bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Validation of Surveillance-Based Algorithms to Estimate Hepatitis C Treatment and Cure in New York City
Authors: Moore Miranda S. , Bocour Angelica , Jordan Lizeyka , McGibbon Emily , Varma Jay K. , Winters Ann , Laraque Fabienne 
Published: December 2017

Context:
Treatment options for chronic hepatitis C virus (HCV) have improved in recent years. The burden of HCV in New York City (NYC) is high. Measuring treatment and cure among NYC residents with HCV infection will allow the NYC Department of Health and Mental Hygiene (DOHMH) to appropriately plan interventions, allocate resources, and identify disparities to combat the hepatitis C epidemic in NYC.

Objective:
To validate algorithms designed to estimate treatment and cure of HCV using RNA test results reported through routine surveillance.

Design:
Investigation by NYC DOHMH to determine the true treatment and cure status of HCV-infected individuals using chart review and HCV test data. Treatment and cure status as determined by investigation are compared with the status determined by the algorithms.

Setting:
New York City health care facilities.

Participants:
A total of 250 individuals with HCV reported to the New York City Department of Health and Mental Hygiene (NYC DOHMH) prior to March 2016 randomly selected from 15 health care facilities.

Main Outcome Measures:
The sensitivity and specificity of the algorithms.

Results:
Of 235 individuals successfully investigated, 161 (69%) initiated treatment and 96 (41%) achieved cure since the beginning of 2014. The treatment algorithm had a sensitivity of 93.2% (95% confidence interval [CI], 89.2%-97.1%) and a specificity of 83.8% (95% CI, 75.3%-92.2%). The cure algorithm had a sensitivity of 93.8% (95% CI, 88.9%-98.6%) and a specificity of 89.4% (95% CI, 83.5%-95.4%). Applying the algorithms to 68 088 individuals with HCV reported to DOHMH between July 1, 2014, and December 31, 2016, 28 392 (41.7%) received treatment and 16 921 (24.9%) were cured.

Conclusions:
The algorithms developed by DOHMH are able to accurately identify HCV treatment and cure using only routinely reported surveillance data. Such algorithms can be used to measure treatment and cure jurisdiction-wide and will be vital for monitoring and addressing HCV. NYC DOHMH will apply these algorithms to surveillance data to monitor treatment and cure rates at city-wide and programmatic levels, and use the algorithms to measure progress towards defined treatment and cure targets for the city.
Contemporary protease inhibitors and cardiovascular risk
Authors: Lundgren Jens , Mocroft Amanda , Ryom Lene 
Published: December 2017

Purpose of review
To review the evidence linking use of HIV protease inhibitors with excess risk of cardiovascular disease (CVD) in HIV+ populations.

Recent findings
For the two contemporary most frequently used protease inhibitors, darunavir and atazanavir [both pharmacologically boosted with ritonavir (/r)], darunavir/r has been shown to be associated with increased CVD risk. The effect is cumulative with longer exposure increasing risk and an effect size comparable to what has been observed for previously developed protease inhibitors. Biological mechanisms may be overlapping and include perturbed lipid metabolism and accumulation of cholesterol derivatives within macrophages. Conversely, atazanavir/r has not been shown to be associated with CVD, possibly because of its ability to increase cardioprotective bilirubin levels.

Summary
Evidence linking protease inhibitors to CVD is based on observational studies only, whereas plausible biological explanations are well established and derived from randomized trials and controlled experiments. Given the possible association with clinical disease, a conservative approach to apply the data in daily practise is proposed which is focused on individualization of care based on underlying risk of CVD.
A Novel Method to Calculate the Volume of Alveolar Cleft Defect Before Surgery
Authors: Chen Guo C. , Sun Min , Yin Ning B. , Li Hai D. 
Published: December 2017

Background:
This study aimed to evaluate a novel subtractive method for the precise calculation of alveolar cleft defect volume before surgery using the three-dimensional imaging software Mimics.

Methods:
Ten patients (3 female, 7 male, age range 8–12 years) with unilateral alveolar cleft were enrolled in the study. Preoperative helical computed tomography scans were performed for all patients. A new subtractive method was introduced to precisely calculate the alveolar cleft defect volume before surgery with the aid of Mimics. The DICOM data of every patient were processed using the subtractive method. Statistical analyses were performed using Pearson's correlation test and t test.

