bluuebunny/crossref_metadata_2025 huggingface dataset:
A Career Exploration Program: An Effective Alternative to the Traditional Use of Faculty Advisors
Authors: Olive Kenneth E. , Kwasigroch Thomas E. , Wooten Daniel J. , Lybrand Cynthia , Peeples Catherine R.
Published: May 2016

Problem

Providing medical students with resources to make effective career choices is challenging for medical schools as career options outnumber the formal clinical rotations students can experience during their undergraduate education.

Approach

In 2009, the authors introduced the Career Exploration (CE) courses into the required curriculum at the Quillen College of Medicine. This three-course sequence includes large-group sessions addressing broad issues related to career choices, small-group specialty interest groups, individual student self-assessments, assignments through which students receive individualized feedback, and individual student advising sessions. The overall objective of the course sequence is to involve all students in career planning from the beginning of medical school so as to help them make more informed career decisions.

Outcomes

The authors used improvement in student satisfaction with career planning activities as a surrogate measure for the outcome of helping students make more informed career choices. Students evaluated the CE courses positively, and overall satisfaction scores averaged 4 (1 = poor to 5 = excellent). Scores on Association of American Medical Colleges Graduation Questionnaire items related to career planning showed improved student satisfaction from 2010 to 2015.

Next Steps

Succession planning for the first- and second-year career advisor is vital—as is faculty development for all clinical advisors to ensure that they have current information regarding both the curriculum and Match process, especially as residency selection becomes increasingly competitive. Enhancing the role of fourth-year students who serve as CE III mentors has the potential to prepare these students to be better teachers as residents.
Unstable Proximal Femur Fractures Treated With Proximal Femoral Locking Plates: A Retrospective, Multicenter Study of 111 Cases
Authors: Collinge Cory A. , Hymes Robert , Archdeacon Michael , Streubel Phillip , Obremskey William , Weber Timothy , Watson J. Tracy , Lowenberg David ,   Members of the Proximal Femur Working Group of the Southeast Trauma Consortium
Published: May 2016

Objectives:

A few small case series have found that proximal femur fractures treated with a proximal femur locking plate (PFLP) have experienced more failures than expected. The purpose of this study was to review the clinical results of patients with acute, unstable proximal femur fractures treated with proximal femoral locking plates in a large, multicenter patient cohort.

Design:

This is a retrospective clinical study.

Setting:

The study included patients from 12 regional trauma centers and tertiary referral hospitals.

Patients:

One hundred eleven consecutive patients with unstable proximal femur fractures stabilized with a PFLP and having required clinical and radiographic follow-up at a minimum of 12 months after injury.

Intervention:

Surgical repair of an unstable proximal femur fracture with a PFLP.

Main outcome measurements:

Treatment failures (failure of fixation, nonunion, and malunion) and need for revision surgery.

Results:

Forty-six patients (41.4%) experienced a major treatment failure, including failed fixation with or without nonunion (39), surgical malalignment or malunion (18), deep infection (8), or a combination of these. Thirty-eight (34%) patients underwent secondary surgeries, including 30 for failed fixation, nonunion, or both. Treatment failure was found to occur at a significantly higher rate in patients with major comorbidities, in femurs repaired in varus malalignment, and using specific plate designs.

Conclusions:

Proximal femoral locking plates are associated with a high complication rate, frequently requiring revision or secondary surgeries in the treatment of unstable proximal femur fractures. Given the high complication rate with PFLPs, careful attention to reduction, use of a PFLP implant, and consideration should be given to alternative implants or fixation techniques when appropriate.

Level of Evidence:

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
A Novel Decision Aid for Surgical Patients with Ulcerative Colitis: Results of a Pilot Study
Authors: Cohan Jessica N. , Ozanne Elissa M. , Sewell Justin L. , Hofer Rebecca K. , Mahadevan Uma , Varma Madhulika G. , Finlayson Emily
Published: May 2016

BACKGROUND:

Up to 30% of patients who have ulcerative colitis are faced with the complex decision between end ileostomy and IPAA. We developed a decision aid to encourage shared decision making between patients and surgeons.

OBJECTIVE:

The aim of this study is to determine whether a decision aid is effective and acceptable for surgical patients with ulcerative colitis and their treating surgeons.

DESIGN:

This was a prospective cohort study.

SETTINGS:

Patients and surgeons were enrolled from 3 colorectal surgery clinics.

PATIENTS:

Consecutive adult patients with ulcerative colitis who were candidates for IPAA and end ileostomy were selected.

INTERVENTIONS:

Patients used a multilingual decision aid before meeting with the surgeon.

MAIN OUTCOME MEASURES:

We measured changes in knowledge, treatment preference, and stage of decision making, as well as preparation for decision making, patient satisfaction, and surgeon satisfaction after using the decision aid.

