bluuebunny/crossref_metadata_2025 huggingface dataset:
The Association of Dry Eye Symptom Severity and Comorbid Insomnia in US Veterans
Authors: Galor Anat , Seiden Benjamin E. , Park Jasmine J. , Feuer William J. , McClellan Allison L. , Felix Elizabeth R. , Levitt Roy C. , Sarantopoulos Constantine D. , Wallace Douglas M.
Published: January 2017

Purpose:

To investigate the association between dry eye (DE) and insomnia symptom severity.

Methods:

Cross-sectional study of 187 individuals seen in the Miami Veterans Affairs eye clinic. An evaluation was performed consisting of questionnaires regarding insomnia (insomnia severity index [ISI]) and DE symptoms, including ocular pain, followed by a comprehensive ocular surface examination. Using a two-step cluster analysis based on intensity ratings of ocular pain, the patient population was divided into two groups (high and low ocular pain groups: HOP and LOP). A control group was ascertained at the same time from the same clinic as defined by no symptoms of DE (Dry Eye Questionnaire 5 [DEQ5], <6). The main outcome measure was the frequency of moderate or greater insomnia in the DE groups.

Results:

The mean age of the study sample was 63 years, and 93% were male. All insomnia complaints were rated higher in the HOP group compared with the LOP and control groups (P<0.0005). Most (61%) individuals in the HOP group experienced insomnia of at least moderate severity (ISI≥15) compared with the LOP (41%) and control groups (18%) (P<0.0005). Black race (odds ratio [OR], 2.7; 95% confidence interval [CI], 1.2–6.0; P=0.02), depression severity (OR, 1.2; 95% CI, 1.1–1.3; P<0.0005), and DE symptom severity (DEQ5; OR, 1.1; 95% CI, 1.01–1.2; P=0.03) were significantly associated with clinical insomnia (ISI≥15) after controlling for potential confounders.

Conclusions:

After adjusting for demographics and medical comorbidities, we show that DE symptom severity is positively associated with insomnia severity.
Crescentic Tuck in Lamellar Keratoplasty—A Novel Technique in a Case of Advanced Pellucid Marginal Corneal Degeneration
Authors: Arora Ritu , Manudhane Aditi , Jain Parul , Goyal Jawahar Lal
Published: January 2017

Purpose:

To describe a new surgical technique “crescentic tuck in lamellar keratoplasty” for the management of advanced pellucid marginal corneal degeneration (PMCD).

Methods:

A 45-year-old man with advanced PMCD and maximal thinning in the inferior juxtalimbal periphery underwent a crescentic lamellar keratoplasty in the right eye. Best-corrected visual acuity was 6/60 with no further improvement because of severe irregular astigmatism. Thinnest pachymetry in the peripheral cornea was 280 μm. Peripheral crescent-shaped lamellar corneal dissection of 3.5-mm width was performed, and an intrastromal pocket was fashioned from 4 to 8 O'clock, extending beyond limbus. A crescent-shaped donor corneal button of 3.5-mm width was denuded of its endothelium and beveled in inferior periphery to create a flange. The flange was tucked into the peripheral scleral pocket. The donor graft was secured to the host bed using 10-0 nylon interrupted sutures.

Results:

Donor cornea integrated with the host bed over time and best spectacle-corrected visual acuity at 1 year improved to 6/9 with –1.25/–3.5 D × 90°. The simK (simulated keratometry) changed from 41.6/56.3 diopters (D) to 45.1/50.6 D. The astigmatism reduced from 14.6 D to 5.5 D.

Conclusion:

Crescentic tuck in lamellar keratoplasty provides good apposition of the donor lenticule and tectonic support to the peripheral thin cornea while preserving the peripheral limbal stem cells. Additionally, there is a significant reduction in the astigmatism, resulting in visual improvement.
Functional rehabilitation in advanced intraoral cancer
Authors: Barret Juan P. , Roodenburg Jan L.
Published: January 2017

Introduction:

Modern treatment of advanced intraoral cancer involves multidisciplinary teams with use of complicated reconstructive techniques to provide improved survival with optimal rehabilitation. Mastication is an important part of this process, and it can be severely impaired by tumor ablation. Whether flap reconstruction is a determinant factor in dental rehabilitation is still in debate.

Patients and methods:

Thirty-five patients with advanced intraoral cancer were reviewed to determine dental rehabilitation of different reconstructive techniques. The patients were treated with a multidisciplinary team approach. The patients’ demographics, primary treatment, reconstructive surgery, dental rehabilitation, and functional outcome were recorded and analyzed.

