Miracle-dz/UniFAR-FTUs huggingface dataset:
Origin, elevation, and evolutionary success of hybrids and polyploids in British Columbia, Canada

Although it is well established that many clades have polyploidization in their evolutionary history, the question of whether polyploidization is actually adaptive is far from resolved. It has been hypothesized that the evolutionary advantages of polyploidy are context-dependent, although we have yet to clearly identify the geographical or ecological contexts in which polyploids are more common. One reason why polyploidy may be displaying idiosyncratic ecological patterns is that previous comparative studies have often not separated polyploids into allopolyploids and autopolyploids, and we posit that there may be important differences in the origin and evolutionary success between the two types. Here, we examine the distribution of allopolyploid, autopolyploid, and diploid hybrid species along an elevation gradient from sea level to ∼4500 m within British Columbia, Canada, and find that polyploids (especially those of hybrid origin) are disproportionately present at high elevations. These processes of hyb.
DETECTION OF HUMAN PAPILLOMAVIRUS 16 AND 18 DNA IN CERVICAL DYSPLASIA AND CERVICAL CARCINOMA BY IN SITU HYBRIDIZATION

We improved the in situ hybridization method using biotinylatyed probes for the detection of human papillomavirus (HPV) 16 and 18 DNA in formalin-fixed and paraffin-embedded tissue sections. Our method included HCl treatment, digestion with 30μg/ml proteinase K, post-fixation with 70% ethanol and incubation with a streptavidin-biotinylated alkaline phosphatase conjugate for visualization of biotin molecules on DNA probes. The sensitivity of this method using biotinylated DNA probes was comparable to using 35S labeled RNA probes. Using this method, 72 cases of cervical dysplasia and 51 cases of squamous cell carcinoma of cervix were examined for the presence of HPV 16 and 18 DNA. HPV 16 DNA was detected by in situ hybridization in 19 (26%) cases: 8 of 17 (47%) with mild dysplasia, 4 of 24 (16%) with moderate dysplasia and 7 of 30 (23%) with severe dysplasia. In 25 cases of carcinoma in situ and 26 cases of invasive carcinoma, HPV 16 or 18 DNA was detected in 8 cases of which 4 cases had an associated nonmalignant lesion. All four cases showed that the intensity in the malignant lesions was less than the dysplasia or benign lesions in the same patients. These findings suggest that replication of HPV DNA might be suppressed in the transformed cells.
Phytoplankton Species' Succession and Nutrients in the Southern Black Sea (Bay of Sinop)

The succession, annual cycle and diversity of phytoplankton species and seasonal changes in nutrients in the southern Black Sea (around Sinop peninsula) were investigated between August 1995 and July 1996. One species of Cyanophyceae, 83 taxa of Dinophyceae, 1 species of Prymnesiophyceae, 5 taxa of Dictyochophyceae, 88 taxa of Bacillariophyceae and 1 species of Euglenophyceae were identified. A list of phytoplankton species together with annual variations was prepared. Changes in community structure, density and diversity are discussed in relation to the physico-chemical features of the water column.
First Record of Philautus petilus Stuart and Heatwole, 2004 (Amphibia: Anura: Rhacophoridae) from Vietnam and Its Phylogenetic Position

Abstract A small rhacophorid, Philautus petilus known from only the female holotype, is recorded for the first time outside of the type locality in Laos. Three specimens, containing the first known males of the species, were collected from Muong Nhe Nature Reserve in Dien Bien Province, northwestern Vietnam. The Vietnamese specimens are identified as P. petilus based on morphological similarities with the holotype from Laos. In addition, our molecular data verify the transfer of this species from Philautus to the genus Theloderma.
The Geonomoid palms

