LLukas22/scidocs huggingface dataset:
Predicting calyptrate fly populations from the weather, and probable consequences of climate change

1. Calyptrate flies include numerous species that are disease vectors and have a high nuisance value, notably Musca domestica . Populations are often associated with livestock farms and domestic waste disposal facilities such as landfill, where the accumulating organic matter provides suitable breeding conditions for a range of species. 2. We examined the relationship between fly numbers and weather conditions using a 4-year data set of weekly fly catches from six sites in southern UK, together with meteorological data. The first 3 years were used to develop predictive models, and these were then used to forecast fly populations in the fourth year. The accuracy of these predictions was assessed by comparison with the actual fly catches for that year. Separate models were developed for M. domestica , Calliphora spp. and all calyptrate flies combined. 3. Predictions based only on humidity, temperature and rainfall were strongly correlated with observed data ( r 2 values ranged from 0·52 to 0·84), suggesting that fly population changes are largely driven by the weather rather than by biotic factors. We can forecast fly populations so that control measures need only be deployed when weather conditions are suitable for a fly outbreak, reducing the need for prophylactic insecticide use. 4. Climate change was simulated using the most recent predictions of future temperature increases. Our models predicted substantial increases in fly populations up to 244% by 2080 compared with current levels, with the greatest increases occurring in the summer months. 5. Synthesis and applications. Models developed use weather data to predict populations of pestiferous flies such as M. domestica , which may prove valuable in integrated control programmes. These models predict substantial increases in fly populations in the future under likely scenarios of climate change. If this occurs we may expect considerable increases in the incidence of fly-borne disease.
UDiTaS™, a genome editing detection method for indels and genome rearrangements

Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Next Generation Sequencing (NGS) or enzymatic digestion, while broadly used in the genome editing field, has critical limitations for detecting and quantifying structural variants such as large deletions (greater than approximately 100 base pairs), inversions, and translocations. To overcome these limitations, we have developed a Uni-Directional Targeted Sequencing methodology, UDiTaS, that is quantitative, removes biases associated with variable-length PCR amplification, and can measure structural changes in addition to small insertion and deletion events (indels), all in a single reaction. We have applied UDiTaS to a variety of samples, including those treated with a clinically relevant pair of S. aureus Cas9 single guide RNAs (sgRNAs) targeting CEP290, and a pair of S. pyogenes Cas9 sgRNAs at T-cell relevant loci. In both cases, we have simultaneously measured small and large edits, including inversions and translocations, exemplifying UDiTaS as a valuable tool for the analysis of genome editing outcomes. UDiTaS is a robust and streamlined sequencing method useful for measuring small indels as well as structural rearrangements, like translocations, in a single reaction. UDiTaS is especially useful for pre-clinical and clinical application of gene editing to measure on- and off-target editing, large and small.
Community-acquired bacterial meningitis in adults in the Netherlands, 2006-14: a prospective cohort study.

BACKGROUND
We studied causative pathogens, clinical characteristics, and outcome of adult community-acquired bacterial meningitis after the introduction of adjunctive dexamethasone treatment and nationwide implementation of paediatric conjugate vaccines.


METHODS
In this cohort study, we prospectively assessed adults (age >16 years) with community-acquired bacterial meningitis in the Netherlands, identified through the National Reference Laboratory for Bacterial Meningitis or individual physicians between Jan 1, 2006, and July 1, 2014. We identified independent predictors of an unfavourable outcome (Glasgow Outcome Scale score 1-4) by logistic regression.


FINDINGS
We assessed 1412 episodes of community-acquired bacterial meningitis. Incidence declined from 1·72 cases per 100,000 adults per year in 2007-08, to 0·94 per 100,000 per year in 2013-14. Streptococcus pneumoniae caused 1017 (72%) of 1412 episodes. Rates of adult bacterial meningitis decreased most sharply among pneumococcal serotypes included in paediatric conjugate vaccine, and in meningococcal meningitis. We found no evidence of serotype or serogroup replacement. The overall case fatality rate was 244 (17%) of 1412 episodes and unfavourable outcome occurred in 531 (38%) of 1412 episodes. Predictors of unfavourable outcome were advanced age, absence of otitis or sinusitis, alcoholism, tachycardia, lower score on the Glasgow Coma Scale, cranial nerve palsy, a cerebrospinal fluid white-cell count lower than 1000 cells per μL, a positive blood culture, and a high serum C-reactive protein concentration. Adjunctive dexamethasone was administered for 1234 (89%) of 1384 assessed episodes. The multivariable adjusted odds ratio of dexamethasone treatment for unfavourable outcome was 0·54 (95% CI 0·39-0·73).