Results:

Nine patients had Stadium III disease, and 26 patients had stadium IV. Thirty-two patients (91.42%) received postoperative radiotherapy. Masticatory and dental functional rehabilitation of patients was very poor. Only 15 patients (42.86%) could eat a normal diet, whereas 18 patients (51.42%) could manage only soft diets, and 2 patients (5.72%) could only be fed with a liquid diet. Denture rehabilitation was even more frustrating and had a direct impact on masticatory rehabilitation. Only 10 patients (28.57%) could use dentures postoperatively and 40% of patients (14 patients) could not use any denture at all. Above all reconstructive techniques, the free radial forearm flap provides the best functional outcome.

Conclusions:

Reconstruction of advanced intraoral cancer results in poor denture rehabilitation, especially when bulky flaps are used. If massive resections are necessary, the free radial forearm flap reconstruction provides the best functional outcome.
Comparison of Impact of Monocular and Integrated Binocular Visual Fields on Vision-related Quality of Life
Authors: Chun Yeoun Sook , Lee Dong Ik , Kwon Jaein , Park In Ki
Published: January 2017

Purpose of the Study:

The purpose of the study was to investigate the relationship between vision-related quality of life (VRQOL) and mean deviation (MD) of the monocular visual field and integrated binocular visual field (IBVF).

Methods:

One hundred eighty VFs (90 pairs) obtained from 90 patients with normal tension glaucoma were included. VRQOL was evaluated using the 25-item National Eye Institute Visual Function Questionnaire (NEI VFQ-25). IBVF was calculated using maximal sensitivity and binocular summation and IBVF MD was calculated. Multiple linear regression analysis was used to assess the impact of IBVF deficit on VRQOL after adjusting for confounding factors. These results were compared to those of monocular visual field.

Results:

Mean subject age was 59.4 years. The average MD of maximal sensitivity was significantly higher than that of binocular summation, the better eye, and the worse eye (−3.27, −3.78, −3.96, and −8.66 dB, respectively, P<0.001). Rasch-analyzed NEI VFQ-25 subscales and composite scores were significantly correlated with IBVF deficit. The impact that IBVF had on VRQOL was similar to that of the better eye (R
2 of 0.431, 0.422, and 0.422 for MD of the better eye, binocular summation, and maximal sensitivity, respectively). In contrast, the worse eye showed the least correlation with VRQOL (0.363).

Conclusions:

The impact of IBVF on VRQOL was similar to that of the better eye irrespective of integration method. Therefore, better eye MD could be a good indicator for VRQOL.
Adverse Events Following Vestibular Schwannoma Surgery: A Comparison of Surgical Approach
Authors: Tolisano Anthony M. , Littlefield Philip D.
Published: January 2017

Objective:

Compare complications of vestibular schwannoma (VS) resection by surgical approach.

Study Design:

Retrospective cohort.

Setting:

The 2008 to 2013 American College of Surgeons-National Surgical Quality Improvement Program.

Patients:

Adult patients with VS resection by an otolaryngologist.

Interventions:

VS resection via transtemporal (TT), retrosigmoid (RS), or middle cranial fossa (MCF) approaches.

Main Outcome Measures:

Hearing preservation approaches were compared with hearing sacrificing approaches. Demographics and intraoperative factors were analyzed to identify predictors of medical and surgical complications, return to the operating room, and death. The effect of trainee presence was evaluated with respect to complications, operative length, and hospital length of stay.

Results:

One hundred eleven VS resections were identified. Patients were predominantly women (57%) and older than 50 years (69%). The TT approach accounted for 50% of the cases, while RS (36%) and MCF (14%) were less common. The risk of any postoperative complication was 17%. There were no patient deaths. There was no difference in the overall complication rate among surgical approaches, nor in the overall, surgical, or medical complication rates between hearing preservation and hearing sacrificing approaches. Trainee presence did not change operation length, hospital length of stay, or complication rates.

