Miracle-dz/UniFAR-FTUs huggingface dataset:
NF-κB Activation during Acute Helicobacter pylori Infection in Mice

ABSTRACT Nuclear factor κB (NF-κB) plays a key regulatory role in host cell responses to Helicobacter pylori infection in humans. Although mice are routinely used as a model to study H. pylori pathogenesis, the role of NF-κB in murine cell responses to helicobacters has not been studied in detail. We thus investigated the abilities of different Helicobacter isolates to induce NF-κB-dependent responses in murine gastric epithelial cells (GECs) and in transgenic mice harboring an NF-κB-responsive lacZ reporter gene. H. pylori and Helicobacter felis strains up-regulated the synthesis in mouse GECs of the NF-κB-dependent chemokines KC (CXCL1) and MIP-2 (CXCL2). These responses were cag pathogenicity island (cagPAI) independent and could be abolished by pretreatment with a pharmacological inhibitor of NF-κB. Consistent with the in vitro data, experimental Helicobacter infection of transgenic mice resulted in increased numbers of GECs with nuclear β-galactosidase activity, which is indicative of specific NF-κB activation. The numbers of β-galactosidase-positive cells in mice were significantly increased at day 1 postinoculation with wild-type H. pylori strains harboring or not harboring a functional cagPAI, compared to naive animals (P = 0.007 and P = 0.04, respectively). Strikingly, however, no differences were observed in the levels of gastric NF-κB activation at day 1 postinoculation with H. felis or at day 30 or 135 postinoculation with H. pylori. This work demonstrates for the first time the induction of NF-κB activation within gastric mucosal cells during acute H. pylori infection. Furthermore, the data suggest that helicobacters may be able to regulate NF-κB signaling during chronic infection.
Demography of the Helmeted Honeyeater (Lichenostomus melanops cassidix)

Abstract Understanding the demography of threatened taxa is essential for formulating effective management strategies for their conservation and for making predictions about their long-term prospects. With fewer than 25 breeding pairs in the current wild population, the Helmeted Honeyeater (Lichenostomus melanops cassidix) is one of the most threatened birds in Australia. Demography of the sole wild population of the Helmeted Honeyeater was investigated by monitoring 526 nests between 1984 and 1996 and 324 colour-banded birds between 1984 and 2008. Throughout the study, the population was effectively closed, there being no evidence of immigration or emigration. Mean survivorship of nests from laying to fledging was 0.17, and mean survivorship of juveniles (from 40 days to 1 year of age) was 0.63. Weighted mean annual survivorship of adult females and males was 0.75 and 0.81 respectively. The population showed little between-year variation in annual productivity and survivorship, with sufficient recruitment for positive population growth. In general, the population dynamics of the Helmeted Honeyeater fit the pattern of an ‘old endemic’ Australian passerine, with low survival of eggs and chicks, extended parental care of juveniles and high survivorship of juveniles and adults. Eggs and chicks that would not naturally survive are a resource that may be used to assist recovery of the population.
Complementarity and selection effects in early and mid‐successional plant communities are differentially affected by plant–soil feedback

Many studies that provided evidence for a positive relationship between plant diversity and productivity have proposed that this effect may be explained by complementarity among species in resources utilization, or selection of particularly productive species in high‐diversity plant communities. Recent studies have related the higher productivity in diverse plant communities to suppression of pathogenic soil biota. If soil biota plays a role in diversity–productivity relationships, the question remains about how they may influence complementarity and selection effects. Here we examine how complementarity and selection effects may depend on soil biota using a plant–soil feedback approach. We used monocultures and mixtures of early successional plant species, which are known to have mostly negative plant–soil feedback effects, and mid‐successional plant species, which generally have neutral plant–soil feedback. We found that plant–soil feedback effects differed between monocultures and mixed plant communities, as well as between early and mid‐successional plants. This resulted in a significant interaction effect between diversity and successional stage. In monocultures, plant–soil feedback tended to be negative for early and positive for mid‐successional plant species. Interestingly, the community feedback responses of the mixed communities were opposite, being positive for early and negative for mid‐successional community. Plant–soil feedback differentially affected complementarity and selection effects of early and mid‐successional plant communities: it enhanced complementarity effects of early and decreased selection effects of mid‐successional species. Synthesis. Soil biota that drive plant–soil feedback effects can influence the diversity–productivity relationship not only through decreased biomass production in monocultures compared to mixtures, but also through influencing complementarity and selection effects among species in mixed plant communities. Our results reveal that biodiversity–productivity relationships depend on plant–soil feedback interactions, which depend on the successional position of the plant. We propose that including successional position and trait‐based analyses of plant–soil feedback in diversity‐functioning studies will enhance understanding consequences of biodiversity loss for productivity and other ecosystem processes.
No evidence for deception over allocation to brood care in a cooperative bird

