bluuebunny/crossref_metadata_2025 huggingface dataset:
Petrology and Geochemistry of Serpentinites Associated with the Ultra-High Pressure Lago di Cignana Unit (Italian Western Alps)
Authors: Gilio Mattia , Scambelluri Marco , Agostini Samuele , Godard Marguerite , Peters Daniel , Pettke Thomas
Published: May 2019

In the Western Alps, the ophiolitic Zermatt–Saas Zone (ZSZ) and the Lago di Cignana Unit (LCU) record oceanic lithosphere subduction to high (540°C, 2·3GPa) and ultra-high pressure (600°C, 3·2GPa), respectively. The top of the Zermatt–Saas Zone in contact with the Lago di Cignana Unit consists of olivine + Ti-clinohumite-bearing serpentinites (the Cignana serpentinite) hosting olivine + Ti-clinohumite veins and dykelets of olivine + Ti-chondrodite + Ti-clinohumite. The composition of this serpentinite reveals a refertilized oceanic mantle peridotite protolith that became subsequently enriched in fluid-mobile elements (FME) during oceanic serpentinization. The olivine + Ti-clinohumite veins in the Cignana serpentinite display Rare Earth Element (REE) and FME compositions quite similar to the host-rock, which suggests closed-system dehydration of this serpentinite during subduction. The Ti-chondrodite-bearing dykelets are richer in REE and FME than the host-rock and the dehydration olivine + Ti-clinohumite veins: their Nd composition points to a mafic protolith, successively overprinted by oceanic metasomatism and by subduction zone recrystallization. These dykelets are comparable in composition to eclogites within the ultra-high pressure LCU that derive from subducted oceanic mafic crust. Different from the LCU, serpentinites from the core domains of the ZSZ display REE compositions indicating a depleted mantle protolith. The oceanic serpentinization of these rocks led to an increase in FME and to seawater-like Sr isotope compositions. The serpentinites sampled at increasing distance from the ultra-high pressure LCU reveal different mantle protoliths, still preserve an oceanic geochemical imprint and contain mafic dykelets affected by oceanic metasomatism. The subduction zone history of these rocks thus occurred under relatively closed system conditions, the only possible change during subduction being an enrichment in As and Sb recorded by the serpentinites closer to the crustal LCU. The ZSZ and Cignana serpentinites thus likely evolved in a slab setting and were weakly exposed to interaction with slab-derived fluids characteristic of plate interface settings. Our data suggest two possible scenarios for the evolution of the studied ZSZ and Cignana serpentinites. They are either part of a coherent ophiolite unit whose initial lithospheric mantle was variably affected by depletion and re-fertilization processes, or they belong to separate tectonic slices derived from two different oceanic mantle sections. In the Cignana serpentinite atop the ZSZ, the presence of Ti-chondrodite dykelets similar in composition to the LCU eclogites suggests these two domains were closely associated in the oceanic lithosphere and shared the same evolution to ultra-high pressure conditions during Alpine subduction.
Flares in rheumatoid arthritis: do patient-reported swollen and tender joints match clinical and ultrasonography findings?
Authors: Kuettel Dorota , Terslev Lene , Weber Ulrich , Østergaard Mikkel , Primdahl Jette , Petersen Randi , Ammitzbøll-Danielsen Mads , Möller Sören , Hørslev-Petersen Kim
Published: May 2019

Objectives

To investigate how patient-reported flares in RA are related to clinical joint examination and inflammation detected by US.

Methods

Eighty RA patients with DAS28-CRP <3.2 and no swollen joints at baseline were followed for 1 year. In case of patient-reported hand flare with swollen and tender joints (SJ and TJ, respectively), patients underwent clinical examination for SJ/TJ and US of bilateral wrists, MCP and PIP 1st–5th, six extensor tendon compartments and wrist flexor tendons for synovitis/tenosynovitis. Percentage agreement and kappa were calculated between patient-reported SJ and TJ, clinical examination for SJ/TJ and US findings indicative of inflammation. With US as reference, sensitivity, specificity, positive/negative predictive value and accuracy of patient-reported and clinically examined joints were determined.

Results

Hand flare was reported by 36% (29/80) of patients. At time of flare, all clinical and ultrasonographic measures of disease activity deteriorated compared with baseline. Agreement between patient-reported SJ/TJ, clinically examined SJ/TJ and US was slight (kappa = 0.02–0.20). Patients and clinicians agreed in 79–93% of joints, more frequently on SJ than TJ. With US as reference, specificities were 86–100% and 88–100%, and sensitivities 12–34% and 4–32% for patient-reported SJ/TJ and clinically examined SJ/TJ, respectively.

