bluuebunny/crossref_metadata_2025 huggingface dataset:
Geography and location are the primary drivers of office microbiome composition
Authors: Chase John H , Fouquier Jennifer , Zare Mahnaz , Sonderegger Derek L , Knight Rob , Kelley Scott , Siegel Jeffrey A , Caporaso J Gregory
Published: January 2018

North Americans spend the majority of their time indoors where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs, and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidates several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ based on surface material (e.g., ceiling tile or carpet), but do differ based on the location in a room (e.g., ceiling or floor), two features which are often conflated, but which we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material were likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces.

Our study highlights several points that should impact the design of future studies of the microbiology of the BEs. First, projects tracking changes to BE bacterial communities should focus sampling effort on surveying different locations in offices and in different cities, but not necessarily different materials or different offices in the same city. Next, disturbance due to repeat sampling, though detectable, is small compared to other variables, opening up a range of longitudinal study designs in the built environment. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples on all sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities.
Behaviour and beliefs related to male aggression: Evidence of intrasexual selection in humans?
Authors: Camilleri Tara-Lyn , Kushnick Geoff
Published: January 2018

Sexual selection favours traits that increase mating and, thus, reproductive success. Some scholars have suggested that intrasexual selection driven by contest competition has shaped human male aggression. If this is the case, one testable hypothesis is that beliefs and behaviour related to male aggression should be more prevalent in societies where the intensity and strength of sexual selection is higher, as measured by factors such as the presence and scope of polygyny, the number of same-sex competitors relative to potential mates, and male contribution to subsistence. Using data from a global sample of 78 societies, we found strong support for this hypothesis. We discuss potential alternative explanations for the relationships, ruling out some using multivariate methods to control for confounding variables such as political complexity, warfare and geographic clustering.
Fighting back: Population recovery and expansion of the range size of the Mitumba chimpanzee community in Gombe National Park, Tanzania
Authors: Mjungu Deus , Wilson Michael L , Foerster Steffen , Pusey Anne E
Published: January 2018

Chimpanzees (Pan troglodytes) compete aggressively for territory with their neighbors. Results from playback experiments and observations of naturally occurring intergroup interactions indicate that success in territorial competition depends mainly on the number of adult males on each side. Communities with more males are therefore expected to win more intergroup contests and, as a result, expand their range. Demography is thus expected to play a decisive role in intergroup competition. Testing this hypothesis, however, has proven difficult. Most studies have focused on a single community, so that the actual number of males is known for only one side. Additionally, because chimpanzees reproduce and grow slowly, many years of data are needed to test the effects of demographic change on territorial behavior. Here we report on 20 years of data from two habituated neighboring communities. We found that numerical advantage plays an important role in territorial competition. During the first part of the study period, the Mitumba community suffered a demographic decline. As a result, males from the larger Kasekela community won the majority of intergroup interactions and expanded their range deep into areas previously used by Mitumba. However, during the last five years, the Mitumba community increased in size, and subsequently recovered a substantial portion of their range from the Kasekela chimpanzees. This study highlights the importance of long-term studies for understanding territorial dynamics.
First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects
Authors: Pangalos Constantinos , Hagnefelt Birgitta , Lilakos Konstantinos , Konialis Christopher
Published: January 2018

