Miracle-dz/UniFAR-FTUs huggingface dataset:
PHENOTYPIC ADJUSTMENT OF CLUTCH SIZE DUE TO NEST PREDATION IN THE GREAT TIT

Nest predation may decrease the optimal clutch size for many reasons. In particular, a smaller clutch size may permit more investment in re-laying or in survival to the next reproductive event. The response to nest predation may be either genetic, as shown by comparative studies on birds, or phenotypic, as found in several aquatic species (in- vertebrates and fish). We have studied the effects of several years of high nest predation on clutch size variation in a Great Tit (Parus major) population. We tested whether nest predation was associated with selection on clutch size or with any phenotypic changes. In the year following peak nest predation, mean clutch size was reduced by about one egg. For nest predation, adult survival, and local recruitment, we failed to detect any dependence on clutch size; the reduction in clutch size was mostly phenotypic. Similarly, the return of clutch size to pre-predation values was explained as a phenotypic change. Surprisingly, individuals that did not experience nest predation themselves also modified their clutch size. This suggests that information on past predation persisted in the population for several years. In years with reduced clutch size, adult survival at the population level was higher, suggesting that a reduction in clutch size would be adaptive in case of nest predation, and that females adjusted their clutch size toward the optimum.
An algorithmic perspective on randomness in quantum mechanics

This thesis investigates the precise kind of randomness generated by quantum measurements. First a rigorous deﬁnition of randomness is given using the theory of algorithmic randomness. Thereafter it is investigated if there are quantum measurements of which it can be shown that they can be used to generate random ﬁnite or inﬁnite binary strings. First, no go theorems from quantum theory are discussed. Second, articles attempting to answer this are studied. Third, the justiﬁcations given by a manufacturer of quantum random number generators are reviewed. Finally, this thesis considers an experimental method for validating the randomness of quantum measurements.
Exploring the role of microRNAs in axolotl regeneration

The axolotl, Ambystoma mexicanum, is used extensively for research in developmental biology, particularly for its ability to regenerate and restore lost organs, including in the nervous system, to full functionality. Regeneration in mammals typically depends on the healing process and scar formation with limited replacement of lost tissue. Other organisms, such as spiny mice (Acomys cahirinus), salamanders, and zebrafish, are able to regenerate some damaged body components. Blastema is a tissue that is formed after tissue injury in such organisms and is composed of progenitor cells or dedifferentiated cells that differentiate into various cell types during regeneration. Thus, identifying the molecules responsible for initiation of blastema formation is an important aspect for understanding regeneration. Introns, a major source of noncoding RNAs (ncRNAs), have characteristic sizes in the axolotl, particularly in genes associated with development. These ncRNAs, particularly microRNAs (miRNAs), exhibit dynamic regulation during regeneration. These miRNAs play an essential role in timing and control of gene expression to order and organize processes necessary for blastema creation. Master keys or molecules that underlie the remarkable regenerative abilities of the axolotl remain to be fully explored and exploited. Further and ongoing research on regeneration promises new knowledge that may allow improved repair and renewal of human tissues.
A Novel Device for the Collection, Storage, Transport, and Delivery of Beneficial Insects, and its Application to Ophraella communa (Coleoptera: Chrysomelidae)

A multi-use device was developed for the collection, short-term storage, transport, and delivery of Ophraella communa (Coleoptera: Chrysomelidae), a biological control agent of common ragweed, Ambrosia artemisiifolia. The device is made from a 125-ml plastic specimen container that can hold O. communa adults or pupae. When used as an aspirator, insect collection and counting times are reduced. O. communa adults and pupae can be stored inside the container at 3°C with median survival of 41 and 21 days, respectively. A cotton wick saturated with water or a 5% sugar solution nourishes insects during transport and the container design minimizes insect mortality by providing an optimum microclimate during insect storage and transport. Designed to protect insects from rainfall and to limit encounters with predators and parasites, the containers can be used for field releases of O. communa adults and pupae. Although the container has been designed and tested for O. communa, it is highly versatile and could possibly be used with a variety of insect species.
Gene expression profiling of Dunaliella sp. acclimated to different salinities

