bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Global Payment and Accountable Care on Medication Treatment for Alcohol and Opioid Use Disorders
Authors: Donohue Julie M. , Barry Colleen L. , Stuart Elizabeth A. , Greenfield Shelly F. , Song Zirui , Chernew Michael E. , Huskamp Haiden A.
Published: November 2017

Objectives:

The Alternative Quality Contract (AQC) implemented in 2009 by Blue Cross Blue Shield of Massachusetts (BCBSMA) is intended to improve quality and control costs by putting providers at risk for total medical spending and tying payment to performance on specified quality measures. We examined the AQC's early effects on use of and spending on medication treatment (MT) for addiction among individuals with alcohol use disorders (AUDs) and opioid use disorders (OUDs), conditions not subject to any performance measurement in the AQC.

Methods:

Using data from 2006 to 2011, we use difference-in-difference estimation of the effect of the AQC on MT using a comparison group of enrollees in BCBSMA whose providers did not participate in the AQC. We compared AQC and non-AQC enrollees with AUDs (n = 37,113 person-years) and/or OUDs (n = 12,727 person-years) on any use of MT, number of prescriptions filled, and MT spending adjusting for demographic and health status characteristics.

Results:

There was no difference in MT use among AQC enrollees with OUD (38.7%) relative to the comparison group (39.1%) (adjusted difference = −0.4%, 95% confidence interval −3.8% to 3.0%, P = 0.82). Likewise, there was no difference in MT use for AUD between the AQC (6.3%) and comparison group (6.5%) (P = 0.64). Similarly, we detected no differences in number of prescriptions or spending.

Conclusions:

Despite incentives for improved integration and quality of care under a global payment contract, the initial 3 years of the AQC showed no impact on MT use for AUD or OUD among privately insured enrollees with behavioral health benefits.
Nursing Care of Infants With a Ventriculoperitoneal Shunt
Authors: Joseph Rachel A. , Killian Michaela R. , Brady Emily E.
Published: November 2017

Background:

Infants with congenital or posthemorrhagic hydrocephalus may require a ventriculoperitoneal (VP) shunt to divert the flow of cerebrospinal fluid, thus preventing increase in intracranial pressure. Knowledge on various aspects of caring for a child with a VP shunt will enable new and experienced nurses to better care for these infants and equip parents for ongoing care at home.

Purpose:

To review the nurses' role in care of infants with hydrocephalus, care after VP shunt placement, prevention of complications, and parental preparation for home care.

Methods/Search Strategy:

A literature review involving electronic databases, such as CINAHL and MEDLINE, Cochrane Database Systematic Reviews, and resources from the Web sites of the National Hydrocephalus Foundation and Hydrocephalus Association, was performed to gather evidence for current practice information.

Findings and Implications for Practice and Research:

Vigilant care can help with early identification of potential complications. The younger the infant at VP shunt placement, the higher the occurrence of complications. All neonatal intensive care unit nurses must be equipped with knowledge and skills to care for infants with hydrocephalus and those who undergo VP shunt placement. Monitoring for early signs of increased intracranial pressure can facilitate timely diagnosis and prompt surgical intervention. Equipping families will be helpful in early identification and timely management of shunt failure. Research on infants with VP shunt placement is essential to develop appropriate guidelines and explore experiences of families to identify caregiver burden and improve parental preparation.
A-Frame free Vascularized Fibular Graft and Femoral Lengthening for Osteosarcoma Pediatric Patients
Authors: Cashin Megan , Coombs Christopher , Torode Ian
Published: November 2017

Background:

Pediatric limb reconstruction after resection of a malignant tumor presents specific challenges. Multiple surgical techniques have been used to treat these patients. This paper describes a staged surgical technique for the reconstruction of large distal femoral defects due to tumor resection in skeletally immature patients.

Methods:

Three pediatric patients with osteosarcoma of the distal femur underwent staged reconstruction. Neoadjuvant chemotherapy was followed by en bloc tumor resection and immediate reconstruction of the distal femoral defect with a vascularized free fibular autograft utilizing a unique A-frame construct combined with intramedullary nail fixation. The second stage was a planned gradual lengthening of the healed construct, over a custom-made magnetically driven expandable intramedullary nail.

Results:

All patients achieved bony union and satisfactory length with minimal complications. The patients all returned to full, unlimited physical activities.

Conclusions:

The early results confirm that the described technique is a safe and reliable procedure for the reconstruction of large femoral defects in pediatric patients with osteosarcoma.

Level of Evidence:

Level IV—therapeutic.
Biomechanical Comparison of Fifth Carpometacarpal Fusion Methods: Kirschner Wires Versus Plate and Screws
Authors: Yoshida Ryu , Obopilwe Elifho , Rodner Craig M.
Published: November 2017

Background:

Fractures and dislocations of the base of the fifth metacarpal can lead to arthritis of the fifth carpometacarpal (CMC) joint. For patients who are symptomatic and fail conservative management, arthrodesis of the fifth CMC joint can be offered. The fusion can be performed using Kirschner wires (K-wires), but can lead to complications such as pin tract infection and pin migration. A low-profile locking plate may represent an attractive alternative. The purpose of this study was to compare the biomechanical stability of these 2 fusion techniques.