Background : Fetal malformations and other structural abnormalities are relatively frequent findings in the course of routine prenatal ultrasonographic examination. Due to their considerable genetic and clinical heterogeneity, the underlying genetic cause is often elusive and the resulting inability to provide a precise diagnosis precludes proper reproductive and fetal risk assessment. We report the development and first applications of an expanded exome sequencing-based test, coupled to a bioinformatics-driven prioritization algorithm, targeting gene disorders presenting with abnormal prenatal ultrasound findings. Methods : We applied the testing strategy to14 euploid fetuses, from 11 on-going pregnancies and 3 products of abortion, all with various abnormalities or malformations detected through prenatal ultrasound examination. Whole exome sequencing (WES) was followed by variant prioritization, utilizing a custom analysis pipeline (Fetalis algorithm), targeting 758 genes associated with genetic disorders which may present with abnormal fetal ultrasound findings. Results :A definitive or highly-likely diagnosis was made in 6 of 14 cases (43%), of which 3 were abortuses (Ellis-van Creveld syndrome, Ehlers-Danlos syndrome and Nemaline myopathy 2) and 3 involved on-going pregnancies (Citrullinemia, Noonan syndrome, PROKR2-related Kallmann syndrome). In the remaining 8 on-going pregnancy cases (57%), a ZIC1 variant of unknown clinical significance was detected in one case, while in 7 cases testing did not reveal any pathogenic variant(s). Pregnancies were followed-up to birth, resulting in one neonate harboring the PROKR2 mutation, presenting with isolated minor structural cardiac abnormalities, and in 7 apparently healthy neonates. Discussion : The expanded targeted exome sequencing-based approach described herein (Fetalis), provides strong evidence suggesting a definite and beneficial increase in our diagnostic capabilities in prenatal diagnosis of otherwise chromosomally balanced fetuses with troubling ultrasound abnormalities. Furthermore, the proposed targeted exome sequencing strategy, designed primarily as a diagnostic rather than a research discovery tool, overcomes many of the problems and limitations associated with clinical wide-scale WES testing in a prenatal setting.
Guideline compliance related to indwelling urinary catheters in 43 Norwegian nursing homes - findings and implications
Authors: Aarnes Laila , Harris Karin , Skaare Aase I , Andersen John R
Published: January 2018

Background For patients in health institutions urinary tract infections often have significant negative health consequences. Indwelling urinary catheters and inappropriate practice related to this is a strong risk factor for urinary tract infections. Thus, a national guideline promotes best practice for handling indwelling urinary catheters. The aim of this study was to assess the prevalence of patients with indwelling urinary catheters in 34 Norwegian nursing homes. Furthermore, we wanted to study whether health professionals followed the national guidelines related to indwelling urinary catheters. If the study reveals room for improvements, it may indicate interventions can contribute to improvements in the health care institutions. Methods We conducted a quantitative survey in health care professionals who worked in nursing homes in from Sogn og Fjordane county (Norway), and asked them how to which extent guidelines related to indwelling urinary catheters were used in at their work place. The study also included data on the prevalence of indwelling urinary catheters in 830 patients (565 women and 265 men) in the 34 nursing homes. We also conducted a clinical audit in these nursing homes in order to study the how the guidelines were implemented. An overall assessment was made (satisfactory or not satisfactory) on whether 11 dimensions of the guidelines were followed (Table 2). When ≥ 80% of the nursing homes had a score = yes/usually to the items above it was considered satisfactory. The evaluations from the clinical audits were based on an overall judgment of the finding at the nursing homes. The study was approved by the Western Norway Hospital Trust as part of a quality assessment strategy. An approval from the regional ethical committee was not needed as the study was a quality assessment project and did not include any individual patient data. Results Our findings shows that 92 of 830 patients had a indwelling urinary catheter the day of prevalence assessment, and significantly more men (21.1%) than women (6.7%) had a indwelling urinary catheter (Fisher's exact test; P <0.001. Overall, the survey showed that compliance with the guidelines was unsatisfactory with one exception; the doctor prescribed the posting of indwelling urinary catheters (Table 2 and 3). Conclusions In conclusion, most areas we investigated need improvements. The survey itself may be a key to change the nursing staff`s attitudes and culture and to gain increased competence. In addition, it seems necessary to have good data solutions as well as leadership anchoring in further work on implementing best practice in handling indwelling urinary catheters. w
Guideline compliance related to indwelling urinary catheters in 34 Norwegian nursing homes - findings and implications
Authors: Aarnes Laila , Harris Karin , Skare Åse I , Andersen John R
Published: January 2018

