Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant Reproductive Characteristics during Secondary Succession in Neotropical Lowland Forest Ecosystems

During secondary succession in tropical America, reproductive characteristics of the constituent plants change as species constitution changes in the direction of 'climax' or equilibrium. Self-compatibility is more prevalent in early stages, while outcrossing is more the rule in later stages as dicliny, dioecism, and self-incompatibility beome more frequent. Observations indicate that plants of increasingly large stature and seral position are more widely spaced, and tend to have larger brightly colored flowers and larger pollinators. Associated understory plants come to have small unicolorous flowers and small pollinators as light availability decreases. Plants of early stages have primarily small, many-seeded dehiscent fruits, while plants with large, few-seeded fleshy fruits come to dominate equilibrium forests, particularly in wet forest. Canopy emergent trees, epiphytes, and lianas of mature forest are exceptional in employing wind-dispersal. Many of these changes correlate well with the thesis that pioneer plants are more highly r-selected, while plants of more mature forest tend to be K-selected. ALTHOUGH THE STUDY OF SECONDARY SUCCESSION in temperate latitudes signalled the onset of ecological endeavor (Cowles 1899, Clements 1916), only in recent years has the study of succession in the tropics made significant advances. The study of reproductive characteristics of plants in seral sequences has lagged even further behind. Our studies and those of others (Bawa 1974, Vasquez-Yanes 1974a, McKey 1975, Ruiz Zapata and Kalin Arroyo 1978) allow some preliminary conclusions and hypotheses on the nature of reproductive characteristics of plants in different seral stages. In this paper we consider the various portions of reproductive biology as a sequence of topics, i.e. floral biology, seed biology, and breeding systems. We then contrast findings from lowland wet and dry forest habitats, and finally integrate our findings and hypotheses with
Molecular analysis of high-level streptomycin resistance in Erwinia amylovora

Streptomycin-resistant and -sensitive strains of Erwinia amylovora from New Zealand and five states in the United States were compared on streptomycin- and myomycin-amended media. Strains with high resistance to streptomycin (HR strains) were insensitive to myomycin, an antibiotic resembling streptomycin in its mode of action, whereas strains with medium resistance (MR) or sensitivity (S) to streptomycin were sensitive to myomycin. No mutations were found in the 16S rRNA gene of nine HR strains of E. amylovora that could account for streptomycin resistance. Nucleotide sequence and allele-specific amplification-polymerase chain reaction analyses were used to examine S, MR, and HR strains for mutations in the rpsL gene. All 102 HR strains of E. amylovora contained a single base-pair mutation in codon 43 of their rpsL gene that resulted in an amino acid substitution in ribosomal protein S12. Codon 43, which encodes lysine in S and MR strains, was converted to a codon for arginine in 96 HR strains, a codon for asparagine in three HR strains, and a codon for threonine in three HR strains. In gene complementation studies, sensitivity to streptomycin and myomycin was restored to E. amylovora and Escherichia coli HR strains with a plasmid carrying the wild-type E. amylovora rpsL gene. Conversely, resistance to streptomycin and insensitivity to myomycin in E. amylovora and E. coli S strains was restored only when the plasmid carried a mutant rpsL gene with the lysine-to-arginine substitution in codon 43. We conclude that mutations in a single codon of ribosomal protein S12 gene rpsL have resulted in high-level streptomycin resistance in E. amylovora. Two genetic bases of streptomycin resistance have now been identified in E. amylovora. These results indicate that the genetic mechanism determines the level of streptomycin resistance and the expression of myomycin resistance and that the presence or relative importance of the two mechanisms differs among various geographic regions
Implications of the Updated 2013 American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations on Human Epidermal Growth Factor Receptor 2 Gene Testing Using Immunohistochemistry and Fluorescence In Situ Hybridization for Breast Cancer

