bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultrasound in Assisted Reproductive Technologies and the First Trimester: Is There a Risk?
Authors: ABRAMOWICZ JACQUES S.
Published: December 2016

Ultrasound is routinely used in assisted reproductive technology for monitoring of follicular growth, oocyte retrieval and embryo transfer, as well as for the assessment of early embryonic development in the first 5 to 8 weeks of pregnancy. Ultrasound is a form of energy, which will affect live tissues it traverses (bioeffects) by being partially transformed into heat (thermal effect) and by alternating positive and negative pressures (nonthermal or mechanical effect). In the United States 2 indices (thermal and mechanical index) must be displayed on-screen to provide the clinicians an indication of possible thermal and nonthermal changes. The thermal index and mechanical index should be kept below 1. The use of Doppler involves much higher levels of energy than B-mode gray scale 2-dimensional or 3-dimensional and special precautions are recommended when utilizing this modality. Information on susceptibility of the oocyte, prefertilization or postfertilization and the possible vulnerability of the very early fetus to such energy is very scarce. Data on whether there is a cumulative effect or an effect of recurrent exposure (eg, oocyte growth follow-up) do not exist. Ultrasound should be used only when medically indicated, for the shortest time and at the lowest intensity compatible with accurate diagnosis, especially when performing Doppler studies. In addition, because of lack of knowledge regarding bioeffects and safety among clinicians, educational effort is needed.
OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY IN PATIENTS WITH BEHÇET UVEITIS
Authors: Khairallah Moncef , Abroug Nesrine , Khochtali Sana , Mahmoud Anis , Jelliti Bechir , Coscas Gabriel , Lupidi Marco , Kahloun Rim , Ben Yahia Salim
Published: December 2016

Purpose:

To describe optical coherence tomography angiography (OCTA) findings in eyes with Behçet uveitis (BU) and to compare these findings with those of fluorescein angiography (FA).

Methods:

Prospective, comparative, cross-sectional study. Patients presenting with clinically active BU involving the posterior segment were evaluated using FA, spectral domain optical coherence tomography (SD-OCT), and OCTA. Optical coherence tomography angiograms were reviewed and analyzed. Foveal avascular zone areas and vessel densities were also reported.

Results:

Twenty-five patients (44 eyes) were included. Perifoveal microvascular changes were more frequently observed on OCTA than on FA (95.5 vs 59.1%;P< 0.001). Disruption of the perifoveal capillary arcade, areas of retinal capillary nonperfusion/hypoperfusion, and perifoveal capillary abnormalities, including rarefied, dilated, or shunting vessels were observed more frequently using OCTA than FA (40.9 vs 25%;P= 0.039, 86.4 vs 34.1%;P< 0.001, and 84.1 vs 36.4%;P< 0.001, respectively). Areas of retinal capillary nonperfusion/hypoperfusion were more frequently observed in the deep than in the superficial capillary plexus (81.8 vs 63.6%;P= 0.039). Capillary abnormalities and disorganization of the normal architecture of the capillary network were more frequent in the deep than in the superficial capillary plexus (P< 0.001). Foveal avascular zone area was not significantly larger in eyes with BU than in control group in both the superficial and the deep capillary plexuses (0.4 vs 0.34 mm2;P= 0.23 and 0.72 vs 0.53 mm2;P= 0.053, respectively). Capillary vessel density was significantly lower in eyes with BU than in control group in the deep capillary plexus (13.7 vs 17.2 mm 21;P= 0.004).

Conclusion:

OCTA allows better visualization and characterization of perifoveal microvascular changes than FA in eyes with active BU. The deep capillary plexus seemed to be more severely involved than the superficial capillary plexus.
Astigmatism Correction With Toric Intraocular Lenses in Descemet Membrane Endothelial Keratoplasty Triple Procedures
Authors: Yokogawa Hideaki , Sanchez P. James , Mayko Zachary M. , Straiko Michael D. , Terry Mark A.
Published: December 2016

Purpose:

To report the clinical efficacy of astigmatism correction with toric intraocular lenses (IOLs) in patients undergoing the Descemet membrane endothelial keratoplasty (DMEK) triple procedure and to evaluate the accuracy of the correction.

Methods:

Fifteen eyes of 10 patients who received cataract extraction, toric IOL placement, and DMEK surgery for Fuchs corneal dystrophy and cataracts were evaluated. The cylinder power of toric IOLs was determined by an online toric calculator with keratoscopy measurements obtained using Scheimpflug corneal imaging. Prediction errors were assessed as a difference vector between the anticipated minus postoperative residual astigmatism.

