Miracle-dz/UniFAR-FTUs huggingface dataset:
Fishpond dams affect leaf-litter processing and associated detritivore communities along intermittent low-order streams

Intermittent streams are common and widespread freshwater ecosystems globally. While dams greatly affect the ecology of permanent streams, the extent of their effects on intermittent streams remains largely unknown. The physical and chemical alterations induced by dams could have particularly strong impacts on the functioning of intermittent low-order streams, especially due to the limitations they place on colonisation of aquatic biota from downstream permanent waters. Leaf-litter breakdown (LLB) and associated communities (microbes and shredders) were studied to investigate the potential ecological continuum rupture caused by fishpond dams along the longitudinal gradient of intermittent streams. Three to four sites were investigated along three reference (no dam) and three impacted (with a fishpond dam) first-order intermittent low-order streams. LLB increased along the longitudinal gradient in all six streams regardless of the presence of dams (from 1.5 to 8.4 fold over <1.5 km distance). This underscores the great variability of low-order stream functioning even at fine scales. Such upstream to downstream gradients need to be taken into account before investigating the effect of any perturbation using LLB as a functional indicator. Fishponds dams tended to increase LLB downstream, and altered the downstream microbial communities (increase in fungal densities) and shredder assemblages (increase in Gammaridae). The effects of fishpond dams on intermittent stream functioning appeared to be most significant when they were associated with changes in hydrology, that is, when fishponds resulted in permanent flows downstream of dams. Our findings suggest that better management of fishpond dams in order to limit hydrological modifications downstream (for instance, by preventing leaks from the dam) could reduce their impact on ecosystem functioning in intermittent streams.
Age determination methods for Northwest Atlantic species

The successful application of techniques to enhance detection of age marks in biological specimens is of vital importance in fisheries research. This manual documents age determination techniques used by staff at the Woods Hole Laboratory, National Marine Fisheries Service. General information on procedures for preparing anatomical structures is described, together with criteria used to interpret growth patterns and assign ages. Annotated photographs of age structures are provided to illustrate criteria. Detailed procedures are given for the following species: Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), Atlantic cod (Gadus morhua), pollock (Pollachius virens), silver hake (Merluccius bilinearis), red hake (Urophycis chuss), black sea bass (Centropristis striata), weakfish (Cynoscion regalis), Atlantic mackerel (Scomber scombrus), butterfish (Peprilus triacanthus), redfish (Sebastes fasciatus), summer flounder (Paralichthys dentatus), winter flounder (Pseudopleuronectes americanus), witch flounder (Glyptocephalus cynoglossus), American plaice (Hippoglossoides platessoides), yellowtail flounder (Limanda ferruginea), surf clam (Spisula solidissima), and ocean quahog (Arctica islandica). (PDF file contains 142 pages.)
The feed value of toasted Mucuna sloanei meal on the performance, haematology and blood biochemistry of broiler finisher birds

An experiment was conducted to determine the feed value of toasted Mucuna sloanei meal (TMSM) on the performance, haematology and blood biochemistry of broiler finisher birds. Mucuna sloanei seeds were processed into toasted Mucuna sloanei meal (TMSM) and analyzed for proximate and phytochemical composition. The meal was then used to formulate broiler finisher diets at 0.0, 5.0, 10.0 and 15.0% inclusion levels respectively, which were then used to raise groups of 30 broiler finisher for 5 weeks. At the end of the 5 weeks (35 days) feeding trial, 3 birds were selected from each group and used for the determination of the blood indices. The daily feed intake and feed conversion ratio increased significantly (P < 0.05) as the dietary levels of TMSM increased. The cost of production also increased as the TMSM increased. The haemoglobin (HB), the packed cell volume and the red blood cell decreased significantly at 15.0% dietary levels. The total proteins, creatinine, urea, cholesterol and serum glutamic oxaloacetic transaminase (SGOT) decreased significantly as toasted Mucuna sloanei meal increased. The results of this trial suggests that broiler finisher chicken can be fed with the toasted Mucuna sloanei meal up to 5.0% inclusion level in their diets without any detrimental effects on performance and blood indices.Keywords: feed value, toasted Mucuna, haematology, blood biochemistry
Morphological and morphometric study of pre-ovigerous and post-ovigerous adults of Tanaisia (Paratanaisia) bragai (Santos, 1934) (Digenea, Eucotylidae)

