bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Burdens of β-Thalassemia Major in Affected Children
Authors: Gharaibeh Huda , Barqawi Moussa A. , Al-Awamreh Khetam , Al Bashtawy Mohammed
Published: February 2018

Background:

β-thalassemia major (BTM) is an inherited blood disorder leading to severe anemia. A better understanding of BTM complications can be considered an important factor in developing effective health care provision.

Method:

A descriptive exploratory design was used to identify the clinical burden of BTM from affected children's perspective. A convenience sample of 45 patients with BTM, accompanied by a family member, was recruited from a governmental hospital during April–May 2015.

Results:

The most reported clinical burden was facial deformity 86.9%, followed by systematic infection (48.8%), growth delay (44.4%), and liver problems (39.9%). Patient age was significantly associated with clinical burdens such as bone pain and facial deformity. The number of blood transfusions received was associated with growth delay and bone pain.

Conclusion:

This study highlights the clinical burdens of thalassemia on affected children, in terms of physical appearance, growth delay and other burdens.
Leading Change
Authors: Nelson-Brantley Heather V. , Ford Debra J. , Miller Karen L. , Stegenga Kristin A. , Lee Robert H. , Bott Marjorie J.
Published: February 2018

OBJECTIVE

The aim of this study was to understand how nurses in a 25-bed critical-access hospital (CAH) led change to become the 1st to achieve Magnet®.

BACKGROUND

Approximately 21% of the US population lives in rural areas served by CAHs. Rural nurse executives are particularly challenged with limited resources.

METHODS

Staff nurses, nurse managers, interprofessional care providers, the chief nursing officer, and board of directors (n = 27) were interviewed. Observations of hospital units and administrative meetings were done, and hospital reports were analyzed.

RESULTS

Nine themes emerged to support a conceptual model of leading change. The CAH spent 3 years of its 6-year journey establishing organizational readiness. Nurses overcame complex challenges by balancing operational support and fostering relationships. The Magnet journey led to significantly improved nurse and patient outcomes. A new organizational culture centered on shared governance, evidence-based practice, and higher education emerged.

CONCLUSIONS

The journey to Magnet leads to improved nurse, patient, and organization outcomes.
Implementation and Evaluation of Shared Medical Appointments in Veterans With Diabetes
Authors: Omogbai Timothy , Milner Kerry A.
Published: February 2018

OBJECTIVE

The aim of this study is to implement and evaluate shared medical appointments (SMA) in veterans with diabetes.

BACKGROUND

Health systems are challenged to meet the complex care needs of veterans with diabetes. Use of SMA has resulted in significant improvements in A1c, blood pressure, and self-management skills in this population.

METHODS

Shared medical appointments were implemented in a Veterans Administration Health System. A1c, blood pressure, total cholesterol, high-density lipoprotein, low-density lipoprotein, triglycerides, weight, and height were collected at baseline, 3 months, and 6 months; hospitalization anytime; and veteran satisfaction at baseline and 6 months.

RESULTS

From October 15, 2015, to March 15, 2016, 30 male veterans with diabetes participated in monthly SMA. Outcome measures except for high-density lipoprotein improved significantly (P < .02) from baseline to 6 months. No veterans were hospitalized. Veteran satisfaction increased significantly (P < .001).

CONCLUSION

Shared medical appointment can be a highly effective intervention for veterans with diabetes. Nursing leaders need to be at the forefront of implementing SMA for populations with chronic conditions.
Realigning Shared Governance With Magnet® and the Organization's Operating System to Achieve Clinical Excellence
Authors: Moreno Janette V. , Girard Anita S. , Foad Wendy
Published: February 2018

In 2012, an academic medical center successfully overhauled a 15-year-old shared governance to align 6 house-wide and 30 unit-based councils with the new Magnet Recognition Program® and the organization's operating system, using the processes of LEAN methodology. The redesign improved cross-council communication structures, facilitated effective shared decision-making processes, increased staff engagement, and improved clinical outcomes. The innovative structural and process elements of the new model are replicable in other health institutions.
LINE-1 Activation After Fertilization Regulates Global Chromatin Accessibility in the Early Mouse Embryo
Authors: Jachowicz Joanna W. , Bing Xinyang , Pontabry Julien , Bošković Ana , Rando Oliver J. , Torres-Padilla Maria-Elena
Published: February 2018

(Abstracted from Nat Genet 2017;49:1502–1510)

After fertilization, gametes undergo dramatic epigenomic reprogramming to initiate embryonic development. Retrotransposons are repetitive elements that form almost half of the mammalian genome; some are transcribed after fertilization.
Reported Primary and Secondary Syphilis Cases in the United States: Implications for HIV Infection
Authors: Kidd Sarah , Torrone Elizabeth , Su John , Weinstock Hillard
Published: February 2018

Background

Recent increases in syphilis among men who have sex with men (MSM) are especially concerning, given the biologic and epidemiologic associations between syphilis and HIV infection. We sought to better describe the current epidemiology of primary and secondary (P&S) syphilis and the prevalence of HIV infection among reported P&S syphilis cases by demographic group, including sex of sex partner, in the United States in 2016.

