Conservation value, biodiversity value and methods of assessment in regenerating and human disturbed tropical forest

Although the value of primary forests for biodiversity conservation is well known, the potential biodiversity and conservation value of regenerating forests remains controversial. Many factors likely contribute to this, including: 1. the variable ages of regenerating forests being studied (often dominated by relatively young regenerating forests); 2. the potential for confounding on-going human disturbance (such as logging and hunting); 3. the relatively low number of multi-taxa studies; 4. the lack of studies that directly compare different historic disturbances within the same location; 5. contrasting patterns from different survey methodologies and the paucity of knowledge on the impacts across different vertical levels of rainforest biodiversity (often due to a lack of suitable methodologies available to assess them). We also know relatively little as to how biodiversity is affected by major current impacts, such as unmarked rainforest roads, which contribute to this degradation of habitat and fragmentation. This thesis explores the potential biodiversity value of regenerating rainforests under the best of scenarios and seeks to understand more about the impact of current human disturbance to biodiversity; data comes from case studies from the Manu and Sumaco Biosphere Reserves in the Western Amazon. Specifically, I compare overall biodiversity and conservation value of a best case regenerating rainforest site with a selection of well-studied primary forest sites and with predicted species lists for the region; including a focus on species of key conservation concern. I then investigate the biodiversity of the same study site in reference to different types of historic anthropogenic disturbance. Following this I investigate the impacts to biodiversity from an unmarked rainforest road. In order to understand more about the differential effects of habitat disturbance on arboreal diversity I directly assess how patterns of butterfly biodiversity vary between three vertical strata. Although assessments within the canopy have been made for birds, invertebrates and bats, very few studies have successfully targeted arboreal mammals. I therefore investigate the potential of camera traps for inventorying arboreal mammal species in comparison with traditional methodologies. Finally, in order to investigate the possibility that different survey methodologies might identify different biodiversity patterns in habitat disturbance assessments, I investigate whether two different but commonly used survey methodologies used to assess amphibians, indicate the same or different responses of amphibian biodiversity to historic habitat change by people. The regenerating rainforest study site contained high levels of species richness; both in terms of alpha diversity found in nearby primary forest areas (87% ±3.5) and in terms of predicted primary forest diversity from the region (83% ±6.7). This included 89% (39 out of 44) of the species of high conservation concern predicted for the Manu region. Faunal species richness in once completely cleared regenerating forest was on average 13% (±9.8) lower than historically selectively logged forest. The presence of the small unmarked road significantly altered levels of faunal biodiversity for three taxa, up to and potentially beyond 350m into the forest interior. Most notably, the impact on biodiversity extended to at least 32% of the whole reserve area. The assessment of butterflies across strata showed that different vertical zones within the same rainforest responded differently in areas with different historic human disturbance. A comparison between forest regenerating after selective logging and forest regenerating after complete clearance, showed that there was a 17% greater reduction in canopy species richness in the historically cleared forest compared with the terrestrial community. Comparing arboreal camera traps with traditional ground-based techniques suggests that camera traps are an effective tool for inventorying secretive arboreal rainforest mammal communities and detect a higher number of cryptic species. Finally, the two survey methodologies used to assess amphibian communities identified contrasting biodiversity patterns in a human modified rainforest; one indicated biodiversity differences between forests with different human disturbance histories, whereas the other suggested no differences between forest disturbance types. Overall, in this thesis I find that the conservation and biodiversity value of regenerating and human disturbed tropical forest can potentially contribute to rainforest biodiversity conservation, particularly in the best of circumstances. I also highlight the importance of utilising appropriate study methodologies that to investigate these three-dimensional habitats, and contribute to the development of methodologies to do so. However, care should be taken when using different survey methodologies, which can provide contrasting biodiversity patterns in response to human disturbance.

Influence of phosphine resistance genes on flight propensity and resource location in Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae): the landscape for selection

Phosphine resistance in Tribolium castaneum Herbst (Coleoptera: Tenebrionidae) has evolved through changes to enzymes involved in basic metabolic pathways. These changes impose metabolic stress and could affect energy-demanding behaviours. We therefore tested whether phosphine resistance alleles impact the movement of these insects in their quest for new resources. We measured walking and flight parameters of four T. castaneum genotypes: (1) a field-derived population, (2) a laboratory cultured, phosphine-susceptible reference strain, (3) a laboratory cultured, phosphine-resistant reference strain, and (4) a resistant introgressed strain that is almost identical genetically to the susceptible population. The temporal pattern of flight was identical across all populations, but resistant beetles took flight significantly less, walked more slowly, and located resources less successfully than did susceptible beetles. Also, the field-derived beetles (proved not to be carrying resistance genes) walked significantly faster and more directly towards food resources, and had a higher propensity for flight when compared to the susceptible laboratory beetles. These negative effects suggest survival of beetles with the resistance alleles will be compromised should they leave phosphine application sites. The field for selection therefore extends beyond the site at which phosphine fumigant imposed its effect, and other mutations are also likely to be affected in this way.