INTERPRETATION
The incidence of adult bacterial meningitis has decreased substantially, which is partly explained by herd protection by paediatric conjugate vaccines. Adjunctive dexamethasone treatment was associated with substantially improved outcome.


FUNDING
European Research Council, National Institute of Public Health and the Environment, European Union, Academic Medical Center, and Netherlands Organization for Health Research and Development.
Impact of race on early treatment termination and outcomes in posttraumatic stress disorder treatment.

OBJECTIVE
The present study investigated the influence of race on posttraumatic stress disorder (PTSD) treatment among 94 African American and 214 Caucasian female victims of interpersonal violence participating in 2 studies of cognitive-behavioral treatment for PTSD that were conducted sequentially and continuously.


METHOD
In each study, participants were randomized into 1 of 3 conditions. The first study compared cognitive processing therapy with prolonged exposure and a delayed treatment condition. In the second study, cognitive processing therapy was compared with its constituent components: cognitive therapy only and written accounts. Participants were assessed with the Clinician Administered PTSD Scale and the Structured Clinical Interview for DSM-IV, as well as through self-report measures of PTSD.


RESULTS
Analyses revealed that African Americans were significantly less likely to complete treatment compared with Caucasians (45% vs. 73%, respectively, p < .001) and that the differences held even after controlling for education and income. Despite racial differences in treatment completion status, analyses with the intent-to-treat sample indicated no racial differences in outcomes on PTSD measures.


CONCLUSIONS
The lack of difference in treatment outcomes despite racial differences in dropout may be explained by greater symptom improvement of African Americans who dropped out compared with Caucasians who dropped out. Implications of these findings and practical approaches to addressing sociocultural barriers to care are explored.
Mediators of exercise maintenance after cardiac rehabilitation.

PURPOSE
Exercise maintenance after completing phase II cardiac rehabilitation (CR) is challenging for many patients. A telephone-based maintenance intervention improved exercise participation compared with a control group at 12 months post-CR discharge. We examined the 6-month mediators of intervention effects on exercise.


METHODS
In a randomized controlled trial, 130 patients who had completed CR (mean age: 63.6 [SD = 9.7] years, 20.8% female) were randomized to Maintenance Counseling (n = 64) or Contact Control (n = 66). Putative mediators examined the following: self-efficacy, behavioral processes of change, decisional balance index, social support for exercise, and enjoyment of exercise.


RESULTS
Multiple mediation analyses showed that the intervention significantly increased social support from friends at 6 months but not the other constructs. Decreasing support from friends mediated greater exercise participation in Maintenance Counseling than in Contact Control at 12 months.


CONCLUSIONS
Social support from friends functioned as a suppressor mediator for exercise maintenance among cardiac patients.
Measuring gratitude in youth: assessing the psychometric properties of adult gratitude scales in children and adolescents.

Before the developmental trajectory, outcomes, and related interventions of gratitude can be accurately and confidently studied among the youth, researchers must ensure that they have psychometrically sound measures of gratitude that are suitable for this population. Thus, considering that no known scales were specifically designed to measure gratitude in youth, this study aimed to answer an important question: Are the existing gratitude scales used with adults valid for use with youth? The present study is an empirical investigation, based on a large youth sample (N = 1,405) with ages ranging from 10 to 19 years old, of the psychometric properties of scores of the Gratitude Questionnaire-6 (GQ-6; M. E. McCullough, R. A. Emmons, & J.-A. Tsang, 2002), the Gratitude Adjective Checklist (GAC; M. E. McCullough, R. A. Emmons, & J.-A. Tsang, 2002), and the Gratitude Resentment and Appreciation Test (GRAT)-short form (M. Thomas & P. Watkins, 2003). Single-group and multiple-group confirmatory factor analyses indicated that the factor structures of these gratitude scales resemble those found with adults and were invariant across age groups. Scores of all three gratitude scales revealed acceptable internal consistency estimates (i.e., >.70) across age groups. Results showed that whereas scores of all three gratitude scales were positively correlated with each other for 14- to 19-year-olds, GRAT-short form scores tended to display relatively low correlations with scores of the other two measures for younger children (10-13 years old). Furthermore, the nomological network analysis showed that scores of all three gratitude scales were positively correlated with positive affect and life satisfaction scores across the age groups. The relationships with negative affect and depression scores, however, seemed dependent on the child's age. Pending results from subsequent research recommendations for researchers interested in studying gratitude in youth are offered.
Low Latency Video Streaming Over Peer-To-Peer Networks

We study peer-to-peer multicast streaming, where a source distributes real-time video to a large population of hosts by making use of their forwarding capacity rather than relying on dedicated media servers. We present a distributed streaming protocol which builds and maintains multiple multicast trees. The protocol is combined with an adaptive scheduling algorithm which ensures packets destined to a large number of peers, or particularly important to decode the video, are sent in priority. Experiments carried out over a simulated network of up to 3000 peers illustrate the performance of the protocol. For low latency video streaming, the prioritization algorithm offers performance gains, especially for large audiences and low latencies
Data Warehouse Life-Cycle and Design