Results:

At 10.1 ± 4.9 months postoperatively, 8/13 (61.5%) of eyes achieved uncorrected distance visual acuity better than 20/40. Mean best spectacle-corrected distance visual acuity (logMAR) improved from 0.21 ± 0.15 preoperatively to 0.08 ± 0.12 postoperatively (P < 0.01). The magnitude of refractive astigmatism was also significantly decreased from 2.23 ± 1.10 D (range 0.75–4.25 D) preoperatively to 0.87 ± 0.75 D (range 0.00–3.00 D) postoperatively (P < 0.01). In 1 eye with rotational misalignment by 43 degrees, we found no improvement of astigmatism. The prediction error of astigmatism at the corneal plane was 0.77 ± 0.54 D (range 0.10–1.77 D). Four eyes with preoperative “with-the-rule” corneal astigmatism had postoperative “against-the-rule” refractive astigmatism.

Conclusions:

For patients with Fuchs corneal dystrophy and cataracts, use of toric IOLs might be a valuable option in triple DMEK surgery. Additionally, care should be taken to prevent excessive IOL rotation.
Anesthesia for functional endoscopic sinus surgery
Authors: Carlton Daniel A. , Govindaraj Satish
Published: December 2016

Purpose of review

The present article summarizes anesthetic techniques used during functional endoscopic sinus surgery to decrease bleeding and aid in creating a clear surgical field. The applicable physiology behind these anesthetic techniques is reviewed with emphasis on the effect on bleeding and the surgical field. Deliberate hypotension, reverse Trendelenburg positioning, regional anesthesia, and cerebral monitoring are discussed.

Recent findings

There are mixed data as to whether traditional inhalation anesthesia or total intravenous anesthesia is superior with respect to better surgical fields and decreased blood loss. A review of the literature tends to favor total intravenous anesthesia. Cerebral oximetry and transcranial Doppler ultrasound are emerging techniques to monitor cerebral perfusion during deliberate hypotension.

Total intravenous anesthesia using propofol and remifentanil is the current favored technique for producing deliberate hypotension during endoscopic sinus surgery due to its hemodynamic stability and smooth rapid emergence.
Angiomyofibroblastoma of the Broad Ligament: A Case Report
Authors: Huang Hsiao-Chin , Chen Ying-Ren , Tsai Horng-Der , Cheng Ya-Min , Hsiao Yi-Hsuan
Published: December 2016

Angiomyofibroblastoma (AMF) is a distinctive, rare, benign mesenchymal tumor that often occurs in the lower genital region of women. The most commonly reported location of an AMF is in the vulvovaginal area. We describe a rare case of an AMF located in the broad ligament in a 47-yr-old woman. The patient experienced menorrhagia, dysmenorrhea, and subsequent menstrual spotting. She sought help at the National Cheng Kung University Hospital. Ultrasonography showed an echo-complex mass in the left adnexal area. The patient underwent laparoscopic surgery to remove the soft tissue mass located in the left broad ligament. The final pathology of the mass was reported as an AMF. We reviewed all of the AMF cases reported in the English-language literature found in Pubmed. This case is the first of AMF located in the broad ligament.
Field Evaluation of Dried Blood Spots for HIV-1 Viral Load Monitoring in Adults and Children Receiving Antiretroviral Treatment in Kenya: Implications for Scale-up in Resource-Limited Settings
Authors: Schmitz Mary E. , Agolory Simon , Junghae Muthoni , Broyles Laura N. , Kimeu Muthusi , Ombayo Joseph , Umuro Mamo , Mukui Irene , Alwenya Kennedy , Baraza Moses , Ndiege Kenneth , Mwalili Samuel , Rivadeneira Emilia , Ng'ang'a Lucy , Yang Chunfu , Zeh Clement ,   for VL-DBS Study Group
Published: December 2016

Background:

The World Health Organization recommends viral load (VL) as the preferred method for diagnosing antiretroviral therapy failure; however, operational challenges have hampered the implementation of VL monitoring in most resource-limited settings. This study evaluated the accuracy of dried blood spot (DBS) VL testing under field conditions as a practical alternative to plasma in determining virologic failure (VF).

Methods:

From May to December 2013, paired plasma and DBS specimens were collected from 416 adults and 377 children on antiretroviral therapy for ≥6 months at 12 clinics in Kenya. DBSs were prepared from venous blood (V-DBS) using disposable transfer pipettes and from finger-prick capillary blood using microcapillary tubes (M-DBS) and directly spotting (D-DBS). All samples were tested on the Abbott m2000 platform; V-DBS was also tested on the Roche COBAS Ampliprep/COBAS TaqMan (CAP/CTM) version 2.0 platform. VF results were compared at 3 DBS thresholds (≥1000, ≥3000, and ≥5000 copies/mL) and a constant plasma threshold of ≥1000 copies/mL.

Results:

On the Abbott platform, at ≥1000-copies/mL threshold, sensitivities, specificities, and kappa values for VF determination were ≥88.1%, ≥93.1%, and ≥0.82%, respectively, for all DBS methods, and it had the lowest percentage of downward misclassification compared with higher thresholds. V-DBS performance on CAP/CTM had significantly poorer specificity at all thresholds (1000%–33.0%, 3000%–60.9%, and 5000%–77.0%). No significant differences were found between adults and children.

