bluuebunny/crossref_metadata_2025 huggingface dataset:
Stretch and hold: The dynamics of a filament governed by a viscoelastic constitutive model with thixotropic yield stress behavior
Authors: Renardy Y. , Grant H. V.
Published: May 2016

The transient behavior of filament stretching is studied for a viscoelastic constitutive model that combines a partially extending strand convection model with a Newtonian solvent. The vertical filament is fixed at the bottom and the top is pulled up and held. Gravity and surface tension are also included in the model though they are not the primary mechanisms in this study. An axisymmetric circular slender jet approximation is applied. An asymptotic analysis for the initial stages of evolution is performed for large relaxation time, so that an interplay of fast and slow time scales emerges, and gives a criterion for whether the fluid yields immediately or whether slow dynamics ensues, depending on elastic stresses, gravity, and capillary stress. The analysis guides the choice of parameters to exemplify thixotropy and yield stress behavior through numerical simulations of the full governing equations from start to finish of the filament evolution. Elastic effects promote a spring back of the filament toward its initial shape, while pulling at the top stretches the filament locally to promote yielding, with the lower portion of the filament remaining unyielded. In addition, a parameter regime that models extensional experiments in the literature for yield stress fluids sheds light on the differences in filament shapes.
Mode-selective chemistry on metal surfaces: The dissociative chemisorption of CH4 on Pt(111)
Authors: Guo Han , Jackson Bret
Published: May 2016

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore CH4 dissociation on Pt(111). Computed sticking probabilities for molecules in the ground, 1v3 and 2v3, states are in very good agreement with the available experimental data, reproducing the variation in reactivity with collision energy and vibrational state. As was found in similar studies on Ni(100) and Ni(111), exciting the 1v1 symmetric stretch of CH4 is more effective at promoting the dissociative chemisorption of CH4 than exciting the 1v3 antisymmetric stretch. This behavior is explained in terms of symmetry, mode-softening, and nonadiabatic transitions between vibrationally adiabatic states. We find that the efficacies of the bending modes for promoting reaction are reasonably large, and similar to the 1v3 state. The vibrational efficacies for promoting reaction on Ni(111) are larger than for reaction on Pt(111), due to the larger nonadiabatic couplings. Our computed sticking probabilities are in good agreement with results from recent ab initio molecular dynamics and reactive force field studies.
Distributed Bragg reflectors obtained by combining Se and Te compounds: Influence on the luminescence from CdTe quantum dots
Authors: Rousset J.-G. , Kobak J. , Janik E. , Parlinska-Wojtan M. , Slupinski T. , Golnik A. , Kossacki P. , Nawrocki M. , Pacuski W.
Published: May 2016

We report on the optical properties of structures containing self assembled CdTe quantum dots (QDs) combined with Te and Se based distributed Bragg reflectors either in a half cavity geometry with a relatively broad cavity mode or in a full cavity geometry where the cavity mode is much narrower. We show that for both structures the extraction coefficient of the light emitted from the QDs ensemble is enhanced by more than one order of magnitude with respect to the QDs grown on a ZnTe buffer. However, a single QD line broadening is observed and attributed to an unintentional incorporation of Se in the vicinity of the CdTe QDs. We show that postponing the QDs growth for 24 h after the distributed Bragg reflector deposition allows recovering sharp emission lines from individual QDs. This two step growth method is proven to be efficient also for the structures with CdTe QDs containing a single Mn2+ ion.
Transmission-spectrum-controllable spoof surface plasmon polaritons using tunable metamaterial particles
Authors: Xu Jie , Zhang Hao Chi , Tang Wenxuan , Guo Jian , Qian Cheng , Li Wenyuan
Published: May 2016

We propose a method to design a transmission-spectrum-controllable spoof surface plasmon polaritons (SPPs) based on the interaction between spoof SPP waveguide and frequency tunable metamaterial (MTM) particles. To achieve the tunable MTM particles, we introduce varactor-diodes into split-ring resonators (SRRs). Taking the advantage of sub-wavelength scale of SRRs, we design and fabricate a compact transmission-spectrum-controllable spoof SPPs. Both simulated and measured results demonstrate excellent dynamic control of transmission coefficients at microwave frequencies.
Structural phase transition, Néel temperature enhancement, and persistent magneto-dielectric coupling in Cr-substituted Mn3O4
Authors: Dwivedi G. D. , Kumar Abhishek , Yang K. S. , Chen B. Y. , Liu K. W. , Chatterjee Sandip , Yang H. D. , Chou H.
Published: May 2016