Conclusions:

Complication rates of VS resection are no different when comparing TT, RS, or MCF approaches. Trainee involvement did not significantly affect complications. This study is limited by the inability to evaluate procedure-specific variables (e.g., facial nerve weakness and hearing preservation rates), but offers a unique survey of global 30-day complication rates reported to a large, multi-institutional, publically available database.
Translating Market Forces Into Frontline Terms
Authors: Zwickel Karen , Koppel Jenna , Katz Marie , Virkstis Katherine , Rothenberger Sarah , Boston-Fleischhauer Carol
Published: January 2017

To transform healthcare delivery, frontline nursing staff must be committed to their work and to driving their organization’s mission forward. However, Advisory Board Survey Solutions data show that nurses are the least engaged as compared with other frontline staff. In this article, the authors identify a top opportunity for improving nurse engagement: ensuring that nurses understand how executives’ actions reflect their organization’s missions and values.
The Influence of Emerging Leadership in Nursing
Authors: Adams Jeffrey M.
Published: January 2017

This department highlights emerging nursing leaders who have demonstrated leadership in advancing innovation and patient care in practice, policy, research, education, and theory. This interview profiles Casey Shillam, PhD, RN, associate dean for baccalaureate education, University of Portland School of Nursing, Oregon.
Developing Competency to Sustain Evidence-Based Practice
Authors: Fisher Cheryl , Cusack Georgie , Cox Kim , Feigenbaum Kathryn , Wallen Gwenyth R.
Published: January 2017

Organizations must ensure that nursing care delivery is based on best evidence. This article describes how a clinical research hospital used a competency-based approach to structure the development and execution of a strategic plan and integrated evidence-based practice concepts into the activities of nurses at all levels. The article will also describe the process for developing and implementing the competency across our department including outcomes achieved.
The Center for Nursing Excellence
Authors: Clavelle Joanne T. , Goodwin Miki
Published: January 2017

An innovative Center for Nursing Excellence model that supports structural empowerment and the achievement of exemplary nursing, patient, and organizational outcomes was implemented in 2 separate health systems in the western United States. Formal leadership roles for nursing practice, research, professional education, and Magnet® continual readiness are aligned to ensure that Magnet designation is attained and maintained in system hospitals.
Mixed Gangliocytoma-Pituitary Adenoma
Authors: Lopes M. Beatriz S. , Sloan Emily , Polder Julie
Published: January 2017

Gangliocytomas originating in the sellar region are rare; most are tumors composed of gangliocytic and pituitary adenomatous elements, forming the so-called mixed gangliocytoma-pituitary adenoma. The majority of mixed gangliocytoma adenomas are associated with endocrinopathies, mainly acromegaly and less often Cushing disease and hyperprolactinemia. In the present study, 10 cases of mixed gangliocytoma and somatotroph adenomas were evaluated for patterns of cellular differentiation and expression of lineage-specific transcription factors. The tumors were characterized by immunohistochemistry for pituitary hormones, cytokeratins, Pit-1, and the neuronal markers NeuN, neurofilaments (NFP), and MAP2. Double-labeling immunohistochemistry for Pit-1/GH, Pit-1/NFP, Pit-1/MAP2, and NeuN/GH was performed in 9/10 tumors. Our data demonstrate that both adenomatous and ganglionic cells express the acidophilic lineage transcription factor Pit-1. Although mixed gangliocytomas and somatotroph adenomas show histologically distinct cellular populations, there is at least a small population of cells that coexpress the Pit-1 transcription factor and neuronal-associated cytoskeletal proteins favoring the theory of transdifferentiation of neuroendocrine cells into neuronal elements of these mixed tumors.
Genital and Extragenital Gonorrhea and Chlamydia in Children and Adolescents Evaluated for Sexual Abuse
Authors: Kellogg Nancy D. , Melville John D. , Lukefahr James L. , Nienow Shalon M. , Russell Edward L.
Published: January 2017

Objective

The aim of this study was to describe the use of a nucleic acid amplification test in detecting genital and extragenital Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) in children and adolescents assessed for sexual abuse/assault.

Methods

The charts of children aged 0 to 17 years, consecutively evaluated for sexual victimization, in emergency department and outpatient settings were reviewed. Data extracted included age, sex, type of sexual contact, anogenital findings, previous sexual contact, toxicology results, and sites tested for NG and CT.

Results

Of the 1319 patients who were tested, 579 were tested at more than 1 site, and 120 had at least 1 infected site. Chlamydia trachomatis was identified in 104 patients, and NG was found in 33. In bivariate analysis, a positive test was associated with female sex, age older than 11 years, previous sexual contact, acute or healed genital injury, drug/alcohol intoxication, and examination within 72 hours of sexual contact. Fifty-one patients had positive anal tests, and 24 had positive oral tests. More than 75% of patients with positive extragenital tests had additional positive tests or anogenital injury. Most with a positive anal (59%) or oral (77%) test did not report that the assailant's genitals came into contact with that site.