Methods:

Twelve fresh frozen cadaver hands were divided into 2 groups. The first group underwent fixation of the fifth CMC joint using 2 1.6 mm (0.062 inches) diameter K-wires in a cross-pin configuration. The second group underwent fixation using a 2.0 mm locking plate with 2 locking screws in the hamate and 3 nonlocking screws in the fifth metacarpal shaft. The specimens were then loaded in extension until failure.

Results:

The stiffness was 15.0±7.2 N/mm for the K-wire group and 14.7±6.0 N/mm (mean±SD) for the plate group (P=0.9366). The peak loads were 62.5±40.0 N and 64.6±24.8 N for K-wire and plate groups, respectively (P=0.9181). The energy to peak load was 294±281 N mm for the K-wire group and 418±190 N mm for the plate group (P=0.3904).

Conclusions:

Fifth CMC fusion using either K-wires or plate and screws showed no significant difference in stiffness, peak load, and energy to peak load. These results suggest the 2 methods provide similar biomechanical stability.
Impact of Quality Bundle Enforcement by a Critical Care Pharmacist on Patient Outcome and Costs*
Authors: Leguelinel-Blache Géraldine , Nguyen Tri-Long , Louart Benjamin , Poujol Hélène , Lavigne Jean-Philippe , Roberts Jason A. , Muller Laurent , Kinowski Jean-Marie , Roger Claire , Lefrant Jean-Yves
Published: November 2017

Objectives:

Surgical and medical ICU patients are at high risk of mortality and provide a significant cost to the healthcare system. The aim of this study is to describe the effect of pharmacist-led interventions on drug therapy and clinical strategies on ICU patient outcome and hospital costs.

Design:

Before and after study in two French ICUs (16 and 10 beds).

Patients:

ICU patients.

Intervention:

From January 1, 2013, to June 30, 2015, a pharmacist observation period was compared with an intervention period in which a critical care pharmacist provided recommendations to clinicians regarding sedative drugs and doses, choice of mechanical ventilation mode and related settings, antimicrobial de-escalation, and central venous and urinary catheters removal. Differences in ICU and hospital length of stay, duration of mechanical ventilation, mortality rate, and hospital costs per patient were quantified between groups with patients matched for severity of illness (Simplified Acute Physiology Score II) at admission.

Measurements and Main Results:

From the 1,519 and 1,268 admitted patients during the observation and intervention periods, respectively, 1,164 patients were evaluable in both groups after matching for Simplified Acute Physiology Score II score. The intervention period was associated with mean (95% CI) reductions in patient hospital length of stay (3.7 d [5.2–2.3 d]; p < 0.001), ICU length of stay (1.4 d [2.3–0.5 d]; p < 0.005), duration of mechanical ventilation (1.2 d [2.1–0.3 d]; p < 0.01), and hospital costs per stay (2,560 euros [3,728–1,392 euros]; p < 0.001). The overall cost savings were 10,840 euros (10,727–10,952 euros) per month, mostly due to reduced consumption of sedatives and antimicrobials. No impact on mortality rate was identified.

Conclusions:

Critical care pharmacist-led interventions were associated with decreases in ICU and hospital length of stays and ICU drug costs.
Preventive, Cumulative Effects of Botulinum Toxin Type A in Facial Aesthetics
Authors: Humphrey Shannon , Jacky Birgitte , Gallagher Conor J.
Published: November 2017

BACKGROUND

Botulinum toxin Type A (BoNTA) is the gold standard for the treatment of dynamic rhytides in the face. Recently, clinical observation suggests that individuals who receive regular injections of BoNTA experience ongoing wrinkle reduction and improvements in overall skin quality not observed in those treated sporadically.

OBJECTIVE

To review scientific evidence of qualitative changes in the skin and the possibility of indirect or direct effects on fibroblasts affecting fibroblast activity, including collagen production, after repeated treatment with BoNTA.

MATERIALS AND METHODS

We examined the literature for supporting evidence of the effect of repeated treatment cycles on wrinkle reduction and skin quality; histological changes in collagen structure; alterations in biomechanical features of the skin; and potential fibroblastic response.

RESULTS

Apparent cumulative improvement on wrinkle reduction and additional skin quality attributes with regular BoNTA treatments suggests an ongoing process of dermal repair. Clinical observation suggests that BoNTA injections stimulate collagen production and lead to a reorganization of the collagen network within the extracellular matrix, which in turn may produce improvements in features associated with more youthful skin. Moreover, evidence suggests that BoNTA may have a direct or indirect effect on fibroblast activity.