Structural phase transition and Néel temperature (TN) enhancement were observed in Cr-substituted Mn3O4 spinels. Structural, magnetic, and dielectric properties of (Mn1−xCrx)3O4 (where x = 0.00, 0.10, 0.20, 0.25, 0.30, 0.40, and 0.50) were investigated. Cr-substitution induces room temperature structural phase transition from tetragonally distorted I41/amd (x = 0.00) to cubic Fd3¯m (x = 0.50). TN is found to increase from 43 K (x = 0.00) to 58 K (x = 0.50) with Cr-substitution. The spin ordering-induced dielectric anomaly near TN ensures that magneto-dielectric coupling persists in the cubic x = 0.50 system. X-ray absorption spectra reveal that Cr exists in a trivalent oxidation state and prefers the octahedral (Oh)-site, replacing Mn3+. Due to a reduction in the Jahn–Teller active Mn3+ cation and an increase in the smaller Cr3+ cation, the system begins to release the geometrical frustration by lowering its degeneracy. Consequently, a phase transition, from distorted tetragonal structure to the more symmetric cubic phase, occurs.
Laser-induced fluorescence measurements of argon and xenon ion velocities near the sheath boundary in 3 ion species plasmas
Authors: Yip Chi-Shung , Hershkowitz Noah , Severn Greg , Baalrud Scott D.
Published: May 2016

The Bohm sheath criterion is studied with laser-induced fluorescence in three ion species plasmas using two tunable diode lasers. Krypton is added to a low pressure unmagnetized DC hot filament discharge in a mixture of argon and xenon gas confined by surface multi-dipole magnetic fields. The argon and xenon ion velocity distribution functions are measured at the sheath-presheath boundary near a negatively biased boundary plate. The potential structures of the plasma sheath and presheath are measured by an emissive probe. Results are compared with previous experiments with Ar–Xe plasmas, where the two ion species were observed to reach the sheath edge at nearly the same speed. This speed was the ion sound speed of the system, which is consistent with the generalized Bohm criterion. In such two ion species plasmas, instability enhanced collisional friction was demonstrated [Hershkowitz et al., Phys. Plasmas 18(5), 057102 (2011).] to exist which accounted for the observed results. When three ion species are present, it is demonstrated under most circumstances the ions do not fall out of the plasma at their individual Bohm velocities. It is also shown that under most circumstances the ions do not fall out of the plasma at the system sound speed. These observations are also consistent with the presence of the instabilities.
The big contradiction between the perturbation theory and the chaotic state. A detailed mathematical analysis indicates when the plasma is stable or unstable
Authors: Xaplanteris C. L. , Xaplanteris S. C.
Published: May 2016

In the present manuscript enough observations and interpretations of three issues of Plasma Physics are presented. The first issue is linked to the common experimental confirmation of plasma waves which appear to be repeated in a standard way while there are also cases where plasma waves change to an unstable state or even to chaotic state. The second issue is associated with a mathematical analysis of the movement of a charged particle using the perturbation theory; which could be used as a guide for new researchers on similar issues. Finally, the suitability and applicability of the perturbation theory or the chaotic theory is presented. Although this study could be conducted on many plasma phenomena (e.g. plasma diffusion) or plasma quantities (e.g. plasma conductivity), here it was decided this study to be conducted on plasma waves and particularly on drift waves. This was because of the significance of waves on the plasmatic state and especially their negative impact on the thermonuclear fusion, but also due to the long-time experience of the plasma laboratory of Demokritos on drift waves.
Phase transitions of ε-HNIW in compound systems
Authors: Zhang Jing-yuan , Guo Xue-yong , Jiao Qing-jie , Zhang Pu
Published: May 2016

The heat-induced phase transitions of ε-HNIW, both neat and coated with various additives used in plastic bonded explosives, were investigated using powder X-ray diffraction and differential scanning calorimetry. It was found that ε-HNIW, after being held at 70°C for 60h, remained in the ε-phase. Applying other conditions, various phase transition parameters were determined, including Tc (the critical phase transition temperature), T50 (the temperature at which 50% of the phase transition is complete) and T180 (the percentage of γ-HNIW present in samples heated to 180°C). According to the above three parameters, additives were divided into three categories: those that delay phase transition, those that raise the critical temperature and the transition rate, and those that promote the phase transition. Based on the above data, a phase transition mechanism is proposed.
Salt tolerance of the halophyte Limonium delicatulum is more associated with antioxidant enzyme activities than phenolic compounds
Authors: Aymen Souid , Morena Gabriele , Vincenzo Longo , Laura Pucci , Lorenza Bellani , Abderrazak Smaoui , Chedly Abdelly , Karim Ben Hamed
Published: May 2016