Conclusions:

VL results from V-DBS, M-DBS, and D-DBS were comparable with those from plasma for determining VF using the Abbott platform but not with CAP/CTM. A 1000-copies/mL threshold was optimal and should be considered for VF determination using DBS in adults and children.
Sex Differences in Tobacco Use Among Persons Living With HIV/AIDS: A Systematic Review and Meta-Analysis
Authors: Weinberger Andrea H. , Smith Philip H. , Funk Allison P. , Rabin Shayna , Shuter Jonathan
Published: December 2016

Background:

Persons living with HIV/AIDS (PLWH) smoke at higher rates than other adults and experience HIV-related and non-HIV–related adverse smoking consequences. This study conducted a systematic review to synthesize current knowledge about sex differences in smoking behaviors among PLWH.

Methods:

Over 3000 abstracts from MEDLINE were reviewed and 79 publications met all the review inclusion criteria (ie, reported data on smoking behaviors for PLWH by sex). Sufficient data were available to conduct a meta-analysis for one smoking variable: current smoking prevalence.

Results:

Across studies (n = 51), the meta-analytic prevalence of current smoking among female PLWH was 36.3% (95% confidence interval [CI]: 28.0% to 45.4%) and male PLWH was 50.3% (95% CI: 44.4% to 56.2%; meta-analytic odds ratio = 1.78, 95% CI: 1.29 to 2.45). When analyses were repeated just on the US studies (n = 23), the prevalence of current smoking was not significantly different for female PLWH (55.1%, 95% CI: 47.6% to 62.5%) compared with male PLWH (55.5%, 95% CI: 48.2% to 62.5%; meta-analytic odds ratio = 1.04, 95% CI: 0.86 to 1.26). Few studies reported data by sex for other smoking variables (eg, quit attempts, noncigarette tobacco product use) and results for many variables were mixed.

Discussion:

Unlike the general US population, there was no difference in smoking prevalence for female versus male PLWH (both >50%) indicating that HIV infection status was associated with a greater relative increase in smoking for women than men. More research is needed in all areas of smoking behavior of PLWH to understand similarities and differences by sex to provide the best interventions to reduce the high smoking prevalence for all sexes.
Nurse Counseling for Physical Activity in Patients Undergoing Esophagectomy
Authors: Komatsu Hiroko , Watanuki Shigeaki , Koyama Yurie , Iino Keio , Kurihara Miho , Uesugi Hideo , Yagasaki Kaori , Daiko Hiroyuki
Published: December 2016

Strong evidence exists regarding multiple benefits of physical activity among cancer patients. Patients undergoing esophagectomy received counseling for physical activity by a nurse and instructions to keep a diary of physical activities before surgery, followed by 2 counseling sessions after surgery. Physical activity, body mass index, psychological distress, and quality of life were measured at baseline, 2–4 weeks, and 3 and 6 months after discharge. Of 29 participants (mean age = 65.9 years), 72.5% underwent thoracoscopic esophagectomy in the prone position with 3-field lymphadectomy. The results of the International Physical Activity Questionnaire indicated that postoperative physical activity returned to nearly preoperative level, and the number of inactive patients gradually decreased by half at 6 months after discharge. Quality of life scores, except those for role function and social function, tended to return to the baseline at 6 months after discharge. Psychological distress measured by the Kessler 6 remained lower than the baseline, whereas the mean score of body mass index gradually declined after discharge. Patients undergoing esophagectomy and receiving nurse counseling can return to preoperative physical activity level in their daily lives after surgery. Nurses should integrate physical activity promotion into cancer care.
Predator diversity reduces habitat colonization by mosquitoes and midges
Authors: Staats Ethan G. , Agosta Salvatore J. , Vonesh James R.
Published: December 2016

Changes in predator diversity via extinction and invasion are increasingly widespread and can have important ecological and socio-economic consequences. Anticipating and managing these consequences requires understanding how predators shape ecological communities. Previous predator biodiversity research has focused on post-colonization processes. However, predators can also shape communities by altering patterns of prey habitat selection during colonization. The sensitivity of this non-consumptive top down mechanism to changes in predator diversity is largely unexamined. To address this gap, we examined patterns of dipteran oviposition habitat selection in experimental aquatic habitats in response to varied predator species richness while holding predator abundance constant. Caged predators were used in order to disentangle behavioural oviposition responses to predator cues from potential post-oviposition consumption of eggs and larvae. We hypothesized that because increases in predator richness often result in greater prey mortality than would be predicted from independent effects of predators, prey should avoid predator-rich habitats during colonization. Consistent with this hypothesis, predator-rich habitats received 48% fewer dipteran eggs than predicted, including 60% fewer mosquito eggs and 38% fewer midge eggs. Our findings highlight the potentially important links between predator biodiversity, prey habitat selection and the ecosystem service of pest regulation.
A trade-off between reproductive investment and maternal cerebellum size in a precocial bird
Authors: Ebneter Christina , Pick Joel L. , Tschirren Barbara
Published: December 2016

