bluuebunny/crossref_metadata_2025 huggingface dataset:
Counter-ion solution modeling in salt-free polyelectrolytes depicts clustering mystery
Authors: Wolverton Mark
Published: December 2017

Polymer chains modeled in a counter-ion solvation lead to polyelectrolyte clustering that is observed in solution, but has so far been mysterious in origin.
The flesh and the bones of cohesive devices: towards a comprehensive model
Authors: Abu-Ayyash Emad A. S. , McKenny John
Published: December 2017

Building on a 1976 model of cohesive devices, this article probes the literature on these linguistic tools with the aim of generating a comprehensive model of cohesion that can be used as an instrument for textual analysis across different text types. This article addresses two main questions: (1) what are the linguistic tools that can be incorporated into the 1976-model of cohesive devices in the creation of an operational model? and (2) what would such a comprehensive model of cohesive devices look like? The contributions of various scholars are examined to determine which elements might be considered as cohesive devices, apart from those introduced in the 1976 model. For almost all the categories within the lexico-grammar taxonomy presented in 1976, more elements are found that can play various cohesive roles in texts and that can be integrated into the 1976 model to form a more all-embracing one. To further illustrate this claim, examples from English and Arabic are used to present a new model of analysis applicable to various languages.
Differences in Molecular Characteristics of Segment 8 in Rice black-streaked dwarf virus and Southern rice black-streaked dwarf virus
Authors: Zhou Yu , Zhang Xiaoming , Wang Dandan , Weng Jianfeng , Di Hong , Zhang Lin , Dong Ling , Zhang Hong , Zu Hongyue , Li Xinhai , Wang Zhenhua
Published: December 2017

Rice black-streaked dwarf virus (RBSDV) and Southern rice black-streaked dwarf virus (SRBSDV) cause maize rough dwarf disease (MRDD) and rice black-streaked dwarf disease (RBSDD) in China. RBSDV segment 8 (S8) contains the only deletion mutation in the genomes of these viruses, which are both members of the genus Fijivirus. To illuminate the molecular differences between the RBSDV and SRBSDV genomes and better understand the evolution of these viruses, and to determine which virus is specifically associated with MRDD and RBSDD in each region, S8 was analyzed in 66 virus isolates collected from 10 geographic locations in China and 14 S8 sequences obtained from the National Center for Biotechnology Information GenBank. Phylogenetic analysis showed that the pathogen associated with MRDD and RBSDD in the Yellow and Huai River valleys was RBSDV, whereas the pathogen associated with these diseases in Sanya was SRBSDV. Codon usage bias in S8 differed significantly between RBSDV and SRBSDV, as indicated by effective number of codons used by a gene (Nc) and GC values, Nc plots, and variation explained by the first axis in correspondence analysis. The nucleotide identities among these 66 RBSDV and SRBSDV isolates ranged from 66.2 to 68.2%, and were considerably lower than the nucleotide identities within RBSDV (from 94.1 to 99.9%) or SRBSDV (from 93.9 to 100%) isolates. Most S8 polymorphisms were identified in the region from 1,000 to 1,200 bp in RBSDV and in the region from 500 to 700 bp in SRBSDV. The difference in the lengths of RBSDV (1,936 bp) and SRBSDV (1,928 bp) was due to an 8-bp deletion in the 3′-untranslated region of SRBSDV. Six recombination events were detected in S8 in RBSDV and two recombination events were detected in S8 in SRBSDV. Recombination breakpoints were found within the region containing the deletion mutation in nine isolates. However, no recombination events were detected between RBSDV and SRBSDV. Both of these viruses were under negative and purifying selection, although the ratio of nonsynonymous mutations to synonymous mutations (Ka/Ks) for RBSDV S8 (0.0530) was not significantly lower than that of SRBSDV S8 (0.0823, P = 0.1550). We found that SRBSDV was more highly genetically differentiated (product of effective population size and the migration rate among populations < 1; values for the among-populations component of genetic variation or normalized variation > 0.33; and P values of the sequence statistic, the rank statistic, and the nearest-neighbor statistic < 0.01) than RBSDV. However, gene flow between RBSDV and SRBSDV was not frequent.
Cutaneous Hypersensitivity-Like Reactions Associated With Breast Implants: A Review
Authors: Labadie Jessica G. , Korta Dorota Z. , Barton Natalie , Mesinkovska Natasha A.
Published: December 2017

BACKGROUND

Breast implantation is an increasingly common procedure for both cosmesis and reconstruction. Risk of cutaneous reactions to breast implants is low and typically described in postsurgical settings. Adverse skin hypersensitivity-like reactions to implants have also been reported but are not well described.

OBJECTIVE

To review the scientific literature on cutaneous hypersensitivity-like reactions to breast implants.

METHODS

A systematic literature review was conducted using PubMed. Articles pertaining to breast implants and cutaneous hypersensitivity-like reactions in humans were included.

