bluuebunny/crossref_metadata_2025 huggingface dataset:
How to Incorporate Experiential Learning in the Classroom to Address Complex Problems in Ecology
Authors: Deslauriers David
Published: March 2017

An alternative to the use of live predators in the context of predator–prey feeding relationships for educational purposes is presented here. A group of 18 students was asked to maneuver a fictional predator (pipette), which was used to capture age-0 Shovelnose Sturgeon under different densities (1–30 fish per 40-L tank) and temperature treatments (13°C, 18°C, and 24°C). The data were then used to estimate the functional feeding response coefficients typical of a type II curve. Results indicated that the temperature treatments did not have a significant influence on the magnitude of the coefficients. However, the use of a fictional predator provided useful insight into behaviors (fish captured head first and off the bottom of the tank) that were more likely to lead to a predation event. This exercise also limited the mortality of organisms typically associated with these types of trials. Conclusions should provide students with a mechanistic understanding of predator–prey interactions by means of an experiential learning experience.
How should we categorise self‐reported data on subsequent injuries?
Authors: Von Rosen Philip , Heijne Annette
Published: March 2017

Classifying subsequent injuries is of high importance in injury epidemiology since a previous injury has been reported to increase the risk of a new injury or increase the risk of a more severe injury. Multiple reports have shown that self‐reported data provide an extensive view of an injury problem and add valuable information to the understanding of the athlete's health. The purpose of this study was to display a method that can be used to facilitate classification of subsequent injuries and to discuss challenges faced when categorising subsequent injuries based on self‐reported data. The suitability of a new model for Subsequent Injuries Adjusted for Self‐reported data (SIAS model) was demonstrated with sport injury data from a cohort of 101 adolescent elite track & field athletes, followed over 52 weeks. A total number of 71 subsequent injuries were identified. Of all subsequent injuries, recurrent injuries represented 69.0% (n = 49) and 31.0% (n = 22) were classified as new injuries. The majority of subsequent injuries (n = 60, 84.5%) occurred after athletes had recovered from a previous injury. Of all subsequent injuries, 15.5% (n = 11) represented injuries where athletes had not fully recovered from a previous injury. Application of the SIAS model allows for classification of subsequent injuries based on self‐reported data on the recovery level of the athletes, the injury onset and injury type. The developed SIAS model follows the consensus recommendations of injury definition, injury classification and is an attempt to increase the understanding of the complex relationship of subsequent injuries in self‐reported data sets.
Totaro’s question for adjoint groups of types 𝐴₁ and 𝐴_{2𝑛}
Authors: Gordon-Phillips Reed
Published: March 2017

Let

G
G

be a smooth connected linear algebraic group over a field

k
k

, and let

X
X

be a

G
G

-torsor. Totaro asked: if

X
X

admits a zero-cycle of degree

d
≥
1

d \geq 1

, then does

X
X

have a closed étalé point of degree dividing

d
d

? We give an affirmative answer for absolutely simple classical adjoint groups of types

A
1

A_1

and

A

2
n

A_{2n}

over fields of characteristic

≠
2

\neq 2

.
Using electronic medical record notes to measure ICU telemedicine utilization
Authors: O’Shea Amy MJ , Vaughan Sarrazin Mary , Nassar Boulos , Cram Peter , Johnson Lynelle , Bonello Robert , Panos Ralph J , Reisinger Heather S
Published: March 2017

Given the complexity of high-acuity health care, designing an effective clinical note template can be beneficial to both document patient care and clarify how telemedicine is used. We characterized documented interactions via a standardized note template between bedside intensive care unit (ICU) providers and teleintensivists in 2 Veterans Health Administration ICU telemedicine support centers. All ICUs linked to support centers and providing care from October 2012 through September 2014 were considered. Interactions were assessed based on initiation site, bedside initiator, contact type, and patient care change. Of 14 511 ICU admissions with teleintensivist access, teleintensivist interaction was documented in 21.6% (N = 3136). In particular, contacts were primarily initiated by bedside staff (74.4%), use increased over time, and of contacts resulting in changes in patient care, most were initiated by a bedside nurse (84.3%). Given this variation, future research necessitates inclusion of utilization in evaluation of Tele-ICU and patient outcomes.
Fair decomposition of group obligations
Authors: Alechina Natasha , van der Hoek Wiebe , Logan Brian
Published: March 2017