Background For patients in health institutions urinary tract infections often have significant negative health consequences. Indwelling urinary catheters and inappropriate practice related to this is a strong risk factor for urinary tract infections. Thus, a national guideline promotes best practice for handling indwelling urinary catheters. The aim of this study was to assess the prevalence of patients with indwelling urinary catheters in 34 Norwegian nursing homes. Furthermore, we wanted to study whether health professionals followed the national guidelines related to indwelling urinary catheters. If the study reveals room for improvements, it may indicate interventions which can contribute to improvements in the health care institutions. Methods We conducted a quantitative survey in health care professionals who worked in nursing homes in from Sogn og Fjordane county (Norway), and asked them to which extent guidelines related to indwelling urinary catheters were used at their work place. The study also included data on the prevalence of indwelling urinary catheters in 830 patients (565 women and 265 men) in the 34 nursing homes. We also conducted a clinical audit in these nursing homes in order to study the how the guidelines were implemented. An overall assessment was made (satisfactory or not satisfactory) on whether 11 dimensions of the guidelines were followed (Table 2). When ≥ 80% of the nursing homes had a score = yes/usually to the items above it was considered satisfactory. The evaluations from the clinical audits were based on an overall judgment of the finding at the nursing homes. The study was approved by the Western Norway Hospital Trust as part of a quality assessment strategy. An approval from the regional ethical committee was not needed as the study was a quality assessment project and did not include any individual patient data. Results Our findings shows that 92 of 830 patients had a indwelling urinary catheter the day of prevalence assessment, and significantly more men (21.1%) than women (6.7%) had a indwelling urinary catheter (Fisher's exact test; P <0.001. Overall, the survey showed that compliance with the guidelines was unsatisfactory with one exception; the doctor prescribed the posting of indwelling urinary catheters (Table 2 and 3). Conclusions In conclusion, most areas we investigated need improvements. The survey itself may be a key to change the nursing staff`s attitudes and culture and to gain increased competence. In addition, it seems necessary to have good data solutions as well as leadership anchoring in further work on implementing best practice in handling indwelling urinary catheters.
Faunal communities are invariant to fragmentation in experimental seagrass landscapes
Authors: Lefcheck Jonathan S , Marion Scott R , Lombana Alfonso V , Orth Robert J
Published: January 2018

Human-driven habitat fragmentation is cited as one of the most pressing threats facing many coastal ecosystems today. Many experiments have explored the consequences of fragmentation on fauna in one such foundational habitat, seagrass beds, but have either surveyed along a gradient of existing patchiness, used artificial materials to mimic a natural bed, or sampled over short timescales. Here, we describe faunal responses to constructed fragmented landscapes varying from 4-400 m2 in two transplant garden experiments incorporating live eelgrass (Zostera marina L.). In experiments replicated within two subestuaries of the Chesapeake Bay, USA across multiple seasons and non-consecutive years, we comprehensively censused faunal communities, from mesopredators to epifaunal grazers, using complementary quantitative methods. We found that community properties, including abundance, species richness, Simpson and functional diversity, and composition were generally unaffected by the amount of habitat, the size of the landscape, or the intensity of sampling. Additionally, an index of competition based on species co-occurrences revealed no trends with increasing patch size, contrary to theoretical predictions. We extend conclusions concerning the invariance of animal communities to habitat fragmentation from small-scale observational surveys and artificial experiments to experiments conducted with actual living plants and at realistic scales. Our findings are likely a consequence of the rapid life histories and high mobility of the organisms common to eelgrass beds in this region, and have implications for both conservation and restoration, suggesting that even small patches can rapidly promote abundant and diverse faunal communities.
A gene expression signature for defining aggressive phenotype and prognosis in intermediate-risk acute myeloid leukemia
Authors: Deng Ailing
Published: January 2018

Intermediate-risk AML is a group of heterogeneous disease, complete and accurate understanding of their molecular pattern are urgent. We downloaded gene expression profile from TCGA, and performed the differential gene expression analysis of 98 intermediate-risk AML patients according to the different clinical outcome. By studying the overlap of differential genes based on OS and EFS classification, we identified 6 distinct genes (SPANXC, ADAMTS15, C8B, FAM183A, FLJ42875 and PXDN). Only FLJ42875 and PXDN were relatively widely expressed in intermediate-risk AML. Moreover, Q1 (0-25%) of PXDN was associated significantly shortened OS and EFS (P=0.0001, P=0.0032, respectively), while OS and EFS of Q2 (25-50%) of FLJ42875 expression group were significantly longer than that of low FLJ42875 expression patients (P=0.0157, P=0.0074, respectively). In the multivariable model of OS, PXDN Q1 group had a shorter OS and EFS (P < 0.001, P =0.009; respectively). While FLJ42875 Q2 group had a tendency of prolonged OS and EFS (P=0.050, P=0.023; respectively). Our results suggest that FLJ42875 and PXDN may play a role in the leukemogenesis of intermediate-risk AML.
Enantioselective organocatalysis in the synthesis of biologically relevant compounds
Authors: Albrecht Lukasz
Published: January 2018

