bluuebunny/crossref_metadata_2025 huggingface dataset:
A linear sigmoid colon passage method in colonoscopy
Authors: Awazu Satoshi , Araki Risa , Awazu Toshihiko
Published: January 2018

A previous study revealed loop formation of the colonoscope in the sigmoid colon in 79% of patients. Colonoscope looping in the sigmoid colon is considered to cause abdominal pain and intestinal perforation. We discovered a phenomenon whereby the rectosigmoid junction becomes linear when the patient is moved from a left lateral to left semiprone position and the colonoscope tip can be readily inserted into the sigmoid colon. Therefore, this phenomenon was applied to our conventional insertion method to determine whether the colonoscope looping rate in the sigmoid colon can be reduced. Thus our new insertion method could reduce the colonoscope looping rate in the sigmoid colon. Our new insertion method may allow safer colonoscope insertion than our conventional insertion method.
Prevalence of disordered eating attitudes in young adults
Authors: Vlachakis Dimitrios , Vlachakis Chrisanthy
Published: January 2018

Objective. The objective of this study was to assess the prevalence of disordered eating and the dietary patterns of young adult female students. Method. 226 young female first and second year students were randomly recruited. The EAT-26 questionnaire was used to measure disordered eating, and the State Trait Anxiety Inventory tool (STAI) to assess anxiety levels. Results. The prevalence of disordered eating (DE group) was quite high and matched previous reported percentages for this age population (18%). DE students showed significantly lower energy intake compared to control group (CON) (1471 ± 357 vs. 1690 ± 563, kcals). Conclusion. Young adult female students show increased tendency towards disordered or restricted eating behaviours. Preventive intervention concerning the negative behaviours may be beneficial for all college students more so to those suffering from anxiety.
Diversity of gastropods in Turnbull National Wildlife Refuge, WA and the regional spread of the invasive European ear snail (Radix auricularia)
Authors: Ponce Jake , Torrieri Christina , Larson Michele
Published: January 2018

Establishing base-line knowledge of native snails in an area and their relative abundance is important in understanding the role of snails in their environment and the possible use of snails as a bioindicator. This information can also be used to determine how an invasive species is affecting the native populations over time. Six genera of gastropods were found in the wetland ponds of Turnbull National Wildlife Refuge (TNWR) from April to June 2012, including the invasive European ear snail (Radix auricularia) which was found in four lakes it was not previously known to inhabit. A dominant snail genus was found for each lake, with Middle Pines Lake being dominated by Radix auricularia. Conductivity was the only abiotic factor studied that positively correlated with genera richness (p = 0.035).
Wireless PC-based phonocardiograph and diagnosis
Authors: Dao Amy
Published: January 2018

Auscultation is used to evaluate heart health and can indicate when it's needed to refer a patient to a cardiologist. Advanced PCG signal processing algorithms are developed to assist the physician in the initial diagnosis but they are primarily designed and demonstrated with research quality equipment. Therefore there is a need to demonstrate the applicability of those techniques with consumer grade instrument. Furthermore, routine monitoring would benefit from a wireless PCG sensor that allows continuous monitoring of cardiac signals of patients in physical activity, e.g., treadmill or weight exercise. In this work, a low-cost portable and wireless healthcare monitoring system based on phonocardiograph signal is implemented to validate and evaluate the most advanced algorithms. Off-the-shelf electronics and a notebook PC are used with MATLAB codes to record and analyze PCG signals which are collected with a notebook computer in tethered and wireless mode. High valued diagnostics based on the S1 and S2 signals and MATLAB codes are demonstrated. While the prototype is based on MATLAB, the later is not an absolute requirement.
Artemisinin mimics calorie restriction to initiate antioxidative responses and compromise telomere shortening
Authors: Wang Da-Ting , Wu Ming , Li Si-ming , Gao Qian , Zeng Qing-Ping
Published: January 2018

Calorie restriction (CR) is known to extend lifespan among organisms with the putative mechanism underlying nitric oxide (NO)-enhanced mitochondrial biogenesis. However, whether NO maintains telomere intact that is implicated in life expectancy remains unknown. We report here the artemisinin derivative artesunate in a low concentration up-regulates mitochondrial SIRT3-SOD2 expression among global activation of antioxidative networks via the NO signaling cascade AMPK→Akt→eNOS→SIRT1→PGC-1α. While the NO donor sodium nitroprusside and the NO precursor L-arginine replicate the antioxidative responses, exogenous low-dose hydrogen peroxide also leads to attenuated oxidative stress. The tumor suppressor BRCA1 and other DNA repair partners are down-regulated after scavenging of reactive oxygen species. Upon treatment, telomere shortening is damped without telomerase up-regulation, highlighting telomere maintenance rather than telomere elongation. In conclusion, artesunate can mimic CR to activate antioxidative responses and alleviate telomere attrition via NO signaling, thereby maintaining the stability and integrity of chromosomes, which are the hallmarks of longevity.
Ebola virus disease outbreak in Nigeria: transmission dynamics and rapid control
Authors: Althaus Christian L , Low Nicola , Musa Emmanuel O. , Shuaib Faisal , Gsteiger Sandro
Published: January 2018

