bluuebunny/crossref_metadata_2025 huggingface dataset:
Use Detective Thinking and Problem Solving for Parents
Authors: Jill Ehrenreich-May , Kennedy Sarah M. , Sherman Jamie A. , Bilek Emily L. , Barlow David H.
Published: December 2017

Chapter 15 covers two sessions. Session 6 teaches parents about the purpose of Detective Thinking. They learn how to help their children use the steps of Detective Thinking to gather evidence for emotional thoughts. They are also taught about the emotional parenting behaviors of overcontrol and overprotection and the opposite parenting behavior of healthy independence-granting. In Session 7, parents are taught to identify the differences between Detective Thinking and Problem Solving and how to help their child apply Problem Solving to conflicts with other people. Parents are taught how to promote independent use of Detective Thinking and Problem Solving skills at home.
Keeping It Going—Maintaining Your Gains
Authors: Ehrenreich-May Jill , Kennedy Sarah M. , Sherman Jamie A. , Bennett Shannon M. , Barlow David H.
Published: December 2017

Chapter 8 reviews the skills adolescents have learned and practiced throughout treatment and celebrates their accomplishments. The client is asked to compare how he or she feels now versus how he or she felt at the beginning of therapy. The client looks back at the new skills acquired and assesses which ones felt most important and helpful. The chapter concludes with the importance of making plans for coping with difficult or strong emotions in the future. Clients are encouraged to “become their own therapist.”
UP-C Sessions 11 Through 14: Facing Our Emotions—Part 2
Authors: Ehrenreich-May Jill , Kennedy Sarah M. , Sherman Jamie A. , Bilek Emily L. , Buzzella Brian A. , Bennett Shannon M. , Barlow David H.
Published: December 2017

Chapter 21 covers Sessions 11 through 14 of the Emotion Detectives program. The goal is to have each child complete several successful situational emotion exposures that reflect increasingly challenging items. Initial exposures allow the children to become accustomed to situational emotion exposures, as well as exposure planning, and allow therapists to assess children’s responses to various emotion triggers. Later sessions provide extensive time to further challenge children and parents as they attempt increasingly difficult items. There is no formal parent group for these sessions. Instead, parents should be directed to review workbook and home learning exercises in the companion materials and assist with exposure activities, as appropriate..
Is Access to Outpatient Neurosurgery Affected by Narrow Insurance Networks? Results From Statewide Analysis of Marketplace Plans in Louisiana
Authors: Dossani Rimal H , Kalakoti Piyush , Nanda Anil , Guthikonda Bharat , Tumialán Luis M
Published: December 2017

BACKGROUND

The main objective of the Affordable Care Act (ACA) was to make health insurance affordable to all Americans while addressing the lack of coverage for 48 million people. In the face of rapidly increasing enrollment and rising demand for inexpensive plans, insurance providers are limiting in-network physicians. Provider networks offering plans with limited in-network physicians have become known as “narrow networks.”

OBJECTIVE

To assesses the adequacy of ACA marketplace plans for outpatient neurosurgery in Louisiana.

METHODS

The Marketplace Public Use Files were searched for all “silver” plans. A total of 7 silver plans were identified in Louisiana. Using the plans’ online directories, a search of in-network neurosurgeons in Louisiana parishes with >100 000 population was performed. The primary outcome was lack of in-network neurosurgeon(s) in silver plans within 50 miles of selected zip code for each parish with >100 000 population. Plans without in-network neurosurgeon(s) are labeled as neurosurgeon-deficient plans.

RESULTS

Several plans in Louisiana are neurosurgeon deficient, ie no in-network neurosurgeon within 50 miles of the designated parish zip code. Company A’s plan 3 is deficient in all 5 parishes, while company C and company D silver plans are deficient in 4 out of 14 (29%). Combined results from all counties and plans demonstrate that 43% (3 out of 7) of all silver plans in Louisiana are neurosurgeon deficient in at least 4 parishes with population >100 000.

CONCLUSION

In Louisiana, narrow networks have limited access to neurosurgical care for those patients with ACA silver plans.
Mechanobiology in vascular remodeling
Authors: Han Yue , Huang Kai , Yao Qing-Ping , Jiang Zong-Lai
Published: December 2017