RESULTS

In total, 10 studies on hypersensitivity-like reactions from breast implants were included in the review. Potential allergenic compounds in breast implants include silicone, polyurethane texturing, and acellular dermal matrix. Perivascular lymphocytic infiltrate was a common finding on histopathology. Patch testing and preoperative silicone cube implantation were used to determine sensitivity. Attempted treatments included topical and oral corticosteroids, montelukast and antibiotics. Most cases required implant removal for resolution of symptoms.

CONCLUSION

Cutaneous hypersensitivity-like reactions to breast implants seem to be rare complications, sometimes necessitating implant removal. Future studies are needed to establish their incidence and etiology, and the diagnostic role of patch testing and preoperative screening.
Cardiovascular and metabolic morbidity after hysterectomy with ovarian conservation: a cohort study
Authors: Laughlin-Tommaso Shannon K. , Khan Zaraq , Weaver Amy L. , Smith Carin Y. , Rocca Walter A. , Stewart Elizabeth A.
Published: December 2017

Objective:

The aim of the study was to determine the long-term risk of cardiovascular disease and metabolic conditions in women undergoing hysterectomy with bilateral ovarian conservation compared with age-matched referent women.

Methods:

Using the Rochester Epidemiology Project records-linkage system, we identified 2,094 women who underwent hysterectomy with ovarian conservation for benign indications between 1980 and 2002 in Olmsted County, Minnesota. Each woman was age-matched (±1 y) to a referent woman residing in the same county who had not undergone prior hysterectomy or any oophorectomy. These two cohorts were followed historically to identify de novo cardiovascular or metabolic diagnoses. We estimated hazard ratios (HRs) and 95% CIs using Cox proportional hazards models adjusted for 20 preexisting chronic conditions and other potential confounders. We also calculated absolute risk increases and reductions from Kaplan–Meier estimates.

Results:

Over a median follow-up of 21.9 years, women who underwent hysterectomy experienced increased risks of de novo hyperlipidemia (HR 1.14; 95% CI, 1.05-1.25), hypertension (HR 1.13; 95% CI, 1.03-1.25), obesity (HR 1.18; 95% CI, 1.04-1.35), cardiac arrhythmias (HR 1.17; 95% CI, 1.05-1.32), and coronary artery disease (HR 1.33; 95% CI, 1.12-1.58). Women who underwent hysterectomy at age ≤35 years had a 4.6-fold increased risk of congestive heart failure and a 2.5-fold increased risk of coronary artery disease.

Conclusions:

Even with ovarian conservation, hysterectomy is associated with an increased long-term risk of cardiovascular and metabolic conditions, especially in women who undergo hysterectomy at age ≤35 years. If these associations are causal, alternatives to hysterectomy should be considered to treat benign gynecologic conditions.
A Modified Bilhaut–Cloquet Procedure for Zigzag Thumb Polydactyly Types III and IV
Authors: Al-Qattan Mohammad M. , Kattan Abdullah E. , Al-Lazzam Abdulmohsen , Gelidan Adnan G.
Published: December 2017

Background:

A review of the English literature over the least 43 years revealed only a total of 53 cases of Wassel types III, IV, and VII treated by the Bilhaut–Cloquet (B–C) procedure. Furthermore, the detailed results and range of motion were only given in 2 series (a total of 9 cases).

Methods:

Four cases of Wassel types III and IV thumb duplications with zigzag deformity were treated with a modified B–C procedure. The main modification was minimal central resections at the joints aiming for joint preservation to improve the postoperative range of motion of the new thumb.

Results:

The results showed an excellent overall functional score (Tada score of 5 of 5 in all cases). The mean range of motion at the metacarpophalangeal joint was excellent (60°), but the mean at the interphalangeal joint was only 20°. Cosmetically, all thumbs were “too wide” and a panel of 3 hand surgeons scored the cosmetic result (0–10 scoring system) between 5.7 and 6.7. No secondary procedures were done, and all parents were “very satisfied” despite the wide thumbs and split nails. This was attributed to the presence of an ugly preoperative zigzag appearance, and hence the comparative postoperative appearance was satisfactory.

Conclusion:

The modified B–C procedure gives a satisfactory function, but the cosmetic outcome is suboptimal.
No Vertical Scar Breast Weight Transfer
Authors: Horndeski Gary M. , Gonzalez Elisa
Published: December 2017

Women desire beautiful breasts that are functional, pain free, and without foreign material. Vertical scars, insufficient elevation, inadequate upper pole fullness, nipple numbness, and loss of breast feeding are undesirable. Relieving pain attributed to enlarged breasts has required significant tissue removal. Software analysis of chest images, physical measurements, and desires are combined to generate a surgical blueprint. The breast is divided horizontally into two components preserving the neurovascular supply and major lactiferous ducts. The skin flap cephalad to the areola provides external coverage. The areola remains attached to a deepithelialized mound, which is rotated into a cone. Dermal straps originating from the base of the cone are looped through the pectoralis major muscle and the cone repeatedly. Weight transfer to the pectoralis major muscles eliminates pain in 54% and decreases pain in 38%. Incisions are concealed at the areola cutaneous junction and in the shadow of the breast. Upper pole fullness increased in 86% without implants or fat transfer. Nipple sensation was increased in 37% and unchanged in 44%. Overall results were excellent in 50% and good in 36%. Complications consisted of dog-ears, periareolar infection, and fat necrosis. No patient required a return to the operation room. Combing computer-aided design with plastic surgical principles creates beautiful, functional breasts without foreign material. Vertical scars are avoided, and weight transfer relieves pain.
Orthognathic Relevant Scales of FACE-Q: Translation and Validation for Hong Kong Chinese Patients
Authors: Tan Su Keng , Leung Wai Keung , Tang Alexander Tin Hong , Tse Edward Chi Man , Zwahlen Roger Arthur
Published: December 2017