The development of methods for the preparation of biologically relevant compounds in an enantiomerically enriched form constitutes one of the most significant tasks in the contemporary organic chemistry. In particular, enantioselective reactions where prochiral substrates are converted into enantiomerically enriched products in the presence of chiral catalyst are of great importance. Recently, asymmetric organocatalysis, where simple organic molecules are used as catalysts of various enantiodifferentiating reactions, has become a highly useful synthetic tool enabling for the efficient asymmetric induction based on diverse activation modes. Herein, we report our studies on organocatalytic, enantioselective strategies for the synthesis of biologically relevant molecules such as: quaternary α-amino acids and their isoelectronic analogs α-aminophosphonates, benzo[1,5]oxazocines, α-methylidene-δ-lactones, α-alkylidene-ketones, furfural derivatives, and benzothiophenes. The devised approaches utilize readily available chiral organocatalysts to control stereo-chemical reaction outcomes. Operational simplicity, efficiency and high enantio- and diastereoselectivities are the main benefits of the developed strategies.
Chimpanzee population response to commercial hunting in south-east Cameroon
Authors: Willie Jacob , Tagg Nikki
Published: January 2018

Wildlife monitoring data provide an objective basis for evaluating conservation efforts and refining conservation strategies. Central chimpanzee nest censuses were conducted in La Belgique Research Site, south-east Cameroon, in 2001 (reference year) and 2014 using the Standing Crop Nest Count methodology. In both study years, 10 6-km transects traversing all habitat types were opened at a constant bearing of 45° to collect nest data. Analyses were performed in Distance 6.2. Chimpanzee nest density values (nests/km²) were 112 and 69 in 2001 and 2014, respectively. These results suggest that chimpanzee numbers in the research site have dropped by 38.4% in 13 years. This is probably due to a strong commercial hunting pressure, especially since 2009, whereby gun hunting has become the de facto method for harvesting wildlife in the region. From the reference year till 2014, the study site had not been subject to devastating disease epidemics or major habitat disturbance from logging and agricultural activities. In the study site−where the presence of conservation scientists and the constant sensitization within the rural communities raise awareness of the need for ape protection−chimpanzees are not particularly targeted by hunters, and it is quite plausible that a number of individuals fled to adjacent forest patches where disturbance shooting is minimal. However, despite observed range shifts, chimpanzees persist in the region. In contexts where laws are not enforced rigorously enough, conservation research presence or other activities aiming at reinforcing the value of living great apes are crucial for the survival of these critically-endangered species.
Transdisciplinary approach to solving conservation challenges: A case of Budongo Conservation Field Station, Uganda
Authors: Asiimwe Caroline , Muhanguzi Geoffrey , Okwir Eric , Okimat Paul , Bugenyi Andrew W , Mugabe Timothy , Babweteera Fred
Published: January 2018

The conservation of chimpanzees (Pan troglodytes) faces complex and dynamic threats, deriving mostly from anthropogenic factors such as high density and poverty in local human populations. One specific threat is poaching, which contributes to both permanent physical disabilities in chimpanzees and cross-species disease transmission. In the Sonso chimpanzee community, Budongo forest, Uganda, over 20% chimpanzees are permanently disabled by indiscriminate poachers’ snare-trap. While severe injuries can sometimes result in death, little is known about the long-term health impacts of poaching to chimpanzees or possible effective mitigation measures. To combat and monitor the complexities of conservation threats, a holistic transdisciplinary approach is required and as a result, the Budongo Conservation Field Station (BCFS) has implemented a comprehensive strategy. Instead of focusing solely on chimpanzee health, our multi-faced tit-for-tat approach also incorporates education and action measures for local communities living adjacent to the forest. To reduce poaching, we provide alternative livelihood sources, veterinary services and education while concurrently employing their local indigenous knowledge of poaching practices to more effectively locate snares/traps in the forest. To mitigate disease transmission across species, beneficiaries in incentive programs must have functional sanitation facilities. To consistently monitor threats and conservation impacts, we routinely collect data on snare recovery and infectious disease prevalence in chimpanzees, humans and livestock. Our preliminary results, since the programs’ inception, show a reduction in respiratory and gastrointestinal infections coupled with an increase in snare recovery from the forest. These findings suggest that our holistic approach is effective in mitigating the threats to chimpanzees in Budongo forest.
Commercial fishing gear modifications to reduce interactions between Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and the southern flounder (Paralichthys lethostigma) fishery in North Carolina (USA)
Authors: Levesque Juan C , Hager Christian , Diaddorio Eric , Dickey R. Jason
Published: January 2018