Tomlinson has suggested (1961) that the palm-collector is a somewhat quixotic character. This statement is illustrated by a quotation from Bailey: “to procure material of the great palms is like setting forth to collect a windmill except that one does not have the advantage of steps built on the derrick”. In general, indeed, palms are unattractive to collect and to handle in the herbarium. The tribe of the Geonomoid palms, however, represents a rather pleasant exception being a group of unarmed and mostly rather small plants with often arundinaceous stems up to a few meters tall. Consequently they are more frequently collected and studied than other palms resulting in a large number of collections and publications. The first author dealing with these palms was Willdenow (1805). He established the genus Geonoma with two species based on Bredemeyer collections from Venezuela near Caracas. The next contribution to our knowledge of this group was Poitbau’s (1822) but he misinterpreted the proterandrous inflorescences as being unisexual. His genus Gynestum, including 5 species from French Guiana, was merged by Kunth (1841) into Geonoma. Contemporaneously with Poiteau and unaware of the efforts of the latter Martius (1823) published the results in Geonoma of his Brazilian itinerary.
Trichodina murmanica (Ciliophora) and Gyrodactylus pleuronecti (Monogenea) parasitizing hatchery‐reared winter flounder, Pseudopleuronectes americanus (Walbaum): effects on host growth and assessment of parasite interaction

Winter flounder, Pseudopleuronectes americanus, caught in Passamaquoddy Bay, New Brunswick, Canada, and held captive under crowded conditions, developed mixed infections of Trichodina murmanica Polyanski, 1955 (Ciliophora) and Gyrodactylus pleuronecti Cone, 1981 (Monogenea). A protocol involving sequential sieving was used to separate the two species of parasites and produce viable experimental baths. Replicate groups of juvenile, hatchery-reared flounder received one of the following treatments: mixed bath of G. pleuronecti and T. murmanica, bath of G. pleuronecti, bath of T. murmanica or parasite-free (controls). The abundance of both parasites correlated negatively with condition factor of the flounder (r=−0.354, P < 0.001 for Trichodina; r=–0.205, P < 0.05 for Gyrodactylus). During the periods of peak parasite abundance (1–2 weeks postinfection), the effect of the two parasite species was additive, as mean condition factor and the percentage change in weight were significantly lower (ANOVA, P < 0.05) among fish with mixed infections compared to single infections or controls. The most common signs of tissue pathology were increased density of epidermal mucous cells on the fins and macrovesicular lipidosis of the hepatocytes. After a significant decline in parasite infrapopulations (3 weeks postinfection), infected fish resumed normal growth, indicating the observed effects were somewhat reversible.
Species differentiation of Sepia officinalis and Sepia hierredda (Cephalopoda: Sepiidae) based on morphological and allozyme analyses

Two taxa of commercially exploited cuttlefish, Sepia officinalis and S. hierredda, are compared for the first time on the bases of quantitative morphology and allozyme polymorphisms. Morphometric measurements and meristic counts of selected soft and hard (cuttlebone) body characters, with allozyme electrophoretic analysis are used. Samples were obtained from north-west Iberian Peninsula and Senegalese waters (West Africa). Significant differences in mantle width, arm and hectocotylus length, numbers of rows of reduced suckers on the hectocotylus and in most cuttlebone measurements were found. Canonical discriminant functions of cuttlebone measurements for males and females were calculated. Allozyme electrophoresis for 33 presumptive loci showed low levels of genetic variability and 13 diagnostic loci between the two Sepia taxa. The genetic identities (I) in pairwise comparisons of populations of both taxa were I=0·582–0·596, which are typical values for congeneric species. These congruent morphological and genetic results strongly suggest that S. officinalis and S. hierredda are different species.
Intestinal regeneration after irradiation: stem cells and Sox9

Brooks Scull: Intestinal Regeneration After Irradiation: Stem Cells and Sox9 (Under the direction of P. Kay Lund) Whole body irradiation is a useful challenge to study the response of intestinal epithelial stem cells (IESC) to genetic damage. High dose irradiation causes complete loss of the proliferative zone within intestinal crypts excluding a few stem/multipotent cells that can regenerate the intestinal epithelial lining. Whole body irradiation models using high dose irradiation are not ideal for studying the regenerative process due to poor animal survival. Little is known about direct effects of irradiation on IESC due to lack of biomarkers. This study developed a high dose abdominal irradiation model with increased survival allowing for analysis of regeneration to day 9 after irradiation and potentially longer. The expression pattern of the putative IESC marker, Sox9, was evaluated and compared with proliferation markers. We provide evidence that differential levels of Sox9 mark subpopulations of proliferating cells. This model will be useful to evaluate therapies that increase IESC survival, proliferation and regeneration. iii Acknowledgments First and foremost, I would like to thank my advisor, Dr. Kay Lund who has been an incredible and irreplaceable mentor. Her scientific knowledge and integity are an inspiration. She started my science career which she continues to nurture and guide for which I am forever in debt. I would also like to thank the members of my committee, Dr. Michael Helmrath and Dr. Scott Magness for their scientific guidance and advise. They have also been inspirational and integral to my development as a scientist. I would like to thank my many colleagues and friends in the Cell and Molecular Physiology department. Most notabley, the past and present members of the Lund Lab, Ramocki for their friendship and support. and especially my wife, Jennifer, for their endless love and support throughout the years.
Humulus lupulus – a story that begs to be told. A review