Conclusion

Over 12 months of follow-up, hand flare was reported by every third RA patient. Self-reported flares were associated with increased disease activity as determined by clinical examination and US. Patient-reported joint assessment may aid in capturing flares between routine clinical visits.
Intake behaviors of yearling steers grazing irrigated pasture and receiving either a free-choice salt-based mineral or a low-moisture molasses-based tub mineral
Authors: Yelich Joel V , Ellison Melinda J , Hall John B , McGee Marcus
Published: May 2019

Mineral intake in grazing cattle is highly variable and research evaluating behavioral aspects of intake are minimal. Development of the GrowSafe System to monitor feed intake allows researchers to record individual feeding behaviors of cattle 24 h per day. In the current experiment conducted during June and July, the GrowSafe System was utilized to evaluate intake behaviors of grazing steers during a short-term free-choice supplementation of either salt-based loose minerals (LM; n = 24; 408 ± 57 kg) or low-moisture molasses-based tub minerals (TUB; n = 24; 396 ± 64 kg). Each treatment was randomized to two of the four irrigated pastures (~5 ha each) consisting of orchard grass (Dactylis glomerat L.), red clover (Trifolium pretense L.), and smooth brome (Bromus inermis). Individual intake was evaluated over three 7-d periods: d – 7 to 0 (adaptation period; AP), d 1 to 7 (period 1; P1), and d 15 to 22 (period 2; P2) of the experiment. The LM mineral mix contained 28% salt during the AP and more salt was added at the initiation of P1 to prevent excessive mineral intake observed during the AP. The LM mineral mix contained 38% salt during P1 and P2. Daily bunk attendance was greater (P < 0.001) for LM (93%) than TUB (67%) steers for the AP. Whereas there was a treatment × period effect (P < 0.001) on daily bunk attendance across P1 (LM: 92%; TUB: 64%) and P2 (LM: 91%; TUB: 82%). Daily mineral intake (as-fed) was greater (P < 0.001) for LM (568 g) than TUB (283 g) during the AP. For P1 and P2, there were no treatment (P = 0.46) and period (P = 0.77) effects on daily mineral intake (LM, 370 g vs. TUB, 343 g), but LM (3.1 visits) had more (P < 0.001) bunk visits per day than TUB (2.0 visits). During the AP, LM (8.5 min) had a greater (P = 0.04) duration of mineral intake per day than TUB (5.6 min); whereas during P1 and P2, TUB (P1 = 8.6; P2 = 12.8 min) had a greater (P ≤ 0.05) duration of mineral intake per day than LM (P1 = 4.9; P2 = 5.7 min). In conclusion, mineral delivery method significantly affected bunk attendance, number of bunk visits per day, and time spent consuming mineral. These results provide additional evidence that mineral type and associated feeding behaviors contribute to the significant variation observed in daily mineral intake in grazing cattle.
The Effects of Smoking on Postoperative Complications After Total Joint Arthroplasty
Authors: Papas Paraskevi Vivian , Gold Christopher A. , Scuderi Giles R.
Published: May 2019

The evidence that preoperative smoking cessation provides decreased postoperative morbidity and complications is continuing to develop and offer stronger results. Although the intensity of the intervention required for a long-term positive impact remains unknown, direct communication between the physician and their patient in combination with nicotine replacement therapy seems to offer the greatest reduction in postoperative morbidity. With many institutions now implementing group classes to prepare patients for their upcoming surgery, adding a smoking cessation group therapy component may further offer patients mutual support to stop smoking before total joint arthroplasty. Preoperative smoking cessation programs not only offer health benefits to the patient by decreasing their risk for periprosthetic joint infection or other complications but also may also lower the cost of care.
Consensus on Reducing Risk in Total Joint Arthroplasty: Revision Surgery
Authors: Hickernell Thomas R. , Cooper H. John
Published: May 2019

Rates of revision hip and knee arthroplasty continue to increase. Patients undergoing revision hip and knee arthroplasty face a different set of challenges than those undergoing primary arthroplasties, with increased rates of medical and surgical complications. Specifically, patients undergoing revision arthroplasty have higher rates transfusion, more unplanned readmissions, greater cardiac and renal complications, and more frequent surgical complications including surgical site infections and need for reoperation and revision surgery. Multiple strategies may be used in an effort to lower these risks, including shifting these surgeries to higher volume medical centers and surgeons, vigorously optimizing revision arthroplasty patients in the preoperative setting, using blood conserving strategies including universal use of tranexamic acid and selective use of blood cell salvage and reinfusion, and closed-incision negative wound pressure therapy to decrease rates of wound complications and surgical site infections.
A Simple RNA Target Capture NGS Strategy for Fusion Genes Assessment in the Diagnostics of Pediatric B‐cell Acute Lymphoblastic Leukemia
Authors: Grioni Andrea , Fazio Grazia , Rigamonti Silvia , Bystry Vojtech , Daniele Giulia , Dostalova Zuzana , Quadri Manuel , Saitta Claudia , Silvestri Daniela , Songia Simona , Storlazzi Clelia T. , Biondi Andrea , Darzentas Nikos , Cazzaniga Giovanni
Published: May 2019

Supplemental Digital Content is available in the text
MALONDIALDEHYDE LEVELS IN PATIENTS WITH AGE-RELATED MACULAR DEGENERATION
Authors: Pinna Antonio , Boscia Francesco , Paliogiannis Panagiotis , Carru Ciriaco , Zinellu Angelo
Published: May 2019

Background/Purpose:

The role of blood malondialdehyde (MDA) in age-related macular degeneration (AMD), the leading cause of new blindness in industrialized countries, is still matter of debate. We performed a systematic review and meta-analysis of the published data on the MDA levels in AMD patients.

