bluuebunny/crossref_metadata_2025 huggingface dataset:
Organic carbon inventories in natural and restored Ecuadorian mangrove forests
Authors: DelVecchia Amanda G , Bruno John F , Benninger Larry K , Alperin Marc , Banerjee Ovik , de Dios Morales Juan
Published: January 2018

Because mangroves can capture and store organic carbon, their protection and restoration is an obvious component of climate change mitigation. However, there are few empirical measurements of long-term carbon storage in mangroves or of how storage varies across environmental gradients. The context dependency of this process combined with geographically limited field sampling has made it difficult to generalize regional and global rates of mangrove carbon sequestration. This has in turn hampered the inclusion of sequestration by mangroves in carbon cycle models and in carbon offset markets. The purpose of this study was to estimate the relative carbon capture and storage potential in natural and restored mangrove forests. We measured depth profiles of soil organic carbon content in 72 cores collected from six sites (three natural, two restored, and one afforested) surrounding Muisne, Ecuador. Samples up to 1 m deep were analyzed for organic matter content using loss-on-ignition and values were converted to organic carbon content using an accepted ratio of 1.72 (g/g). Results suggest that average soil carbon storage is 0.055 ± 0.002 g∙cm-3 (11.3 ± 0.8% carbon content by dry mass, mean ± 1 SE) up to 1 m deep in natural sites, and 0.058 ± 0.002 g∙cm-3 (8.0 ± 0.3%) in restored sites. These estimates are concordant with published global averages. Evidence of equivalent carbon stocks in restored and afforested mangrove patches emphasizes the carbon sink potential for reestablished mangrove systems. We found no relationship between sediment carbon storage and aboveground biomass, forest structure, or within-patch location. Our results demonstrate the long-term carbon storage potential of natural mangroves, high effectiveness of mangrove restoration and afforestation, a lack of predictability in carbon storage strictly based on aboveground parameters, and the need to establish standardized protocol for quantifying mangrove sediment carbon stocks.
Earthworm assemblages in different intensity of agricultural uses and their relation to edaphic variables
Authors: Falco Liliana B , Sandler Rosana V , Momo Fernando R , Di Ciocco César A , Saravia Leonardo A , Coviella Carlos E
Published: January 2018

The objective of this study was to relate earthworm assemblage structure with three different soil use intensities, and to indentify the physical, chemical, and microbiological variables that are associated to the observed differences in earthworm assemblage structure between soils. Three soil uses were evaluated: 1- Fifty year old naturalized grasslands; 2- Cattle-grazing fields converted to feedlot within the two years before the start of this work, and 3- Fifty year old intensive agricultural fields. Three different sites for each soil use were evaluated from winter 2008 through summer 2011. Nine earthworm species were identified across all sampling sites. The sites shared five species: the native Microscolex dubius, and the introduced Aporrectodea caliginosa, A. rosea, Octalasion cyaneum, and O. lacteum, but they differed in their relative abundances according to the system. The results show that earthworm community structure is linked to and modulated by soil properties. Both, species abundance and diversity showed significant differences depending on soil use intensity. A PCA analysis showed that species composition is closely related to the environmental variability. The ratio of native to exotic species was significantly lower in the intensive agricultural system when compared to the other two, lower disturbance Systems. Microscolex dubius was shown to be related to the naturalized grasslands and it was associated to Ca, pH, Mechanical Resistance, and to respiration. Aporrectodea caliginosa was related to high K levels, low enzymatic activity, slightly low pH, and low Ca, and appeared related to the highly disturbed environment. Eukerria stagnalis and Aporrectodea rosea, commonly found un the cattle-grazing system, were related to high soil humidity, low pH, low Ca and low enzymatic activity. These results show that earthworm assamblages can be good descriptors of different soil use intensities. In particular, Microscolex dubius, Aporrectodea caliginosa, and Aporrectodea rosea, showed different temporal patterns and species associations, due to the changes in soil properties attributable tos oil use intensity.
Natal host plants can alter herbivore competition
Authors: Pan Huipeng , Preisser Evan , Su Qi , Jiao Xiaoguo , Xie Wen , Wang Shaoli , Wu Qingjun , Zhang Youjun
Published: January 2018

