Miracle-dz/UniFAR-FTUs huggingface dataset:
EPICARDIAL AUTO-FLUORESCENCE NAD(P)H KINETICS IN THE ISCHEMICALLY PRECONDITIONED LANGERDORFF RAT HEART. EFFECTS OF CAPSAICIN. PART 2.

--------------------------------+ Corresponding author. Partially on leave of absence from I.M. O Pharmacotoxicology, the University of Ancona Medical School, Via Tronto 10 A, 60020 Ancona, Italy. E-mail l.rossini@univpm.it; Tel. n. 0039-071-2181028; Fax n. 0039-071-2206037. L.R. is recipient of a grant from the Medical Research Council Canada and the Centro Nazionale delle Ricerche Italy. The work represents a contribution to celebrate the teaching and research activities of Professors Britton Chance, Roxanne Deslauriers, Anna Maria Di Giorgio, Joseph Larner, Eugenio Meda, Ferid Murad, Giorgio Segre, and Carlo Terzuolo.
Morphology, host range and phylogenetic diversity of Sphingomonas phages in the floodwater of a Japanese paddy field

Abstract Members of the Sphingomonas-related genera (Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis) are dominant in bacterial isolates from the floodwater of Japanese paddy fields. Fifty-eight Sphingomonas/Novosphingobium bacteriophages (phages) were isolated to elucidate their morphology, host range and phylogenetic diversity based on the capsid gene (g23) sequence. All of the phages were siphoviruses with isometric or elongated, icosahedral capsids and a long, non-contractile tail. The genomes were double-stranded DNA measuring either 40, 60, 100 or 160 kb. The host range of the phages was examined by infecting 16 bacterial isolates from the floodwater, belonging to Sphingomonas, Novosphingobium, Sphingopyxis and Porphyrobacter. The host range was widely different and varied between infection of only the host used for isolation and infection of hosts belonging to the three genera of Sphingomonas, Novosphingobium and Porphyrobacter. All phages had g23, indicating the ubiquity of the g23 gene among Myoviridae and Siphoviridae members. Every g23 sequence of the phages belonged to one of the six uncharacterized Paddy Groups proposed by Fujii et al. (2008). The g23 sequences were identical at the nucleotide level for several phages with isometric and elongated capsids with 60 and 160 kb genomes, and between some phages and the clones that were retrieved from distant paddy fields. This indicates the common occurrence of horizontal transfer of g23 in the paddy fields. The g23 sequence does not correlate with the host range of those phages. In addition, a larger degree of divergence of g23 from coliphage T4 in paddy fields compared to marine environments was estimated from the present study.
Clone culture studies of a new rosalinid foraminifer from Plymouth, England and Wellington, New Zealand

A formal description of Rosalina leei sp.nov. (Foraminifera) includes an account of the great morphological variation found among adult agamonts obtained over a period of 14 months from clone cultures. Variation in chamber number, direction of coiling, overall shape, the degree of inflation of the final chamber and suture characters are detailed.
The use of museum samples for large-scale sequence capture: A study of congeneric horseshoe bats (family Rhinolophidae)

Museums hold most of the world’s most valuable biological specimens and tissues collected, including type material that is often decades or even centuries old. Unfortunately, traditional museum collection and storage methods were not designed to preserve the nucleic acids held within the material, often reducing its potential viability and value for many genetic applications. High-throughput sequencing technologies and associated applications offer new opportunities for obtaining sequence data from museum samples. In particular, target sequence capture offers a promising approach for recovering large numbers of orthologous loci from relatively small amounts of starting material. In the present study, we test the utility of target sequence capture for obtaining data from museum-held material from a speciose mammalian genus: the horseshoe bats (Rhinolophidae: Chiroptera). We designed a ‘bait’ for capturing > 3600 genes and applied this to 10 species of horseshoe bat that had been collected between 93 and 7 years ago and preserved using a range of methods. We found that the mean recovery rate per species was approximately 89% of target genes with partial sequence coverage, ranging from 3024 to 3186 genes recovered. On average, we recovered 1206 genes with ≥ 90% sequence coverage, per species. Our findings provide good support for the application of large-scale bait capture across congeneric species spanning approximately 15 Myr of evolution. On the other hand, we observed no clear association between the success of capture and the phylogenetic distance from the bait model, although sample sizes precluded a formal test. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. ADDITIONAL KEYWORDS: DNA – high-throughput sequencing – phylogenomics – pull-down – Rhinolophus – systematics – target enrichment.
The odour of pyrazine increases the egg mass of domestic chickens (Gallus gallus domesticus L.)