The evolutionary route(s) to cooperative breeding, wherein individuals provide care to the offspring of others, remains contentious. Two hypotheses propose that such helping behavior constitutes a signal, either to remain on the current territory (pay-to-stay) or to advertise quality to potential partners (social prestige). As such, both hypotheses predict that helpers gain from perceived, rather than actual, levels of care provided. Using the chestnut-crowned babbler (Pomatostomus ruficeps), we test whether individuals attempt to increase their perceived level of care by visiting the nest without food (nonfeeding [NF]) or with food but fail to deliver it (false-feeding [FF]). We found no evidence that either NF or FF was used as a deceptive tactic, with both being more parsimoniously explained by current levels of brood demand. Most notably, categories of helpers (males, adults, immigrants) expected to be “charged” more for staying or to benefit more from advertising quality, neither nonfed nor false-fed more than other categories (females, yearlings, natals). In addition, there was no evidence that the presence of an audience (the breeding females in their domed nests) influenced the probability of NF or FF in a manner consistent with either hypothesis. Finally, the incidences of both NF and FF were low and insufficient to have significant effects on the per ceived levels of care provided, even if they were used in an attempt to deceive other group members over their contributions to rearing young. We conclude that signaling-based hypotheses have, at best, a weak role in selecting for helping behavior in chestnut-crowned babblers. Key wor ds: cheating, cooperative breeding, false-feeding, pay-to-stay , policing, signaling, social prestige. [Behav Ecol]
Genetic diversity analysis of Moroccan lentil (Lens culinaris Medik.) landraces using Simple Sequence Repeat and Amplified Fragment Length Polymorphisms reveals functional adaptation towards agro‐environmental origins

In the absence of previous molecular characterization, we assessed genetic diversity of 53 Moroccan lentil landraces including two local cultivars using simple sequence repeat (SSR) and amplified fragment length polymorphisms (AFLP). Nineteen SSRs yielded 213 alleles, and seven AFLP primer combinations gave 766 fragments of which 422 were polymorphic. Moderate to high genetic variation was observed. Several small groups of landraces were differentiated. Interestingly, one of the smallest groups contained short-cycle landraces with high early vegetative growth. Landraces in that group were from the dry land location of Abda, where they were likely selected for adaptation to drought and heat stress over centuries. Another group contained two landraces from highland areas that may have been selected for specific adaptation to cold stress. A third group contained one landrace from the Zear region known for its seed quality and has been proposed for the protected designation of origin (PDO) quality mark. Both techniques gave evidence of differentiation of the latter landrace supporting the idea of PDO attribution. Functional grouping according to agro-environmental origins, cycle duration and early vegetative vigour was observed.
Nitrogen and water requirements of fertigated cabbage in Ontario

Increasing nutrient and water regulations have necessitated development of best management practices for application of nitrogen (N) and water. This study was conducted to determine if there was an optimal balance of N and water applied for late storage cabbage (Brassica oleracea L. var. capitata). Five rates of N and five irrigation rates arranged in a response surface design replicated three times were supplied to Huron cabbage grown on sandy loam soil to study the interaction of N and water applied. Plots were located at the University of Guelph, Simcoe Research Station, Ontario, Canada from 2003 to 2005. Total and marketable yields were maximized from a low of 278 kg ha-1 N in 2005 to above the highest rate tested (400 kg ha-1 N) in the other 2 yr. In 2005, there were 29 d above 30 °C and marketable yield was 49% lower than 2004, which had only 1 d above 30 °C. A target soil water value of 100% of field capacity was required to maximize yield in all 3 yr. More N is required as the water supply increas.
Changes seen in the body of an elderly patient suffering from diabetes