To investigate which genes may be important for growth under extreme conditions such as very low or high salinities, a survey of the Dunaliella sp. transcriptome was performed with a cDNA microarray which had been generated previously representing 778 expressed sequence tags. The comparative microarray analysis indicated that 142 genes differed in expression levels by more than twofold in cells grown at extreme salinities (0.08 M and 4.5 M NaCl) when compared with cells grown at intermediate salinity (1.5 M NaCl). Of these genes, 28 had increased expression and 57 were suppressed in cells grown at low salinity. In cells grown at high salinity, 43 genes showed increased expression and 69 genes showed suppressed expression. However, we did observe a large overlap in the expression of extreme salinity‐responsive genes based on Venn diagram analysis, which found 55 genes that responded to both of the two extreme salinity conditions. Further, we found that several genes had similar expression levels under low and high salinities, including some general stress response genes that were upregulated in both extreme salinity conditions. For confirmation of the validity of the cDNA microarray analysis, expression of several genes was independently confirmed by the use of gene‐specific primers and real‐time polymerase chain reaction. The present study is the first large‐scale comparative survey of the transcriptome from the microalga Dunaliella sp. acclimated to extreme salinities, thus providing a platform for further functional investigation of differentially expressed genes in Dunaliella.
Aspects of the regulation of expression of pcnB, which encodes poly (A) polymerase I of Escherichia coli

The pcnB gene encodes poly(A) polymerase I (PAP I), the major Escherichia coli poly(A) polymerase involved in mRNA processing, and the decay of small plasmid copy number control RNAs. Prior to the study presented here, the transcriptional and translational organisation of the pcnB region was illdefined. In this work, the pcnB promoter, identified by sub-cloning and primer extension analysis, was found to resemble closely a consensus 70 promoter in both sequence and activity. Operon fusions of pcnB with lacZ are only slightly derepressed in a ApcnB background, providing little evidence of autoregulation at the level of transcription. Translation of the pcnB message was shown, by site-directed mutagenesis, to commence from the ribonucleotides AUU, a triplet that is very rarely used as an initiation codon. Furthermore, it was demonstrated that at the level of translation, the in vivo expression of pcnB is specifically subject to negative regulation, over a fourfold range, by Initiation Factor-3 (IF-3), whose own translation is also initiated from an AUU codon. Additional tests showed that a single chromosomal copy of wild-type infC (which encodes IF-3) can induce maximal IF-3-mediated repression of pcnB. Apart from the Shine-Dalgarno region, pcnB appears to lack any of the known sequence determinants encoded by infC that are believed to facilitate the use of AUU as an initiation codon. Several pcnB homologues are identified from other eubacteria that potentially could utilise an AUU triplet as a translational initiation codon. A conserved run of T residues (five to seven nucleotides long) exactly nine nucleotides downstream from the -10 region of these homologues suggested that the expression of pcnB might be subject to regulation by pyrimidinesensitive selection of transcriptional start sites, coupled with UTP-dependent reiterative transcription. This possibility was investigated.
Differential modulation of the contextual conditioned emotional response by CB1 and TRPV1 receptors in the ventromedial prefrontal cortex: Possible involvement of NMDA/nitric oxide-related mechanisms

Background: Blockade of cannabinoid CB1 or vanilloid TRPV1 receptors in the ventromedial prefrontal cortex of rats respectively increases or decreases the conditioned emotional response during re-exposure to a context previously paired with footshocks. Although these mechanisms are unknown, they may involve local modulation of glutamatergic and nitrergic signaling. Aim: We investigated whether these mechanisms are involved in the reported effects of CB1 and TRPV1 modulation in the ventromedial prefrontal cortex. Methods: Freezing behavior and autonomic parameters were recorded during the conditioned response expression. Results: The CB1 receptors antagonist NIDA, or the TRPV1 agonist capsaicin (CPS) in the ventromedial prefrontal cortex increased the conditioned emotional response expression, and these effects were prevented by TRPV1 and CB1 antagonism, respectively. The increased conditioned emotional response evoked by NIDA and CPS were prevented by an NMDA antagonist or a neuronal nitric oxide synthase inhibitor. A nitric oxide scavenger or a soluble guanylate cyclase inhibitor prevented only the NIDA effects and the CPS effect was prevented by a non-selective antioxidant drug, as nitric oxide can also induce reactive oxygen species production. Conclusion: Our results suggest that CB1 and TRPV1 receptors in the ventromedial prefrontal cortex differently modulate the expression of conditioned emotional response through glutamatergic and nitrergic mechanisms, although different pathways may be involved.
First glimpse into the origin and spread of the Asian longhorned tick, Haemaphysalis longicornis, in the United States