Methods

We reviewed national P&S syphilis case report data from 2016, including available risk factor information such as sex of sex partner and HIV status. Data were extracted from the National Electronic Telecommunications System for Surveillance, the system through which Centers for Disease Control and Prevention receives notifiable sexually transmitted disease data from all 50 states and the District of Columbia. The proportion of cases with HIV coinfection was calculated using cases with known HIV status as the denominator.

Results

Of 27,814 P&S syphilis cases reported in 2016, 58.1% were among MSM, 13.9% were among men who have sex with women only, 11.0% were among women, and 16.9% were among men without data on sex of sex partners. Similar patterns were observed across geographic regions, race/ethnicity groups, and most age groups. Overall, 38.5% of reported P&S syphilis cases with known HIV status were coinfected with HIV. The prevalence of HIV coinfection was highest among MSM (47.0%) compared with men who have sex with women only (10.7%) or women (4.1%). Among MSM with P&S syphilis, the prevalence of HIV coinfection was highest among black MSM, ranging from 33.8% among black MSM aged 15 to 19 years to 77.8% among black MSM aged 45 to 49 years.

Conclusions

These data underscore the epidemiologic linkages between syphilis and HIV, particularly among MSM. Primary and secondary syphilis may represent an opportunity to prevent HIV infection among persons who are HIV negative and identify and link to care persons living with HIV infection but not currently engaged in care.
Impact of Cognitive Demand during Sustained Near Tasks in Children and Adults
Authors: Roberts Tawna L. , Manny Ruth E. , Benoit Julia S. , Anderson Heather A.
Published: February 2018

SIGNIFICANCE

These results demonstrate that accommodation in children is more accurate and less variable when performing a sustained near task with increased cognitive demand. In addition, children with increased uncorrected hyperopia have less stable accommodative responses, which may have visual implications during sustained near tasks.

PURPOSE

This study investigated accommodative accuracy (lag) and variability during sustained viewing for passive and active tasks in children and adults with emmetropia and uncorrected hyperopia.

METHODS

Lag and variability (root mean square [RMS] and low-frequency component) were measured in 54 children aged 3 to younger than 10 years with mean spherical equivalent of +1.31 ± 1.05 diopters (D) (range, −0.37 to +4.58 D) and 8 adults aged 22 to 32 years with mean spherical equivalent +0.65 ± 0.62 D (range, −0.13 to +1.15 D). Subjects viewed 20/50 stimuli at 33 cm during both a 10-minute passive and active task. Group 1 (<6 years or nonreaders) viewed shapes; group 2 (≥6 years and reading) and adults read passages.

RESULTS

Groups 1 and 2 had larger lags, RMS, and low-frequency component for passive versus active tasks (P < .001). Lag and RMS did not differ between tasks in adults (P > .05), but low-frequency component was larger during passive viewing (P = .04). Group 1 had significantly higher RMS and low-frequency component than group 2 and the adults in the passive condition had greater low-frequency component in the active condition. In children, hyperopia was independently associated with RMS and low-frequency component under passive (RMS 95% confidence interval [CI], 0.04 to 0.15; low-frequency component 95% CI, 0.00011 to 0.00065) and active (RMS 95% CI, 0.001 to 0.06; 95% CI, 0.000014 to 0.00023) viewing.

CONCLUSIONS

Accommodation is more accurate and less variable when children are engaged in the task. Children also have more variable accommodation than adults. In addition, children with greater hyperopia have more variable accommodation during sustained near tasks.
Educational Effectiveness of an Easily Made New Simulator Model for Ultrasound-Guided Vascular Access and Foreign Body Management Procedures on Pediatric Patients
Authors: Chang Ikwan , Kwak Young Ho , Kim Do Kyun , Lee Jin Hee , Jung Jae Yun , Kwon Hyuksool , Jung Jin Hee , Lee Bongjin , Paek So Hyun
Published: February 2018

Objectives

This study aimed to introduce an easily made chicken breast simulator for ultrasound (US)-guided vascular access, foreign body (FB) detection, and hydrodissection in pediatric patients and to validate the effectiveness for training using this phantom tissue model.

Methods

The authors made the tissue phantom simulator using a chicken breast and rubber tourniquet for vascular access and fragments of a tongue blade and steel clip for FB detection and hydrodissection using a very simple method. We provided training on US-guided vascular access (following the tip [FTT] method), FB detection, and hydrodissection using this model for novice physicians to learn US-guided procedures for pediatric patients. In addition, we provided a questionnaire to solicit their thoughts on their knowledge and confidence to perform these procedures before and after training and to learn their thoughts on the similarity to actual patients and usefulness of this model on a 10-point Likert scale.