Natural selection favours increased investment in reproduction, yet considerable variation in parental investment is observed in natural populations. Life-history theory predicts that this variation is maintained by a trade-off between the benefits of increased reproductive investment and its associated costs for the parents. The nature of these costs of reproduction, however, remains poorly understood. The brain is an energetically highly expensive organ and increased reproductive investment may, therefore, negatively affect brain maintenance. Using artificial selection lines for high and low prenatal maternal investment in a precocial bird, the Japanese quail (
Coturnix japonica
), we provide experimental evidence for this hypothesis by showing that increased prenatal provisioning negatively affects the size of a particular brain region of the mother, the cerebellum. Our finding suggests that cognitive demands may constrain the evolution of parental investment, and vice versa, contributing to the maintenance of variation in reproductive behaviour in animal populations.
An experimental evolution study confirms that discontinuous gas exchange does not contribute to body water conservation in locusts
Authors: Talal Stav , Ayali Amir , Gefen Eran
Published: December 2016

The adaptive nature of discontinuous gas exchange (DGE) in insects is contentious. The classic ‘hygric hypothesis’, which posits that DGE serves to reduce respiratory water loss (RWL), is still the best supported. We thus focused on the hygric hypothesis in this first-ever experimental evolution study of any of the competing adaptive hypotheses. We compared populations of the migratory locust (Locusta migratoria) that underwent 10 consecutive generations of selection for desiccation resistance with control populations. Selected locusts survived 36% longer under desiccation stress but DGE prevalence did not differ between these and control populations (approx. 75%). Evolved changes in DGE properties in the selected locusts included longer cycle and interburst durations. However, in contrast with predictions of the hygric hypothesis, these changes were not associated with reduced RWL rates. Other responses observed in the selected locusts were higher body water content when hydrated and lower total evaporative water loss rates. Hence, our data suggest that DGE cycle properties in selected locusts are a consequence of an evolved increased ability to store water, and thus an improved capacity to buffer accumulated CO2, rather than an adaptive response to desiccation. We conclude that DGE is unlikely to be an evolutionary response to dehydration challenge in locusts.
piRNA-associated proteins and retrotransposons are differentially expressed in murine testis and ovary of aryl hydrocarbon receptor deficient mice
Authors: Rico-Leo Eva M. , Moreno-Marín Nuria , González-Rico Francisco J. , Barrasa Eva , Ortega-Ferrusola Cristina , Martín-Muñoz Patricia , Sánchez-Guardado Luis O. , Llano Elena , Alvarez-Barrientos Alberto , Infante-Campos Ascensión , Catalina-Fernández Inmaculada , Hidalgo-Sánchez Matías , de Rooij Dirk G. , Pendás Alberto M. , Peña Fernando J. , Merino Jaime M. , Fernández-Salguero Pedro M.
Published: December 2016

Previous studies suggested that the aryl hydrocarbon receptor (AhR) contributes to mice reproduction and fertility. However, the mechanisms involved remain mostly unknown. Retrotransposon silencing by Piwi-interacting RNAs (piRNAs) is essential for germ cell maturation and, remarkably, AhR has been identified as a regulator of murine
B1-SINE
retrotransposons. Here, using littermate

AhR
+/+

and
AhR
−/−
mice, we report that AhR regulates the general course of spermatogenesis and oogenesis by a mechanism likely to be associated with piRNA-associated proteins, piRNAs and retrotransposons. piRNA-associated proteins MVH and Miwi are upregulated in leptotene to pachytene spermatocytes with a more precocious timing in
AhR
−/−
than in

AhR
+/+

testes. piRNAs and transcripts from
B1-SINE
,
LINE-1
and
IAP
retrotransposons increased at these meiotic stages in AhR-null testes. Moreover,
B1-SINE
transcripts colocalize with MVH and Miwi in leptonema and pachynema spermatocytes. Unexpectedly,
AhR
−/−
males have increased sperm counts, higher sperm functionality and enhanced fertility than

AhR
+/+

mice. In contrast, piRNA-associated proteins and
B1-SINE
and
IAP
-derived transcripts are reduced in adult
AhR
−/−
ovaries. Accordingly, AhR-null female mice have lower numbers of follicles when compared with

AhR
+/+

mice. Thus, AhR deficiency differentially affects testis and ovary development possibly by a process involving piRNA-associated proteins, piRNAs and transposable elements.
A decision underlies phototaxis in an insect
Authors: Gorostiza E. Axel , Colomb Julien , Brembs Björn
Published: December 2016