Established populations of Asian longhorned ticks (ALT), Haemaphysalis longicornis, were first identified in the United States (US) in 2017 by sequencing the mitochondrial cytochrome c oxidase subunit I (cox1) ‘barcoding’ locus followed by morphological confirmation. Subsequent investigations detected ALT infestations in 12, mostly eastern, US states. To gain information on the origin and spread of US ALT, we (1) sequenced cox1 from ALT populations across 9 US states and (2) obtained cox1 sequences from potential source populations [China, Japan and Republic of Korea (ROK) as well as Australia, New Zealand and the Kingdom of Tonga (KOT)] both by sequencing and by downloading publicly available sequences in NCBI GenBank. Additionally, we conducted epidemiological investigations of properties near its initial detection locale in Hunterdon County, NJ, as well as a broader risk analysis for importation of ectoparasites into the area. In eastern Asian populations (China/Japan/ROK), we detected 35 cox1 haplotypes that neatly clustered into two clades with known bisexual versus parthenogenetic phenotypes. In Australia/New Zealand/KOT, we detected 10 cox1 haplotypes all falling within the parthenogenetic cluster. In the United States, we detected three differentially distributed cox1 haplotypes from the parthenogenetic cluster, supporting phenotypic evidence that US ALT are parthenogenetic. While none of the source populations examined had all three US cox1 haplotypes, a phylogeographic network analysis supports a northeast Asian source for the US populations. Within the United States, epidemiological investigations indicate ALT can be moved long distances by human transport of animals, such as horses and dogs, with smaller scale movements on wildlife. These results have relevant implications for efforts aimed at minimizing the spread of ALT in the United States and preventing additional exotic tick introductions.
open-japanese-mesh: assigning MeSH UIDs to Japanese medical terms via open Japanese-English glossaries

The Medical Subject Headings (MeSH) thesaurus is a controlled vocabulary for indexing biomedical documents that is used for document retrieval and other natural language processing purposes. However, although the original English MeSH is freely available, its Japanese translation has a restricted license. We attempted to create an open alternative, and for this purpose we made a script for assigning MeSH UIDs to Japanese medical terms using Japanese-English glossaries. From the MeSpEn glossary and MEDUTX dictionary, we generated a 12,457-word Japanese-MeSH dictionary.
ER-α variants and the cardiovascular effects of hormone replacement therapy

There is an accumulating body of evidence linking estrogen receptor-α (ER-α) gene polymorphisms with variation in cardiovascular risk factors or disease. The ER-α IVS1-397 T/C (PvuII), IVS1-351 A/C (XbaI) and the promoter region TA repeat polymorphisms have received the most attention. If ER-α genetic variants identify women at high risk for cardiovascular events, this information could be used to improve clinical decisions regarding the use of hormone replacement therapy (HRT). More detailed haplotype and genome-wide studies of many of the major HRT clinical trial cohorts are currently underway and these efforts promise to clarify many outstanding issues concerning estrogen action and cardiovascular disease.
The effect of plant structure on the intake of tropical pasture. III.* Influence of fertilizer nitrogen on the size of bite harvested by Jersey cows grazing Setaria anceps cv. Kazungula swards