The aim of this study was to obtain data on the morphology and morphometry of pre-ovigerous and post-ovigerous adults of the species Tanaisia (Paratanaisia) bragai , using confocal laser scanning microscopy to obtain tomographic images of the suckers and tegument. For morphometric analysis, 45 specimens (30 pre-ovigerous adults and 15 post-ovigerous adults) were measured with the aid of an ocular micrometer coupled to the objective of a photonic microscope. Pre-ovigerous and post-ovigerous adult individuals, stained with Mair carmalumen and mounted in permanent preparations, were analyzed by means of confocal laser scanning microscopy. Positive correlation was detected between the body length and ovary length of post-ovigerous adults (rs: 0.774; p<0.01), as well as between the body length and testes (rs: 0.604 and 0.659; p< 0.05), the body length and the length of uterus (rs: 0.839; p< 0,01) and between the ovary width and egg length (rs: 0.777; p<0.01). Morphological study of the pre-ovigerous adults demonstrated that the ovary and testes develop simultaneously before the development of the uterus and vitelline glands. The acetabulum was detected in pre-ovigerous adults stained with hematoxilin and observed using light microscopy. In these specimens, the acetabulum measured 36.7 ± 6.9 µm (25-50 µm) in width and 39.91 ± 6.8 µm (25-55 µm) in length. The acetabulum was not detected in post-ovigerous adults observed with light microscopy. However, this structure was detected using confocal miscrocopy. In the post-ovigerous specimens, the acetabulum presented a reduced size compared to the pre-ovigerous adults. This may imply that this structure has more functional significance in the larval and pre-ovigerous stages.
Utility of the Cytochrome Oxidase I gene (COI) for Species Identification and Phylogeographic Analysis in Black Flies (Diptera: Simuliidae)

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene correctly discriminated among morphologically distinct species with nearly 100% of efficacy and also proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed the areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained largely concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.
Accumulating knowledge on the dimensions of biodiversity: systematic perspectives on Neotropical mammals

Rates of species discovery shape our per- ceptions of biodiversity, whether or not accumulation curves are used to generate precise diversity esti- mates. In addition to earlier-noted problems of esti- mating diversity by this approach, variation in body size, geographic range size, and geographic provin- cialism all serve to make organisms differentially apparent to sampling efforts. Another striking limita- tion of the approach is that rates of systematic
Distribution of Aminoglycoside Resistance Genes Among Acinetobacter baumannii Strains Isolated From Burn Patients in Tehran, Iran

Background: Acinetobacter baumannii is an important cause of nosocomial infections, particularly in burn patients. Hospital Infections caused by these bacteria are difficult to treat. Objectives: The present study aimed at determining the frequency of genes encoding aminoglycoside-modifying enzymes in A. baumannii strains isolated from burn patients in Shahid Motahari hospital. Methods: This study was performed on 100 A. baumannii strains collected from Shahid Motahari hospital in Tehran during 2013 and 2014. The bacteria were cultured and identified. Antibiotic susceptibility testing was performed by disk diffusion method according to the CLSI guidelines. PCR assay was done to find the genes encoding aminoglycoside-modifying enzymes. Results: In this study, highest resistance to antibiotic was reported for ceftriaxone, ciprofloxacin, and ceftizoxime (100%), whereas the highest susceptibility was observed for colistin (100%), followed by gentamicin, amikacin, and tobramycin with (93%), (90%), and (87%), respectively. In the total of 100 strains studied, aphA6, aadB, aacC1 and aadA1 genes were found in 657 221 and 37 of A. baumannii isolates, respectively; 8 isolates had aadB and aphA6 genes and 3 had aadB, aadA1, aacC1, and aphA6 genes. Conclusions: This study showed the high frequency aminoglycoside-resistance genes among A. baumanni strains. Thus, the implementation of appropriate programs to prevent the spread of the bacteria seems necessary in the Shahid Motahari hospital.
PHYSIOLOGICAL AND HISTOLOGICAL EFFECT OF LEAD ACETATE IN KIDNEY OF MALE MICE