Methods:

PubMed, ISI Web of Sciences, and Scopus searches were performed according to MOOSE guidelines. Case–control studies were eligible for inclusion. Participants and controls were AMD patients and subjects without AMD, respectively. The main outcome measures were wet AMD and dry AMD. MDA level was the main exposure variable. Data were pooled using a random-effects model.

Results:

Twelve case–control studies were identified. A total of 634 AMD patients (mean age 66.7 years) and 656 controls without AMD (mean age 67.8 years) were evaluated. Extreme between-study heterogeneity was observed (I2= 96.8%,P< 0.001). Pooled standardized mean difference showed that MDA values were significantly higher in patients with AMD (standardized mean difference = 1.91µmol/L, 95% confidence interval = 1.08–2.74;P< 0.001). In a model including five studies, homogenous for age, sample matrix, and laboratory testing for MDA, heterogeneity decreased from extreme to moderate (I2= 46.4%,P= 0.113), and pooled standardized mean difference, though attenuated, remained significantly higher in AMD patients (standardized mean difference = 1.07µmol/L, 95% confidence interval = 0.82–1.31;P< 0.001).

Conclusion:

There is some evidence of higher levels of MDA in AMD patients compared with healthy controls; however, this result should be interpreted with caution because of extreme between-study heterogeneity and the possible effect of publication bias. Future studies, preferably well age-matched and of cohort design, are necessary before any firm conclusions on the putative role of elevated MDA on AMD can be drawn.
Medicare for All's Political Reality
Authors: Millenson Michael L.
Published: May 2019

Attempting to enact Medicare for All in today's political climate is akin to a Starbucks barista saying he is torn between staying with his girlfriend and marrying Jennifer Lawrence: it is an unrealistic ideal. But if one also takes into account the genuine threat to the Affordable Care Act (ACA) from the Trump administration's decision to support a federal judge's controversial under-appeal ruling that the entire ACA is unconstitutional, the Medicare for All enthusiasm is even more alarming. It also ignores the unprecedented disruption to the lives of tens of millions of Americans such a massive change would create.
Simple Endoscopic Score of Crohn Disease and Magnetic Resonance Enterography in Children
Authors: Weiss Batia , Turner Dan , Griffiths Anne , Walters Tom , Herman‐Sucharska Izabela , Coppenrath Eva , Anupindi Sudha A. , Towbin Alexander J. , O’Brien Kathy , Silverstein Jared , Navas Victor , Koletzko Sibylle , Sladek Malgorzata , Gavish Matan , Amitai Michal M. ,   ImageKids study group. NCT01881490
Published: May 2019

Objectives:

We aimed to explore the ability of magnetic resonance enterography (MRE) to impute the simple endoscopic score of Crohn disease (SES‐CD) in children with CD, in whom failure of ileal intubation is common and may impair SES‐CD calculation in clinical studies.

Methods:

This is a substudy of the prospective ImageKids study in which children with CD underwent ileocolonoscopy (scored by SES‐CD) and MRE (scored on a 100 mm visual analogue scale [VAS] and by MaRIA). Mucosal healing (MH) was defined as SES‐CD <3, MRE‐VAS <20 mm, and/or MaRIA <7.

Results:

A total of 237 children (22 centers, age 11.5 ± 3.3 years), were enrolled. Ileal intubation has failed in 40 of 237 (17%). The agreement between SES‐CD and MRE was 75% (k = 0.508, P < 0.001) in the ileum, and 68% to 85% in the colonic segments (k = 0.21–0.50, P < 0.001). The sensitivity and specificity of ileal MRE‐VAS for MH were 91.7% (95% confidence interval 0.84–0.96) and 53.1% (95% confidence interval 0.43–0.63), respectively. The ileal MaRIA score (calculated in 33/40) was higher in the children without ileal intubation than in the others (20.5 ± 7.1 vs 15.1 ± 10.8, respectively, P = 0.0018). In 7% (16/237) of children, isolated active ileal disease would have been missed when considering SES‐CD only. A multivariable model predicted the ileal SES‐CD subscore from the MaRIA: SES‐CDileum = 1.145 + 0.169 × MaRIAileum rounded to the nearest whole number (R2 = 0.17). Applying this model to the children without ileal intubation revealed that 29 of 33 (88%) had ileal disease; 8 of 29 patients (28%) with normal colonic SES‐CD had imputed ileal SES‐CD ≥3.

Conclusions:

MRE is useful for imputing the ileal disease in pediatric clinical studies, overcoming the problem of ileal nonintubation.
De Novo Crohn's Disease of the Pouch in Children Undergoing Ileal Pouch‐Anal Anastomosis for Ulcerative Colitis
Authors: Jarchin Lauren , Spencer Elizabeth A. , Khaitov Sergey , Greenstein Alexander , Jossen Jacqueline , Lai Joanne , Dunkin David , Pittman Nanci , Benkov Keith , Dubinsky Marla C.
Published: May 2019

Background:

Approximately 10% of children with ulcerative colitis (UC) undergo colectomy with ileal pouch‐anal anastomosis (IPAA). We aimed to describe the postoperative outcomes, with an emphasis on chronic pouch inflammation including de novo Crohn disease (CD) at a tertiary care inflammatory bowel disease center.