RESULTS:

Twenty-five patients were enrolled; 5 had previously undergone subtotal colectomy. After using the decision aid, patients’ knowledge scores improved by 39% (p < 0.006), 6 patients changed their treatment preference, and 8 reported increased certainty in treatment preference. The median for preparation for decision making was 75 of 100. Patient satisfaction with the decision aid (median score, 37/41) and surgeon satisfaction with the clinical encounter (median score, 38/45) were high. Patients who previously underwent subtotal colectomy had lower preparation for decision-making scores (median score, 58 vs 78 for surgery-naïve patients, p = 0.06), and did not report increased certainty in treatment preference after using the decision aid.

LIMITATIONS:

The study included a small sample with no comparison group.

CONCLUSIONS:

A novel decision aid for surgical patients with ulcerative colitis appears to be effective and acceptable in patients and surgeons from diverse clinical settings. Patients who have not yet initiated surgical treatment seem to benefit most. Future studies to validate the knowledge questionnaire and test the decision aid in a randomized fashion are warranted.
Transverse Perineal Support: A Novel Surgical Treatment for Perineal Descent in Patients With Obstructed Defecation Syndrome
Authors: Renzi Adolfo , Brillantino Antonio , Di Sarno Giandomenico , d’Aniello Francesco , Bianco Pasquale , Iacobellis Francesca , Reginelli Alfonso , Grassi Roberto
Published: May 2016

BACKGROUND:

We hypothesized that pathological perineal descent may be responsible for the failure of operations for obstructed defecation syndrome and that correcting excessive perineal descent may improve the outcome in this group of patients.

OBJECTIVE:

The purpose of this study was to report the short-term preliminary results of a novel surgical procedure, transverse perineal support, for the correction of pathological perineal descent.

DESIGN:

This was a prospective, uncontrolled, open-label study.

SETTINGS:

The study was conducted in a hospital and a university center.

PATIENTS:

Among 25 patients observed with failure of previous surgery for obstructed defecation syndrome, 12 with pathological perineal descent underwent transverse perineal support, were followed-up at 6 months, and constituted the object of analysis.

INTERVENTIONS:

The surgical procedure was performed positioning a porcine dermal implant just above the perineum superficial fascia sutured to the periosteum membrane of ischiatic tuberosities at the insertion of the superficial transverse perineal muscle.

MAIN OUTCOME MEASURES:

The main outcome measures were obstructed defecation syndrome score and x-ray and magnetic resonance defecographic imaging evaluation of perineal descent and anorectal manometric parameters.

RESULTS:

The postoperative median obstructed defecation syndrome score was 7.0 (range, 3–8), showing a statistically significant difference if compared with the preoperative score of 13.5 (range, 9–18; p = 0.0005). The mean postoperative maximum intrarectal pressure was 69.4 ± 11.1 mm Hg, significantly higher than the preoperative pressure of 45.9 ± 12.8 mm Hg (p < 0.0001). At postoperative x-ray and magnetic resonance imaging defecography, the mean fixed and dynamic perineal descents were significantly lower than the preoperative descents (p = 0.02 for fixed perineal descent and p = 0.0004 for dynamic perineal descent). Of the 4 patients (33.3%) with preoperative pathological dynamic perineal descent, only 1 showed a persistent pathological dynamic perineal descent. No early or late complication was observed.

LIMITATIONS:

The study was limited by its small size and short follow-up time.

CONCLUSIONS:

Transverse perineal support appears to be a promising, safe, and effective procedure in the treatment of obstructed defecation syndrome associated with pathological perineal descent (see Video, Supplemental Digital Content 1, http://links.lww.com/DCR/A225).
The “Studded” Rectum: Phenotypic Evidence of MYH-Associated Polyposis
Authors: Church James , Kravochuck Sara
Published: May 2016

BACKGROUND:

MYH-associated polyposis is a recessively inherited syndrome of colorectal cancer predisposition attributed to biallelic germline mutations in the base excision repair gene MYH. Clinically it overlaps with attenuated familial adenomatous polyposis, sporadic oligopolyposis, serrated polyposis, familial colorectal cancer type X, and Lynch syndrome. There is no specific phenotypic feature of MYH-associated polyposis. We have noticed that a proportion of patients with MYH-associated polyposis presenting for yearly colonoscopy surveillance have rectums that are studded with small hyperplastic polyps.

OBJECTIVE:

We report this as a possible unique phenotypic feature of the syndrome.

DESIGN:

This was a descriptive study.

SETTINGS:

The study was conducted at a department of colorectal surgery in a tertiary referral center.

PATIENTS:

Patients affected with oligopolyposis or MYH-associated polyposis presenting for endoscopic surveillance and polyp control were included.

INTERVENTIONS:

Interventions included colonoscopy or proctoscopy with excision or biopsy of mucosal lesions.

MAIN OUTCOME MEASURES:

The presence of rectal studding was measured.

