Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic susceptibility to chronic obstructive pulmonary disease

Summary The reasons why only a fraction of smokers develop clinical manifestations of chronicobstructive pulmonary disease (COPD) have been a focus of research. The variableresponse to cigarette smoke clearly suggests a degree of genetic susceptibility.Among the candidate genes that have been studied in COPD are those regulatingproteases and antiproteases (e.g. a 1 -antitrypsin, serpine2, a 1 -antichymotrypsin, a2-macroglobulin, secretory leukocyte proteinase inhibitor, matrix metalloproteinases,ADAM33 and protease activated receptor-2), antioxidant genes (e.g. microsomalepoxide hydrolase, glutathione-S-transferase, cytochrome P4501A1 and extracellularsuperoxide dismutase), genes regulating mucociliary clearance (e.g. cystic ﬁbrosistransmembrane regulator and mucins), and genes that inﬂuence inﬂammatorymediators (e.g. vitamin D-binding protein, tumour necrosis factor-a, interleukin(IL)-11, the IL-1 family, IL-13, transforming growth factor-b1, immunoglobulindeﬁciency, blood group antigens and the human leukocyte antigen locus). Recently, detection of microsatellite DNA instability (MSI) has suggested that MSIcan be considered as a useful genetic screening marker for the "susceptible" smoker.Keywords: Antioxidant, chronic obstructive pulmonary disease, cigarette smoking,inﬂammatory mediators, microsatellite DNA, proteases–antiproteases.
Morphological channeling by structural constraint: convergence in styles of dwarfing and gigantism in Cerion, with a description of two new fossil species and a report on the discovery of the largest Cerion

A survey of all Cerion taxa and geographic variants reveals that a distinctive shape—a narrowly spired “smokestack” shell more than three times higher than wide—occurs only in dwarfs and giants and never in the much more common populations of normal size. The smokestack shape evolved once in giants (in the newly described species C. excelsior from Great Inagua and Mayaguana—the largest of all Cerion), but at least seven and probably eight times independently in dwarfs. A study of complex allometric patterns in Cerion's ontogeny, and of covariance sets in growth, indicates that smokestacks can easily evolve in dwarfs and giants by the common route of relative increase in whorl number during an allometric phase that adds height but no width to the shell. (Giants simply add more whorls to a shell with whorls of normal size; dwarfs grow a normal number of whorls in a shell with small whorls and reduced maximum width.) This pathway is not open to Cerion of normal size, and the restriction of smokestacks to both extremes of the size range records a channel set by Cerion's invariant allometries and the geometry of spiral growth in general, not an immediate adaptation conferring special advantages via the elevated spire itself.
Taxonomy of the Plethodontid salamander Genus ensatina

Highton (1998) argued that published data warrant a taxonomic revision of the Ensatina complex. The complex comprises units that have varying degrees of phenetic and phylogenetic differentiation, but morphological/coloration, protein, and mtDNA data sets are less concordant than Highton believed. We employ different criteria to discover species than did Highton. His proposed species do not fulfill our criteria. Several are not diagnosable, nor do they have identity as evolutionarily independent lineages or as genetically cohesive units. Furthermore, he misinterpreted Stebbins' (1949) conception of a ring species, which was an evolutionary and biogeographic hypothesis. As observed as long ago as Stebbins' original work, taxonomic resolution of the complex is neither simple nor will a changed taxonomy solve the biological problems identified. The biological complexity of Ensatina argues against a simple taxonomic resolution, because the evolutionary realities of diversification in old and persistent complexes require compromises if Linnean taxonomies are to be used. We prefer a taxonomy that clarifies the evolutionary relationships among the components and that highlights, rather than obscures, the complex interactions of the past and present. Accordingly, while we recognize that a new taxonomy may be required when studies in progress are concluded, for the present we recommend continued recognition of the Ensatina complex as a single polytypic taxonomic species.
Preliminary study on Ethno-medicinal plants used for treating malarial fever in Pilibhit Tiger Reserve, Uttar Pradesh, India.