DEFINITION The term data warehouse life-cycle is used to indicate the phases (and their relationships) a data warehouse system goes through between when it is conceived and when it is no longer available for use. Apart from the type of software, life-cycles typically include the following phases: requirements analysis, design (including modeling), construction, testing, deployment, operation, maintenance and retirement. On the other hand, different life-cycles differ in the relevance and priority with which the phases are carried out, that can vary according to the implementation constraints (i.e. economic constraints, time constraints, etc.) and the software specificities and complexity; in particular, the specificities in the data warehouse life cycle derive from the presence of the operational database that feeds the system and by the extent of this kind of system that must be considered in order to keep under control the cost and the complexity of the project. Although the design phase is only a step within the overall life-cycle, the identification of a proper lifecycle model and the adoption of a correct design methodology are strictly related since each one influences the other.
LBP maps for improving fractal based texture classification

This paper presents an innovative manner of obtaining discriminative texture signatures by using the LBP approach to extract additional sources of information from an input image and by using fractal dimension to calculate features from these sources. Four strategies, called Min, Max, Diff Min and Diff Max , were tested, and the best success rates were obtained when all of them were employed together, resulting in an accuracy of 99.25%, 72.50% and 86.52% for the Brodatz, UIUC and USPTex databases, respectively, using Linear Discriminant Analysis. These results surpassed all the compared methods in almost all the tests and, therefore, confirm that the proposed approach is an effective tool for texture analysis. © 2017 Elsevier B.V. All rights reserved.
Widespread uplift and ‘trapdoor’ faulting on Galápagos volcanoes observed with radar interferometry

Volcanic uplift, caused by the accumulation of magma in subsurface reservoirs, is a common precursor to eruptions. But, for some volcanoes, uplift of metres or more has not yet led to an eruption. Here we present displacement maps of volcanoes in the Galápagos Islands, constructed using satellite radar interferometry, that might help explain this dichotomy. We show that all but one of the seven volcanoes on the islands of Isabela and Fernandina deformed during 1992–99. Cerro Azul and Fernandina erupted during the observation period and show evidence of inflation, co-eruptive deflation and shallow dyke intrusion. In contrast, the largest volcano, Sierra Negra, has not erupted, yet exhibits spatially and temporally variable deformation, with a maximum uplift of 2.7 m between 1992 and 1999, which can be modelled by a shallow inflating sill. Inflation during 1997–98, however, was accompanied by ‘trapdoor’ faulting on a steeply dipping fracture system within the caldera. Repeated trapdoor faulting over geological time has formed an arcuate intra-caldera ridge within Sierra Negra and may have acted to relax stresses above the magma chamber, inhibiting summit eruptions. Similar processes may help explain large uplift unaccompanied by eruptive activity at other volcanoes.
Physician-assisted deaths under the euthanasia law in Belgium: a population-based survey.

BACKGROUND
Legalization of euthanasia and physician-assisted suicide has been heavily debated in many countries. To help inform this debate, we describe the practices of euthanasia and assisted suicide, and the use of life-ending drugs without an explicit request from the patient, in Flanders, Belgium, where euthanasia is legal.


METHODS
We mailed a questionnaire regarding the use of life-ending drugs with or without explicit patient request to physicians who certified a representative sample (n = 6927) of death certificates of patients who died in Flanders between June and November 2007.


RESULTS
The response rate was 58.4%. Overall, 208 deaths involving the use of life-ending drugs were reported: 142 (weighted prevalence 2.0%) were with an explicit patient request (euthanasia or assisted suicide) and 66 (weighted prevalence 1.8%) were without an explicit request. Euthanasia and assisted suicide mostly involved patients less than 80 years of age, those with cancer and those dying at home. Use of life-ending drugs without an explicit request mostly involved patients 80 years of older, those with a disease other than cancer and those in hospital. Of the deaths without an explicit request, the decision was not discussed with the patient in 77.9% of cases. Compared with assisted deaths with the patient's explicit request, those without an explicit request were more likely to have a shorter length of treatment of the terminal illness, to have cure as a goal of treatment in the last week, to have a shorter estimated time by which life was shortened and to involve the administration of opioids.