RESULTS:

There were 49 patients, 16 with biallelic germline mutations of MYH; 10 of these had rectal studding. A sampling of rectal polyps was biopsied and all were hyperplastic. Five patients with biallelic MYH mutations had no studding, and 1 had not been prospectively examined. The studding was independent of the nature of the MYH mutation(s). The 33 patients other patients included 21 with serrated polyposis, 2 with a germline APC mutation, 1 with a PTEN mutation, 2 with mixed polyposis, 3 with oligoadenomatous polyposis and no germline mutation, and 4 patients with oligoadenomatous polyposis who had not been genetically tested. Only 1 of these (oligoadenomatous polyposis, not tested) had studding.

LIMITATIONS:

The study was limited by its small number of biallelic MYH mutation carriers.

CONCLUSIONS:

Rectal studding may be a sign of MYH-associated polyposis and raises questions about the biology of abnormal base excision repair.
Risk of Surgical Site Infection Varies Based on Location of Disease and Segment of Colorectal Resection for Cancer
Authors: Murray Alice Charlotte Adelaide , Pasam Ravi , Estrada David , Kiran Ravi P.
Published: May 2016

BACKGROUND:

Current quality-monitoring initiatives do not accurately evaluate surgical site infections based on type of surgical procedure.

OBJECTIVE:

This study aimed to characterize the effect of the anatomical site resected (right, left, rectal) on wound complications, including superficial, deep, and organ space surgical site infections, in patients who have cancer.

SETTINGS:

Data were retrieved from the American College of Surgeons National Surgical Quality Improvement Program database.

DESIGN:

This study was designed to determine the independent risk associated with the anatomical location of cancer resection for all subtypes of surgical site infection. Statistical methods included the Fisher exact test, the χ2 test, and univariable and multivariable analyses for each outcome of interest.

PATIENTS:

All colon and rectal resections for colorectal cancer between 2006 and 2012 were selected. Included were 45,956 patients: 17,993 (39.2%) underwent right colectomy, 11,538 (25.1%) underwent left colectomy, and 16,425 (35.7%) underwent rectal resections.

RESULTS:

The overall surgical site infection rate was 12.3%: 3.7% organ space, 1.4% deep, and 7.2% superficial. On multivariable analysis, rectal resection was associated with the greatest odds of overall surgical site infections in comparison with left- or right-sided resections (rectal OR, 1.51; 95% CI, 1.35–1.69 vs left OR, 1.09; 95% CI, 0.97–1.23 vs right OR, 1). Rectal resections were also associated with greater odds of developing a deep surgical site infection than either right (rectal OR, 1.45; 95% CI, 1.06–1.99) or left (OR, 0.89; 95% CI, 0.62–1.27). The likelihood of organ space surgical site infection followed a similar pattern (rectal OR, 1.83; 95% CI 1.49–2.25; left colon, OR, 0.95; 95% CI, 0.75–1.19). Rectal and left resections had increased odds of superficial surgical site infections compared with right resections (rectal OR, 1.31; 95% CI, 1.14–1.51; left OR, 1.19; 95% CI, 1.03–1.37).

LIMITATIONS:

This is a retrospective observational study.

CONCLUSIONS:

Rectal resections for cancer are independently associated with an increased likelihood of superficial, deep, and organ space infections. The policy on surgical site infections as a quality measure currently in place requires modification to adjust for the location of pathology and, hence, the anatomical segment resected when assessing the risk for type of surgical site infection.
Short-term Outcomes After Open and Laparoscopic Colostomy Creation
Authors: Ivatury Srinivas Joga , Bostock Rosenzweig Ian C. , Holubar Stefan D.
Published: May 2016

BACKGROUND:

Colostomy creation is a common procedure performed in colon and rectal surgery. Outcomes by technique have not been well studied.

OBJECTIVE:

This study evaluated outcomes related to open versus laparoscopic colostomy creation.

DESIGN:

This was a retrospective review of patients undergoing colostomy creation using univariate and multivariate propensity score analyses.

SETTINGS:

Hospitals participating in the American College of Surgeons National Surgical Quality Improvement Program database were included.

PATIENTS:

Data on patients were obtained from the American College of Surgeons National Surgical Quality Improvement Program 2005–2011 Participant Use Data Files.

MAIN OUTCOME MEASURES:

We measured 30-day mortality, 30-day complications, and predictors of 30-day mortality.

RESULTS:

A total of 2179 subjects were in the open group and 1132 in the laparoscopic group. The open group had increased age (open, 64 years vs laparoscopic, 60 years), admission from facility (17.0% vs 14.9%), and disseminated cancer (26.1% vs 21.4%). All were statistically significant. The open group had a significantly higher percentage of emergency operations (24.9% vs 7.9%). Operative time was statistically different (81 vs 86 minutes). Thirty-day mortality was significantly higher in the open group (8.7% vs 3.5%), as was any 30-day complication (25.4% vs 17.0%). Propensity-matching analysis on elective patients only revealed that postoperative length of stay and rate of any wound complication were statistically higher in the open group. Multivariate analysis for mortality was performed on the full, elective, and propensity-matched cohorts; age >65 years and dependent functional status were associated with an increased risk of mortality in all of the models.

LIMITATIONS:

This study has the potential for selection bias and limited generalizability.