Background:

A validated questionnaire is needed to study a more holistic outcome assessment including postsurgical aesthetic satisfaction and psychosocial changes in orthognathic patients. The aim of this study was to determine the reliability and validity of 9 orthognathically relevant translated FACE-Q scales among Hong Kong Chinese orthognathic patients.

Methods:

Two hundred fifty adult Cantonese-speaking patients of 18 years or older who underwent orthognathic treatment were recruited in the Prince Philip Dental Hospital of Hong Kong. Nine of an overall of 40 independent FACE-Q scales were selected and translated into Hong Kong Chinese. The reliability, validity, and test–retest reliability were examined using Cronbach’s alpha, paired t test and Pearson’s correlation coefficients.

Results:

The Hong Kong Chinese version of the 9 FACE-Q scales was obtained by forward-backward translation. One hundred eight male (mean age, 25.57 ± 4.49) and 142 female (mean age, 24.61 ± 4.54) patients were recruited for the reliability and validation process. The internal consistency (0.89–0.97) and the test–retest reliability (0.73–0.90) were found to be high. The validity of the translated questionnaires was comparable with that of the original FACE-Q.

Conclusion:

The results presented here prove that the 9 translated FACE-Q scales are reliable and valid instruments for research and clinical purposes in Hong Kong Chinese orthognathic patients.
Prepectoral Implant-Based Breast Reconstruction and Postmastectomy Radiotherapy: Short-Term Outcomes
Authors: Sigalove Steven , Maxwell G. Patrick , Sigalove Noemi M. , Storm-Dickerson Toni L. , Pope Nicole , Rice Jami , Gabriel Allen
Published: December 2017

Background:

Prosthetic breast reconstruction in the setting of radiotherapy is associated with poor outcomes. Until recently, prosthetic breast reconstruction was predominantly performed by placing the prosthesis in a subpectoral space. Placement of the prosthesis in a prepectoral space is currently emerging as a simpler, alternative approach to subpectoral placement. The impact of postmastectomy radiotherapy (PMRT) on prepectoral reconstruction has not yet been specifically assessed. This study compared the outcomes of patients who underwent immediate, direct-to-implant, or 2-staged, prepectoral breast reconstruction followed by PMRT with those from patients who did not receive PMRT.

Methods:

Patients with well-perfused skin flaps and without contraindications, including uncontrolled diabetes-mellitus, previous irradiation, and current tobacco use, were offered the prepectoral approach. Following implant or expander placement, patients underwent planned or unplanned radiotherapy. Complications after each stage of reconstruction were recorded.

Results:

Thirty-three patients underwent 52 breast reconstructions via the prepectoral approach. Sixty-five percentage of the breasts were irradiated, including 21% after expander and 44% after implant placement. Patients were followed for a mean of 25.1 ± 6.4 months. Complication rate in irradiated breasts was 5.9% (1 incidence of seroma and 1 incidence of wound dehiscence followed by expander removal) and 0% in nonirradiated breasts. Capsular contracture rate was 0% in both irradiated and nonirradiated breasts.

Conclusions:

Immediate implant-based prepectoral breast reconstruction followed by PMRT appears to be well tolerated, with no excess risk of adverse outcomes, at least in the short term. Longer follow-up is needed to better understand the risk of PMRT in prepectorally reconstructed breasts.
Effectiveness of a Clinical Reasoning Course on Willingness to Think Critically and Skills of Self-Reflection
Authors: Huhn Karen
Published: December 2017

Background and Purpose.

One may possess the skills of good critical thinking but may be unwilling to use them in certain situations, and conversely one may have the habits of the mind of good critical thinking but may fail to possess the requisite skills to use them effectively. Students entering a Doctor of Physical Therapy (DPT) program are most likely already quite good at conceptualizing, analyzing, and synthesizing information. However, during a curriculum review, the faculty of a DPT program agreed that students failed to exhibit sufficient higher-order thinking required for clinical reasoning, one of the primary intended outcomes of the curriculum. The faculty members hypothesized that making the skills and attributes of clinical reasoning more explicit early in the program would help set the stage for improving students' clinical reasoning skills throughout the rest of the DPT curriculum.

Case Description.

A course entitled “Critical Reasoning” was created as an introduction to the habits of the mind and traits required for good critical thinking and reflective skills. The intentions of the course were to provide a framework for the development of clinical reasoning skills and to make these skills, attributes, and habits of good clinical thinking explicit. The purpose of this study was to explore the effectiveness of this Critical Reasoning course on increasing students' awareness of and willingness to think and reflect critically.

