bluuebunny/crossref_metadata_2025_split huggingface dataset:
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FM: an encrypted and compressed full-text index for collections of genomic sequences
Authors: Montecuollo Ferdinando , Schmid Giovannni , Tagliaferri Roberto 
Published: May 2017

Abstract

Motivation
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets—as those related to personalized medicine—require the compliance with regulations about the storage and processing of sensitive data.

Results
We have designed and carefully engineered E2FM-index, a new full-text index in minute space which was optimized for compressing and encrypting nucleotide sequence collections in FASTA format and for performing fast pattern-search queries. E2FM-index allows to build self-indexes which occupy till to 1/20 of the storage required by the input FASTA file, thus permitting to save about 95% of storage when indexing collections of highly similar sequences; moreover, it can exactly search the built indexes for patterns in times ranging from few milliseconds to a few hundreds milliseconds, depending on pattern length.

Availability and implementation
Source code is available at https://github.com/montecuollo/E2FM.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Political Case of Penetrating Cranial Trauma: The Injury of James Scott Brady
Authors: Menger Richard , Kalakoti Piyush , Hanif Rimal , Ahmed Osama , Nanda Anil , Guthikonda Bharat 
Published: May 2017

Abstract
James Brady, the White House press secretary during President Ronald Reagan's first term in office, was 1 of 4 people (including the President) wounded during an attempted assassination attempt on President Reagan's life on March 30, 1981. John Hinckley, Jr. was found not guilty of this attempt by reason of insanity. The assassination attempt was a ploy by Hinckley, Jr. to impress the actress Jodie Foster. Brady was the most seriously injured of the 4 who were wounded. He suffered a gunshot wound to the left forehead that traveled through the left frontal lobe, corpus callosum, and then into the right frontal and temporal lobes. He initially required a bifrontal craniotomy for evacuation of a right frontotemporal intraparenchymal hemorrhage and debridement of tract. His postoperative course was complicated by seizures, cerebrospinal fluid leakage (necessitating multiple reparative procedures), aspiration pneumonia, and pulmonary emboli. Despite the severity of his injury and perioperative morbidities, Mr. Brady made good recovery. Although permanently left with residual weakness on the left side of his body, making a wheelchair necessary, Brady maintained cognitive and personality traits that were very close to his preinjury baseline. As a result, James Brady and his wife, Sarah, led a call to create legislative reform subsequently known as the “Brady Bill.” This bill controversially made mandatory background checks for the purchase of firearms from licensed dealers. Our work aims to describe the assassination attempt, the neurosurgical injury and management of Mr. Brady's case, and the brief historical sequel that followed.
Intraoperative Transpedicular Onyx Injection to Reduce Vascularity of a Thoracic Hemangiopericytoma After Unsuccessful Preoperative Endovascular Embolization: a Technical Report
Authors: Mashaly Hazem , Zhang Zoe , Shaw Andrew , Youssef Patrick , Mendel Ehud 
Published: May 2017

Abstract

BACKGROUND AND IMPORTANCE
Hemangiopericytoma is a rare vascular tumor with central nervous system involvement representing only 1% of central nervous system tumors. They rarely affect the vertebral column. Complete surgical resection is the treatment of choice for hemangiopericytoma given their high rates of local recurrence. However, the high vascularity of such tumors with the risk of massive bleeding during surgery represents a significant challenge to surgeons. Therefore, preoperative endovascular embolization via the transarterial route has been advocated.

CLINICAL PRESENTATION
In the current study, we present a case of a T12 hemangiopericytoma that was managed by a 2-stage surgical resection, with the use of intraoperative transpedicular onyx injection to reduce intraoperative blood loss following an unsuccessful trial of preoperative endovascular embolization.