CONCLUSIONS:

Colostomy creation at American College of Surgeons National Surgical Quality Improvement Program hospitals is more commonly performed open rather than laparoscopically. Patient age >65 years and dependent functional status are associated with an increased risk of 30-day mortality.
LOCATING AND CHARACTERIZING ANGIOID STREAKS WITH EN FACE OPTICAL COHERENCE TOMOGRAPHY
Authors: Hanhart Joel , Greifner Hillel , Rozenman Yaakov
Published: May 2016

Purpose:

To characterize angioid streaks (AS) with en face optical coherence tomography (OCT).

Methods:

Case report of a patient with myopia presenting with choroidal neovascularization secondary to AS. Swept-source en face OCT ability to image the streaks was compared with spectral-domain and swept-source B-scans as well as color and red-free pictures. A 48-year-old man with myopia presented with sudden central visual loss. Choroidal neovascularization secondary to AS was diagnosed and intraocular anti–vascular endothelial growth factor given with clinical and OCT features improvement.

Results:

Angioid streaks were visualized as less dark than the overlying retinal and the underlying choroidal vasculature. En face OCT located the changes at the level of Bruch membrane. An AS was found to be interrupted by the choroidal neovascularization, what was not captured by other modalities.

Conclusion:

En face OCT allows to assess the extent of changes in Bruch membrane and their spatial relationship to choroidal neovascularization.
Virtual Fitting, Selection, and Cutting of Preformed Anatomic Orbital Implants
Authors: Mahoney Nicholas R. , Peng Michelle Y. , Merbs Shannath L. , Grant Michael P.
Published: May 2016

Purpose:

To evaluate the usage of preoperative digital anatomic implant evaluation in internal orbital fractures.

Methods:

An IRB-approved review of cases of orbital fracture repair was conducted and cases where digital implant modeling was performed were selected for comprehensive review. The surgical time of these cases was also compared with surgeon and implant matched controls.

Results:

A total of 25 patients and 26 orbits underwent preoperative virtual fitting and were reviewed. There were no complications or revision surgeries needed. Postoperative assessment demonstrated accuracy to the preoperative target with an average maximum deviation of 1.9 mm.

Conclusions:

Preoperative digital fracture assessment, implant manufacturer and size selection, and virtual cutting guide creation provides additional tools for orbital surgeons to achieve anatomic restoration without significant differences in operating time.
Periorbital Autologous Fat Grafting in Facial Nerve Palsy
Authors: Siah We Fong , Litwin Andre S. , Nduka Charles , Malhotra Raman
Published: May 2016

Purpose:

To report outcomes and complications of periorbital autologous fat grafting (AFG) in improving volume loss-related symmetry and function in facial nerve palsy patients and to assess patient satisfaction.

Methods:

A retrospective, noncomparative review of all facial nerve palsy patients who underwent periorbital AFG at single center over a 4-year period. Two independent graders objectively assessed standard photographs for any change in volume loss and symmetry: pre- and postoperative periods (early, 0–2 months; intermediate, 3–9 months; and late, >10 months). Any adverse outcomes were recorded. Patient satisfaction was assessed by questionnaire survey.

Results:

A total of 18 facial nerve palsy patients (13 females) underwent periorbital AFG between February 2011 and 2015. Mean age was 51.9 ± 15.3 years (range, 26–76). Mean follow up was 6.8 ± 4.6 (range, 0.5–15) months. Photographs of 14 patients were eligible for evaluation. Tear trough visibility (p < 0.01), infraorbital rim visibility (p = 0.03), and lower eyelid-cheek junction symmetry (p < 0.01) improved in the early postoperative period with persistence of improvement in the latter parameter at intermediate postoperative period (p < 0.01). Lagophthalmos significantly improved (p = 0.03) in the early postoperative period. Two patients developed cheek cellulitis and 4 had persistent malar edema (3 had existing edema). Questionnaire survey showed a reduction in daytime ocular lubricants and an improvement in nocturnal-lagophthalmos symptoms.

Conclusion:

Periorbital AFG is a useful adjunct in improving symmetry and lagophthalmos in facial nerve palsy patients where volume loss is a contributory factor but effects were not long lasting. Patient satisfaction is high. Those with preexisting malar bags are at higher risk of developing persistent malar edema following periorbital AFG.
Does Simulation Improve Recognition and Management of Pediatric Septic Shock, and If One Simulation Is Good, Is More Simulation Better?*
Authors: Dugan Mark C. , McCracken Courtney E. , Hebbar Kiran B.
Published: May 2016

Objectives:

Determine whether serial simulation training sessions improve resident recognition and initial septic shock management in a critically ill simulated septic shock patient, and to determine whether serial simulations further improve resident task performance when compared with a single simulation session.

Design:

Prospective observational cohort study with a live expert review of trainee simulation performance. Expert reviewers blinded to prior trainee performance.

Setting:

A PICU room in a quaternary-care children’s hospital, featuring a hi-fidelity pediatric patient simulator.