Context. —Human epidermal growth factor receptor 2 (HER2/neu) amplification is used as a predictive marker for trastuzumab treatment in breast cancer. Both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) testing algorithms have been based on the 2007 American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guidelines. In late 2013, the guidelines were updated with new scoring criteria. Objective. —To assess the impact of the revised ASCO/ CAP recommendations on both IHC and FISH results by using the dual-color HER2/neu and centromeric FISH probes. Design. —Retrospective analysis of 590 invasive carcinomas with concurrent IHC and dual-color HER2/neu and centromeric 17 (CEP17) FISH results, based on 2007 ASCO/CAP guidelines, was conducted from July 2011 to June 2013. With the revised guidelines, patients were recategorized and concordance rates between the 2 assays were recalculated. Results. —Overall concordance rates for FISH and IHC decreased from 94.9% to 93.8% with reclassification. Negative FISH cases decreased from 79.1% to 69.3%. However, equivocal FISH cases were significantly increased from 0.7% to 9.5%, leading to more retesting. Both positive IHC and FISH cases were also noted to be increased, leading to more patients being eligible for trastuzumab treatment, especially those patients with concurrent HER2/neu and CEP17 polysomy. Approximately 1% of patients with initial FISH negative results were reclassified as having positive results when both the ratios and average copy number of HER2/neu were considered under the revised guidelines. Conclusions. —The revised 2013 ASCO/CAP guidelines can potentially lead to more patients being eligible for trastuzumab therapy but additional retesting is to be expected owing to an increased number of equivocal FISH cases. (Arch Pathol Lab Med. 2016;140:140–147; doi: 10.5858/ arpa.2015-0108-OA)
Regulation of sodium transport across epithelia derived from human mammary gland

The first aim of this project is to define the cellular mechanisms that account for the low Na concentration in human milk. MCF10A cells, which were derived from human mammary epithelium and grown on permeable supports, exhibit amilorideand benzamil-sensitive short circuit current (Isc), suggesting activity of the epithelial Na channel, ENaC. When cultured in the presence of cholera toxin (Ctx), MCF10A cells exhibit greater amiloride sensitive Isc at all time points tested, an effect that is not reduced with Ctx washout for 12 hours or by cytosolic pathways inhibitors. Ctx increases the abundance of both β and -ENaC in the apical membrane and increases its monoubiquitination but without changing total protein and mRNA levels. Additionally, Ctx increases the levels of both the phosphorylated and the nonphosphorylated forms of Nedd4-2, a ubiquitin-protein ligase that regulates ENaC degradation. The results reveal a novel mechanism in human mammary gland epithelia by which Ctx regulates ENaC-mediated Na transport. The second project aim is to develop a protocol to isolate mammary gland epithelia for subsequent in vitro culture. Caprine (1CME) and bovine mammary epithelia (1BME) were isolated and cultured on permeable supports to study hormoneand neurotransmitter-sensitive ion transport. Both 1CME and 1BME cells were passed for multiple subcultures and all passages formed electrically tight barriers. 1 CME were cultured in the presence of hydrocortisone and exhibited high electrical resistance and amiloride-sensitive Isc, suggesting the presence of ENaC-mediated Na transport. 1 BME were grown in a complex media in the presence or absence of dexamethasone. In contrast to 1CME, 1BME exhibited no detectable amiloride-sensitive Isc in either culture condition. However, 1BME monolayers responded to an adrenergic agonist, norepinephrine, and a cholinergic agonist, carbamylcholine, with rapid increases in Isc. Thus, this protocol for isolation and primary cell culture can be used for future studies that focus on mammary epithelial cell regulation and functions. In conclusion, the results from these projects demonstrate that mammary epithelial cells form electrically tight monolayers and can exhibit neurotransmitterand/or hormone-induced net ion transport. The mechanisms that regulate Na transport across mammary gland may provide clues to prevent or treat mastitis. REGULATION OF SODIUM TRANSPORT ACROSS EPITHELIA DERIVED FROM HUMAN MAMMARY GLAND
Role of Acinetobacter sp. in arsenite As(III) oxidation and reducing its mobility in soil