The hop cones of the female plant of the common hop species Humulus lupulus L. are grown almost exclusively for the brewing industry. Only the cones of the female plants are able to secrete the fine yellow resinous powder (i.e. lupulin glands). It is in these lupulin glands that the main brewing principles of hops, the resins and essential oils, are synthesized and accumulated. Hops are of interest to the brewer since they impart the typical bitter taste and aroma to beer and are responsible for the perceived hop character. In addition to the comfortable bitterness and the refreshing hoppy aroma delivered by hops, the hop acids also contribute to the overall microbial stability of beer. Another benefit of the hop resins is that they help enhance and stabilize beer foam and promote foam lacing. In an attempt to understand these contributions, the very complex nature of the chemical composition of hops is reviewed. First, a general overview of the hop chemistry and nomenclature is presented. Then, the different hop resins found in the lupulin glands of the hop cones are discussed in detail. The major hop bitter acids (α- and β-acids) and the latest findings on the absolute configuration of the cis and trans iso-α-acids are discussed. Special attention is given to the hard resins; the known δ-resin is reviewed and the e-resin is introduced. Recent data on the bittering potential and the antimicrobial properties of both hard resin fractions are disclosed. Attention is also given to the numerous essential oil constituents as well as their contributions to beer aroma. In addition to the aroma contribution of the well-known essential oil compounds, a number of recently identified sulfur compounds and their impact on beer aroma are reviewed. The hop polyphenols and their potential health benefits are also addressed. Subsequently, the importance of hops in brewing is examined and the contributions of hops to beer quality are explained. Finally, the beer and hop market of the last century, as well as the new trends in brewing, are discussed in detail. Hop research is an ever growing field of central importance to the brewing industry, even in areas that are not traditionally associated with hops and brewing. This article attempts to give a general overview of the different areas of hop research while assessing the latest advances in hop science and their impact on brewing. Copyright © 2014 The Institute of Brewing & Distilling
Distribuição vertical do fósforo no solo em função dos modos de aplicação = Vertical distribution of phosphorus in soil in function of modes of application

A demanda de estudos sobre a dinâmica das adubacoes e uso eficiente de fosforo na agricultura do cerrado brasileiro, foi proposito para este trabalho, cujo objetivo foi verificar a eficiencia da combinacao de modos de aplicacao de fertilizantes fosfatados na distribuicao vertical do nutriente no solo. O experimento foi realizado no sudoeste goiano, juntamente com o sistema de producao de soja e milho. O delineamento experimental foi em blocos casualizados, em esquema fatorial 6x6, entre os modos de adubacao (100% da adubacao a lanco, 75% a lanco e 25% na linha, 50% a lanco e 50% na linha, 25% a lanco e 75% na linha, 100% na linha e a testemunha) e as profundidades 0,0-2,5; 2,5-5,0; 5,0-7,5; 7,5-10,0; 10,0-15,0; 15,0-20,0 cm. Foi utilizado uma dose padrao de 120 Kg . ha -1 de P 2 O 5 na forma de Fosfato Monoamonico (MAP). As avaliacoes foram teor de P no solo e foliar, altura e produtividade das plantas de soja, alem da altura e produtividade do milho de segunda safra. A associacao da adubacao em 75% a lanco e 25% na linha, mostrou insuficiencia para suprir toda necessidade das plantas pelo fosforo. Quando o fertilizante foi aplicado em maior percentual a lanco em area total proporcionou maior acumulo de fosforo na camada de 0,0- 2,5 cm, entretanto, quando houve predominio da aplicacao na linha de plantio os maiores acumulos ocorreram na camada de 5,0-7,5 cm.
The Differential Contribution of Behavior and Biology to Breslow Thickness and Melanoma Survival in Males Compared to Females