CONCLUSION

Clinical observation of progressive wrinkle reduction and qualitative improvements in a number of skin attributes that accumulate with more frequent injections of BoNTA suggest an ongoing process of repair leading to prolonged and cumulative effects.
Botulinum Toxin for Eyebrow Shaping: A Systematic Review
Authors: Jabbour Samer , Awaida Cyril , Kechichian Elio , Rayess Youssef , Abdelmassih Youssef , Noel Warren , Hachem Lena el , Nasr Marwan
Published: November 2017

BACKGROUND

Currently, there is no standardized approach for eyebrow shaping with botulinum toxin, and controversies still exist regarding this subject.

OBJECTIVE

The objective of this systematic review is to summarize and compare all the published data regarding eyebrow shaping with botulinum toxin.

METHODS

On March 10, 2017, an online search of published articles in the Medline, Embase, and Cochrane databases were conducted. All articles that used objective measurements to quantify the eyebrow changes after botulinum toxin injection were included in this review.

RESULTS

Eleven studies were selected for inclusion with a total of 585 patients. All the included studies used onabotulinumtoxin A. Seven studies injected both the lateral and the medial eyebrow depressors, 2 studies injected the lateral depressors alone, and 2 studies injected the medial depressors alone. The highest elevation was observed in the lateral brow (0.4–4.8 mm). Bruising and headache were the most frequently reported complications, and only 5 cases of eyelid ptosis were noted.

CONCLUSION

Botulinum toxin injection for eyebrow shaping is a noninvasive, safe, and reproducible procedure. Eyebrow reshaping can be achieved by targeting different muscle groups. However, further randomized controlled trials are warranted.
Risk Factors for Complications in Expander-Based Breast Reconstruction: Multivariate Analysis in Asian Patients
Authors: Suga Hirotaka , Shiraishi Tomohiro , Tsuji Naoko , Takushima Akihiko
Published: November 2017

Background:

There have been many studies examining risk factors for complications in expander-based breast reconstruction after mastectomy, and some patient factors have been identified as risk factors. However, most of the previous studies were based on Caucasian patients.

Methods:

Asian patients who had a tissue expander placed for immediate breast reconstruction between January 2006 and December 2015 (363 patients and 371 expanders) were analyzed retrospectively. Univariate and multivariate analyses were performed to elucidate risk factors for complications.

Results:

The rate of skin necrosis was significantly higher in nipple-sparing mastectomy than in other types of mastectomies (12 patients among 107 patients, P = 0.001). The weight of the resected specimen was significantly higher in the group with complications than in the group without complications (444 g compared with 363 g, P = 0.027). Other factors (age, body mass index, smoking, expander type, preoperative chemotherapy, axillary dissection) had no significant effect on complications. Multivariate analysis with a logistic regression showed that a large breast (over 500 g) was the only significant risk factor for complications, with an odds ratio of 3.20 and a 95% confidence interval of 1.33–7.54 (P = 0.010).

Conclusion:

In this series of Asian patients, breast size, rather than body mass index, is the most important predictor for complications in expander-based breast reconstruction.
Are sex and history of pruritic skin conditions factors which affect the phenomenon of visually evoked itch? An exploratory study
Authors: Lloyd Donna M. , Dodd Rebecca , Higgins Caroline , Burke Melanie R. , McGlone Francis
Published: November 2017

Introduction:

We have previously shown that sensations of itch and the scratch response can be evoked using itch-related images. However, we did not determine whether individual differences in a person’s experience of itch could moderate this effect. This exploratory study aimed to determine whether sex or a history of pruritic skin conditions (PSCs) could influence the effects of visually evoked itch and scratch.

Methods:

Forty-one participants (19 males; 16 with a history of PSCs) viewed static images that could either be itch or nonitch related. These were further separated by picture type: “skin contact” (ants crawling on the hand vs. a butterfly on the finger); “skin response” (scratching an insect bite vs. washing the hands); “skin condition” (psoriasis vs. freckles) or “context only” (insects vs. birds). Images were rated using a 10-point scale by answering: “How itchy do you feel?” (Self-rating) and “How itchy do you think the person in the picture feels?” (Other-rating). Frequency and location of scratching was also recorded.

Results:

The highest itch scores were to itch-related skin contact pictures. Females gave higher itch ratings than males, and people with a history of PSCs gave higher itch ratings when viewing images of people scratching. There was no correlation between itch ratings and scratch response, and no relationship between body site viewed and location of scratching.