Bycatch of protected species in commercial fishing operations is a primary concern to fishery managers because it threatens the conservation, protection, and recovery of fragile species, such as the Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). One potential solution to reduce the risk associated with commercial fishing operations is to design commercial fishing gear that is more selective in terms of interactions between Atlantic sturgeon and commercial fisheries. Given the need to reduce commercial fishery interactions, the overarching goal was to reduce Atlantic sturgeon fishery interactions and maintain southern flounder (Paralichthys lethostigma) catch in North Carolina. The specific objectives of this study were to design and evaluate the effectiveness of a modified gillnet. Overall, the results proved that lowering the profile and amount of webbing had a beneficial impact at reducing Atlantic sturgeon encounters and bycatch. The modified gillnet reduced bycatch and Atlantic sturgeon encounters by 49.4% and 60.9%, respectively. We also found the modified gear entangled 51.6% less southern flounder, which corresponded to a 32% reduction in total weight; the experimental sections entangled slightly larger individuals than the control sections. Our findings showed the number of Atlantic sturgeon encounters was positively associated with mean water depth, with more Atlantic sturgeon encountered in deeper than shallower waters; 75% were encountered at depths between 4.6 and 6.1 m. In addition, we found that 41% of the Atlantic sturgeon encountered were in warmer (26‒30°C) than colder water.
Arctium lappa – Burdock pappus bristles can cause skin irritation and burdock ophthalmia
Authors: Cole Theodor C H , Su Shan , Hilger Hartmut H
Published: January 2018

Contact with and handling of burs (the flowering heads or infructescences) from the greater burdock (Arctium lappa L., Asteraceae) and other members of the same genus, is a potential hazard for humans, horses, and dogs. The minute, sharply-pointed, bristly pappus hairs easily detach from the top of the 'seeds' and are carried by the slightest breeze – attaching to skin, mucous membranes, and eyes where they can cause severe dermal irritation, possible respiratory manifestations, and ophthalmia.
Microbial diversity of extreme habitats in human homes
Authors: Savage Amy M. , Hills Justin , Driscoll Katherine , Fergus Daniel J , Grunden Amy M , Dunn Robert R
Published: January 2018

High throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.
Injury surveillance in a rural sub-Saharan setting: Results from a surveillance initiative in Nzega District, Tanzania
Authors: Davis Laura , Bechtold Alyssa , Kaeraa Marc , Lacava Lukas , L. Wilson Michael
Published: January 2018

Introduction: Ninety percent of all injuries occur in low- and middle-income countries (LMIC) and most of these injuries are largely preventable. Most injury surveillance systems are focused in large urban settings, which largely ignore injury mechanisms in rural contexts which are critical settings for planning future prevention efforts. Methods: Injury data was collected from July 1 to July 31, 2013 at Nzega District Hospital (NDH) in central Tanzania in the form of an injury questionnaire based off of the WHO’s injury surveillance guidelines. One hundred patients were enrolled and asked questions about the location of their injury, cause of their injury, and many other contextual and demographic factors. Results: Seventy-nine percent of participants were males and the most prevalent injury cause for all participants was road traffic collisions, making up 31% of the injuries. Violence was the second most prevalent cause, accounting for 28% of the injuries, and the number one cause of injuries for women. Twenty-three percent (n=7) of patients suffering from injuries due to road traffic collisions were given a prognosis of long-term disability of six months or more. Forty-four percent of all injuries occurred in the home setting. Conclusion: The incidence rate of injuries overall of 346 per 10 000 per year is consistent with others studies conducted in LMICs and is higher than many infectious diseases that are already considered a pressing public health problem. Injuries create disabilities, which in turn creates an economic burden on the individual, health care system, and society as a whole.
Time-variant species pools shape competitive dynamics and diversity-ecosystem function relationships
Authors: Armitage Dave W
Published: January 2018

Biodiversity-ecosystem function (BEF) experiments routinely employ common garden designs, drawing samples from a local biota. The communities from which taxa are sampled may not, however, be at equilibrium. To test for temporal changes in BEF relationships, I assembled pools of aquatic bacterial strains isolated at different time points from leaves on the pitcher plant Darlingtonia californica in order to evaluate the strength, direction, and drivers of the BEF relationship across a natural host-associated successional gradient. I constructed experimental communities using bacterial isolates from each time point and measured their respiration rates and competitive interactions. Communities assembled from mid-successional species pools showed the strongest positive relationships between community richness and respiration rates, driven primarily by linear additivity among isolates. Diffuse competition was common among all communities but greatest within mid-successional isolates. These results demonstrate the dependence of the BEF relationship on the temporal dynamics of the local species pool, implying that ecosystems may respond differently to the addition or removal of taxa at different points in time during succession.
Method of discovery of effective components in herbals based on evidence by reversed-directed analysis
Authors: Zhang Jianyi
Published: January 2018

