bluuebunny/crossref_metadata_2025_split huggingface dataset:
Termites and a changing climate.
Authors: Ewart D. , Nunes L. , Troya T. de , Kutnik M. 
Published: January 2017

Abstract

To understand how termites react to changing climatic conditions, it is important to first explore what termites are and the parameters that control their bio-ecology. This chapter first reviews the factors that limit termite behaviour, including food, water, reproduction, and dispersal. It then discusses the impact of environmental temperature, distance from the equator, and climate change on the distribution pattern, diversity and survival of termites. The effects of a changing climate on the activities of termites are complex but can be projected from our knowledge of termites around the globe. The chief factors are likely to be heat, changes to precipitation, and the frequency of extreme weather events, sea-level rise, and the impact of rising carbon dioxide on their food resource.
Fly populations and problems in a changing climate.
Authors: Sallam M. F. , Pereira R. M. , Koehler P. G. 
Published: January 2017

Abstract

The geographic expansion and development rate of flies are climate-induced. Their importance as potential vectors of diseases and as forensic tools depends on where flies can occur in large numbers and the suitable habitats for their distribution. This chapter examines the effects of environmental (including temperature, precipitation, surface water, and vegetation) and host factors on the survival, development, distribution/range, and ability to transmit disease of flies. It presents new georeferenced data for temperature-related development of flies, and discusses current and future prediction scenarios for fly distribution at times of natural disasters, such as tornadoes or tsunamis in 2 different temperature-gradient areas in USA (New York City, New York, and Miami-Dade County, Florida).
Climate change and its effect on urban mosquitoes in South America.
Authors: Lima-Camara T. N. de , Honório N. A. 
Published: January 2017

Abstract

This chapter reviews available evidence on the impact of climate change on the distribution of urban mosquitoes in South America, and on the transmission of mosquito-borne diseases of humans and animals. The following vector-pathogen pairs are covered: Aedes and arboviruses (e.g. Dengue virus, Chikungunya virus, and Zika virus); Culex quinquefasciatus and West Nile virus; and Anopheles darlingi and malaria. Climate variables that should be considered when modelling the geographical expansion of urban mosquito vectors to new areas are discussed.
Ecotourism and environmental management: a case study of a partnership for conservation in Fiji.
Authors: Bricker K. S. , Kerstetter D. L. 
Published: January 2017

Abstract

This chapter provides an overview of environmental management in Fiji. This is accomplished through a review of the current situation in Fiji as well as the presentation of a case study of Rivers Fiji, an ecotourism company that partnered with native landowners to facilitate a lease for conservation of the Upper Navua River.
The various faces of competitiveness in tourism: a survey of the extant literature.
Authors: Croes R. , Kubickova M. 
Published: January 2017

Abstract

This chapter sets out to reveal the conceptual and empirical discussion pertaining to tourism competitiveness and the foundational challenges it faces. Furthermore, it considers a number of research pathways that aim at gaining more meaningful insights into the concept of tourism competitiveness. The review reveals that the foundational underpinnings of the construct are not wholly defined - and this lack of proper definition hampers the theoretical advancement of the tourism competitiveness framework. Sifting through the multiple definitions, the chapter identifies three dimensions and four characteristics revealed in four interrelated components of tourism competiveness; these are productivity, human agency, satisfaction and quality of life.
Stakeholders' perceived impact of wind farms at a tourism destination: a case study of Jeju Island, South Korea.
Authors: Lee SeungWoo [Lee S. W. J. ] 
Published: January 2017

Abstract

This chapter explores the opinions of two stakeholder groups (residents and government officials) regarding tourism and wind farm development on Jeju Island. The findings indicate that both stakeholders believe tourism to be a major economic entity on the island. In regard to wind farm development, both parties demonstrate mixed perceptions. The notable disparity between residents and government officials is that residents characterize the economic-cultural and local impacts of wind farm development more positively while government officials are less convinced of both impacts.
BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution
Authors: Psomopoulos Fotis E , Vitsios Dimitrios M , Baichoo Shakuntala , Ouzounis Christos A 
Published: January 2017

Abstract

Summary
BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway. Thus, BioPAXViz can significantly facilitate, and contribute to, the study of metabolic pathway evolution and engineering.

Availability and Implementation
BioPAXViz has been developed as a Cytoscape app and is available at: https://github.com/CGU-CERTH/BioPAX.Viz. The software is distributed under the MIT License and is accompanied by example files and data. Additional documentation is available at the aforementioned GitHub repository.
ntCard: a streaming algorithm for cardinality estimation in genomics data
Authors: Mohamadi Hamid , Khan Hamza , Birol Inanc 
Published: January 2017

Abstract

Motivation
Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k-mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k-mers, or even better, to build a histogram of k-mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools. However, calculating a k-mer histogram from large volumes of sequencing data is a challenging task.