Subjects:

Postgraduate year-2 and postgraduate year-3 pediatric residents who rotate through the PICU.

Interventions:

Postgraduate year-3 residents as the control cohort, completing one simulation near the start of their third residency year. Postgraduate year-2 residents as the intervention cohort, completing two simulations during their second residency year and one near the start of their third residency year.

Measurements and Main Results:

Resident objective performance was measured using a validated 27-item checklist (graded 0/1) related to monitoring, data gathering, and interventions in the diagnosis and management of pediatric septic shock. The intervention cohort had a higher mean performance percentage score during their third simulation than the control cohort completing their single simulation (87% vs 77%; p < 0.001). Septic shock was correctly diagnosed more often in the intervention cohort at the time of their third simulation (100% vs 78%; p < 0.001). Appropriate broad-spectrum antibiotics were administered correctly more often in the intervention cohort (83% vs 50%; p < 0.001).

Conclusions:

Simulations significantly improved resident performance scores in the management of septic shock with repetitive simulation showing significant ongoing improvements. Further studies are needed to determine long-term impact on knowledge and skill retention and whether results attained in a simulation environment are translatable into clinical practice in improving bedside care.
Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses
Authors: Guillerme Thomas , Cooper Natalie
Published: May 2016

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.
Apoptosis in snowflake yeast: novel trait, or side effect of toxic waste?
Authors: Pentz Jennifer T. , Taylor Bradford P. , Ratcliff William C.
Published: May 2016

Recent experiments evolving
de novo
multicellularity in yeast have found that large cluster-forming genotypes also exhibit higher rates of programmed cell death (apoptosis). This was previously interpreted as the evolution of a simple form of cellular division of labour: apoptosis results in the scission of cell–cell connections, allowing snowflake yeast to produce proportionally smaller, faster-growing propagules. Through spatial simulations, Duran-Nebreda and Solé (
J. R. Soc. Interface
12, 20140982 (
doi:10.1073/pnas.1115323109
)) develop the novel null hypothesis that apoptosis is not an adaptation,
per se
, but is instead caused by the accumulation of toxic metabolites in large clusters. Here we test this hypothesis by synthetically creating unicellular derivatives of snowflake yeast through functional complementation with the ancestral
ACE2
allele. We find that multicellular snowflake yeast with elevated apoptosis exhibit a similar rate of apoptosis when cultured as single cells. We also show that larger snowflake yeast clusters tend to contain a greater fraction of older, senescent cells, which may explain why larger clusters of a given genotype are more apoptotic. Our results show that apoptosis is not caused by side effects of spatial structure, such as starvation or waste product accumulation, and are consistent with the hypothesis that elevated apoptosis is a trait that co-evolves with large cluster size.
Ex vivo
mammalian prions are formed of paired double helical prion protein fibrils
Authors: Terry Cassandra , Wenborn Adam , Gros Nathalie , Sells Jessica , Joiner Susan , Hosszu Laszlo L. P. , Tattum M. Howard , Panico Silvia , Clare Daniel K. , Collinge John , Saibil Helen R. , Wadsworth Jonathan D. F.
Published: May 2016

Mammalian prions are hypothesized to be fibrillar or amyloid forms of prion protein (PrP), but structures observed to date have not been definitively correlated with infectivity and the three-dimensional structure of infectious prions has remained obscure. Recently, we developed novel methods to obtain exceptionally pure preparations of prions from mouse brain and showed that pathogenic PrP in these high-titre preparations is assembled into rod-like assemblies. Here, we have used precise cell culture-based prion infectivity assays to define the physical relationship between the PrP rods and prion infectivity and have used electron tomography to define their architecture. We show that infectious PrP rods isolated from multiple prion strains have a common hierarchical assembly comprising twisted pairs of short fibres with repeating substructure. The architecture of the PrP rods provides a new structural basis for understanding prion infectivity and can explain the inability to systematically generate high-titre synthetic prions from recombinant PrP.
Vibrations of an elastic cylindrical shell near the lowest cut-off frequency
Authors: Kaplunov J. , Manevitch L. I. , Smirnov V. V.
Published: May 2016

A new asymptotic approximation of the dynamic equations in the two-dimensional classical theory of thin-elastic shells is established for a circular cylindrical shell. It governs long wave vibrations in the vicinity of the lowest cut-off frequency. At a fixed circumferential wavenumber, the latter corresponds to the eigenfrequency of in-plane vibrations of a thin almost inextensible ring. It is stressed that the well-known semi-membrane theory of cylindrical shells is not suitable for tackling a near-cut-off behaviour. The dispersion relation within the framework of the developed formulation coincides with the asymptotic expansion of the dispersion relation originating from full two-dimensional shell equations. Asymptotic analysis also enables refining the geometric hypotheses underlying various ad hoc set-ups, including the assumption on vanishing of shear and circumferential mid-surface deformations used in the semi-membrane theory. The obtained results may be of interest for dynamic modelling of elongated cylindrical thin-walled structures, such as carbon nanotubes.
Topology optimization for three-dimensional electromagnetic waves using an edge element-based finite-element method
Authors: Deng Yongbo , Korvink Jan G.
Published: May 2016