Conventional methods in this field include identifying and screening compounds in a laboratory setting with cells and animals, and then moving on to clinical trials with promising compounds. To complicate the issue with these methods, effective compounds might not exist in the original herbals, multiple components might be involved with outcomes, long study period and high cost. The method described above might bypass bottlenecks such as, 1) promising compounds are identified from test patients who demonstrate preferred and safe results, 2) more than one compound might be identified, 3) safe and effective compounds might be metabolites and not exist in herbals. The process includes a website to collect clinical information. The promising compounds can be determined by analyzing common components from patients. Both internal and external tests could be done with promising compounds, the entire process would be very efficient and economical.
Predation in multi-prey multi-predator communities: Seeking common patterns between North America and Africa
Authors: Owen-Smith Norman
Published: January 2018

The impact that large mammalian carnivores can have on the abundance of their ungulate prey remains contentious and achieving scientific consensus has proved elusive. Several studies in temperate latitudes in North America have documented how increases in the abundance of wolves have been associated with declines in the abundance of certain large ungulate species, and vice versa. In contrast, in African savanna ecosystems in both southern and eastern Africa, variations in the abundance of ungulate populations seem to be primarily associated with fluctuations in rainfall affecting vegetation growth and consequent food availability for herbivores. In this review, I will explain how the functional mechanisms operating in these distinct ecosystems are basically similar, despite contrasts in their diversity of predators and prey. I will describe how predation constrains the abundance of African savanna herbivores, despite resource controls over their population dynamics. For case histories I will draw particularly on findings from South Africa’s Kruger National Park, where the most comprehensive information is available.
Application of nitrones in the stereoselective synthesis of important β-lactam compounds
Authors: Chmielewski Marek
Published: January 2018

The copper(I)-mediated reaction of nitrones with terminal acetylenes, known as the Kinugasa reaction, represents an attractive method of direct formation of the β-lactam ring. The reaction can be performed in many ways. Diastereoselective versions, including cyclic chiral nitrones or chiral acetylenes and open-chain nitrones, are the most attractive. An alternative method yielding β-lactams with high stereoselectivity, in which nitrones are used, is their 1,3-dipolar cycloaddition to unsaturated lactones. After N- O bond cleavage, cycloadducts can be easily transformed into β-lactams via an intramolecular acylation of the nitrogen atom. Both methodologies are demonstrated in the synthesis of carbapenems (Thienamycin and 4AA azetidinone), monobactams (Carumonam) and Ezetimibe, a powerful cholesterol absorption inhibitor.
Hypersaline lakes harbor more active bacterial communities
Authors: Aanderud Zachary T , Vert Joshua C , Lennon Jay T , Magnusson Tylan W , Breakwell Donald P , Harker Alan R
Published: January 2018

Extremophiles employ a diverse array of resistance strategies to thrive under harsh environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves to drop too low, extremophiles may enter a dormant state of reduced metabolic activity to survive. Dormancy is frequently offered as a plausible explanation for the persistence of bacteria under suboptimal environmental conditions with the prevalence of this mechanism only expected to rise as stressful conditions intensify. We estimated dormancy in ten hypersaline and freshwater lakes across the Western United States. To our surprise, we found that extreme environmental conditions did not induce higher levels of bacterial dormancy. Based on our approach using rRNA:rDNA gene ratios to estimate activity, halophilic and halotolerant bacteria were classified as inactive at a similar percentage as freshwater bacteria, and the proportion of the community exhibiting dormancy was considerably lower (16%) in hypersaline than freshwater lakes across a range of cutoffs estimating activity. Of the multiple chemical characteristics we evaluated, salinity and, to a lesser extent, total phosphorus concentrations influenced activity. But instead of dormancy being more common as stressful conditions intensified, the percentage of the community residing in an inactive state decreased with increasing salinity in freshwater and hypersaline lakes, suggesting that salinity acts as a strong environmental filter selecting for bacteria that persist and thrive under saltier conditions. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results demonstrate that extreme environments may not necessarily be stressful or suboptimal for highly adapted extremophiles causing them to need dormancy less often to survive.
Decomposition of Ethiopian life expectancy by age and cause of mortality; 1990-2010
Authors: Balew Gizachew , Cho Youngtae
Published: January 2018