There are many well-documented differences between males and females regarding melanoma including incidence rates, presentation, markers of progression, and survival. A common hypothesis to explain the female survival advantage is that males are less aware of their skin, resulting in thicker lesions at diagnosis, and ultimately poorer survival. However, there are also multiple hypotheses attributing the female survival advantage to biological differences between males and females, mostly regarding sexsteroid hormones. Sex has been identified as an independent prognostic marker in multiple studies, supporting the hypothesis that melanoma progression varies between men and women. Despite these findings, stratifying by sex in melanoma studies is uncommon. Here we present four studies investigating both behavioral and biological differences as they relate to Breslow thickness and melanoma survival in analyses stratified by sex.
Regulation of Anti-Viral Cd8+ T Cell Responses by the Pd-1 Pathway

PD-1 and its ligands, PD-L1 and PD-L2, constitute a critical immunoregulatory pathway for modulating CD8+ T cell responses. This pathway has become an important therapeutic target in cancer and chronic viral infections, where blockade of PD-1/PD-L1 reverses CD8+ T cell exhaustion and improves outcomes. However, it remains unclear how PD-1 pathway signals shape the development and maintenance of memory CD8+ T cell responses following acutely-resolved infection or exhausted CD8+ T cell responses following chronic infection. Absence of PD-1 results in early over-activation, excessive proliferation and diminished survival of virus-specific CD8+ T cells during both acutely-resolved and chronic viral infections. Following influenza infection, PD-1 pathway deficiency led to sub-optimal CD8+ T cell memory development. Defects were observed in the magnitude of the influenza-specific CD8+ T cell responses, as well as in cytokine production and recall capacity. Similarly, during chronic LCMV infection, PD-1 deficient CD8+ T cells were more dysfunctional than their WT counterparts. Permanent absence of PD-1 dramatically dysregulated lineage dynamics and long-term stability of exhausted CD8+ T cell populations through a mechanism involving the transcription factors T-bet and Eomesodermin. As a result, PD-1 deficiency led to the accumulation of terminally-differentiated, but more cytotoxic, exhausted CD8+ T cells. These findings reveal a novel dual role for PD-1 signals during acutely-resolved and chronic viral infections. PD-1 pathway signals clearly restrict CD8+ T cell activation, expansion and function early, consistent with previous work. However, in doing this, PD-1 also preserves the quantity and quality of long-term memory or exhausted CD8+ T cell responses. Thus, PD-1 acts as a critical "rheostat" on CD8+ T cells, balancing the need for activation to achieve pathogen clearance with the establishment and maintenance of long-term memory or exhausted T cell responses. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor E. John Wherry
Assessment of the potential for hybridisation between Laricobius nigrinus (Coleoptera: Derodontidae) and Laricobius osakensis, predators of the hemlock woolly adelgid (Hemiptera: Adelgidae)

In 2003, Laricobius nigrinus Fender was introduced into the eastern United States as a biological control agent of the hemlock woolly adelgid (Adelges tsugae Annand). Following its release, it was discovered that L. nigrinus was hybridising and producing viable progeny with Laricobius rubidus LeConte, a species native to eastern North America. Recently, Laricobius osakensis Montgomery and Shiyake was imported from Japan into the USA as a potential biological control agent of hemlock woolly adelgid. Hybridisation between L. nigrinus and L. rubidus led to interest in the outcome of interactions between L. osakensis and the other two Laricobius spp. The purpose of this study was to determine if L. osakensis could mate with L. nigrinus, if they could produce hybrid progeny, and whether mating interferes with reproductive output. Laricobius spp. were observed mating directly following emergence and found to be capable of producing sterile eggs in the absence of a mating event. Laboratory and confined field studies found no evidence that L. osakensis and L. nigrinus could produce hybrid progeny and the interaction between the two species did not result in a lower reproduction associated with interspecific mating attempts. Interbreeding should therefore not have an impact on biological control using these species. Fecundity experiments showed that L. osakensis produced eggs earlier in the season and at a higher rate than L. nigrinus, suggesting that L. osakensis may have the potential to be an even more successful biological control agent than L. nigrinus.
Nest-Site Selection and Nest Survival of Early Successional Birds in Central Pennsylvania