Interspecific competition between herbivores is widely recognized as an important determinant of community structure. Although researchers have identified a number of factors capable of altering competitive interactions, few studies have addressed the influence of neighboring plant species. If adaptation to/ epigenetic effects of an herbivore’s natal host plant alter its performance on other host plants, then interspecific herbivore interactions may play out differently in heterogeneous and homogenous plant communities. We tested the impact of natal host plants on interactions between the Middle-east Asia Minor 1 (MEAM1) and Mediterranean (MED) cryptic species of the whitefly Bemisia tabaci by rearing the offspring of a cabbage-derived MEAM1 population and a poinsettia-derived MED population together on three different host plants: cotton, poinsettia, and cabbage. We found that MED excluded MEAM1 on poinsettia and that MEAM1 excluded MED on cabbage, results consistent with previous research. MED also excluded MEAM1 when reared together on cotton, however, a result at odds with multiple otherwise-similar studies that reared both species on the same natal plant. Our work provides evidence that natal plants affect competitive interactions on another plant species, and highlights the potential importance of neighboring plant species on herbivore community composition.
Extreme leg action and hip-joint dynamics in wild primates
Authors: Madden Derek S , Madden Erinn H. , Madden Sierra L.
Published: January 2018

We measure how leg actions of cadaver monkeys are transferred within the hip-joint, and we compare physical femoral mobility of wild and captive monkeys in Panama, Costa Rica, and in zoological parks of California. We acquire leg movement data of howler, capuchin and spider monkeys with random 1 second digital photography during 4 months in Central America, and weekly visits for 2 months in California zoos (n=47 wild primates, 1879 focal events; 24 captive primates, 959 focal events). We employ computer software to objectively assess leg angle in regards to flexion, neutral and extension postures of the femur, relative to the hip socket. We apply leg action data to cadaver pelvises in primate bone collections at University of California, Davis, University of Oregon Osteology Lab, and the Denver Museum. Our study reveals that extreme femoral action translates as high diversity of articular contacts within the primate hip joint, and that captive monkeys in artificial habitats have less femoral movements than wild monkeys, with statistical comparisons being: Full leg flexion P = 0.0012; Flexion P = 0.023; Ambulatory as in walking P = 0.075; Extension P = 0.002; and Full extension with leg in line with body P = 0.00011. We speculate that the primate body is built to move in extreme but non-traumatic, wide-ranging appendicular actions. Such movements may help to simulate peripheral articular cartilage, contributing to the longevity of joints, and perhaps extending the life of primates who move in this manner.
Synthetic neuronal datasets for benchmarking directed connectivity metrics
Authors: Rodrigues João , Andrade Alexandre
Published: January 2018

Background: Datasets consisting of synthetic neural data generated with quantifiable and controlled parameters are a valuable asset in the process of testing and validating directed connectivity metrics. Considering the recent debate in the neuroimaging community concerning the use of directed functional connectivity metrics for fMRI data, synthetic datasets that emulate BOLD dynamics have played a central role by supporting claims that argue in favor, or against, certain metrics. Generative models often used in studies that simulate neuronal activity, with the aim of gaining insight into specific brain regions and functions, have different requirements from the generative models for benchmarking datasets. Even though the latter must be realistic, there is a tradeoff between realism and computational demand that needs to be contemplated and simulations that efficiently mimic the real behavior of single neurons or neuronal populations are preferred, instead of more cumbersome and marginally precise ones. Methods: this work explores how simple generative models are able to produce neuronal datasets, for benchmarking purposes, that reflect the simulated effective connectivity and, how these can be used to obtain synthetic recordings of EEG and fMRI BOLD. The generative models covered here are AR processes, neural mass models consisting of linear and non-linear stochastic differential equations and populations with thousands of spiking units. Forward models for EEG consist in the simple three-shell head model while fMRI BOLD is modeled with the Balloon-Windkessel model or by convolution with a hemodynamic response function. Results: the simulated datasets are tested for causality with the original spectral formulation for Granger causality. Modeled effective connectivity can be detected in the generated data for varying connection strengths and interaction delays. Discussion: all generative models produce synthetic neuronal data with detectable causal effects although the relation between modeled and detected causality varies and less biophysically realistic models offer more control in causal relations such as modeled strength and frequency location.
Long live the wasp: adult longevity in captive colonies of the eusocial paper wasp Polistes canadensis (L.)
Authors: Southon Robin J , Bell Emily F , Graystock Peter , Sumner Seirian
Published: January 2018

Insects have been used as an exemplary model in studying longevity, from extrinsic mortality pressures to intrinsic senescence. In the highly eusocial insects great degrees of variation in lifespan exist between morphological castes in relation to extreme divisions of labour, but of particular interest is the primitively eusocial orders. These species represent the ancestral beginnings of eusociality, in which castes are flexible and based on behaviour rather than morphology. Here we present data on the longevity of the primitively eusocial Neotropical paper wasp Polistes canadensis, in a captive setting removed of all environmental hazards. In comparison to other eusocial wasps’ P. canadensis had an average lifespan of 193±10.5 days, with one individual living longer than 450 days. Although this is shorter than most highly eusocial bee and ant queens. Natal colony variation does exist between P. canadensis colonies, possibly due to nutritional and genetic factors. This study provides a foundation for future investigations on the effects of intrinsic and extrinsic factors on longevity in primitively eusocial insects, as well as the relationship with caste and genome.
Organization and distribution of glomeruli in the bowhead whale olfactory bulb
Authors: Kishida Takushi , Thewissen J. G. M. , Usip Sharon , George John C , Suydam Robert S
Published: January 2018