We consider the problem of decomposing a group norm into a set of individual obligations for the agents comprising the group, such that if the individual obligations are fulfilled, the group obligation is fulfilled. Such an assignment of tasks to agents is often subject to additional social or organizational norms that specify permissible ways in which tasks can be assigned. An important role of social norms is that they can be used to impose ‘fairness constraints’, which seek to distribute individual responsibility for discharging the group norm in a ‘fair’ or ‘equitable’ way. We propose a simple language for this kind of fairness constraints and analyse the problem of computing a fair decomposition of a group obligation, both for non-repeating and for repeating group obligations.
Supramolecular organic frameworks (SOFs): homogeneous regular 2D and 3D pores in water
Authors: Tian Jia , Wang Hui , Zhang Dan-Wei , Liu Yi , Li Zhan-Ting
Published: March 2017

Studies on periodic porosity and related properties and functions have been limited to insoluble solid-state materials. Self-assembly provides a straightforward and efficient strategy for the construction of soluble periodic porous supramolecular organic frameworks (SOFs) in water from rationally designed molecular building blocks. From rigid tri- and tetra-armed building blocks and cucurbitu[8]ril (CB[8]), a number of two-dimensional (2D) honeycomb, square and rhombic SOFs can be generated, which is driven by CB[8]-encapsulation-enhanced dimerization of two aromatic units on the periphery of the multi-armed molecules. By utilizing the same three-component host−guest motif as the driving force, three-dimensional (3D) diamondoid and cubic SOFs can be obtained from tetrahedral and [Ru(bipy)3]2+-derived octahedral monomers and CB[8]. All of the 2D and 3D periodic frameworks are soluble in water, and are able to maintain the periodicity as well as the pore sizes in the solid state. 3D SOFs are highly efficient homogeneous polycationic frameworks for reversible adsorption of anionic species including organic dyes, peptides, nucleic acids, drugs, dendrimers and Wells-Dawson-typed polyoxametallates (WD-POMs). WD-POM molecules adsorbed in the [Ru(bipy)3]2+-based SOF can catalyse the reduction of proton to H2 upon visible-light sensitization of [Ru(bipy)3]2+, which allows multiple electron transfer from [Ru(bipy)3]2+ to WD-POM. This review summarizes the design, formation and characterization of this new family of self-assembled frameworks, highlights their applications as homogeneous porous materials and finally outlines some future research directions.
Early Development, Identification of Mode of Action, and Use of Dantrolene Sodium
Authors: Pollock Neil A. , Machon Roslyn G. , Rosenberg Henry
Published: March 2017

Dantrolene—a nitrofurantoin derivative—was developed by Snyder et al. in 1967. After initial discovery of its muscle relaxation potential, investigations in a number of species demonstrated dose-dependent reductions in skeletal muscle tone that were long lasting, relatively nontoxic, and free of adverse effects such as respiratory impairment. Ellis et al. then published a number of papers investigating the means by which dantrolene produced these effects. Using a series of classic physiologic models, Ellis investigated potential sites of action for the new drug, eventually narrowing this down to the intracellular calcium-release mechanism. Ellis went on to play a pivotal role in the discovery of dantrolene’s effectiveness for the treatment of malignant hyperthermia, after reading a scientific bulletin about muscle rigidity in pigs affected by porcine stress syndrome, contacting Gaisford Harrison and sending dantrolene to him for trial.
SPONTANEOUS SUPRACHOROIDAL HEMORRHAGE ASSOCIATED WITH IATROGENIC COAGULOPATHY
Authors: Akkan Aydoğmuş Fatma Sema , Serdar Kurtulus , Kalayci Defne , Çelik Ayşenur
Published: March 2017

Purpose:

To present a case of spontaneous suprachoroidal hemorrhage in a patient on anticoagulation.

Methods:

Single case report.

Results:

A 68-year-old woman with a history of hypertension, atherosclerosis, and heart failure presented with massive spontaneous suprachoroidal hemorrhage in the left eye. She had no known ophthalmic pathology. She was taking warfarin and she had a high international normalization ratio. Despite medical and surgical therapy, there was no improvement and vision deteriorated to no light perception.