Methods:

Electronic medical records of all children who underwent colectomy ≤18 years between 2008 and 2017 were reviewed. Clinical and laboratory data were recorded. Primary outcome was frequency of chronic pouch inflammation including de novo CD. Secondary outcomes included early (≤30 days from index surgery) and late postoperative complications. Descriptive statistics (median and interquartile range) summarized the data and univariate analysis tested associations with outcomes.

Results:

Fifty‐eight children underwent colectomy and 56 completed IPAA. Median age at diagnosis was 14 years (12–16.2) and at colectomy 16.2 years (14.2–17.7) with median follow‐up of 13 months (5–43). Sixty‐six percent underwent 3‐stage IPAA and 78% were biologic exposed. Eleven had chronic pouchitis, 73% antibiotic refractory and 25% met criteria for de novo CD by median of 19 months (9–41). A total of 21% and 50% experienced early and late surgical complications, most commonly ileus and recurrent IPAA stricture. The pouch failure rate was 3.6%. Chronic pouch inflammation was associated with a later diagnosis of de novo CD (P = 0.0025).

Conclusions:

In pediatric UC, CD is not uncommon after IPAA. Chronic pouch inflammation often precedes a diagnosis of de novo CD. Families should be informed of the short‐ and long‐term outcomes in children before UC surgery.
Leveraging Electronic Health Records and Machine Learning to Tailor Nursing Care for Patients at High Risk for Readmissions
Authors: Brom Heather , Brooks Carthon J. Margo , Ikeaba Uchechukwu , Chittams Jesse
Published: May 2019

Background:

Electronic health record–derived data and novel analytics, such as machine learning, offer promising approaches to identify high-risk patients and inform nursing practice.

Purpose:

The aim was to identify patients at risk for readmissions by applying a machine-learning technique, Classification and Regression Tree, to electronic health record data from our 300-bed hospital.

Methods:

We conducted a retrospective analysis of 2165 clinical encounters from August to October 2017 using data from our health system's data store. Classification and Regression Tree was employed to determine patient profiles predicting 30-day readmission.

Results:

The 30-day readmission rate was 11.2% (n = 242). Classification and Regression Tree analysis revealed highest risk for readmission among patients who visited the emergency department, had 9 or more comorbidities, were insured through Medicaid, and were 65 years of age and older.

Conclusions:

Leveraging information through the electronic health record and Classification and Regression Tree offers a useful way to identify high-risk patients. Findings from our algorithm may be used to improve the quality of nursing care delivery for patients at highest readmission risk.
The Advanced Practice Nurse Will See You Now
Authors: McClain Jesse V. , Chance Elisha A.
Published: May 2019

Background:

There is a paucity of evidence-based, posthospital stroke care in the United States proven to reduce preventable hospital readmissions.

Local Problem:

Follow-up with a provider after hospitalization for stroke or transient ischemic attack had low compliance rates. This may contribute to preventable readmissions.

Methods:

A retrospective, descriptive chart review to determine whether an advanced practice registered nurse (APRN)-led transitional care clinic for stroke survivors impacted 30- and 90-day hospital readmissions. Readmissions between clinic patients and nonclinic patients were compared.

Interventions:

The site implemented an APRN-led transitional care stroke clinic to improve patient transitions from hospital to home.

Results:

The 30-day readmission proportion was significantly higher in nonclinic patients (n = 335) than in clinic patients (n = 68) (13.4% vs 1.5%, respectively; P = .003). The 90-day readmission proportion was numerically higher in nonclinic patients (12.8% vs 4.4%, respectively; P = .058).

Conclusions:

The results suggest the APRN-led clinic may impact 30-day hospital readmissions in stroke/transient ischemic attack survivors.
Evidence-Based Quality Improvement Training Programs
Authors: Sarff Laura , O'Brien Roxanne
Published: May 2019

Background:

Patient harm from medical errors is frequently the result of poorly designed systems. Quality improvement (QI) training programs should build staff capability and organizational capacity for improving systems.

Problem:

Lack of internal expertise in QI and financial impact of hiring consultants deter organizations from developing QI training.

Approach:

One safety net hospital, with minimal resources, used evidence-based elements to create a Quality Academy Program.

Outcomes:

Significant outcomes demonstrated individual capability in undertaking QI initiatives. Staff who continued QI posttraining and the number of initiatives launched demonstrated organizational capacity. Feedback showed an increase in confidence with projects intended to improve care processes and patient outcomes.

Conclusions:

The elements shown to be essential in QI programs to build capability and capacity for organizational improvement can improve patient outcomes and organizational work processes as well as impact staff engagement and morale.
Central Conditions Mimicking Benign Paroxysmal Positional Vertigo: A Case Series
Authors: Power Laura , Murray Kate , Bullus Kristian , Drummond Katherine J. , Trost Nicholas , Szmulewicz David J.
Published: May 2019

Background and Purpose:

Benign paroxysmal positional vertigo (BPPV) is the most common cause of positional vertigo. The term “benign” is consistent with a peripheral vestibular disorder that does not carry the potentially sinister sequelae of a central nervous system (CNS) cause. However, in 12% to 20% of cases, positional vertigo may be attributed to CNS pathology, including tumors of the cerebellum.