Outcomes.

There was a statistically significant increase from pre- to post-intervention in students' willingness to think critically as measured by the California Critical Thinking Disposition Inventory. The Self Reflection and Insight Scale also indicated improvement in students' insight into their thinking and their reflective skills.

Discussion and Conclusion.

It would seem that, given the statistically significant improvement in both outcome measures, the course may have had a positive effect on improving students' willingness and ability to think about their thinking. Making the habits of the mind and the skills of critical reflection explicit early in a curriculum can lead to improvements in students' willingness to think and reflect critically. However, the course's effect on students' overall clinical reasoning skills cannot be assumed without further investigation.
Student Physical Therapists Achieve Similar Patient Outcomes as Licensed Physical Therapists: A Retrospective Comparison of Outcomes of Patients With Low Back Pain
Authors: Rindflesch Aaron B. , Calley Darren Q. , Dobson Benjamin J. , Steele Tess G. , Yonkovich Sarah E. , Hollman John H.
Published: December 2017

Introduction.

Third-party payer reimbursement for outpatient physical therapy services is typically fee for service. For many payers, services delivered by supervised student physical therapists (SPTs) that meet legal and regulatory guidelines are reimbursed equivalently to services delivered by licensed physical therapists (PTs). Few studies have compared patient outcomes for physical therapy services provided by SPTs with those provided by licensed PTs. Therefore, we compared outcomes of patients with low back pain (LBP) treated primarily by supervised SPTs with those of patients treated primarily by PTs. We hypothesized that each patient group would have similar outcomes.

Methods.

From 2012 through 2015, 128 patients treated for LBP were selected for review by convenience sampling: 67 primarily by a PT and 61 primarily by a supervised SPT. We conducted a retrospective cohort study using electronic health records at an outpatient orthopedic clinic in the Midwest. A mixed-model analysis of covariance was used to analyze differences in outcomes between patients treated by SPTs and PTs (α = .05).

Results.

For both groups, outcomes measured using the Patient-Specific Functional Scale improved from the initial to final session during the episode of care (P < .001). No significant difference existed in the initial and final Patient-Specific Functional Scale scores between groups (P = .74).

Discussion and Conclusion.

For outpatients with LBP, the plan of care designed and delivered by supervised SPTs was as effective as that of licensed PTs. This study shows that use of properly supervised SPTs does not decrease the effectiveness of outpatient physical therapy services for patients with LBP. Additional research is needed in other clinical settings.
Looking Outside Health Care to Teach Innovation in Physical Therapy Business Practice: Use of Harvard Business School Cases at Emory University
Authors: Kapasi Zoher F. , Davis Beth P.
Published: December 2017

Background and Purpose.

With profound changes in health care and the need for innovation to deliver exceptional value to patients receiving physical therapy, it is incumbent that students are prepared to look outside health care to adopt business practices from other industries and foster innovation as they begin to practice physical therapy. The purpose of this paper is to describe how the case-based analysis of Harvard Business School (HBS) cases from a variety of industries was implemented to teach business disciplines and promote innovative thinking in Doctor of Physical Therapy students at Emory University.

Method/Model Description and Evaluation.

The process for developing the course including course content and objectives, pedagogical, methods, student assessment including course evaluation and alumni survey at Emory University is described in this study. In addition, quantitative and qualitative analysis of students' course evaluation outcomes has been described in this paper.

Outcomes.

A total of 57 students participated in the elective course over the past 4 academic years. Class participation, written assignments, and quantitative analysis of course evaluations indicate that students agree the course objectives were met. Qualitative analysis of anonymous student comments revealed core themes of innovative course format and innovative learning, showing that the course instilled an innovation mindset in our students. Finally, 94% of course alumni survey respondents agreed that the course created an entrepreneurial and innovative mindset that impacted their practice of physical therapy.

Discussion and Conclusion.

We successfully introduced a course in a physical therapist education program to include training in innovation using HBS cases. To deliver exceptional value to patients receiving physical therapy, we must innovate. Thus, preparation of physical therapist practitioners who can innovate is critical to achieve our vision of optimizing movement to improve human experience and thereby transform society.
Predicting Academic and Licensure Examination Success Among Physical Therapist Assistant Students
Authors: Kabiri Laura S. , Voight Michele , Gleeson Peggy B. , Mitchell Katy
Published: December 2017

Introduction.

Identifying and admitting students most likely to succeed is key to physical therapist assistant (PTA) student and program success. However, there is currently no information available regarding admission criteria outcomes among PTA students. The purpose of this research was to examine quantitative PTA program admission criteria and their ability to predict student academic and National Physical Therapy Examination (NPTE) success.

Methods.

All CAPTE-accredited PTA programs were asked to return data for each student admitted to the program since 2009 including those who graduated, were dismissed, or left the program. Data on 2809 PTA students from 31 programs in 24 states were used for this research. Predictor variables included prerequisite course grades, overall prerequisite GPA, and standardized test scores. Outcome variables included dichotomized academic success (academic difficulty/no academic difficulty) based on research by Utzman et al and ultimate NPTE status (pass/fail). Binary logistic regression with multiple models was used for data analysis.