Conclusion:

Spontaneous expulsive suprachoroidal hemorrhage is a rare entity. Advanced age, systemic anticoagulation, and hypertension are strong risk factors. It is important to monitor international normalization ratio in warfarinized patients; particularly, uncontrolled high levels may cause spontaneous suprachoroidal hemorrhage in the absence of predisposing ocular pathology.
Can We Improve the Tolerance of an Ocular Prosthesis by Enhancing Its Surface Finish?
Authors: Litwin Andre S. , Worrell Emma , Roos Jonathan C. P. , Edwards Barry , Malhotra Raman
Published: March 2017

Purpose:

Patients who wear an ocular prosthesis frequently suffer with dry eye symptoms and socket discharge, often on a daily basis. The aim of the study was to determine whether a smoother, optical quality polish of the prosthesis’ surface could improve symptoms and wear tolerance. The study was designed as single-center, single-masked, prospective randomized controlled trial. Eighty-eight consecutive patients undergoing annual ocular prosthesis maintenance review were approached from the prosthesis clinic. Forty-one out of 49 eligible patients were recruited.

Methods:

Participants were randomized to either a standard or a higher “optical quality” polish of their prosthesis. At entry to the trial, at 1 month, and 12 months they completed a questionnaire covering cleaning, lubricant use, inflammation, discomfort, and discharge. Lower scores indicated better tolerance of the prosthesis. At each visit, the prosthesis was stained and photographed against a standard background to assess deposit build up. Primary outcome measures were 1) a subjective questionnaire score and 2) an objective assessment of surface deposit build-up on prosthetic eyes by standardized photographic grading.

Results:

Forty-one patients participated in the study. The median age of their prosthesis was 36 months (range 9 months–40 years). There was no statistically significant difference in questionnaire scores or deposit build up between the 2 groups at baseline. By 12-months, the higher optical quality polish showed a statistically significant reduction in symptoms and frequency of discharge (2.19 vs. 3.85; p = 0.05—lower scores better). Scoring of the prosthesis’ deposit build-up showed a significant difference at 1 month, but this was not sustained at 12 months.

Conclusions:

Creating an optical quality finish to an ocular prosthesis reduces deposit build up on artificial eyes. The authors found this modification improved patient tolerance at 12 months.
Secondary Posttraumatic Stress and Nurses' Emotional Responses to Patient's Trauma
Authors: Missouridou Evdokia
Published: March 2017

Alarmingly high percentages of secondary posttraumatic stress have been reported in several nursing domains such as critical care and emergency nursing, oncology, pediatric nursing, mental health nursing, and midwifery. The purpose of this review is to examine and describe nurses' emotional responses in the face of their exposure to patients' trauma. Lack of understanding of the dynamics of trauma may limit nurses' ability to interact in a meaningful and safe way with patients and their families. Spirituality can be a precious compass in the long-term journey of resolving feelings of grief and loss at work and of building a strong professional identity.
Alcohol Use at the Time of Traumatic Brain Injury: Screening and Brief Intervention in a Community Hospital
Authors: Eyer Madeline M. , Renier Colleen M. , Woehrle Theo A. , Vogel Linda E. , Conway Pat G. , McCarty Catherine A.
Published: March 2017

The use of screening and brief interventions (SBI) has been proposed to reduce future alcohol misuse and injury in traumatic brain injury (TBI) patients. As a result a SBI protocol for TBI patients was introduced with nursing training at a community hospital. In the 2 years following the implementation of a SBI protocol and nursing training, the number of patients with positive alcohol results decreased. The number of brief interventions increased to 83 (40.1%, 95% confidence limit [CL] = 33.4, 46.8), and CAGE questionnaire screenings decreased to 88 (42.5%, 95% CL = 35.8, 49.2), with 31 (35.2%) having positive results. These results highlight the need to assess processes and training in the emergency department to ensure that SBIs occur.
Development and Function of Immune Cells in an Adolescent Patient With a Deficiency in the Interleukin‐10 Receptor
Authors: Veenbergen Sharon , van Leeuwen Marieke A. , Driessen Gertjan J. , Kersseboom Rogier , de Ruiter Lilian F. , Raatgeep Rolien (H.)C. , Lindenbergh‐Kortleve Dicky J. , Simons‐Oosterhuis Ytje , Biermann Katharina , Halley Dicky J.J. , de Ridder Lissy , Escher Johanna C. , Samsom Janneke N.
Published: March 2017

Objective:

Monogenic defects in the interleukin‐10 (IL‐10) pathway are extremely rare and cause infantile‐onset inflammatory bowel disease (IBD)‐like pathology. Understanding how immune responses are dysregulated in monogenic IBD‐like diseases can provide valuable insight in “classical” IBD pathogenesis. Here, we studied long‐term immune cell development and function in an adolescent IL‐10 receptor (IL10RA)‐deficient patient who presented in infancy with severe colitis and fistulizing perianal disease and is currently treated with immune suppressants.