Forty leghorn chickens at the commencement of egg laying, were divided into two groups, each with 10 females and 10 males. One group was exposed to the odour of synthetic pyrazine (2-methoxy-3-isobutylpyrazine) for 16 weeks while the other acted as a control. During the first 4 weeks the hens exposed to pyrazine odour laid significantly fewer eggs (unfertilized) than the controls, but thereafter both groups laid a similar number. Mean egg mass of the pyrazine exposed hens was significantly ( P = 0.012) greater (5.5%) than that of the control group. No significant difference was found in body mass or eggshell thickness. Similarly, there were no consistent significant differences between groups in oestrogen and testosterone concentrations in the blood of females and males, respectively. No pyrazine could be detected in cloacal extracts. The experiment shows that an external odour can affect the internal reproductive system of the chicken. It is suggested that the pyrazine-engendered increase in egg mass involves neuroendocrine regulation within the hypothalamus rather than hormonal interactions ‘downstream’ of the brain.
The origin and early evolution of birds

Birds evolved from and are phylogenetically recognized as members of the theropod dinosaurs; their first known member is the Late Jurassic Archaeopteryx, now represented by seven skeletons and a feather, and their closest known non‐avian relatives are the dromaeosaurid theropods such as Deinonychus. Bird flight is widely thought to have evolved from the trees down, but Archaeopteryx and its outgroups show no obvious arboreal or tree‐climbing characters, and its wing planform and wing loading do not resemble those of gliders. The ancestors of birds were bipedal, terrestrial, agile, cursorial and carnivorous or omnivorous. Apart from a perching foot and some skeletal fusions, a great many characters that are usually considered ‘avian’ (e.g. the furcula, the elongated forearm, the laterally flexing wrist and apparently feathers) evolved in non‐avian theropods for reasons unrelated to birds or to flight. Soon after Archaeopteryx, avian features such as the pygostyle, fusion of the carpometacarpus, and elongated curved pedal claws with a reversed, fully descended and opposable hallux, indicate improved flying ability and arboreal habits. In the further evolution of birds, characters related to the flight apparatus phylogenetically preceded those related to the rest of the skeleton and skull. Mesozoic birds are more diverse and numerous than thought previously and the most diverse known group of Cretaceous birds, the Enantiornithes, was not even recognized until 1981. The vast majority of Mesozoic bird groups have no Tertiary records: Enantiornithes, Hesperornithiformes, Ichthyornithiformes and several other lineages disappeared by the end of the Cretaceous. By that time, a few Linnean ‘Orders’ of extant birds had appeared, but none of these taxa belongs to extant ‘families’, and it is not until the Paleocene or (in most cases) the Eocene that the majority of extant bird ‘Orders’ are known in the fossil record. There is no evidence for a major or mass extinction of birds at the end of the Cretaceous, nor for a sudden ‘bottleneck’ in diversity that fostered the early Tertiary origination of living bird ‘Orders’.
LEUKOCYTE ALKALINE PHOSPHATASE CYTOCHEMISTRY: APPLICATIONS AND METHODS *