Background: Diabetes is a foreign disease today. This is a chronic, metabolic disease that is characterized by elevated blood glucose levels. There are many types of disease. Each of them has different characteristics. The key in the fight against the disease is to perform appropriate laboratory tests to diagnose diabetes and to introduce appropriate treatment to prevent many complications, e.g. impairment of: vision, kidneys, cardiovascular system or hearing. Material and methods: A proper review of the literature was used, which identifies risk factors, complications and proper management in diagnosing diabetes. Results: The growing problem of diabetes forces us to find the most accurate way to treat the disease. Performing reliable diagnostics is crucial. The reference method (IDMS) and
Biosynthesis of anthracydines: enzymic conversion of aklanonic acid to aklavinone and ɛ-rhodomycinone by anthracycline-producing streptomycetes

Summary: Aklanonic acid, a substituted anthraquinone, is the earliest stable intermediate isolated so far in the biosynthesis of anthracycline antibiotics. Desalted, soluble cell extracts of Streptomyces sp. C5 and Streptomyces peucetius (ATCC 29050) converted aklanonic acid to ɛ-rhodomycinone in an S-adenosyl-L-methionine- and NADPH-dependent sequence of reactions. Aklanonic acid was methylated to form aklanonic acid methyl ester (AAME), which was cyclized to form aklaviketone. Aklaviketone was reduced to aklavinone by an NADPH-linked reductase. When extracts of Streptomyces sp. C5 and S. peucetius were used, aklavinone was hydroxylated at C-11 by an NADPH- and oxygen-dependent reaction to form ɛ-rhodomycinone. Cell extracts of Streptomyces galilaeus strains ATCC 31133 and 31671 converted aklanonic acid to aklavinone in the same manner, but neither of the S. galilaeus strains hydroxylated aklavinone to ɛ-rhodomycinone. Mutants of Streptomyces sp. C5 blocked at steps in the conversion of aklanonic acid to aklavinone, and which accumulated aklanonic acid (SC5-39; dauC), AAME (SC5-138; dauD, dauE), and aklaviketone (SC5-159; dauE, dauF), lacked the expected enzymic activities. In a mutant (SC5-24; dauE) lacking aklaviketone reductase, but retaining aklavinone 11-hydroxylase activity, maggiemycin was formed as an apparent shunt product. An enzymic pathway for ɛ-rhodomycinone and maggiemycin formation is consistent with the data presented.
A Chemosensory Adaptation Module for the Physiology Laboratory from Student-Directed C. elegans Research

of comparative physiology laboratory exercises in my first semester as an assistant professor, I turned to my research and found what I had always suspected—the model organism, Caenorhabditis elegans, is as useful in the teaching laboratory as it is in the research laboratory. Since 1974 (Brenner, 1974), research with this common, free-living nematode has yielded numerous significant discoveries in areas ranging from cell signaling and early development to cell death and aging (Table 1). And for good reason; the C. elegans system, a.k. a. “the worm,” boasts many salient features including being the first multi-cellular organism with a sequenced genome (The C. elegans Sequencing Consortium, 1998), a fully described cell lineage (Sulston & Horvitz, 1977; Kimble & Hirsh, 1979; Kimble & White, 1981; Sulston, Schierenberg et al., 1983), and a growing, friendly research community. Many of the attributes that make C. elegans an attractive research specimen, such as its relative low cost and simple body plan (Figure 1), also make it an ideal system for the teaching laboratory. In particular, C. elegans is well suited to genetics and cell biology teaching applications (Guziewicz, Vitullo et al., 2002; Griffin, McMiller et al., 2003). Similarly, as C. elegans physiologists already know, I have found it is well suited to the physiology laboratory. Here, I will describe how students in my junior level college Comparative Physiology course have made use of C. elegans in semester-long, student-directed research projects. One of these projects, chemosensory adaptation, can be implemented as a stand alone laboratory module suitable for high school and college students and will be described in detail. Additionally, some general tips to incorporate C. elegans into your teaching laboratory will be mentioned throughout this paper.
Complementing Human Behavior Assessment by Leveraging Personal Ubiquitous Devices and Social Links: An Evaluation of the Peer-Ceived Momentary Assessment Method