Case Description:

Here, we present a series of 3 cases in which positional vertigo and nystagmus were the only presenting features in 2 cases of cerebellar tumor and 1 case of obstructive hydrocephalus.

Intervention:

All patients underwent surgical intervention for removal of posterior fossa tumors or posterior fossa decompression for obstructive hydrocephalus. Following surgery, all 3 patients underwent a period of vestibular rehabilitation for postoperative motion sensitivity and balance impairment.

Outcomes:

Despite the continuing presence of central positioning nystagmus, all 3 patients recovered well, putatively with the aid of vestibular rehabilitation.

Discussion:

The presence of central positioning nystagmus may be the sole presenting feature of serious neurological conditions such as posterior fossa tumor. It is recommended that a diagnosis of BPPV can only be made if Dix-Hallpike or supine roll maneuver elicits nystagmus that is consistent with BPPV. Any features of the nystagmus, which are not consistent with BPPV, should raise suspicion of central pathology, and warrant further investigation.

Video Abstract available for more insights from the authors (see Video Abstract, Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A265).
Exergaming-Based Dexterity Training in Persons With Parkinson Disease: A Pilot Feasibility Study
Authors: van Beek Judith J. W. , van Wegen Erwin E. H. , Bohlhalter Stephan , Vanbellingen Tim
Published: May 2019

Background and Purpose:

Many individuals with Parkinson disease (PD) suffer from impaired dexterity, which impacts activities of daily living and quality of life. Exergaming, video game-based training with augmented virtual reality, may have value for improving function. The aim of the present pilot study was to comprehensively evaluate the feasibility of a dexterity training program using exergaming, in individuals with PD.

Methods:

Ten participants with PD (aged between 55 and 75 years, Hoehn and Yahr stages II-IV) trained over a period of 4 weeks, twice a week for 30 minutes. Baseline (T0) and postintervention (T1) assessments were done. Primary outcomes with respect to feasibility were the adherence rate, open-end questions, the level of participation (Pittsburgh Rehabilitation Participation Scale), and the usability (System Usability Scale). Dexterous function was measured with the Nine-Hole Peg Test and the Dexterity Questionnaire-24. Upper limb motor impairment was assessed by a modified version of the Movement Disorders Society Unified Parkinson's Disease Rating Scale III. Finally, quality of life was assessed by the 39-item Parkinson's Disease Questionnaire (PDQ-39).

Results:

Adherence rate was 99%, motivation increased significantly from 3.9 to 4.8 (Pittsburgh Rehabilitation Participation Scale, P = 0.03), and system usability of the exergaming system was acceptable to very good. Regarding potential efficacy, participants with impaired dexterity at T0 significantly improved in the Nine-Hole Peg Test and the PDQ-39.

Discussions and Conclusions:

The outcomes of this pilot study suggest that exergaming is feasible and has potential to improve dexterity in individuals with PD. Its efficacy should be investigated in a properly powered randomized controlled trial.

Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A270).
Optimizing Dietary Protein for Lifelong Bone Health
Authors: Wallace Taylor C.
Published: May 2019

Bone undergoes continuous remodeling; therefore, an adequate supply of amino acid and mineral substrate is needed to support the formation and maintenance of bone across the life span. Although a considerable amount of research has been given to the type and amount of dietary protein intake necessary to achieve optimal bone health, authoritative bodies have varying recommendations around intake, largely established on nonbone health outcomes and/or early nitrogen-balance studies. The relationship of dietary protein intake and bone health has sparked intense debate for many decades, and there are inconsistencies in how healthcare providers counsel patients about protein in relation to bone health and prevention of osteoporosis. However, a recent series of investigations from various researches and leading bone health societies have contradicted these early hypotheses and led to a clearer understanding of the role dietary protein plays in optimizing bone health across the life span. This article reviews the existing evidence to date and summarizes a recent webinar cohosted by the American Society for Nutrition and American Bone Health.
Developing Safe Syringe Exchange Programs: Role of the North Carolina Division of Public Health
Authors: Novick Lloyd F. , Staley Danny , Novick Carole G.
Published: May 2019

Syringe exchange programs became legal in North Carolina on July 11, 2016. A combination of forces led to this progressive public health measure, including advocacy of the State Health Official, in a state characterized by a conservative political climate. Data collected by the division of public health were a key contributor to the initiative. Nearly 5 North Carolinians died each day from unintentional medication or drug overdose. High rates of coinfection including hepatitis B and C, human immunodeficiency virus, and endocarditis were shown to have substantial economic consequences. The North Carolina Harm Reduction Coalition and use of Moral Foundations Theory in crafting messages were important in influencing legislation. North Carolina now has 30 active syringe exchange programs serving 40 counties. Individuals using intravenous drugs who take advantage of these syringe exchange programs are provided with clean needles to not only help prevent the spread of illness but also learn more about safe health practices.
Measuring Alcohol Outlet Density: An Overview of Strategies for Public Health Practitioners
Authors: Sacks Jeffrey J. , Brewer Robert D. , Mesnick Jessica , Holt James B. , Zhang Xingyou , Kanny Dafna , Elder Randy , Gruenewald Paul J.
Published: May 2019

Context:

Excessive alcohol use is responsible for 88 000 deaths in the United States annually and cost the United States $249 billion in 2010. There is strong scientific evidence that regulating alcohol outlet density is an effective intervention for reducing excessive alcohol consumption and related harms, but there is no standard method for measuring this exposure.