This paper develops a topology optimization procedure for three-dimensional electromagnetic waves with an edge element-based finite-element method. In contrast to the two-dimensional case, three-dimensional electromagnetic waves must include an additional divergence-free condition for the field variables. The edge element-based finite-element method is used to both discretize the wave equations and enforce the divergence-free condition. For wave propagation described in terms of the magnetic field in the widely used class of non-magnetic materials, the divergence-free condition is imposed on the magnetic field. This naturally leads to a nodal topology optimization method. When wave propagation is described using the electric field, the divergence-free condition must be imposed on the electric displacement. In this case, the material in the design domain is assumed to be piecewise homogeneous to impose the divergence-free condition on the electric field. This results in an element-wise topology optimization algorithm. The topology optimization problems are regularized using a Helmholtz filter and a threshold projection method and are analysed using a continuous adjoint method. In order to ensure the applicability of the filter in the element-wise topology optimization version, a regularization method is presented to project the nodal into an element-wise physical density variable.
Homogenized boundary conditions and resonance effects in Faraday cages
Authors: Hewett D. P. , Hewitt I. J.
Published: May 2016

We present a mathematical study of two-dimensional electrostatic and electromagnetic shielding by a cage of conducting wires (the so-called ‘Faraday cage effect’). Taking the limit as the number of wires in the cage tends to infinity, we use the asymptotic method of multiple scales to derive continuum models for the shielding, involving homogenized boundary conditions on an effective cage boundary. We show how the resulting models depend on key cage parameters such as the size and shape of the wires, and, in the electromagnetic case, on the frequency and polarization of the incident field. In the electromagnetic case, there are resonance effects, whereby at frequencies close to the natural frequencies of the equivalent solid shell, the presence of the cage actually amplifies the incident field, rather than shielding it. By appropriately modifying the continuum model, we calculate the modified resonant frequencies, and their associated peak amplitudes. We discuss applications to radiation containment in microwave ovens and acoustic scattering by perforated shells.
Encoding Gaussian curvature in glassy and elastomeric liquid crystal solids
Authors: Mostajeran Cyrus , Warner Mark , Ware Taylor H. , White Timothy J.
Published: May 2016

We describe shape transitions of thin, solid nematic sheets with smooth, preprogrammed, in-plane director fields patterned across the surface causing spatially inhomogeneous local deformations. A metric description of the local deformations is used to study the intrinsic geometry of the resulting surfaces upon exposure to stimuli such as light and heat. We highlight specific patterns that encode constant Gaussian curvature of prescribed sign and magnitude. We present the first experimental results for such programmed solids, and they qualitatively support theory for both positive and negative Gaussian curvature morphing from flat sheets on stimulation by light or heat. We review logarithmic spiral patterns that generate cone/anti-cone surfaces, and introduce spiral director fields that encode non-localized positive and negative Gaussian curvature on punctured discs, including spherical caps and spherical spindles. Conditions are derived where these cap-like, photomechanically responsive regions can be anchored in inert substrates by designing solutions that ensure compatibility with the geometric constraints imposed by the surrounding media. This integration of such materials is a precondition for their exploitation in new devices. Finally, we consider the radial extension of such director fields to larger sheets using nematic textures defined on annular domains.
The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing
Authors: Bocak L. , Kundrata R. , Fernández C. Andújar , Vogler A. P.
Published: May 2016

The ongoing exploration of biodiversity and the implementation of new molecular tools continue to unveil hitherto unknown lineages. Here, we report the discovery of three species of neotenic beetles for which we propose the new family Iberobaeniidae. Complete mitochondrial genomes and rRNA genes recovered Iberobaeniidae as a deep branch in Elateroidea, as sister to Lycidae (net-winged beetles). Two species of the new genus
Iberobaenia
,
Iberobaenia minuta
sp. nov. and
Iberobaenia lencinai
sp. nov. were found in the adult stage. In a separate incidence, a related sequence was identified in bulk samples of soil invertebrates subjected to shotgun sequencing and mitogenome assembly, which was traced to a larval voucher specimen of a third species of
Iberobaenia
.
Iberobaenia
shows characters shared with other elateroid neotenic lineages, including soft-bodiedness, the hypognathous head, reduced mouthparts with reduced labial palpomeres, and extremely small-bodied males without strengthening structures due to miniaturization. Molecular dating shows that Iberobaeniidae represents an ancient relict lineage originating in the Lower Jurassic, which possibly indicates a long history of neoteny, usually considered to be evolutionarily short-lived. The apparent endemism of Iberobaeniidae in the Mediterranean region highlights the importance of this biodiversity hotspot and the need for further species exploration even in the well-studied European continent.
Organic membranes determine the pattern of the columnar prismatic layer of mollusc shells
Authors: Checa Antonio G. , Macías-Sánchez Elena , Harper Elizabeth M. , Cartwright Julyan H. E.
Published: May 2016