Although modern baleen whales still possess a functional olfactory systems that includes olfactory bulbs, cranial nerve I and olfactory receptor genes, their olfactory capabilities have been reduced profoundly. This is probably in response to their fully aquatic lifestyle. The glomeruli that occur in the olfactory bulb can be divided into two non-overlapping domains, a dorsal domain and a ventral domain. Recent molecular studies revealed that all modern whales have lost olfactory receptor genes and marker genes that are specific to the dorsal domain, and that a modern baleen whale possess only 60 olfactory receptor genes. Here we show that olfactory bulb of bowhead whales (Balaena mysticetus, Mysticeti) lacks glomeruli on the dorsal side, consistent with the molecular data. In addition, we estimate that there are more than 4,000 glomeruli in the bowhead whale olfactory bulb. Olfactory sensory neurons that express the same olfactory receptor in mice generally project to two specific glomeruli in an olfactory bulb, meaning that ratio of the number of olfactory receptors : the number of glomeruli is approximately 1:2. However, we show here that this ratio is not applicable to whales, indicating the limitation of mice as model organisms for understanding the initial coding of odor information among mammals.
Quantifying the impact of environmental factors on the spatiotemporal structure of insect communities in a semi-arid Sabkha ecosystem
Authors: Chenchouni Haroun , Menasria Taha , Neffar Souad , Chafaa Smail , Bradai Liès , Chaibi Rachid , Mekahlia Mohamed Nacer , Bendjoudi Djamel , Si Bachir Abdelkrim
Published: January 2018

The current study highlights some knowledge on the diversity and structure of insect communities and trophic groups living in Sabkha Djendli (semi-arid area of Northeastern Algeria). The entomofauna was monthly sampled from March to November 2006 using pitfall traps at eight sites located at the vicinity of the Sabkha. Structural and diversity parameters (species richness, Shannon index, evenness) were measured for both insect orders and trophic guilds. The canonical correspondence analysis (CCA) was applied to determine how vegetation parameters (species richness and cover) influence spatial and seasonal fluctuations of insect assemblages. The catches totalled 434 insect individuals classified into 75 species, 62 genera, 31 families and 7 orders, where Coleoptera and Hymenoptera were the most abundant and constant over seasons and study stations. Spring and autumn presented the highest values of diversity parameters. Individual-based Chao-1 species richness estimator indicated 126 species for the total individuals captured in the Sabkha. Based on catch abundances, the structure of functional trophic groups was predators (37.3%), saprophages (26.7%), phytophages (20.5%), polyphages (10.8%), coprophages (4.6%); whereas in terms of numbers of species, they can be classified as phytophages (40%), predators (25.3%), polyphages (13.3%), saprophages (12%), coprophages (9.3%). The CCA demonstrated that phytophages and saprophages as well as Coleoptera and Orthoptera were positively correlated with the two parameters of vegetation, especially in spring and summer. While the abundance of coprophages was positively correlated with species richness of plants, polyphage density was positively associated with vegetation cover. The insect community showed high taxonomic and functional diversity that is closely related to diversity and vegetation cover in different site stations and seasons.
Patient exposure in the basic science classroom enhances differential diagnosis formation and clinical decision-making
Authors: Peacock Justin G. , Grande Joseph P.
Published: January 2018

Purpose: The authors proposed that introducing real patients into a pathology classroom early in medical education would help integrate fundamental principles and disease pathology with clinical presentation and medical history. Methods: Three patients with different pathologies described their history and presentation without revealing their diagnosis. Students were required to submit a differential diagnosis in writing, and then they were able to ask questions to arrive at the correct diagnosis. Students were surveyed on the efficacy of patient-based learning. Results: Average student scores on the differential diagnosis assignments significantly improved 32% during the course. From the survey, 72% of students felt that patient encounters should be included in the pathology course next year. 74% felt that the differential diagnosis assignments helped them develop clinical decision-making skills. 73% felt that the experience helped them know what questions to ask patients. 86% felt that they obtained a better understanding of patients’ social and emotional challenges. Discussion: Having students work through the process of differential diagnosis formulation when encountering a real patient and their clinical presentation improved clinical decision-making skills and integrated fundamental concepts with disease pathology during a basic science pathology course. o
Powerline noise elimination in neural signals via blind source separation and wavelet analysis
Authors: Akwei-Sekyere Samuel
Published: January 2018