Results.

A&P I grade (academic: odds ratio = 1.44, P = .0005; NPTE: odds ratio = 1.72, P = .007), overall prerequisite GPA (academic: odds ratio = 2.02, P = .0005; NPTE: odds ratio = 2.14, P = .0005), and TEAS total score (academic: odds ratio = 1.05, P = .0005; NPTE: odds ratio = 1.06, P = .006) were the only significant predictors of both academic and NPTE success. For both outcomes, A&P I, GPA, and TEAS remained the significant predictors regardless of the program type (public/private/for-profit), students' sex, and students' ethnicity.

Discussion and Conclusion.

When establishing the PTA program admission criteria, A&P I grade, overall prerequisite GPA, and TEAS total score offer predictive values for both academic and NPTE success regardless of the program type, students' sex, and students' ethnicity. These scores should be important contributors to admission decisions for PTA education.
The Differential Effects of Insurance Mandates on Health Care Spending for Children’s Autism Spectrum Disorder
Authors: Candon Molly K. , Barry Colleen L. , Epstein Andrew J. , Marcus Steven C. , Kennedy-Hendricks Alene , Xie Ming , Mandell David S.
Published: December 2017

Objectives:

There is substantial variation in treatment intensity among children with autism spectrum disorder (ASD). This study asks whether policies that target health care utilization for ASD affect children differentially based on this variation. Specifically, we examine the impact of state-level insurance mandates that require commercial insurers to cover certain treatments for ASD for any fully-insured plan.

Methods:

Using insurance claims between 2008 and 2012 from three national insurers, we used a difference-in-differences approach to compare children with ASD who were subject to mandates to children with ASD who were not. To allow for differential effects, we estimated quantile regressions that evaluate the impact of mandates across the spending distributions of three outcomes: (1) monthly spending on ASD-specific outpatient services; (2) monthly spending on ASD-specific inpatient services; and (3) quarterly spending on psychotropic medications.

Results:

The change in spending on ASD-specific outpatient services attributable to mandates varied based on the child’s level of spending. For those children with ASD who were subject to the mandate, monthly spending for a child in the 95th percentile of the ASD-specific outpatient spending distribution increased by $1460 (P<0.001). In contrast, the effect was only $2 per month for a child in the fifth percentile (P<0.001). Mandates did not significantly affect spending on ASD-specific inpatient services or psychotropic medications.

Conclusions:

State-level insurance mandates have larger effects for those children with higher levels of spending. To the extent that spending approximates treatment intensity and the underlying severity of ASD, these results suggest that mandates target children with greater service needs.
Preceptorship in a Nurse Practitioner Program
Authors: McQueen Karen A. , Poole Karen , Raynak Andrea , McQueen Ainsley
Published: December 2017

Preceptorship has been identified as an effective strategy for facilitating clinical learning among diverse health care professionals. The benefits of preceptored experiences are well documented; however, the preceptorship model is also vulnerable to challenges. There has been limited evaluation of preceptorship with nurse practitioner (NP) students. This article describes an evaluation of the preceptorship experience from the perspective of NP students. In particular, the facilitators and barriers to clinical learning are described.
Broad Spectrum Proteomics Analysis of the Inferior Colliculus following Acute Hydrogen Sulfide Exposure
Authors: Kim Dong-Suk , Anantharam Poojya , Hoffmann Andrea , Meade Mitchell L. , Grobe Nadja , Gearhart Jeffery M. , Whitley Elizabeth M. , Mahama Belinda , Rumbeiha Wilson K.
Published: December 2017

Acute exposure to high concentrations of H2S causes severe brain injury and long-term neurological disorders. The mechanisms of H2S-induced neurodegeneration are not known. To better understand the cellular and molecular mechanisms of H2S-induced neurodegeneration we used a broad-spectrum proteomic analysis approach to search for key molecules in H2S-induced neurotoxicity. Mice were subjected to acute whole body exposure of up to750 ppm of H2S. The H2S-treated group showed behavioral motor deficits and developed severe lesions in the inferior colliculus (IC), part of the brainstem. The IC was microdissected for proteomic analysis. Tandem mass tags (TMT) liquid chromatography mass spectrometry (LC-MS/MS)-based quantitative proteomics was applied for protein identification and quantitation. LC-MS/MS was able to identify 598, 562, and 546 altered proteomic changes for day 1 (2 h post H2S exposure), day 2, and day 4 of H2S exposure, respectively. Mass spectrometry data were analyzed by Perseus 1.5.5.3 statistical analysis, and gene ontology heat map clustering. Quantitative real-time PCR was used to confirm some of the H2S-dependent proteomics changes. Taken together, acute exposure to H2S induced behavioral motor deficits along with progressive neurodegeneration including disruption of several biological processes in the IC such as cellular morphology, energy metabolism, and calcium signaling. The obtained broad-spectrum proteomics data may provide important clues to elucidate mechanisms of H2S-induced neurotoxicity.