Vascular remodeling is a common pathological process in cardiovascular diseases and includes changes in cell proliferation, apoptosis and differentiation as well as vascular homeostasis. Mechanical stresses, such as shear stress and cyclic stretch, play an important role in vascular remodeling. Vascular cells can sense the mechanical factors through cell membrane proteins, cytoskeletons and nuclear envelope proteins to initiate mechanotransduction, which involves intercellular signaling, gene expression, and protein expression to result in functional regulations. Non-coding RNAs, including microRNAs and long non-coding RNAs, are involved in the regulation of vascular remodeling processes. Mechanotransduction triggers a cascade reaction process through a complicated signaling network in cells. High-throughput technologies in combination with functional studies targeting some key hubs and bridging nodes of the network can enable the prioritization of potential targets for subsequent investigations of clinical translation. Vascular mechanobiology, as a new frontier field of biomechanics, searches for principles of stress-growth in vasculature to elucidate how mechanical factors induce biological effects that lead to vascular remodeling, with the goal of understanding the mechanical basis of the pathological mechanism of cardiovascular diseases at the cellular and molecular levels. Vascular mechanobiology will play a unique role in solving the key scientific problems of human physiology and disease, as well as generating important theoretical and clinical results.
Breaking the barriers: advances in acoustic functional materials
Authors: Ge Hao , Yang Min , Ma Chu , Lu Ming-Hui , Chen Yan-Feng , Fang Nicholas , Sheng Ping
Published: December 2017

Acoustics is a classical field of study that has witnessed tremendous developments over the past 25 years. Driven by the novel acoustic effects underpinned by phononic crystals with periodic modulation of elastic building blocks in wavelength scale and acoustic metamaterials with localized resonant units in subwavelength scale, researchers in diverse disciplines of physics, mathematics, and engineering have pushed the boundary of possibilities beyond those long held as unbreakable limits. More recently, structure designs guided by the physics of graphene and topological electronic states of matter have further broadened the whole field of acoustic metamaterials by phenomena that reproduce the quantum effects classically. Use of active energy-gain components, directed by the parity–time reversal symmetry principle, has led to some previously unexpected wave characteristics. It is the intention of this review to trace historically these exciting developments, substantiated by brief accounts of the salient milestones. The latter can include, but are not limited to, zero/negative refraction, subwavelength imaging, sound cloaking, total sound absorption, metasurface and phase engineering, Dirac physics and topology-inspired acoustic engineering, non-Hermitian parity–time synthetic active metamaterials, and one-way propagation of sound waves. These developments may underpin the next generation of acoustic materials and devices, and offer new methods for sound manipulation, leading to exciting applications in noise reduction, imaging, sensing and navigation, as well as communications.
Anglican Mission in Twentieth-Century Africa
Authors: Prevost Elizabeth E.
Published: December 2017

Anglican mission in Africa had the capacity to challenge and unseat social, political, and religious hierarchies and identities as much as to create and reinforce them. This chapter considers how twentieth-century movements in colonial statecraft, welfare and development, anti-colonial nationalism, and decolonization found expression in Anglican mission in sub-Saharan Africa. Specifically, it looks at how the Anglican missionary commitment to indigenization played out in government and society, education and knowledge production, ritual and spirituality, political dissent, and devolution—often in unexpected ways that thwarted the intent of mission establishments and reshaped the character of Anglicanism. Approaching missions as communities, structured by changing norms of authority and social cohesion, can reveal the complex interrelationships of local, regional, and global dynamics of Anglican ideology and practice.
A molecular line survey toward the nearby galaxies NGC 1068, NGC 253, and IC 342 at 3 mm with the Nobeyama 45 m radio telescope: Impact of an AGN on 1 kpc scale molecular abundances
Authors: Nakajima Taku , Takano Shuro , Kohno Kotaro , Harada Nanase , Herbst Eric
Published: December 2017

It is important to investigate the relationships between the power sources and the chemical compositions of galaxies in order to understand the scenario of galaxy evolution. We carried out an unbiased molecular line survey towards active galactic nucleus (AGN) host galaxy NGC1068, and prototypical starburst galaxies, NGC 253 and IC 342, with the Nobeyama 45 m telescope in the 3 mm band. The advantage of this line survey is that the obtained spectra have the highest angular resolution ever obtained with single-dish telescopes. In particular, the beam size of this telescope is ∼15″–19″, which is able to separate spatially the nuclear molecular emission from that of the starburst ring (d ∼ 30″) in NGC 1068. We successfully detected approximately 23 molecular species in each galaxy, and calculated rotation temperatures and column densities. We estimate the molecular fractional abundances with respect to 13CO and CS molecules and compare them among three galaxies in order to investigate the chemical signatures of an AGN environment. As a result, we found clear trends in the abundances of molecules surrounding the AGN on a 1-kpc scale. HCN, H13CN, CN, 13CN, and HC3N are more abundant, and CH3CCH is deficient in NGC 1068 compared with the starburst galaxies. High abundances of HCN, H13CN, and HC3N suggest that the circumnuclear disk in NGC 1068 is in a high-temperature environment. The reason for the non-detection of CH3CCH is likely to be dissociation by high-energy radiation or less sublimation of a precursor of CH3CCH from grains.
Isolate Specificity and Polygenic Inheritance of Resistance in Barley to Diverse HeterologousPuccinia striiformisIsolates
Authors: Haghdoust R. , Singh D. , Garnica D. P. , Park R. F. , Dracatos P. M.
Published: December 2017

