Evaluating the success of phased-release reintroductions for captive-born cheetah (Acinonyx jubatus) in South Africa

Thesis (MScConsEcol)--Stellenbosch University, 2022.ENGLISH ABSTRACT: The global cheetah population has declined to an estimated 7,100 individuals, with half the global population currently found in southern Africa. Where natural metapopulation dynamics are no longer possible, human mediated gene flow is coordinated in the form of managed metapopulations. In 2011, the Endangered Wildlife Trust (EWT, South Africa) established a Cheetah Metapopulation Project (CMP) to ensure the genetic and demographic viability of cheetah on small, fenced reserves in South Africa. Research from the CMP indicates that a new source population is required to ensure new genetics enter the metapopulation as the current rate is below the required four individuals per year. A phased-release method, consisting of two distinct phases, allows for the reintroduction of captive-born cheetah into the cheetah metapopulation in South Africa. The limited research on the reintroduction of captive-born carnivore studies indicates that captive-born cheetah are able to express behaviour seen in wild-born cheetah. This study aimed to provide an evaluation of a phased-release methodology for the reintroduction of captive-born cheetah in South Africa. This was achieved by determining criteria to evaluate the behavioural, spatial, and foraging ecology of each captive-born cheetah at both an individual-level and a population-level to allow for comparisons with wild-born cheetah and other methods of captive release. Post-release movements were calculated at month intervals, using data from GPS collars and post-release monitoring data from October 2019 to August 2021. Home-range (95%) and home-range overlap estimates were established for all cheetah. Of the twelve cheetah released following the phased-release method, five individuals settled after an exploration period, while five other individuals were still in their exploration stage at the end of the current study. The twelve cheetah used all available habitat types at some point during their movements, and all females birthed their first litter within seven months post-release. Alterations to a male cheetah’s social group also caused a change in habitat utilisation. Nineteen different prey species were identified at kill sites and prey consumption estimates indicated that the majority of the cheetah were able to reach the monthly energy requirement, although excessive supplement feeding was provided unjustifiably for four individuals. Body condition scoring and monitoring of kill sites was dependant on consistent monitoring which, when compromised or inconsistent, proved to limit the accuracy of these criteria. The criteria used for the evaluation of behavioural, spatial, and foraging ecology, proved successful on an individual level, and indicated areas that needed further investigation. When applied to a population level, phased-release cheetah showed similar characteristics to those of wild-born cheetah. It is recommended that the evaluation of this phased-release method is continued over a longer time period to further determine the success of this release method.AFRIKAANSE OPSOMMING: Die wêreldwye jagluiperdbevolking het tot 'n geraamde 7,100 individue afgeneem, met die helfte van die wêreldbevolking wat tans in Suider-Afrika voorkom. Waar natuurlike metapopulasiedinamika nie meer moontlik is nie, word mens-gemedieerde geenvloei gekoördineer in die vorm van bestuurde metapopulasies. In 2011 het die Trust vir Bedreigde Natuurlewe (EWT, Suid-Afrika) ’n Jagluiperd-metabevolkingsprojek (CMP) gestig om die genetiese en demografiese lewensvatbaarheid van jagluiperds op klein, omheinde reservate in Suid-Afrika te verseker. Navorsing van die CMP dui daarop dat 'n nuwe bronpopulasie nodig is om te verseker dat nuwe genetika die metapopulasie binnedring aangesien die huidige koers onder die vereiste vier individue per jaar is. 'n Gefaseerde vrystellingmetode, wat uit twee afsonderlike fases bestaan, maak voorsiening vir die herinvoering van jagluiperds wat in gevangenskap gebore is in die jagluiperd-metapopulasie in Suid-Afrika. Die beperkte navorsing oor die herinvoering van gevangene-gebore karnivoor studies dui daarop dat gevangen gebore jagluiperds in staat is om gedrag uit te druk wat gesien word in wild gebore jagluiperds. Hierdie studie het ten doel gehad om 'n evaluering te verskaf van 'n gefaseerde vrystellingmetodologie vir die herinvoering van jagluiperds wat in gevangenskap gebore is in Suid-Afrika. Dit is bereik deur kriteria te bepaal om die gedrags, ruimtelike en vreet-ekologie van elke jagluiperd wat in gevangenskap gebore is te evalueer op beide 'n individuele vlak en 'n bevolkingsvlak om vergelykings met wildgebore jagluiperds en ander metodes van vrylating in gevangenskap moontlik te maak. Na-vrystelling-bewegings is met maandelikse tussenposes bereken, met behulp van data van GPS-halsbande en na-vrystelling moniteringsdata van Oktober 2019 tot Augustus 2021. Tuisafstand- (95%) en tuisafstand oorvleuelingsskattings is vir alle jagluiperds vasgestel. Van die twaalf jagluiperds wat vrygelaat is volgens die gefaseerde vrystelling-metode, het vyf individue na 'n eksplorasieperiode gevestig, terwyl vyf ander individue nog in hul eksplorasiestadium was aan die einde van die huidige studie. Die twaalf jagluiperds het op 'n stadium tydens hul bewegings alle beskikbare habitattipes gebruik, en alle wyfies het hul eerste werpsel binne sewe maande na vrylating gebore. Veranderinge aan 'n jagluiperdman se sosiale groep het ook 'n verandering in habitatbenutting veroorsaak. Negentien verskillende prooispesies is by doodmaakplekke geïdentifiseer en prooiverbruikskattings het aangedui dat die meerderheid van die jagluiperds in staat was om die maandelikse energiebehoefte te bereik, alhoewel oormatige aanvullingsvoeding onregverdig vir vier individue verskaf is. Liggaamstoestandtelling en monitering van doodmaakplekke was afhanklik van konsekwente monitering wat, wanneer dit gekompromitteer of teenstrydig was, bewys het om die akkuraatheid van hierdie kriteria te beperk. Die kriteria wat gebruik is vir die evaluering van gedrags-, ruimtelike en vreet-ekologie, was suksesvol op individuele vlak, en het gebiede aangedui wat verdere ondersoek benodig. Wanneer dit op 'n bevolkingsvlak toegepas word, het gefaseerde vrystelling jagluiperds soortgelyke eienskappe getoon as dié van wildgebore jagluiperds. Dit word aanbeveel dat die evaluering van hierdie gefaseerde vrystellingmetode oor 'n langer tydperk voortgesit word om die sukses van hierdie vrystellingmetode verder te bepaal.Master