Results:
The mean volume of the alveolar cleft defect was 1811.97 ± 817.90 mm3. The mean time spent to calculate an alveolar cleft defect volume was 60.60 ± 11.67 minutes. The Pearson correlation test (r = 0.38, P = 0.279) indicated a poor correlation between alveolar cleft defect volume and calculation time.

Conclusions:
Preoperative knowledge of defect volume is crucial in alveolar cleft repair. Accurate estimation of graft volume in alveolar cleft patients can be performed using this new subtractive method. Compared with previous methods, this new subtractive method is time-saving and suitable for both unilateral and bilateral clefts. Surgeons can use this method to design a surgical plan for each patient before surgery within a short time, and with less cost.
The experience of head and neck cancer survivorship (including laryngectomy): an integrated biopsychosocial model
Authors: Jacobson Marlene C. 
Published: December 2017

Purpose of review
The head and neck cancer (HNC) survivorship experience is unique among cancer populations. This review seeks to explore the HNC survivor experience associated with altered upper aerodigestive tract (UADT) function using principles of survivorship.

Recent findings
HNC survivors experience complex physical, functional, and psychosocial challenges related to UADT dysfunction. Interventions need to address all of these dimensions being mindful of the survivor experience. Studies reveal related unmet needs of both HNC survivors and their family members. An expose of the HNC survivorship experience is timely since 2016/2017 contains the release of landmark position papers and guidelines in the field. These address the unique challenges faced by the HNC population, their management, and the triad psychosocial, functional, and physical survivor burden. Such developments will drive future care.

Summary
The head and neck survivorship experience is characterized by complex changes with broad impact when examined in an experiential framework. HNC survivor care demands clinical excellence from multiple disciplines that are positioned to enact recent HNC guidelines and adopt survivorship principles. Future research in this population that explores experiential aspects of altered UADT function would be valuable in informing clinical practice. A biopsychosocial framework is presented for conceptualizing the HNC survivorship experience.
Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses
Authors: Pénzes Judit J , Marsile-Medun Soledad , Agbandje-McKenna Mavis , Gifford Robert James 
Published: December 2017

ABSTRACTAmdoparvoviruses (familyParvoviridae:genusAmdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify PVe disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived PVe in the genome of the Transcaucasian mole vole (Ellobius lutescens). Furthermore, we identify four further PVe in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identify a genome-length PVe in the genome of a pit viper (Protobothrops mucrosquamatus) that is more like a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features including: (i) a putative middle ORF gene; (ii) a capsid gene that lacks a phospholipase A2 (PLA2) domain; (iii) a genome structure consistent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range has extended to rodents in the past, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that PVe in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species.
High-efficiency optogenetic silencing with soma-targeted anion-conducting channelrhodopsins
Authors: Mahn Mathias , Gibor Lihi , Cohen-Kashi Malina Katayun , Patil Pritish , Printz Yoav , Oring Shir , Levy Rivka , Lampl Ilan , Yizhar Ofer 
Published: December 2017

AbstractOptogenetic silencing allows time-resolved functional interrogation of defined neuronal populations. However, the limitations of inhibitory optogenetic tools impose stringent constraints on experimental paradigms. The high light power requirement of light-driven ion pumps and their effects on intracellular ion homeostasis pose unique challenges, particularly in experiments that demand inhibition of a widespread neuronal population in vivo. Guillardia theta anion-conducting channelrhodopsins (GtACRs) are promising in this regard, due to their high single-channel conductance and favorable photon-ion stoichiometry. However, GtACRs show poor membrane targeting in mammalian cells, and the activity of such channels can cause transient excitation in the axon due to an excitatory chloride reversal potential in this compartment. Here we address both problems by enhancing membrane targeting and subcellular compartmentalization of GtACRs. The resulting GtACR-based optogenetic tools show improved photocurrents, greatly reduced axonal excitation, high light sensitivity and rapid kinetics, allowing highly efficient inhibition of neuronal activity in the mammalian brain.
Cross-reactive immunity drives global oscillation and opposed alternation patterns of seasonal influenza A viruses
Authors: Gatti Lorenzo , Zhang Jitao David , Anisimova Maria , Schutten Martin , Osterhaus Ab , van der Vries Erhard 
Published: December 2017