Barley is a host to Puccinia striiformis f. sp. hordei, and is an intermediate or near nonhost to the formae speciales adapted to wheat (P. striiformis f. sp. tritici) and to barley grass (P. striiformis f. sp. pseudo-hordei). The genetic basis of resistance to these forms of P. striiformis is not well understood. Accordingly, a recombinant inbred line (RIL) population was developed using a P. striiformis-susceptible accession (Biosaline-19) and the immune cultivar Pompadour. We investigated the genetic basis of resistance to four diverse P. striiformis isolates (P. striiformis f. sp. pseudo-hordei, and P. striiformis f. sp. tritici pathotypes 104 E137 A−, 134 E16 A+, and 64 E0 A−). and determined that the immunity in Pompadour at the seedling stage to the different P. striiformis isolates was due to quantitative trait loci (QTL) on chromosomes 1H, 3H, 5H, and 7H with both overlapping and distinct specificities. Further histological analysis confirmed the presence of isolate specificity. The RILs were also assessed in the field for resistance to P. striiformis f. sp. pseudo-hordei, P. striiformis f. sp. hordei, and the leaf rust pathogen (P. hordei) to identify pleiotropic QTL loci effective at the adult plant stage and determine whether the leaf rust resistance in Pompadour (Rph20) was also effective to P. striiformis. RILs that were seedling susceptible to P. striiformis f. sp. pseudo-hordei were resistant in the field, implicating the involvement of adult plant resistance (APR). Additional QTLs were identified on chromosome 7H at the same genetic position as Rph23 (APR to leaf rust), suggesting either pleiotropic resistance or the presence of a stripe rust resistance gene closely linked to or allelic with Rph23. Unlike many pleiotropic APR genes identified and isolated in wheat, our data suggest that the Rph20 locus does not confer resistance to the P. striiformis isolates used in this study (P. striiformis f. sp. hordei [χ2(independence) = 2.47 P > 0.12] and P. striiformis f. sp. pseudo-hordei [χ2(independence) = 0.42 P > 0.60]).
Does Self-compassion Benefit Couples Coping With Vulvodynia? Associations With Psychological, Sexual, and Relationship Adjustment
Authors: Santerre-Baillargeon Marie , Rosen Natalie O. , Steben Marc , Pâquet Myriam , Macabena Perez Rocio , Bergeron Sophie
Published: December 2017

Objectives:

Vulvodynia, a chronic vulvovaginal pain condition, has deleterious consequences for the psychological, relational, and sexual well-being of affected women and their partners. Protective factors, which can reduce these negative effects, are increasingly studied in the field of chronic pain. One of these, self-compassion, entails qualities such as kindness toward oneself, and has been associated with better adjustment in individuals with chronic pain. Because many women with vulvodynia have a negative image of themselves in the context of sexuality, self-compassion may be especially relevant for this population. This study aimed to investigate self-compassion among couples coping with vulvodynia and its associations with psychological, sexual, and relationship adjustment, as well as pain during sexual intercourse.

Materials and Methods:

Data were gathered from 48 women diagnosed with provoked vestibulodynia—a subtype of vulvodynia—and their partners, using self-report questionnaires pertaining to anxiety, depression, sexual distress, relationship satisfaction, and pain intensity during sexual intercourse.

Results:

For both women and their partners, higher levels of self-compassion were associated with their own lower anxiety and depression. When partners reported higher levels of self-compassion, they were more satisfied with their relationship, and both partners and women reported lower sexual distress. No significant association was found for pain during intercourse.

Discussion:

Findings suggest that self-compassion is a promising protective factor in the experience of vulvodynia and associated distress. Interventions aimed at increasing self-compassion could enhance the efficacy of psychological treatments for these women and their partners. Further studies are needed to better understand the correlates of self-compassion among this population.
Surgically Induced Scleral Necrosis in a Patient With Rheumatoid Arthritis After AGV Implantation
Authors: Kumar Suresh , Ichhpujani Parul , Thakur Sahil
Published: December 2017

Introduction:

Surgically induced scleral necrosis (SINS) is a rare entity that has till date not been reported in a patient of glaucoma undergoing Ahmed glaucoma valve (AGV) implantation.

Methods:

We present a case of primary open-angle glaucoma who underwent AGV implantation followed by development of scleral necrosis, involving both the scleral patch graft and host sclera. After failure of surgical and medical management, AGV had to be explanted. The patient was diagnosed with rheumatoid arthritis and had to be treated with steroids and azathioprine for the same.

Results:

SINS is a potentially disastrous complication of ocular surgery that can occur in patients with systemic diseases like rheumatoid arthritis and requires aggressive management to salvage the eye.