Discussion:

There is a heightened response to itch-related cues in females and those with PSCs, indicating a more centrally mediated pathway bringing subconscious itch sensations into conscious awareness in these populations. These findings could influence personalized treatment interventions aimed at reducing awareness of itch sensations in susceptible individuals.
Psyllium Is Superior to Wheat Dextrin for Lowering Elevated Serum Cholesterol
Authors: McRorie Johnson W. , Gibb Roger D. , Womack Joyce B. , Pambianco Daniel J.
Published: November 2017

The Dietary Reference Intakes for fiber are based on an association between a high-fiber diet and a reduced risk of cardiovascular disease. Only 5% of Americans consume the recommended levels of dietary fiber; most consume approximately half the recommended level. If a fiber supplement is used to achieve the recommended level, it is important that the isolated fiber has the requisite physical properties to reduce the risk of cardiovascular disease by lowering elevated serum low-density lipoprotein and total cholesterol. The current study was designed to directly assess the cholesterol-lowering effects of psyllium, a natural nonfermented viscous/gel-forming fiber, versus wheat dextrin, a semisynthetic, readily fermented nonviscous supplement. The study was a 3-month, randomized, parallel-group design (n = 20 enrolled) that assessed psyllium husk (3.4 g) and wheat dextrin (3.5 g) dosed 3 times a day before meals. The results showed that gel-forming psyllium significantly (P < .05) lowered both low-density lipoprotein cholesterol (−17%) and total cholesterol (−11%), without affecting high-density lipoprotein cholesterol, versus wheat dextrin. In conclusion, clinicians and consumers should be aware that the physical characteristics of a fiber supplement determine whether it will provide specific health benefits, and it is recommended to only take those fiber supplements with evidence of clinically meaningful health benefits from well-controlled clinical studies.
Farming and Food Production
Authors: Wilde Parke
Published: November 2017

The Farm Bill is the complex law that reauthorizes nutrition assistance programs and agricultural programs, approximately once every 5 years. This article describes the Farm Bill titles other than the nutrition title, especially commodity subsidy programs, crop insurance programs, conservation programs, and several small programs that support organic, local, and sustainable production. A current policy question is whether the nutrition and agricultural components will remain part of the Farm Bill going forward.
The Royal College of Pathologists of Australasia Quality Assurance Program: Immunohistochemistry Breast Marker Audit Overview 2005-2015
Authors: Haffajee Zenobia Ayesha Mohamed , Kumar Beena , Francis Glenn , Peck Martyn , Badrick Tony
Published: November 2017

The Royal College of Pathologists of Australasia Quality Assurance Program (RCPAQAP) Anatomical Pathology provides a comprehensive External Quality Assurance (EQA) exercise to review the reporting of immunohistochemistry (IHC) and in-situ hybridization (ISH) breast markers through an audit of clinical results. The aim of this exercise was to provide information regarding the quality of breast marker testing within clinical laboratories from 2005 to 2015. This comprehensive audit included estrogen, progesterone, and HER2 marker reporting. This was an important quality assurance activity established in response to ongoing difficulties experienced in laboratories in this area of testing.
Neural Breathing Pattern and Patient-Ventilator Interaction During Neurally Adjusted Ventilatory Assist and Conventional Ventilation in Newborns
Authors: Mally Pradeep V. , Beck Jennifer , Sinderby Christer , Caprio Martha , Bailey Sean M.
Published: November 2017

Objective:

To compare neurally adjusted ventilatory assist and conventional ventilation on patient-ventilator interaction and neural breathing patterns, with a focus on central apnea in preterm infants.

Design:

Prospective, observational cross-over study of intubated and ventilated newborns. Data were collected while infants were successively ventilated with three different ventilator conditions (30 min each period): 1) synchronized intermittent mandatory ventilation (SIMV) combined with pressure support at the clinically prescribed, SIMV with baseline settings (SIMVBL), 2) neurally adjusted ventilatory assist, 3) same as SIMVBL, but with an adjustment of the inspiratory time of the mandatory breaths (SIMV with adjusted settings [SIMVADJ]) using feedback from the electrical activity of the diaphragm).

Setting:

Regional perinatal center neonatal ICU.

Patients:

Neonates admitted in the neonatal ICU requiring invasive mechanical ventilation.

Measurements and Main Results:

Twenty-three infants were studied, with median (range) gestational age at birth 27 weeks (24–41 wk), birth weight 780 g (490–3,610 g), and 7 days old (1–87 d old). Patient ventilator asynchrony, as quantified by the NeuroSync index, was lower during neurally adjusted ventilatory assist (18.3% ± 6.3%) compared with SIMVBL (46.5% ±11.7%; p < 0.05) and SIMVADJ (45.8% ± 9.4%; p < 0.05). There were no significant differences in neural breathing parameters, or vital signs, except for the end-expiratory electrical activity of the diaphragm, which was lower during neurally adjusted ventilatory assist. Central apnea, defined as a flat electrical activity of the diaphragm more than 5 seconds, was significantly reduced during neurally adjusted ventilatory assist compared with both SIMV periods. These results were comparable for term and preterm infants.