INTERPRETATION
Physician-assisted deaths with an explicit patient request (euthanasia and assisted suicide) and without an explicit request occurred in different patient groups and under different circumstances. Cases without an explicit request often involved patients whose diseases had unpredictable end-of-life trajectories. Although opioids were used in most of these cases, misconceptions seem to persist about their actual life-shortening effects.
Mosaics from Arbitrary Stereo Video Sequences

Although mosaics are well established as a compact and nonredundant representation of image sequences, their application still suffers from restrictions of the camera motion or has to deal with parallax errors. We present an approach that allows construction of mosaics from arbitrary motion of a head-mounted camera pair. As there are no parallax errors when creating mosaics from planar objects, our approach first decomposes the scene into planar sub-scenes from stereo vision and creates a mosaic for each plane individually. The power of the presented mosaicing technique is evaluated in an office scenario, including the analysis of the parallax error.
Improving Tolerance to Variations in Memristor-Based Applications Using Parallel Memristors

Memristors are being explored for a wide variety of applications such as neuromorphic computing, memory and digital logic. However, they suffer from process variations like any other nanodevice, which in turn impacts their applicability. The effect of process variations, specifically variation in thickness, is highly non-linear on memristors; the effect is greater near the lower memristance region (near Mon) than in the higher memristance region (near Moff). Due to this non-linear effect, many applications do not use the lower memristance values. Consequently, the application's functionality and performance is affected. In this work, we propose a technique called parallel memristors. In this technique, instead of using a single memristor, the application uses several memristors connected in parallel. Each memristor in this parallel structure is programmed to a higher memristance value to tolerate variations. Since many memristors are connected in parallel, the effective memristance value can be near the Mon value, thereby achieving high-speed operation. We evaluate the parallel memristor technique in two different applications-memristor-based threshold logic and memristor-based memory. We also perform various optimizations to tradeoff between variation tolerance, power, delay, and area.
Rational choice or Hobson’s Choice? The “new political economy” as development theory

One of the most striking intellectual developments of the past two decades has been the growing influence of rational choice-based thinking among non-economists in the social sciences. By 1992 rational choice-based articles accounted for two fifths of the contents of the American Political Science Review, and rational choice fundamentalists were increasingly making over US political science departments and graduate curricula in their image.
Computed tomography--an increasing source of radiation exposure.

Copyright © 2007 Massachusetts Medical Society. The advent of computed tomography (ct) has revolutionized diagnostic radiology. Since the inception of CT in the 1970s, its use has increased rapidly. It is estimated that more than 62 million CT scans per year are currently obtained in the United States, including at least 4 million for children.1 By its nature, CT involves larger radiation doses than the more common, conventional x-ray imaging procedures (Table 1). We briefly review the nature of CT scanning and its main clinical applications, both in symptomatic patients and, in a more recent development, in the screening of asymptomatic patients. We focus on the increasing number of CT scans being obtained, the associated radiation doses, and the consequent cancer risks in adults and particularly in children. Although the risks for any one person are not large, the increasing exposure to radiation in the population may be a public health issue in the future.
Educating the engineer of 2020: Adapting engineering education to the new century

This publication contains reprint articles for which IEEE does not hold copyright. Full text is not available on IEEE Xplore for these articles.
TextRank: Bringing Order Into Texts

In this paper, we introduce TextRank – a graph-based ranking model for text processing, and show how this model can be successfully used in natural language applications. In particular, we propose two innovative unsupervised methods for keyword and sentence extraction, and show that the results obtained compare favorably with previously published results on established benchmarks.
Surgical checklists: a systematic review of impacts and implementation

BACKGROUND
Surgical complications represent a significant cause of morbidity and mortality with the rate of major complications after inpatient surgery estimated at 3-17% in industrialised countries. The purpose of this review was to summarise experience with surgical checklist use and efficacy for improving patient safety.


METHODS
A search of four databases (MEDLINE, CINAHL, EMBASE and the Cochrane Database of Controlled Trials) was conducted from 1 January 2000 to 26 October 2012. Articles describing actual use of the WHO checklist, the Surgical Patient Safety System (SURPASS) checklist, a wrong-site surgery checklist or an anaesthesia equipment checklist were eligible for inclusion (this manuscript summarises all but the anaesthesia equipment checklists, which are described in the Agency for Healthcare Research and Quality publication).


RESULTS
We included a total of 33 studies. We report a variety of outcomes including avoidance of adverse events, facilitators and barriers to implementation. Checklists have been adopted in a wide variety of settings and represent a promising strategy for improving the culture of patient safety and perioperative care in a wide variety of settings. Surgical checklists were associated with increased detection of potential safety hazards, decreased surgical complications and improved communication among operating staff. Strategies for successful checklist implementation included enlisting institutional leaders as local champions, incorporating staff feedback for checklist adaptation and avoiding redundancies with existing systems for collecting information.


CONCLUSIONS
Surgical checklists represent a relatively simple and promising strategy for addressing surgical patient safety worldwide. Further studies are needed to evaluate to what degree checklists improve clinical outcomes and whether improvements may be more pronounced in particular settings.