The distortion of neural signals by powerline noise from recording biomedical devices has the potential to reduce the quality and convolute the interpretations of neural data. State of the art electrophysiology employs band-stop filters with which powerline noise are attenuated to low-amplitudes. Due to the instability of neural signals, the distribution of signals filtered out may not be centered at \(50/60Hz\). As a result, self-correction methods are needed to optimize the performance of these filters. Since powerline noise is additive in nature, it is intuitive to model powerline noise in a raw electrophysiological recording and subtract it from the raw data in order to obtain neural data. This paper proposes a method that utilizes this approach by decomposing the recorded signal and extracting powerline noise via blind source separation and wavelet analysis. The performance of this algorithm was compared with that of a band-stop finite impulse response filter. The proposed method was able to expel sinusoidal signals within powerline noise frequency range with higher fidelity in comparison with the mentioned band-stop finite impulse response filter, especially at low signal-to-noise ratio.
On the complementation of Saccharomyces cerevisiae MET16 in Schizosaccharomyces pombe
Authors: Kelly Thomas B
Published: January 2018

Metabolically active pathways tend to be more highly conserved between ecologically similar relatives than other pathways for their critical role in life-functions. The developmental features of Schizosaccharomyces pombe and Saccharomyces cerevisiae may have become quite divergent, but their ecological niche is still quite similar. The functional homology between S. cerevisiae’s MET16p and S. pombe’s was investigated through plasmid insertion and sulfate assimilation assays in S. pombe. Although the S. cerevisiae:MET16p was produced, the S. pombe colonies were unable to utilize extracellular sulfate in the synthesis of Methionine.
Does evolution of plumage patterns and of migratory behaviour in Apodini swifts (Aves: Apodiformes) follow distributional range shifts?
Authors: Tietze Dieter Thomas , Wink Michael , Päckert Martin
Published: January 2018

The Apodini swifts in the Old World serve as an example for a recent radiation on an intercontinental scale on the one hand. On the other hand they provide a model for the interplay of trait and distributional range evolution with speciation, extinction and trait transition rates on a low taxonomic level (23 extant taxa). Swifts are well adapted to a life mostly in the air and to long-distance movements. Their overall colouration is dull, but lighter feather patches of chin and rump stand out as visual signals. Only few Apodini taxa breed outside the tropics; they are the only species in the study group that migrate long distances to wintering grounds in the tropics and subtropics. We reconstructed a dated molecular phylogeny including all species, numerous outgroups and fossil constraints. Several methods were used for historical biogeography and two models for the study of trait evolution. We finally correlated trait expression with geographic status. The differentiation of the Apodini took place in less than 9 Ma. Their ancestral range most likely comprised large parts of the Old-World tropics, although the majority of extant taxa breed in the Afrotropic and the closest relatives occur in the Indomalayan. The expression of all three investigated traits increased speciation rates and the traits were more likely lost than gained. Chin patches are found in almost all species, so that no association with phylogeny or range could be found. Rump patches showed a phylogenetic signal and were correlated with Indomalayan distribution. Apodini swifts performed long-distance migration whenever they expanded their range to temperate latitudes during warm periods, repeatedly in the Pleistocene.
New methods for computational drug design
Authors: Kromann Jimmy Charnley
Published: January 2018

This thesis describes the work that has been carried out in connection with my Masters at the University of Copenhagen. This work has led to new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. This work also included the implementation of the new HF-3c method in GAMESS and its interface with the fragmentation method FMO. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. HF-3c also shows interaction energies within the same order of accuracy as the PM6 based methods. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. PM6-D3H+ and FMO2-HF- 3c in GAMESS was used to optimize two small proteins which resulted in a much more reliable structure compared to the reference structures, than PM6-DH+ in MOPAC, most likely due to the different optimization algorithms associated with the programs. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.
A ten-year demographic history of a population of howler monkeys (Alouatta palliata) living in a fragmented landscape in Mexico
Authors: Cristóbal Azkarate Jurgi , Dunn Jacob Charles , Domingo Balcells Cristina , Veà Baró Joaquim
Published: January 2018