Conclusions:

Patient-ventilator interaction appears to be improved with neurally adjusted ventilatory assist. Analysis of the neural breathing pattern revealed a reduction in central apnea during neurally adjusted ventilatory assist use.
Procedural Training and Assessment for Pediatric Emergency Medicine Physicians Within the United States and Canada
Authors: Burns Rebekah A. , Uspal Neil G.
Published: November 2017

Objectives

The aims of this study were to determine current practices in procedural training and skill assessment for attending physicians working in pediatric emergency departments within the United States and Canada and identify barriers to providing training and assessment.

Methods

This was a cross-sectional survey study. Members of the pediatric emergency medicine fellowship program directors and associate program directors Listserv were invited to participate in an anonymous survey about attending physician training and assessment practices for 9 specific procedures and barriers to training and assessment.

Results

Eighty-two (56.2%) of 146 recipients responded, with 79 surveys fully completed; 58.5% of responders report that their division offers procedural training, whereas 14.6% report assessment of procedural skills. The most common procedure for which participants report training and assessment is orotracheal intubation (53.1% and 7.5%, respectively), with training rates for other procedures ranging from 2.5% to 43.0%. Most sites that report training use simulation in some form for education. For assessment, simulation is used almost exclusively. Cost (50.6%), lack of faculty interest (36.7%), and lack of standardized guidelines (36.7%) are the most common barriers to training. Lack of standardized guidelines (51.9%), cost (43.0%), and lack of faculty interest (38.0%) are the most common barriers for assessment.

Conclusions

Although pediatric emergency medicine physicians may be required to perform emergent procedures, opportunities to receive training and assessment in these procedures are limited. Simulation and other educational modalities are being used to provide skill training and assessment, but cost and lack of resources, standardized protocols, and faculty interest are barriers to the implementation of training and assessment programs.
Innovative Methods for Designing Actionable Program Evaluation
Authors: Nesbit Brandon , Hertz Marci , Thigpen Sally , Castellanos Ted , Brown Michelle , Porter Jamila , Williams Amber
Published: November 2017

Context:

For most programs, whether funded through governmental agencies or nongovernmental organizations, demonstrating the impact of implemented activities is vital to ensuring continued funding and support.

Objective:

Program evaluation is a critical tool that serves the dual purpose of describing impact and identifying areas for program improvement. From a funder's perspective, describing the individual and collective impact of state-based programs can be challenging due to variations in strategies being implemented and types of data being collected.

Design:

A case study was used to describe the actionable, mixed-methods evaluation of the Core Violence and Injury Prevention Program (Core VIPP), including how the evaluation design and approach shifted to address evolving challenges faced by award recipients over time. Particular emphasis is given to innovative methods for collecting, analyzing, and disseminating data for key state and federal stakeholders.

Results:

The results of the Core VIPP evaluation showed how this funding played a vital role in building injury and violence prevention capacity in state health departments, leading to a decrease in both intermediate and long-term outcomes.

Conclusions:

The lessons learned through the mixed-method evaluation of the Core VIPP informed the structure of the subsequent funding cycle (Core SVIPP) to include more prescriptive requirements for evidence-based implementation and a state support team structure for delivery of training and technical assistance.
State Injury Programs' Response to the Opioid Epidemic: The Role of CDC's Core Violence and Injury Prevention Program
Authors: Deokar Angela J. , Dellapenna Alan , DeFiore-Hyrmer Jolene , Laidler Matt , Millet Lisa , Morman Sara , Myers Lindsey
Published: November 2017

The Centers for Disease Control and Prevention's (CDC's) Core Violence and Injury Prevention Program (Core) supports capacity of state violence and injury prevention programs to implement evidence-based interventions. Several Core-funded states prioritized prescription drug overdose (PDO) and leveraged their systems to identify and respond to the epidemic before specific PDO prevention funding was available through CDC. This article describes activities employed by Core-funded states early in the epidemic. Four case examples illustrate states' approaches within the context of their systems and partners. While Core funding is not sufficient to support a comprehensive PDO prevention program, having Core in place at the beginning of the emerging epidemic had critical implications for identifying the problem and developing systems that were later expanded as additional resources became available. Important components included staffing support to bolster programmatic and epidemiological capacity; diverse and collaborative partnerships; and use of surveillance and evidence-informed best practices to prioritize decision-making.
Rehabilitation Outcomes in Spinal Abscess Patients With and Without a History of Intravenous Substance Abuse
Authors: Raut Namrata , Nagar Vittal R. , Springer Joe E. , Sawaki Lumy , Salles Sara S.
Published: November 2017

Objective

The aim of the study was to compare functional outcomes of acute inpatient rehabilitation for spinal epidural abscess patients with and without history of intravenous substance abuse.

Design

This is a retrospective case series study in freestanding rehabilitation hospital.

Methods

Charts of 28 spinal epidural abscess patients admitted from January 2012 to September 2015: 13 with intravenous substance abuse and 15 without intravenous substance abuse were reviewed. Both groups received standard-of-care rehabilitation. Statistical analyses of Functional Independence Measure scores were conducted using individual 2 (substance use) × 2 (rehabilitation status) repeated measures analysis of variance. Functional outcomes were defined by total Functional Independence Measure scores as well as motor and cognitive subsets. Length of stay and morphine equivalents were also compared.