Like a moth into the flame—phototaxis is an iconic example for innate preferences. Such preferences probably reflect evolutionary adaptations to predictable situations and have traditionally been conceptualized as hard-wired stimulus–response links. Perhaps for that reason, the century-old discovery of flexibility in
Drosophila
phototaxis has received little attention. Here, we report that across several different behavioural tests, light/dark preference tested in walking is dependent on various aspects of flight. If we temporarily compromise flying ability, walking photopreference reverses concomitantly. Neuronal activity in circuits expressing dopamine and octopamine, respectively, plays a differential role in photopreference, suggesting a potential involvement of these biogenic amines in this case of behavioural flexibility. We conclude that flies monitor their ability to fly, and that flying ability exerts a fundamental effect on action selection in
Drosophila
. This work suggests that even behaviours which appear simple and hard-wired comprise a value-driven decision-making stage, negotiating the external situation with the animal's internal state, before an action is selected.
Primase is required for helicase activity and helicase alters the specificity of primase in the enteropathogen
Clostridium difficile
Authors: van Eijk Erika , Paschalis Vasileios , Green Matthew , Friggen Annemieke H. , Larson Marilynn A. , Spriggs Keith , Briggs Geoffrey S. , Soultanas Panos , Smits Wiep Klaas
Published: December 2016

DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms.
Clostridium difficile
is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of
C. difficile
, and reconstitute helicase and primase activities
in vitro
. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. Furthermore, we find that helicase activity is dependent on the presence of primase
in vitro
. The inherent trinucleotide specificity of primase is determined by a single lysine residue and is similar to the primase of the extreme thermophile
Aquifex aeolicus.
However, the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, loader–helicase–primase interactions, which crucially mediate helicase loading and activation during DNA replication in all organisms, differ critically in
C. difficile
from that of the well-studied Gram-positive
Bacillus subtilis
model.
Phylogenomics-guided discovery of a novel conserved cassette of short linear motifs in BubR1 essential for the spindle checkpoint
Authors: Tromer Eelco , Bade Debora , Snel Berend , Kops Geert J. P. L.
Published: December 2016

The spindle assembly checkpoint (SAC) maintains genomic integrity by preventing progression of mitotic cell division until all chromosomes are stably attached to spindle microtubules. The SAC critically relies on the paralogues Bub1 and BubR1/Mad3, which integrate kinetochore–spindle attachment status with generation of the anaphase inhibitory complex MCC. We previously reported on the widespread occurrences of independent gene duplications of an ancestral ‘MadBub’ gene in eukaryotic evolution and the striking parallel subfunctionalization that lead to loss of kinase function in BubR1/Mad3-like paralogues. Here, we present an elaborate subfunctionalization analysis of the Bub1/BubR1 gene family and perform de novo sequence discovery in a comparative phylogenomics framework to trace the distribution of ancestral sequence features to extant paralogues throughout the eukaryotic tree of life. We show that known ancestral sequence features are consistently retained in the same functional paralogue: GLEBS/CMI/CDII/kinase in the Bub1-like and KEN1/KEN2/D-Box in the BubR1/Mad3-like. The recently described ABBA motif can be found in either or both paralogues. We however discovered two additional ABBA motifs that flank KEN2. This cassette of ABBA1-KEN2-ABBA2 forms a strictly conserved module in all ancestral and BubR1/Mad3-like proteins, suggestive of a specific and crucial SAC function. Indeed, deletion of the ABBA motifs in human BUBR1 abrogates the SAC and affects APC/C–Cdc20 interactions. Our detailed comparative genomics analyses thus enabled discovery of a conserved cassette of motifs essential for the SAC and shows how this approach can be used to uncover hitherto unrecognized functional protein features.
Language as a coordination tool evolves slowly
Authors: David-Barrett Tamas , Dunbar Robin I. M.
Published: December 2016

Social living ultimately depends on coordination between group members, and communication is necessary to make this possible. We suggest that this might have been the key selection pressure acting on the evolution of language in humans and use a behavioural coordination model to explore the impact of communication efficiency on social group coordination. We show that when language production is expensive but there is an individual benefit to the efficiency with which individuals coordinate their behaviour, the evolution of efficient communication is selected for. Contrary to some views of language evolution, the speed of evolution is necessarily slow because there is no advantage in some individuals evolving communication abilities that much exceed those of the community at large. However, once a threshold competence has been achieved, evolution of higher order language skills may indeed be precipitate.
Influence of environmental parameters on movements and habitat utilization of humpback whales (Megaptera novaeangliae) in the Madagascar breeding ground
Authors: Trudelle Laurène , Cerchio Salvatore , Zerbini Alexandre N. , Geyer Ygor , Mayer François-Xavier , Jung Jean-Luc , Hervé Maxime R. , Pous Stephane , Sallée Jean-Baptiste , Rosenbaum Howard C. , Adam Olivier , Charrassin Jean-Benoit
Published: December 2016