Program:

We overview the strategies available for measuring outlet density, discuss their advantages and disadvantages, and provide examples of how they can be applied in practice.

Implementation:

The 3 main approaches for measuring density are container-based (eg, number of outlets in a county), distance-based (eg, average distance between a college and outlets), and spatial access–based (eg, weighted distance between town center and outlets).

Evaluation:

While container-based measures are the simplest to calculate and most intuitive, distance-based or spatial access–based measures are unconstrained by geopolitical boundaries and allow for assessment of clustering (an amplifier of certain alcohol-related harms). Spatial access–based measures can also be adjusted for population size/demographics but are the most resource-intensive to produce.

Discussion:

Alcohol outlet density varies widely across and between locations and over time, which is why it is important to measure it. Routine public health surveillance of alcohol outlet density is important to identify problem areas and detect emerging ones. Distance- or spatial access–based measures of alcohol outlet density are more resource-intensive than container-based measures but provide a much more accurate assessment of exposure to alcohol outlets and can be used to assess clustering, which is particularly important when assessing the relationship between density and alcohol-related harms, such as violent crime.
The Relationship Between Demographic Characteristics and Noninflammatory Complaints in Rheumatoid Arthritis Patients on Remission
Authors: Karatas Gulsah , Umay Ebru , Gurcay Eda
Published: May 2019

Objectives

The aim of this study was to investigate the noninflammatory complaints in rheumatoid arthritis (RA) patients on remission and the relationship between these complaints and disease characteristics.

Methods

This is a medical records review study of 103 RA patients who sustained a remission period for at least 6 months. Clinical features and demographic characteristics of patients, such as laboratory parameters, current number of sensitive and swollen joints, pain level and Patient Global Assessment, previously used medications, and modified Health Assessment Questionnaire, were carefully recorded. Patients were divided into 2 groups according to the presence of noninflammatory complaints as patients with or without noninflammatory complaints (group 1, n = 56; group 2, n = 47, respectively).

Results

The most common complaints with a decreasing frequency were as follows: low back pain (n = 13 [23.2%]), degenerative knee pain (n = 11 [19.6%]), and widespread body pain due to fibromyalgia (n = 7 [12.5%]). The mean age and age at diagnosis were higher in group 1 than in those in group 2 (p = 0.039, and p = 0.014, respectively).

Conclusions

Noninflammatory complaints can be observed in about 50% of RA patients on remission. These complaints were more common in elderly patients with old-age disease onset. Therefore, while evaluating and treating this patient population, noninflammatory complaints and disease-specific parameters should be considered carefully in order to fully improve the clinical outcomes.
Ultrasonic Classification of Multicategory Thyroid Nodules Based on Logistic Regression
Authors: Zheng Yi , Xu Shangyan , Zheng Zhan , Wu Lili , Chen Lin , Zhan Weiwei
Published: May 2019

This study aims to screen out significant ultrasonic features to establish different predictive models of thyroid nodules based on logistic regression, with different indicators being included and nodular size being differentiated, and then compare them.

Ultrasonic features of 1906 thyroid nodules in 1761 patients who had undergone sonography and fine-needle aspiration or surgery in our hospital were retrospectively analyzed. According to nodule size and whether vascular or elastographic indicators being included or not, nodules were divided into 12 groups. By univariate and multivariate analysis, the significant sonographic features to diagnose nodules of each group were screened and compared. The logistic regression models were built, and the cutoff values were calculated. The diagnostic performance of newly established models was validated, and the best model was compared with the American College of Radiology Thyroid Imaging Reporting and Data System.

Significant features used to diagnose nodules in all models were hypoechoic, irregular margin, and microcalcification. Predominantly solid was an important indicator to differentiate benign and malignant macronodules. A taller-than-wide shape was a significant indicator of malignant micronodules. Strain elastographic character did show diagnostic value. The area under the curve of logistic regression models for malignant risk prediction were all higher than 0.7, and the best one was model 7, but the diagnostic performance was significantly reduced when models performed bivariate prediction.

The most valuable indicators of malignant thyroid nodules are hypoechoic, irregular margin, and microcalcification. New models are suitable for nodules of different sizes and with or without vascular or elastographic features being described.
The Value of Elasticity Contrast Index in the Differential Diagnosis of Thyroid Solid Nodules
Authors: Di Zhixin , Li Ziyao , Tian Jiawei , Wang Dongmo , Liu Li , Liu Cong
Published: May 2019

Objectives

To assess the clinical value of elasticity contrast index (ECI) in differentiating malignant thyroid nodules from benign ones.

Methods

Conventional ultrasound and elastography with pulsation of the carotid artery used as the compression source were retrospectively reviewed on 175 patients (143 females and 32 males; mean ± SD age, 45.17 ± 11.45 years) with 236 solid nodules (113 malignant and 123 benign). All nodules were confirmed by fine-needle aspiration or surgery to be accurately diagnosed. Elasticity contrast index values were computed and used to quantify local stiffness contrast within a nodule as determined with elastography. Elasticity contrast index values between the malignant and benign groups were compared and then related with pathological results. Diagnostic performance of this method was evaluated with use of the receiver operating characteristic curve.