Results
Here, we present ntCard, a streaming algorithm for estimating the frequencies of k-mers in genomics datasets. At its core, ntCard uses the ntHash algorithm to efficiently compute hash values for streamed sequences. It then samples the calculated hash values to build a reduced representation multiplicity table describing the sample distribution. Finally, it uses a statistical model to reconstruct the population distribution from the sample distribution. We have compared the performance of ntCard and other cardinality estimation algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB in size, where the first two representing whole genome shotgun sequencing experiments on the human genome and the last one on the white spruce genome. Results show ntCard estimates k-mer coverage frequencies &gt;15× faster than the state-of-the-art algorithms, using similar amount of memory, and with higher accuracy rates. Thus, our benchmarks demonstrate ntCard as a potentially enabling technology for large-scale genomics applications.

Availability and Implementation
ntCard is written in C ++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ntCard.

Supplementary information
Supplementary data are available at Bioinformatics online.
MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites
Authors: Olarerin-George Anthony O , Jaffrey Samie R 
Published: January 2017

Abstract

Summary
An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Availability and Implementation
The code and associated tutorial are available at https://github.com/olarerin/metaPlotR.
Reflex impairment, physiological stress, and discard mortality of European plaice Pleuronectes platessa in an otter trawl fishery
Authors: Methling Caroline , Skov Peter V. , Madsen Niels 
Published: January 2017

AbstractThe reformed European Common Fisheries Policy introduced a discard ban, with a possibility of exempting species where a high discard survival can be demonstrated. This necessitates a validation of the methods used for estimating the discard mortality of candidate species. In this study, we assess whether reflex impairment can predict short-term mortality in commercially trawled European plaice upon landing and after air exposure of up to 90 min. Sub-lethal stress was assessed by a suite of physiological variables. Over a 10-day period, mortality was monitored for a total of 199 plaice following trawl and air exposure of varying duration, and for 50 control fish scored for reflex impairment on board the vessel. Mortality was only observed in fish exposed to air for &gt;60 min, and averaged 11.1% (95% CI = 7.1–16.3%). Reflex impairment was found to be a significant (P &lt; 0.001) predictor of mortality in a generalized linear model, excluding other initially included variables by using a stepwise method. Plasma cortisol, haematocrit, and plasma osmolality all indicated a profound and increasing level of stress with air exposure, accompanied by a near depletion of muscle phosphocreatine and nucleotides. Fishing site had an unexpected, but significant (p &lt; 0.05) effect on stress levels, which was also reflected in reflex impairment and mortality. Based on these findings, a possible exemption from the discard ban should include considerations on the duration of air exposure.
Movement patterns in women at risk for perinatal depression: use of a
mood-monitoring mobile application in pregnancy
Authors: Faherty Laura J , Hantsoo Liisa , Appleby Dina , Sammel Mary D , Bennett Ian M , Wiebe Douglas J 
Published: January 2017

Abstract
Objectives: To examine, using a smartphone application, whether mood is related to daily movement patterns in pregnant women at risk for perinatal depression.
Materials and Methods: Thirty-six women with elevated depression symptoms (PHQ-9 ≥ 5) in pregnancy used the application for 8 weeks. Mood was reported using application-administered surveys daily (2 questions) and weekly (PHQ-9 and GAD-7). The application measured daily mobility (distance travelled on foot) and travel radius. Generalized linear mixed-effects regression models estimated the association between mood and movement.
Results: Women with milder depression symptoms had a larger daily radius of travel (2.7 miles) than women with more severe symptoms (1.9 miles), P = .04. There was no difference in mobility. A worsening of mood from the prior day was associated with a contracted radius of travel, as was being in the group with more severe symptoms. No significant relationships were found between anxiety and either mobility or radius.
Discussion: We found that the association of mood with radius of travel was more pronounced than its association with mobility. Our study also demonstrated that a change in mood from the prior day was significantly associated with radius but not mood on the same day that mobility and radius were measured.
Conclusion: This study lays the groundwork for future research on how smartphone mood-monitoring applications can combine actively and passively collected data to better understand the relationship between the symptoms of perinatal depression and physical activity that could lead to improved monitoring and novel interventions.
Airway Management With a Stereotactic Headframe In Situ—A Mannequin Study
Authors: Brockerville Melissa , Unger Zoe , Rowland Nathan C. , Sammartino Francesco , Manninen Pirjo H. , Venkatraghavan Lashmi 
Published: January 2017

Background:
Stereotactic headframe-based imaging is often needed for target localization during surgery for insertion of deep brain stimulators. A major concern during this surgery is the need for emergency airway management while an awake or sedated patient is in the stereotactic headframe. The aim of our study was to determine the ease of emergency airway management with a stereotactic headframe in situ.