Results

A total of 16 emergency residents participated in this study. We obtained US images during vascular access (FTT) and FB detection/ hydrodissection procedures using this phantom tissue model. Residents' knowledge of and confidence to perform US-guided FTT method and FB detection/hydrodissection procedures after training increased to a statistically significant degree (P< 0.001 in all items). The median Likert scores regarding the similarity to actual patients and usefulness of this model were 8.5 (interquartile range, 7.5–9) and 10 (interquartile range, 8–10), respectively.

Conclusions

The model for US-guided procedures used in this study can be constructed by simple and easy methods, presents realistic procedural images, and was useful for training novice physicians to conduct US-guided procedures on pediatric patients.
Characterization of Small Renal Tumors With Magnetic Resonance Elastography
Authors: Prezzi Davide , Neji Radhouene , Kelly-Morland Christian , Verma Hema , O'Brien Tim , Challacombe Ben , Fernando Archana , Chandra Ashish , Sinkus Ralph , Goh Vicky
Published: February 2018

Objectives

The aim of this study was to explore the feasibility of magnetic resonance elastography (MRE) for characterizing indeterminate small renal tumors (SRTs) as part of a multiparametric magnetic resonance (MR) imaging protocol.

Materials and Methods

After institutional review board approval and informed consent were obtained, 21 prospective adults (15 men; median age, 55 years; age range, 25–72 years) with SRT were enrolled. Tumors (2–5 cm Ø) were imaged using 3-directional, gradient echo MRE. Viscoelastic parametric maps (shear wave velocity [c] and attenuation [α]) were analyzed by 2 independent radiologists. Interobserver agreement (Bland-Altman statistics and intraclass correlation coefficients) was assessed. Anatomical T2-weighted, dynamic contrast-enhanced (DCE) and diffusion sequences completed the acquisition protocol. Imaging parameters were compared between groups (Mann-Whitney U test).

Results

Quality of MRE was good in 18 cases (mean nonlinearity <50%), including 1 papillary renal cell carcinoma and 1 metanephric adenoma. A cohort of 5 oncocytomas and 11 clear-cell renal cell carcinomas (ccRCCs) was analyzed for statistical differences. The MRE viscoelastic parameters were the strongest imaging discriminators: oncocytomas displayed significantly lower shear velocity c (median, 0.77 m/s; interquartile range [IQR], 0.76–0.79) (P = 0.007) and higher shear attenuation α (median, 0.087 mm−1; IQR, 0.082–0.087) (P = 0.008) than ccRCC (medians, 0.92 m/s and 0.066 mm−1; IQR, 0.84–0.97 and 0.054–0.074, respectively). T2 signal intensity ratio (tumor/renal cortex) was lower in oncocytomas (P = 0.02). The DCE and diffusion MR parameters overlapped substantially (P ≥ 0.1). Oncocytomas displayed a consistent MRE viscoelastic profile, corresponding to data point clustering in a bidimensional scatter plot. Values for MRE intraclass correlation coefficient were 0.982 for c and 0.984 for α, indicating excellent interobserver agreement.

Conclusions

Magnetic resonance elastography is feasible for SRT characterization; MRE viscoelastic parameters were stronger discriminators between oncocytoma and ccRCC than anatomical, DCE and diffusion MR imaging parameters.
The opioid epidemic in acute care surgery—Characteristics of overprescribing following laparoscopic cholecystectomy
Authors: Hanson Kristine T. , Thiels Cornelius A. , Polites Stephanie F. , Gazelka Halena M. , Ray-Zack Mohamed D. , Zielinski Martin D. , Habermann Elizabeth B.
Published: February 2018

BACKGROUND

Postoperative prescribing following acute care surgery must be optimized to limit excess opioids in circulation as misuse and diversion are frequently preceded by a prescription for acute pain. This study aimed to identify patient characteristics associated with higher opioid prescribing following laparoscopic cholecystectomy (LC).

METHODS

Among patients aged 18 years or older who underwent LC at a single institution in 2014 to 2016, opioids prescribed at discharge were converted to oral morphine equivalents (OME) and compared with developing state guidelines (maximum, 200 OME). Preoperative opioid use was defined as any opioid prescription 1 month to 3 months before LC or a prescription unrelated to gallbladder disease less than 1 month before LC. Univariate and multivariable methods determined characteristics associated with top quartile opioid prescriptions among opioid-naive patients.

RESULTS

Of 1,606 LC patients, 34% had emergent procedures, and 14% were preoperative opioid users. Nonemergent LC patients were more likely to use opioids preoperatively (16% vs. 11%, p = 0.006), but median OME did not differ by preoperative opioid use (225 vs. 219, p = 0.40). Among 1,376 opioid-naive patients, 96% received opioids at discharge. Median OME was 225 (interquartile range, 150–300), and 52% were prescribed greater than 200 OME. Top quartile prescriptions (≥300 OME) were associated with gallstone pancreatitis diagnosis, younger age, higher pain scores, and longer length of stay (all p < 0.05). While median OME did not differ by emergent status (median, 225; interquartile range, 150–300 for both, p = 0.15), emergent had more top quartile prescriptions (32% vs. 25%, p = 0.005). After adjusting for diagnosis, age, and sex, emergent status showed evidence of being associated with top quartile prescription (odds ratio, 1.3; 95% confidence interval, 1.0–1.8). Thirty-day refill rate was 5%.