Results

Mean ± SD ECI values for malignant thyroid nodules were significantly greater than those for benign nodules (3.67 ± 1.20 vs 1.80 ± 0.74, P < 0.01). Area under the receiver operating characteristic curve of ECI values was 0.907 (95% confidence interval, 0.867–0.948), and the best cutoff point was 2.16, leading to a sensitivity of 90.3%, specificity of 82.9%, positive predictive value of 83.7% and negative predictive value of 91.2%.

Conclusions

Elasticity contrast index values can serve as a useful parameter in the differential diagnosis of solid thyroid nodules. With the use of ECI values, objective quantitative information on the tumor stiffness can be achieved to improve diagnostic confidence.
Implicit Measures of Receptive Vocabulary Knowledge in Individuals With Level 3 Autism
Authors: Coderre Emily L. , Chernenok Mariya , O’Grady Jessica , Bosley Laura , Gordon Barry , Ledoux Kerry
Published: May 2019

Implicit measures of cognition are essential for assessing knowledge in people with Level 3 autism because such individuals are often unable to make reliable overt behavioral responses. In this study, we investigated whether three implicit measures—eye movement (EM) monitoring, pupillary dilation (PD), and event-related potentials (ERPs)—can be used to reliably estimate vocabulary knowledge in individuals with Level 3 autism. Five adults with Level 3 autism were tested in a repeated-measures design with two tasks. High-frequency ‘known’ words (eg, bus, airplane) and low-frequency ‘unknown’ words (eg, ackee, cherimoya) were presented in a visual world task (during which EM and PD data were collected) and a picture-word congruity task (during which ERP data were collected). Using a case-study approach with single-subject analyses, we found that these implicit measures have the potential to provide estimates of receptive vocabulary knowledge in individuals with Level 3 autism. Participants differed with respect to which measures were the most sensitive and which variables best predicted vocabulary knowledge. These implicit measures may be useful to assess language abilities in individuals with Level 3 autism, but their use should be tailored to each individual.
Ferroic multipolar order and disorder in cyanoelpasolite molecular perovskites
Authors: Coates C. S. , Gray H. J. , Bulled J. M. , Boström H. L. B. , Simonov A. , Goodwin A. L.
Published: May 2019

We use a combination of variable-temperature high-resolution synchrotron X-ray powder diffraction measurements and Monte Carlo simulations to characterize the evolution of two different types of ferroic multipolar order in a series of cyanoelpasolite molecular perovskites. We show that ferroquadrupolar order in [C
3
N
2
H
5
]
2
Rb[Co(CN)
6
] is a first-order process that is well described by a four-state Potts model on the simple cubic lattice. Likewise, ferrooctupolar order in [NMe
4
]
2
B[Co(CN)
6
] (B = K, Rb, Cs) also emerges via a first-order transition that now corresponds to a six-state Potts model. Hence, for these particular cases, the dominant symmetry breaking mechanisms are well understood in terms of simple statistical mechanical models. By varying composition, we find that the effective coupling between multipolar degrees of freedom—and hence the temperature at which ferromultipolar order emerges—can be tuned in a chemically sensible manner.

This article is part of the theme issue ‘Mineralomimesis: natural and synthetic frameworks in science and technology’.
Geomimetic approaches in the design and synthesis of metal-organic frameworks
Authors: Huskić Igor , Friščić Tomislav
Published: May 2019

The recent discovery of minerals with metal-organic framework (MOF) structures has challenged the view of MOFs as purely synthetic materials. At the same time, the application of geo-inspired synthetic methodologies, such as accelerated ageing and pseudomorphic replication, has enabled a cleaner, more environmentally friendly synthesis of MOFs from mineral-like feedstocks, as well as the assembly of materials with structure controlled at both micro- and meso-scales. These almost concomitant developments have highlighted the previously unknown relationships between geology and MOF chemistry. Here, we outline examples of MOF structures found in minerals, and note geologically inspired approaches to MOF synthesis, as a means to highlight how the emergent geomimetic concepts in MOF chemistry can lead to advances in the design and synthesis of MOFs.

This article is part of the theme issue ‘Mineralomimesis: natural and synthetic frameworks in science and technology’.
Flexibility of network materials and the Rigid Unit Mode model: a personal perspective
Authors: Dove Martin T.
Published: May 2019

The Rigid Unit Mode model was initially developed to understand the origin of displacive phase transitions in network silicate structures. Here, we review the successes of the model, and consider how it might apply to a wider range of network structures.