In this work we studied the effect of salinity (ranging from 50 to 500 mM NaCl) on the physiological and the antioxidant responses of the local halophyte Limonium delicatulum Kuntze. We based our analysis on 12 biochemical assays that are commonly used to measure the antioxidant responses under stress such as oxidative stress markers, enzymes activities and polyphenolic compounds. Our aim was to study parameters that are strongly correlated with the growth response to salinity. Results showed two different growth responses depending on the concentration of NaCl in the medium. Under 50 to 200 mM, the growth was stimulated before it decreased significantly at 300–500 mM. L. delicatulum revealed a good aptitude to maintain photosynthetic machinery by increasing the concentrations of photosynthetic pigments, which is essential for the stabilisation of photosystems and the photosynthesis process under optimal NaCl concentration. Their breakdown at higher salinity decreased the photosynthetic performance of plants resulting in growth inhibition. Moreover, to reduce the damaging effect of oxidative stress and to tolerate the accumulation of salt ions, L. delicatulum induced the activities of their antioxidant enzymes more than their contents in polyphenolic compounds.
Other-constituency theories and firm governance: is the benefit corporation sufficient?
Authors: Jonsen Richard Harvey
Published: May 2016

Stakeholder theory creates a core conflict between managers in publicly held corporations and their boards of directors. Benefit corporation legislation recently adopted in 31 states attempts to address this conflict between shareholder primacy doctrine and stakeholder theory. While
benefit corporation statutes offer improvement over traditional corporate structure for firms operating according to instrumental stakeholder theory, they do not fully support the ends of normative stakeholder theory or alternative normative other-constituency approaches, such as recently
introduced common good models of the firm. Managers choosing to employ normative other-constituency approaches may choose to put benefit corporation regulations to use in the states where these tools are available, but they will continue to be faced with conflicts between benefit corporation
structure/governance and applying normative other-constituency approaches on a day-to-day basis in their operations.
Prediction and Uncertainty in Associative Learning: Examining Controlled and Automatic Components of Learned Attentional Biases
Authors: Luque David , Vadillo Miguel A. , Le Pelley Mike E. , Beesley Tom
Published: May 2016

It has been suggested that attention is guided by two factors that operate during associative learning: a predictiveness principle, by which attention is allocated to the best predictors of outcomes, and an uncertainty principle, by which attention is allocated to learn about the less known features of the environment. Recent studies have shown that predictiveness-driven attention can operate rapidly and in an automatic way to exploit known relationships. The corresponding characteristics of uncertainty-driven attention, on the other hand, remain unexplored. In two experiments we examined whether both predictiveness and uncertainty modulate attentional processing in an adaptation of the dot probe task. This task provides a measure of automatic orientation to cues during associative learning. The stimulus onset asynchrony of the probe display was manipulated in order to explore temporal characteristics of predictiveness- and uncertainty-driven attentional effects. Results showed that the predictive status of cues determined selective attention, with faster attentional capture to predictive than to non-predictive cues. In contrast, the level of uncertainty slowed down responses to the probe regardless of the predictive status of the cues. Both predictiveness- and uncertainty-driven attentional effects were very rapid (at 250 ms from cue onset) and were automatically activated.
Nanomechanics of phospholipid bilayer failure under strip biaxial stretching using molecular dynamics
Authors: Murphy M A , Horstemeyer M F , Gwaltney Steven R , Stone Tonya , LaPlaca Michelle , Liao Jun , Williams Lakiesha , Prabhu R
Published: May 2016

The current study presents a nanoscale in silico investigation of strain rate dependency of membrane (phospholipid bilayer) failure when placed under strip biaxial tension with two planar areas. The nanoscale simulations were conducted in the context of a multiscale modelling framework in which the macroscale damage (pore volume fraction) progression is delineated into pore nucleation (number density of pores), pore growth (size of pores), and pore coalescence (inverse of nearest neighbor distance) mechanisms. As such, the number density, area fraction, and nearest neighbor distances were quantified in association with the stress–strain behavior. Deformations of a 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer were performed using molecular dynamics to simulate mechanoporation of a neuronal cell membrane due to injury, which in turn can result in long-term detrimental effects that could ultimately lead to cell death. Structures with 72 and 144 phospholipids were subjected to strip biaxial tensile deformations at multiple strain rates. Formation of a water bridge through the phospholipid bilayer was the metric to indicate structural failure. Both the larger and smaller bilayers had similar behavior regarding pore nucleation and the strain rate effect on pore growth post water penetration. The applied strain rates, planar area, and cross-sectional area had no effect on the von Mises strains at which pores greater than 0.1 nm2 were detected (0.509  ±  7.8%) or the von Mises strain at failure (ε
failure  =  0.68  ±  4.8%). Additionally, changes in bilayer planar and cross-sectional areas did not affect the stress response. However, as the strain rate increased from 2.0  ×  108 s−1 to 1.0  ×  109 s−1, the yield stress increased from 26.5 MPa to 66.7 MPa and the yield strain increased from 0.056 to 0.226.
Learning statistical models of phenotypes using noisy labeled training data
Authors: Agarwal Vibhu , Podchiyska Tanya , Banda Juan M , Goel Veena , Leung Tiffany I , Minty Evan P , Sweeney Timothy E , Gyang Elsie , Shah Nigam H
Published: May 2016