Long-term field studies of primates are critical for our understanding of life history and the processes driving changes in demography. Here, we present the first long-term demographic data for the northernmost population of the mantled howler monkey (Alouatta palliata). We followed 10 groups of howler monkeys living in a highly fragmented landscape between 2000 and 2011. Forest fragmentation did not seem to play a major role in the dynamics of our population, as the population size remained relatively stable over the 10-year study period, and birth rates and inter-birth intervals were comparable to those of howler monkeys at other sites. Moreover, dispersal events were commonplace, particularly secondary dispersal (individuals emigrating from groups that they had previously immigrated into), which supports the suggestion that this may be an important component of the reproductive strategy of the mantled howler monkey. Finally, we found a marked effect of seasonality on the population dynamics of our study population. In particular, the period of lowest temperatures and resource scarcity between November and March was associated with higher mortality and reproductive inhibition, while the period of resource abundance between April and May was associated with the majority of conceptions and weaning of offspring. This, in turn, could be influencing dispersal patterns in our study area, as male howler monkeys seem to time some of their immigrations into new groups to coincide with the start of the period of higher fertility, while females preferentially joined new groups several months before the onset of this period.
Pooling morphometric estimates: a statistical equivalence approach
Authors: Pardoe Heath R , Cutter Gary , Alter Rachel A , Kucharsky Hiess Rebecca , Semmelroch Mira , Parker Donna , Farquharson Shawna , Jackson Graeme , Kuzniecky Ruben
Published: January 2018

Changes in hardware or image processing settings are a common issue for large multi-center studies. In order to pool MRI data acquired under these changed conditions, it is necessary to demonstrate that the changes do not affect MRI-based measurements. In these circumstances classical inference testing is inappropriate because it is designed to detect differences, not prove similarity. We used a method known as statistical equivalence testing to address this limitation.

Equivalence testing was carried out on three datasets: (i) cortical thickness and automated hippocampal volume estimates obtained from healthy individuals imaged using different multi-channel head coils; (ii) manual hippocampal volumetry obtained using two readers; and (iii) corpus callosum area estimates obtained using an automated method with manual cleanup carried out by two readers. Equivalence testing was carried out using the “two one-sided tests” (TOST) approach. Power analyses of the two one-sided tests were used to estimate sample sizes required for well-powered equivalence testing analyses. Mean and standard deviation estimates from the automated hippocampal volume dataset were used to carry out an example power analysis.

Cortical thickness values were found to be equivalent over 61% of the cortex when different head coils were used (q < 0.05, FDR correction). Automated hippocampal volume estimates obtained using the same two coils were statistically equivalent (TOST p = 4.28 × 10-15). Manual hippocampal volume estimates obtained using two readers were not statistically equivalent (TOST p = 0.97). The use of different readers to carry out limited correction of automated corpus callosum segmentations yielded equivalent area estimates (TOST p = 1.28 × 10-14). Power analysis of simulated and automated hippocampal volume data demonstrated that the equivalence margin affects the number of subjects required for well-powered equivalence tests.

We have presented a statistical method for determining if morphometric measures obtained under variable conditions can be pooled. The equivalence testing technique is applicable for analyses in which experimental conditions vary over the course of the study.
The influence of belief conflict on stress and burnout syndrome in healthcare workers: using structural equation modeling in a cross-sectional study
Authors: Kyougoku Makoto , Teraoka Mutsumi
Published: January 2018

Purpose: Belief conflict has been hypothesized to contribute to increased stress and burnout syndrome among healthcare workers. However, tests on this hypothesis have been limited. The aim of this study was to evaluate the effect of belief conflict on stress and burnout syndrome in healthcare workers using structural equation modeling (SEM). Method: A sample of 488 participants (4.3% physicians, 32.4% nurses, 16.2% occupational therapists, 10.7% physical therapists, 36.4% other) responded to a questionnaire based on the Assessment of Belief Conflict in Relationship-14 (ABCR-14), Stress Response Scale-18 (SRS-18), and Japanese Burnout Scale (JBS). These data were examined using descriptive statistics and a causal sequence model. Results : The hypothesized model exhibited an excellent model fit (RMSEA = 0.041, CFI = 0.937, TLI = 0.933). The results suggested that belief conflict has positive causal effects on stress and burnout syndrome: standardized total effect = 0.676 (S.E. = 0.041, Est . /S.E. = 16.334, p-value = 0.000, 95% CI = 0.411; 0.646), standardized total indirect effect = 0.221 (S.E. = 0.031, Est . /S.E. = 7.066, p-value = 0.000, 95% CI = 0.115; 0.231), standardized direct effect = 0.455 (S.E. = 0.048, Est . /S.E. = 9.497, p-value = 0.000, 95% CI = 0.257; 0.455). Conclusion: This study indicated that healthcare workers suffer stress and burnout related to belief conflict. Therefore, assessment of belief conflict in healthcare workers, followed by appropriate intervention where indicated, would be beneficial in preventing stress and burnout.
A new screw and technique for the treatment of ruptured multiaxial joint ligaments: a preliminary study on the scapholunate dissociation of the wrist
Authors: Nikolopoulos Fotios , Poulilios Apostolos , Vidalis George , Kefalas Vassilios
Published: January 2018