AbstractSeveral human pathogens exhibit distinct patterns of seasonality and circulate as pairs of discrete strains. For instance, the activity of the two co-circulating influenza A virus subtypes oscillates and peaks during winter seasons of the world’s temperate climate zones. These periods of increased activity are usually caused by a single dominant subtype. Alternation of dominant strains in successive influenza seasons makes epidemic forecasting a major challenge. From the start of the 2009 influenza pandemic we enrolled influenza A virus infected patients (n = 2,980) in a global prospective clinical study. Complete hemagglutinin (HA) sequences were obtained from 1,078 A/H1N1 and 1,033 A/H3N2 viruses and were linked to patient data. We then used phylodynamics to construct high resolution spatio-temporal phylogenetic HA trees and estimated global influenza A effective reproductive numbers (R) over time (2009-2013). We demonstrate that R, a parameter to define host immunity, oscillates around R = 1 with a clear opposed alternation pattern between phases of the A/H1N1 and A/H3N2 subtypes. Moreover, we find a similar alternation pattern for the number of global virus migration events between the sampled geographical locations. Both observations suggest a between-strain competition for susceptible hosts on a global level. Extrinsic factors that affect person-to-person transmission are a major driver of influenza seasonality, which forces influenza epidemics to coincide with winter seasons. The data presented here indicate that also cross-reactive host immunity is a key intrinsic driver of global influenza seasonality, which determines the outcome of competition between influenza A virus strains at the onset of each epidemic season.Significance statementAnnual influenza epidemics coincide with winter seasons in many parts of the world. Environmental factors, such as air humidity variation or temperature change, are commonly believed to drive these seasonality patterns. Interestingly, three out of the four latest pandemics (1918, 1968 and 2009) did not spread in winter initially, but during summer. This questions to what extent other factors could also impact virus spread among humans. We demonstrate that cross-reactive host immunity is a key factor. It drives the well-known seasonal patterns of virus activity oscillation and alternation of the dominant influenza virus subtype in successive seasons. Furthermore, this factor may also explain the efficient spread of pandemic viruses during summer when cross-reactive host immunity is relatively low.
Excess deaths associated with the chikungunya epidemic of 2014 in Jamaica were higher among children under 5 and over 40 years of age, an analysis based on official data
Authors: Freitas André Ricardo Ribas , Donalisio Maria Rita 
Published: December 2017

AbstractWe assessed the excess of all causes of mortality by age groups during the chikungunya epidemics in Jamaica, 2014. Excess mortality was estimated by subtracting deaths observed in 2014 from that expected based on the average mortality rate of 2012-2013, with confidence interval of 99%.Overall mortality 91.9 / 100,000 population, 2,499 additional deaths than expected coincided with the peak of the epidemic, there was a strong correlation between the monthly incidence and the excess of deaths (Spearman Rho = 0.939; p <0.005). No other significant epidemiological phenomenon occurred on that island that could explain this increase in mortality. Thus, we suggest that mortality associated with chikungunya is underestimated in Jamaica, as in other countries.The excess of deaths could be a strategic tool for the epidemiological surveillance of chikungunya as it has already been used in influenza and respiratory syncytial.
Excess mortality in Guadeloupe and Martinique, islands of the French West Indies, during the chikungunya epidemic of 2014
Authors: Freitas A. R. R. , Alarcon-Elbal P. M. , Donalisio M. R. 
Published: December 2017

AbstractIn some chikugunya epidemics, deaths are not fully captured by the traditional surveillance system, based on case reports and death reports. This is a time series study to evaluate the excess of mortality associated with epidemic of chikungunya virus (CHIKV) in Guadeloupe and Martinique, Antilles, 2014. The population (total 784,097 inhabitants) and mortality data estimated by sex and age were accessed at the Institut National de la Statistique et des Etudes Economiques - France. Age adjusted mortality rates were calculated also in Reunion, Indian Ocean for comparison. Epidemiological data on CHIKV (cases, hospitalizations, and deaths) were obtained in the official epidemiological reports of the Cellule de Institut de Veille Sanitaire - France. The excess of deaths for each month in 2014 and 2015 was the difference between the expected and observed deaths for all age groups, considering the 99% confidence interval threshold. Pearson coefficient of correlation between monthly excess of deaths and reported cases of chikungunya show a strong correlation (R = 0.81, p <0.005), also with a 1-month lag (R = 0.87, p <0.001), and between monthly rates of hospitalization for CHIKV and the excess of deaths with a delay of 1 month (R = 0.87, p <0.0005).The peak of the epidemic occurred in the month with the highest mortality, returning to normal soon after the end of the CHIKV epidemic. The overall mortality estimated by this method (639 deaths) was about 4 times greater than that obtained through death declarations (160 deaths). Excess mortality increased with age. Although etiological diagnosis of all deaths associated with CHIKV infection is not possible, already well-known statistical tools can contribute to an evaluation of the impact of this virus on the mortality and morbidity in the different age groups.
Behavior Variability of a Conditional Gene Knockout Mouse as a Measure of Subtle Phenotypic Trait Expression. The Case of Mouse Executive Function Distortion
Authors: Prosselkov Pavel , Zhang Qi , Goto Hiromichi , Polygalov Denis , McHugh Thomas J. , Itohara Shigeyoshi 
Published: December 2017