Human exposure to lead continues to be a serious public health problem, because lead can cause renal disease and the kidney has the highest concentrations among the soft tissues. Exposure to lead is associated with adverse effects on renal function in laboratory animals and man. An experiment was conducted to study the effect of oral feeding of lead acetate on kidney by estimation the levels of uric acid, urea and creatinine in the serum of mice and the histological parameters of kidney in three different durations. Mice were treated with 0.4 mg/100 ml lead acetate (LA) for 10 days (group A) and for 20 days (group B) and for 30 days (group C). levels of urea in the serum of group A, B, and C increased significantly comparing with the control group, also there was significant differences between group A and group B and between group A and group C, but there was no significant differences between Group B and group C. Level of serum uric acid in groups A, B, C increased significantly comparing with the control group but there was no significant differences among treated group.Serum creatinine levels in group A increased none significantly comparing with the control group. While increased significantly in both of group B and group C, there was significant differences between group A and group C, but there was no significant differences between group A and group B.Kidney sections in group A characterized by foci of congestion and heamorrhage.Glomerular swelling revealed in the kidneys of group B, but the kidney of group C revealed vasculitis, heamorrhage and early hyalinization, normal gromeruli appear in all treated groups.
Calendula officinalis -An Important Medicinal Plant with Potential Biological Properties

Calendula officinalis L. (Marigold) is globally known for its medicinal importance containing various phyto-chemicals including carbohydrates, amino acids, lipids, fatty acids, carotenoids, terpenoids, flavonoids, quinones, coumarins and other constituents, showing some important biological activities like wound healing, immuno-stimulant, spasmogenic and spasmolytic, hepatoprotective, genotoxic and antigenotoxic, anti-amylase, anti-inflammatory, anti-oedematous, anti-bacterial and anti-fungal, antioxidant, antidiabetic, anti-HIV and anti-cancerous, nephron-protective, prevention of oropharyngeal mucositis, hypoglycemic and gastroprotective activities with no toxic effect . In this review, a detailed account of different phytochemicals and their medicinal properties of C. officinalis have been addressed.
Nematodes associated with terrestrial slugs from canola fields and ornamental nurseries in South Africa

A survey of nematodes that use terrestrial slugs as definitive hosts, was conducted in canola fields and ornamental nurseries located in the Western Cape province of South Africa. A total of 3290 slugs were collected from 22 different sites. On the identification of the slugs, they were vivisected and examined for internal nematodes. After identifying the nematodes found, on the basis of their morphological characteristics, their identity was confirmed using molecular sequence data for the internal transcribed spacer (ITS-1, 5.8S, ITS-2), D2-D3 expansion segments of the large subunit (LSU or 28S) and small subunit (SSU or 18S) ribosomal DNA. Of the 22 sites investigated, 13 had nematodes present, with 8 % of the slugs being found to be infected with nematodes. Seven nematode species were confirmed, including Agfa flexilis , Angiostoma margaretae , Angiostoma sp. (SA1), Caenorhabditis elegans , mermithid sp. (SA1), Phasmarhabditis sp. (SA3) and Phasmarhabditis sp. (SA4). In addition, several Angiostoma spp. were also isolated, but could only be identified to genus level due to limited material. Of the seven confirmed species, four were previously undescribed. This is the first record of A. margaretae associating with Deroceras panormitanum , Deroceras reticulatum , Lehmannia valentiana and Oopelta polypunctata . Also, this is the first time that a mermithid has been found associating with molluscs in South Africa.
Xyela fusca spec. nov. from Japan elucidates East Asian–North American relationships of Xyela (Hymenoptera, Xyelidae)

Morphological and genetic data indicate that Xyela fusca Blank, Kramp & Shinohara spec. nov. from Shikoku, Japan, plus an undescribed species from China are closely related to the Nearctic X. bakeri Konow, 1898. These species form the X. bakeri group, which is considered to be the sister clade of the Eurasian X. julii group. In addition to the X. alpigena group, the X. bakeri group is the second species group of Xyela with representatives occurring in both the Old and the New World. While X. bakeri is associated with Pinus ( Pinus ) species as the larval hosts, collection data of imagines suggest P. ( Strobus ) parviflora for X. fusca . This appears to be the second case, in which closely related Xyela species have switched hosts between species belonging to different subgenera of Pinus . Based on distribution data, migration of the common ancestor across Beringia appears likely, which would also have involved the change of the host subgenus. The six species of Xyela of Japan are keyed and new distribution data are presented. New, most northwesterly records of imagines from Yukon Territory (Canada) and field observations in Colorado and California (USA) suggest P. contorta as an additional larval host of X. bakeri .
Development and evaluation of fish ball from fish powder supplemented with potato flour