Conclusions

Positive tests for NG and CT in patients evaluated for sexual victimization may represent infection from sexual contact, contiguous spread of infection, or the presence of infected assailant secretions. Relying on patient reports of symptoms, or types of sexual contact, to determine need for testing may miss NG and CT infections in patients evaluated for sexual victimization.
Clinical Applicability of Monitoring the Time Interval Between Anesthesia and Electroconvulsive Therapy
Authors: Gálvez Verònica , Loo Colleen K.
Published: January 2017

The anesthetic–electroconvulsive therapy (ECT) time interval (time interval elapsed from the beginning of anesthesia injection to the beginning of ECT stimulus) has been reported to have an important impact on seizure quality outcomes, because it is an indirect measure of the anesthetic plasma concentration when the ECT electrical stimulus is administered. We report the importance of the routine monitoring of this time interval in clinical settings, as an additional measure to interpret seizure quality outcomes at each ECT session, to further assist on ECT dosing decisions during the treatment course.
Chirality and the angular momentum of light
Authors: Cameron Robert P. , Götte Jörg B. , Barnett Stephen M. , Yao Alison M.
Published: January 2017

Chirality is exhibited by objects that cannot be rotated into their mirror images. It is far from obvious that this has anything to do with the angular momentum of light, which owes its existence to rotational symmetries. There is nevertheless a subtle connection between chirality and the angular momentum of light. We demonstrate this connection and, in particular, its significance in the context of chiral light–matter interactions.

This article is part of the themed issue ‘Optical orbital angular momentum’.
Optical angular momentum and atoms
Authors: Franke-Arnold Sonja
Published: January 2017

Any coherent interaction of light and atoms needs to conserve energy, linear momentum and angular momentum. What happens to an atom’s angular momentum if it encounters light that carries orbital angular momentum (OAM)? This is a particularly intriguing question as the angular momentum of atoms is quantized, incorporating the intrinsic spin angular momentum of the individual electrons as well as the OAM associated with their spatial distribution. In addition, a mechanical angular momentum can arise from the rotation of the entire atom, which for very cold atoms is also quantized. Atoms therefore allow us to probe and access the quantum properties of light’s OAM, aiding our fundamental understanding of light–matter interactions, and moreover, allowing us to construct OAM-based applications, including quantum memories, frequency converters for shaped light and OAM-based sensors.

This article is part of the themed issue ‘Optical orbital angular momentum’.
Normal modes and mode transformation of pure electron vortex beams
Authors: Thirunavukkarasu G. , Mousley M. , Babiker M. , Yuan J.
Published: January 2017

Electron vortex beams constitute the first class of matter vortex beams which are currently routinely produced in the laboratory. Here, we briefly review the progress of this nascent field and put forward a natural quantum basis set which we show is suitable for the description of electron vortex beams. The normal modes are truncated Bessel beams (TBBs) defined in the aperture plane or the Fourier transform of the transverse structure of the TBBs (FT-TBBs) in the focal plane of a lens with the said aperture. As these modes are eigenfunctions of the axial orbital angular momentum operator, they can provide a complete description of the two-dimensional transverse distribution of the wave function of any electron vortex beam in such a system, in analogy with the prominent role Laguerre–Gaussian (LG) beams played in the description of optical vortex beams. The characteristics of the normal modes of TBBs and FT-TBBs are described, including the quantized orbital angular momentum (in terms of the winding number
l
) and the radial index
p
>0. We present the experimental realization of such beams using computer-generated holograms. The mode analysis can be carried out using astigmatic transformation optics, demonstrating close analogy with the astigmatic mode transformation between LG and Hermite–Gaussian beams.