The degree to which biological control is exercised compared to physical control of the organization of biogenic materials is a central theme in biomineralization. We show that the outlines of biogenic calcite domains with organic membranes are always of simple geometries, while without they are much more complex. Moreover, the mineral prisms enclosed within the organic membranes are frequently polycrystalline. In the prismatic layer of the mollusc shell, organic membranes display a dynamics in accordance with the von Neumann–Mullins and Lewis Laws for two-dimensional foam, emulsion and grain growth. Taken together with the facts that we found instances in which the crystals do not obey such laws, and that the same organic membrane pattern can be found even without the mineral infilling, our work indicates that it is the membranes, not the mineral prisms, that control the pattern, and the mineral enclosed within the organic membranes passively adjusts to the dynamics dictated by the latter.
Differences in male coloration are predicted by divergent sexual selection between populations of a cichlid fish
Authors: Selz O. M. , Thommen R. , Pierotti M. E. R. , Anaya-Rojas J. M. , Seehausen O.
Published: May 2016

Female mating preferences can influence both intraspecific sexual selection and interspecific reproductive isolation, and have therefore been proposed to play a central role in speciation. Here, we investigate experimentally in the African cichlid fish
Pundamilia nyererei
if differences in male coloration between three para-allopatric populations (i.e. island populations with gene flow) of
P. nyererei
are predicted by differences in sexual selection by female mate choice between populations
.
Second, we investigate if female mating preferences are based on the same components of male coloration and go in the same direction when females choose among males of their own population, their own and other conspecific populations and a closely related para-allopatric sister-species,
P. igneopinnis
. Mate-choice experiments revealed that females of the three populations mated species-assortatively, that populations varied in their extent of population-assortative mating and that females chose among males of their own population based on different male colours. Females of different populations exerted directional intrapopulation sexual selection on different male colours, and these differences corresponded in two of the populations to the observed differences in male coloration between the populations. Our results suggest that differences in male coloration between populations of
P. nyererei
can be explained by divergent sexual selection and that population-assortative mating may directly result from intrapopulation sexual selection.
The Australian saltwater crocodile (Crocodylus porosus) provides evidence that the capacitation of spermatozoa may extend beyond the mammalian lineage
Authors: Nixon Brett , Anderson Amanda L. , Smith Nathan D. , McLeod Robby , Johnston Stephen D.
Published: May 2016

Although mammalian spermatozoa only acquire functional maturity as they are conveyed through the male (epididymal maturation) and female (capacitation) reproductive tracts, the degree of post-testicular development necessary to achieve fertilization in other vertebrate species remains far less clear. Indeed, despite reports that the epididymis of birds and reptiles is capable of secreting proteins that bind and modify the sperm surface characteristics, it remains unclear whether capacitation is a pre-requisite for fertilization in these species. Using the ancient reptilian Australian saltwater crocodile as a model, this study was undertaken to explore whether reptile sperm do undergo capacitation-like changes following ejaculation. Our studies revealed that crocodile spermatozoa experienced a rapid and sustained, cyclic-AMP mediated increase in progressive motility following incubation under conditions optimized for the induction of capacitation in mammalian species such as the mouse and human. This response was coupled with elevated levels of phosphorylation associated with both protein kinase A and tyrosine kinase substrates, the latter of which were predominantly localized within the sperm flagellum. In findings that also accord with mammalian spermatozoa, we confirmed a homologue of outer dense fibre 2 as one of the principal substrates for tyrosine phosphorylation. Overall, our findings support the concept that crocodile spermatozoa do undergo a process that is homologous to capacitation in preparation for fertilization of an ovum.
Generating an Executable Model of the Drosophila Central Complex
Authors: Givon Lev E. , Lazar Aurel A.
Published: May 2016

The central complex (CX) is a set of neuropils in the center of the fly brain that have been implicated as playing an important role in vision-mediated behavior and integration of spatial information for locomotor control. In contrast to currently available data regarding the neural circuitry of neuropils in the fly's vision and olfactory systems, comparable data for the CX neuropils is relatively incomplete; many categories of neurons remain only partly characterized, and the synaptic connectivity between CX neurons has yet to be experimentally determined. Successful modeling of the information processing functions of the CX neuropils therefore requires a means of easily constructing and testing a range of hypotheses regarding both the high-level structure of their neural circuitry and the properties of their constituent neurons and synapses. This document demonstrates how NeuroArch and Neurokernel may be used to algorithmically construct and evaluate executable neural circuit models of the CX neuropils and their interconnects based upon currently available information regarding the geometry and polarity of the arborizations of identified local and projection neurons in the CX.
Mutational signatures associated with tobacco smoking in human cancer
Authors: Alexandrov Ludmil B. , Ju Young Seok , Haase Kerstin , Van Loo Peter , Martincorena Iñigo , Nik-Zainal Serena , Totoki Yasushi , Fujimoto Akihiro , Nakagawa Hidewaki , Shibata Tatsuhiro , Campbell Peter J. , Vineis Paolo , Phillips David H. , Stratton Michael R.
Published: May 2016