Present study provides significant information on ethno-medicinal plants used for treating malarial fever by the Tharu tribe of Pilibhit Tiger Reserve . The ethno-medicinal data was collected by using prescribed questionnaire. A total 30 informants were critically interviewed for data collection. A total of 23 plant species representing 22 families were found to be commonly used to treat malarial fever. The families most represented were Lamiaceae (4 species) followed by Solanaceae (3 species), Cucurbitaceae and Menispermaceae (2 species each). Some novel traditional uses of certain plants as medicines for treating malarial fever were also recorded. The medicinal plants with botanical name and collection number are arranged in alphabetical order followed by the family, local name growth form parts used and mode of administration. This study generates first-hand information on antimalarial plants used in the region. Present study is a precursor for a detailed pharmacological analysis to ensure scientific validation.
Effect of scarification, gibberellic acid and temperature on seed germination of two multipurpose Albizia species from Ethiopia

Seeds of Albizia grandibracteata and Albizia gummifera possess seedcoat-imposed dormancy hampering complete, rapid and uniform germination. To overcome this dormancy, seeds of both species were pre-treated with mechanical scarification or concentrated sulphuric acid for 10, 20, 30, 40 and 60 minutes or hot water at 60, 70, 80, 90 and ca. 100°C. Besides, scarified seeds of A. grandibracteata were treated with three concentrations of gibberellic acid: 10 -3 , 10 -4 and 10 -5 M. To determine the effects of temperature on seed germination, pre-treated seeds from each species were germinated at 15, 20, 25, 30 and 35°C. All scarification treatments improved the germination capacity and vigour of A. gummifera seeds, the highest being after mechanical scarification followed by sulphuric acid and 80°C hot water treatments. Only mechanical scarification gave the highest germination in A. grandibracteata seeds. GA treatment of mechanically scarified seeds resulted in more than 50% germination, and GA 3 , 10 -4 M was better than the others were. Germination capacity and the speed of germination were higher at 20 and 25°C in both species; but A. gummifera seeds gerntinated well over a wider range of temperatures.
The Case for Archetypal Vertebrate Ichnofacies

ABSTRACT Vertebrate and invertebrate ichnology have different traditions—the ethological and the biotaxonomic—resulting in corresponding ethoichnofacies and biotaxonichnofacies. Archetypal vertebrate ichnofacies are Chelichnus, Grallator, Brontopodus, Batrachichnus, and Characichnos. Ichnofacies are discernable in nonmarine environments. Tetrapod trace fossils can be utilized in the definition of ichnofacies. It is reasonable to use trace fossils of only one phylum (Vertebrata) to define ichnofacies because vertebrate ichnofossils yield biotaxonichnofacies, whereas Seilacherian ichnofacies are ethoichnofacies. Early named vertebrate ichnofacies are ichnocoenoses of limited temporal extent. Archetypal vertebrate ichnofacies are biotaxonomic in nature, so they are neither directly comparable nor subsumable within Seilacherian ethoichnofacies.
A new in vitro method to evaluate digestibility of commercial diets for dogs

Abstract The aim of the present study was to develop a new in vitro method for evaluating the digestibility of commercial diets for dogs. First, in order to develop the in vitro method, the digestibility of four commercial diets for dogs was evaluated through several in vitro trials and results were compared with those that were retrieved from the literature. The in vitro method that was developed consists of two incubation phases, a first lasting 2h and taking place in the presence of pepsin, gastric lipase and HCl (gastric phase) and a second 4h one with pancreatin and bile salts (intestinal phase). Later, digestibility of 16 extruded diets for dogs was evaluated both in vivo with adult dogs and in vitro. There was a close linear relationship between in vivo total tract and in vitro dry matter digestibility (r2 = .81), whereas accuracy of crude protein digestibility using the in vitro method was lower (r2 = .51). Linear regression accuracy for ether extract and starch digestibility was low, but the digestibility results obtained with the in vitro method (95.3 and 98.7% for ether extract and starch, respectively) were very close to those from the in vivo trial (average digestibility of ether extract and starch was 94.8 and 99.1%, respectively). The present in vitro method has proved to be a relatively simple, quick procedure for predicting the digestibility of commercial diets for dogs. The utilisation of such a method may significantly reduce the need for in vivo digestion trials with dogs.
Targeting STAT3 in Ovarian Cancers: Reciprocal Activation of NF-kB by STAT3 Inhibition