Introduction Almost 20 years ago 0. P. Jones’ in a special issue of Blood stated, “. the use of dry fixed smears is not necessarily limited to the field of descriptive or morphologic hematology but, with the proper selection of experimental material, may be utilized to good advantage in determining cell potentialities. ” In the same publication Dameshek wrote, “. morphology when appropriately interpreted, can be both physiology and chemistry. far from being dead, morphologic hematology is undoubtedly in for a renaissance period, a period in which it is hoped that appropriate staining techniques will point directly to chemical and physiopathologic alteration^. "^ That such an era has indeed emerged is evident from the titles of the papers presented in this monograph and is well exemplified by the cytochemical demonstration and assessment of leukocyte alkaline phosphatase activity (LAPA). The demonstration of enzyme activity in situ is dependent upon fixation methods that will preserve cytological detail with minimal inhibition of enzyme activity and upon an enzyme-substrate reaction product which is either insoluble in its immediate environment or which can combine to form an insoluble product with other substances already present in, or to be added to, the incubation mixture. Preferably, this product should be colored so as to be visible under ordinary transmitted light, or a colorless product may be reacted on by other reagents SO as to produce a final colored precipitate that is localized at the theoretical sites of enzyme activity. There are important advantages to be gained in the study of blood, which’are denied when working with solid tissues. Blood smears, monocellular in thickness, permit the briefest of fixation and staining times and require neither embedding nor mounting. Furthermore, cellular units are intact; the cell membrane is not cut as is unavoidable in tissue sections. The intracellular detail that can be discerned in properly prepared blood smears is generally superior to that seen on sectioned tissues. Above all, blood is a unique tissue. It is readily biopsied and a minute sample is not only representative of the circulating blood-cell population but may also reflect the physiological state of the whole organism. Blood cells have been categorized according to their morphology and on the basis of their tinctorial staining characteristics (Giemsa-Wright’s stain). Thus, mature neutrophilic granulocytes have been thought of as members of a homogeneous group of cells with similar function and similar capabilities. Cytochemical techniques readily destroy such concepts. This is well exemplified by staining for LAPA, which reveals that two adjacent neutrophils, lying within a single microscopic field, appearing almost identical by conventional staining techniques, may differ markedly in alkaline phosphatase activity (FIGURE 1). Whether these
Activity of plant wastes on acute phase proteins in cows

Abstract The effect of two patented protected plants wastes (PW), named in the paper as PE and CO, has been evaluated in dairy heifers under ACTH challenge. The experimental protocol used for each compound involved 3 groups of 5 heifers, 18 days of adaptation to the experimental diets and 5 days (22-26) of ACTH treatment (0.5 mg of Synachten – Novartis - twice a day). In addition to the basal diet, 1 kg of a mixture of dehy beet pulp and PW in the ratio of 1.0:0.0 (EXP-0), 0.1:0.9 (EXP-1) and 0.3:0.7 (EXP-2) was fed in the morning meal to the experimental groups. Blood was sampled before (days 19 and 22) and during (days 24 and 26) ACTH treatment and analysed for cortisol, glucose, ceruloplasmin and haptoglobin. Acute phase proteins increased in the EXP-1 group for PE (P<0.01) and in EXP-2 group for CO (P<0.05), while the higher concentration of CO reduced haptoglobin concentration (P=0.01). These results suggest that the efficacy of PW integration is dose dependent and the optimal dose seems to be different between the 2 selected compounds.
Annual rhythms of some physiological parameters in Ovis aries and Capra hircus

The aim of this study was to evaluate the annual variation of some physiological parameters (total lipid, NEFA, phospholipids, triglycerides, creatinine, β-idrossibutirrate, albumin, total protein, total cholesterol, urea, uric acid, glucose, rectal temperature and heart rate) in five female goats and five female sheep housed under natural photoperiod and natural ambient temperature in a 12 m2 sound proof box equipped with 50 × 100 cm opening window, that allowed natural ventilation. ANOVA was used to determine significant differences (p values < 0.05 were considered statistically significant). A trigonometric statistical model was applied to describe the periodic phenomenon analytically, by individuating the main rhythmic parameters according to the single cosinor procedure. Serum total lipid, NEFA, phospholipids, triglycerides, rectal temperature and heart rate, both in sheep and goats, showed an annual rhythm with acrophases in autumn. The results show that sheep and goats present similar annual patterns, probably influenced by various environmental factors.
Molecular Communication: Application areas of molecular communication