CONCLUSION

Over half of opioid-naive patients undergoing LC were prescribed opioids exceeding draft state guidelines. Variation in prescribing patterns was not fully explained by patient factors. Acute care surgeons have an opportunity to optimize prescribing practices with the ultimate goal of reducing opioid misuse.

LEVEL OF EVIDENCE

Therapeutic study, level IV; Epidemiologic study, level III.
Vascular surgery during U.S. combat operations from 2002 to 2016: Analysis of vascular procedures performed to inform military training
Authors: Turner Caryn A. , Stockinger Zsolt T. , Gurney Jennifer M.
Published: February 2018

BACKGROUND

Vascular surgery constitutes approximately 6.5% of surgical procedures performed for combat injuries, yet general surgeons are increasingly unfamiliar with vascular surgery. This study examines the frequency and type of vascular surgical procedures performed during recent US Military operations from 2002 to 2016.

METHODS

A retrospective analysis of the Department of Defense Trauma Registry was performed for all Role (R)2 and R3 medical treatment facilities (MTFs), from January 2002 to May 2016. A total of 106 International Classification of Diseases—9th Rev.—Clinical Modification (ICD-9-CM) procedure codes were categorized as vascular and were included in the present analysis. Procedure codes were separated by anatomic location and procedure type. Ligation as part of an amputation was excluded. Grafts were further subdivided by type: synthetic, autologous, and unknown. Procedure grouping and categorization were determined by subject matter experts. Data analysis used Stata Version 14 (College Station, TX).

RESULTS

A total of 25,816 vascular surgical procedures were identified at R2 and R3 MTFs. Role 3 MTFs reported more than four times the number of procedures compared to R2 MTFs. The most common anatomic locations documented were extremity (64.96%) and not otherwise specified (28.1%). The most common procedures overall were amputation (33.36%) and fasciotomy (18.83%). The most common graft type was autologous (68.87%), and the least common was synthetic (5.69%).

CONCLUSION

While amputation, fasciotomy, and ligation were the most common vascular procedures performed for combat trauma, the need for definitive repair including grafting is common at both R2 and R3 MTFs. Vascular surgery therefore remains a necessary skill set for the deployed US Military surgeon; military general surgeons need to train and sustain their vascular skills, including proficiency at amputation and fasciotomy.

LEVEL OF EVIDENCE

Epidemiologic study, level III.
Nonocclusive mesenteric ischemia in patients with methamphetamine use
Authors: Anderson Jamie E. , Brown Ian E. , Olson Kristin A. , Iverson Katherine , Cocanour Christine S. , Galante Joseph M.
Published: February 2018

BACKGROUND

Data suggest that methamphetamine may increase the risk of nonocclusive mesenteric ischemia (NOMI). We describe patterns of presentation and outcomes of patients with methamphetamine use who present with NOMI to a single institution.

METHODS

This is an observational study of patients from January 2015 to September 2017 with methamphetamine use who presented with NOMI at an academic medical center in Northern California. We summarize patient comorbidities, clinical presentation, operative findings, pathologic findings, hospital course, and survival.

RESULTS

Ten patients with methamphetamine use and severe NOMI were identified. One patient was readmitted with a perforated duodenal ulcer, for a total of 11 encounters. Most presented with acute (n = 3) or acute-on-chronic (n = 4) abdominal pain. Distribution of ischemia ranged from perforated duodenal ulcer (n = 3), ischemia of the distal ileum (n = 1), ischemia of entire small bowel (n = 2), and patchy necrosis of entire small bowel and colon (n = 5). Six patients died, three within 1 week of admission and three between 3 months and 8 months.

CONCLUSION

Methamphetamine use may be associated with significant microvascular compromise, increasing the risk of mesenteric ischemia. Providers in areas with high prevalence of methamphetamine use should have a high index of suspicion for intestinal ischemia in this patient population. Patients with methamphetamine use admitted for trauma or other pathology may be at particular risk of ischemia and septic shock, especially in the setting of dehydration. Use of vasoconstrictors in this patient population may also exacerbate intestinal ischemia.

LEVEL OF EVIDENCE

Therapeutic Case series study, level V.
Emergent management of primary headache: a review of current literature
Authors: Naeem Farnia , Schramm Chris , Friedman Benjamin W.
Published: February 2018

Purpose of review

The current article reviews recent data on treatment of acute headache patients in the acute care setting.