Methods:

Biomaterial was collected from the IL10RA‐deficient patient, pediatric patients with IBD, and healthy controls. The frequency and phenotype of immune cells were determined in peripheral blood and intestinal biopsies by flow cytometry and immunohistochemistry. Functional changes in monocyte‐derived dendritic cells and T cells were assessed by in vitro activation assays.

Results:

The IL10RA‐deficient immune system developed normally with respect to numbers and phenotype of circulating immune cells. Despite normal co‐stimulatory molecule expression, bacterial lipopolysaccharide‐stimulated monocyte‐derived dendritic cells from the IL10RA‐deficient patient released increased amounts of tumor necrosis factor α compared to healthy controls. Upon T‐cell receptor ligation, IL10RA‐deficient peripheral blood mononuclear cells released increased amounts of T‐cell cytokines interferon γ and IL‐17 agreeing with high numbers of T‐bet+ and IL‐17+ cells in intestinal biopsies taken at disease onset. In vitro, the immunosuppressive drug thalidomide used to treat the patient's decreased peripheral blood mononuclear cell‐derived tumor necrosis factor production.

Conclusions:

With time and during immunosuppressive treatment the IL10RA‐deficient immune system develops relatively normally. Upon activation, IL‐10 is crucial for controlling excessive inflammatory cytokine release by dendritic cells and preventing interferon γ and IL‐17‐mediated T‐cell responses.
Transfer of disrupted-in-schizophrenia 1 aggregates between neuronal-like cells occurs in tunnelling nanotubes and is promoted by dopamine
Authors: Zhu Seng , Abounit Saïda , Korth Carsten , Zurzolo Chiara
Published: March 2017

The disrupted-in-schizophrenia 1 (
DISC1
) gene was identified as a genetic risk factor for chronic mental illnesses (CMI) such as schizophrenia, bipolar disorder and severe recurrent depression. Insoluble aggregated DISC1 variants were found in the cingular cortex of sporadic, i.e. non-genetic, CMI patients. This suggests protein pathology as a novel, additional pathogenic mechanism, further corroborated in a recent transgenic rat model presenting DISC1 aggregates. Since the potential role of aggregation of DISC1 in sporadic CMI is unknown, we investigated whether DISC1 undergoes aggregation in cell culture and could spread between neuronal cells in a prion-like manner, as shown for amyloid proteins in neurodegenerative diseases. Co-culture experiments between donor cells forming DISC1 aggregates and acceptor cells showed that 4.5% of acceptor cells contained donor-derived DISC1 aggregates, thus indicating an efficient transfer
in vitro
. DISC1 aggregates were found inside tunnelling nanotubes (TNTs) and transfer was enhanced by increasing TNT formation and notably by dopamine treatment, which also induces DISC1 aggregation. These data indicate that DISC1 aggregates can propagate between cells similarly to prions, thus providing some molecular basis for the role of protein pathology in CMI.
Effects of 25 mg oxazepam on emotional mimicry and empathy for pain: a randomized controlled experiment
Authors: Nilsonne Gustav , Tamm Sandra , Golkar Armita , Sörman Karolina , Howner Katarina , Kristiansson Marianne , Olsson Andreas , Ingvar Martin , Petrovic Predrag
Published: March 2017

Emotional mimicry and empathy are mechanisms underlying social interaction. Benzodiazepines have been proposed to inhibit empathy and promote antisocial behaviour. First, we aimed to investigate the effects of oxazepam on emotional mimicry and empathy for pain, and second, we aimed to investigate the association of personality traits to emotional mimicry and empathy. Participants (
n
=76) were randomized to 25 mg oxazepam or placebo. Emotional mimicry was examined using video clips with emotional expressions. Empathy was investigated by pain stimulating the participant and a confederate. We recorded self-rated experience, activity in major zygomatic and superciliary corrugator muscles, skin conductance, and heart rate. In the mimicry experiment, oxazepam inhibited corrugator activity. In the empathy experiment, oxazepam caused increased self-rated unpleasantness and skin conductance. However, oxazepam specifically inhibited neither emotional mimicry nor empathy for pain. Responses in both experiments were associated with self-rated empathic, psychopathic and alexithymic traits. The present results do not support a specific effect of 25 mg oxazepam on emotional mimicry or empathy.
Suicides on the Austrian railway network: hotspot analysis and effect of proximity to psychiatric institutions
Authors: Strauss Markus J. , Klimek Peter , Sonneck Gernot , Niederkrotenthaler Thomas
Published: March 2017