We began this book with a short example about targeted drug delivery, an important application area for molecular communication; we now elaborate on this significant and motivating example for molecular communication. We also discuss other potential application areas of molecular communication, such as tissue engineering, lab-on-a-chip technology, and unconventional computation. For each application area, we start with a brief introduction to the area and describe potential application scenarios where bio-nanomachines communicate through molecular communication to achieve the goal of an application. We then describe in detail selected designs of molecular communication systems as well as experimental results in the area. Drug delivery Drug delivery provides novel methodologies for drug administration that can maximize the therapeutic effect of drug molecules [1,2]. One goal of drug delivery is to develop drug delivery carriers that can carry and deliver drug molecules to a target site in a body. Such drug delivery carriers are made from synthetic or natural particles (e.g., pathogens or blood cells) and they are typically nano to micrometer in size, so they can be injected into the circulatory system to propagate in a body. Targeting of drug delivery carriers in a body can be performed by exploiting pathological conditions that appear at a target site (e.g., tumor tissues). For instance, tumor tissues develop small gaps between nearby endothelial cells in a blood vessel, so drug delivery carriers, if small enough, can propagate through the gaps to accumulate in the tumor tissues.
Efficacy of RT-PCR for the detection of E. coli in drinking water

Background: Escherichia coli (E. coli) is an indicator of potential human fecal contamination. Polymerase Chain Reaction (PCR) as an ideal detection method for detecting E. coli has some advantages like rapidity, high sensitivity and accuracy, easy performance, ability to run in high numbers and inexpensiveness. On the other hand, the disadvantage of PCR is possibility of its false positive results. In this study, reverse transcriptase polymerase chain reaction (RT-PCR) method was used to overcome the problem, and the results were compared to most probable number (MPN). Materials and Methods: 16srRNA forward (SF) and 16srRNA reverse (SR) primers were designed using E. coli 16srRNA sequence. After preparing different diluted samples of E. coli in distilled water, the bacteria were separated by FHLP and HAWP filters and its 16srRNA was propagated using mentioned primers. To confirm the sensitivity of the RT- PCR method compared to MPN one, samples obtained from 15 water sources in Arak city were examined. Results: The number of bacteria in dilutions were confirmed with culture. RT-PCR data showed that FHLP compared to HAWP filters have a higher capability in separating of bacteria in different dilutions. Also there was a higher sensitivity of RT-PCR compared to RT- PCR and MPN. Conclusion: RT-PCR can detect the bacteria in lower dilutions of bacterial suspension. Hydrophobic filters (e.g. FHLP) compared to hydrophilic filters (e.g. HAWP) have higher capability in separating bacteria. To detect all coliform bacteria RT-PCR amplifications achieved by cells concentrated with hydrophobic filters are recommended. Keywords: Water pollution, Escherichia coli, Reverse transcriptase polymerase chain reaction,
From 18S ribosomal sequence data to evolution of morphology among the fungi

From ribosomal DNA sequence data we can estimate ascomycete relationships, the time of divergence of major ascomycete lineages, and the history of morphological evolutionary change. Groups long accepted by mycologists such as the filamentous ascomycetes with fruiting bodies, (the plectomycetes and pyrenomycetes) are supported by 18S rDNA sequence data. After generating a phylogenetic tree showing relationships, the geological time of divergence of major fungal lineages may be estimated, inferring elapsed time using the calibrated percent substitutions between sequences. Determining the pathway of evolution of morphological characters is more difficult than inferring the relationships among these taxa. To establish the history of morphological evolution, we need accurate trees receiving strong support from our data set. We also need taxa with the intermediate characters to reveal the sequence of events in morphological evolution. Soon, however, we may be able to take a more direct approach to evolution of .
Likely Changes in Habitat Quality for Fish and Wildlife in Coastal Louisiana during the Next Fifty Years