International air travel has already spread Ebola virus disease (EVD) to major cities as part of the unprecedented epidemic that started in Guinea in December 2013. An infected airline passenger arrived in Nigeria on July 20, 2014 and caused an outbreak in Lagos and then Port Harcourt. After a total of 20 reported cases, including 8 deaths, Nigeria was declared EVD free on October 20, 2014. We quantified the impact of early control measures in preventing further spread of EVD in Nigeria and calculated the risk that a single undetected case will cause a new outbreak. We fitted an EVD transmission model to data from the outbreak in Nigeria and estimated the individual reproduction number of the index case at 9.0 (95% confidence interval [CI]: 5.2-15.6). We also found that the net reproduction number fell below unity 15 days (95% CI: 11-21 days) after the arrival of the index case. Hence, our study illustrates the time window for successful containment of EVD outbreaks caused by infected air travelers.
Comprehensive, structurally-curated alignment and phylogeny of vertebrate biogenic amine receptors
Authors: Spielman Stephanie , Kumar Keerthana , Wilke Claus O.
Published: January 2018

Biogenic amine receptors play critical roles in regulating behavior and physiology, particularly within the central nervous system, in both vertebrates and invertebrates. These receptors belong to the G-protein coupled receptor (GPCR) family and interact with endogenous bioamine ligands, such as dopamine, serotonin, and epinephrine, and they are targeted by a wide array of pharmaceuticals. Despite these receptors’ clear clinical and biological importance, their evolutionary history remains poorly characterized. In particular, the relationships among biogenic amine receptors and any specific evolutionary constraints acting within distinct receptor subtypes are largely unknown. To advance and facilitate studies in this receptor family, we have constructed a comprehensive, high-quality, structurally-curated sequence alignment of vertebrate biogenic amine receptors. We demonstrate that aligning GPCR sequences without considering structure produces an alignment with substantial error, whereas a structurally-aware approach greatly improves alignment accuracy. Moreover, we show that phylogenetic inference with our structurally-curated alignment offers dramatic improvements over a structurally-naive alignment. Using the structural alignment and its corresponding phylogeny, we deduce novel biogenic amine receptor relationships and uncover previously unrecognized lineage-specific receptor clades. Moreover, we find that roughly 1% of the 3039 sequences in our final alignment are either misannotated or unclassified, and we propose updated classifications for these receptors. We release our comprehensive alignment and its corresponding phylogeny as a resource for future research into the evolution and diversification of biogenic amine receptors.
Subject-specific body segment parameter estimation using 3D photogrammetry with multiple cameras
Authors: Peyer Kathrin E , Morris Mark , Sellers William I
Published: January 2018

Inertial properties of body segments, such as mass, centre of mass or moments of inertia, are important parameters when studying movements of the human body. These quantities are, however, not directly measurable. Current approaches include using regression models which have limited accuracy; geometric models with lengthy measuring procedures; or acquiring and post-processing MRI scans of participants. We propose a geometric methodology based on 3D photogrammetry using multiple cameras to provide subject-specific body segment parameters while minimizing the interaction time with the participants. A low-cost body scanner was built using multiple cameras and 3D point cloud data generated using structure from motion photogrammetric reconstruction algorithms. The point cloud was manually separated into body segments and convex hulling applied to each segment to produce the required geometric outlines. The accuracy of the method can be adjusted by choosing the number of subdivisions of the body segments. The body segment parameters of six participants (four male and two female) are presented using the proposed method. The multi-camera photogrammetric approach is expected to be particularly suited for studies including populations for which regression models are not available in literature and where other geometric techniques or MRI scanning are not applicable due to time or ethical constraints.
Development of new psychometric instruments to measure appearance distress during adolescence: the Adolescent Appearance Distress Scales
Authors: Moss Timothy P , Bailey Chantelle , Griffiths Catrin , Lawson Victoria , Williamson Heidi
Published: January 2018