The effect of fertilizing Setaria anceps cv. Kazungula swards with nitrogen on the size of bite harvested by cattle was determined and the influence of sward canopy structure upon bite size was investigated in two experiments. The first experiment measured the effect of nitrogen at 0, 40, 60 and 100 kg/ha on 6-week regrowth, and the second measured the effect at 50 and 100 kg/ha on 4- and 6-week regrowths of both unfertilized swards and others which had received 350 kg nitrogen per hectare in each of the previous three years. The mean bite size of cows grazing immature (4-week) regrowths increased linearly with increasing applications of nitrogen, averaging 0.29, 0.33 and 0.37 g organic matter (OM) per bite on the 0, 50 and 100 kg/ha treatments respectively. Swards which allowed the largest bites to be prehended had the highest leaf yields and the highest leaf bulk densities. The mean bite size on 6-week regrowths was lower (0.28 g OM/bite) than on 4-week regrowths (0.33 g OM/bite). Cows selected leaf from the upper layers of the swards, and inaccessibility of leaf resulting from a high stem and inflorescence content prevented animals from taking larger bites. In both experiments high levels of nitrogen fertilizer advanced the maturity of 6-week regrowths, and the bite size of cows grazing these pastures did not increase beyond the level recorded at intermediate nitrogen levels. It was concluded that fertilizer nitrogen increases dry matter and leaf yields, particularly in the uppermost layers of the sward, allowing cows to harvest large bites of immature herbage. A higher stem and inflorescence content in heavily fertilized swards can result in inaccessibility of leaf when mature herbage is grazed. ________________ *Part II, Aust. J. Agric. Res., 24: 821 (1973).
UPF1-Mediated RNA Decay—Danse Macabre in a Cloud

Nonsense-mediated RNA decay (NMD) is the prototype example of a whole family of RNA decay pathways that unfold around a common central effector protein called UPF1. While NMD in yeast appears to be a linear pathway, NMD in higher eukaryotes is a multifaceted phenomenon with high variability with respect to substrate RNAs, degradation efficiency, effector proteins and decay-triggering RNA features. Despite increasing knowledge of the mechanistic details, it seems ever more difficult to define NMD and to clearly distinguish it from a growing list of other UPF1-mediated RNA decay pathways (UMDs). With a focus on mammalian NMD, we here critically examine the prevailing NMD models and the gaps and inconsistencies in these models. By exploring the minimal requirements for NMD and other UMDs, we try to elucidate whether they are separate and definable pathways, or rather variations of the same phenomenon. Finally, we suggest that the operating principle of the UPF1-mediated decay family could be considered similar to that of a computing cloud providing a flexible infrastructure with rapid elasticity and dynamic access according to specific user needs.
ANTIBACTERIAL ACTIVITY OF PHYLLANTHUS MADERASPATENSIS LEAVES EXTRACT

Nature has been a source of medicinal agents for thousands of years and an impressive number of modern drugs have been isolated from natural sources; many of these isolations were based on the uses of the agents in traditional medicine. This plant-based, traditional medicine system continues to play an essential role in health care, with about 80% of the world’s inhabitants relying mainly on traditional medicines for their primary health care. According to World Health Organization, medicinal plants would be the best source to obtain a variety of drugs. Therefore, such plants should be investigated to better understand their properties, safety and efficacy. Phyllanthus maderaspatensis commonly known as a “Madras Leaf Flower” have promising therapeutic value with its various phytochemical constituents such as tannins, alkaloids, steroids, flavonoids, terpenoids, fatty acids, phenols, minerals, carbohydrates and vitamins. The present study was done to determine the antibacterial activity of P. maderaspatensis leaves extract against clinical isolates of some bacteria using well diffusion method. The extracts showed inhibitory activity against clinical isolates of gram negative bacteria such as Salmonella typhi, Shigella dysentriae, Klebsiella pneumonia, Pseudomonas aeruginosa and Escherichia coli and gram positive bacteria such as Bacillus subtilis and Staphylococcus aureus. The results showed that the acetone extracts were more potent than the other extracts. The acetone extracts of Phyllanthus maderaspatensis showed best activity against Klebsiella pneumonia with a minimum inhibitory concentration(MIC) of 10 mg/ml.
Association of plasma exosomes with severity of organ failure and mortality in patients with sepsis