Sea otter predation and the distribution of bivalve prey in the Elkhorn Slough National Estuarine Research Reserve

The California sea otter population is gradually expanding in size and geographic range and is consequently invading new feeding grounds, including bays and estuaries that are home to extensive populations of bivalve prey. One such area is the Elkhorn Slough, where otters have apparently established a spring and summer communal feeding and resting area. In anticipation of future otter foraging in the slough, an extensive baseline database on bivalve densities, size distributions, biomasses, and burrow depths has been established for three potential bivalve prey species, Saxidomus nuttalli, Tresus nutallii, and Zirphaea pilsbryi. In 1986, the Elkhorn Slough otters were foraging predominately at two areas immediately east and west of the Highway 1 bridge (Skipper's and the PG&E Outfall). Extensive subtidal populations of Saxidomus nuttalli and Tresus nuttallii occur in these areas. Shell records collected at these study areas indicated that sea otters were foraging selectively on Saxidomus over Tresus. The reason for this apparent preference was not clear. At the Skipper's study site, 51% of the shell record was composed of Saxidomus, yet this species accounted for only 16% of the in situ biomass, and only 39% of the available clams. Tresus represented 49% of the shell record at Skipper's, yet this species accounted for 84% of the in situ biomass and 61% of the available clams. There was no difference in mean burrow depth between the two species at this site so availability does not explain the disparity in consumption. At the PG&E Outfall, Saxidomus represents 66% of the in situ biomass and 81% of the available clams, while Tresus accounts for 34% of the in situ biomass and 19% of the available clams. Saxidomus accounts for 96% of the shell record at this site vs. 4% for Tresus, again indicating that the otters were preying on Saxidomus out of proportion to their density or biomass. High densities and biomasses of a third species, Zirphaea pilsbryi, occur in areas where sea otters were observed to be foraging, yet no cast-off Zirphaea shells were found. Although it is possible this species was not represented in the shell record because the otters were simply chewing up the shells, it is more likely this species is avoided by sea otters. There were relatively few sea otters in the Elkhorn Slough in 1986 compared to the previous two years. This, coupled with high bivalve densities, precluded any quantitative comparison of bivalve densities before and after the 1986 sea otter occupation. Qualitative observations made during the course of this study, and quantitative observations from previous studies indicate that, after 3 years, sea otters are not yet significantly affecting bivalve densities in the Elkhorn Slough.

L’industrie osseuse des Iroquoiens du site Mailhot-Curran (BgFn-2) : une étude des déchets de fabrication

Bien que l’os soit une matière première ayant joué un rôle essentiel au sein des activités quotidiennes des Iroquoiens du Saint-Laurent, il existe à ce jour très peu d’analyses systématiques de l’outillage en os et des débris de fabrication retrouvés en Iroquoianie. Afin de pallier ces lacunes, ce mémoire de maitrise porte sur l’analyse des vestiges en os ouvragés récupérés sur le site villageois Mailhot-Curran (BgFn-2), occupé durant le Sylvicole supérieur tardif par une communauté iroquoienne du Saint-Laurent. Plus précisément, l’étude consiste à analyser l’industrie osseuse en portant une attention particulière aux déchets de fabrication. Cet examen attentif a pour principal objectif de documenter les modes de gestion et de sélection de la matière première ainsi que d’améliorer la compréhension des techniques préhistoriques employées pour la fabrication des objets en os. Au moyen d’analyses technologiques, zooarchéologiques et tracéologiques, il sera possible de classifier les déchets de fabrication, de documenter leur origine technologique et, ultimement, de reconstituer un certain nombre de chaines opératoires. Une étude détaillée de la distribution spatiale des artéfacts permettra également de mieux comprendre l’organisation des activités dans l’espace villageois. Ce mémoire a aussi pour objectif de fournir des balises méthodologiques et empiriques relatives à l’étude des déchets de fabrications en os, afin de démontrer la pertinence de considérer ces derniers dans la compréhension des systèmes socioéconomiques et culturels.