Measures of adolescent appearance distress have focused on weight and body shape, excluding other aspects of appearance. The absence of a psychometrically sound, general measure of appearance distress has limited evaluation of interventions and curtailed investigation of psychological processes in adolescent appearance adjustment. This paper describes the development of scales assessing adolescent appearance distress to address this dearth of appropriate measures, validated through cross-sectional design involving 617 adolescents. Two scales were developed, comprising 13 items for younger adolescents and 17 items for older adolescents. Two similar factors were generated for each scale, “fear of negative appearance evaluation” and “salience and investment in appearance.” A third factor was identified for older adolescents, “social appearance comparison.” Sound psychometric properties were demonstrated.
HIV-positive parents’ accounts on disclosure preparation activities for a parent’s and/or a child’s illness in Kenya
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

The aim of this research brief is to describe a study that examined how HIV-positive parents prepared themselves and their children for HIV disclosure in Kenya. This is the first study from Sub-Saharan Africa (SSA) that provides comprehensive data on how HIV-positive parents prepare themselves and their HIV-positive and negative children for disclosure of a parent’s and/or a child’s illness. Prior studies in SSA have provided limited details about the activities performed by parents to prepare for disclosure of a parent’s or a child’s illness. Key aspects of preparing for disclosure to children: 1. Most parents take years to prepare for disclosure, proceeding when they judge themselves ready to impart the news and their children receptive to receive the news. 2. Parents’ preparation activities for disclosure proceed through four major phases which include secrecy, exploration, readiness, and finally full disclosure of illness. 3. In the secrecy phase parents do not disclose; in the exploration phase they plan how they will disclose; in the readiness phase they seek activities that will help them to fully disclose; finally when ready they fully disclose to their children based on birth order. 4. Parents who have many children remain simultaneously within the different preparation phases as they move their children from a state where none are disclosed to, to a state when all of them have been fully disclosed to. The original research article is located at: http://scholarworks.waldenu.edu/jsbhs/vol8/iss1/1/
HIV disclosure perspectives from HIV-positive parents, HIV-positive children, and HIV-negative children
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

The aim of this research brief is to describe a study that examined the lived experiences of HIV-positive parents and their biological HIV-positive and negative children before, during, and after the HIV disclosure process in Kenya. This is the first study from Sub-Saharan Africa (SSA) that provides perspectives on HIV disclosure of a parent’s and a child’s illness from the viewpoints of HIV-positive parents, HIV-positive children, and HIV-negative children. Prior studies in SSA have mostly centered on disclosure to HIV-positive children (of their own illnesses) and others have reported on parents disclosing their illnesses to their children. Key Aspects of HIV Disclosure to Children: 1. Disclosure should be performed as a process. 2. It is a parent’s decision on when to disclose but also a child’s right to be told about his/her own, a parent’s, and other family member’s illnesses and deaths. 3. Healthcare professionals should help parents prepare for and disclose family member’s illnesses and prior deaths to their children. 4. Disclosure should preferably be performed when both the parent and child are in good health. 5. Disclosure should be performed when a child shows understanding of the illness and/or maturity. 6. Disclosure planning should include a determination of who is the most suitable person to disclose to a child. 7. Disclosure should be postponed until animportant life event (e.g., taking a national school examination) has occurred. The original research article is located at: https://peerj.com/articles/486.pdf
Free flow of sweat due to loss of surface tension at sweat droplets causes water-induced skin wrinkling
Authors: Marasakatla Soumya , Marasakatla Karunakar
Published: January 2018

Water immersion skin wrinkling has long been used as a test for sympathetic nerve function. However, the cause of underlying mechanism remained elusive. In this article, we theoretically investigate a possible cause of the phenomenon by taking various properties of sweating into consideration. The pressure exerted by the surface tension of sweat droplets counterbalances the secretory pressure of sweat glands at the pore. When a hand is immersed in water, sweat droplets easily merge with the water, causing the pressure to drop at the pore. Our calculations, using earlier measurements of secretory pressure, show that the water pressure at the sweat pore will be less than the secretory pressure of sweat glands when the hand is immersed at a shallow depth. The resulting pressure imbalance enables the sweat to flow freely into the water. We believe that there will be an initial vasodilation to feed the excess generation of sweat. Sweat flow continues as long as there is blood flow to the hand. To prevent excessive loss of sweat from the body and to maintain homeostasis, sympathetic nerves trigger vasoconstriction to reduce the blood flow to the hand. The overlying skin wrinkles due to loss of volume under the skin. It is possible that denerved fingers remain in the vasodilation state during immersion due to a lack of sympathetic nerve function.
Fault bars and stable isotope signatures reveal effects of severe weather stressors on fledgling sparrows
Authors: Ross Jeremy D , Kelly Jeffrey F , Bridge Eli S , Engel Michael H , Reinking Dan L , Boyle W Alice
Published: January 2018