CONCLUSION
Preoperative endovascular embolization is not feasible in some cases due to the location of the segmental or radiculomedullary arteries in relation to tumor feeders and, rarely, small size of these arterial feeders. Percutaneous injection of onyx is an option. In this case report, we discuss direct intraoperative injection via a transpedicular route as a safe and effective method for decreasing the vascularity of some lesions and improving intraoperative blood loss.
Preventing Radicalization in the UK: Expanding the Knowledge-Base on the Channel Programme
Authors: Thornton Amy , Bouhana Noémie 
Published: May 2017

AbstractThe Channel programme is part of the Prevent Strategy, one of the four strands of the UK counter-terrorism strategy known as CONTEST. While the programme has been running since 2007 and thousands of purportedly ‘vulnerable’ individuals are referred to the programme each year, there are still gaps in public knowledge about the programme, and this article seeks to fill some of those gaps while raising issues to consider in the future. With empirical data from interviews with individuals who have worked on the Channel programme, issues discussed include the type of individuals who are placed onto the programme, the suitability of intervention providers who aim to assist these vulnerable individuals, and the vital role of schools and the community in the success of the programme. The way in which the programme is designed and framed is of vital importance, as the mechanisms by which a deradicalization programme should work are very different from those which a counter-radicalization programme should employ. Finally suggestions are made for future empirical work in order to be able to understand and evaluate Channel.
Validation of Innovative Techniques for Monitoring Nociception during General Anesthesia
Authors: Funcke Sandra , Sauerlaender Sven , Pinnschmidt Hans O. , Saugel Bernd , Bremer Kai , Reuter Daniel A. , Nitzschke Rainer 
Published: May 2017

Abstract

Background
This study compares the analgesic indices Analgesia Nociception Index (heart rate variability), Surgical Pleth Index (photoplethysmography), and pupillary dilatation, to heart rate, mean arterial pressure, and bispectral index, with regard to diagnostic accuracy and prediction probability for nociceptive response. The primary endpoint was the correlation between Δ values and the remifentanil dose administered.

Methods
We anesthetized 38 patients with propofol and increasing doses of remifentanil and applied standardized tetanic and intracutaneous electrical painful stimulations on each analgesic level. Baseline and Δ values of the Analgesia Nociception Index, the Surgical Pleth Index, pupillary dilatation, heart rate, mean arterial pressure, and bispectral index and their relation to remifentanil doses were analyzed by receiver operating characteristic curves, prediction probability (PK), and mixed-model analysis.

Results
Under propofol sedation, sensitivity and specificity of the Analgesia Nociception Index (PK = 0.98), the Surgical Pleth Index (PK = 0.87), and pupillary dilatation (PK = 0.98) for detecting both painful stimulations were high compared to heart rate (PK = 0.74), mean arterial pressure (PK = 0.75), and bispectral index (PK = 0.55). Baseline values had limited prediction probability toward the nociceptive response (Analgesia Nociception Index: PK = 0.7; Surgical Pleth Index: PK = 0.63; pupillary dilatation: PK = 0.67; and bispectral index: PK = 0.67). The remifentanil dose had an effect (P < 0.001) on all parameters except for bispectral index (P = 0.216).

Conclusions
The Analgesia Nociception Index, the Surgical Pleth Index, and pupillary dilatation are superior in detecting painful stimulations compared to heart rate and mean arterial pressure but had limited predictive value. These effects are attenuated by increasing dosages of remifentanil. Our data confirm that bispectral index is not a marker of analgesia.
RETINAL AND CHOROIDAL VASCULAR OCCLUSION FOLLOWING AQUEOUS MISDIRECTION SYNDROME IN A PATIENT WITH SICKLE CELL TRAIT
Authors: Dewundara Samantha , Nassiri Nariman , Kim Johnstone M. , Kadikoy Huseyin , Amde Wendewessen , Tannir Justin , Hughes Bret A. , Abrams Gary W. 
Published: May 2017

Purpose:
To report a patient with retinal and choroidal vascular occlusion as a presenting sign of sickle cell trait following the development of aqueous misdirection syndrome.

Methods:
Retrospective chart review.