Objective Traditionally, patient groups with a phenotype are selected through rule-based definitions whose creation and validation are time-consuming. Machine learning approaches to electronic phenotyping are limited by the paucity of labeled training datasets. We demonstrate the feasibility of utilizing semi-automatically labeled training sets to create phenotype models via machine learning, using a comprehensive representation of the patient medical record.

Methods We use a list of keywords specific to the phenotype of interest to generate noisy labeled training data. We train L1 penalized logistic regression models for a chronic and an acute disease and evaluate the performance of the models against a gold standard.

Results Our models for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.90, 0.89, and 0.86, 0.89, respectively. Local implementations of the previously validated rule-based definitions for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.96, 0.92 and 0.84, 0.87, respectively.

We have demonstrated feasibility of learning phenotype models using imperfectly labeled data for a chronic and acute phenotype. Further research in feature engineering and in specification of the keyword list can improve the performance of the models and the scalability of the approach.

Conclusions Our method provides an alternative to manual labeling for creating training sets for statistical models of phenotypes. Such an approach can accelerate research with large observational healthcare datasets and may also be used to create local phenotype models.
Restoration of Blood Flow to the Proximal Femoral Epiphysis in Unstable Slipped Capital Femoral Epiphysis by Modified Dunn Procedure: A Preliminary Angiographic and Intracranial Pressure Monitoring Study
Authors: Jackson J. Benjamin , Frick Steven L. , Brighton Brian K. , Broadwell Scott R. , Wang Eric A. , Casey Virginia F.
Published: May 2016

Background:

The major complication of unstable slipped capital femoral epiphysis (SCFE) is avascular necrosis (AVN) of the femoral head. The purpose of this study was to document by angiography the preoperative and postoperative perfusion to the proximal femoral epiphysis following an unstable SCFE. A specific aim was to determine whether blood flow could be restored. A secondary aim was to determine the efficacy of an intracranial pressure (ICP) monitor to assess blood flow within the femoral head intraoperatively.

Methods:

Nine patients with an unstable SCFE underwent superselective angiogram of the medial circumflex femoral artery preoperatively, followed by operative fixation with an open reduction using a modified Dunn approach. Femoral head blood flow was evaluated with an ICP monitor. Angiography was repeated postoperatively. Patients were followed radiographically to assess for AVN.

Results:

Follow-up averaged 22 months. Six patients did not have arterial flow to the femoral head on the preoperative angiogram. Flow was restored postoperatively on angiogram in 4 of the 6 patients. Two patients developed AVN. One had no flow to the femoral head preoperatively or postoperatively on angiogram and complete tearing of the periosteum was noted. In 1 patient, there was no ICP waveform after the initial reduction. After removing more callous and repeating reduction, the waveform returned. Of the 2 patients with AVN, 1 had an ICP waveform after reduction.

Conclusions:

This study documents that some patients with unstable SCFE present with reduced femoral head blood supply due to SCFE. It also demonstrates blood flow restoration in 4 patients by angiogram and 5 by ICP monitor after surgical treatment. No patient immediately lost blood flow due to surgery. ICP monitor is a safe intraoperative tool for real-time assessment of femoral head blood flow during open reduction of unstable SCFE. Presence of flow by ICP is not a guarantee that AVN will not develop, but absence of flow was predictive of AVN.