ABSTRACT Microbial arsenite oxidation was observed by Acinetobacter sp. XS21, this strain oxidised arsenite As(III) up to 80 mM within 48–72 h of incubation. The present strain XS21 oxidised As(III) at a very high concentration in a shorter interval of time than any of the previous reported microbes. Further, XS21 was applied to the soil to observe its ability in reducing the mobility of As(III), and we found that Acinetobacter sp. XS21 efficiently removed arsenite from soluble-exchangeable fraction and removed 70% of the arsenite as compared to control. This feature makes it a potential candidate for bioremediation. Arsenic-resistant bacteria with strong As(III)-oxidising ability may have potential to improve bioremediation of As(III)-contaminated sites. To understand their basis of resistance and transformation we found the As(III) oxidase gene using degenerate primer and amplified ∼550 bp of aioA gene. Amplified aioA gene sequence exhibiting 52% identity in terms of gene and deduced protein sequence to Uncultured bacterium, and Achromobacter sp. arsenite oxidase of larger subunit. Arsenite oxidase, an enzyme, was also observed in this isolate, which may provide a resistance and transforming ability. This bacterium was identified as Acinetobacter sp. , by sequencing 16s rRNA gene sequence analysis.
Comparison of immune electron microscopy with direct negative staining for detection of Bovine Viral Diarrhoea Virus

The objective of this study was to optimize an immune electron microscopy protocol for detection of Bovine Viral Diarrhoea Virus (BVDV) and to compare its detection limit with that of direct negative staining technique. Indian non-cytopathic BVDV isolate (Ind S1449) infected SFTR cell supernatant with a titre of 105.3 TCID 50 per ml was used. For IEM, various parameters including anti-BVDV polyclonal serum dilution, virus-antibody incubation temperature and time, and centrifugation time were optimized using the undiluted BVDV stock. Incubation with 1: 400 dilution of anti-BVDV polyclonal serum at 37°C for one hour was found to be optimum. To compare the detection limits of both the protocols, serial ten-fold dilutions of the virus stock (undiluted to 10−4 containing 105.3 to 101.3 TCID 50per ml, respectively) were used. Phosphotungstic acid stained grids were viewed under transmission electron microscope. BVDV was visualized as immune-aggregates of varying sizes distributed diffusely across IEM grids. In direct negative stained grids, the virus was detected mostly as individual particles. The detection limit of the IEM protocol was 103.3 TCID 50 per ml which was one hundred-fold more than that of direct negative staining protocol. The present study demonstrates that examination of suspected sample by immune electron microscopic procedures is feasible for BVDV detection and it can be used as routine diagnostic tool, especially for screening of cell culture supernatants infected with suspected clinical specimens. Suitability of this assay for direct screening for identification of persistently infected animals which are of great concern for control programmes, needs to be explored.
A physics-constrained three-dimensional three-component particle-based velocimetry method for constant-density flows

A physics-constrained three-dimensional three-component particle-based velocimetry method for constant-density flows Keishi Kumashiro Master of Applied Science Institute for Aerospace Studies University of Toronto 2019 A physics-constrained method of inferring three-dimensional three-component (3D3C) velocity fields in constant-density flows from reconstructed 3D Mie-scattering fields of tracer particles is introduced. The proposed method is based on the representation of the estimated velocity field as a linear combination of divergence-free polynomial basis functions; the piecewise constant representation of the estimated velocity field that is inherent to tomographic particle image velocimetry (T-PIV) is replaced by a smooth representation that automatically satisfies conservation of mass. The appropriate linear combination is determined using a non-regularized motion estimation framework that is influenced by optical flow motion estimation. A detailed evaluation of the proposed method is provided in terms of accuracy and spatial resolution, treating 3D constant-density direct numerical simulation data as the ground truth. It is shown that the proposed method (i) yields as much as a twofold improvement in both accuracy and spatial resolution compared to an idealized implementation of T-PIV and (ii) achieves comparable accuracy and spatial resolution to an idealized estimate that corresponds to the theoretical one-vector-per-particle limit.
EVOLUTION OF INTRAHOST HIV ‐ 1 GENETIC DIVERSITY DURING CHRONIC INFECTION