This article is part of the themed issue ‘Optical orbital angular momentum’.
Recent advances in high-capacity free-space optical and radio-frequency communications using orbital angular momentum multiplexing
Authors: Willner Alan E. , Ren Yongxiong , Xie Guodong , Yan Yan , Li Long , Zhao Zhe , Wang Jian , Tur Moshe , Molisch Andreas F. , Ashrafi Solyman
Published: January 2017

There is a continuing growth in the demand for data bandwidth, and the multiplexing of multiple independent data streams has the potential to provide the needed data capacity. One technique uses the spatial domain of an electromagnetic (EM) wave, and space division multiplexing (SDM) has become increasingly important for increased transmission capacity and spectral efficiency of a communication system. A subset of SDM is mode division multiplexing (MDM), in which multiple orthogonal beams each on a different mode can be multiplexed. A potential modal basis set to achieve MDM is to use orbital angular momentum (OAM) of EM waves. In such a system, multiple OAM beams each carrying an independent data stream are multiplexed at the transmitter, propagate through a common medium and are demultiplexed at the receiver. As a result, the total capacity and spectral efficiency of the communication system can be multiplied by a factor equal to the number of transmitted OAM modes. Over the past few years, progress has been made in understanding the advantages and limitations of using multiplexed OAM beams for communication systems. In this review paper, we highlight recent advances in the use of OAM multiplexing for high-capacity free-space optical and millimetre-wave communications. We discuss different technical challenges (e.g. atmospheric turbulence and crosstalk) as well as potential techniques to mitigate such degrading effects.

This article is part of the themed issue ‘Optical orbital angular momentum’.
Helically twisted photonic crystal fibres
Authors: Russell P. St.J. , Beravat R. , Wong G. K. L.
Published: January 2017

Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with
N
cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic ‘space’, cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of ‘numerical experiments’ based on finite-element solutions of Maxwell's equations in a helicoidal frame.

This article is part of the themed issue ‘Optical orbital angular momentum’.
Optical orbital angular momentum
Authors: Barnett Stephen M. , Babiker Mohamed , Padgett Miles J.
Published: January 2017

We present a brief introduction to the orbital angular momentum of light, the subject of our theme issue and, in particular, to the developments in the 13 years following the founding paper by Allenet al.(Allenet al.1992Phys. Rev. A45, 8185 (doi:10.1103/PhysRevA.45.8185)). The papers by our invited authors serve to bring the field up to date and suggest where developments may take us next.

This article is part of the themed issue ‘Optical orbital angular momentum’.
In vitroassembly of the Rous Sarcoma Virus capsid protein into hexamer tubes under physiological conditions
Authors: Jaballah Soumeya A. , Bailey Graham D. , Desfosses Ambroise , Hyun Jaekyung , Mitra Alok K. , Kingston Richard L.
Published: January 2017

During a proteolytically-driven maturation process, the ortho-retroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assemblesin vitroat physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.
Parasite escape through trophic specialization in a species flock
Authors: Hablützel Pascal I. , Vanhove Maarten P.M. , Deschepper Pablo , Grégoir Arnout F. , Roose Anna K. , Volckaert Filip A.M. , Raeymaekers Joost A.M.
Published: January 2017

In adaptive radiations species diversify rapidly to occupy an array of ecological niches. In these different niches, species might be exposed to parasites through different routes and at different levels. If this is the case, adaptive radiations should be accompanied by a turnover in parasite communities. How the adaptive radiation of host species might be entangled with such a turnover of parasite communities is poorly documented in nature. In the present study, we examined the intestinal parasite faunas of eleven species belonging to the tribe Tropheini, one of several adaptive radiations of cichlid fishes in Lake Tanganyika. The most parsimonious ancestral foraging strategy among Tropheini is relatively unselective substrate ingestion by browsing of aufwuchs. Certain lineages however evolved more specialized foraging strategies, such as selective combing of microscopic diatoms or picking of macro-invertebrates. We found that representatives of such specialized lineages bear reduced infection with intestinal acanthocephalan helminths. Possibly, the evolution of selective foraging strategies entailed reduced ingestion of intermediate invertebrate hosts of these food-web transmitted parasites. In Tropheini, trophic specialization is therefore intertwined with divergence in parasite infection. We conclude that the study of parasite communities could improve our understanding of host evolution, ecological speciation and the origin of adaptive radiations.
Spontaneous Neural Encoding of Social Network Position
Authors: Parkinson Carolyn M. , Kleinbaum Adam M. , Wheatley Thalia
Published: January 2017

Humans form complex social networks that include numerous non-reproductive bonds with non-kin. Navigating these networks presents a considerable cognitive challenge thought to have comprised a driving force in human brain evolution. Yet, little is known about how and to what extent the human brain encodes the structure of the social networks in which it is embedded. By combining social network analysis and multi-voxel pattern analysis of functional magnetic resonance imaging (fMRI) data, we show that social network information about direct relationships, bonds between third parties, and aspects of the broader network topology is accurately perceived and automatically activated upon seeing a familiar other.
Epidemiological and ecological modelling reveal diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study
Authors: Coughtrie Abigail L. , Morris Denise E. , Anderson Rebecca , Begum Nelupha , Cleary David W. , Faust Saul N. , Jefferies Johanna M. , Kraaijeveld Alex R. , Moore Michael V. , Mullee Mark A. , Roderick Paul J. , Tuck Andrew , Whittaker Robert N. , Yuen Ho Ming , Doncaster C. Patrick , Clarke Stuart C.
Published: January 2017