Railway suicide is a significant public health problem. In addition to the loss of lives, these suicides occur in public space, causing traumatization among train drivers and passengers, and significant public transport delays. Prevention efforts depend upon accurate knowledge of clustering phenomena across the railway network, and spatial risk factors. Factors such as proximity to psychiatric institutions have been discussed to impact on railway suicides, but analytic evaluations are scarce and limited. We identify 15 hotspots on the Austrian railway system while taking case location uncertainties into account. These hotspots represent 0.9% of the total track length (5916 km/3676 miles) that account for up to 17% of all railway suicides (N=1130). We model suicide locations on the network using a smoothed inhomogeneous Poisson process and validate it using randomization tests. We find that the density of psychiatric beds is a significant predictor of railway suicide. Further predictors are population density, multitrack structure and—less consistently—spatial socio-economic factors including total suicide rates. We evaluate the model for the identified hotspots and show that the actual influence of these variables differs across individual hotspots. This analysis provides important information for suicide prevention research and practice. We recommend structural separation of railway tracks from nearby psychiatric institutions to prevent railway suicide.
Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?
Authors: Akkaynak Derya , Siemann Liese A. , Barbosa Alexandra , Mäthger Lydia M.
Published: March 2017

Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation ofperfect camouflagein which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging.
Dynamics of cilia length in left–right development
Authors: Pintado P. , Sampaio P. , Tavares B. , Montenegro-Johnson T. D. , Smith D. J. , Lopes S. S.
Published: March 2017

Reduction in the length of motile cilia in the zebrafish left–right organizer (LRO), also known as Kupffer's vesicle, has a large impact on left–right development. Here we demonstrate through genetic overexpression in zebrafish embryos and mathematical modelling that the impact of increased motile cilia length in embryonic LRO fluid flow is milder than that of short cilia. Through Arl13b overexpression, which increases cilia length without impacting cilia beat frequency, we show that the increase in cilium length is associated with a decrease in beat amplitude, resulting in similar flow strengths for Arl13b overexpression and wild-type (WT) embryos, which were not predicted by current theory. Longer cilia exhibit pronounced helical beat patterns and, consequently, lower beat amplitudes relative to WT, a result of an elastohydrodynamic shape transition. For long helical cilia, fluid dynamics modelling predicts a mild (approx. 12%) reduction in the torque exerted on the fluid relative to the WT, resulting in a proportional reduction in flow generation. This mild reduction is corroborated by experiments, providing a mechanism for the mild impact on organ
situs
.
G
-Strands on symmetric spaces
Authors: Arnaudon Alexis , Holm Darryl D. , Ivanov Rossen I.
Published: March 2017

We study the
G
-strand equations that are extensions of the classical chiral model of particle physics in the particular setting of broken symmetries described by symmetric spaces. These equations are simple field theory models whose configuration space is a Lie group, or in this case a symmetric space. In this class of systems, we derive several models that are completely integrable on finite dimensional Lie group
G
, and we treat in more detail examples with symmetric space
SU
(2)/
S
1
and
SO
(4)/
SO
(3). The latter model simplifies to an apparently new integrable nine-dimensional system. We also study the
G
-strands on the infinite dimensional group of diffeomorphisms, which gives, together with the Sobolev norm, systems of 1+2 Camassa–Holm equations. The solutions of these equations on the complementary space related to the Witt algebra decomposition are the odd function solutions.
Experimental duration and predator satiation levels systematically affect functional response parameters
Authors: Li Yuanheng , Rall Björn C. , Kalinkat Gregor
Published: March 2017

Empirical feeding studies where density-dependent consumption rates are fitted to functional response models are often used to parametrize the interaction strengths in models of population or food-web dynamics. However, the relationship between functional response parameter estimates from short-term feeding studies and real-world, long-term, trophic interaction strengths remains largely untested. In a critical first step to address this void, we tested for systematic effects of experimental duration and predator satiation on the estimation of functional response parameters, namely attack rate and handling time. Analyzing a large data set covering a wide range of predator taxonomies and body sizes we show that attack rates decrease with increasing experimental duration, and that handling times of starved predators are consistently shorter than those of satiated predators. Therefore, both the experimental duration and the predator satiation level have a strong and systematic impact on the predictions of population dynamics and food-web stability. Our study highlights potential pitfalls at the intersection of empirical and theoretical applications of functional responses. We conclude our study with some practical suggestions how these implications should be addressed in the future to improve predictive abilities and realism in models of predator-prey interactions.
High variability impairs motor learning regardless of whether it affects task performance
Authors: Cardis Marco , Casadio Maura , Ranganathan Rajiv
Published: March 2017