Materials and Methods:
We conducted an observational study using a mannequin. A Leksell stereotactic headframe was placed on a mannequin in the operating room and the frame was fixed to the operating room table. Anesthesia personnel were asked to insert a #4 laryngeal mask and then to intubate the mannequin, using both direct (DL) and video laryngoscopy (VL). In addition, participants were asked to perform the same airway techniques in the mannequin without the headframe. Data were analyzed for time taken for airway management using different devices with and without the headframe. In addition, we compared the time taken to secure the airway between different participant groups.

Results:
Thirty anesthesia personnel (7 residents, 12 fellows, and 11 consultants) participated in the study. With the headframe in situ, 97% of participants were able to insert a laryngeal mask on their first attempt; 93% and 97% of participants were able to intubate the mannequin using DL and VL respectively on their first attempt. Without the stereotactic headframe, all participants were able to insert the laryngeal mask and intubate on the first attempt. The average time taken to insert a laryngeal mask and intubate the mannequin using DL and VL with the headframe in situ was 39.3, 58.6, and 54.8 seconds, respectively.

Conclusions:
Our study showed that both laryngeal mask insertion and tracheal intubation can be performed with a stereotactic headframe in situ. A laryngeal mask is the quickest airway device to insert and can be inserted while the mannequin is in the standard surgical position. Further study is needed to validate the results in patients.
Surgery for Refractory Coccygodynia
Authors: Kleimeyer John P. , Wood Kirkham B. , Lønne Greger , Herzog Tyler , Ju Kevin , Beyer Lisa , Park Christine 
Published: January 2017

Study Design.
This is a retrospective cohort study.

Objective.
To evaluate the long-term outcomes for patients with refractory coccygodynia treated with coccygectomy compared to a nonsurgical regimen of sitting aids, physical therapy, medications, and injections.

Summary of Background Data.
The surgical treatment of coccygodynia remains controversial. To date, there has only been one small comparative study of surgical versus nonsurgical treatment.

Methods.
From 2004 to 2014, 109 patients presenting with coccygodynia were treated with either total coccygectomy or a nonsurgical course of sitting aids, physical therapy, anti-inflammatory medications, and injections. All had at least 2 years of symptoms before surgery. The patient principally made the treatment decision, counseled by the treating physician. Before surgery, all subjects underwent at least 2 years of conservative treatment and three-dimensional imaging (computed tomography and/or magnetic resonance imaging). Subjects completed visual analog pain scales, EuroQol five-dimension, components of the PROMIS measure, and a novel Coccygodynia Disability Index evaluation. Work status, complications, and satisfaction were recorded.

Results.
A total of 61 patients received nonsurgical care; eight declined participation and five could not be located. Forty-eight patients underwent total coccygectomy; three declined participation and five could not be located. At an average 4.8 years of follow-up (range: 2–9), the nonsurgical visual analog pain scales was 5 and the surgical 2 (P = 0.001); 79% of surgically treated patients were improved at 2 years versus 43% for the nonsurgical group. EuroQol five-dimension (P = 0.002), Coccygodynia Disability Index (0.01), and PROMIS Pain interference scores (0.02) were also significantly improved in the surgical group. Eleven surgical patients (26%) had complications, all wound related with successful resolution; seven treated with dressing changes and four with surgical debridement.

Conclusion.
Total coccygectomy is a safe and effective surgical treatment of coccygodynia refractory to nonoperative care. Patient-reported outcome measures were improved after surgery compared with nonsurgical management. Postoperative wound care remains a concern.

Level of Evidence: 4
Long-term Pulmonary Function After Open Anterior Thoracolumbar Surgery in Thoracolumbar/Lumbar Idiopathic Adolescent Scoliosis
Authors: Ruiz-Juretschke Cristina , Pizones Javier , Delfino Renato , Sánchez-Mariscal Felisa , Zúñiga Lorenzo , Izquierdo Enrique 
Published: January 2017

Study Design.
A prospectively updated, long-term case series analysis.

Objective.
The aim of this study was to report the effect of thoracolumbar anterior open surgery performed during adolescence on adult pulmonary function.