Level of Evidence:

Therapeutic level I—prognostic. See Instructions for Authors for a complete description of levels of evidence.
A Novel Technique of a Transcorneal Suture to Manage an Iris Tuck into the Tube of a Glaucoma Drainage Device
Authors: Kataria Pankaj , Kaushik Sushmita , Singh Simar R. , Pandav Surinder S.
Published: May 2016

Backgrounds:

Glaucoma drainage devices create an alternative pathway of aqueous drainage from the anterior chamber by channelling aqueous out of the eye through a tube to a subconjunctival bleb or the suprachoroidal space. They may be associated with a number of potential complications including tube malpositioning. This malpositioning may have serious sequelae such as corneal endothelial damage, chronic iritis, tube iris touch, cataract formation, or tube occlusion. Occlusion of the mouth of the tube by the iris impedes aqueous drainage and results in the failure of intraocular pressure (IOP) control. Tube repositioning in cases of occlusion of the mouth of the tube by the iris often involves extensive and potentially complicated surgery requiring tube removal and reinsertion.

Observation:

We describe a new minimally invasive surgical technique for correcting posterior tube malposition resulting in tube occlusion by the iris. The iris had occluded the tube of a Baerveldt prototype glaucoma drainage devices and caused an intractable increased IOP. After our tube sling suture, the tube was free, and the IOP normalized. The procedure entailed no difficult dissection or major surgical intervention. The technique is illustrated by a surgical video.

Conclusions:

This novel technique is a simple method that relieved the occlusion successfully, and avoided the need to redissect the conjunctiva or shorten the tube.
Ocular Decompression Retinopathy After Uncomplicated Cataract Surgery in a Patient With a History of Narrow-Angle Glaucoma
Authors: Dohlman Thomas H. , Chee Ru-ik , Seidman Carly , Rafla-Demetrious Leila , Gupta Mrinali P.
Published: May 2016

Purpose:

To describe a case of ocular decompression retinopathy following uncomplicated cataract surgery in a patient with phacomorphic narrow-angle glaucoma.

Methods:

Case report with wide-field fundus imaging.

Results:

A 57-year-old woman with a history of phacomorphic narrow-angle glaucoma presented 1 day after uncomplicated cataract extraction with intraocular lens insertion of the left eye with hand motion vision. She was found to have decompression retinopathy with large prefoveal subhyaloid hemorrhage. The hemorrhages gradually improved over time with observation.

Conclusions:

We report a case of decompression retinopathy after uncomplicated cataract extraction in a patient with phacomorphic narrow-angle glaucoma. This report expands upon the procedures after which decompression retinopathy has been diagnosed and suggests a need for careful perioperative management in patients with glaucoma.
Fungal Appendicitis in Immunocompromised Children. Indications and Contraindications for Laparoscopic Appendectomy: A Report on 2 Successful Cases
Authors: Carlini Veronica , Calcaterra Valeria , Decembrino Nunzia , Rubert Laura , Pasqua Noemi , Novario Mattia , Lucioni Marco , Brunero Marco , Pelizzo Gloria
Published: May 2016

In leukemic patients, appendectomy must be approached with caution because of the increased risk of complications. Fungal appendicitis is rare and only a few cases have been described in the literature, particularly in immunocompromised individuals in whom this infection can be fatal. We present 2 pediatric patients with acute myeloid leukemia, who developed appendicitis during the postchemotherapy neutropenic phase, while receiving antifungal prophylaxis. Fever was the first sign of infection. Laparoscopic appendectomy was performed without postoperative complications. The histologic examination and the culture analysis showed the presence of fungal elements; systemic fungal infection was also excluded. The risk is increased in immunocompromised children with fungal appendicitis and the signs of peritoneal irritation are not always obvious. The histopathologic demonstration of fungal elements and tissue reaction is mandatory for a definitive diagnosis. Laparoscopic appendectomy should be considered as the gold standard procedure to avoid fungal dissemination. Moreover, laparoscopic surgery and its inherent mini-invasive surgical advantages may improve the overall survival without incurring significant complications.
Juvenile Nasopharyngeal Angiofibroma
Authors: Bakshi Satvinder S. , Bhattacharjee Sumita
Published: May 2016

A 9 year old male presented with nasal obstruction and recurrent, unprovoked epistaxis for 1 week. Imaging revealed a highly vascular mass in the nasopharynx. The feeding vessels were subsequently embolized and the mass was removed completely. Juvenile nasopharyngeal angiofibroma is a benign but locally invasive tumor accounting for about 0.05% of all head and neck tumors. Patients usually present with nasal obstruction and epistaxis. The tumor can however be extensive on presentation with intra orbital and intra cranial extension. The treatment is surgical removal of the tumor and the approach depends on the size of the tumor by either endoscopic or open approach.
Safety and Role of Gastrointestinal Endoscopy in the Management of Gastrointestinal Acute GVHD in Children After Hematopoietic Stem Cell Transplantation
Authors: Gassas Adam , Krueger Joerg , Schechter Tal , Zaidman Irina , Asim Muhammad , Ali Muhammad
Published: May 2016