Recent findings

Intravenous fluid hydration, a common component of emergency department (ED) migraine therapy, does not improve pain outcomes and leads to longer ED lengths of stay. Therefore, intravenous fluids should be administered only to migraine patients with clinical evidence of dehydration. Similarly, intravenous ketamine has garnered interest as a treatment for acute pain but does not provide substantial relief to migraine patients. New studies on the serotonin (5-HT3; 5-hydroxytryptamine-3) antagonist granisetron, intranasal lidocaine, and high-flow oxygen have reported conflicting results for migraine patients. Finally, although experts recommend avoiding opioids in migraine treatment, opioid administration remains prevalent in the ED. A new study has demonstrated that patients who receive intravenous hydromorphone in the ED are much less likely to attain acute headache relief. Standardized headache protocols may decrease opioid use and provide significant pain relief for patients.

Recent data have clarified the role of opioids and ketamine in the ED (do not use!). The role of treatment protocols and intravenous fluids is still ill-defined. Subpopulations of migraine patients may benefit from high-flow oxygen and intranasal lidocaine.
On the utilization of novel spectral laser scanning for three-dimensional classification of vegetation elements
Authors: Li Zhan , Schaefer Michael , Strahler Alan , Schaaf Crystal , Jupp David
Published: February 2018

The Dual-Wavelength Echidna Lidar (DWEL), a full waveform terrestrial laser scanner (TLS), has been used to scan a variety of forested and agricultural environments. From these scanning campaigns, we summarize the benefits and challenges given by DWEL's novel coaxial dual-wavelength scanning technology, particularly for the three-dimensional (3D) classification of vegetation elements. Simultaneous scanning at both 1064 nm and 1548 nm by DWEL instruments provides a new spectral dimension to TLS data that joins the 3D spatial dimension of lidar as an information source. Our point cloud classification algorithm explores the utilization of both spectral and spatial attributes of individual points from DWEL scans and highlights the strengths and weaknesses of each attribute domain. The spectral and spatial attributes for vegetation element classification each perform better in different parts of vegetation (canopy interior, fine branches, coarse trunks, etc.) and under different vegetation conditions (dead or live, leaf-on or leaf-off, water content, etc.). These environmental characteristics of vegetation, convolved with the lidar instrument specifications and lidar data quality, result in the actual capabilities of spectral and spatial attributes to classify vegetation elements in 3D space. The spectral and spatial information domains thus complement each other in the classification process. The joint use of both not only enhances the classification accuracy but also reduces its variance across the multiple vegetation types we have examined, highlighting the value of the DWEL as a new source of 3D spectral information. Wider deployment of the DWEL instruments is in practice currently held back by challenges in instrument development and the demands of data processing required by coaxial dual- or multi-wavelength scanning. But the simultaneous 3D acquisition of both spectral and spatial features, offered by new multispectral scanning instruments such as the DWEL, opens doors to study biophysical and biochemical properties of forested and agricultural ecosystems at more detailed scales.
Estimation of vegetation water content at leaf and canopy level using dual-wavelength commercial terrestrial laser scanners
Authors: Elsherif Ahmed , Gaulton Rachel , Mills Jon
Published: February 2018

Vegetation water content, quantified as the leaf equivalent water thickness (EWT), can serve as an indicator of vegetation stress. The intensity data recorded by terrestrial laser scanning (TLS) instruments, operating at shortwave infrared wavelengths, can be used to estimate the three-dimensional distribution of EWT, after a full and rigorous calibration for the range and incidence angle effects. However, TLS instruments do not record the incidence angles automatically, making calibration challenging. In this study, intensity data from two commercially available TLS instruments (Leica P40, 1550 nm shortwave infrared wavelength, and Leica P20, 808 nm near-infrared wavelength) were combined in a normalized difference index (NDI). The NDI was found to minimize the incidence angle effects with no need for further calibration. A dry-down experiment was conducted using deciduous and conifer canopies. The NDI was found to be highly correlated to EWT at leaf level (
R
2
of 0.91 and 0.74) and at canopy level (
R
2
of 0.89 and 0.74) for the deciduous and conifer canopies, respectively. Three-dimensional distributions of EWT at canopy level were generated, which revealed some vertical heterogeneity.
Bounding uncertainty in volumetric geometric models for terrestrial lidar observations of ecosystems
Authors: Paynter Ian , Genest Daniel , Peri Francesco , Schaaf Crystal
Published: February 2018

Volumetric models with known biases are shown to provide bounds for the uncertainty in estimations of volume for ecologically interesting objects, observed with a terrestrial laser scanner (TLS) instrument. Bounding cuboids, three-dimensional convex hull polygons, voxels, the Outer Hull Model and Square Based Columns (SBCs) are considered for their ability to estimate the volume of temperate and tropical trees, as well as geomorphological features such as bluffs and saltmarsh creeks. For temperate trees, supplementary geometric models are evaluated for their ability to bound the uncertainty in cylinder-based reconstructions, finding that coarser volumetric methods do not currently constrain volume meaningfully, but may be helpful with further refinement, or in hybridized models. Three-dimensional convex hull polygons consistently overestimate object volume, and SBCs consistently underestimate volume. Voxel estimations vary in their bias, due to the point density of the TLS data, and occlusion, particularly in trees. The response of the models to parametrization is analysed, observing unexpected trends in the SBC estimates for the drumlin dataset. Establishing that this result is due to the resolution of the TLS observations being insufficient to support the resolution of the geometric model, it is suggested that geometric models with predictable outcomes can also highlight data quality issues when they produce illogical results.
The potential to characterize ecological data with terrestrial laser scanning in Harvard Forest, MA
Authors: Orwig D. A. , Boucher P. , Paynter I. , Saenz E. , Li Z. , Schaaf C.
Published: February 2018