Results:
A patient treated for bilateral chronic angle-closure glaucoma with sequential EX-PRESS glaucoma filtration device surgery developed sequential bilateral aqueous misdirection syndrome. The left eye developed retinal arterial and localized choroidal vascular occlusions subsequent to an acute elevation in intraocular pressure and possibly the use of oral acetazolamide. The patient was subsequently found to have sickle cell trait. The right eye developed aqueous misdirection with acute elevation of intraocular pressure as well, but the patient was not treated with oral acetazolamide and did not develop vascular occlusion.

Conclusion:
Retinal and choroidal vascular occlusions can be the presenting sign of a patient with sickle cell trait. Sickle cell screening may be beneficial in African American or Middle Eastern patients after an acute rise in intraocular pressure, particularly before initiation of treatment with oral carbonic anhydrase inhibitors.
Pilot Study Comparing Closed Versus Open Tracheal Suctioning in Postoperative Neonates and Infants With Complex Congenital Heart Disease
Authors: Tume Lyvonne N. , Baines Paul B. , Guerrero Rafael , Hurley Margaret A. , Johnson Robert , Kalantre Atul , Ramaraj Ram , Ritson Paul C. , Walsh Laura , Arnold Philip D. 
Published: May 2017

Objectives:
To determine the hemodynamic effect of tracheal suction method in the first 36 hours after high-risk infant heart surgery on the PICU and to compare open and closed suctioning techniques.

Design:
Pilot randomized crossover study.

Setting:
Single PICU in United Kingdom.

Participants:
Infants undergoing surgical palliation with Norwood Sano, modified Blalock-Taussig shunt, or pulmonary artery banding in the first 36 hours postoperatively.

Interventions:
Infants were randomized to receive open or closed (in-line) tracheal suctioning either for their first or second study tracheal suction in the first 36 hours postoperatively.

Measurements and Main Results:
Twenty-four infants were enrolled over 18 months, 11 after modified Blalock-Taussig shunt, seven after Norwood Sano, and six after pulmonary artery banding. Thirteen patients received the open suction method first followed by the closed suction method second, and 11 patients received the closed suction method first followed by the open suction method second in the first 36 hours after their surgery. There were statistically significant larger changes in heart rate (p = 0.002), systolic blood pressure (p = 0.022), diastolic blood pressure (p = 0.009), mean blood pressure (p = 0.007), and arterial saturation (p = 0.040) using the open suction method, compared with closed suctioning, although none were clinically significant (defined as requiring any intervention).

Conclusions:
There were no clinically significant differences between closed and open tracheal suction methods; however, there were statistically significant greater changes in some hemodynamic variables with open tracheal suctioning, suggesting that closed technique may be safer in children with more precarious physiology.
Five Community-wide Approaches to Physical Activity Promotion: A Cluster Analysis of These Activities in Local Health Jurisdictions in 6 States
Authors: Bekemeier Betty , Pui-Yan Yip Michelle , Flaxman Abraham D. , Barrington Wendy 
Published: May 2017

Objective:
Local health departments (LHDs) have essential roles to play in ensuring the promotion of physical activity (PA) in their communities in order to reduce obesity. Little research exists, however, regarding the existence of these PA interventions across communities and how these interventions may impact community health.

Design:
In this exploratory study, we used cluster analysis to identify the structure of co-occurring PA interventions, followed by regression analysis to quantify the association between the patterns of PA interventions and prevalence of PA and obesity at a population level.

Setting:
Our study setting included local health jurisdictions in Colorado, Florida, Minnesota, New Jersey, Tennessee, and Washington.

Participants:
Participating jurisdictions were those 218 local health jurisdictions (mostly counties) from which LHD leaders had provided data in 2013 for the Multi-Network Practice and Outcome Variation Examination Study.

Main Outcome Measures:
We obtained unique public health activities data on PA interventions conducted in 2012 from 218 LHDs in 6 participating states. We categorized jurisdictions using cluster analysis, based on PA intervention approaches indicated by LHD leaders as available in their communities and then examined associations between categories and prevalence of obesity and of residents engaged in PA.