Current sepsis biomarkers may be helpful in determining organ failure and evaluating patient clinical course; however, direct molecular biomarkers to predict subsequent organ failure have not yet been discovered. Exosomes, a small population of extracellular vesicles, play an important role in the inflammatory response, coagulation process and cardiac dysfunction in sepsis. Nonetheless, the association of plasma exosome with severity and mortality of sepsis is not well known. Therefore, the overall levels of plasma exosome in sepsis patients were assessed and whether exosome levels were associated with organ failure and mortality was evaluated in the present study. Plasma level of exosomes was measured by ELISA. Among 220 patients with sepsis, 145 (66%) patients were diagnosed with septic shock. A trend of increased exosome levels in control, sepsis and septic shock groups was observed (204 µg/mL vs 525 µg/mL vs 802 µg/mL, P < 0.001). A positive linear relationship was observed between overall exosome levels and Sequential Organ Failure Assessment (SOFA) score in the study cohorts (r value = 0.47). When patients were divided into two groups according to best cut‐off level, a statistical difference in 28‐ and 90‐day mortality between patients with high and low plasma exosomes was observed. Elevated levels of plasma exosomes were associated with severity of organ failure and predictive of mortality in critically ill patients with sepsis.
The role of seasonally altering photoperiod in regulating physiology in Atlantic cod (Gadus morhua). Part I. Sexual maturation

While the Atlantic cod (Gadus morhua) displays clear seasonality in its reproductive cycle, the exact photic signal that entrains this rhythm is yet undefined. This present work developed a model to describe the photic regulation of reproduction in the species in comparison with other commercially important temperate teleosts. This was achieved through the strategic masking of the natural photoperiod cycle during the first 2 years of life with the application of continuous illumination. The results demonstrated that it is the falling autumnal photoperiod signal after the summer solstice, more specifically after October, that is responsible for recruiting individuals to enter the sexual maturation cycle. Furthermore, in all treatments where this signal was masked through the application of continuous illumination, there was no significant reproductive activity and growth was improved by up to 60% at 27 months posthatch. This information is of particular value to the developing cod aquaculture industry in w.
Evaluation of antioxidant potential of Indian wild leafy vegetable Tribulus terrestris .

Antioxidants play an important role in inhibiting and scavenging free radicals, thus providing protection to human against various infections and degenerative diseases. Polyphenols have been proved to possess antioxidant activities and thus have been used for the prevention and cure of diseases which are mainly associated with free radicals. The present investigation was undertaken to screen the phytochemicals, in vitro antioxidant and assessment of free radical scavenging activity of aqueous and alcoholic extracts of Tribulus terrestris Linn. (Zygophyllaceae) by using different analytical methods viz, 1, 1-diphenyl-2-picryl-hydrazyl (DPPH) free radical scavenging assay, hydrogen peroxide radical scavenging assay, polyphenol contents, etc. Aqueous and alcoholic extracts of T. terrestris exhibited concentration dependent free radical scavenging activity in all models studied. Total phenolic content of alcoholic extract of T. terrestris is higher than corresponding aqueous extract.
Effect of Abscisic Acid and Benzyladenine on Fruit Set and Fruit Quality of Apples

Experiments were conducted over a 5-year period to determine the effects of abscisic acid (ABA) and benzyladenine (BA) applied alone and in combination on fruit set, fruit quality, and return bloom of 'McIntosh' and 'Fuji' apples. ABA thinned in 3 of the 5 years used and it thinned 'McIntosh' when applied at bloom, petal fall, and at the 10-mm fruit size stage. On 'Fuji', ABA thinned over a range of concentrations from 150 to 1000 mgL -1 . It caused leaf yellowing on 'McIntosh' but not on 'Fuji'. When BA was applied with ABA on 'McIntosh', even at a rate as high as 1000 mgL -1 , it either dramatically reduced or prevented leaf yellowing and leaf abscission. The usefulness of applyingBA withABA was inconclusive because ofvariability in thinning response. ABA advanced surface red color on 'McIntosh' and when combined with BA, it reversed the reduction in red color caused by BA.
Physiological response to sub lethal concentra­ tion of nickel on marine and fresh water algae

Effect of nickel at low levels on chlorophycean alga and a diatom was studied. A comparative study of the growth parameters made on both the microalgae showed that divalent nickel retarded the growth of algae at the higher concentration used even though low test concentrations had a stimulatory effect. It was found that nickel toxicity is related to the presence of divalent nickel and can be influenced by environmental factors.