Gastrointestinal (GI) endoscopy and biopsy is a common procedure to confirm the diagnosis of acute graft-versus-host disease (aGVHD) in children after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Its safety and benefits in aGVHD management is unclear. We aimed to review the safety and benefits of GI endoscopy and biopsy for GI-aGVHD management. From January 2000 to December 2009, 450 Children received allo-HSCT at SickKids. Seventy-nine (17.5%) patients underwent GI endoscopy and biopsy for suspicion of GI-aGVHD. GI-aGVHD grading was I (n=5), II (n=39), III (n=23), and IV (n=12). GI biopsy confirmed aGVHD in 49 (62%) patients and results were negative in 30 (38%). Thirty-two (40%) patients started treatment based on clinical criteria before procedure. Twenty-four out of 79 patients had a change in therapy because of biopsy results. Treatment change was significantly more common in patients who had a positive biopsy results compared with those with negative results (24/49 vs. 4/30, P=0.02). Comparing patients who started therapy before the biopsy results (n=32) and the remaining patients (n=47) who were not started on therapy, the biopsy results had more impact in altering/starting therapy in these patients (24/47 vs. 0/32, P<0.00001). For the 32 patients who started therapy before the procedure, the biopsy confirmed aGVHD diagnosis in 20 of them (63%). Only 1 patient (1.25%) had duodenal hematoma and needed prolong GI rest and ultimately recovered. GI endoscopy and biopsy was safe and useful in guiding therapy for GI-aGVHD.
Examining hand dominance using dynamometric grip strength testing as evidence for overwork weakness in Charcot–Marie–Tooth disease: a systematic review and meta-analysis
Authors: Roberts-Clarke Daniel , Fornusek Che , Fiatarone Singh Maria A. , Burns Joshua , Hackett Daniel A.
Published: May 2016

This systematic review with a meta-analysis of studies was carried out to evaluate the potential of overwork weakness on the basis of grip strength of dominant and nondominant hands in individuals with Charcot–Marie–Tooth disease (CMT). Numerous electronic databases were searched from the earliest records to February 2016. Studies of any design including participants older than 18 years of age with a confirmed diagnosis of CMT that measured grip strength of both hands using dynamometric testing were eligible for inclusion. Of 12 593 articles identified following removal of duplicates, five articles fulfilled the criteria. A total of 166 participants, mostly with CMT1 or CMT2, were described from the studies included. Hand and finger pinch grip strength for the dominant compared with the nondominant hand was not statistically different. There is no definitive evidence that preferential use of the dominant hand in CMT impairs function relative to the nondominant hand. Thus, robust exercise trials of progressive resistance training are needed to understand the extent of adaptations possible and provide evidence of the safety of such regimens.
Student Engagement in Online Nursing Courses
Authors: Hampton Debra , Pearce Patricia F.
Published: May 2016

The purposes of this study were to determine the level of engagement of registered nurse (RN) to Bachelor of Science in Nursing (BSN), Master of Science in Nursing (MSN), and Doctor of Nursing Practice (DNP) nursing students enrolled in online nursing degree programs and to understand whether there are generational differences in level of student engagement. Significant differences were noted for engagement level between generations of students, but no significant difference was noted in the engagement level of students from RN to BSN, MSN, or DNP programs.
The Pseudosubarachnoid Sign
Authors: Kim Jung-Min , Eom Tae-Hoon
Published: May 2016

Several radiographic mimics of subarachnoid hemorrhage (SAH) have been reported. The pseudosubarachnoid sign may be seen in patients with marked hypoxic–ischemic injury. Our case was a 12-year-old boy with a known history of autism spectrum disorder. He was submersed in water for 20 minutes, after diving into a river, and brought to our emergency department where resuscitation was performed. He achieved a return of spontaneous circulation 45 minutes after the accident but was in a coma. Brain computed tomography showed severe brain edema and loss of sulci with increased attenuation of the basal cisterns that was compatible with SAH, but was later revealed as the pseudosubarachnoid sign. In this case, the misdiagnosis of SAH had several clinical implications for the management of the patient. This could have clinical implications if a patient with the Glasgow Coma Score greater than 3 were inappropriately treated for SAH. Furthermore, there are possible medical–legal implications regarding child abuse with SAH misdiagnosis.
search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles
Authors: Iwema Carrie L. , LaDue John , Zack Angela , Chattopadhyay Ansuman
Published: May 2016