Motor variability plays an important role in motor learning, although the exact mechanisms of how variability affects learning is not well understood. Recent evidence suggests that motor variability may have different effects on learning in redundant tasks, depending on whether it is present in the task space (where it affects task performance), or in the null space (where it has no effect on task performance). Here we examined the effect of directly introducing null and task space variability using a manipulandum during the learning of a motor task. Participants learned a bimanual shuffleboard task for 2 days, where their goal was to slide a virtual puck as close as possible towards a target. Critically, the distance traveled by the puck was determined by the sum of the left and right hand velocities, which meant that there was redundancy in the task. Participants were divided into five groups – based on both the dimension in which the variability was introduced and the amount of variability that was introduced during training. Results showed that although all groups were able to reduce error with practice, learning was affected more by the amount of variability introduced rather than the dimension in which variability was introduced. Specifically, groups with higher movement variability during practice showed larger errors at the end of practice compared to groups that had low variability during learning. These results suggest that although introducing variability can increase exploration of new solutions, this may come at a cost of decreased stability of the learned solution.
Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test
Authors: Toro Israel Del , Berberich Gabriele , Ribbons Relena R. , Berberich Martin B. , Sanders Nathan J. , Ellison Aaron M.
Published: March 2017

Ecological studies aim to better understand the distribution and abundances of organisms. Yet ecological works often are subjected to unintentional biases thus an improved framework for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants(Formica rufa,RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 meters of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE-SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research.
Evolution of the sex ratio and effective number under gynodioecy and androdioecy
Authors: Uyenoyama Marcy K. , Takebayashi Naoki
Published: March 2017

We address the evolution of effective number of individuals under androdioecy and gynodioecy. We analyze dynamic models of autosomal modifiers of weak effect on sex expression. In our zygote control models, the sex expressed by a zygote depends on its own genotype, while in our maternal control models, it depends on the genotype of its maternal parent. Our analysis unifies full multi-dimensional local stability analysis with the Li-Price equation, which for all its heuristic appeal, describes evolutionary change over a single generation. We define a point in the neighborhood of a fixation state from which a single-generation step indicates the asymptotic behavior of the frequency of a modifier allele initiated at an arbitrary point near the fixation state. A concept of heritability appropriate for the evolutionary modification of sex emerges from the Li-Price framework. We incorporate our theoretical analysis into our previously-developed Bayesian inference framework to develop a new method for inferring the viability of gonochores (males or females) relative to hermaphrodites. Applying this approach to microsatellite data derived from natural populations of the gynodioecious plantSchiedea salicariaand the androdioecious killifishKryptolebias marmoratus, we find that while female and hermaphroditeS. salicariaappear to have similar viabilities, maleK. marmoratusappear to survive to reproductive age at less than half the rate of hermaphrodites.
Novelty by Furcation and Fusion: How tree-like is evolution?
Authors: Oakley Todd H.
Published: March 2017

Novelty and innovation are fundamental yet relatively understudied concepts in evolution. We may study novelty phylogenetically, with a key question of whether evolution occurs by tree-like branching, or through exchange of distantly related parts in processes akin to horizontal transfer. Here, I argue that except at the lowest levels of biological organization, evolution is not usually tree-like. Perfectly vertical inheritance, an assumption of evolutionary trees, requires simultaneous co-duplication of all the parts of a duplicating or speciating (which I collectively call 'furcating') biological feature. However, simultaneous co-duplication of many parts usually requires variational processes that are rare. Therefore, instead of being perfectly tree-like, evolution often involves events that incorporate or fuse more distantly related parts into new units during evolution, which herein I call 'fusion'. Exon shuffling, horizontal gene transfer, introgression and co-option are such fusion processes at different levels of organization. In addition to co-duplication, units under phylogenetic study must individuate (gaining evolutionary independence) before they can diverge. A lack of individuation erases evolutionary history, and provides another challenge to tree-like evolution. In particular, biological units in the same organism that are the products of development always share the same genome, perhaps making full individuation difficult. The ubiquity of processes that fuse distantly related parts or oppose individuation has wide ranging implications for the study of macroevolution. For one, the central metaphor of a tree of life will often be violated, to the point where we may need a different metaphor, such as economic public goods, or a ‘web of life’. Secondly, we may need to expand current models. For example, even under the prevailing model of cell-type evolution, the sister-cell-type model, a lack of complete individuation and evolution by co-option will often be involved in forming new cell-types. Finally, these processes highlight a need for an expansive toolkit for studying evolutionary history. Multivariate methods are particularly critical to discover co-variation, the hallmark of an absence of complete individuation. In addition to studying phylogenetic trees, we may often need to analyze and visualize phylogenetic networks. Even though furcation - the splitting and individuation of biological features - does happen, fusion of distant events is just as critical for the evolution of novelties, and must formally be incorporated into the metaphors, models, and visualization of evolutionary history.
Salt-bridge Networks within Globular and Disordered Proteins – Characterizing Trends for Designable Interactions
Authors: Basu Sankar , Mukharjee Debasish
Published: March 2017