Contemporary terrestrial laser scanning (TLS) is being used widely in forest ecology applications to examine ecosystem properties at increasing spatial and temporal scales. Harvard Forest (HF) in Petersham, MA, USA, is a long-term ecological research (LTER) site, a National Ecological Observatory Network (NEON) location and contains a 35 ha plot which is part of Smithsonian Institution's Forest Global Earth Observatory (ForestGEO). The combination of long-term field plots, eddy flux towers and the detailed past historical records has made HF very appealing for a variety of remote sensing studies. Terrestrial laser scanners, including three pioneering research instruments: the Echidna Validation Instrument, the Dual-Wavelength Echidna Lidar and the Compact Biomass Lidar, have already been used both independently and in conjunction with airborne laser scanning data and forest census data to characterize forest dynamics. TLS approaches include three-dimensional reconstructions of a plot over time, establishing the impact of ice storm damage on forest canopy structure, and characterizing eastern hemlock (
Tsuga canadensis
) canopy health affected by an invasive insect, the hemlock woolly adelgid (
Adelges tsugae
). Efforts such as those deployed at HF are demonstrating the power of TLS as a tool for monitoring ecological dynamics, identifying emerging forest health issues, measuring forest biomass and capturing ecological data relevant to other disciplines. This paper highlights various aspects of the ForestGEO plot that are important to current TLS work, the potential for exchange between forest ecology and TLS, and emphasizes the strength of combining TLS data with long-term ecological field data to create emerging opportunities for scientific study.
Non-intersecting leaf insertion algorithm for tree structure models
Authors: Åkerblom Markku , Raumonen Pasi , Casella Eric , Disney Mathias I. , Danson F. Mark , Gaulton Rachel , Schofield Lucy A. , Kaasalainen Mikko
Published: February 2018

We present an algorithm and an implementation to insert broadleaves or needleleaves into a quantitative structure model according to an arbitrary distribution, and a data structure to store the required information efficiently. A structure model contains the geometry and branching structure of a tree. The purpose of this work is to offer a tool for making more realistic simulations of tree models with leaves, particularly for tree models developed from terrestrial laser scanning (TLS) measurements. We demonstrate leaf insertion using cylinder-based structure models, but the associated software implementation is written in a way that enables the easy use of other types of structure models. Distributions controlling leaf location, size and angles as well as the shape of individual leaves are user definable, allowing any type of distribution. The leaf generation process consist of two stages, the first of which generates individual leaf geometry following the input distributions, while in the other stage intersections are prevented by carrying out transformations when required. Initial testing was carried out on English oak trees to demonstrate the approach and to assess the required computational resources. Depending on the size and complexity of the tree, leaf generation takes between 6 and 18 min. Various leaf area density distributions were defined, and the resulting leaf covers were compared with manual leaf harvesting measurements. The results are not conclusive, but they show great potential for the method. In the future, if our method is demonstrated to work well for TLS data from multiple tree types, the approach is likely to be very useful for three-dimensional structure and radiative transfer simulation applications, including remote sensing, ecology and forestry, among others.
Weighing trees with lasers: advances, challenges and opportunities
Authors: Disney M. I. , Boni Vicari M. , Burt A. , Calders K. , Lewis S. L. , Raumonen P. , Wilkes P.
Published: February 2018

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods.
Spectral and spatial information from a novel dual-wavelength full-waveform terrestrial laser scanner for forest ecology
Authors: Mark Danson F. , Sasse Fadal , Schofield Lucy A.
Published: February 2018

The Salford Advanced Laser Canopy Analyser (SALCA) is an experimental terrestrial laser scanner designed and built specifically to measure the structural and biophysical properties of forest canopies. SALCA is a pulsed dual-wavelength instrument with co-aligned laser beams recording backscattered energy at 1063 and 1545 nm; it records full-waveform data by sampling the backscattered energy at 1 GHz giving a range resolution of 150 mm. The finest angular sampling resolution is 1 mrad and around 9 million waveforms are recorded over a hemisphere above the tripod-mounted scanner in around 110 min. Starting in 2010, data pre-processing and calibration approaches, data analysis and information extraction methods were developed and a wide range of field experiments conducted. The overall objective is to exploit the spatial, spectral and temporal characteristics of the data to produce ecologically useful information on forest and woodland canopies including leaf area index, plant area volume density and leaf biomass, and to explore the potential for tree species identification and classification. This paper outlines the key challenges in instrument development, highlights the potential applications for providing new data for forest ecology, and describes new avenues for exploring information-rich data from the next generation of terrestrial laser scanners instruments like SALCA.
New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning
Authors: Malhi Yadvinder , Jackson Tobias , Patrick Bentley Lisa , Lau Alvaro , Shenkin Alexander , Herold Martin , Calders Kim , Bartholomeus Harm , Disney Mathias I.
Published: February 2018

Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describehowecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understandwhytrees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.
The terrestrial laser scanning revolution in forest ecology
Authors: Danson F. Mark , Disney Mathias I. , Gaulton Rachel , Schaaf Crystal , Strahler Alan
Published: February 2018

New laser scanning technologies are set to revolutionize the way in which we measure and understand changes in ecosystem structure and function. Forest ecosystems present a particular challenge because of their scale, complexity and structural dynamics. Traditional forestry techniques rely on manual measurement of easy-to-measure characteristics such as tree girth and height, along with time-consuming, logistically difficult and error-prone destructive sampling. Much more detailed and accurate three-dimensional measurements of forest structure and composition are key to reducing errors in biomass estimates and carbon dynamics and to better understanding the role of forests in global ecosystem and climate change processes. Terrestrial laser scanners are now starting to be deployed in forest ecology research and, at the same time, new terrestrial laser scanning (TLS) technologies are being developed to enhance and extend the range of measurements that can be made. These new TLS measurements provide a tantalizing glimpse of a completely new way to measure and understand forest structure. It is therefore a good time to take stock, assess the state of the art and identify the immediate challenges for continued development of TLS in forest ecology.
The upstrap
Authors: Crainiceanu Ciprian M.
Published: February 2018

Bootstrap [2] is a landmark method for quantifying variability. It uses sampling with replacement with a sample size equal to that of the original data. We propose the upstrap, which samples with replacement either more or fewer samples than the original sample size. We illustrate the upstrap by solving a hard, but common, sample size calculation problem.
Medical consequences of pathogenic CNVs in adults: Analysis of the UK Biobank
Authors: Crawford Karen , Bracher-Smith Matthew , Kendall Kimberley M , Rees Elliott , Pardiñas Antonio F , Einon Mark , Escott-Price Valentina , Walters James TR , O’Donovan Michael C , Owen Michael J , Kirov George
Published: February 2018

Background

Genomic copy number variants (CNVs) increase risk for early-onset neurodevelopmental disorders but their impact on medical outcomes in later life is poorly understood. The UK Biobank, with half a million well-phenotyped adults, presents an opportunity to study the medical consequences of CNV in middle and old age.

Methods

We called 54 CNVs associated with clinical phenotypes or genomic disorders, including their reciprocal deletions or duplications, in all Biobank participants. We used logistic regression analysis to test CNVs for associations with 58 common medical phenotypes.

Findings

CNV carriers had an increased risk of developing 37 of the 58 phenotypes at nominal levels of statistical significance, with 19 associations surviving Bonferroni correction (p<8·6×10−4). Tests of each of the 54 CNVs for association with each of the 58 phenotypes identified 18 associations that survived Bonferroni correction (p<1·6×10−5) and a further 57 that were associated at a false discovery rate (FDR) threshold of 0·1. Thirteen CNVs had three or more significant associations at FDR=0·1, with the largest number of phenotypes (N=15) found for deletions at 16p11·2. The most common CNVs (frequency 0·5-0·7%) have no or minimal impact on medical outcomes in adults.

Interpretation

Some of the 54 tested CNVs have profound effects on physical health, even in people who have largely escaped early neurodevelopmental outcomes. Our work provides clinicians with a morbidity map of potential outcomes among carriers of these CNVs.

Funding

MRC UK, Wellcome Trust UK
Building a local community of practice in scientific programming for Life Scientists
Authors: Stevens Sarah L. R. , Kuzak Mateusz , Martinez Carlos , Moser Aurelia , Bleeker Petra , Galland Marc
Published: February 2018

In this paper, we describe why and how to build a local community of practice in scientific programming for life scientists that use computers and programming in their research. A community of practice is a small group of scientists that meet regularly to help each other and promote good practices in scientific programming. While most life scientists are well-trained in the laboratory to conduct experiments, good practices with (big) datasets and their analysis are often missing. We propose a model on how to build such a community of practice at a local academic institution, present two real-life examples and introduce challenges and implemented solutions. We believe that the current data deluge that life scientists face can benefit from the implementation of these small communities. Good practices spread among experimental scientists will foster open, transparent and sound scientific results beneficial to society.
CRISPR-based editing reveals edge-specific effects in biological networks
Authors: Li Yi , Nowak Chance M. , Withers Daniel , Pertsemlidis Alexander , Bleris Leonidas
Published: February 2018