Abstract We studied nest-site selection and nest survival of early successional birds at the Barrens Grouse Habitat Management Area in central Pennsylvania in 2006 and 2007. We compared vegetation at nests to that at sites 30 m distant to examine microhabitat characteristics related to nest-site selection and which characteristics were associated with nest survival. Daily nest survival probability was 0.968 ± 0.006 (SE) for Chestnut-sided Warblers (Dendroica pensylvanica), 0.935 ± 0.014 for Field Sparrows (Spizella pusilla), 0.955 ± 0.011 for Indigo Buntings (Passerina cyanea), and 0.960 ± 0.005 for all species combined. Nest-site selection was best characterized by high woody stem density for Chestnut-sided Warblers, Indigo Buntings, and all species combined. Nest survival increased with woody stem density, indicating that nest-site preferences may be adaptive. Ground cover best predicted nest placement for Field Sparrows but no measured variable affected nest survival for this species. We suggest that severe defoliation by gypsy moths (Lymantria dispar) in 2007 had little effect on nest predation risk for early successional birds.
Metallo-β-lactamases among Enterobacteriaceae from routine samples in an Italian tertiary-care hospital and long-term care facilities during 2008: Metallo-β-lactamases among Enterobacteriaceae from routine samples

Abstract The emergence of metallo-β-lactamase (MBL)-producing Enterobacteriaceae is a serious public health concern. Producers have been repeatedly isolated from patients and long-term care facility (LTCF) residents around Bolzano, and we sought to assess their prevalence and clinical impact. All routine Enterobacteriaceae isolates from a Bolzano tertiary-care hospital and associated long-term care facilities in 2008 ( n = 5500) were screened for MBLs, with case details reviewed for the source patients. In total, 36 producers were obtained from 29 patients, comprising 14 Escherichia coli , six Klebsiella pneumoniae , four Klebsiella oxytoca , four Citrobacter freundii , two Enterobacter cloacae and two Morganella morganii , as well as single Citrobacter amalonaticus, Enterobacter aerogenes, Providencia stuartii and Proteus mirabilis isolates. All were PCR-positive for bla VIM and 25 were PCR-positive for qnrS ; 19 non- K. pneumoniae had bla SHV and one had bla CTX-M-group1 ; 13 were from 12 LTCF residents and 23 were from 17 acute-care patients. All these patients had serious underlying diseases with prolonged hospitalization or LTCF stay; only seven had infections due to the MBL producers, comprising four urinary tract infections, two catheter-related bloodstream infections and one patient with both a surgical site infection and pneumonia. Five patients had more than one MBL-producing organism. Pulsed-field gel electrophoresis identified a cluster of six related E. coli , whereas pairs of K. pneumoniae and C. freundii isolates had >85% profile similarity. Transformants prepared from two isolates were shown to be PCR-positive for bla VIM , qnrS and bla SHV ; their plasmids gave similar restriction fragment length polymorphism patterns, and bla VIM-1 , qnrSI and bla SHV-12 were detected by sequencing.
Mineralização e efeitos de biocarvão de cama de frangosobre a capacidade de troca catiônica do solo

The objective of this work was to characterize carbon mineralization process in poultry litter samples and in its biochar, as well as to determine the soil cation exchange capacity (CEC) and the C mineralization rates in soils treated with poultry litter and biochar. Carbon mineralization was evaluated through the quantification of released C‑CO 2 from mixtures of soil and poultry litter and of soil and biochar at doses equivalent to 0, 1,000, 2,000, 4,000, and 8,000 mg kg -1 C, in a 64‑day incubation experiment. At the end of the incubation period, carbon content, pH, and CEC were determined in soil samples. Carbon mineralization of the materials fitted to first order kinetics equation. Fluxes of C‑CO 2 were more intense from 20 to 40 days of incubation, followed by flux decreases until their stabilization. Carbon mineralization rates of poultry litter and its biochar were respectively 49.7 and 5.1%. Increases of CEC were observed in the biochar treatments, as a consequence of pH rising, and in both materials due to soil‑carbon content alterations.