Background: Ethiopia, a sub-Saharan country with over 94 million populations growing at a rate of 2.6 percent is showing a fast socio-economic improvement. According to World Health Organization 2014, life expectancy in the country has increased by about 19 years with in the last two decades. It has also reduced child mortality by 2/3rd; two years ahead of millennium development goal deadline. This research will focus in decomposing the improvement in life expectancy in the country from 1990 to 2010. Methods: We used a secondary data on cause and age specific mortality estimate of Ethiopia from institute of health metrics and evaluation. Burden of disease is measured using potential life years lost and potential life years gained using survival 6 program and compared across time. Further improvement in life expectancy is decomposed across age and specific causes using Pollard’s life expectancy decomposition method. Results: Burden of disease measured in weighted years of life lost (YLL) shows that lower respiratory infection at a value of 5.35, neonatal disorders [4.058], diarrheal diseases [3.6], neglected tropical diseases [2.4], meningitis [1.49] and tuberculosis [1.19] are the top causes of burden in 1990 which showed a slight shift in 2010. Lower respiratory tract infections showed the highest reduction in YLL by about 41.27%, followed by diarrheal disease (32.8%) and meningitis (26.46%). Decomposition of life expectancy shows among the total 15.25 years increase in life expectancy from 1990 to 2010, about 5.8 (35.78%) years of increase in life expectancy is achieved through improved longevity in children’s aged 1- 4 year. On the other hand diarrheal diseases reduction contributes about 3.12 [15.96%] followed by lower respiratory infection about 2.54 [12.98%], neglected tropical diseases by 1.45 [7.43%] and tuberculosis by 1.2 [6.25%] years. Conclusions and recommendation: Burden of disease in Ethiopia has declined dramatically which has contributed to the improvement in life expectancy, with the highest reduction already recorded in major communicable diseases. Though it is encouraging that mortality from children has reduced in the country, the slow change in mortality and burden of disease in the general adult population needs future public attention.
Phage on Tap – A quick and efficient protocol for the preparation of bacteriophage laboratory stocks
Authors: Bonilla Natasha , Rojas Maria Isabel , Netto Flores Cruz Giuliano , Hung Shr-Hau , Rohwer Forest , Barr Jeremy J
Published: January 2018

A major limitation with traditional phage preparations is the variability in titer, salts, and bacterial contaminants between successive propagations. Here we introduce the Phage On Tap (PoT) protocol for the quick and efficient preparation of homogenous bacteriophage (phage) stocks. This method produces homogenous, laboratory-scale, high titer (up to 1010-11 PFU∙ml-1), endotoxin reduced phage banks that can be used to eliminate the variability between phage propagations and improve the molecular characterizations of phage. The method consists of five major parts, including phage propagation, phage clean up by 0.22 µm filtering and chloroform treatment, phage concentration by ultrafiltration, endotoxin removal, and the preparation and storage of phage banks for continuous laboratory use. From a starting liquid lysate of >100 mL, the PoT protocol generated a clean, homogenous, laboratory phage bank with a phage recovery efficiency of 85% within just two days. In contrast, the traditional method took upwards of five days to produce a high titer, but lower volume phage stock with a recovery efficiency of only 4%. Phage banks can be further purified for the removal of bacterial endotoxins, reducing endotoxin concentrations by over 3,000-fold while maintaining phage titer. The PoT protocol focused on T-like phages, but is broadly applicable to a variety of phages that can be propagated to sufficient titer, producing homogenous, high titer phage banks that are applicable for molecular and cellular assays.
Moose refugia from predation by wolves near mines in the Athabasca oil sands
Authors: Neilson Eric , Boutin Stan
Published: January 2018