Fish ball was formulated with fish mince powder supplemented with potato flour along with other ingredients. Higher percentage of fish mince powder contained higher amount of protein, fat and ash but lower amount of total carbohydrate and moisture compared to that containing lower percentage of fish mince powder. The water absorption and frying time increased with the increasing percentage of fish mince powder. Fish balls prepared from the ingredients having 35% fish mince powder had the highest score in flavor rating and fish ball containing 30% fish mince powder had the highest overall acceptability. The scores on color and texture of fish balls prepared from all samples were almost same, but the scores on flavor and over all acceptability varied due to the fishy flavor because some of the panelist disliked the fishy flavor. While studying the storage period, there were no remarkable changes in case of color, flavor and texture of the prepared fish ball. No molds growth was noticed on the storage period of 90 days. So, the percentage of fish mince powder had no influence on the stability of the fish ball at room temperature. J. Bangladesh Agril. Univ. 15(1): 95-102, January 2017
Role of the Adapter Protein 3BP2 in BCR-ABL-mediated Signal Transduction and Leukemogenesis

3BP2 was originally identified through its interaction with the ABL kinase. Fusion of ABL with the BCR gene forms the BCR-ABL onco-protein, which is causative in Chronic Myeloid Leukemia (CML) and acute lymphoid leukemia (ALL). Due to the ability of 3BP2 to regulate ABL activity in osteoblasts, we hypothesize that 3BP2 modulates BCR-ABL signalling. Overexpression of 3BP2 in the CML-T1 cell line produced a marked decrease in global tyrosine phosphorylation. 3BP2 overexpression also resulted in a significant increase in CML-T1 cell growth, accompanied by altered ERK1/2, AKT, SYK, LYN, HCK, and CBL phosphorylation and expression. A phospho-SRC family protein and a 116 kDa phospho-protein were identified as 3BP2 interaction partners in response to BCR-ABL activation. BCR-ABL bone marrow transplantation (BMT) models in 3bp2 mice exhibit accelerated disease compared to wild-type mice, with altered leukemic phenotype. In conclusion, 3BP2 is able to modulate signalling through BCR-ABL and affect BCR-ABL-induced disease outcome.
Red clover varieties of Mattenklee type have higher production, protein yield and persistence than Ackerklee types in grass–clover mixtures

Dairy farmers have increased interest in multiyear red clover–ryegrass ley pasture swards because of their high productivity and protein concentration but the adoption of such mixtures has been restricted because of poor persistency of many red clover cultivars currently used. We aimed (i) to assess dry-matter yield (DMY), persistence and nutritive value of four Mattenklee and four Ackerklee cultivars and (ii) to investigate the underlying plant morphological traits. We conducted a 4-year field experiment with red clover–ryegrass mixtures, in combination with a short-term pot experiment in which the red clover cultivars were grown both in monoculture and in mixture with Lolium perenne L. In the field, Mattenklees showed higher production (on average 42% higher) and clover content (on average 34% higher) in the third and fourth year of production compared to Ackerklees. In the fourth year, Mattenklees had slightly lower digestibility and lower protein concentration compared to Ackerklees cultivars; however, the digestible DMY and the protein yield were higher for Mattenklees. Both persistence and nutritive value of the different red clover cultivars were closely correlated with plant morphological traits. For stem length, there was close correlation (r > .77) between the results from the pot experiment and the field experiment, suggesting that stem length may be an important trait for plant breeding.
Impact of Male Reproductive Hormones on Sperm Activity via Regulation of Semen Antioxidant Levels