Abstract —HIV‐1 is one of the fastest evolving entities known. Given that census population sizes of HIV‐1 within individuals are much greater than the inverse mutation rate, every possible singel point mutation in the viral genome occurs each generation. This enormous capability to generate genetic variation allows for escape from immune surveillance and antiviral therapy. However, compared to generate genetic variation allows for escape from immune surveillance and ativiral therapy. However, compared to this potential, populations of HIV‐1 within individuals exhibit little genetic variation. This discrepancy between the known mutatiton rate of HIV‐1 and the average level of genetic variation in the env gene observed in vivo is reflected in comparisons of the actual numbers of productively infected cells, estimated as 107, and the effectrive population size, estimated as 103. Using approximate Bayesian computation, we evaluated several hypotheses based on a variety of selective and demorgaphic processes to explain the low effective populations size of HIV‐1. Of the models we examined, the metapopulation model, in which HIV‐1 evolves within an individual as a large collection of small subpopulations subject to frequent migration, extinction, and recolonization, was most consistent with the observed levels of genetic variation and the average frequencies of those variants. The metapopulation model links previous studies of viral dynamics and population genetics.
Restriction endonuclease analysis of various strains of Mycobacterium paratuberculosis isolated from cattle.

: Deoxyribonucleic acid (DNA) preparations from 3 reference strains of Mycobacterium paratuberculosis and from 23 isolates of M paratuberculosis obtained from cattle in New Zealand were characterized by restriction endonuclease analysis, using the enzymes BstE II, Pvu II, and Bcl I. Patterns of DNA fragments for strain 18 (one of the reference strains) differed markedly from patterns of other strains, indicating genetic differences between strain 18 and the other strains of M paratuberculosis evaluated. The other 2 reference strains (TMC 1613 and Weybridge strain 316) and all but 1 of the isolates from cattle had identical patterns with the 3 enzymes. These 2 reference strains differed from each other in their dependence on exogenous mycobactin, but this was not reflected in their restriction patterns. The single variant isolate from cattle had patterns identical to those of the other isolates, using Pvu II and Bcl I, and had only 1 fragment line difference with BstE II. Although close genetic homogeneity of cattle strains of M paratuberculosis prevented development of a typing system on the basis of restriction endonuclease analysis, the results provided a basis for genomic comparison with other closely related organisms.
Cardiac-evoked long-range quantum entanglement in the conscious brain

We report observations of cardiac-evoked long-range zero quantum coherence (ceZQC) in human brain tissue which were not accompanied by an alternation of short-range quantum coherence. For every cardiac pulsation, ceZQC emerged over the entire brain tissue for a period of 270 ± 180 ms. We observed this quantum eﬀect in 40 human volunteers, if and only if they were awake. This link to conscious awareness suggests that the information held in the long-range quantum phenomenon is used and manipulated in conscious-related computation
Energy Rate Density as a Technosignature : The Case for Stellivores

The energy rate density (ERD) metric is the central scientific measure underlying all of big history. It measures the rate at which free energy transits in a complex system of a given mass. How could it inform SETI and astrobiology? One simple way to proceed is to look for high ERD systems in the universe and binary systems in accretion are excellent candidates. I argue that these accreting binary systems might be instances of Type II stellar civilizations on Kardashev’s scale, civilizations feeding on stars, or stellivores. I review living clues, such as their sheer variety, their existence far from thermodynamic equilibrium, the fine-tuning of their models, the existence of reserves, accretion and ejection control. I summarize these clues using living systems theory. I use known binary stars masses and accretion rates to compute the ERD of putative stellivores, such as cataclysmic variables (130), neutron stars (30) and transient black holes (19). The results support an anomalously high ERD. I discuss objections and counterarguments regarding the stellivore hypothesis, and implications for big history.
Authors’ reply

dry-Guillain-Barré syndrome. A clinicopathological study of fifty fatal cases and a critique of the literature. Medicine (Baltimore) 28:59–141. Powell HC, Myers RR, Mizisin AP, Olee T, Brotoff SW (1991). Response of the axon and barrier endothelium to experimental allergic neuritis induced by autoreactive T cell lines. Acta Neuropathol 82:364–377. Rauschka H, Jellinger K, Lassmann H, Braier F, Schmidbauer M (2003). Guillain-Barré syndrome with marked pleocytosis or a significant proportion of polymorphonuclear granulocytes in the cerebrospinal fluid: neuropathological investigation of five cases and review of differential diagnoses. Eur J Neurol 10:479–486.
Satellite Symposia