L’industrie osseuse des Iroquoiens du site Mailhot-Curran (BgFn-2) : une étude des déchets de fabrication

Bien que l’os soit une matière première ayant joué un rôle essentiel au sein des activités quotidiennes des Iroquoiens du Saint-Laurent, il existe à ce jour très peu d’analyses systématiques de l’outillage en os et des débris de fabrication retrouvés en Iroquoianie. Afin de pallier ces lacunes, ce mémoire de maitrise porte sur l’analyse des vestiges en os ouvragés récupérés sur le site villageois Mailhot-Curran (BgFn-2), occupé durant le Sylvicole supérieur tardif par une communauté iroquoienne du Saint-Laurent. Plus précisément, l’étude consiste à analyser l’industrie osseuse en portant une attention particulière aux déchets de fabrication. Cet examen attentif a pour principal objectif de documenter les modes de gestion et de sélection de la matière première ainsi que d’améliorer la compréhension des techniques préhistoriques employées pour la fabrication des objets en os. Au moyen d’analyses technologiques, zooarchéologiques et tracéologiques, il sera possible de classifier les déchets de fabrication, de documenter leur origine technologique et, ultimement, de reconstituer un certain nombre de chaines opératoires. Une étude détaillée de la distribution spatiale des artéfacts permettra également de mieux comprendre l’organisation des activités dans l’espace villageois. Ce mémoire a aussi pour objectif de fournir des balises méthodologiques et empiriques relatives à l’étude des déchets de fabrications en os, afin de démontrer la pertinence de considérer ces derniers dans la compréhension des systèmes socioéconomiques et culturels.

Occurrence of OsHV-1 in Crassostrea gigas cultured in Ireland during an exceptionally warm summer. Selection of less susceptible oysters

The occurrence of OsHV-1, a herpes virus causing mass mortality in the Pacific oyster Crassostrea gigas was investigated with the aim to select individuals with different susceptibility to the infection. Naïve spat transferred to infected areas and juveniles currently being grown at those sites were analyzed using molecular and histology approaches. The survey period distinguishes itself by very warm temperatures reaching up to 3.5°C above the average. The virus was not detected in the virus free area although a spread of the disease could be expected due to high temperatures. Overall mortality, prevalence of infection and viral load was higher in spat confirming the higher susceptibility in early life stages. OsHV-1 and oyster mortality were detected in naïve spat after 15 days of cohabitation with infected animals. Although, infection was associated with mortality in spat, the high seawater temperatures could also be the direct cause of mortality at the warmest site. One stock of juveniles suffered an event of abnormal mortality that was significantly associated with OsHV-1 infection. Those animals were infected with a previously undescribed microvariant whereas the other stocks were infected with OsHV-1 μVar. Cell lesions due to the infection were observed by histology and true infections were corroborated by in situ hybridization. Survivors from the natural outbreak were exposed to OsHV-1 μVar by intramuscular injection and were compared to naïve animals. The survival rate in previously exposed animals was significantly higher than in naïve oysters. Results derived from this study allowed the selection of animals that might possess interesting characteristics for future analysis on OsHV-1 resistance.

Early reserve effects linked to small home ranges of a commercial fish, Diplodus sargus, Sparidae

Studies that combine both the ecological responses of marine species and protection measures with movement patterns and habitat use are of major importance in order to better understand the performance of marine protected areas (MPA) and how species respond to their implementation. However, few studies have assessed MPA performance by relating local individual movement patterns and the observed reserve effects. In this study, we combined acoustic telemetry with abundance estimates to study the early effects of a recently established small coastal MPA on the local populations of white seabream. The results show that even small, recently established coastal MPAs can increase the abundance and biomass of commercial fish species, provided that target species have small home ranges and exhibit high site fidelity.

Hypertrophic Adenoid Is A Major Infection Site Of Human Bocavirus 1.

Human bocavirus 1 (HBoV1) is associated with respiratory infections worldwide, mainly in children. Similar to other parvoviruses, it is believed that HBoV1 can persist for long periods of time in humans, probably through maintaining concatemers of the virus single-stranded DNA genome in the nuclei of infected cells. Recently, HBoV-1 was detected in high rates in adenoid and palatine tonsils samples from patients with chronic adenotonsillar diseases, but nothing is known about the virus replication levels in those tissues. A 3-year prospective hospital-based study was conducted to detect and quantify HBoV1 DNA and mRNAs in samples of the adenoids (AD), palatine tonsils (PT), nasopharyngeal secretions (NPS), and peripheral blood (PB) from patients undergoing tonsillectomy for tonsillar hypertrophy or recurrent tonsillitis. HBoV1 was detected in 25.3% of the AD samples, while the rates of detection in the PT, NPS, and PB samples were 7.2%, 10.5%, and 1.7%, respectively. The viral loads were higher in AD samples, and 27.3% of the patients with HBoV had mRNA detectable in this tissue. High viral loads and detectable mRNA in the AD were associated with HBoV1 detection in the other sample sites. The adenoids are an important site of HBoV1 replication and persistence in children with tonsillar hypertrophy. The adenoids contain high HBoV1 loads and are frequently positive for HBoV mRNA, and this is associated with the detection of HBoV1 in secretions.