Assessing the movement patterns and key habitat features of breeding humpback whales is a prerequisite for the conservation management of this philopatric species. To investigate the interactions between humpback whale movements and environmental conditions off Madagascar, we deployed 25 satellite tags in the northeast and southwest coast of Madagascar. For each recorded position, we collated estimates of environmental variables and computed two behavioural metrics: behavioural state of ‘transiting’ (consistent/directional) versus ‘localized’ (variable/non-directional), and active swimming speed (i.e. speed relative to the current). On coastal habitats (i.e. bathymetry < 200 m and in adjacent areas), females showed localized behaviour in deep waters (191 ± 20 m) and at large distances (14 ± 0.6 km) from shore, suggesting that their breeding habitat extends beyond the shallowest waters available close to the coastline. Males' active swimming speed decreased in shallow waters, but environmental parameters did not influence their likelihood to exhibit localized movements, which was probably dominated by social factors instead. In oceanic habitats, both males and females showed localized behaviours in shallow waters and favoured high chlorophyll-aconcentrations. Active swimming speed accounts for a large proportion of observed movement speed; however, breeding humpback whales probably exploit prevailing ocean currents to maximize displacement. This study provides evidence that coastal areas, generally subject to strong human pressure, remain the core habitat of humpback whales off Madagascar. Our results expand the knowledge of humpback whale habitat use in oceanic habitat and response to variability of environmental factors such as oceanic current and chlorophyll level.
It is lonely at the front: contrasting evolutionary trajectories in male and female invaders
Authors: Hudson Cameron M. , Brown Gregory P. , Shine Richard
Published: December 2016

Invasive species often exhibit rapid evolutionary changes, and can provide powerful insights into the selective forces shaping phenotypic traits that influence dispersal rates and/or sexual interactions. Invasions also may modify sexual dimorphism. We measured relative lengths of forelimbs and hindlimbs of more than 3000 field-caught adult cane toads (Rhinella marina) from 67 sites in Hawai'i and Australia (1–80 years post-colonization), along with 489 captive-bred individuals from multiple Australian sites raised in a ‘common garden’ (to examine heritability and reduce environmental influences on morphology). As cane toads spread from east to west across Australia, the ancestral condition (long limbs, especially in males) was modified. Limb length relative to body size was first reduced (perhaps owing to natural selection on locomotor ability), but then increased again (perhaps owing to spatial sorting) in the invasion vanguard. In contrast, the sex disparity in relative limb length has progressively decreased during the toads' Australian invasion. Offspring reared in a common environment exhibited similar geographical divergences in morphology as did wild-caught animals, suggesting a genetic basis to the changes. Limb dimensions showed significant heritability (2–17%), consistent with the possibility of an evolved response. Cane toad populations thus have undergone a major shift in sexual dimorphism in relative limb lengths during their brief (81 years) spread through tropical Australia.
Paradigm shifts and the interplay between state, business and civil sectors
Authors: Encarnação Sara , Santos Fernando P. , Santos Francisco C. , Blass Vered , Pacheco Jorge M. , Portugali Juval
Published: December 2016

The recent rise of the civil sector as a main player of socio-political actions, next to public and private sectors, has largely increased the complexity underlying the interplay between different sectors of our society. From urban planning to global governance, analysis of these complex interactions requires new mathematical and computational approaches. Here, we develop a novel framework, grounded on evolutionary game theory, to envisage situations in which each of these sectors is confronted with the dilemma of deciding between maintaining a
status quo
scenario or shifting towards a new paradigm. We consider multisector conflicts regarding environmentally friendly policies as an example of application, but the framework developed here has a considerably broader scope. We show that the public sector is crucial in initiating the shift, and determine explicitly under which conditions the civil sector—reflecting the emergent reality of civil society organizations playing an active role in modern societies—may influence the decision-making processes accruing to other sectors, while fostering new routes towards a paradigm shift of the society as a whole. Our results are shown to be robust to a wide variety of assumptions and model parametrizations.
Effect of wall-mediated hydrodynamic fluctuations on the kinetics of a Brownian nanoparticle
Authors: Yu Hsiu-Yu , Eckmann David M. , Ayyaswamy Portonovo S. , Radhakrishnan Ravi
Published: December 2016

The reactive flux formalism (Chandler 1978
J. Chem. Phys.
68
, 2959–2970. (
doi:10.1063/1.436049
)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu
et al.
2015
Phys. Rev. E
91
, 052303. (
doi:10.1103/PhysRevE.91.052303
)) makes a significant step towards solving the coupled processes of molecular reactions and hydrodynamic relaxation by examining how the wall-mediated hydrodynamic memory impacts the two-stage temporal relaxation of the reaction rate for a nanoparticle transition between two bound states in the bulk, near-wall and lubrication regimes.
A computational framework for ptychographic reconstructions
Authors: Enders B. , Thibault P.
Published: December 2016