In August 2013, we observed a high incidence (44%) of synchronous fault bars across the rectrices of juvenile Grasshopper Sparrows (Ammodrammus savannarum) captured near El Reno, Oklahoma. Earlier that year, on May 31, the site was struck by a severe storm which rained hailstones exceeding 5.5 cm diameter and spawned an historic 4.2 km-wide tornado <8 km to the south of the site. An assessment of Grasshopper Sparrow nesting phenology indicated that a large number of nestlings were likely growing tail feathers when the storm hit. To assess the nature of the fault bars, we measured δ15N and δ13C stable isotope ratios within four 0.25-0.40 mg feather sections taken from the distal end of a tail feather from 18 juveniles captured at the site in August. The fault bar, if present, was contained within only one section. Fault bars were located at various positions on the distal half of feathers, and fault bar width significantly increased as a function of distance from the tip (i.e., age at formation). After correcting for consistent, natural δ15N variation across sections, we found that feather sections containing or located immediately proximal to fault bars showed significantly higher δ15N than sections from the same feathers located distal to or further from the fault bar region. We also observed significantly higher δ13C but lower δ15N in the feathers of juveniles with fault bars compared to normal appearing juveniles. Our findings support the hypothesis that an abrupt environmental stressor affected Grasshopper Sparrow chicks of various ages, and caused short term catabolism of muscle tissue that resulted in a spike in δ15N deposited into growing feathers. Furthermore, higher δ15N and lower δ13C among juveniles lacking fault bars suggested a seasonal change in diet consistent with these individuals hatching after the May 31 storm. Severe weather events may represent major stressors to ground-nesting birds, and we recommend exploiting opportunities to study the effects of severe weather as part of ongoing research efforts.
Transcriptome analyses of Anguillicola crassus from native and novel hosts
Authors: Heitlinger Emanuel , Taraschewski Horst H. , Weclawski Urszula , Gharbi Karim , Blaxter Mark
Published: January 2018

Anguillicola crassus is a swim bladder nematode of eels. The parasite is native to the Asian eel Anguilla japonica, but was introduced to Europe and the European eel Anguilla anguilla in the early 1980s. A Taiwanese source has been proposed for this introduction. In the new host in the recipient area, the parasite appears to be more pathogenic. As a reason for these differences, genetically fixed differences in infectivity and development between Taiwanese and European A.crassus have been described and disentangled from plasticity induced by different host environments.To explore whether transcriptional regulation is involved in these lifecycle differences, we have analysed a “common garden”, cross infection experiment, using deep-sequencing transcriptomics. Surprisingly, in the face of clear phenotypic differences in life history traits, we identified no significant differences in gene expression between parasite populations or between experimental host species. From 120,000 SNPs identified in the transcriptome data we found that European A. crassus were not a genetic subset of the Taiwanese nematodes sampled. The loci that have the major contribution to the European-Taiwanese population differentiation show an enrichment of synonymous and non-coding polymorphism. This argues against positive selection in population differentiation. However, genes involved in protein processing in the endoplasmatic reticulum membrane and genes bearing secretion signal sequences were enriched in the set of genes most differentiated between European and Taiwanese A. crassus. These genes could be a source for the phenotypically visible genetically fixed differences between European and Taiwanese A. crassus.
Identification of the underlying factor structure of the Derriford Appearance Scale 24
Authors: Moss Timothy P , Lawson Victoria , White Paul , Collaboration Appearance Research
Published: January 2018

Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n=1265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was found to be the best fit to the data. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC subscale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale.
Epidemiological evaluation of rubella virus infection among pregnant women in Ibadan, Nigeria
Authors: Adewumi Olubusuyi M , Olayinka Adebowale O. , Olusola Babatunde A. , Faleye Temitope O.C. , Sule Waidi F. , Adesina Olubukola
Published: January 2018