Primary Relapse Site Pattern In Women With Triple-negative Breast Cancer.

Despite the remarkable improvements in breast cancer (BC) characterization, accurate prediction of BC clinical behavior is often still difficult to achieve. Some studies have investigated the association between the molecular subtype, namely the basal-like BC and the pattern of relapse, however only few investigated the association between relapse pattern and immunohistochemical defined triple-negative breast cancers (TNBCs). The aim of this study was to evaluate the pattern of relapse in patients with TNBC, namely the primary distant relapse site. One-hundred twenty nine (129) invasive breast carcinomas with follow-up information were classified according to the molecular subtype using immunohistochemistry for ER, PgR and Her2. The association between TNBC and distant relapse primary site was analyzed by logistic regression. Using multivariate logistic regression analysis patients with TNBC displayed only 0.09 (95% CI: 0.00-0.74; p=0.02) the odds of the non-TNBC patients of developing bone primary relapse. Regarding visceral and lymph-node relapse, no differences between in this cohort were found. Though classically regarded as aggressive tumors, TNBCs rarely development primary relapse in bone when compared to non-TNBC, a clinical relevant fact when investigating a metastasis of an occult or non-sampled primary BC.

Petroleomics By Electrospray Ionization Ft-icr Mass Spectrometry Coupled To Partial Least Squares With Variable Selection Methods: Prediction Of The Total Acid Number Of Crude Oils.

Negative-ion mode electrospray ionization, ESI(-), with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was coupled to a Partial Least Squares (PLS) regression and variable selection methods to estimate the total acid number (TAN) of Brazilian crude oil samples. Generally, ESI(-)-FT-ICR mass spectra present a power of resolution of ca. 500,000 and a mass accuracy less than 1 ppm, producing a data matrix containing over 5700 variables per sample. These variables correspond to heteroatom-containing species detected as deprotonated molecules, [M - H](-) ions, which are identified primarily as naphthenic acids, phenols and carbazole analog species. The TAN values for all samples ranged from 0.06 to 3.61 mg of KOH g(-1). To facilitate the spectral interpretation, three methods of variable selection were studied: variable importance in the projection (VIP), interval partial least squares (iPLS) and elimination of uninformative variables (UVE). The UVE method seems to be more appropriate for selecting important variables, reducing the dimension of the variables to 183 and producing a root mean square error of prediction of 0.32 mg of KOH g(-1). By reducing the size of the data, it was possible to relate the selected variables with their corresponding molecular formulas, thus identifying the main chemical species responsible for the TAN values.

Surgical Site Infections In Women And Their Association With Clinical Conditions.

Surgical site infections (SSIs) can affect body tissues, cavities, or organs manipulated in surgery and constitute 14% to 16% of all infections. This study aimed to determine the incidence of SSIs in women following their discharge from a gynecology outpatient clinic, to survey different types of SSIs among women, and to verify the association of SSIs with comorbidities and clinical conditions. Data were collected via analytical observation with a cross-sectional design, and the study was conducted in 1,026 women who underwent gynecological surgery in a teaching hospital in the municipality of Teresina, in the northeast Brazilian State of Piauí, from June 2011 to March 2013. The incidence of SSIs after discharge was 5.8% among the women in the outpatient clinic. The most prevalent surgery among the patients was hysterectomy, while the most prevalent type of SSI was superficial incisional. Comorbidities in women with SSIs included cancer, diabetes mellitus, and hypertension. Surveillance of SSIs during the post-discharge period is critical for infection prevention and control. It is worth reflecting on the planning of surgical procedures for patients who have risk factors for the development of SSIs.

Site Specific Spin Dynamics In Bafe2as2: Tuning The Ground State By Orbital Differentiation.