Ptychography is now a well-established X-ray microscopy tool for synchrotron end-stations equipped with a scanning stage and a pixelated detector. Ptychographic phasing algorithms use information from coherent diffraction to deliver quantitative images of the specimen at a resolution higher than the scanning resolution. These algorithms have traditionally been implemented in software on a per-instrument basis in various degrees of user-friendliness and sophistication. Here, we present Ptypy, a ptychography software written with the intention to serve as a framework across the diverse sets of available instruments and usage cases. A distinctive feature of the software is its formalism, which provides a convenient abstraction of the physical model, thus allowing for concise algorithmic implementations and portability across set-up geometries. We give an overview of the supported usage cases, explain the abstraction layer and design principles, and provide a step-by-step guide describing how an algorithm may be realized in a concise and readable manner. The software capabilities are illustrated with reconstructions from visible light and X-ray data.
Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone”
Authors: Thrash J. Cameron , Seitz Kiley W. , Baker Brett J. , Temperton Ben , Gillies Lauren E. , Rabalais Nancy N. , Henrissat Bernard , Mason Olivia U.
Published: December 2016

Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called ‘dead zones,’ are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as those belonging to Candidate Phyla usually associated with anoxic environments-Parcubacteria (OD1) and Peregrinibacteria. Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter.

Importance

Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon—many of which occur in bacterioplankton from poorly understood lineages—have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these “microbial dark matter” taxa during hypoxia.
Multivariate pattern analysis of MEG and EEG: a comparison of representational structure in time and space
Authors: Cichy Radoslaw Martin , Pantazis Dimitrios
Published: December 2016

1

Multivariate pattern analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data can reveal the rapid neural dynamics underlying cognition. However, MEG and EEG have systematic differences in sampling neural activity. This poses the question to which degree such measurement differences consistently bias the results of multivariate analysis applied to MEG and EEG activation patterns. To investigate, we conducted a concurrent MEG/EEG study while participants viewed images of everyday objects. We applied multivariate classification analyses to MEG and EEG data, and compared the resulting time courses to each other, and to fMRI data for an independent evaluation in space. We found that both MEG and EEG revealed the millisecond spatio-temporal dynamics of visual processing with largely equivalent results. Beyond yielding convergent results, we found that MEG and EEG also captured partly unique aspects of visual representations. Those unique components emerged earlier in time for MEG than for EEG. Identifying the sources of those unique components with fMRI, we found the locus for both MEG and EEG in high-level visual cortex, and in addition for MEG in early visual cortex. Together, our results show that multivariate analyses of MEG and EEG data offer a convergent and complimentary view on neural processing, and motivate the wider adoption of these methods in both MEG and EEG research.
Cleanliness in context: reconciling hygiene with a modern microbial perspective
Authors: Vandegrift Roo , Bateman Ashley C. , Siemens Kyla N. , Nguyen May , Green Jessica L. , Van Den Wymelenberg Kevin G. , Hickey Roxana J.
Published: December 2016

The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with that of sterilization. Recent research on microbial ecology is demonstrating that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (ourmicrobiota). Human skin is home to a diverse, skin habitat specific community of microorganisms; this includes members that exist across the ecological spectrum from pathogen through commensal to mutualist. Most evidence suggests that the skin microbiota is likely of direct benefit to the host, and only rarely exhibits pathogenicity. This complex ecological context suggests that the conception of hygiene as a unilateral reduction or removal of microbes has outlived its usefulness. As such, we suggest the explicit definition of hygiene as ‘those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease’. To examine the implications of this definition, we review the literature related to hand drying as an aspect of hand hygienic practice. Research on hand drying generally focuses on ‘hygienic efficacy’, a concept not typically defined explicitly, but nearly always including alterations to bulk microbial load. The corresponding literature is differentiable into two divisions: research supporting the use of forced air dryers, which typically includes effectiveness of drying as an aspect of hygienic efficacy; and research supporting the use of paper towels, which typically includes risk of aerosolized spread of microbes from hands as an aspect of hygienic efficacy. Utilizing a definition of hygiene that explicitly relies onreduction in disease spreadrather than alterations to bulk microbial load would address concerns raised on both sides of the debate. Future research should take advantage of cultivation-independent techniques, working to bridge the gap between the two existing divisions of research by using health outcomes (such as the spread of disease) as dependent variables, taking into account the microbial community context of the skin microbiota, and focusing on understanding the relative contribution of bioaerosols and residual moisture to the risk of disease transmission.
How to improve parameter estimates in GLM-based fMRI data analysis: cross-validated Bayesian model averaging
Authors: Soch Joram , Meyer Achim Pascal , Haynes John-Dylan , Allefeld Carsten
Published: December 2016

In functional magnetic resonance imaging (fMRI), model quality of general linear models (GLMs) for first-level analysis is rarely assessed. In recent work (Soch et al., 2016: “How to avoid mismodelling in GLM-based fMRI data analysis: cross-validated Bayesian model selection”, NeuroImage, vol. 141, pp. 469-489; DOI: 10.1016/j. neuroimage.2016.07.047), we have introduced cross-validated Bayesian model selection (cvBMS) to infer the best model for a group of subjects and use it to guide second-level analysis. While this is the optimal approach given that the same GLM has to be used for all subjects, there is a much more efficient procedure when model selection only addresses nuisance variables and regressors of interest are included in all candidate models. In this work, we propose cross-validated Bayesian model averaging (cvBMA) to improve parameter estimates for these regressors of interest by combining information from all models using their posterior probabilities. This is particularly useful as different models can lead to different conclusions regarding experimental effects and the most complex model is not necessarily the best choice. We find that cvBMS can prevent not detecting established effects and that cvBMA can be more sensitive to experimental effects than just using even the best model in each subject or the model which is best in a group of subjects.
Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification
Authors: Zhu Wentao , Lou Qi , Vang Yeeleng Scott , Xie Xiaohui
Published: December 2016