Rubella is a vaccine-preventable, mild rash-inducing viral disease with complications that include a spectrum of birth defects in the developing foetus, especially if the infection is acquired in the early months of pregnancy. Consequently, the primary objective of global rubella control programmes is prevention of congenital rubella infection and associated birth defects often collectively referred to as CRS. Despite the availability of safe and effective vaccines, and elimination of rubella virus in many developed countries, substantial commitment to rubella control has not been demonstrated in the developing countries. This study appraises immunity to rubella, and consequently makes appropriate recommendations aimed at facilitating effective control. A cross-sectional sero-surveillance study was carried out among 272 consenting ante-natal clinic attendees in southwestern, Nigeria. Prevalence rates of 91.54% and 1.84% were recorded for anti-rubella virus (anti-RV) IgG and IgM respectively. Also, 90.7% and 92.3% of the women aged ≤ 30 years and ˃ 30 years respectively had detectable anti-RV IgG. No significant association (p=0.94) was recorded between anti-RV IgG detection and age of the women. Previous exposure and susceptibility of significant fraction of the population to rubella infection were confirmed. Considerable political commitment and promotion of free rubella immunization specifically for women of childbearing potential were recommended.
Fluctuating asymmetry could be reliable proxy for oxidative stress in vertebrates
Authors: Canovas Miguel , Mentaberre Gregorio GMG , Tvarijonaviciute Asta , Casas-Díaz Encarna , Navarro Nora , Lavín Santiago , Soriguer Ramón , Candela Mónica G , Serrano Ferron Emmanuel
Published: January 2018

The study of fluctuating asymmetry (FA) in living organisms has produced contradictory results over the past few decades. Though the protocol for measuring FA is firmly established, the sources of FA remain unclear in many cases. Our goal is to study the relationship between FA and both the concentration of biomarkers of reactive oxygen species (ROS) and the body condition in a medium-sized mammal, the European wild boar (Sus scrofa). Using a Partial Least Squares regression (PLSr) we found a positive significant relationship between oxidative stress and FA but a negative relationship between oxidative stress and body condition of boar. Our results may suggest that FA can be used to assess the physiological cost associated with oxidative stress in mammals.
Serial sampling provides chronological evidence that endogenous protein is used for primary growth in a molt-migrant goose
Authors: Rohwer Sievert , Fox Anthony D , Daniel Thomas , Kelly Jeffery F
Published: January 2018

This is a proof of concept paper based on chronological samples of growing feathers from geese thought to be molt-migrants. When molt-migrant birds initiate molt shortly after migrating to a new isoscape, isotope values measured along the length of their feathers should change continuously. To assess long-term changes and daily cycling in δ15N and δ13C values, we serially sampled growing primaries of three presumed molt-migrant geese. Two showed changing δ15N signatures along the length of their growing primaries, indicating they were molt-migrants, while the third, presumably a resident, showed no change. We then resampled these feathers at closer intervals for evidence of the predicted diel cycle in the use of exogenous and endogenous protein for feather growth, generated by the diel feeding cycle of these geese. As predicted, the two geese that were equilibrating to a new isoscape showed oscillations of approximately 24-hour periodicity in δ15N values, measured along the length of their primaries. In contrast, the goose that was not equilibrating to a new isoscape showed no 24-hour periodicity in its δ15N values. Our results demonstrate that chronological sampling along the length of individual primaries holds great potential for identifying individuals that are molt-migrants.
The CombineArchiveWeb application – A web based tool to handle files associated with modelling results
Authors: Scharm Martin , Wendland Florian , Peters Martin , Wolfien Markus , Theile Tom , Waltemath Dagmar
Published: January 2018

Sharing in silico experiments is essential for the advance of research in computational biology. Consequently, the COMBINE archive was designed as a digital container format. It eases the management of files related to a modelling result, fosters collaboration, and ultimately enables the exchange of reproducible simulation studies. However, manual handling of COMBINE archives is tedious and error prone. We therefore developed the CombineArchiveWeb application to support scientists in promoting and publishing their research by means of creating, exploring, modifying, and sharing archives. All files are equipped with meta data and can be distributed over the Web through shareable workspaces.
Carbon-driven eco-agriculture without nitrogen deficiency
Authors: Oda Masato , Tamura Kenji , Nakatsuka Hiroko , Nakata Miki , Hayashi Yukimi
Published: January 2018

A farmer grew crops by adding only organic material with a high C:N ratio (40) to the soil for 30 years. He focused on the role of carbon in increasing the number of microorganisms. This idea was based on the concepts of 1) indirect crop management via microorganisms and 2) providing carbon to microorganisms for energy. Here, we name this practice “carbon -driven eco-agriculture” (CDEA). We determined the effect of CDEA on a laterite soil vegetable field in Sao Paulo for 4 years. The yield exceeded the national average. Soil aggregates formed to 29 cm thickness, and the microbial activity was one order of magnitude higher than that in a conventional control field. The output/input ratios of carbon and nitrogen were 1.88 –2.35 and 3.58–6.00, respectively, indicating a sustainable system for these elements. Incorporating high-C:N-ratio (>20) organic material results in nitrogen deficiency. However, our results indicate that large numbers of microorganisms provide crops with sufficient nitrogen at low concentrations. This method overcomes the yield limitation of chemical fertilizer application and reverses soil degradation.
An algorithm to detect and communicate the differences in computational models describing biological systems
Authors: Scharm Martin , Wolkenhauer Olaf , Waltemath Dagmar
Published: January 2018