Conclusion:

SINS can occur with AGV implantation. Treatment may require aggressive medical and surgical intervention. It is imperative to evaluate patients for systemic illness before planning an AGV implant.
Screening Tool to Determine Risk of Having Muscle Dysmorphia Symptoms in Men Who Engage in Weight Training at a Gym
Authors: Palazón-Bru Antonio , Rizo-Baeza María M. , Martínez-Segura Asier , Folgado-de la Rosa David M. , Gil-Guillén Vicente F. , Cortés-Castell Ernesto
Published: December 2017

Objective:

Although 2 screening tests exist for having a high risk of muscle dysmorphia (MD) symptoms, they both require a long time to apply. Accordingly, we proposed the construction, validation, and implementation of such a test in a mobile application using easy-to-measure factors associated with MD.

Design:

Cross-sectional observational study.

Setting:

Gyms in Alicante (Spain) during 2013 to 2014.

Participants:

One hundred forty-one men who engaged in weight training.

Assessment of Risk Factors:

The variables are as follows: age, educational level, income, buys own food, physical activity per week, daily meals, importance of nutrition, special nutrition, guilt about dietary nonadherence, supplements, and body mass index (BMI). A points system was constructed through a binary logistic regression model to predict a high risk of MD symptoms by testing all possible combinations of secondary variables (5035). The system was validated using bootstrapping and implemented in a mobile application.

Main Outcome Measures:

High risk of having MD symptoms (Muscle Appearance Satisfaction Scale).

Results:

Of the 141 participants, 45 had a high risk of MD symptoms [31.9%, 95% confidence interval (CI), 24.2%-39.6%]. The logistic regression model combination providing the largest area under the receiver operating characteristic curve (0.76) included the following: age [odds ratio (OR) = 0.90; 95% CI, 0.84-0.97, P = 0.007], guilt about dietary nonadherence (OR = 2.46; 95% CI, 1.06-5.73, P = 0.037), energy supplements (OR = 3.60; 95% CI, 1.54-8.44, P = 0.003), and BMI (OR = 1.33, 95% CI, 1.12-1.57, P < 0.001). The points system was validated through 1000 bootstrap samples.

Conclusions:

A quick, easy-to-use, 4-factor test that could serve as a screening tool for a high risk of MD symptoms has been constructed, validated, and implemented in a mobile application.
Expression of PD-L1 on Immune Cells Shows Better Prognosis in Laryngeal, Oropharygeal, and Hypopharyngeal Cancer
Authors: Birtalan Ede , Danos Kornel , Gurbi Bianka , Brauswetter Diana , Halasz Judit , Kalocsane Piurko Violetta , Acs Balazs , Antal Biborka , Mihalyi Reka , Pato Anna , Fent Zoltan , Polony Gabor , Timar Jozsef , Tamas Laszlo
Published: December 2017

Despite great enthusiasm towards immunotherapy, reliable biomarkers are still lacking. The importance of subsets based on human papillomavirus (HPV) status is supported by a growing body of evidence. However, role of other possible subgroups such as anatomic localization of primary tumor remains controversial. Our objective was to investigate immune cell infiltrate and checkpoint inhibitor proteins in above-mentioned head and neck cancer subsets. Archival tumor samples of 106 laryngeal, oropharyngeal, and hypopharyngeal cancer patients were stained with PD-L1, PD-L2, PD-1, and CTLA-4 antibodies. Proportion of tumor-infiltrating lymphocytes was assessed as well. In HPV-negative tumors, PD-L1 immune cell positivity was associated with better disease-specific survival. PD-L1 expression on immune cells correlated with improved disease-specific survival in laryngeal tumors. Furthermore, PD-L1 immune cell positivity correlated with CTLA-4 expression on immune cells and it was accompanied by high tumor-infiltrating lymphocyte rate. PD-L1 expression on tumor cells and PD-1 status showed strong correlation in all patients and in oropharyngeal and laryngeal localization, but not in hypopharynx. HPV-negative oropharyngeal cancers showed negative PD-L1 status on tumor cells. CTLA-4 positivity was observed in 49.5% and 20.6% on immune cells and on tumor cells, respectively. We concluded that PD-L1 expression on immune cells indicates better prognosis in laryngeal squamous cell carcinoma and in HPV-negative head and neck squamous cell carcinoma. We have not found any essential differences between anatomic subgroups. A possibly distinct role of hypopharyngeal localization regarding immune activity requires further clarification.
Immunohematology Mesenchymal Stromal Cell-based Therapy: From Research to Clinic
Authors: Najar Mehdi , Krayem Mohammad , Meuleman Nathalie , Bron Dominique , Hélène Busser , Lagneaux Laurence
Published: December 2017

Mesenchymal stromal cells (MSC) are nonhematopoietic cells that can be isolated from several adult and fetal tissues. MSC present specific features as the capacity to support hematopoiesis and to regulate immune response. Thus, the use of MSC as a cell therapeutic product in the field of immune-hematology is of great importance. In this review, we focused on human MSC and discussed their immune-hematologic properties and their translation toward therapeutic clinical applications. Thus, these features hold great promise for cell-based therapy and are of important relevance for the field.
Why Videos Matter So Much in Plastic Surgery Today: A Complete Index of Videos in Plastic and Reconstructive Surgery and Plastic and Reconstructive Surgery Global Open
Authors: Boehm Kaitlin S. , Rohrich Rod J. , Lalonde Donald H.
Published: December 2017