A wide range of techniques on ligament reconstruction have been proposed, summarized in three main categories: The direct suturing or indirect reconstruction of the ligament using adjuvant devices, the “biological ligament ” substitution with the use of autografts or allograft and the “artificial ligament substitution”, with polyester fibers. We propose a new orthopedic screw, the Flexy Screw (FS) and the FS technique for repairing unstable joints due to ligament damage. The tools used for the FS insertion and removal, is all included in the overall flexyscrew system (FSS).In this work we have particularly developed the FS technique for the scapholunate ligament rupture (SLR). The value 18.03N/mm (SD9.6) for the linear elastic mean stiffness for the SLIL, and 14.4N/mm for the FS, furthermore the FS max load 138N at 10mm, in comparison with the average elastic limit of 47N at 3mm for the SLIL are considered satisfactory. Furthermore, the FS technique is aiming to be applied in a wide spectrum of unstable joints needing “ligament substitution”, because, as a mechanical orthopedic device can be adapted in order to simulate more closely the physiological mechanical properties of the ligaments.
Cell death via remote heating of microparticles with potential applications in atherosclerosis and thrombosis therapy
Authors: Gaitas Angelo , Kim Gwangseong
Published: January 2018

We report a method to cause cell death by remotely heating microparticles by induction heating, this technique could be used to remove vascular deposits and thrombosis. In this preliminary work, we used micrometer size spherical (ferromagnetic) particles and (pure) iron particles to heat remotely macrophages using inductive heating. Iron particles achieved maximum temperatures of 51 ± 0.5 oC after 30 minutes of inductive heating, while spherical particles achieved a maximum temperature of 43.9 ± 0.2 oC (N=6). The therapeutic outcome was determined by monitoring cell re-growth for 2 days following inductive heating treatment. The initial density of cells in the first day prior to induction heating was 105,000 ± 20,820 cells/ml (N=3). 24 hours after induction heating this number was reduced to 6,666 ± 4,410 cells/ml for the spherical particles and 16,666 ± 9,280 cells/ml for the iron particles. The second day the cells grew to 26,667 ± 6,670 cells/ml and 30,000 ± 15,280 cells/ml respectively. Compared to cell cultures with iron and spherical particles that were not subjected to induction heating, we observed a 97% reduction in cell count for the spherical particles and a 91% reduction for the iron particles after the first 24 hours. After 48 hours we observed a 95% reduction in cell growth for both spherical and iron particles. Induction heating of microparticles was highly effective in reducing the macrophage population and preventing their growth.
Geographic Feature Type Topic Model (GFTTM): grounding topics in the landscape
Authors: Adams Benjamin
Published: January 2018

Probabilistic topic models are a class of unsupervised machine learning models used for understanding the latent topics in a corpus of documents. A new method for combining geographic feature data with text from geo-referenced documents to create topic models that are grounded in the physical environment is proposed. The Geographic Feature Type Topic Model (GFTTM) models each document in a corpus as a mixture of feature type topics and abstract topics. Feature type topics are conditioned on additional observation data of the relative densities of geographic feature types co-located with the document's location referent, whereas abstract topics are trained independently of that information. The GFTTM is evaluated using geo-referenced Wikipedia articles and feature type data from volunteered geographic information sources. A technique for the measurement of semantic similarity of feature types and places based on the mixtures of topics associated with the types is also presented. The results of the evaluation demonstrate that GFTTM finds two distinct types of topics that can be used to disentangle how places are described in terms of its physical features and more abstract topics such as history and culture.
A rapid assessment of post-disclosure experiences of urban HIV-positive and HIV-negative school-aged children in Kenya
Authors: Gachanja Grace
Published: January 2018