Repositories, such as the BioModels Database and the Physiome Model Repository support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available, a framework to track the differences between models and their versions is essential to compare and combine models. Difference detection allows users to study the history of models but also helps in the detection of errors and inconsistencies. However, current repositories lack suitable methods to track a model’s development over time. Consequently, researchers have problems to grasp the differences between models and their versions.

Focusing on SBML and CellML, we developed an algorithm to accurately detect and describe differences between versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks, and (iii) mathematical expressions. Our method is implemented in a comprehensive and open library called BiVeS. Our work facilitates the reuse and extension of existing models. It also supports collaborative modelling. Finally, it contributes to better reproducibility of modelling results and to the challenge of model provenance.

Our algorithm is the first tailor-made detector of differences between versions of computational models in standard formats.
COZMO - A new lightweight stream cipher
Authors: Bonnerji Rhea , Sarkar Simanta , Rarhi Krishnendu , Bhattacharya Abhishek
Published: January 2018

This paper deals with the merger of the two lightweight stream ciphers – A5/1 and Trivium. The idea is to make the key stream generation more secure and to remove the attacks of the individual algorithms. The bits generated by the Trivium cipher (output) will act as the input of the A5/1 cipher. The registers used in the A5/1 cipher will be filled by the output bits of the Trivium cipher. The three registers will then be connected to generate an output which will be our required key stream. we are using Trivium and A5/1 algorithm and making changes to suit our needs.
Effects of forest fragmentation on bird communities in NW Ethiopia
Authors: Yineger Haile , Hughes Jane M
Published: January 2018

Anthropogenic disturbance regimes in areas that were once large continuous habitats have been major drivers of habitat fragmentation and loss which in turn form the largest worldwide threat to avian biodiversity. Studies suggest that functional trait based approaches provide better understanding of fragmentation effects on ecological processes in human-modified landscapes. However, research on these thematic areas is limited in many tropical regions, such as Ethiopia. In this study, we evaluated sensitivity of bird communities and functional groups to fragmentation processes in Ethiopia. Standard point counts were used to survey birds in 16 remnant forest patches of variable sizes and degrees of isolation. The information theoretic model selection approach was used for precise understanding of avian functional group responses to habitat loss and fragmentation. Results showed strong impacts of forest loss and fragmentation on forest specialists, insectivores, frugivores, open nesters, understorey nesters and resident birds. Protection and restoration of the remnant forest patches may help mitigate the negative effects of fragmentation on such specialist bird functional groups.
Introduction to Meta Analysis
Authors: Basu Arindam
Published: January 2018

Meta analysis refers to secondary data analysis where information from individual research articles are synthesised to arrive at a summary estimate. Meta analysis thus refers to several related steps of framing a question or a problem, formulating search strategies, collection of journal articles or primary studies, abstraction of data from the studies, critical appraisal of studies, judging homogeneity of studies, and synthesis of information from them. In this paper, we describe the key processes of how to conduct each of these steps to conduct a meta analysis.
The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines
Authors: Taylor Michael P , Wedel Mathew J
Published: January 2018

Barosaurus is a diplodocid sauropod from the Upper Jurassic Morrison Formation of the western United States, and is known for its very long neck. It is related to the sympatric Diplodocus, and often thought of as more or less identical except with a longer neck. The holotype YPM 429 includes three and a half posterior cervical vertebrae, somewhat distorted and damaged, which are nevertheless very distinctive and quite different from those of Diplodocus. The cervicals of the better known and more complete referred Barosaurus specimen AMNH 6341 show the same characteristic features as the holotype, though not to the same extent: transversely broad but anteroposteriorly short zygapophyseal facets; prezygapophyses carried on broad, squared-off rami; zygapophyses shifted forward relative to the centrum; diapophyses, parapophyses and neural spines shifted backwards; and broad diapophyseal “wings”. These features form a single functional complex, enabling great lateral ﬂexibility, but restricting vertical ﬂexibility. This may indicate that Barosaurus used a different feeding style from other sauropods perhaps sweeping out long arcs at ground level. The Morrison Formation contains at least nine diplodocid species in six to eight genera whose relationships are not yet fully understood, but Barosaurus remains distinct from its relatives.
Test re-test reliability and construct validity of the star-track test of manual dexterity
Authors: Kildebro Niels , Amirian Ilda , Gögenur Ismail , Rosenberg Jacob
Published: January 2018