Highlights

Mice exposed to H2S recapitulated H2S-induced neurotoxicity manifested in humans.

The IC in the mouse brain is the most sensitive to H2S-induced neurodegeneration.

Proteomic expressions of key proteins were validated at transcription level.

Several biological pathways were dysregulated by H2S exposure.
High-Order Organization of Guanine-Based Reflectors Underlies the Dual Functionality of the Fish Iris
Authors: Gur Dvir , Nicolas Jan-David , Brumfeld Vlad , Bar-Elli Omri , Oron Dan , Levkowitz Gil
Published: December 2017

Many marine organisms have evolved a reflective iris to prevent unfocused light from reaching the retina. The fish iris has a dual function, both to camouflage the eye and serving as a light barrier. Yet, the mechanism that enables this dual functionality and the benefits of using a reflective iris have remained unclear. Using synchrotron micro-focused diffraction, cryo-SEM imaging and optical analyses on zebrafish at different stages of development, we show that the complex optical response of the iris is facilitated by the development a high-order organization of multilayered guanine-based crystal reflectors and pigments. We further demonstrate how the efficient light reflector is established during development to allow the optical functionality of the eye, already at early developmental stages. These results shed light on the evolutionary drive for developing a compact reflective iris, which is widely used by many animal species.

Significance Statement

The fish iris is an exquisite example of nature’s remarkable engineering where specialized cells, dubbed iridophores, produce an efficient light reflector made of guanine-based crystals. This unique structure of the fish iris serves a dual function: In addition to its role as a light barrier, the iris has a second role of camouflaging the eye by creating a silvery reflectance, which merges with the fish skin. The underlying mechanism that enables the aforementioned dual functionality of the fish iris as well as the structural morphogenesis of the guanine reflector during embryonic development, remained unclear. We show that complex optical response of the iris is facilitated by the establishment of a high-order organization of multilayered guanine-based crystal reflectors and pigments.
A measure of vascular reactivity to overcome neurovascular uncoupling in functional imaging of brain tumors: initial results
Authors: Voss Henning U. , Peck Kyung K. , Brennan Nicole M. Petrovich , Holodny Andrei I.
Published: December 2017

Purpose

Preoperative functional MRI (fMRI) is limited by a muted BOLD response caused by abnormal vasoreactivity and resultant neurovascular uncoupling adjacent to malignant brain tumors. We propose to overcome this limitation and more accurately identify eloquent areas adjacent to brain tumors by independently assessing vasoreactivity using breath-holding and incorporating these data into the BOLD analysis.

Methods

Local vasoreactivity using a breath-holding paradigm with the same timing as the functional motor and language tasks was determined in 16 patients (9 glioblastomas, 1 anaplastic astrocytoma, 5 low grade astrocytomas, and 1 metastasis). We derived a model based on coherence for analyzing BOLD fMRI that takes into account the altered hemodynamics adjacent to brain tumors.

Results

Activation maps computed using the coherence model were overall similar to standard activation maps. However, the coherence maps demonstrated clinically meaningful areas of activation that were not seen using the standard method in 12/16 cases. This included localization of language areas adjacent to brain tumors, where the coherence method results were confirmed by intra-operative direct cortical stimulation. Enhanced task response maps based on vasoreactivity mapping demonstrated more robust, anatomically-correct activation, in particular adjacent to tumors as compared to maps obtained without vasoreactivity information.

Conclusions

The present preliminary results demonstrate the principle that the neurovascular uncoupling known to affect the accuracy of BOLD fMRI adjacent to brain tumors may be, at least partially, overcome by incorporating an independent measurement of vasoreactivity into the BOLD analysis.
Muon Radiation Dose and Marine Megafaunal Extinction at the end-Pliocene Supernova
Authors: Melott Adrian L. , Marinho Franciole , Paulucci Laura
Published: December 2017

Considerable data and analysis support the detection of a supernova at a distance of about 50 pc, ~2.6 million years ago. This is possibly related to the extinction event around that time and is a member of a series of explosions which formed the Local Bubble in the interstellar medium. We build on the assumptions made in previous work, and propagate the muon flux from supernova-initiated cosmic rays from the surface to the depths of the ocean. We find that the radiation dose from the muons will exceed the total present surface dose from all sources at depths up to a kilometer and will persist for at least the lifetime of marine megafauna. It is reasonable to hypothesize that this increase in radiation load may have contributed to a newly documented marine megafaunal extinction at that time.
Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases
Authors: Welch David , Buonanno Manuela , Grilj Veljko , Shuryak Igor , Crickmore Connor , Bigelow Alan W. , Randers-Pehrson Gerhard , Johnson Gary W. , Brenner David J.
Published: December 2017

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207–222 nm) efficiently kills bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently kills airborne aerosolized viruses, a very low dose of 2 mJ/cm2of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.
Mendelian inheritance errors in whole genome sequenced trios are enriched in repeats and cluster within copy number losses
Authors: Kothiyal Prachi , Wong Wendy S. , Bodian Dale L. , Niederhuber John E.
Published: December 2017