There has been limited involvement of HIV-negative children in HIV disclosure studies; most studies conducted on the effects of disclosure on children have been with HIVpositive children and HIV-positive mother-child dyads. Seven HIV-positive and five HIVnegative children participated in a larger study conducted to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. In this study, the experiences of these 12 children after receiving disclosure of their own and their parents’ illnesses respectively are presented. Each child underwent an indepth qualitative semi-structured digitally recorded interview. The recorded interviews were transcribed and loaded into NVivo8 for phenomenological data analysis. Five themes emerged from the data, indicating that HIV-positive and negative children appear to have differing post-disclosure experiences revolving around acceptance of illness, stigma and discrimination, medication consumption, sexual awareness, and use of coping mechanisms. Following disclosure, HIV-negative children accepted their parents’ illnesses within a few hours to a few weeks; HIV-positive children took weeks to months to accept their own illnesses. HIV-negative children knew of high levels of stigma and discrimination within the community; HIV-positive children reported experiencing indirect incidences of stigma and discrimination. HIV-negative children wanted their parents to take their medications, stay healthy, and pay their school fees so they could have a better life in the future; HIV-positive children viewed medication consumption as an ordeal necessary to keep them healthy. HIV-negative children wanted their parents to speak to them about sexual-related matters; HIV-positive children had lingering questions about relationships, use of condoms, marriage, and childbearing options. All but one preadolescent HIV-positive child had self-identified a person to speak with for social support. When feeling overwhelmed by their circumstances, most children self-withdrew and performed positive activities (e.g., praying, watching TV, listening to the radio, singing, dancing) to help themselves feel better. Many HIV-affected families have a combination of HIV-positive and negative siblings within the household. Pending further studies conducted with larger sample sizes, the results of this study should assist healthcare professionals to better facilitate disclosure between HIV-positive parents and their children of mixed HIV statuses.
Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana
Authors: Winterbach Hanlie EK , Winterbach Christiaan W , Boast Lorraine , Klein Rebecca , Somers Michael MJ
Published: January 2018

Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus) suitable conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs’ preferred prey and small livestock biomass can be used to explore the current potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana’s agricultural areas which provide additional large areas with high conservation potential. Twenty percent wild prey biomass proved to be possibly the critical point to distinguish between high and low predicted levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana’s still large and contiguous cheetah population.
Development of an agent based model illustrating the usage of deferred acceptance algorithm in the admission process
Authors: Bhatia Abhishek , Sharma Chetan , Goyal Rinkaj
Published: January 2018

Agent based modelling framework successfully models real life problems that support simulation with diverse strategies and mechanisms devoid of the restrictions set by mathematical tractability. Union of game theory and agent based modelling has elucidated the dynamics of different social and economic scenarios. In this study, we present our efforts to develop an agent based model through embracing a customized version of the deferred acceptance algorithm. This study considers two widely adopted admission process scenarios i.e. partially and fully centralized as a case study, wherein a University acts as a nodal bureau and admits students to affiliated colleges. In this paper, an agent based model has been developed in the Netlogo simulation environment, which advocates fully centralized procedure and simulates deferred acceptance algorithm. The simulation results in a strategy-proof, optimum and stable allocation of available seats in the admission process.
Impact of copper toxicity on stone-head cabbage (Brassica oleracea var. capitata) in hydroponics
Authors: Ali Sajid , Shahbaz Muhammad , Shahzad Ahmad Naeem , Fatima Ammara , Khan Hafiz Azhar Ali , Anees Moazzam , Haider Muhammad Saleem
Published: January 2018

Arable soils are frequently subjected to contamination with copper as the consequence of imbalanced fertilization with manure and organic fertilizers and/or extensive use of copper-containing fungicides. In the present study, the exposure of Stone-head cabbage (Brassica oleracea Var. capitata) to elevated Cu2+ levels resulted in leaf chlorosis and lesser biomass yield at ≥ 2 µM. Root nitrate content was not statistically affected by Cu2+ levels, although it was substantially decreased at ≥ 5 µM Cu2+ in the shoot. The decrease in nitrate contents can be related to lower nitrate uptake rates because of growth inhibition by Cu-toxicity. Shoot sulfate content increased strongly at ≥ 2 µM Cu2+ indicating an increase in demand for sulfur under Cu stress. Furthermore, at ≥ 2 µM concentration, concentration of water-soluble non-protein thiol increased markedly in the roots and to a smaller level in the shoot. When exposed to elevated concentrations of Cu2+ the improved sulfate and water-soluble non-protein thiols need further studies for the evaluation of their direct relation with the synthesis of metal-chelating compounds (i.e. phytochelatins).
Genotoxic evaluation of Mexican welders occupationally exposed to welding-fumes using the micronucleus test on exfoliated oral mucosa cells: a cross-sectional, case-control study
Authors: Jara-Ettinger Ana C. , López-Tavera Juan C. , Zavala-Cerna Guadalupe , Torres-Bugarín Olivia
Published: January 2018