Clinical Trials and Novel Pathogens: Lessons Learned from SARS

During the recent global outbreak of severe acute respiratory syndrome (SARS), thousands of patients received treatments of uncertain efficacy and known toxicity such as ribavirin and corticosteroids. Despite this, no controlled clinical trials assessing the efficacy of these agents were conducted. If a second global SARS outbreak occurred, clinicians would not have controlled data on which to base therapeutic decisions. We discuss the unique methodologic and logistical challenges faced by researchers who attempt to conduct controlled trials of therapeutic agents during an outbreak of a novel or unknown infectious pathogen. We draw upon our own experience in attempting to conduct a randomized controlled trial (trial) of ribavirin therapy for SARS and discuss the lessons learned. Strategies to facilitate future clinical trials during outbreaks of unknown or novel pathogens are also presented

Dynamic Fuzzy c-Means (dFCM) Clustering and its Application to Calorimetric Data Reconstruction in High Energy Physics

In high energy physics experiments, calorimetric data reconstruction requires a suitable clustering technique in order to obtain accurate information about the shower characteristics such as position of the shower and energy deposition. Fuzzy clustering techniques have high potential in this regard, as they assign data points to more than one cluster,thereby acting as a tool to distinguish between overlapping clusters. Fuzzy c-means (FCM) is one such clustering technique that can be applied to calorimetric data reconstruction. However, it has a drawback: it cannot easily identify and distinguish clusters that are not uniformly spread. A version of the FCM algorithm called dynamic fuzzy c-means (dFCM) allows clusters to be generated and eliminated as required, with the ability to resolve non-uniformly distributed clusters. Both the FCM and dFCM algorithms have been studied and successfully applied to simulated data of a sampling tungsten-silicon calorimeter. It is seen that the FCM technique works reasonably well, and at the same time, the use of the dFCM technique improves the performance.Comment: 15 pages, 10 figures. It is accepted for publication in NIM

Variations in water use by a mature mangrove of Avicennia germinans, French Guiana