New relationship between Hormones and Antioxidants has been proposed. The levelsof several hormones correlate well with different Antioxidants activities in different tissues.The study conducted to find a relationship between serum male reproductive hormonesandsemen Antioxidantlevels and sperm activity.Samples of infertile group consist of Asthenozoospermia ASZ (n=31) and healthy fertile menas a control (n=24). The patients have been selected and examined according to (W.H.O2010) semen analysis manual criteria. In addition th biochemical analysis of seminal plasmaincluding (Total antioxidant capacity TAC, Glutathione Reductase GRD, glutathione andMalondialdehyde MDA) and serum (LH, FSH and Testosterone) were assayed for eachsample.Results show a decrease in TAC level of ASZ group as compared to control (439.1±207.9 and834.5±253.7 μM), and a significant decrease in seminal glutathione levels of (127.77±59.08and 174.12±61.25 μM) respectively, and show an increase in MDA level (131.45±119.61 and44.13±13.07 nmol/ml) respectively, while no significant difference in GRD level(24.00±17.69 and 16.02± 9.66 U/mL) respectively. Also there is an increase in LH and FSHhormones level (5.26±2.92, 5.81±5.46 mIU/ml), in ASZ as compared to control (2.29±1.15,1.970±1.547 IU/ml) respectively, and no significance difference in the testosterone level(5.60±1.92 and 4.35±1.65 ng/mL).
Pathoadaptation of the Intracellular Bacteria Shigella and Chlamydia: Virulence, Antivirulence, and Tissue Tropism

Abstract : Horizontal transfer of pathogenicity islands or plasmids can enable bacterial adaptation to novel pathogenic niches. Success in the new niche is dependent on conservation of advantageous genes and concomitant inactivation or loss of deleterious or unnecessary alleles. For example, the acquisition of type three secretion systems (T3SSs) by Shigella and Chlamydia species facilitated entry into and exploitation of eukaryotic host cells. Conversely, both microbes experienced significant pseudogenization and genome reduction as a result of adaptation to the intracellular lifestyle. The pathogenic Shigella evolved from commensal Escherichia coli ancestors following acquisition of a large virulence plasmid carrying the T3SS. Antivirulence genes (AVGs) inhibitory to the new intracellular niche have been inactivated or lost from all strains. To identify novel Shigella AVGs, a contracted version of the large virulence plasmid was created using the minimal genes required for T3SS expression and assembly. Termed the Shigella minimally invasive plasmid (Smip), this construct was transformed into a S. flexneri strain cured of the large virulence plasmid (BS103), and the virulence phenotypes of the resulting strain characterized. BS103/Smip was capable of host cell entry, demonstrating the presence of a functional T3SS. However, although expression of the Smip in commensal E. coli isolates permitted host cell entry, invasion was severely attenuated compared to wild type Shigella. In two E. coli/Smip isolates, T3SS expression was severely inhibited at the level of the T3SS transcriptional regulators, virF and virB, indicating that that multiple virulence inhibitors (potential AVGs) are likely present in these strains. As part of a second project exploring pathogen evolution, the activity and expression of the arginine decarboxylase enzyme (AaxB) in Chlamydia was examined. Chlamydia species infect a wide variety of different hosts and tissues.
Seed yield and quality of soybean [Glycine Max (L.) Merill] as influenced by cultivar and sowing date in vertisols of Andhra Pradesh during kharif season

In order to study the effect of planting date and cultivar on seed yield and germinating ability of soybean, an experiment was conducted for two seasons (2014 – 15 and 2015 – 16 ) at Regional Agricultural Research Station, Nandyal, Andhra Pradesh. Two popular varieties, viz., JS-335 and JS-93-05 were sown on four sowing dates i.e. July 2nd fortnight (FN), August 1st FN, August 2nd FN and September 1st FN during the two consecutive kharif crop seasons in FRBD design, replicated thrice. The variety JS-335 recorded significantly higher yield (1296 kg ha-1) than JS-93-05 (690 kg ha-1) . Early sowings during July 2nd FN and August Ist FN recorded significantly at par yields (1087 kg ha-1, 1101 kg ha-1 respectively) with good initial and aging germination percentage (81%, 58.8% respectively). Though September 1st FN sown crop recorded significantly lowest seed yield (860 kg ha-1), the initial and aging germination percentage were highest (88.6%, 66.0%).