Areas near human disturbance may become prey refugia when predators avoid human activities more than their prey leading to decreased predation rates and/or increased prey population growth. Alberta’s Athabasca oil sands region (AOSR) is home to moose (Alces alces) and wolf (Canis lupus) populations and is characterized by extensive human disturbance including open pit mines, tailings ponds and industrial facilities. We examined the extent to which moose could be released from predation near Alberta’s Athabasca oil sands due to wolf avoidance of mining infrastructure. Using moose and wolves GPS telemetry, we compared the use of natural habitats and distance to mining features to the availability of these variables. We split mining features into high human-use facilities and low human-use pit mines and tailings ponds. We binned distance to mining features variables into distance buffers covering the range of moose home range diameters resulting in buffers of < 2.5 km, 2.5-5 km and 5-10 km. Moose models included an interaction between distance to mining features buffers and the distribution of wolves to assess whether moose exposure to wolves varies with proximity to human activity. We compared a habitat model including forest cover type, streams and rivers to a disturbance model using AIC. The model fitting habitat and distance to facilities was top-ranked for both species. Moose selection for areas near facilities was higher than wolves. Wolves avoided areas within 10 and 5 km of facilities but exhibited an equivocal response within 2.5 km. Moose exposure to wolves increased with distance to mines indicating that use of areas in proximity to human disturbance releases moose from predation by wolves. Human induced prey refugia could increase moose population growth and increase human-moose conflict. Additionally, moose dispersal out of the refuge areas could produce subsequent increases in the wolf population.
A mathematical theory of knowledge, science, bias and pseudoscience
Authors: Fanelli Daniele
Published: January 2018

This essay unifies key epistemological concepts in a consistent mathematical framework built on two postulates: 1-information is finite; 2-knowledge is information compression. Knowledge is expressed by a function \( K(Y;X) \) and two fundamental operations, \( \oplus, \otimes \). This \( K \) function possesses fundamental properties that are intuitively ascribed to knowledge: it embodies Occam's razor, has one optimal level of accuracy, and declines with distance in time. Empirical knowledge differs from logico-deductive knowledge solely in having measurement error and therefore a "chaos horizon". The \( K \) function characterizes knowledge as a cumulation and manipulation of patterns. It allows to quantify the amount of knowledge gained by experience and to derive conditions that favour the increase of knowledge complexity. Scientific knowledge operates exactly as ordinary knowledge, but its patterns are conditioned on a "methodology" component. Analysis of scientific progress suggests that classic Popperian falsificationism only occurs under special conditions that are rarely realised in practice, and that reproducibility failures are virtually inevitable. Scientific "softness" is simply an encoding of weaker patterns, which are simultaneously cause and consequence of higher complexity of subject matter and methodology. Bias consists in information that is concealed in ante-hoc or post-hoc methodological choices. Disciplines typically classified as pseudosciences are sciences expressing extreme bias and therefore yield \( K(Y;X) \leq 0 \). All knowledge-producing activities can be ranked in terms of a parameter \(\Xi \in (-\infty,\infty) \), measured in bits, which subsumes all quantities defined in the essay.
Managing elk in a world with complex predator-prey (and social!) dynamics: A case study from the Kootenays
Authors: Szkorupa Tara , Kuzyk Gerald
Published: January 2018

I will present current challenges to managing elk in a multi-predator/multi-prey system in the Kootenay Region of southeast BC. Elk in this region are highly valued by licensed hunters, First Nations and the general public and are one of the most controversial and closely monitored wildlife populations in the province. In 2010, BC Fish and Wildlife developed an elk management plan for the Kootenay Region following extensive stakeholder involvement. At that time there was relatively little regard for predation since elk populations were increasing and thought to be at or near carrying capacity in many areas. Concerns centered around the effects of large elk populations on grassland ecosystems, other wildlife species (such as bighorn sheep) and agricultural operations. Objectives for elk population targets were established by considering social and ecological criteria, and focused on reducing or maintaining populations using hunting as the primary management tool. Elk management from 2010 to 2014 followed guidance from the plan and objectives were largely achieved. Since 2014, managing elk populations has been largely reactive to the effects of predation. Information on predation is gathered from elk population and composition surveys, radio-collared elk, and anecdotal observations (e.g., from First Nations, the general public, biologists, and Conservation Officers). This information is then applied to management, in consideration of social perspectives identified through public surveys and focus group meetings. For example, wildlife staff consider predation effects on population size and trend when setting cow/calf elk seasons and number of Limited Entry Hunt authorizations. In the fall of 2015, wildlife staff began developing a provincial management plan for Rocky Mountain elk. A key part of this plan will be a management tool table, which will identify potential tools (e.g., predator management to increase elk populations), their likely biological effectiveness, as well as relevant policy, social, and economic considerations. I will provide an overview of these tools, focusing on those related to predator-prey dynamics.