Background: An estimated of 800,000 people worldwide are occupationally exposed to welding-fumes. Previous studies show that the exposure to such fumes is associated with damage to genetic material and increased cancer risk. In this study, we evaluate the genotoxic effect of welding-fumes using the Micronucleus Test on oral mucosa cells of Mexican welders. Material and Methods: We conducted a cross-sectional, matched case-control study of n = 66 (33 exposed welders, and 33 healthy controls). Buccal mucosa smears were collected and stained with acridine orange, observed under 100x optical amplification with a fluorescence lamp, and a single-blinded observer counted the number of micronuclei and other nuclear abnormalities per 2000 observed cells. We compared the frequencies of micronuclei and other nuclear abnormalities, and fitted generalised linear models to investigate the interactions between nuclear abnormalities and the exposure to welding-fumes, while controlling for smoking and age. Results: Binucleated cells and condensed-chromatin cells showed statistically significant differences between cases and controls. The frequency of micronuclei and the rest of nuclear abnormalities (lobed-nuclei, pyknosis, karyolysis, and karyorrhexis) did not differ significantly between the groups. After adjusting for smoking, the regression results showed that the occurrence of binucleated cells could be predicted by the exposure to welding-fumes plus the presence of tobacco consumption; for the condensed-chromatin cells, our model showed that the exposure to welding-fumes is the only reliable predictor. Conclusions: Our findings suggest that Mexican welders who are occupationally exposed to welding-fumes have increased counts of binucleated and condensed-chromatin cells. Nevertheless, the frequencies of micronuclei and the rest of nuclear abnormalities did not differ between cases and controls. Further studies, should shed more light on this subject.
Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828
Authors: Read Timothy D , Petit III Robert A , Joseph Sandeep J , Alam Md T , Weil Ryan , Ahmad Maida , Bhimani Ravila , Vuong Jocelyn S , Haase Chad P , Webb Harry , Dove Alistair D. M.
Published: January 2018

The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species and is therefore also the largest extant species of the paraphyletic assemblage commonly referred to as “fishes”. As both a phenotypic extreme and a member of the group basal to the remaining gnathostomes, which includes all tetrapods and therefore also humans, its genome is of substantial comparative interest. Whale sharks are also listed as a “vulnerable” species on the International Union for Conservation of Nature (IUCN)'s Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which assembled into 11,347,816 contigs and 3,606,038 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the Holocephali Elephant shark. The whale shark contained a novel Toll-like-receptor protein with sequence conservation to both the TLR4 and TLR13 proteins of mammals. The data are publicly available on a Galaxy bioinformatic server (http://whaleshark.georgiaaquarium.org). This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.
The fragile legacy of Amphicoelias fragillimus (Dinosauria: Sauropoda; Morrison Formation - Latest Jurassic)
Authors: Woodruff Cary , Foster John R
Published: January 2018

In the summer of 1878, American paleontologist Edward Drinker Cope published the discovery of a sauropod dinosaur that he named Amphicoelias fragillimus. What distinguishes A. fragillimus in the annals of paleontology is the immense magnitude of the skeletal material. The single incomplete dorsal vertebra as reported by Cope was a meter and a half in height, which when fully reconstructed, would make A. fragillimus the largest vertebrate ever. After this initial description Cope never mentioned A. fragillimus in any of his scientific works for the remainder of his life. More than four decades after its description, a scientific survey at the American Museum of Natural History dedicated to the sauropods collected by Cope failed to locate the remains or whereabouts of A. fragillimus. For nearly a century the remains have yet to resurface. The enormous size of the specimen has generally been accepted despite being well beyond the size of even the largest sauropods known from verifiable fossil material (e.g. Argentinosaurus). By deciphering the ontogenetic change of Diplodocoidea vertebrae, the science of gigantism, and Cope’s own mannerisms, we conclude that the reported size of A. fragillimus is most likely an extreme over-estimation.
Influence of the mother's preceding pregnancy on the gestation length of the current pregnancy. An immunological explanation?
Authors: Vernier Michel C , Schulzer Michael , Vernier Pierre
Published: January 2018

Introduction. A number of epidemiological studies on various diseases have drawn attention to relationships between fetal life events, as measured by health indicators and pathological events later in life. This accounts for the renewed interest in fetal health indicators. The objective of this retrospective study is to investigate the relationship between the sex of conceptuses of the mother’s preceding pregnancies and the gestation length of the current pregnancy. Methods. A population of 7773 neonates were divided into cohorts, according to the sex of the current neonate and number and sex of the mother’s preceding pregnancies. Average gestation lengths for each cohort were measured and compared between different configurations of preceding pregnancies. Results. There a positive association between the length of gestation of the neonate and its mother’s preceding pregnancies of same sex as its own. Gestation length increases with the number of conceptuses of same sex among the preceding pregnancies. Likewise, there is a negative association between the length of gestation of the neonate and its mother’s preceding pregnancies of opposite sex to its own. Gestation length decreases with the number of conceptuses of opposite sex among the preceding pregnancies. Discussion. The results of our study are compatible with the immunological hypothesis, based on the sex-linked concepto-gravidic antigenic dissimilarity, proposed to explain the association between preceding pregnancy and fetal development. The influence of the preceding pregnancy is significant enough to be taken into account for effective management of current pregnancies as well as for efficient clinical trial analysis.