Summary of Background Data.
There seems to be subclinical impairment of pulmonary function in the mid-term (2–5 years) in patients who underwent thoracotomy or thoraco-phreno-laparotomy after adolescent idiopathic scoliosis (AIS) surgery. However, long-term results when patients reach adulthood are lacking.

Methods.
Prospective data of pulmonary function tests (PFTs) on adult patients who underwent anterior open surgery during adolescence due to main thoracolumbar/lumbar curves were collected. Forced vital capacity (FVC), forced expiratory volume in the first second (FEV1), and the Tiffeneau index (TI: FEV1/FVC) with a 12-year minimum follow-up were recorded. These figures were compared with reference (predicted) values and preoperative data.

Results.
Twenty-four patients were included. All patients had undergone a thoraco-phreno-laparotomy. None of the patients had pulmonary disease. Mean age was 15.83 years at the time of surgery and the mean follow-up was 18.26 years (12–29 years).
Long-term results of the 24 operated patients (mean ± SD: FVC = 3.3 ± 0.39; FEV1 = 2.6 ± 0.38; TI = 80.3 ± 5.7) showed a similar FVC and slightly worse FEV1 than reference values (FVC = 3.4 ± 0.48; FEV1 = 3.03 ± 0.42; TI = 82.4 ± 1.3), (P = 0.21; P = 0.02; P = 0.3, respectively). Nevertheless, the values were within the normal percent-predicted range for FVC (93.5% ± 11.2) and FEV1 (91.4% ± 12.8). In 14 patients, long-term figures (median ± IQR): FVC = 3.2 ± 0.6; FEV1 = 2.54 ± 0.42; TI = 81.5 ± 11.2) were compared with preoperative values (median ± IQR: FVC = 2.9 ± 0.8; FEV1 = 2.47 ± 0.93; TI = 84.8 ± 34.2), (P = 0.08, P = 0.92, P = 0.026, respectively). Only the TI showed significant differences due to disproportionate improvement of FVC and FEV1 during the follow-up years.

Conclusion.
Thoracolumbar/lumbar AIS patients who underwent a thoraco-phreno-laparotomy during adolescence showed, in the long-term (18 years follow-up), a similar FVC compared with the reference values that was slightly superior than the values before surgery. Despite the lower FEV1 than the reference values and taking into consideration our limitations, the percent-predicted values were within the normal range, indicating no major pulmonary impairment in the long run.

Level of Evidence: 4
Risk Factors for Recurrence After Laparoscopic Ventral Rectopexy
Authors: Fu Cherylin W. P. , Stevenson Andrew R. L. 
Published: January 2017

BACKGROUND:
Laparoscopic ventral rectopexy effectively treats posterior compartment prolapse. However, recurrence after laparoscopic ventral rectopexy is poorly understood.

OBJECTIVE:
This study aimed to evaluate factors contributing to recurrence after laparoscopic ventral rectopexy.

DESIGN:
A retrospective cohort analysis was performed of patients who underwent laparoscopic ventral rectopexy between June 2008 and June 2014. Patients presenting with full-thickness rectal prolapse were compared against the rest. Cox proportional hazards regression was used to determine predictors for recurrence. Operative findings of redo cases were evaluated.

SETTINGS:
This study was conducted under the supervision of a single pelvic floor surgeon.

PATIENTS:
A total of 231 patients with a median follow-up of 47 months were included.

MAIN OUTCOME MEASURES:
Clinicopathological risk factors and technical failures contributing to recurrence were analyzed.

RESULTS:
The overall recurrence rate was 11.7% (n = 27). Twenty-five recurrences occurred in patients with full-thickness rectal prolapse, of which 16 were full-thickness recurrences (14.2% (16/113)). Multivariate analyses showed predictors for recurrence to be prolonged pudendal nerve terminal motor latency (HR = 5.57 (95% CI, 1.13 – 27.42); p = 0.04) and the use of synthetic mesh as compared with biologic grafts (HR = 4.24 (95% CI, 1.27–14.20); p = 0.02). Age >70 years and poorer preoperative continence were also associated with recurrence on univariate analysis. Technical failures contributing to recurrence included mesh detachment from the sacral promontory and inadequate midrectal mesh fixation.

LIMITATIONS:
Modifications to the operative technique were made throughout the study period. A postoperative defecating proctogram was not routinely performed.

CONCLUSIONS:
Recurrence after laparoscopic ventral rectopexy is multifactorial, and risk factors are both clinical and technical. The use of biologic grafts was associated with lower recurrence as compared with synthetic mesh. Patients with full-thickness rectal prolapse who are elderly, have poorer baseline continence, and have prolonged pudendal nerve terminal motor latency are at increased risk of recurrence.