ABSTRACT Nyman, J.A. ; Baltz, D.M. ; Kaller, M.D.; Leberg, P.L. ; Parsons Richards, C. ; Romaire, R.P., and Soniat, T.M. , 2013. Likely changes in habitat quality for fish and wildlife in coastal Louisiana during the next fifty years. Louisiana's 2012 Master Plan for a sustainable coast was designed to minimize economic damage from storm surges and to maximize wetland habitat for fish and wildlife. Selecting projects for inclusion in the master plan depended partly on models that simulated the effects of management options on environmental factors that control habitat quality for fish and wildlife. We used 13 models to predict the effects of the master plan on habitat quality for fish and wildlife in coastal Louisiana. Habitat quality was predicted to change more for the Neotropical songbirds and seven other modeled species losing habitat quality with the status quo (−37%) than it was predicted to increase for five modeled species gaining habitat quality with the status quo (+18%). The master plan was predicted to slow or negate all changes associated with the status quo. All of the modeled fish and wildlife belong to people of the state of Louisiana, people living in countries bordering the Gulf of Mexico, and to people throughout the Americas. Thus, declining fish and wildlife habitat quality in Louisiana probably will cause market and nonmarket losses, which although concentrated in Louisiana, will extend across the Americas. As funding for Louisiana's master plan is pursued, it is important to consider that almost all of the causes for net wetland losses in Louisiana are external to the owners of these wetlands but that the fish and wildlife that use these wetlands belong to and benefit people throughout the Americas.
Effect of spiking of young males in different percentage on economic performance of broiler breeder flock

In order to improve fertility performances of a broiler breeder flock and investigate its effect on economic performance of flock, males existing in flock at laying period were divided in 7 separated treatments by completely random design (CRD) with different management treatments. The results of hatching egg percent of fertile eggs in different treatments were considered as fertility index of flock. Treatment 7 was control and repeats of design were age of flock at the weeks of 28 to 66. Sex ratio of males to females was reduced at the weeks of 30, 35, 40 and 62. At the week 44, spiking of young males in the main flock was performed for treatments 1 to 6 in different percentage of 100, 80, 60, 40, 20 and 10. Hatching egg percent values of treatments in three periods of weeks 28 to 44 (before spiking), weeks 44 to 66 (after spiking) and weeks 28 to 66 (before and after spiking) compared with each other by least significant difference (LSD) procedure. Results showed that by except of treatments 1 and 2, reduction of spiking percentage caused no significant decrease in hatching eggs percent, but treatment 2 compared with treatment 1 had no significant increase in hatching egg percent (P>0.01). Effect of spiking on culling percent of females resulted from physical damages of males were not significant between treatments 1 to 5 (P>0.01); but it was significant with treatments 6 and 7 (P 0.01). Therefore, spiking of young males in different percentages and decrease of sex ratio of males to females had no significant effect on hatching egg percent and flock fertility. Study of economic performance of different treatments showed that treatments with the most spiked male percentage had the least and treatments with the least spiked male percentage the most economic performance of the male’s fertility management.
Notch1 induces enhanced expression of Δ-like-1 in the U251MG glioma cell line

The Notch signaling pathway takes part in coordinated regulation of cell growth, survival and differentiation. Previous findings have shown that Notch1 and Delta-like-1 (DLL1) are overexpressed in many glioma cell lines and primary human gliomas. Down-regulation of DLL1 by RNA interference inhibits proliferation and induces apoptosis in multiple glioma cell lines. Our studies showed that Notch1 expression plasmid induced more expression of DLL1 in the U251MG glioma cell line. Adversely, blocking Notch1 receptors down-regulated the expression of DLL1. Both down-regulating DLL1 and blocking Notch1 receptors induced U251MG cell apoptosis and proliferation inhibition, and combining the two treatments produced stronger effects than the sum of a single treatment. These findings suggest a positive feedback loop between Notch1 and DLL1, which may become an effective combined therapeutic target.