integration of nutrients released from fish decomposition. This study provides evidence that large inputs of autochthonous fish-derived nutrients contribute to nutrient availability within winterkilled systems and increase the maximum attainable biomass of the phytoplankton community.
The relationships between echolocation calls, morphology and diet in insectivorous bats

In this study we explored quantitatively the relationships between the size of bats, the frequencies in their echolocation calls, and the incidence of moths and beetles in their diets. We focused on the predictions of the allotonic frequency hypothesis which states that some insectivorous bats increase their access to moths that can hear echolocation calls by shifting to frequencies to which the ears of these insects are less sensitive. The hypothesis predicts that the frequencies dominating the echolocation calls of bats may be correlated with the incidence of moths in their diets. We collected data for 62 species of bats that take airborne prey, usually flying insects, 25 species of high duty cycle echolocating bats (Rhinolophidae and Hipposideridae) and 37 species that are low duty cycle echolocators (Vespertilionidae and Molossidae). For bats whose echolocation calls are dominated by frequencies 100 kHz, the relationship was not statistically significant, suggesting that morphological characteristics rather than echolocation call frequency may limit the range of potential prey items. Our analyses also demonstrate the importance of jaw morphology as a predictor of the incidence of beetles or moths in the diets of bats, and reveal that generally bigger species (as defined by forearm length) use echolocation calls dominated by lower frequencies than smaller species. In both high duty and low duty cycle echolocating bats the relationship between body size and dominant call frequency was best described by a linear model. We also propose that perch hunting was central in the development of the high duty cycle approach to echolocation.
Improved Lossless Depth Image Compression

Since RGB-D sensors became massively popular and are used in a wide range of applications, depth data compression became an important research topic. Live-streaming of depth data requires quick compression and decompression. Accurate preservation of information is crucial in order to prevent geometric distortions. Custom algorithms are needed considering the unique characteristics of depth images. We propose a real-time, lossless algorithm which can achieve significantly higher compression ratios than RVL. The core elements are an adaptive span-wise intra-image prediction, and parallelization. Additionally, we extend the algorithm by inter-frame difference computation and evaluate the performance regarding different conditions. Lastly, the compression ratio can be further increased by a second encoder, circumventing the lower limit of four-bit per valid pixel of the original RVL algorithm.
Comparative study of selenium requirements of three phytoplankton species: Gymnodinium catenatum, Alexandrium minutum (Dinophyta) and Chaetoceros cf. tenuissimus (Bacillariophyta)

This study investigated the selenium (Se) requirements of three phytoplankton species which commonly bloom in southern Australian estuaries. The present study showed that the toxic dinoflagellate Gymnodinium catenatum Graham had an obligate requirement for Se (IV) in culture. After two transfers (~4 weeks ￻7 generations) in Se-deficient seawater medium, this phytoplankton species exhibited a decline in growth rate (25%) and biomass yield (90%), while complete cessation of cell division occurred under prolonged (8 weeks ￻ 12 generations) Se starvation. Addition of 10-9-10-7 M H2SeO3 to nutrient-enriched seawater medium resulted in increased G.catenatum growth and biomass yields in direct proportion to the Se concentrations offered. In contrast to G.catenatum, Se limitation was observed in the dinoflagellate Alexandrium minutum Halim after four transfers (5 weeks ￻20 generations) in Se-deficient medium. Exponential growth rates of A.minutum decreased slightly (5-10%) when Se was not supplied, but biomass yields decreased as much as 80-90%. The diatom Chaetoceros cf. tenuissimus Meunier showed no evidence of Se limitation even after eight transfers (8 weeks; >60 generations) in Se-deficient medium. Variations in growth rates and biomass yields between transfers provide valuable information about the relative potential for Se limitation in the three species studied. In addition, differences in Se requirement between these bloom-forming phytoplankton species suggest that this micronutrient may play a role in structuring phytoplankton communities in southern Australian waters.
The Elementary Nervous System Revisited

Parker's theory of the origin of the nervous system is discussed along with later interpretations. Attention today has shifted from the cellular to the molecular level, and it has become clear that many of the molecules and mechanisms thought of as typically neuronal have homologs or counterparts in non-nervous cells and unicellular organisms. This applies to signalling chemicals, receptors, second messenger systems and ion channels, and also to the production of electrical events. Parker's view of sponges as a group lacking nerves but possessing independent effectors is still acceptable, but some sponges (and also higher animals) employ non-nervous signalling pathways to coordinate their effectors. Thus, nerves are not always necessary for coordinated behavior. Cnidarians like hydra have seemingly simple, two-dimensional nervous systems with little or no centralization, but even such systems can be surprisingly complex, and the more advanced cnidarians show neurophysiological specializations as sophisticated as those of many higher invertebrates. Examples of ingenious cnidarian solutions to behavioral problems are given. No existing animals have ‘elementary’ nervous systems if that term implies the existence of crude or inefficient functional adaptations
PAPER Distinguishing local from global climate influences in the variation of carbon status with altitude in a tree line species

geb_598 1.12 Aim Two alternative hypotheses attempt to explain the upper elevation limit of tree lines world-wide, the carbon-limitation hypothesis (CLH) and the growthlimitation hypothesis (GLH); the altitudinal decrease of temperature is considered the driver constraining either carbon gain or growth. Using a widely distributed tree line species (Nothofagus pumilio) we tested whether tree line altitude is explained by the CLH or the GLH, distinguishing local from global effects. We elaborated expectations based on most probable trends of carbon charging with altitude according to both hypotheses, considering the alternative effects of drought. Location Two climatically contrasting tree line ecotones in the southern Andes of Chile: Mediterranean (36°54′ S) and Patagonia (46°04′ S). Methods At both locations, 35–50 trees of different ages were selected at each of four altitudes (including tree line), and stem and root sapwood tissues were collected to determine non-structural carbohydrate (NSC) concentrations. NSC accumulates whenever growth is more limited than photosynthesis. An altitudinal increase in NSCs means support for the GLH, while the opposite trend supports the CLH. We also determined stable carbon isotope ratios (d 13