Respiratory tract infections (RTI) are responsible for over 4 million deaths per year worldwide with pathobiont carriage a required precursor to infection. Through a cross-sectional community-based nasal self-swabbing study we sought to determine carriage epidemiology for respiratory pathogens amongst bacteria (Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, Staphylococcus aureus, Pseudomonas aeruginosaandNeisseria meningitidis) and viruses (RSV, Influenza viruses A and B, Rhinovirus/Enterovirus, Coronavirus, Parainfluenza viruses 1-3 and Adenovirus (ADV)). Carriage of bacterial and viral species was shown to vary with participant age, recent RTI and the presence of other species. The spatial structure of microbial respiratory communities was less nested (more disordered) in the young (0-4 years) and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals (X2= 20.42,p= 0.002), indicating spatial clumping of species consistent with facilitative relationships amongst them. Deviations from a neutral model of ecological niches were observed for samples collected in the summer and from older individuals (those aged 5-17, 18-64 and ≥65 years) but not in samples collected from winter, younger individuals (those aged 0-4 years), individuals with recent RTI and individuals without recent RTI, demonstrating the importance of both neutral and niche processes in respiratory community assembly. The application of epidemiological methods and ecological theory to sets of respiratory tract samples has yielded novel insights into the factors that drive microbial community composition, such as seasonality and age, as well as species patterns and interactions within the nose.
Using high-throughput barcode sequencing to efficiently map connectomes
Authors: Peikon Ian D , Kebschull Justus M , Vagin Vasily V , Ravens Diana I , Sun Yu-Chi , Brouzes Eric , Corrêa Ivan R , Bressan Dario , Zador Anthony
Published: January 2017

The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision—a “connectome”—is based on imaging methods that are slow, labor-intensive and expensive. Here we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence—an RNA “barcode”—which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and then joined into a form suitable for sequencing. Although at present the inefficiency in our hands of barcode joining precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost.
Visual motion computation in recurrent neural networks
Authors: Pachitariu Marius , Sahani Maneesh
Published: January 2017

Populations of neurons in primary visual cortex (V1) transform direct thalamic inputs into a cortical representation which acquires new spatio-temporal properties. One of these properties, motion selectivity, has not been strongly tied to putative neural mechanisms, and its origins remain poorly understood. Here we propose that motion selectivity is acquired through the recurrent mechanisms of a network of strongly connected neurons. We first show that a bank of V1 spatiotemporal receptive fields can be generated accurately by a network which receives only instantaneous inputs from the retina. The temporal structure of the receptive fields is generated by the long timescale dynamics associated with the high magnitude eigenvalues of the recurrent connectivity matrix. When these eigenvalues have complex parts, they generate receptive fields that are inseparable in time and space, such as those tuned to motion direction. We also show that the recurrent connectivity patterns can be learnt directly from the statistics of natural movies using a temporally-asymmetric Hebbian learning rule. Probed with drifting grating stimuli and moving bars, neurons in the model show patterns of responses analogous to those of direction-selective simple cells in primary visual cortex. These computations are enabled by a specific pattern of recurrent connections, that can be tested by combining connectome reconstructions with functional recordings.*