The main purpose of this article is to provide the reader with an easily searchable online index of the first 1976 videos published in Plastic and Reconstructive Surgery and Plastic and Reconstructive Surgery Global Open to facilitate access to readers. The authors also describe the history and evolution of video articles in the first journal to provide a large offline video library of plastic surgery. The importance of videos in plastic surgery education is explored.
Association of postoperative organ space infection after intraoperative irrigation in appendicitis
Authors: Hernandez Matthew C. , Finnesgard Eric J. , Aho Johnathon M. , Jenkins Donald H. , Zielinski Martin D.
Published: December 2017

BACKGROUND

The benefit of intraoperative irrigation on postoperative abscess rates compared to suction alone is unclear. The American Association for the Surgery of Trauma grading system provides distinct disease severity stratification to determine if prior analyses were biased by anatomic severity. We hypothesized that for increasing appendicitis severity, patients receiving (high, ≥2 L) intraoperative irrigation would have increased postoperative organ space infection (OSI) rate compared to (low, <2 L) irrigation.

METHODS

Single-institution review of adults (>18 years) undergoing appendectomy for appendicitis during 2010-2016. Demographics, operative details, irrigation volumes, duration of stay, and complications (Clavien-Dindo classification) were collected. American Association for the Surgery of Trauma grades were assigned by two independent reviewers based on operative findings. Summary, univariate, and area under the receiver operating curve analyses were performed.

RESULTS

Patients (n = 1187) were identified with a mean (SD) age of 41.6 (18.4) years (45% female). Operative approach included laparoscopy (n = 1122 [94.5%]), McBurney incision (n = 10 [0.8%]), midline laparotomy (n = 16 [1.3 %]), and laparoscopy converted to laparotomy (n = 39 [3.4%)]. The mean (SD) volume of intraoperative irrigation was 410 (1200) mL. Complication rate was 26.1%. Median volume of intraoperative irrigation in patients who developed postoperative OSI was 3 [0–4] compared to 0 [0–0] in those without infection (p < 0.0001). Area under the receiver operating curve analysis determined that 2 or more liters of irrigation was associated with postoperative OSI (c statistic: 0.83, 95% confidence interval, 0.76–0.89; p < 0.001).

CONCLUSION

Irrigation is used for increasingly severe appendicitis with wide variation. Irrigation volumes of 2 L or greater are associated with postoperative OSI. Improving standardization of irrigation volume (<2 L) may prevent morbidity associated with this high-volume disease.

LEVEL OF EVIDENCE

Therapeutic, level IV.
Study on Linear Combination of Long Memory Processes Corrupted by Additive Noises for fMRI Time Series Analysis
Authors: You Wonsang , Limperopoulos Catherine
Published: December 2017

Estimating the long memory parameter of the fMRI time series enables us to understand the fractal behavior of neural activity of the brain through fMRI time series. However, the existence of white noise and physiological noise compounds which also have fractal properties prevent us from making the estimation precise. As basic strategies to overcome noises, we address how to estimate the long memory parameter in the presence of additive noises, and how to estimate the long memory parameters of linearly combined long memory processes.
The Phagocyte Oxidase Controls Tolerance toMycobacterium tuberculosisinfection
Authors: Olive Andrew J , Smith Clare M , Kiritsy Michael C , Sassetti Christopher M
Published: December 2017

Protection from infectious disease relies on two distinct mechanisms. “Antimicrobial resistance” directly inhibits pathogen growth, whereas “infection tolerance” controls tissue damage. A single immune-mediator can differentially contribute to these mechanisms in distinct contexts, confounding our understanding of protection to different pathogens. For example, the NADPH-dependent phagocyte oxidase complex (Phox) produces anti-microbial superoxides and protects from tuberculosis in humans. However, Phox-deficient mice do not display the expected defect in resistance toM. tuberculosisleaving the role of this complex unclear. We re-examined the mechanisms by which Phox contributes to protection from TB and found that mice lacking the Cybb subunit of Phox suffered from a specific defect in tolerance, which was due to unregulated Caspase1 activation, IL-1β production, and neutrophil influx into the lung. These studies demonstrate that Phox-derived superoxide protect against TB by promoting tolerance to persistent infection, and highlight a central role for Caspase1 in regulating TB disease progression.
Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities
Authors: Gumbs Rikki , Gray Claudia L. , Wearn Oliver R. , Owen Nisha R.
Published: December 2017

The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. The EDGE metric, which prioritises species based on their Evolutionary Distinctiveness (ED) and Global Endangerment (GE), relies on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic analyses of large clades are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to impute ED for species missing from a phylogeny whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogeny, the new method provided the closest estimates of their “true” score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous imputation methods. Previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogeny. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.
The structure of the influenza A virus genome
Authors: Dadonaite Bernadeta , Barilaite Egle , Fodor Ervin , Laederach Alain , Bauer David L. V.
Published: December 2017