3 GLOSSARY 4 INTRODUCTION 5 METHODS AND MATERIALS 10 RESULTS 14 STAT3 is associated with increased proliferation and spheroid formation of epithelial derived serous ovarian tumor------------------------------------------------14 STAT3 inhibitors appear to reduce the viability of ovarian cancer cells that have constitutively activated STAT3---------------------------------------------------------15 Not all STAT3 inhibitors block the STAT3 function via inhibition of STAT3 phosphorylation--------------16 STAT3 inhibitors disrupt cell-cell adhesion and formation of spheroids in ovarian cancers-------------17 STAT3 inhibition via STAT3 RNAi leads to upregulation of IL-8----------------------------------------18 STAT3 inhibitors such as ST3-01 can also lead to upregulation of IL-8----------------------------------------19 IL-8 upregulation is specific to STAT3 inhibition---20 IL-8 upregulation caused by STAT3 inhibition may be a marker for NF-κB pathway activation------------21 NF-κB activation is related to STAT3 inhibition in both OVCAR8 cells and in primary ovarian cancer cells------------------------------------------------------------23 A reciprocal relationship between NF-κB activity and STAT3 activity exists in ovarian cancer cells----------24 The reciprocal relationship between NF-κB and STAT3 is also observed in Renal Cell Carcinoma with constitutively activated STAT3--------------------------26 NF-κB subunit p65 translocates into the nucleus upon NF-κB activation------------------------------------27 NF-κB subunit P65 is crucial for the NF-κB activity and NF-κB target gene expression----------------------27 No significant p65 nuclear translocation is observed when STAT3 is inhibited----------------------------------30 DISCUSSION 33 SUMMARY 41 FIGURES 42 REFERENCES 83 FUNDING 90
Oscillation in expression of Adenylyl Cyclase isoforms: new insight to regulation of molecular clock

Abstract Background: Mammalian cells contain a cell-autonomous circadian clock that couples endogenous rhythms with changes of cellular environment. Some recent reports have been shown that circadian clock regulates glucose homeostasis; but, their molecular basis is little understood. Adenylyl Cyclase (AC) is a key enzyme in glucose metabolism. We aimed to investigate circadian mRNA expression of two circadian clock genes Cry1, Cry2, and nine Adenylyl Cyclase isoforms. Methods: MCF7 cell culture shocked using horse serum. Every four hours (over a 48-h period), total RNA was extracted and cDNA was synthesized. Expression level of AC isoforms and Cry genes was evaluated by quantitative RT-PCR. Results: Two AC isoforms; AC3, AC6 showed a circadian expression pattern in which they had a significant correlation with Cry1 and Cry2 transcripts. AC3 isoform was also up-regulated after serum shock. Time lags results indicated that AC3 expression was coincided with Cry2 and leads Cry1 expression. Conclusions: Adenylyl Cyclase isoforms, especially AC3, may play an important role in molecular clock regulation and response to external factors.
An Assessment of the Family Asteraceae at Shadullapur Upazila of Gaibandha District, Bangladesh with Particular Reference to Medicinal Plants

An assessment of the family Asteraceae at Sadullapur upazila of Gaibandha district, Bangladesh was carried out from August 2014 to October 2015. A total of 32 species under 27 genera belonging to the family Asteraceae were collected and identified. Frequent field trips were made during August 2014 to October 2015 to record medicinal information by interviewing local people of various age groups, mostly ranging between 18 to 67 years, including medicinal healers (herbalists/hakims). A total of 28 plant species under 24 genera of the family Asteraceae have been documented which are used for the treatment of 57 diseases/illness. In majority cases, leaves of the medicinal plants were found leading in terms of their use followed by whole plant, stem, bark, flower, seed and root. For each species scientific name, local name, chromosome number, voucher number, ailments to be treated and part(s) used are provided.
Conservation Status and Habitat Preferences of the Cozumel Curassow

I assessed the population status and habitat preferences of the Cozumel Cu-rassow, Crax rubra griscomi, in the forests of Cozumel Island, Mexico, from October 1994 to June 1995. The estimated density was 0.9 curassows km -2 with a population size of about 300 birds. These numbers and the fact that the Cozumel Curassow is restricted to the island, place this endemic cracid within the conservation status of Critically Endangered. Hunting is likely the main cause of its present conservation status. This curassow showed a greater preference for the tropical semi-deciduous forest than for the low tropical deciduous forest. Likewise, older stands of forest have a positive influence on its distribution. Freshwater sources within the forests have a positive influence on the Cozumel Curassow distribution within a radius of about 2 km. Human settlements and human accesses to the forest interior showed a negative influence on its distribution within a radius of 4.5 km.
The role of the relaxin receptor RXFP1 in brain cancer