Mammogram classification is directly related to computer-aided diagnosis of breast cancer. Traditional methods requires great effort to annotate the training data by costly manual labeling and specialized computational models to detect these annotations during test. Inspired by the success of using deep convolutional features for natural image analysis and multi-instance learning for labeling a set of instances/patches, we propose end-to-end trained deep multiinstance networks for mass classification based on whole mammogram without the aforementioned costly need to annotate the training data. We explore three different schemes to construct deep multi-instance networks for whole mammogram classification. Experimental results on the INbreast dataset demonstrate the robustness of proposed deep networks compared to previous work using segmentation and detection annotations in the training.
The SPECIES beamline at the MAX IV Laboratory: a facility for soft X-ray RIXS and APXPS
Authors: Urpelainen Samuli , Såthe Conny , Grizolli Walan , Agåker Marcus , Head Ashley R. , Andersson Margit , Huang Shih-Wen , Jensen Brian N. , Wallén Erik , Tarawneh Hamed , Sankari Rami , Nyholm Ralf , Lindberg Mirjam , Sjöblom Peter , Johansson Niclas , Reinecke Benjamin N. , Arman M. Alif , Merte Lindsay R. , Knudsen Jan , Schnadt Joachim , Andersen Jesper N. , Hennies Franz
Published: December 2016

SPECIES is an undulator-based soft X-ray beamline that replaced the old I511 beamline at the MAX II storage ring. SPECIES is aimed at high-resolution ambient-pressure X-ray photoelectron spectroscopy (APXPS), near-edge X-ray absorption fine-structure (NEXAFS), X-ray emission spectroscopy (XES) and resonant inelastic X-ray scattering (RIXS) experiments. The beamline has two branches that use a common elliptically polarizing undulator and monochromator. The beam is switched between the two branches by changing the focusing optics after the monochromator. Both branches have separate exit slits, refocusing optics and dedicated permanent endstations. This allows very fast switching between two types of experiments and offers a unique combination of the surface-sensitive XPS and bulk-sensitive RIXS techniques both in UHV and at elevated ambient-pressure conditions on a single beamline. Another unique property of the beamline is that it reaches energies down to approximately 27 eV, which is not obtainable on other current APXPS beamlines. This allows, for instance, valence band studies under ambient-pressure conditions. In this article the main properties and performance of the beamline are presented, together with selected showcase experiments performed on the new setup.
Cult of the “I”
Authors: Golub Koraljka , Hansson Joacim , Selden Lars
Published: December 2016

Purpose

The purpose of the paper is to analyse three Scandinavian iSchools in Denmark, Norway and Sweden with regard to their intentions of becoming iSchools and curriculum content in relation to these intentions. By doing so, a picture will be given of the international expansion of the iSchool concept in terms of organisational symbolism and practical educational content. In order to underline the approaches of the Scandinavian schools, comparisons are made to three American iSchools.

Design/methodology/approach

The study is framed through theory on organisational symbolism and the intentions of the iSchool movement as formulated in its vision statements. Empirically, the study consists of two parts: close readings of three documents outlining the considerations of three Scandinavian LIS schools before applying for the iSchool status, and statistical analysis of 427 syllabi from master level courses at three Scandinavian and three American iSchools.

Findings

All three Scandinavian schools, analysed, have recently become iSchools, and though some differences are visible, it is hard to distinguish anything in their syllabi as carriers of what can be described as an iSchool identity. In considering iSchool identity, it instead benefits on a symbolic level that are most prominent, such as branding, social visibility and the possible attraction of new student groups. The traditionally strong relation to national library sectors are emphasised as important to maintain, specifically in Norway and Sweden.

Research limitations/implications

The study is done on iSchools in Denmark, Norway and Sweden with empirical comparison to three American schools. These comparisons face the challenge of meeting the educational system and programme structure of each individual country. Despite this, findings prove possible to use as ground for conclusions, although empirical generalisations concerning, for instance, other countries must be made with caution.

Practical implications

This study highlights the practical challenges met in international expansion of the iSchool movement, both on a practical and symbolic level. Both the iSchool Caucus and individual schools considering becoming iSchools may use these findings as a point of reference in development and decision making.

Originality/value

This is an original piece of research from which the results may contribute to the international development of the iSchool movement, and extend the theoretical understanding of the iSchool movement as an educational and organisational construct.