Influenza A viruses (IAVs) are segmented single-stranded negative sense RNA viruses that constitute a major threat to human health. The IAV genome consists of eight RNA segments contained in separate viral ribonucleoprotein complexes (vRNPs) that are packaged together into a single virus particle1,2. While IAVs are generally considered to have an unstructured single-stranded genome, it has also been suggested that secondary RNA structures are required for selective packaging of the eight vRNPs into each virus particle3,4. Here, we employ high-throughput sequencing approaches to map both the intra and intersegment RNA interactions inside influenza virions. Our data demonstrate that a redundant network of RNA-RNA interactions is required for vRNP packaging and virus growth. Furthermore, the data demonstrate that IAVs have a much more structured genome than previously thought and the redundancy of RNA interactions between the different vRNPs explains how IAVs maintain the potential for reassortment between different strains, while also retaining packaging selectivity. Our study establishes a framework towards further work into IAV RNA structure and vRNP packaging, which will lead to better models for predicting the emergence of new pandemic influenza strains and will facilitate the development of antivirals specifically targeting genome assembly.
A memory element imposes epigenetic behavior on intrinsically labile RNAi-induced heterochromatin spread
Authors: Greenstein R.A. , Jones Stephen K. , Spivey Eric C. , Rybarski James R. , Finkelstein Ilya J. , Al-Sady Bassem
Published: December 2017

ABTRACT

The heterochromatin spreading reaction is a central contributor to the formation of gene-repressive structures, which are re-established with high fidelity following replication. The high fidelity of this process is not obviously encoded in the primary spreading reaction. To resolve origins of stable inheritance of repression, we probed the intrinsic fidelity of spreading events in fission yeast using a system that quantitatively describes the spreading reaction in live single cells. We show that spreading from RNAi-nucleated elements is stochastic, multimodal, and fluctuates dynamically across time. In contrast, a second form of spreading, nucleated by thecis-acting elementREIII, is deterministic, has high memory capacity and acts as the source of locus fidelity.REIIIenables fidelity in part by endowing the locus with resistance to perturbations. Together, our results suggest that epigenetic capacity may not be intrinsically encoded in the spreading reaction, but rather requires collaboration with specialized memory elements.
Osterixfunctions downstream of anti-Müllerian hormone signaling to regulate Müllerian duct regression
Authors: Mullen Rachel D. , Wang Ying , Liu Bin , Moore Emma L. , Behringer Richard R.
Published: December 2017

In mammals, the developing reproductive tract primordium of male and female fetuses consists of the Wolffian duct and the Müllerian duct (MD), two epithelial tube pairs surrounded by mesenchyme. During male development, mesenchyme-epithelia interactions mediate MD regression to prevent its development into a uterus, oviduct and upper vagina. It is well established that transforming growth factor-beta family member anti-Müllerian hormone (AMH) secreted from the fetal testis and its type 1 and 2 receptors expressed in MD mesenchyme regulate MD regression. However, little is known about the molecular network regulating downstream actions of AMH signaling. To identify potential AMH-induced genes and regulatory networks controlling MD regression in a global non-biased manner, we examined transcriptome differences in MD mesenchyme between males (AMH signaling on) and females (AMH signaling off) by RNA-Seq analysis of purified fetal MD mesenchymal cells. This analysis found 82 genes up-regulated in males during MD regression and identifiedOsterix (Osx)/Sp7, a key transcriptional regulator of osteoblast differentiation and bone formation, as a novel downstream effector of AMH signaling during MD regression. Osx/OSX was expressed in a male-specific pattern in MD mesenchyme during MD regression. OSX expression was lost in mutant males without AMH signaling. In addition, transgenic mice ectopically expressing human AMH in females induced a male pattern ofOsxexpression. Together these results indicate that AMH signaling is necessary and sufficient forOsxexpression in the MD mesenchyme. In addition, MD regression was delayed inOsxnull males, identifyingOsxas a new factor that regulates MD regression.

Significance

In mammals, each embryo forms both male and female reproductive tract organ progenitor tissues. Anti-Müllerian hormone (AMH) secreted by fetal testes acts on mesenchyme cells adjacent to the Müllerian duct (MD) epithelium, the progenitor tissue of the female reproductive tract, to induce MD regression. While AMH and early AMH signaling components are elucidated, downstream gene networks directing this process are largely unknown. A global non-biased approach using whole transcriptome sequencing of fetal MD mesenchymal cells identified 82 factors as potential target genes of AMH includingOsterix (Osx). Our findings providein vivoevidenceOsxis an AMH-induced gene that regulates MD regression. Identification ofOsxmay provide key insights into gene regulatory networks underlying MD regression and male sex differentiation.
Challenges in Using ctDNA to Achieve Early Detection of Cancer
Authors: Haque Imran S , Elemento Olivier
Published: December 2017

Early detection of cancer is a significant unmet clinical need. Improved technical ability to detect circulating tumor-derived DNA (ctDNA) in the cell-free DNA (cfDNA) component of blood plasma via next-generation sequencing and established correlations between ctDNA load and tumor burden in cancer patients have spurred excitement about the possibilities of detecting cancer early by performing ctDNA mutation detection.