Results

There were no significant differences between the two groups. There was a significant main effect of treatment on total Functional Independence Measure scores (P < 0.001), Functional Independence Measure motor scores (P < 0.001), and Functional Independence Measure cognitive scores (P < 0.01) from admission to discharge. Subsequent Student's t tests revealed that the scores of both groups significantly improved on all Functional Independence Measure components. There were no group differences on length of stay and morphine equivalents at discharge.

Conclusions

Acute inpatient rehabilitation can effectively improve functional outcomes in spinal epidural abscess patients with or without intravenous substance abuse, even though these two patient groups can vary in clinical factors.
Preoperative Exposure of Sigmoid Sinus Trajectory in Posterolateral Cranial Base Approaches Using a New Landmark Through a Neurosurgical Perspective
Authors: Doğan Ihsan , Özgüral Onur , Eroğlu Ümit , Al-Beyati Eyyub S. M. , Kilinç Cemil M. , Cömert Ayhan , Uğur Hasan Çağlar
Published: November 2017

The location of burr holes in posterolateral cranial base approaches should be appropriate to provide an adequate operative field, and surgical freedom is crucial for bone window opening. The aim of this study was to search for more convenient and easily detectable landmarks in comparison with current landmarks in posterolateral cranial base surgery. Twenty 3-dimensional reconstructed head and neck computed tomography angiography images (group 1) and 20 cadaver heads (group 2) were evaluated. An imaginary line connecting the angle of the mandible and the mastoid tip was extended upward. A second line passing through the lateral edge of the zygomatic arch was also extended posteriorly. The authors examined if the first line met with the sigmoid sinus throughout its course and determined the location of the intersection point of these 2 lines relative to the sigmoid-transverse sinus junction. The intersection point did not correspond to the sinus region in 3 images from group 1 and 4 specimens from group 2. The matching of the mandibula-mastoid line trajectory with the sigmoid sinus course was unacceptable in 4 images and 5 cadavers. For venous anatomy preservation and anatomic skull base fossa orientation during posterolateral cranial base approaches, upward extension of the mandibula-mastoid line can be a proper landmark for surgical planning in this region. The authors’ proposed superficial anatomical line and intersection point over the skull could be used as a reliable indicator for the external projection of the sigmoid sinus and an appropriate initial burr-hole location.
BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data
Authors: McNally Colin P , Eng Alexander , Noecker Cecilia , Gagne-Maynard William C , Borenstein Elhanan
Published: November 2017

The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce BURRITO, a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information. BURRITO simultaneously visualizes the taxonomic and functional compositions of multiple samples and dynamically highlights relationships between taxa and functions to capture the underlying structure of these data. Users can browse for taxa and functions of interest and interactively explore the share of each function attributed to each taxon across samples. BURRITO supports multiple input formats for taxonomic and metagenomic data, allows adjustment of data granularity, and can export generated visualizations as static publication-ready formatted figures. In this paper, we describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes.
Novel bacterial lineages associated with boreal moss species
Authors: Holland-Moritz Hannah , Stuart Julia , Lewis Lily R. , Miller Samantha , Mack Michelle C. , McDaniel Stuart F. , Fierer Noah
Published: November 2017

Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local environmental conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss species collected near Fairbanks, AK USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbor diverse lineages of potential N2- fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.
No changes in parieto-occipital alpha during neural phase locking to visual quasi-periodic theta-, alpha-, and beta-band stimulation
Authors: Keitel Christian , Benwell Christopher SY , Thut Gregor , Gross Joachim
Published: November 2017

Recent studies have probed the role of the parieto-occipital alpha rhythm (8 – 12 Hz) in human visual perception through attempts to drive its neural generators. To that end, paradigms have used high-intensity strictly-periodic visual stimulation that created strong predictions about future stimulus occurrences and repeatedly demonstrated perceptual consequences in line with an entrainment of parieto-occipital alpha. Our study, in turn, examined the case of alpha entrainment by non-predictive low-intensity quasi-periodic visual stimulation within theta-(4 – 7 Hz), alpha-(8 – 13 Hz) and beta (14 – 20 Hz) frequency bands, i.e. a class of stimuli that resemble the temporal characteristics of naturally occurring visual input more closely. We have previously reported substantial neural phase-locking in EEG recording during all three stimulation conditions. Here, we studied to what extent this phase-locking reflected an entrainment of intrinsic alpha rhythms in the same dataset. Specifically, we tested whether quasi-periodic visual stimulation affected several properties of parieto-occipital alpha generators. Speaking against an entrainment of intrinsic alpha rhythms by non-predictive low-intensity quasi-periodic visual stimulation, we found none of these properties to show differences between stimulation frequency bands. In particular, alpha band generators did not show increased sensitivity to alpha band stimulation and Bayesian inference corroborated evidence against an influence of stimulation frequency. Our results set boundary conditions for when and how to expect effects of entrainment of alpha generators and suggest that the parieto-occipital alpha rhythm may be more inert to external influences than previously thought.
ChIPdig: a comprehensive user-friendly tool for mining multi-sample ChIP-seq data
Authors: Esse Ruben , Grishok Alla
Published: November 2017