Results:
We identified 5 distinct PA intervention categories representing community-wide approaches—Comprehensive Approach, Built Environment, Personal Health, School-Based Interventions, and No Apparent Activities. Prevalence rates of obesity and PA among jurisdictions in the intervention clusters were significantly different from jurisdictions with No Apparent Activities, with more population-level approaches most significantly related to beneficial outcomes.

Conclusion:
Our findings suggest the importance of standardized public health services data for generating evidence regarding health-related outcomes. The intervention categories we identified appear to reflect broad, local community-wide prevention approaches and demonstrated that population-level PA interventions can be testable and may have particularly beneficial relationships to community health. Widespread adoption of such standardized data depicting local public health prevention activity could support monitoring practice change, performance improvement, comparisons across communities that could reduce unnecessary variation, and the generation of evidence for public health practice and policy-making.
Measuring Subcounty Differences in Population Health Using Hospital and Census-Derived Data Sets: The Missouri ZIP Health Rankings Project
Authors: Nagasako Elna , Waterman Brian , Reidhead Mathew , Lian Min , Gehlert Sarah 
Published: May 2017

Context:
Measures of population health at the subcounty level are needed to identify areas for focused interventions and to support local health improvement activities.

Objective:
To extend the County Health Rankings population health measurement model to the ZIP code level using widely available hospital and census-derived data sources.

Design:
Retrospective administrative data study.

Setting:
Missouri.

Population:
Missouri FY 2012-2014 hospital inpatient, outpatient, and emergency department discharge encounters (N = 36 176 377) and 2015 Nielsen data.

Main Outcome Measures:
ZIP code–level health factors and health outcomes indices.

Results:
Statistically significant measures of association were observed between the ZIP code–level population health indices and published County Health Rankings indices. Variation within counties was observed in both urban and rural areas. Substantial variation of the derived measures was observed at the ZIP code level with 20 (17.4%) Missouri counties having ZIP codes in both the top and bottom quintiles of health factors and health outcomes. Thirty of the 46 (65.2%) counties in the top 2 county quintiles had ZIP codes in the bottom 2 quintiles.

Conclusions:
This proof-of-concept analysis suggests that readily available hospital and census-derived data can be used to create measures of population health at the subcounty level. These widely available data sources could be used to identify areas of potential need within counties, engage community stakeholders, and target interventions.
Improved HIV-1 Viral Load Monitoring Capacity Using Pooled Testing With Marker-Assisted Deconvolution
Authors: Liu Tao , Hogan Joseph W. , Daniels Michael J. , Coetzer Mia , Xu Yizhen , Bove Gerald , DeLong Allison K. , Ledingham Lauren , Orido Millicent , Diero Lameck , Kantor Rami 
Published: May 2017

Objective:
Improve pooled viral load (VL) testing to increase HIV treatment monitoring capacity, particularly relevant for resource-limited settings.

Design:
We developed marker-assisted mini-pooling with algorithm (mMPA), a new VL pooling deconvolution strategy that uses information from low-cost, routinely collected clinical markers to determine an efficient order of sequential individual VL testing and dictates when the sequential testing can be stopped.

Methods:
We simulated the use of pooled testing to ascertain virological failure status on 918 participants from 3 studies conducted at the Academic Model Providing Access to Healthcare in Eldoret, Kenya, and estimated the number of assays needed when using mMPA and other pooling methods. We also evaluated the impact of practical factors, such as specific markers used, prevalence of virological failure, pool size, VL measurement error, and assay detection cutoffs on mMPA, other pooling methods, and single testing.

Results:
Using CD4 count as a marker to assist deconvolution, mMPA significantly reduces the number of VL assays by 52% [confidence interval (CI): 48% to 57%], 40% (CI: 38% to 42%), and 19% (CI: 15% to 22%) compared with individual testing, simple mini-pooling, and mini-pooling with algorithm, respectively. mMPA has higher sensitivity and negative/positive predictive values than mini-pooling with algorithm, and comparable high specificity. Further improvement is achieved with additional clinical markers, such as age and time on therapy, with or without CD4 values. mMPA performance depends on prevalence of virological failure and pool size but is insensitive to VL measurement error and VL assay detection cutoffs.