Background Ecological momentary assessment (EMA) enables individuals to self-report their subjective momentary physical and emotional states. However, certain conditions, including routine observable behaviors (eg, moods, medication adherence) as well as behaviors that may suggest declines in physical or mental health (eg, memory losses, compulsive disorders) cannot be easily and reliably measured via self-reports. Objective This study aims to examine a method complementary to EMA, denoted as peer-ceived momentary assessment (PeerMA), which enables the involvement of peers (eg, family members, friends) to report their perception of the individual’s subjective physical and emotional states. In this paper, we aim to report the feasibility results and identified human factors influencing the acceptance and reliability of the PeerMA Methods We conducted two studies of 4 weeks each, collecting self-reports from 20 participants about their stress, fatigue, anxiety, and well-being, in addition to collecting peer-reported perceptions from 27 of their peers. Results Preliminary results showed that some of the peers reported daily assessments for stress, fatigue, anxiety, and well-being statistically equal to those reported by the participant. We also showed how pairing assessments of participants and peers in time enables a qualitative and quantitative exploration of unique research questions not possible with EMA-only based assessments. We reported on the usability and implementation aspects based on the participants’ experience to guide the use of the PeerMA to complement the information obtained via self-reports for observable behaviors and physical and emotional states among healthy individuals. Conclusions It is possible to leverage the PeerMA method as a complement to EMA to assess constructs that fall in the realm of observable behaviors and states in healthy individuals.
SYNONYMISED AND FORGOTTEN, THE BIRD'S HEAD STOUT-TAILED SNAKES, CALAMOPHIS MEYER (SQUAMATA: SERPENTES: HOMALOPSIDAE)

Calamophis jobiensis Meyer disappeared into the synonymy of Brachyorrhos albus in1893. Although the holotype of jobiensis was destroyed in World War II, six museum specimens similar to jobiensis were subsequently found in three museum collections. Morphological analysis suggests that Calamophis is a valid genus distinct from Brachyorrhos and the six museum specimens, none of which are conspecifi c with jobiensis, represent three undescribed species. Calamophis appears to be endemic to Yapen Island in the Bird's Head region of West Papua, Indonesia. Based upon their body form, two of the species with cylindrical bodies and stout tails appear to be cryptozoic/fossorial/ aquatic species. The third species has a remarkable lateral compression of the body, an exceptionally abbreviated tail and narrow ventrals that suggest it is an aquatic form, possibly evolved from a fossorial ancestor.
FIRST REPORT ON IDENTIFICATION OF RASPBERRY BUSHY DWARF VIRUS IN RED RASPBERRY ( RUBUS IDEAUS L.) IN BULGARIA

Raspberry bushy dwarf virus (RBDV), classified to genus Idaeovirus , is a seed- and pollen-borne virus that is commonly found in red raspberry ( Rubus ideaus L.). The virus seems to occur worldwide, including the neighbouring to Bulgaria countries ‐ Romania and Serbia. In Bulgaria, however, RBDV has not been reported so far and, therefore, this is the first report for RBDV occurrence in our country. The investigations were carried out during four suc cessive vegetative cycles in two raspberry plantati ons located in Plovdiv district and included two cultiv ars: ‘Lyulin’ grown in an experimental plot at the Fruit Growing Institute in Plovdiv, and ‘Heritage’ grown in a commercial plantation. The RBDV identification and corroboration was done using visual observations, s erological analyses by enzyme‐linked immunosorbent assay (ELISA), and biological tests by mechanical inocula tions onto herbaceous indicators. In some bushes, visual observations revealed decrea sing of cane vigour (dwarfing), leaf yellows and sometimes crumbly fruits. ELISA data showed that RBDV was identified in single infection in 12 % of th e tested samples from ‘Lyulin’ (experimental plantati on) and in 8.1 % of the samples from ‘Heritage’ (commercial plantation). The virus was detected als o in mixed infection with other raspberry viruses a s the infection levels in ‘Lyulin’ and ‘Heritage’ being 3 2 % and 16 % respectively. Biotests were carried out by mechanical inoculation onto Celosia argentea, Chenopodium amaranticolor, C. foedidum и C. quinoa . RBDV infected C. amaranticolor and C. quinoa . Both species reacted with local and systemic symptoms. The presence of RBDV in Bulgaria was confirmed by both methods: ELISA and mechanical inoculation onto herbaceous indicators.
Depletion of marine megafauna and shifting baselines among artisanal fishers in eastern Brazil