The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any website to be integrated with articles from preprint servers. The bioPreprint search engine is publicly available athttp://www.hsls.pitt.edu/resources/preprint.
Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations
Authors: Bourgeois Yann , Hazzouri Khaled Michel , Warren Ben
Published: May 2016

1. Characterizing species history and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species.
2. The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a burst of analytical tools that can confuse users.
3. Such confusion can limit the amount of information effectively retrieved from complex genomic datasets. In addition, the lack of a unified analytical pipeline impairs the diffusion of the most recent analytical tools into fields like conservation biology.
4. To address this need, we describe possible analytical protocols and link these with more than 70 methods dealing with genome-scale datasets. We summarise the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
Refining the role ofde novoprotein truncating variants in neurodevelopmental disorders using population reference samples
Authors: Kosmicki Jack A. , Samocha Kaitlin E. , Howrigan Daniel P. , Sanders Stephan J. , Slowikowski Kamil , Lek Monkol , Karczewski Konrad J. , Cutler David J. , Devlin Bernie , Roeder Kathryn , Buxbaum Joseph D. , Neale Benjamin M. , MacArthur Daniel G. , Wall Dennis P. , Robinson Elise B. , Daly Mark J.
Published: May 2016

Recent research has uncovered an important role forde novovariation in neurodevelopmental disorders. Using aggregated data from 9246 families with autism spectrum disorder, intellectual disability, or developmental delay, we show ~1/3 ofde novovariants are independently observed as standing variation in the Exome Aggregation Consortium’s cohort of 60,706 adults, and thesede novovariants do not contribute to neurodevelopmental risk. We further use a loss-of-function (LoF)-intolerance metric, pLI, to identify a subset of LoF-intolerant genes that contain the observed signal of associatedde novoprotein truncating variants (PTVs) in neurodevelopmental disorders. LoF-intolerant genes also carry a modest excess of inherited PTVs; though the strongestde novoimpacted genes contribute little to this, suggesting the excess of inherited risk resides lower-penetrant genes. These findings illustrate the importance of population-based reference cohorts for the interpretation of candidate pathogenic variants, even for analyses of complex diseases andde novovariation.
Synaptonemal complex components are required for meiotic checkpoint function inC. elegans
Authors: Bohr Tisha , Ashley Guinevere , Eggleston Evan , Firestone Kyra , Bhalla Needhi
Published: May 2016

Synapsis involves the assembly of a proteinaceous structure, the synaptonemal complex (SC), between paired homologous chromosomes and is essential for proper meiotic chromosome segregation. InC. elegans, the synapsis checkpoint selectively removes nuclei with unsynapsed chromosomes by inducing apoptosis. This checkpoint depends on Pairing Centers (PCs),cis-acting sites that promote pairing and synapsis. We have hypothesized that the stability of homolog pairing at PCs is monitored by this checkpoint. Here, we report that SC components SYP-3, HTP-3, HIM-3 and HTP-1 are required for a functional synapsis checkpoint. Mutation of these components does not abolish PC function, demonstrating they are bonafide checkpoint components. Further, we identify mutant backgrounds in which the instability of homolog pairing at PCs does not correlate with the synapsis checkpoint response. Altogether, these data suggest that, in addition to homolog pairing, SC assembly may be monitored by the synapsis checkpoint.
Soft selective sweeps in evolutionary rescue
Authors: Wilson Benjamin A. , Pennings Pleuni S. , Petrov Dmitri A.
Published: May 2016

Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps in our model. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens.
Antibiotic Stress Selects against Cooperation in a Pathogenic Bacterium
Authors: Vasse Marie , Noble Robert , Akhmetzhanov Andrei R. , Torres-Barceló Clara , Gurney James , Benateau Simon , Gougat-Barbera Claire , Kaltz Oliver , Hochberg Michael E.
Published: May 2016