Author summary

Dynamic visual scenes provide our eyes with enormous quantities of visual information, particularly when the visual scene changes rapidly. Even at modest moving speeds, individual small objects quickly change their location causing single points in the scene to change their luminance equally fast. Furthermore, our own movements through the world add to the velocities of objects relative to our retinas, further increasing the speed at which visual inputs change. How can a biological system process efficiently such vast amounts of information, while keeping track of objects in the scene? Here we formulate and analyze a solution that is enabled by the temporal dynamics of networks of neurons.
Improved annotation of the insect vector of Citrus greening disease: Biocuration by a diverse genomics community
Authors: Saha Surya , Hosmani Prashant S , Villalobos-Ayala Krystal , Miller Sherry , Shippy Teresa , Flores Mirella , Rosendale Andrew , Cordola Chris , Bell Tracey , Mann Hannah , DeAvila Gabe , DeAvila Daniel , Moore Zachary , Buller Kyle , Ciolkevich Kathryn , Nandyal Samantha , Mahoney Robert , Voorhis Joshua Van , Dunlevy Megan , Farrow David , Hunter David , Morgan Taylar , Shore Kayla , Guzman Victoria , Izsak Allison , Dixon Danielle E , Cridge Andrew , Cano Liliana , Cao Xialong , Jiang Haobo , Leng Nan , Johnson Shannon , Cantarel Brandi L , Richardson Stephen , English Adam , Shatters Robert G , Childers Chris , Chen Mei-Ju , Hunter Wayne , Cilia Michelle , Mueller Lukas A , Munoz-Torres Monica , Nelson David , Poelchau Monica F , Benoit Joshua B , Wiersma-Koch Helen , D’elia Tom , Brown Susan J
Published: January 2017

The Asian citrus psyllid (Diaphorina citriKuwayama) is the insect vector of the bacteriumCandidatusLiberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of theD. citrigenome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that ofDrosophila melanogasterto newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles inD. citribiology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. All data are available onhttps://citrusgreening.org/.
Comparison of one-stage and two-stage genome-wide association studies
Authors: Xue Shang , Ogut Funda , Miller Zachary , Verma Janu , Bradbury Peter J. , Holland James B.
Published: January 2017

Linear mixed models are widely used in humans, animals, and plants to conduct genome-wide association studies (GWAS). A characteristic of experimental designs for plants is that experimental units are typically multiple-plant plots of families or lines that are replicated across environments. This structure can present computational challenges to conducting a genome scan on raw (plot-level) data. Two-stage methods have been proposed to reduce the complexity and increase the computational speed of whole-genome scans. The first stage of the analysis fits raw data to a model including environment and line effects, but no individual marker effects. The second stage involves the whole genome scan of marker tests using summary values for each line as the dependent variable. Missing data and unbalanced experimental designs can result in biased estimates of marker association effects from two-stage analyses. In this study, we developed a weighted two-stage analysis to reduce bias and improve power of GWAS while maintaining the computational efficiency of two-stage analyses. Simulation based on real marker data of a diverse panel of maize inbred lines was used to compare power and false discovery rate of the new weighted two-stage method to single-stage and other two-stage analyses and to compare different two-stage models. In the case of severely unbalanced data, only the weighted two-stage GWAS has power and false discovery rate similar to the one-stage analysis. The weighted GWAS method has been implemented in the open-source software TASSEL.
Targeted capture of complete coding regions across divergent species
Authors: Schott Ryan K , Panesar Bhawandeep , Card Daren C , Preston Matthew , Castoe Todd A , Chang Belinda SW
Published: January 2017

Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.
WinPSSP: a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest
Authors: Pagola Silvina , Polymeros Alekos , Kourkoumelis Nikolaos
Published: January 2017

The direct-space methods software Powder Structure Solution Program (PSSP) [Pagola & Stephens (2010). J. Appl. Cryst.
43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.
Experimental inhibition of a key cellular antioxidant affects vocal communication
Authors: Messina Simone , Eens Marcel , Casasole Giulia , AbdElgawad Hamada , Asard Han , Pinxten Rianne , Costantini David
Published: January 2017

There is substantial interest of evolutionary ecologists in the proximate mechanisms that modulate vocal communication. In recent times, there has been growing interest in the role of oxidative stress as a mediator of avian song expression.

Here, we tested whether the experimental inhibition of the synthesis of a key cellular antioxidant (glutathione) reduces song rate metrics of male European starlings (Sturnus vulgaris). We measured the effect of our treatment on total song rate and on its two components, undirected and nest‐box‐oriented song, outside the breeding season.

Treated males that did not own a nest‐box (subordinate males likely to be of lower quality) suffered increased oxidative stress relative to untreated males, while treated males that owned a nest‐box (dominant males likely to be of higher quality) did not. Treated non‐owners also reduced their undirected song rate, whereas treated nest‐box owners did not suffer any reduction in song rate.

Our results revealed that inhibition of a key cellular antioxidant results in decreased vocal communication in a social vertebrate, and that this effect is dependent on its social status (nest‐box owner vs. non‐owner).

This work provides support for the hypothesis that acoustic signals may honestly convey information about the individual oxidative status and capacity to regulate the oxidative balance. Our findings raise the possibility of hitherto unexplored impacts of oxidative stress on fitness traits in social species.