Increasing exploitation effort and efficiency have been leading to population declines and extinctions among large marine animals. Understanding the magnitude of such losses is challenging because current baselines about species' abundances and distributions in the sea were mostly established after humans had started affecting marine populations. For artisanal fisheries, from which written historical records are rarely, if ever, available, approaches based on gathering anecdotal information from fishers' knowledge are a promising method to know the past environmental conditions. We interviewed coastal artisanal fishers, with ages varying from 15 to 85 years, to detect temporal changes in the catch abundance of large fish species, particularly the largetooth sawfish Pristis pristis and the goliath grouper Epinephelus itajara within Abrolhos Bank, Brazil. Most fishers considered that fishing has led to species depletion. However, older fishers reported significantly more species and larger species as depleted than young fishers. Older fishers caught significantly larger largetooth sawfish and goliath grouper in the past than younger fishers. The largetooth sawfish has not been caught or sought for more than 10 years. Probabilistic tests provided no definitive evidence for local extinction, although the past record of sightings indicates a population decline close to the threshold level for extinction probability. We provide evidence that small‐scale artisanal fisheries can decimate the abundance of large coastal fishes, one of those almost close to local extinction. Finally, our results suggest that the younger generation is not aware of past ecological conditions, indicating the occurrence of a shifting baseline syndrome among the fishing community.
Congenital syphilis.

The majority of paediatricians and family physicians in practice in Canada today have never seen a case of congenital syphilis. However, there have been outbreaks of syphilis across Canada since 2001, such that the incidence of syphilis in Canada in 2007 was projected to be almost 10-fold compared with what it was in 1994 to 2000 [1]-[3]. The initial increase in incidence was concentrated in men who have sex with men, but heterosexual transmission in inner-city populations now accounts for a large percentage of cases in some provinces. The incidence of syphilis in 2007 was highest in British Columbia and Alberta, followed by Quebec and Ontario [2]. This has led to an increase in reported congenital cases from approximately two per year to 10 per year nationally [1][4]; it is likely that other cases have been missed because infants are asymptomatic or the diagnosis has not been considered.
Survival of Microorganisms on HEPA Filters

High Efficiency Particulate Air (HEPA) filters are required to minimize the release of microorganisms from laboratories and other settings. This study was carried out to assess whether a range of microorganisms captured on HEPA filters would survive under normal operating conditions. Bacillus atrophaeus (NCTC 10073), Staphylococcus epidermidis (NCIMB 12721), MS-2 coliphage, Escherichia coli (NCIMB 9481), Brevundimonas diminuta (NCIMB 11091), and Aspergillus brasiliensis (ATCC 16404) were individually aerosolized using a Collison nebulizer and captured on HEPA filter material. Clean air was drawn through the loaded filters for 6 days at a constant rate (face velocity of 0.4-0.5 m/s−1) for all organisms and for 210 days for B. atrophaeus to simulate the use of a HEPA filter. Pre-packed sterile filters were also contaminated with B. atrophaeus which survived on the HEPA filter material for 210 days with no significant loss of viability. MS-2 coliphage and A. brasiliensis survived over the 6 days with no significant loss of viability. There was a 5-log reduction in viability of S. epidermidis over 6 days, while both Gram-negative bacteria, E. coli and B. diminuta, were not recoverable after 48 hours of exposure. This study highlights the need for risk assessments and rigorous guidelines on the use and handling of air filtration membranes exposed to resistant pathogenic agents to minimize the risks of occupational exposure.