There has been fare amount of debate regarding the contribution of salt-bridges in the stabilization of protein folds. However, their participation in crucial protein functions are well established. The current study analyzes their modes of association, in terms of networks, both within globular proteins and also at protein-protein interfaces. Apart from the most common and trivial case of isolated salt-bridges, bifurcated salt-bridges appear to be a special salt-bridge motif both in terms of its topology and geometry and found ubiquitously in proteins and inter-protein complexes. Interesting and attractive examples presenting different interaction-modes have been highlighted. Bifurcated salt-bridges appear to function as molecular clips instrumental in stitching large surface contours of interacting protein-protein interfaces. The work also emphasizes the key role of salt-bridge mediated interactions in the partial folding of proteins containing large amount of disordered regions. Salt-bridge mediated interactions seem pivotal in promoting ‘disorder-to-order’ transitions for small disordered protein fragments and their stabilization upon binding. The results should guide to elucidate the modus operandi of these partially disordered proteins and also should be helpful to conceptualize how these proteins manage to keep necessary amount of disorder even in their functionally active bound forms, encouraging future studies. It should also be potentially beneficial towards the proposed notion of geometrically specific designable interactions involving salt-bridges.
Humans are colonized by many uncharacterized and highly divergent microbes
Authors: Kowarsky Mark , Camunas Joan , Kertesz Michael , Iwijn De Vlaminck , Koh Winston , Pan Wenying , Martin Lance , Neff Norma , Okamoto Jennifer , Wong Ron , Kharbanda Sandhya , El-Sayed Yasser , Blumenfeld Yair , Stevenson David K. , Shaw Gary , Wolfe Nathan D. , Quake Stephen R.
Published: March 2017

Blood circulates throughout the entire body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analysing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.
Assessing the relationship of ancient and modern populations
Authors: Schraiber Joshua G.
Published: March 2017

Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population while accounting for sequencing error and post-mortem damage by analyzing raw read from multiple ancient individuals simultaneously. We show that when analyzing SNP data, it is better to sequence more ancient samples to low coverage: two samples sequenced to 0.5x coverage provide better resolution than a single sample sequenced to 2x coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that with even a few high cover-age individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.
Coral reefs in crisis: The reliability of deep-time food web reconstructions as analogs for the present
Authors: Roopnarine Peter D. , Dineen Ashley A.
Published: March 2017

Ongoing anthropogenic alterations of the biosphere have shifted emphasis in conservation biology from individual species to entire ecosystems. Modern measures of ecosystem change, however, lack the extended temporal scales necessary to forecast future change under increasingly stressful environmental conditions. Accordingly, the assessment and reconstruction of ecosystem dynamics during previous intervals of environmental stress and climate change in deep time has garnered increasing attention. The nature of the fossil record, though, raises questions about the difficulty of reconstructing paleocommunity and paleoecosystem-level dynamics. In this study, we assess the reliability of such reconstructions by simulating the fossilization of a highly threatened and disturbed modern ecosystem, a Caribbean coral reef. Using a high-resolution coral reef food web from Jamaica, we compare system structures of the modern and simulated fossil reefs, including guild richness and evenness, trophic level distribution, predator dietary breadth, food chain lengths, and modularity. Results indicate that despite the loss of species, guilds, and trophospecies interactions, particularly zooplankton and other soft-bodied organisms, the overall guild diversity, structure, and modularity of the reef ecosystem remained intact. These results have important implications for the integrity of fossil food web studies and coral reef conservation, demonstrating that fossil reef communities can be used to understand reef community dynamics during past regimes of environmental change.
Abnormally high levels of serum α-klotho result in a poor outcome for clinical pregnancy-A prospective cohort study
Authors: Funabiki Miyako , Taguchi Sagiri , Nakamura Yoshitaka
Published: March 2017

Background

The klotho protein has been extensively studied. However, there are no studies examining the association between serum alpha klotho levels and the clinical outcome of post-clinical pregnancy.