Objectives: To determine test re-test reliability and construct validity of the star-track test of manual dexterity. Design: Test re-test reliability was tested in a controlled study. Construct validity was tested in a blinded randomized crossover study. Setting: The study was performed at a university hospital in Denmark.Participants: A total of 11 subjects for test re-test and 20 subjects for the construct validity study were included. All were healthy volunteers. Intervention: The test re-test trial had two measurements with 2 days pause in between. The interventions in the construct validity study included baseline measurement, intervention 1: fatigue, intervention 2: stress, and intervention 3: fatigue and stress. There was a 2 day pause between each intervention. Main outcome measure: Integrated measure of completion time and number of errors. Results: All participants completed the study (test re-test n = 11; construct validity n=20). Test re-test showed a strong Pearson product-moment correlation (r= 0.90, n= 11, P < 0.01) with no sign of learning effect. The 20 subjects in the construct validity trial were randomized to the order of the four interventions, so that all subjects completed each intervention once. A repeated measures ANOVA determined that mean integrated measure differed between interventions (p = 0.003). Post hoc tests using Bonferroni correction revealed that compared with baseline all interventions had significantly higher integrated scores ranging from 47-59% difference in mean. Conclusion: The star track test of manual dexterity had a strong test re-test reliability, and was able to discriminate between a subject´s normal manual dexterity and dexterity after exposure to fatigue and/or stress.
Morphology of the jaw, suspensorial, and opercle musculature of Beloniformes and related species (Teleostei: Acanthopterygii), with a special reference to the m. adductor mandibulae complex
Authors: Werneburg Ingmar
Published: January 2018

The taxon Beloniformes represents a heterogeneous group of teleost fishes that show an extraordinary diversity of jaw morphology. I present new anatomical descriptions of the jaw musculature in six selected beloniforms and four closely related species. A reduction of the external jaw adductor (A1) and a changed morphology of the intramandibular musculature were found in many Beloniformes. This might be correlated with the progressively reduced mobility of the upper and lower jaw bones. The needlefishes and sauries, which are characterised by extremely elongated and stiffened jaws, show several derived characters, which in combination enable the capture of fish at high velocity. The ricefishes are characterised by several derived and many plesiomorphic characters that make broad scale comparisons difficult. Soft tissue characters are highly diverse among hemiramphids and flying fishes reflecting the uncertainty about their phylogenetic position and interrelationship. The morphological findings presented herein may help to interpret future phylogenetic analyses using cranial musculature in Beloniformes.
Bayesian inference of protein structure from chemical shift data
Authors: Bratholm Lars A , Christensen Anders Steen , Hamelryck Thomas , Jensen Jan H
Published: January 2018

Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.
Characterization of four new monoclonal antibodies against the distal N-terminal region of PrPc
Authors: Didonna Alessandro , Venturini Anja Colja , Hartman Katrina , Vranac Tanja , Curin Serbec Vladka , Legname Giuseppe
Published: January 2018

Prion diseases are a group of fatal neurodegenerative disorders that affect humans and animals. They are characterized by the accumulation in the central nervous system of a pathological form of the host-encoded prion protein (PrPC). The prion protein is a membrane glycoprotein that consists of two domains: a globular, structured C-terminus and an unstructured N-terminus. The N-terminal part of the protein is involved in different functions in both health and disease. In the present work we discuss the production and biochemical characterization of a panel of four monoclonal antibodies (mAbs) against the distal N-terminus of PrPC using a well-established methodology based on the immunization of Prnp0/0 mice. Additionally, we show their ability to block prion (PrPSc) replication at nanomolar concentrations in a cell culture model of prion infection. These mAbs represent a promising tool for prion diagnostics and for studying the physiological role of the N-terminal domain of PrPC.
Whale Shark Provisioning: What do we know and where do we stand; The case study of Oslob, Philippines
Authors: Ponzo Alessandro , Araujo Gonzalo , Labaja Jessica , So Catherine L. , Snow Sally J. , Geary Daniel , Craven Samantha , Lucey Anna R.
Published: January 2018

Background. Provisioning is a growing practice used to facilitate wildlife-tourist interaction, especially with elusive marine species, but still little is known about its effect on the host species. This work discusses the practice, effect and proposed measures to manage the whale shark provisioning activities and related tourism industry in the waters of Oslob, Philippines.