Unraveling the properties of biological networks is central to understanding normal and disease cellular phenotypes. Networks consist of functional elements (nodes) that form a variety of diverse connections (edges) with each node being a hub for multiple edges. Herein, in contrast to node-centric network perturbation and analysis approaches, we present a high-throughput CRISPR-based methodology for delineating the role of network edges. Ablation of network edges using a library targeting 93 miRNA target sites in 71 genes reveals numerous edges that control, with variable importance, cellular survival under stress. To compare the impact of removing nodes versus edges in a biological network, we dissect a specific p53-microRNA pathway. In summary, we demonstrate that network edges are critical to the function and stability of biological networks. Our results introduce a novel genetic screening opportunity via edge ablation and highlight a new dimension in biological network analysis.
Yellow Fever, Dengue Fever and West Nile Viruses Co-Circulation in Ogbomoso
Authors: Oladipo E.K. , Awoyelu E.H. , Oloke J.K.
Published: February 2018

Arboviruses are an emerging threat of significant impact on human health and well-being. With increasing proportion of the world living in urban environments, inadvertently, there is the creation of better habitats for vector species. This study is aimed at establishing the occurrence of arboviruses within Ogbomoso, with a view to providing baseline data for further study. Ninety-three plasma samples from consenting individuals in the age range 1-75 years were collected and screened for IgM to dengue fever (DENV), West Nile (WNV) and yellow fever (YFV) viruses using third generation Enzyme Linked Immuno-Sorbent Assay (WKEA Med Supplies Corp, China) kits. An overall prevalence of 52.7% (49/93) were recorded from the recruited individuals. IgM antibodies to Dengue, Yellow fever and West Nile viruses were found in 16/49 (17.2%), 16/49 (17.2%) and 17/49 (18.3%), respectively. High prevalence were recorded in the age groups 16-30, 31-45 and 61-75 years. Gender analysis of the positive samples showed higher prevalence among females than males. The result also showed high prevalence in urban settings than rural settings for DENV and WNV, however, for YNF, higher prevalence was found in the rural area. The prevalence of dual and trio arboviral infection showed 17.2% and 11.8% respectively. This study confirms the circulation of Dengue fever, Yellow fever and West Nile viruses in Ogbomoso and therefore suggest the need for public awareness on vector control.
Transcription initiation RNAs are associated with chromatin activation mark H3K4me3
Authors: Hobbs Matthew , Ender Christine , Baillie Gregory J. , Crawford Joanna , Ru Kelin , Taft Ryan J. , Taft Ryan J. , Mattick John S.
Published: February 2018

Transcription initiation RNAs (tiRNAs) are small, predominantly 18 nt, RNAs whose biogenesis is associated with nucleosomes adjacent to active transcription initiation sites. These loci usually contain modified histones associated with transcription initiation, including histone H3 trimethylated at lysine 4 (H3K4me3). To further characterize the relationship of tiRNAs and H3K4me3 marked nucleosomes, H3K4me3-targeted RNA:chromatin immunoprecipitations were performed in a murine macrophage cell line, and small RNA sequence libraries were constructed and subjected to deep sequencing. The H3K4me3 libraries exhibited a distinct profile of read lengths with a noticeable enrichment of sequences 17-26 nt in length, with a peak at ∼18nt that included tiRNAs. These RNAs show clear enrichment of sequences that map to genomic features known to be associated with transcription initiation, including CAGE transcription initiation sites (TSSs), sites of RNAPII occupancy, and H3K4me3 sites. The distribution of sequences that map in the vicinity of TSSs is consistent with previous descriptions of tiRNAs; viz. a major peak at approximately 40 nt downstream of the TSS, and a minor broader peak approximately 150-200 nt upstream of, and on the opposite strand to, the TSS. These results show that tiRNAs are physically associated with H3K4me3-marked chromatin. tiRNAs may be markers of RNAPII pausing and it remains a possibility that their association with H3K4me3 is part of an epigenetic signaling system.
A common goodness-of-fit framework for neural population models using marked point process time-rescaling
Authors: Tao Long , Weber Karoline E. , Arai Kensuke , Eden Uri T.
Published: February 2018

A critical component of any statistical modeling procedure is the ability to assess the goodness-of-fit between a model and observed data. For neural spike train models of individual neurons, many goodness-of-fit measures rely on the time-rescaling theorem to assess the statistical properties of rescaled spike times. Recently, there has been increasing interest in statistical models that describe the simultaneous spiking activity of neuron populations, either in a single brain region or across brain regions. Classically, such models have used spike sorted data to describe relationships between the identified neurons, but more recently clusterless modeling methods have been used to describe population activity using a single model. Here we develop a generalization of the time-rescaling theorem that enables comprehensive goodness-of-fit analysis for either of these classes of population models. We use the theory of marked point processes to model population spiking activity, and show that under the correct model, each spike can be rescaled individually to generate a uniformly distributed set of events in time and the space of spike marks. After rescaling, multiple well-established goodness-of-fit procedures and statistical tests are available. We demonstrate the application of these methods both to simulated data and real population spiking in rat hippocampus.