Methods

We conducted a prospective cohort study in 42 patients (median age 37.4 years) to evaluate the association between serum alpha klotho levels during the follicular phase of preimplantation and the clinical outcome data of post-clinical pregnancy. The patients provided informed consent at our clinic. The serum alpha klotho levels were evaluated using a human soluble alpha klotho assay kit. The fetal chromosomal abnormalities were investigated at our clinic. We also assessed the clinical outcomes of post-clinical pregnancies.

Results

The serum alpha klotho level during the follicular phase of preimplantation for non-pregnant women was 544.31 pg/ml (mean). The clinical pregnancy rate was 38.1%. There were chromosomal abnormalities observed in four unborn children (9.5%; Down syndrome, etc). The serum alpha klotho levels during the follicular phase of preimplantation in the chromosomal abnormalities group were higher than in the group without chromosomal abnormalities (P=0.029, abnormalities group 659.26 pg/ml [mean] versus control 530.23 pg/ml [mean]). A multiple logistic regression analysis showed the chromosomal abnormalities rates in unborn children were positively influenced by serum alpha klotho levels during the follicular phase of preimplantation (p=0.0008) and the patient’s age (p=0.008).

Conclusion

Previous studies have demonstrated that increased alpha klotho levels in human serum are positively correlated with health. However, abnormally high levels of serum alpha klotho during the follicular phase of preimplantation may predict a poor outcome for clinical pregnancy.
Combining molecular gut content analysis and functional response models shows how body size affects prey choice in soil predators
Authors: Eitzinger Bernhard , Rall Björn C. , Traugott Michael , Scheu Stefan
Published: March 2017

Predator-prey interactions are a core concept of animal ecology and functional response models provide a powerful tool to predict the strength of trophic links and assess motives for prey choice. However, due to their reductionist set-up, these models may not display field conditions, possibly leading to skewed results.

We tested the validity of functional response models for multiple prey by comparing them with empirical data from DNA-based molecular gut content analysis of two abundant and widespread macrofauna soil predators, lithobiid and geophilomorph centipedes.

We collected soil and litter dwelling centipedes, screened their gut contents for DNA of nine abundant decomposer and intraguild prey using specific primers and tested for different prey and predator traits explaining prey choice. In order to calculate the functional response of same predators, we used natural prey abundances and functional response parameters from published experiments and compared both approaches.

Molecular gut content results showed that prey choice of centipedes is driven by predator body size and prey identity. Results of functional response models significantly correlated with results from molecular gut content analysis for the majority of prey species.

Overall, the results suggest that functional response models are a powerful tool to predict trophic interactions in soil, however, species-specific traits have to be taken into account to improve predictions.
Bayesian weighing of electron cryo-microscopy data for integrative structural modeling
Authors: Bonomi Massimiliano , Hanot Samuel , Greenberg Charles H. , Sali Andrej , Nilges Michael , Vendruscolo Michele , Pellarin Riccardo
Published: March 2017

Cryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map and other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-sourceIntegrative Modeling Platform(http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.

Highlights

We present a modeling approach to integrate cryo-EM data with other sources of information

We benchmark our approach using synthetic data on 21 complexes of known structure

We apply our approach to the GroEL/GroES, RNA polymerase II, and exosome complexes
Substrate-triggered position-switching of TatA and TatB is an essential step in theEscherichia coliTat protein export pathway
Authors: Habersetzer Johann , Moore Kristoffer , Cherry Jon , Buchanan Grant , Stansfeld Phillip , Palmer Tracy
Published: March 2017

The twin arginine protein transport (Tat) machinery mediates the translocation of folded proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. TheEscherichia coliTat system comprises TatC and two additional sequence-related proteins, TatA and TatB. Here we use disulfide crosslinking and molecular modelling to show there are two binding sites for TatA/B proteins on TatC. TatA and TatB are each able to occupy both sites if they are the only TatA/B protein present. However, under resting conditions the sites are differentially occupied with TatB occupying the ‘polar cluster’ site while TatA binds adjacently at the TatC transmembrane helix 6 binding site. When the Tat system is activated by the overproduction of a substrate, TatA and TatB switch their binding sites. We propose that this substrate-triggered positional exchange is a key step in the assembly of an active Tat translocase.