Relaxin (RLN2) promotes cell migration/invasion, cell growth, and neoangiogenesis through binding to the relaxin receptor RXFP1 in many types of cancers. However, there have been no studies to determine the role of this system in brain tumors, especially in Glioblastoma Multiforme (GB), the most lethal primary brain tumor in adults. GB is a systemic brain disease and aggressively invades brain tissue. In this study, we have identified RXFP1 receptor, but not RLN2, in GB cell lines and primary GB cells from patients. RLN2 treatment resulted in a significant increase in migration of GB cell line and primary GB cells. To determine molecular mechanisms that facilitate RXFP1-mediated migration in GB cells, we employed a pseudopodia assay and 2D LC-MS/MS to investigate the protein composition at cell protrusions (pseudopodia) during GB cell migration. We also observed the expression of known mediators promoting tissue invasion upon RLN2 treatment. We identified PGRMC1, a candidate protein from 2D LC-MS/MS as a novel relaxin target protein in RXFP1-expressing brain tumor cells. RLN2 treatment also caused an increase in cathepsin (cath)-B and -L and enhanced production of as the small Rho-GTPases Rac1 and Cdc42 in GB cells. Collectively, these findings indicate that RXFP1-induced cell migration is mediated by the upregulation and intracellular actions of Rac1, Cdc42 and by cath-B and cath–L who serve as matrix modulating factors to facilitate brain tumor cells migration. PGRMC1 also contributes to RXFP1-mediated cell migration through an as yet unknown mechanism. RLN2 is not present in the brain. We determined the role of a peptide ligand of RXFP1, the newly discovered C1q/TNF related peptide (CTRP)8-derived P74 peptide, in promoting migration in GB cells. Similar to relaxin, P74 was found to have pro-migratory effects on GB cells. The biological activity of this peptide was also similar to relaxin and caused the upregulation of cath-B, cath-D and cath-L in the primary GB cells, thus, indicating that P74 might serve as a novel RXFP1 activating peptide ligand. We conclude that RXFP1 receptor signaling plays a key role in brain tumors cell migration and invasion.
A molecular characterisation of PsaN: a nuclear-encoded subunit of the photosystem I complex of Chlamydomonas reinhardtii.

Photosystem I (PSI) is a membrane protein complex composed of a large number of polypeptide subunits, designated PsaA to PsaN. In eukaryotes, the genes for these subunits are distributed between the nuclear and chloroplast genomes with the core subunits encoded by chloroplast genes. The function of many of the small nuclear-encoded subunits is unknown. Primarily, we are investigating the role of a nuclear-encoded subunit PsaN, which is absent in prokaryotic PSI complexes. PsaN is an extrinsic subunit located entirely on the lumenal side of the thylakoid membrane. We have isolated and sequenced the psaN gene in Chlamydomonas and shown that it is a single copy gene with an unusual exon structure. We are currently generating nuclear PSI mutants by random mutagenesis, in order to isolate tagged Chlamydomonas mutants disrupted in psaN or the other nuclear genes. The isolation of such mutants will provide an insight into their function and a valuable null background for structure-function studies, in which site-directed variants of the gene are re-introduced into the nuclear genome. In addition, we are analysing an existing psaF-deficient mutant of Chlamydomonas reinhardtii [1] in order to determine the function of the C-terminal region of the PsaF subunit. [1] Farah, J. et al. (1995). EMBO J. 14: 4976-4984.
Prediction of egg and larval development times in the field under variable temperatures