In the tropical intertidal zones, little is known on water uptake by mangroves. Transpiration rates are generally measured at leaf level, but few studies exist on water use at tree or stand levels. The objective of this study was to measure sap flow in trees of different sizes to appreciate the range of variation in water use that may exist in a site dominated by 80% mature Avicennia germinans. The results showed that from the dry to the wet season the mean water use increased from 3.2 to 5.3 dm3 d−1 in small trees (DBH ∼ 13 cm), from 11.5 to 30.8 dm3 d−1 in medium trees (∼24 cm) and from 40.8 to 64.1 dm3 d−1 in large ones (∼45 cm). Sapwood remained active up to a depth of 8 cm with radial variations within the stem. Weak correlations were obtained with VPD and net radiation. This study confirmed that transpiration was larger under low levels of salinity. Water use at stand level (∼1900 living stems ha−1) was estimated to be in the range of 5.8 to 11.8 m3 ha−1 d−1 according to the season

Vector Correlators in Lattice QCD: methods and applications

We discuss the calculation of the leading hadronic vacuum polarization in lattice QCD. Exploiting the excellent quality of the compiled experimental data for the e^+e^- --> hadrons cross-section, we predict the outcome of large-volume lattice calculations at the physical pion mass, and design computational strategies for the lattice to have an impact on important phenomenological quantities such as the leading hadronic contribution to (g-2)mu and the running of the electromagnetic coupling constant. First, the R(s) ratio can be calculated directly on the lattice in the threshold region, and we provide the formulae to do so with twisted boundary conditions. Second, the current correlator projected onto zero spatial momentum, in a Euclidean time interval where it can be calculated accurately, provides a potentially critical test of the experimental R(s) ratio in the region that is most relevant for (g-2)mu. This observation can also be turned around: the vector correlator at intermediate distances can be used to determine the lattice spacing in fm, and we make a concrete proposal in this direction. Finally, we quantify the finite-size effects on the current correlator coming from low-energy two-pion states and provide a general parametrization of the vacuum polarization on the torus.Comment: 16 pages, 9 figure files; corrected a factor 2 in Eq. (7) over the published versio

Nursing Home Residents and Enterobacteriaceae Resistant to Third-Generation Cephalosporins

Limited data identify the risk factors for infection with Enterobacteriaceae resistant to third-generation cephalosporins among residents of long-term-care facilities. Using a nested case-control study design, nursing home residents with clinical isolates of Enterobacteriaceae resistant to third-generation cephalosporins were compared to residents with isolates of Enterobacteriaceae susceptible to third-generation cephalosporins. Data were collected on antimicrobial drug exposure 10 weeks before detection of the isolates, facility-level demographics, hygiene facilities, and staffing levels. Logistic regression models were built to adjust for confounding variables. Twenty-seven case-residents were identified and compared to 85 controls. Exposure to any cephalosporin (adjusted odds ratio [OR] 4.0, 95% confidence interval [CI] 1.2 to13.6) and log percentage of residents using gastrostomy tubes within the nursing home (adjusted OR 3.9, 95% CI 1.3 to 12.0) were associated with having a clinical isolate resistant to third-generation cephalosporins

Global gene expression analysis of human erythroid progenitors

This article is available open access through the publisher’s website. Copyright @ 2011 American Society of Hematology. This article has an erratum: http://bloodjournal.hematologylibrary.org/content/118/26/6993.3.Understanding the pattern of gene expression during erythropoiesis is crucial for a synthesis of erythroid developmental biology. Here, we isolated 4 distinct populations at successive erythropoietin-dependent stages of erythropoiesis, including the terminal, pyknotic stage. The transcriptome was determined using Affymetrix arrays. First, we demonstrated the importance of using defined cell populations to identify lineage and temporally specific patterns of gene expression. Cells sorted by surface expression profile not only express significantly fewer genes than unsorted cells but also demonstrate significantly greater differences in the expression levels of particular genes between stages than unsorted cells. Second, using standard software, we identified more than 1000 transcripts not previously observed to be differentially expressed during erythroid maturation, 13 of which are highly significantly terminally regulated, including RFXAP and SMARCA4. Third, using matched filtering, we identified 12 transcripts not previously reported to be continuously up-regulated in maturing human primary erythroblasts. Finally, using transcription factor binding site analysis, we identified potential transcription factors that may regulate gene expression during terminal erythropoiesis. Our stringent lists of differentially regulated and continuously expressed transcripts containing many genes with undiscovered functions in erythroblasts are a resource for future functional studies of erythropoiesis. Our Human Erythroid Maturation database is available at https://cellline.molbiol.ox.ac.uk/eryth/index.html.National Health Service Blood and Transplant, National Institute for Health Research Biomedical Research Center Program, and National Institute for Health Research

ALMACAL VI: Molecular gas mass density across cosmic time via a blind search for intervening molecular absorbers