Background

In recent years, epigenetic research has enjoyed explosive growth as high-throughput sequencing technologies become more accessible and affordable. However, this advancement has not been matched with similar progress in data analysis capabilities from the perspective of experimental biologists not versed in bioinformatic languages. For instance, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is at present widely used to identify genomic loci of transcription factor binding and histone modifications. Basic ChIP-seq data analysis, including read mapping and peak calling, can be accomplished through several well-established tools, but more sophisticated analyzes aimed at comparing data derived from different conditions or experimental designs constitute a significant bottleneck. We reason that the implementation of a single comprehensive ChIP-seq analysis pipeline could be beneficial for many experimental (wet lab) researchers who would like to generate genomic data.

Results

Here we present ChIPdig, a stand-alone application with adjustable parameters designed to allow researchers to perform several analyzes, namely read mapping to a reference genome, peak calling, annotation of regions based on reference coordinates (e.g. transcription start and termination sites, exons, introns, 5′ UTRs and 3′ UTRs), and generation of heatmaps and metaplots for visualizing
coverage. Importantly, ChIPdig accepts multiple ChIP-seq datasets as input, allowing genome-wide differential enrichment analysis in regions of interest to be performed. ChIPdig is written in R and enables access to several existing and highly utilized packages through a simple user interface powered by the Shiny package. Here, we illustrate the utility and user-friendly features of ChIPdig by analyzing H3K36me3 and H3K4me3 ChIP-seq profiles generated by the modENCODE project as an example.

Conclusions

ChIPdig offers a comprehensive and user-friendly pipeline for analysis of multiple sets of ChIP-seq data by both experimental and computational researchers. It is open source and available at https://github.com/rmesse/ChIPdig.
Behavioral and neural representations of spatial directions across words, schemas, and images
Authors: Weisberg Steven M. , Marchette Steven A. , Chatterjee Anjan
Published: November 2017

Modern spatial navigation requires fluency with multiple representational formats, including visual scenes, signs, and words. These formats convey different information. Visual scenes are rich and specific, but contain extraneous details. Arrows, as an example of signs, are schematic representations in which the extraneous details are eliminated, but analog spatial properties are preserved. Words eliminate all spatial information and convey spatial directions in a purely abstract form. How does the human brain compute spatial directions within and across these formats? To investigate this question, we conducted two experiments on men and women: a behavioral study that was preregistered, and a neuroimaging study using multivoxel pattern analysis of fMRI data to uncover similarities and differences among representational formats. Participants in the behavioral study viewed spatial directions presented as images, schemas, or words (e.g., “left”), and responded to each trial, indicating whether the spatial direction was the same or different as the one viewed previously. They responded more quickly to schemas and words than images, despite the visual complexity of stimuli being matched. Participants in the fMRI study performed the same task, but responded only to occasional catch trials. Spatial directions in images were decodable in the intraparietal sulcus (IPS) bilaterally, but were not in schemas and words. Spatial directions were also decodable between all three formats. These results suggest that IPS plays a role in calculating spatial directions in visual scenes, but this neural circuitry may be bypassed when the spatial directions are presented as schemas or words.

Significance Statement

Human navigators encounter spatial directions in various formats: words (“turn left”), schematic signs (an arrow showing a left turn), and visual scenes (a road turning left). The brain must transform these spatial directions into a plan for action. Here, we investigate similarities and differences between neural representations of these formats. We found that bilateral intraparietal sulci represents spatial directions in visual scenes and across the three formats. We also found that participants respond quickest to schemas, then words, then images, suggesting that spatial directions in abstract formats are easier to interpret than concrete formats. These results support a model of spatial direction interpretation in which spatial directions are either computed for real world action, or computed for efficient visual comparison.
Exploring Applications of Crowdsourcing to Cryo-EM
Authors: Bruggemann Jacob , Lander Gabriel C. , Su Andrew I.
Published: November 2017

Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too time-consuming to perform on data sets of thousands of images. In recent years, crowdsourcing has proven effective at leveraging the open web to manually curate datasets. In particular, citizen science projects such as Galaxy Zoo have shown the power of appealing to users' scientific interests to process enormous amounts of data. To this end, we explored the possible applications of crowdsourcing in cryo-EM particle picking, presenting a variety of novel experiments including the production of a fully annotated particle set from untrained citizen scientists. We show the possibilities and limitations of crowdsourcing particle selection tasks, and explore further options for crowdsourcing cryo-EM data processing.
Genome variants associated with RNA splicing variation in bovine are extensively shared between tissues
Authors: Xiang Ruidong , Hayes Ben J. , Jagt Christy J. Vander , MacLeod Iona M. , Khansefid Majid , Bowman Phil J. , Yuan Zehu , Prowse-Wilkins Claire P. , Reich Coralie M. , Mason Brett A. , Garner Josie B. , Marett Leah C. , Chen Yizhou , Bolormaa Sunduimijid , Daetwyler Hans D. , Chamberlain Amanda J. , Goddard Michael E.
Published: November 2017

Background

Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i.e., geQTLs and 2) variants associated with variations in exon expression, i.e., eeQTLs, in different tissues.

Results

Using whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios were verified by matching their effects on adjacent intron excision ratios. sQTLs contained the highest percentage of variants that are within the intronic region of genes and contained the lowest percentage of variants that are within intergenic regions, compared to eeQTLs and geQTLs. Many geQTLs and sQTLs are also detected as eeQTLs. Many expression QTLs, including sQTLs, were significant in all four tissues and had a similar effect in each tissue. To verify such expression QTL sharing between tissues, variants surrounding (±1Mb) the exon or gene were used to build local genomic relationship matrices (LGRM) and estimated genetic correlations between tissues. For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues. Thus, an effective but simple-to-implement meta-analysis combining information from three tissues is introduced to increase power to detect and validate sQTLs. sQTLs and eeQTLs together were more enriched for variants associated with cattle complex traits, compared to geQTLs. Several putative causal mutations were identified, including an sQTL at Chr6:87392580 within the 5th exon of kappa casein (CSN3) associated with milk production traits.

Conclusions

Using novel analytical approaches, we report the first identification of numerous bovine sQTLs which are extensively shared between multiple tissue types. The significant overlaps between bovine sQTLs and complex traits QTL highlight the contribution of regulatory mutations to phenotypic variations.
Suboptimal eye movements for seeing fine details
Authors: Ağaoğlu Mehmet N. , Sheehy Christy K. , Tiruveedhula Pavan , Roorda Austin , Chung Susana T. L.
Published: November 2017

Human eyes are never stable, even during attempts of maintaining gaze on a visual target. Considering transient response characteristics of retinal ganglion cells, a certain amount of motion of the eyes is required to efficiently encode information and to prevent neural adaptation. However, excessive motion of the eyes leads to insufficient exposure to the stimuli which creates blur and reduces visual acuity. Normal miniature eye movements fall in between these extremes but it is unclear if they are optimally tuned for seeing fine spatial details. We used a state-of-the-art retinal imaging technique with eye tracking to address this question. We sought to determine the optimal gain (stimulus/eye motion ratio) that corresponds to maximum performance in an orientation discrimination task performed at the fovea. We found that miniature eye movements are tuned, but may not be optimal, for seeing fine spatial details.
Secondary metabolites and the antimicrobial potential of five differentColeusspecies in response to salinity stress
Authors: Kotagiri Divya , Khasim Beebi Shaik , Viswanatha Chaitanya Kolluru
Published: November 2017

Salinity is one of the major abiotic stresses that affects the growth and productivity of plants. The presence of soluble salts at high concentration near the root system restricts the uptake of water by plants. Plants grown under saline conditions possess higher amounts of secondary metabolites compared with those grown under normal conditions. The use of traditional medicine to treat infectious diseases is increasing day by day throughout the world. Developing novel drugs with antimicrobial potential from the source of medicinal plants is receiving attention to replace the use of synthetic drugs and to combat the growth of multi-drug resistant strains. Thus screening of medicinal plant extracts is carried out to evaluate their antimicrobial potency. The present study aimed at determining the secondary metabolites and antimicrobial potential of leaf, stem and root ethanol and chloroform extracts of five differentColeusspecies;C.aromaticus, C.amboinicus, Cbarbatus, C.forskohliiandC.zeylanicussubjected to salinity stress. The up regulation in the content of plant bioactive compounds along with the antimicrobial activities of ethanol and chloroform extracts under the influence of salinity stress have been observed during the study inColeus.The leaf, stem and root extracts of all the fiveColeusspecies showed good antimicrobial activity against the tested pathogenic strains. The leaf extracts ofColeusshowed higher inhibitory activity compared to the stem and root extracts. Ethanol extracts showed higher anti-microbial activity ranging from 1.5-100 mg/ml compared with the chloroform extracts ranging from 0.97-250 mg/ml respectively. The study revealed that the increased antimicrobial activity with increasing salinity might be due to the up regulation of secondary metabolites. The leaf, stem and root extracts ofColeusshowed effective antimicrobial activity against the pathogenic strains even under saline conditions is due to the up regulation of secondary metabolites which provides a scope of developing novel drugs to treat infectious diseases.