This article is part of the theme issue ‘Mineralomimesis: natural and synthetic frameworks in science and technology’.
Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacteria via Dynamic RNA Nanotechnology
Authors: Hanewich-Hollatz Mikhail H. , Chen Zhewei , Huang Jining , Hochrein Lisa M. , Pierce Niles A.
Published: May 2019

A guide RNA (gRNA) directs the function of a CRISPR protein effector to a target gene of choice, providing a versatile programmable platform for engineering diverse modes of synthetic regulation (edit, silence, induce, bind). However, the fact that gRNAs are constitutively active places limitations on the ability to confine gRNA activity to a desired location and time. To achieve programmable control over the scope of gRNA activity, here we apply principles from dynamic RNA nanotechnology to engineer conditional guide RNAs (cgRNAs) whose activity is dependent on the presence or absence of an RNA trigger. These cgRNAs are programmable at two levels, with the trigger-binding sequence controlling the scope of the effector activity and the target-binding sequence determining the subject of the effector activity. We demonstrate molecular mechanisms for both constitutively active cgRNAs that are conditionally inactivated by an RNA trigger (ON→OFF logic) and constitutively inactive cgRNAs that are conditionally activated by an RNA trigger (OFF→ON logic). For each mechanism, automated sequence design is performed using the reaction pathway designer within NUPACK to design an orthogonal library of three cgRNAs that respond to different RNA triggers. In E. coli expressing cgRNAs, triggers, and silencing dCas9 as the protein effector, we observe programmable conditional gene silencing with a median dynamic range of ≈6-fold for an ON→OFF “terminator switch” mechanism, ≈15-fold for an ON→OFF “splinted switch” mechanism, and ≈3.6-fold for an OFF→ON “toehold switch” mechanism; the median crosstalk within each cgRNA library is <2%, <2%, and ≈20% for the three mechanisms. By providing programmable control over both the scope and target of protein effector function, cgRNA regulators offer a promising platform for synthetic biology.
Prediction of specific TCR-peptide binding from large dictionaries of TCR-peptide pairs
Authors: Springer Ido , Besser Hanan , Tickotsky-Moskovitz Nili , Dvorkin Shirit , Louzoun Yoram
Published: May 2019

Current sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. Currents tools are based on conserved motifs and are applied to peptides with many known binding TCRs.

Given any TCR and peptide, we employ new NLP-based methods to predict whether they bind. We combined large-scale TCR-peptide dictionaries with deep learning methods to produce ERGO (pEptide tcR matchinG predictiOn), a highly specific and generic TCR-peptide binding predictor.

A set of standard tests are defined for the performance of peptide-TCR binding, including the detection of TCRs binding to a given peptide/antigen, choosing among a set of candidate peptides for a given TCR and determining whether any pair of TCR-peptide bind. ERGO significantly outperforms current methods in these tests even when not trained specifically for each test.

The software implementation and data sets are available at https://github.com/louzounlab/ERGO
Persistent features of intermittent transcription
Authors: Wilkinson Michael , Darmanis Spyros , Pisco Angela Oliveira , Huber Greg
Published: May 2019

Here we report statistical studies of single-cell mRNA counts from cells derived from different tissues of adult mice. By examining correlations between mRNA gene counts we find strong evidence that when genes are only observed in a small fraction of cells, this is as a consequence of intermittent transcription rather than of expression only in specialized cell types. Count statistics are used to estimate a peak transcription level for each gene, and a probability for the gene to be active in any given cell. We find that the peak transcription levels are approximately constant across different tissue types, but the gene expression probabilities may be markedly different. Both these quantities have very wide ranges of values, with a probability density function well approximated by a power law.

Author summary

Using evidence from single-cell mRNA counts, we argue that the expression of many genes in individual mouse cells is highly intermittent. Comparing cells from different tissues, we find that the peak activity of a given gene is approximately the same in all tissue types, whereas the probability of a gene being active can differ markedly.
Population history and genetic adaptation of the Fulani nomads: Inferences from genome-wide data and the lactase persistence trait
Authors: Vicente Mário , Priehodová Edita , Diallo Issa , Podgorná Eliska , Poloni Estella S. , Černý Viktor , Schlebusch Carina M.
Published: May 2019

Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt. Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. Our findings further suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first Genome Wide Association study (GWAS) of the lactase persistence trait. We also further explored signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.
TEMPO: Detecting Pathway-Specific Temporal Dysregulation of Gene Expression in Disease
Authors: Pietras Christopher Michael , Ocitti Faith , Slonim Donna K.
Published: May 2019

While many transcriptional profiling experiments measure dynamic processes that change over time, few include enough time points to adequately capture temporal changes in expression. This is especially true for data from human subjects, for which relevant samples may be hard to obtain, and for developmental processes where dynamics are critically important. Although most expression data sets sample at a single time point, it is possible to use accompanying temporal information to create a virtual time series by combining data from different individuals.

We introduce TEMPO, a pathway-based outlier detection approach for finding pathways showing significant temporal changes in expression patterns from such combined data. We present findings from applications to existing microarray and RNA-seq data sets. TEMPO identifies temporal dysregulation of biologically relevant pathways in patients with autism spectrum disorders, Huntington’s disease, Alzheimer’s disease, and COPD. Its findings are distinct from those of standard temporal or gene set analysis methodologies.

Overall, our experiments demonstrate that there is enough signal to overcome the noise inherent in such virtual time series, and that a temporal pathway approach can identify new functional, temporal, or developmental processes associated with specific phenotypes.

Availability

An R package implementing this method and full results tables are available at bcb.cs.tufts.edu/tempo/.