Nous proposons une methode pour modeliser la relation entre le developpement d'un insecte et des temperatures variables. Classiquement, les modeles sont construits a partir d'insectes eleves au laboratoire a plusieurs temperatures constantes ; les resultats peuvent rarement etre extrapoles aux conditions naturelles. Les modeles que nous avons utilises permettent d'introduire une vitesse de developpement dependante de la temperature, ainsi qu'une variabilite entre individus. Les parametres de ces modeles sont directement estimes a partir de donnees de populations naturelles. Nous nous sommes limites a l'etude de deux stades de developpement : embryonnaire et larvaire. Les experiences sur le terrain se sont deroulees de 1985 a 1992 et concernent le balanin de la châtaigne (Curculio elephas) qui se developpe dans les châtaignes. Une relation lineaire entre vitesse et temperature a conduit a de bons ajustements statistiques pour les developpements embryonnaire et larvaire. Une relation non lineaire n'ameliore pas l'ajustement de maniere notable. La duree mediane du developpement embryonnaire a ete estimee a 108.9 degres-jours (DJ) (base 6,5°C). Pour le developpement larvaire, les repetitions, malgre une base commune estimee a 0°C, n'ont pas pu etre regroupees. Les durees medianes s'echelonnent de 562 a 624 DJ. Il est possible d'estimer la variabilite interne a chaque repetition : par exemple pour l'une d'entre elles, le developpement varie de 516 DJ pour le premier decile (25,8 jours a la temperature constante de 20°C) a 704 DJ pour le dernier decile (35,2 jours a 20°C). L'utilisation de deux mesures differentes de la temperature (sous les châtaigniers ou a partir d'une station meteorologique) a modifie notablement les parametres du modele. Nous discutons du choix d'une relation entre vitesse et temperature, lineaire ou non, en considerant, entre autres, la sensibilite de notre modele aux mesures de la temperature. Finalement, nous examinons les differentes origines possibles de la forte variabilite du developpement du balanin de la châtaigne.
Anti‐acetylcholinesterase, antidiabetic, anti‐inflammatory, antityrosinase and antixanthine oxidase activities of Moroccan propolis

Summary Biological properties of Moroccan propolis have been scarcely studied. In the present work, the total phenols and flavonoids from 21 samples of propolis collected in different places of Morocco or 3 supplied in the market were determined, as well as the in vitro capacity for inhibiting the activities of acetylcholinesterase, α-glucosidase, α-amylase, lipoxygenase, tyrosinase, xanthine oxidase and hyaluronidase. The results showed that samples 1 (region Fez-Boulemane, Sefrou city) (IC50 = 0.065, 0.006, 0.020, 0.050, 0.014 mg mL−1) and 23 (marketed) (IC50 = 0.018, 0.002, 0.046, 0.037, 0.008 mg mL−1) had the best in vitro capacity for inhibiting the α-amylase, α-glucosidase, lipoxygenase, tyrosinase and xanthine oxidase activities, respectively. A negative correlation between IC50 values and concentration of phenols, flavones and flavanones was found. These activities corresponded to the generally higher amounts of phenols and flavonoids. In the same region, propolis samples have dissimilar phenol content and enzyme inhibitory activities.
Determining fine‐scale migratory connectivity and habitat selection for a migratory songbird by using new GPS technology

Migratory aerial insectivores are among the fastest declining avian groups, but our understanding of these trends has been limited by poor knowledge of migratory connectivity and the identification of critical habitat across the vast distances they travel annually. Using new, archival GPS loggers, we tracked individual purple martins Progne subis from breeding colonies across North America to determine precise ( 10 m) locations of migratory and overwintering roost locations in South America and to test hypotheses for fine-scale migratory connectivity and habitat use. We discovered weak migratory connectivity at the roost scale, and extensive, fine-scale mixing of birds in the Amazon from distant (> 2000 km) breeding sites, with some individuals sharing the same roosting trees. Despite vast tracts of contiguous forest in this region, birds occupied a much more limited habitat, with most (56%) roosts occurring on small habitat islands that were strongly associated with water. Only 17% of these roosts were in current protected areas. These data reflect a critical advance in our ability to remotely determine precise migratory connectivity and habitat selection across vast spatial scales, enhancing our understanding of population dynamics and enabling more effective conservation of species at risk.
Global analysis of protein-RNA interactions

It is becoming increasingly evident that post-transcriptional regulation has profound impact on when, where, and to what level genes are expressed. Hundreds of RNA-binding proteins and non-coding RNAs mediate post-transcriptional gene regulation – but how they are coordinated and what their RNA targets are remains largely elusive. The development of genome-wide analysis tools enables us now to systematically study the extent and logic of post-transcriptional gene regulation on global scale. In this book, the author Andre Gerber explains some of these new techniques, which led to the discovery of novel principles of gene expression control such as RNA regulons. He also provides an overview of current knowledge about the implications of RNA-binding proteins and non-coding RNAs in human disease, and the chances and pitfalls towards the development of novel therapeutics. This book is written for everyone with basic knowledge in molecular biology and who wishes to get an introduction into this fascinating field of RNA research.