We reanalyze published data on the expected ctDNA allele fraction in early-stage cancer and the population statistics of cfDNA concentration to show that under conservative technical assumptions, high-sensitivity cancer detection by ctDNA mutation detection will require either more blood volume (150-300mL) than practical for a routine screen or variant filtering that may be impossible given our knowledge of cancer evolution, and will likely remain out of economic reach for routine population screening without multiple-order-of-magnitude decreases in sequencing cost. Instead, new approaches that integrate ctDNA mutations with multiple other blood-based analytes (such as exosomes, circulating tumor cells, ctDNA epigenetics, metabolites) as well as integration of these signals over time for each individual may be needed.
Computational docking reveals evolutionary conservation of a specific interaction between 15d-Prostaglandin-J2 and eIF4A
Authors: Yun So Jeong , Kim Hyunjoon , Lee Seung Gee , Jung Seung-Hyun , Kim Joon Hyun , Ryu Jeong Eun , Singh N. Jiten , Jeon Jouhyun , Han Jin-Kwan , Kim Cheol-Hee , Kim Sanguk , Kim Kwang S. , Jang Sung Key , Kim Woo Jae
Published: December 2017

15-deoxy-delta 12,14-prostaglandin J2 (15d-PGJ2) is anti-inflammatory/antineoplastic prostaglandin which functions through covalent binding to cysteine residues of various target proteins. We previously showed that 15d-PGJ2 mediated anti-inflammatory responses are dependent on the translational inhibition through its interaction with eIF4A. Binding of 15d-PGJ2 to eIF4A specifically blocks the interaction between eIF4G and eIF4A leads to the formation of stress granules (SGs), which cluster mRNAs with inhibited translation. Here we show that the binding between 15d-PGJ2 and eIF4A specifically blocks the interaction between the MIF4G domain of eIF4G and eIF4A. To reveal the mechanism of this interaction, we used computational simulation-based docking studies and identified that the carboxyl tail of 15d-PGJ2 could stabilize the binding of 15d-PGJ2 to eIF4A through arginine 295 of eIF4A, which is the first suggestion that the 15d-PGJ2 tail play a physiological role. Interestingly, the putative 15d-PGJ2 binding site on eiF4A is conserved across many species, suggesting a biological role. Our data propose that studying 15d-PGJ2 and its targets will may uncover new therapeutic approaches in anti-inflammatory drug discovery.
Gaze Behaviour During Sensorimotor Adaptation Parcellates the Explicit and Implicit Contributions to Learning
Authors: de Brouwer Anouk J. , Albaghdadi Mohammed , Randall Flanagan J. , Gallivan Jason P.
Published: December 2017

Successful motor performance relies on our ability to adapt to changes in the environment by learning novel mappings between motor commands and sensory outcomes. Such adaptation is thought to involve two distinct mechanisms: An implicit, error-based component linked to slow learning and an explicit, strategic component linked to fast learning and savings (i.e., faster relearning). Because behaviour, at any given moment, is the resultant combination of these two processes, it has remained a challenge to parcellate their relative contributions to performance. The explicit component to visuomotor rotation (VMR) learning has recently been measured by having participants verbally report their aiming strategy used to counteract the rotation. However, this procedure has been shown to magnify the explicit component. Here we tested whether task-specific eye movements, a natural component of reach planning—but poorly studied in motor learning tasks—can provide a direct read-out of the state of the explicit component during VMR learning. We show, by placing targets on a visible ring and including a delay between target presentation and reach onset, that individual differences in gaze patterns during sensorimotor adaptation are linked to participants’ rates of learning and can predict the expression of savings. Specifically, we find that participants who, during reach planning, naturally fixate an aimpoint, rotated away from the target location, show faster initial adaptation and readaptation 24 hrs. later. Our results demonstrate that gaze behaviour can not only uniquely identify individuals who implement cognitive strategies during learning, but also how their implementation is linked to differences in learning.
Dr.Paso: Drug response prediction and analysis system for oncology research
Authors: Azuaje Francisco , Kaoma Tony , Jeanty Céline , Nazarov Petr V. , Muller Arnaud , Kim Sang-Yoon , Golebiewska Anna , Dittmar Gunnar , Niclou Simone P.
Published: December 2017