Trio-based whole genome sequencing (WGS) data can contribute significantly towards the development of quality control methods that can be applied to non-family WGS. Mendelian inheritance errors (MIEs) in parent-offspring trios are commonly attributed to erroneous sequencing calls, as the rate of true de novo mutations is extremely low compared to the incidence of MIEs. Here, we analyzed WGS data from 1,314 trios across diverse human populations with the goal of studying the characteristics of MIEs. We applied filters based on genotype call quality and observed that filtering has a greater impact on frequent MIEs. Our results indicate that MIEs are enriched in repeats and MIE density correlates with short interspersed nuclear elements (SINEs) density. We also observed clustered MIEs in regions overlapping large deletions. We created population-specific MIE profiles and discovered regions that represent different MIE distributions across populations. Finally, we have provided population-specific MIE tracks that can be loaded in UCSC Genome Browser. These profiles can be used for flagging calls in proximity of clustered MIEs before allele frequency and admixture calculations, annotating candidate de novo mutations, discovering population-specific putative deletions, and for distinguishing between regions that have errors due to sequence quality vs. chromosomal anomalies.
Tissue disorder strength measured by quantitative phase imaging as intrinsic cancer marker
Authors: Takabayashi Masanori , Majeed Hassaan , Kajdacsy-Balla Andre , Popescu Gabriel
Published: December 2017

Tissue refractive index provides important information about morphology at the nanoscale. Since the malignant transformation involves both intra- and inter-cellular changes in the refractive index map, the tissue disorder measurement can be used to extract important diagnosis information. Quantitative phase imaging (QPI) provides a practical means of extracting this information as it maps the optical path-length difference (OPD) across a tissue sample with sub-wavelength sensitivity. In this work, we employ QPI to compare the tissue disorder strength between benign and malignant breast tissue histology samples. Our results show that disease progression is marked by a significant increase in the disorder strength. Since our imaging system can be added as an upgrading module to an existing microscope, we anticipate that it can be integrated easily in the pathology work flow.
De novo profile generation based on sequence context specificity with the long short-term memory network
Authors: Yamada Kazunori D , Kinoshita Kengo
Published: December 2017

Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Amino acid sequence profiles are widely used for bioinformatics studies, such as sequence similarity searches, multiple alignments, and evolutionary analyses. Currently, many biological sequences are becoming available, and the rapidly increasing amount of sequence data emphasizes the importance of scalable generators of amino acid sequence profiles. We employed the LSTM network and developed a novel profile generator to construct profiles without any assumptions, except for input sequence context. Our method could generate better profiles than existing de novo profile generators, including CSBuild and RPS-BLAST, on the basis of profile-sequence similarity search performance with linear calculation costs against input sequence size. In addition, we analyzed the effects of the memory power of LSTM and found that LSTM had high potential power to detect long-range interactions between amino acids, as in the case of beta-strand formation, which has been a difficult problem in protein bioinformatics using sequence information. We demonstrated the importance of sequence context and the feasibility of LSTM on biological sequence analyses. Our results demonstrated the effectiveness of memories in LSTM and showed that our de novo profile generator, SPBuild, achieved higher performance than that of existing methods for profile prediction of beta-strands, where long-range interactions of amino acids are important and are known to be difficult for the existing window-based prediction methods. Our findings will be useful for the development of other prediction methods related to biological sequences by machine learning methods.
B1a B cells require autophagy for metabolic homeostasis and self-renewal
Authors: Clarke Alexander J , Riffelmacher Thomas , Braas Daniel , Cornall Richard J , Simon Anna Katharina
Published: December 2017

Specific metabolic programs are activated by immune cells to fulfil their functional roles, which include adaptations to their microenvironment. B1 B cells are tissue-resident, innate-like B cells. They have many distinct properties, such as the capacity to self-renew and the ability to rapidly respond to a limited repertoire of epitopes. The metabolic pathways that support these functions are unknown. We show that B1 B cells are bioenergetically more active than B2 B cells, with higher rates of glycolysis and oxidative phosphorylation, and depend on glycolysis. They acquire exogenous fatty acids, and store lipids in droplet form. Autophagy is differentially activated in B1a B cells, and deletion of the autophagy gene Atg7 leads to a selective loss of B1a B cells due to a failure of self-renewal. Autophagy-deficient B1a B cells downregulate critical metabolic genes and accumulate dysfunctional mitochondria. B1 B cells therefore, have evolved a distinct metabolism adapted to their residence and specific functional properties.
Examining molecular determinants underlying heterogeneity of synaptic release probability using optical quantal imaging
Authors: Akbergenova Yulia , Zhang Yao V. , Weiss-Sharabi Shirley , Cunningham Karen L. , Littleton J. Troy
Published: December 2017