The role of orbital differentiation on the emergence of superconductivity in the Fe-based superconductors remains an open question to the scientific community. In this investigation, we employ a suitable microscopic spin probe technique, namely Electron Spin Resonance (ESR), to investigate this issue on selected chemically substituted BaFe2As2 single crystals. As the spin-density wave (SDW) phase is suppressed, we observe a clear increase of the Fe 3d bands anisotropy along with their localization at the FeAs plane. Such an increase of the planar orbital content is interestingly independent of the chemical substitution responsible for suppressing the SDW phase. As a consequence, the magnetic fluctuations in combination with this particular symmetry of the Fe 3d bands are propitious ingredients for the emergence of superconductivity in this class of materials.

Selection And Validation Of Reference Genes For Functional Studies In The Calliphoridae Family.

The genera Cochliomyia and Chrysomya contain both obligate and saprophagous flies, which allows the comparison of different feeding habits between closely related species. Among the different strategies for comparing these habits is the use of qPCR to investigate the expression levels of candidate genes involved in feeding behavior. To ensure an accurate measure of the levels of gene expression, it is necessary to normalize the amount of the target gene with the amount of a reference gene having a stable expression across the compared species. Since there is no universal gene that can be used as a reference in functional studies, candidate genes for qPCR data normalization were selected and validated in three Calliphoridae (Diptera) species, Cochliomyia hominivorax Coquerel, Cochliomyia macellaria Fabricius, and Chrysomya albiceps Wiedemann . The expression stability of six genes ( Actin, Gapdh, Rp49, Rps17, α -tubulin, and GstD1) was evaluated among species within the same life stage and between life stages within each species. The expression levels of Actin, Gapdh, and Rp49 were the most stable among the selected genes. These genes can be used as reliable reference genes for functional studies in Calliphoridae using similar experimental settings.

Strict Criteria For Selection Of Laparoscopy For Women With Adnexal Mass.

We compared the indication of laparoscopy for treatment of adnexal masses based on the risk scores and tumor diameters with the indication based on gynecology-oncologists' experience. This was a prospective study of 174 women who underwent surgery for adnexal tumors (116 laparotomies, 58 laparoscopies). The surgeries begun and completed by laparoscopy, with benign pathologic diagnosis, were considered successful. Laparoscopic surgeries that required conversion to laparotomy, led to a malignant diagnosis, or facilitated cyst rupture were considered failures. Two groups were defined for laparoscopy indication: (1) absence of American College of Obstetrics and Gynecology (ACOG) guideline for referral of high-risk adnexal masses criteria (ACOG negative) associated with 3 different tumor sizes (10, 12, and 14 cm); and (2) Index of Risk of Malignancy (IRM) with cutoffs at 100, 200, and 300, associated with the same 3 tumor sizes. Both groups were compared with the indication based on the surgeon's experience to verify whether the selection based on strict rules would improve the rate of successful laparoscopy. ACOG-negative and tumors ≤10 cm and IRM with a cutoff at 300 points and tumors ≤10cm resulted in the same best performance (78% success = 38/49 laparoscopies). However, compared with the results of the gynecology-oncologists' experience, those were not statistically significant. The selection of patients with adnexal mass to laparoscopy by the use of the ACOG guideline or IRM associated with tumor diameter had similar performance as the experience of gynecology-oncologists. Both methods are reproducible and easy to apply to all women with adnexal masses and could be used by general gynecologists to select women for laparoscopic surgery; however, referral to a gynecology-oncologist is advisable when there is any doubt.

[comparative Study Between Fast And Slow Induction Of Propofol Given By Target-controlled Infusion: Expected Propofol Concentration At The Effect Site. Randomized Controlled Trial].

studies have shown that rate of propofol infusion may influence the predicted propofol concentration at the effect site (Es). The aim of this study was to evaluate the Es predicted by the Marsh pharmacokinetic model (ke0 0.26min(-1)) in loss of consciousness during fast or slow induction. the study included 28 patients randomly divided into two equal groups. In slow induction group (S), target-controlled infusion (TCI) of propofol with plasma, Marsh pharmacokinetic model (ke0 0.26min(-1)) with target concentration (Tc) at 2.0-μg.mL(-1) were administered. When the predicted propofol concentration at the effect site (Es) reached half of Es value, Es was increased to previous Es + 1μg.mL(-1), successively, until loss of consciousness. In rapid induction group (R), patients were induced with TCI of propofol with plasma (6.0μg.ml(-1)) at Es, and waited until loss of consciousness. in rapid induction group, Tc for loss of consciousness was significantly lower compared to slow induction group (1.67±0.76 and 2.50±0.56μg.mL(-1), respectively, p=0.004). the predicted propofol concentration at the effect site for loss of consciousness is different for rapid induction and slow induction, even with the same pharmacokinetic model of propofol and the same balance constant between plasma and effect site.