Ecological antagonisms such as predation, parasitism, competition, and abiotic environmental stress play key roles in shaping population biology, in particular by inducing stress responses and selecting for tolerant or resistant phenotypes. Little is known, however, about their impact on social traits, such as the production of public goods. Evolutionary trade-off theory predicts that adaptation to stresses should lessen investments in costly helping behaviours when cooperation does not increase resistance or tolerance, but support for this prediction is scarce. We employed theory and experiments to investigate how ecological antagonism influences social dynamics and resistance evolution in the pathogenic bacteriumPseudomonas aeruginosa. We subjected two clones of bacterium to four doses of antibiotics and assessed growth and frequencies of public goods producing and non-producing genotypes. Our results show that abiotic stress selects against public goods production. Specifically, we found that non-producers of costly iron chelating molecules (siderophores) most rapidly increased in frequency under intermediate antibiotic pressure. Moreover, the dominance of non-producers in mixed cultures was associated with higher survival and resistance to antibiotics than in either producer or non-producer monocultures. Mathematical modelling explains this counterintuitive result, and shows how these qualitative patterns are predicted to generalise to many other systems. Our results shed light on the complex interactions between social traits and ecological antagonisms, and in particular the consequences for bacterial social evolution and antibiotic resistance.
Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses
Authors: Roux Simon , Brum Jennifer R. , Dutilh Bas E. , Sunagawa Shinichi , Duhaime Melissa B. , Loy Alexander , Poulos Bonnie T. , Solonenko Natalie , Lara Elena , Poulain Julie , Pesant Stéphane , Kandels-Lewis Stefanie , Dimier Céline , Picheral Marc , Searson Sarah , Cruaud Corinne , Alberti Adriana , Duarte Carlos M. , Gasol Josep M. , Vaqué Dolors ,   Tara Oceans Coordinators, Bork Peer , Acinas Silvia G. , Wincker Patrick , Sullivan Matthew B. , Acinas Silvia G. , Bork Peer , Boss Emmanuel , Bowler Chris , Vargas Colomban de , Follows Michael , Gorsky Gabriel , Grimsley Nigel , Hingamp Pascal , Iudicone Daniele , Jaillon Olivier , Kandels-Lewis Stefanie , Karp-Boss Lee , Karsenti Eric , Krzic Uros , Not Fabrice , Ogata Hiroyuki , Pesant Stephane , Raes Jeroen , Reynaud Emmanuel G. , Sardet Christian , Sieracki Mike , Speich Sabrina , Stemmann Lars , Sullivan Matthew B. , Sunagawa Shinichi , Velayoudon Didier , Wincker Patrick
Published: May 2016

Ocean microbes drive global-scale biogeochemical cycling1, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories2–5. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ‘known’5. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during theTaraOceans andMalaspinaresearch expeditions6,7. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups8,9). This roughly triples known ocean viral populations10, doubles known candidate bacterial and archaeal virus genera9, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predictedin silicoto infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks.
Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast
Authors: Booth Gregory T. , Wang Isabel X. , Cheung Vivian G. , Lis John T.
Published: May 2016

Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.
Distinctly perturbed metabolic networks underlie differential tumor tissue damages induced by immune modulator β-glucan in a two-case ex vivo non-small-cell lung cancer study
Authors: Fan Teresa W.-M. , Warmoes Marc O. , Sun Qiushi , Song Huan , Turchan-Cholewo Jadwiga , Martin Jeremiah T. , Mahan Angela , Higashi Richard M. , Lane Andrew N.
Published: May 2016

Cancer and stromal cell metabolism is important for understanding tumor development, which highly depends on the tumor microenvironment (TME). Cell or animal models cannot recapitulate the human TME. We have developed an ex vivo paired cancerous (CA) and noncancerous (NC) human lung tissue approach to explore cancer and stromal cell metabolism in the native human TME. This approach enabled full control of experimental parameters and acquisition of individual patient's target tissue response to therapeutic agents while eliminating interferences from genetic and physiological variations. In this two-case study of non-small-cell lung cancer, we performed stable isotope-resolved metabolomic (SIRM) experiments on paired CA and NC lung tissues treated with a macrophage activator β-glucan and 13C6-glucose, followed by ion chromatography–Fourier transform mass spectrometry (IC-FTMS) and nuclear magnetic resonance (NMR) analyses of 13C-labeling patterns of metabolites. We demonstrated that CA lung tissue slices were metabolically more active than their NC counterparts, which recapitulated the metabolic reprogramming in CA lung tissues observed in vivo. We showed β-glucan-enhanced glycolysis, Krebs cycle, pentose phosphate pathway, antioxidant production, and itaconate buildup in patient UK021 with chronic obstructive pulmonary disease (COPD) and an abundance of tumor-associated macrophages (TAMs) but not in UK049 with no COPD and much less macrophage infiltration. This metabolic response of UK021 tissues was accompanied by reduced mitotic index, increased necrosis, and enhaced inducible nitric oxide synthase (iNOS) expression. We surmise that the reprogrammed networks could reflect β-glucan M1 polarization of human macrophages. This case study presents a unique opportunity for investigating metabolic responses of human macrophages to immune modulators in their native microenvironment on an individual patient basis.