Conclusions:
mMPA can substantially increase the capacity of VL monitoring.
Defining Quality of Rheumatologic Care: Mexico
Authors: Pineda Carlos , Sandoval Hugo 
Published: May 2017

Abstract
We present an overview of rheumatology practices in Mexico, describing the national health care system as segmented and fragmentary, with a population separated into 3 main categories, according to employment-based coverage and income level: (1) private sector, (2) Social Security System, and (3) public insurance subsector.
The rheumatology practice in the public and private sectors are described. We estimate that between 85%–90% of Mexican rheumatologists have a mixed (public and private)–type practice. Payments to rheumatologists are not currently affected by quality and value metrics, with low penetrance of electronic health records. Recent changes and challenges to health insurance coverage are illustrated.
Human brain-derived Aβ oligomers bind to synapses and disrupt synaptic activity in a manner that requires APP
Authors: Wang Zemin , Jackson Rosemary J. , Hong Wei , Walter Taylor M. , Moreno Arturo , Liu Wen , Li Shaomin , Frosch Matthew P. , Slutsky Inna , Young-Pearse Tracy , Spires-Jones Tara L. , Walsh Dominic M. 
Published: May 2017

AbstractCompelling genetic evidence links the amyloid precursor protein (APP) to Alzheimer’s disease (AD), and several theories have been advanced to explain the involvement of APP in AD. A leading hypothesis proposes that a small amphipathic fragment of APP, the amyloid β-protein (Aβ), self-associates to form soluble aggregates which impair synaptic and network activity. Here, we report on the plasticity-disrupting effects of Aβ isolated from AD brain and the requirement of APP for these effects. We show that Aβ-containing AD brain extracts block hippocampal long-term potentiation (LTP), augment glutamate release probability and disrupt the excitation/inhibition balance. Notably, these effects are associated with Aβ localizing to synapses, and genetic ablation of APP prevents both Aβ binding and Aβ-mediated synaptic dysfunctions. These findings indicate a role for APP in AD pathogenesis beyond the generation of Aβ and suggest modulation of APP expression as a therapy for AD.AcknowledgmentsWe thank Dr. Tiernan T. O’Malley for useful discussions and technical advice. This work was supported by grants to DMW from the National Institutes of Health (AG046275), Bright Focus, and the United States-Israel Binational Science Foundation (2013244, DMW and IS); grants to TSJ from Alzheimer’s Research UK and the Scottish Government (ARUK-SPG2013-1), Wellcome Trust-University of Edinburgh Institutional Strategic Support funds, and the H2020 European Research Council (ALZSYN); and to the Massachusetts Alzheimer’s Disease Research Center (AG05134).
DNA.Land: A digital biobank using a massive crowdsourcing approach
Authors: Yuan Jie , Gordon Assaf , Speyer Daniel , Aufrichtig Richard , Zielinski Dina , Pickrell Joseph , Erlich Yaniv 
Published: May 2017

AbstractPrecision medicine necessitates large scale collections of genomes and phenomes. Despite decreases in the costs of genomic technologies, collecting these types of information at scale is still a daunting task that poses logistical challenges and requires consortium-scale resources. Here, we describe DNA.Land, a digital biobank to collect genome and phenomes with a fraction of the resources of traditional studies at the same scale. Our approach relies on crowd-sourcing data from the rapidly growing number of individuals that have access to their own genomic datasets through Direct-to-Consumer (DTC) companies. To recruit participants, we developed a series of automatic return-of-results features in DNA.Land that increase users’ engagement while stratifying human subject research protection. So far, DNA.Land has collected over 43,000 genomes in 20 months of operation, orders of magnitude higher than previous digital attempts by academic groups. We report lessons learned in running a digital biobank, our technical framework, and our approach regarding ethical, legal, and social implications.