A lay summary is available for this article.
The tortoise and the hare: reducing resource availability shifts competitive balance between plant species
Authors: Pearson Dean E. , Ortega Yvette K. , Maron John L.
Published: January 2017

Determining how changes in abiotic conditions influence community interactions is a fundamental challenge in ecology. Meeting this challenge is increasingly imperative in the Anthropocene where climate change and exotic species introductions alter abiotic context and biotic composition to reshuffle natural systems.

We created plant assemblages consisting of monocultures or equal abundance of the native community dominant bluebunch wheatgrass (Pseudoroegneria spicata) and the exotic spotted knapweed (Centaurea stoebe), a co‐occurring invasive forb that has overtaken grasslands across the western United States. We subjected these composition treatments to drought (20% of average precipitation vs. average) and herbivory on C. stoebe by its biocontrol agent Cyphocleonus achates to explore how reduced precipitation might influence the effects of competition and biocontrol herbivory on C. stoebe's abundance.

At the end of 7 years, C. stoebe dominated mixed‐species plots under normal precipitation conditions, with biomass 50% greater than that of the native P. spicata. However, under drought stress, P. spicata's biomass was >200% greater than C. stoebe's. Interestingly, both species were impervious to drought in monoculture, indicating the importance of the drought by competition interaction. The biocontrol herbivore reduced C. stoebe abundance and indirectly increased P. spicata biomass in mixed‐species drought plots, but these effects were only marginally significant and relatively weak. Overall, C. stoebe abundance was primarily driven by the drought by competition interaction, with negatively additive but weak effects of the drought by herbivory interaction.

The response of the exotic to the treatments was driven by rapid changes in population density linked to its fast life‐history strategy, while the native's response was driven by changes in per capita plant biomass linked to its slower life‐history strategy. Individual plant performance metrics did not predict overall population responses for the invader, indicating the importance of longer term population measures.

Synthesis. These results demonstrate that reduced precipitation inputs linked to climate change can dramatically shift the balance of plant competition, even toggling the advantage from exotic to native dominance. They also illustrate the importance of biotic interactions in predicting species responses to abiotic change.
Comparison of Parent, Peer, Psychiatric, and Cannabis Use Influences Across Stages of Offspring Alcohol Involvement: Evidence from the COGA Prospective Study
Authors: Bucholz Kathleen K. , McCutcheon Vivia V. , Agrawal Arpana , Dick Danielle M. , Hesselbrock Victor M. , Kramer John R. , Kuperman Samuel , Nurnberger John I. , Salvatore Jessica E. , Schuckit Marc A. , Bierut Laura J. , Foroud Tatiana M. , Chan Grace , Hesselbrock Michie , Meyers Jacquelyn L. , Edenberg Howard J. , Porjesz Bernice
Published: January 2017

Background

All stages of development of alcohol use disorder (AUD) have not been equally studied. While initiation of drinking has been given considerable attention, other stages have not been as thoroughly investigated. It is not clear whether the same factors are associated consistently across early and late transitions in AUD involvement. High‐risk family samples that are enriched for AUD vulnerability and transitions in AUD development offer an opportunity to examine influences across multiple stages of AUD development.

Methods

Data from adolescents and young adults from high‐risk families were used to study 4 transitions in AUD development—time to first drink, first drink to first problem, first drink to first diagnosis, and first problem to first diagnosis. Cox modeling was used to compare associations of parental AUD, parental separation, peer substance use, offspring ever‐use of cannabis, trauma exposures, and internalizing and externalizing psychopathology across transitions.

Results

Hazards of most transitions were elevated for those who had ever used cannabis, those who attributed substance use to their peers, those with externalizing disorders, and those with parents with AUD. Many risk factors were linked to early initiation of alcohol, particularly cannabis use. Internalizing disorders were associated with later stages. Nonassaultive trauma was associated only with early initiation; assaultive trauma was not associated with any transition.

Conclusions

In this large, ethnically diverse sample of high‐risk youth, significant influences across transitions were fairly consistent, with externalizing disorders and cannabis ever‐use elevating the likelihood of each stage, and peer and parental (and especially maternal AUD) influences linked to initiation and some later stages. Finally, in light of the increasingly permissive legal and social stances toward cannabis in the United States, the marked elevations of all alcohol outcomes observed for cannabis use underscore the importance of studying the underpinnings of this relationship.