Tobacco smoking increases the risk of at least 15 classes of cancer. We analyzed somatic mutations and DNA methylation in 5,243 cancers of types for which tobacco smoking confers an elevated risk. Smoking is associated with increased mutation burdens of multiple distinct mutational signatures, which contribute to different extents in different cancers. One of these signatures, mainly found in cancers derived from tissues directly exposed to tobacco smoke, is attributable to misreplication of DNA damage caused by tobacco carcinogens. Others likely reflect indirect activation of DNA editing by APOBEC cytidine deaminases and of an endogenous clock-like mutational process. The results are consistent with the proposition that smoking increases cancer risk by increasing the somatic mutation load, although direct evidence for this mechanism is lacking in some smoking-related cancer types.

ONE SENTENCE SUMMARY

Multiple distinct mutational processes associate with tobacco smoking in cancer reflecting direct and indirect effects of tobacco smoke.
Elevated nonlinearity as indicator of transition to overexploitation in fish stocks
Authors: Dakos Vasilis , Glaser Sarah M. , Hsieh Chih-hao , Sugihara George
Published: May 2016

Ecosystems may experience abrupt changes such as species extinctions, reorganisations of trophic structure, or transitions from stable population dynamics to strongly irregular fluctuations. Although most of these changes have important ecological and at times economic implications, they remain notoriously difficult to detect in advance. Here, we use a Ricker-type model to simulate the transition of a hypothetical stable fisheries population either to irregular boom-bust dynamics or to overexploitation. Our aim is to infer the risk of extinction in these two scenarios by comparing changes in variance, autocorrelation, and nonlinearity between unexploited and exploited populations. We find that changes in these statistical metrics reflect the risk of extinction but depend on the type of dynamical transition. Variance and nonlinearity increase similarly in magnitude along both transitions. In contrast, autocorrelation depends strongly on the presence of underlying oscillating dynamics. We also compare our theoretical expectations to indicators measured in long-term datasets of fish stocks from the California Cooperative Oceanic Fisheries Investigation in the Eastern Pacific and from the Northeast Shelf in the Western Atlantic. Our results suggest that elevated variance and nonlinearity could be potentially used to rank exploited fish populations according to their risk of extinction.
Evolutionary dynamics of abundant stop codon readthrough inAnophelesandDrosophila
Authors: Jungreis Irwin , Chan Clara S , Waterhouse Robert M , Fields Gabriel , Lin Michael F , Kellis Manolis
Published: May 2016

Translational stop codon readthrough was virtually unknown in eukaryotic genomes until recent developments in comparative genomics and new experimental techniques revealed evidence of readthrough in hundreds of fly genes and several human, worm, and yeast genes. Here, we use the genomes of 21 species ofAnophelesmosquitoes and improved comparative techniques to identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector,Anopheles gambiae, and 51 additionalDrosophila melanogasterstop codons, with several cases of double and triple readthrough including readthrough of two adjacent stop codons, supporting our earlier prediction of abundant readthrough in pancrustacea genomes. Comparisons betweenAnophelesandDrosophilaallow us to transcend the static picture provided by single-clade analysis to explore the evolutionary dynamics of abundant readthrough. We find that most differences between the readthrough repertoires of the two species are due to readthrough gain or loss in existing genes, rather than to birth of new genes or to gene death; that RNA structures are sometimes gained or lost while readthrough persists; and that readthrough is more likely to be lost at TAA and TAG stop codons. We also determine which characteristic properties of readthrough predate readthrough and which are clade-specific. We estimate that there are more than 600 functional readthrough stop codons inA. gambiaeand 900 inD. melanogaster. We find evidence that readthrough is used to regulate peroxisomal targeting in two genes. Finally, we use the sequenced centipede genome to refine the phylogenetic extent of abundant readthrough.
Capturing Evolutionary Signatures in Transcriptomes with myTAI
Authors: Drost Hajk-Georg , Gabel Alexander , Domazet-Lošo Tomislav , Quint Marcel , Grosse Ivo
Published: May 2016

Combining transcriptome data of biological processes or response to stimuli with evolutionary information such as the phylogenetic conservation of genes or their sequence divergence rates enables the investigation of evolutionary constraints on these processes or responses. Suchphylotranscriptomicanalyses recently unraveled that mid-developmental transcriptomes of fly, fish, and cress were dominated by evolutionarily conserved genes and genes under negative selection and thus recapitulated the developmental hourglass on the transcriptomic level. Here, we present a protocol for performing phylotranscriptomic analyses on any biological process of interest. When applying this protocol, users are capable of detecting different evolutionary constraints acting on different stages of the biological process of interest in any species. For each step of the protocol, modular and easy-to-use open-source software tools are provided, which enable a broad range of scientists to apply phylotranscriptomic analyses to a wide spectrum of biological questions.