Methods. Since March 2012, the research team has been studying daily the whale shark population, the tourism industry and its compliances with the local and national laws. During 443 days of survey, 135 individual whale sharks where identified within the interaction area, 197h of shark behavioral observations and tourist compliance surveys have been collected along with 45 biopsy samples, 1000h of dive profiles from TDR tags and 500 tourist satisfaction questionnaires.

Results. Since its official opening in January 2012 more than 140,000 interaction tickets have been sold bringing over 1M USD to the local community and making it one of the largest marine wildlife tourist attractions in South East Asia. The benefits for the community and regional economy are undeniable, however behavioral modification, extended residency time, poor nutritional value of provided food and thermal stress related to the extended permanence in shallow water together with habitat destruction caused by poor diving practices and unregulated coastal developments are some of the quantified side effects of this industry.

Conclusion. A series of meeting with the stakeholders and an education campaign have been initiated as bottom up approach and an adaptive management model based on the identification of the limits of acceptable change is being developed in collaboration with the Authorities to address current limitations in the long-term sustainable management of the whale shark watching industry in Oslob.
Parcellating connectivity in spatial maps
Authors: Baldassano Christopher , Beck Diane M , Fei-Fei Li
Published: January 2018

A common goal in biological sciences is to model a complex web of connections using a small number of interacting units. We present a general approach for dividing up elements in a spatial map based on their connectivity properties, allowing for the discovery of local regions underlying large-scale connectivity matrices. Our method is specifically designed to respect spatial layout and identify locally-connected clusters, corresponding to plausible coherent units such as strings of adjacent DNA base pairs, subregions of the brain, animal communities, or geographic ecosystems. Instead of using approximate greedy clustering, our nonparametric Bayesian model infers a precise parcellation using collapsed Gibbs sampling. We utilize an infinite clustering prior that intrinsically incorporates spatial constraints, allowing the model to search directly in the space of spatially-coherent parcellations. After showing results on synthetic datasets, we apply our method to both functional and structural connectivity data from the human brain. We find that our parcellation is substantially more effective than previous approaches at summarizing the brain's connectivity structure using a small number of clusters, produces better generalization to individual subject data, and reveals functional parcels related to known retinotopic maps in visual cortex. Additionally, we demonstrate the generality of our method by applying the same model to human migration data within the United States. This analysis reveals that migration behavior is generally influenced by state borders, but also identifies regional communities which cut across state lines. Our parcellation approach has a wide range of potential applications in understanding the spatial structure of complex biological networks.
Physiological performance of Persian acroporid corals in summer versus winter temperatures
Authors: Vajed Samiei Jahangir , Saleh Abolfazl , Mehdinia Ali , Shirvani Arash , Kayal Mohsen
Published: January 2018

With ongoing climate change, coral susceptibility to thermal stress constitutes a central concern in reef conservation. In the Persian Gulf, coral reefs are confronted with the most extreme temperatures. Over the last decades, both annual hot and cold peak periods in this region have been associated with episodes of coral bleaching and mortality. Using physiological performance as a measure of coral health, we investigated the thermal susceptibility of the common acroporid coral from the Persian Gulf, Acropora downingi, in Hengam Island where temperature oscillates seasonally in the range 20.2-34.2°C. In a series of two short-term experiments, we exposed corals (1) to the constant temperature levels of summer versus winter, and (2) to progressive temperature deviations from the annual mean toward the two extreme seasonal values and beyond. We monitored four indictors of coral physiological performance: net photosynthesis (Pn), dark respiration (R), autotrophic capability (Pn/R), and survival. Warming revealed detrimental for Pn and survival of corals, while equivalent cooling did not. Pn/R was lower at the warmer thermal level within each season, and during summer compared to winter. Corals exposed to the maximum temperature of summer displayed Pn/R<1, inferring that photosynthetic performance could not support basal metabolic needs under this environment and that corals had to import organic matter or draw on their reserves to compensate for carbon losses during respiration. We therefore suggest that the Persian Gulf populations of A. downingi are more sensitive to the extreme temperatures endured in summer compared to that experienced in winter; and they may be impacted by future increases in water temperature.
NxRepair: Error correction in de novo sequence assembly using Nextera mate pairs
Authors: Murphy Rebecca R , O'Connell Jared M , Cox Anthony J , Schulz-Trieglaff Ole B
Published: January 2018

Scaffolding errors and incorrect traversals of the de Bruijn graph during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub; a tutorial and user documentation are also available.