Background: Alzheimer’s disease (AD) is a progressive disorder that evolves over time, and also varies from patient to patient. Therefore, defining relevant clinical outcomes in AD can be challenging. Results: Several assessment scales are commonly used to assess AD symptoms and disease status. Examples include SIB (cognitive measure in moderate to severe disease), ADCS-ADL (functional measure for all stages of AD), and the NPI (carer interview on patient behaviour). The MMSE scale is included in all clinical studies of AD as a cognitive screening tool, and has become the standard scale for monitoring treatment in many guidelines. However, it is a relatively crude measure, with pronounced floor and ceiling effects, poor inter-test consistency, and poor discrimination between disease severities. Therefore, it is important to consider other evaluation options such as the prevention of clinical worsening (i.e., concurrent worsening in overall cognitive, functional and global status) – a highly relevant assessment in a progressive disorder such as AD, where rapidly deteriorating patients are most in need of treatment. The emergence of specific symptoms may also be a clinically relevant outcome, e.g., behavioural symptoms such as agitation/aggression are frequently cited as the most difficult/disruptive aspects of AD.Another example is communication, which is important for many aspects of daily life, and its loss can contribute to the development of other reported symptoms. Conclusions: The selection of outcome measures for the assessment of AD should be re-evaluated, in order to define endpoints that are clinically relevant to AD patients and carers.
Rapid detection of Escherichia coli O157∶H7 by using real-time fluorescence PCR assays

In order to establish a TaqMan-based real-time PCR assay for the detection of E.coli O157∶H7, the primers and TaqMan-based probe were designed according to the conserved region of rfb E.coli O157 gene published on GenBank.The primers, probes and the reactive condition were optimized to improve the sensitivity and specificity of the assay. The pure culture and raw milk samples were detected to evaluate the sensitivity of the assay. Analysis of 32 bacterial strains demonstrated that the real-time PCR assay successfully distinguished the E.coli O157 serotype from non-E.coli O157 serotypes and other common enteric bacteria. All bacterial strains that lacked this gene were not detected by this assay. The quantitative ranges of the real-time PCR assay were linear for DNA concentrations ranging from 100 to 104 cfu/μL of E.coli O157 in pure culture, but the detection sensitivity of the real-time PCR assay ranged from 102 to 104 cfu/μL for raw milk samples without enrichment. The overall test could be finished within about 3 hours.The TaqMan-based real-time PCR assay for rfb E. coli O157 gene was proved to be a rapid, sensitive and specific test for the quantitative detection of E.coli O157 from the contaminated food samples.
POSTGLACIAL POPULATION EXPANSION DRIVES THE EVOLUTION OF LONG‐DISTANCE MIGRATION IN A SONGBIRD

Abstract The evolution of long‐distance migratory behavior from sedentary populations is a central problem in studies of animal migration. Three crucial issues that remain unresolved are: (1) the biotic and abiotic factors promoting evolution of migratory behavior, (2) the geographic origin of ancestral sedentary populations, and (3) the time scale over which migration evolves. We test the role of postglacial population expansions during the Quaternary in driving the evolution of songbird migration against prevailing views favoring the role of intraspecific competition. In contrast to previous attempts to investigate these questions using interspecific phylogenies, we adopt an intraspecific approach and examine the phylogeography of a North American songbird, the chipping sparrow (Spizella passerina), which exhibits both long‐distance migratory behavior in temperate North America and sedentary behavior in Mexico and Central America. We show that migratory populations descend from sedentary populations in southern Mexico and that migration has evolved as a result of a northward population expansion into temperate North America since the last glacial maximum 18,000 years ago. Migration appears to have evolved rapidly in some species as populations colonized areas of high seasonality in the temperate zone. The phylogeography of the yellow‐eyed junco (Junco phaeonotus), a strictly sedentary species, provides a null model supporting the view that northward range expansions were driven solely by environmental factors and not by a predisposition to evolve migratory behavior. These results provide the strongest evidence to date that historical climate patterns can drive the rapid evolution of avian migration in natural populations, and they suggest a general mechanism for the repeated evolution of migration within and across bird lineages.