Neurons communicate through neurotransmitter release at specialized synaptic regions known as active zones (AZs). Using transgenic biosensors to image postsynaptic glutamate receptor activation following single vesicle fusion events at Drosophila neuromuscular junctions, we analyzed release probability (Pr) maps for a defined connection with ~300 AZs between synaptic partners. Although Pr was very heterogeneous, it represented a stable and unique feature of each AZ. Pr heterogeneity was not abolished in mutants lacking Synaptotagmin 1, suggesting the AZ itself is likely to harbor a key determinant(s). Indeed, AZ Pr was strongly correlated with presynaptic Ca2+ channel density and Ca2+ influx at single release sites. In addition, Pr variability was reflected in the postsynaptic compartment, as high Pr AZs displayed a distinct pattern of glutamate receptor clustering. Developmental analysis suggests that high Pr sites emerge from earlier formed AZs, with a temporal maturation in transmission strength occurring over several days.
Task Engagement Enhances Population Encoding of Stimulus Meaning in Primary Auditory Cortex
Authors: Bagur Sophie , Averseng Martin , Elgueda Diego , David Stephen , Fritz Jonathan , Yin Pingbo , Shamma Shihab , Boubenec Yves , Ostojic Srdjan
Published: December 2017

The main functions of primary sensory cortical areas are classically considered to be the extraction and representation of stimulus features. In contrast, higher cortical sensory association areas are thought to be responsible for combining these sensory representations with internal motivations and learnt associations. These regions generate appropriate neural responses that are maintained until a motor command is executed. Within this framework, responses of the primary sensory areas during task performance are expected to carry less information about the behavioral meaning of the stimulus than higher sensory, association, motor and frontal cortices. Here we demonstrate instead that the neuronal population responses in the early primary auditory cortex (A1) display many aspects of responses generally associated with higher-level areas. A1 activity was recorded in awake ferrets while they were either passively listening or actively discriminating two periodic click trains of different rates in a Go/No-Go paradigm. By applying population-level dimensionality reduction techniques, we found that task-engagement induced a shift in the nature of the encoding from a sensory-driven representation of the two stimuli to a behaviorally relevant representation of the two categories that specifically enhances the target stimulus. We demonstrate that this shift in encoding relies partly on a novel mechanism of change in spontaneous activity patterns upon engagement in the task. We show that this population-level representation of stimuli in A1 population activity bears strong similarities to responses in the frontal cortex, but appears earlier following stimulus presentation. Analysis of neural activity recorded in various Go/No-Go tasks, with different sounds and reinforcement paradigms, reveals that this striking population-level enhancement of target representation is a general property of task engagement. These findings indicate that primary sensory cortices play a highly flexible role in the processing of incoming stimuli and implement a crucial change in the structure of population activity in order to extract task-relevant information during behavior.
A genetically encoded adhesin toolbox for programming multicellular morphologies and patterns
Authors: Glass David S. , Riedel-Kruse Ingmar H.
Published: December 2017

Synthetic multicellular systems hold promise for understanding natural development of biofilms and higher organisms1,2, as well as for engineering complex multi-component metabolic pathways2,3and materials4. However, such efforts will require tools to adhere cells into defined morphologies and patterns, and these tools are currently lacking1,5,6. Here we report the first 100% genetically encoded synthetic platform for modular cell-cell adhesion inEscherichia coli, which provides control over multicellular self-assembly. Adhesive selectivity is provided by a library of outer membrane-displayed nanobody7,8and antigen peptides with orthogonal intra-library specificities, while affinity is controlled by intrinsic adhesin affinity, competitive inhibition, and inducible expression. We demonstrate the resulting capabilities for rational design of well-defined morphologies and patterns through homophilic and heterophilic interactions, lattice-like self-assembly, phase separation, differential adhesion, and sequential layering. This adhesion toolbox, compatible with synthetic biology standards9, will enable construction of high-level multicellular designs and shed light on the evolutionary transition to multicellularity6,10.
Effect of hydrophobic finishing on drag force of swimwear
Authors: Nazemi Siamak , Khajavi Ramin , Rabie Far Hamidreza , Yazdanshenas Mohammad Esmail , Raad Manouchehr
Published: December 2017

Purpose

During 2008 Olympics, Michael Phelps had a record-breaking performance. One contributing factor to his success was the full-body swimsuit he was wearing. Cases like these were the reason for the initiation of study and research for improvement in the new generation of sport gears. The purpose of this paper is to show that drag force plays a significant role in swimmers’ speed through the water; thus, using swimsuit with minimized drag force becomes imperative for Olympians like Michael Phelps.

Design/methodology/approach

This paper shows a comparative evaluation of hydrodynamics of three PET fabrics with different finishings that have hydrophobic behavior over a range of Reynolds number 1.0218×103 and 1.365×103 in the air medium at 20°C ambient temperature, and Reynolds number ranging from 15.68856×103 to 20.958×103 in the water medium at 20°C ambient temperature under stable stretch conditions.

Findings

The results show that hydrophobic finishing reduces the drag force by 1.5 percent at the angles of attack of 0 and 90 degrees.

Originality/value

If all the factors are considered to be stable for the swimmer, the drag force reduces by 1.5 percent, thereby increasing the speed of swimmer by 1.22 percent, which means that the record of the swimmer improves by 0.819 seconds.