The prediction of anticancer drug response is crucial for achieving a more effective and precise treatment of patients. Models based on the analysis of large cell line collections have shown potential for investigating drug efficacy in a clinically-meaningful, cost-effective manner. Using data from thousands of cancer cell lines and drug response experiments, we propose a drug sensitivity prediction system based on a 47-gene expression profile, which was derived from an unbiased transcriptomic network analysis approach. The profile reflects the molecular activity of a diverse range of cancer-relevant processes and pathways. We validated our model using independent datasets and comparisons with published models. A high concordance between predicted and observed drug sensitivities was obtained, including additional validated predictions for four glioblastoma cell lines and four drugs. Our approach can accurately predict anti-cancer drug sensitivity and will enable further pre-clinical research. In the longer-term, it may benefit patient-oriented investigations and interventions.
The essential genome ofEscherichia coliK-12
Authors: Goodall Emily C. A. , Robinson Ashley , Johnston Iain G. , Jabbari Sara , Turner Keith A. , Cunningham Adam. F. , Lund Peter A. , Cole Jeffrey A. , Henderson Ian R.
Published: December 2017

Transposon-Directed Insertion-site Sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries and therefore it remains unclear whether the two methodologies are comparable. To address this, a high density transposon library was constructed inEscherichia coliK-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false positive identification of essential gene candidates, statistical data analysis included corrections for both gene length and genome length. Through this analysis new essential genes and genes previously incorrectly designated as essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects and fine resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis datasets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry.

IMPORTANCE

Incentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes inE. coli, we constructed a very high density transposon mutant library. Initial automated analysis of the resulting data revealed many discrepancies when compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high density TraDIS sequencing data for each putative essential gene for the model laboratory organism,Escherichia coli. This paper is important because it provides a better understanding of the essential genes ofE. coli, reveals the limitations of relying on automated analysis alone and a provides new standard for the analysis of TraDIS data.
RANbodies: reporter-nanobody fusions as versatile, small, sensitive immunohistochemical reagents
Authors: Yamagata Masahito , Sanes Joshua R.
Published: December 2017

Sensitive and specific antibodies are essential for detecting molecules in cells and tissues. However, currently used polyclonal and monoclonal antibodies are often less sensitive than desired, difficult to produce, and available in limited quantities. A promising recent approach to circumvent these limitations is to employ chemically-defined antigen-combining sites called nanobodies, derived from single chain camelid antibodies. Here, we used nanobodies to prepare sensitive unimolecular detection reagents by genetically fusing cDNAs encoding nanobodies to enzymatic or antigenic reporters. We call these fusions between a reporter and a nanobody RANbodies. They can be used to localize epitopes and to amplify signals from fluorescent proteins. They be generated and purified simply and in unlimited amounts, and can be preserved safely and inexpensively in the form of DNA or digital sequence.
Sequence determinants of protein phase behavior from a coarse-grained model
Authors: Dignon Gregory L. , Zheng Wenwei , Kim Young C. , Best Robert B. , Mittal Jeetain
Published: December 2017

Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid phase separation (LLPS). However, many proteins involved in this phase separation are at least partially disordered. The molecular mechanism and the sequence determinants of this process are challenging to determine experimentally owing to the disordered nature of the assemblies, motivating the use of theoretical and simulation methods. This work advances a computational framework for conducting simulations of LLPS with residue-level detail, and allows for the determination of phase diagrams and coexistence densities of proteins in the two phases. The model includes a short-range contact potential as well as a simplified treatment of electrostatic energy. Interaction parameters are optimized against experimentally determined radius of gyration data for multiple unfolded or intrinsically disordered proteins (IDPs). These models are applied to two systems which undergo LLPS: the low complexity domain of the RNA-binding protein FUS and the DEAD-box helicase protein LAF-1. We develop a novel simulation method to determine thermodynamic phase diagrams as a function of the total protein concentration and temperature. We show that the model is capable of capturing qualitative changes in the phase diagram due to phosphomimetic mutations of FUS and to the presence or absence of the large folded domain in LAF-1. We also explore the effects of chain-length, or multivalency, on the phase diagram, and obtain results consistent with Flory-Huggins theory for polymers. Most importantly, the methodology presented here is flexible so that it can be easily extended to other pair potentials, be used with other enhanced sampling methods, and may incorporate additional features for biological systems of interest.

Author summary

Liquid liquid phase separation (LLPS) of low-complexity protein sequences has emerged as an important research topic due to its relevance to membraneless organelles and intracellular compartmentalization. However a molecular level understanding of LLPS cannot be easily obtained by experimental methods due to difficulty of determining structural properties of phase separated protein assemblies, and of choosing appropriate mutations. Here we advance a coarse-grained computational framework for accessing the long time scale phase separation process and for obtaining molecular details of LLPS, in conjunction with state of the art enhanced sampling methods. We are able to capture qualitatively the changes of phase diagram due to specific mutations, inclusion of a folded domain, and to variation of chain length. The model is flexible and can be used with different knowledge-based potential energy functions, as we demonstrate. We expect a wide application of the presented framework for advancing our understanding of the formation of liquid-like protein assemblies.