We are just starting to understand the physical processes driving the dramatic change in cosmic star-formation rate between z ∼ 2 and the present day. A quantity directly linked to star formation is the molecular gas density, which should be measured through independent methods to explore variations due to cosmic variance and systematic uncertainties. We use intervening CO absorption lines in the spectra of mm-bright background sources to provide a census of the molecular gas mass density of the Universe. The data used in this work are taken from ALMACAL, a wide and deep survey utilizing the ALMA calibrator archive. While we report multiple Galactic absorption lines and one intrinsic absorber, no extragalactic intervening molecular absorbers are detected. However, thanks to the large redshift path surveyed (Δz = 182), we provide constraints on the molecular column density distribution function beyond z ∼ 0. In addition, we probe column densities of N(H2) > 1016 atoms cm−2, five orders of magnitude lower than in previous studies. We use the cosmological hydrodynamical simulation IllustrisTNG to show that our upper limits of ρ(H2) ≲ 108.3M⊙Mpc−3 at 0 < z ≤ 1.7 already provide new constraints on current theoretical predictions of the cold molecular phase of the gas. These results are in agreement with recent CO emission-line surveys and are complementary to those studies. The combined constraints indicate that the present decrease of the cosmic star-formation rate history is consistent with an increasing depletion of molecular gas in galaxies compared to z ∼ 2

Physical mechanisms controlling self-aggregation of convection in idealized numerical modeling simulations

We elucidate the physics of self-aggregation by applying a new diagnostic technique to the output of a cloud resolving model. Specifically, the System for Atmospheric Modeling is used to perform 3- D cloud system resolving simulations of radiative-convective equilibrium in a nonrotating framework, with interactive radiation and surface fluxes and fixed sea surface temperature (SST). We note that self-aggregation begins as a dry patch that expands, eventually forcing all the convection into a single clump. Thus, when examining the initiation of self-aggregation, we focus on processes that can amplify this initial dry patch. We introduce a novel method to quantify the magnitudes of the various feedbacks that control self-aggregation within the framework of the budget for the spatial variance of column-integrated frozen moist static energy. The absorption of shortwave radiation by atmospheric water vapor is found to be a key positive feedback in the evolution of aggregation. In addition, we find a positive wind speed-surface flux feedback whose role is to counteract a negative feedback due to the effect of air-sea enthalpy disequilibrium on surface fluxes. The longwave radiation feedback can be either positive or negative in the early and intermediate stages of aggregation; however, it is the dominant positive feedback that maintains the aggregated state once it develops. Importantly, the mechanisms that maintain the aggregate state are distinct from those that instigate the evolution of self-aggregation.National Science Foundation (U.S.) (Grant 1032244)National Science Foundation (U.S.) (Grant 1136480)National Science Foundation (U.S.) (Grant 0850639)Massachusetts Institute of Technology. Joint Program on the Science & Policy of Global Chang

Serum cytokine profile of neonatal broiler chickens infected with Salmonella Typhimurium

The avian immune system responds to Salmonella infection by expressing cytokines and chemokines. We hypothesized that the immune status of Salmonella Typhimurium (ST) challenged neonatal broilers would differ from the uninfected treatment. The objective of this experiment was to evaluate 12 cytokines. Day of hatch male chicks were randomly allocated into a control or ST challenged group. At day three of age, sterile diluent or 5.0 × 108 CFU of ST was given orally to each chick. Blood was obtained 24 h post challenge and serum separated for later analysis (n = 30 chicks/treatment). Significant (p ≤ 0.05) increases in pro-inflammatory cytokines-interleukin-6 (IL-6), IL-16, and IL-21; anti-inflammatory cytokines- IL-10; chemokines-regulated on activation, normal T cell expressed and secreted (RANTES), macrophage inflammatory protein-1β (MIP-1β), and MIP-3α; colony stimulating factors-macrophage colony-stimulating factor (M-CSF); and growth factors-vascular endothelial growth factor (VEGF) were observed in the serum of the challenged chicks when compared to the control. No significant differences were observed in IL-2, interferon gamma (IFNγ), and IFNα. These data indicate the detection of mucosal immune responses in broiler chickens following ST infection. The heightened levels of pro-inflammatory cytokines, chemokines, and colony stimulating factors align with known inflammatory mechanisms, like the influx of immune cells. However, the elevation of IL-10 was unexpected, due to its immunoregulatory properties. Notably, the rise in VEGF levels is compelling, as it suggests the possibility of tissue repair and angiogenesis in ST infected birds