ABSTRACTTask learning relies on brain executive function (EF), the construct of controlling and coordinating behavior under the everlasting flow of environmental changes. We have previously shown, that a complete knockout of a vertebrate brain-specific pair of gene paralogs (Ntng1/2) distorts the mouse EF, making behavior less predictable (more variable) via the affected working memory and attention (1). In the current study, conditionally targeting either serotonin transporter (5-HTT) or Emx1-expressing neurons, we show that the cell type-specific ablation of Ntng1 within the excitatory circuits of either cortex or thalamus does not have a profound impact on the EF but rather affects its certain modalities, i.e. impulsivity and/or selective attention, modulated by cognitive demand. Several mice of both conditional genotypes simultaneously occupy either top or bottom parameter-specific behavioral ranks, indicative of a subject-unique antagonistic either proficit or deficit of function within the same behavior. Employing genotype-attributable behavior variability as a phenotypic trait, we deduce, that Ntng1-parsed excitatory pathways contribute but do not fully reconstitute the attention-impulsivity phenotypes, associated with the mouse EF deficit. However, complete knockdown of Ntng1/2, and associated with it behavior variability, explains the deficit of executive function and task learning.
Decoding the chromatin proteome of a single genomic locus by DNA sequencing
Authors: Korthout Tessy , Poramba-Liyanage Deepani W. , Verzijlbergen Kitty F. , van Welsem Tibor , van Leeuwen Fred 
Published: December 2017

AbstractTranscription, replication and repair involve interactions of specific genomic loci with many different proteins. How these interactions are orchestrated at any given location and under changing cellular conditions is largely unknown because systematically measuring protein-DNA interactions at a specific locus in the genome is challenging. To address this problem, we developed Epi-Decoder, a Tag-ChIP-Barcode-Seq technology in budding yeast to identify and quantify in an unbiased and systematic manner the proteome of an individual genomic locus. Epi-Decoder is orthogonal to proteomics approaches because it does not rely on mass spectrometry but instead takes advantage of DNA sequencing. Analysis of the proteome of a transcribed locus proximal to an origin of replication revealed more than 400 proteins. Moreover, replication stress induced changes in local chromatin-proteome composition prior to local origin firing, affecting replication proteins as well as transcription proteins. Epi-Decoder will enable the delineation of complex and dynamic protein-DNA interactions across many regions of the genome.
Farm productive realities and the dynamics of bovine viral diarrhea (BVD) transmission
Authors: Iotti Bryan , Valdano Eugenio , Savini Lara , Candeloro Luca , Giovannini Armando , Rosati Sergio , Colizza Vittoria , Giacobini Mario 
Published: December 2017

AbstractBovine Viral Diarrhea (BVD) is a viral disease that affects cattle and that is endemic to many European countries. It has a markedly negative impact on the economy, through reduced milk production, abortions, and a shorter lifespan of the infected animals. Cows becoming infected during gestation may give birth to Persistently Infected (PI) calves, which remain highly infective throughout their life, due to the lack of immune response to the virus. As a result, they are the key driver of the persistence of the disease both at herd scale, and at the national level. In the latter case, the trade-driven movements of PIs, or gestating cows carrying PIs, are responsible for the spatial dispersion of BVD. Past modeling approaches to BVD transmission have either focused on within-herd or between-herd transmission. A comprehensive portrayal, however, targeting both the generation of PIs within a herd, and their displacement throughout the Country due to trade transactions, is still missing. We overcome this by designing a multiscale metapopulation model of the spatial transmission of BVD, accounting for both within-herd infection dynamics, and its spatial dispersion. We focus on Italy, a country where BVD is endemic and seroprevalence is very high. By integrating simple within-herd dynamics of PI generation, and the highly-resolved cattle movement dataset available, our model requires minimal arbitrary assumptions on its parameterization. Notwithstanding, it accurately captures the dynamics of the BVD epidemic, as demonstrated by the comparison with available prevalence data. We use our model to study the role of the different productive realities of the Italian market, and test possible intervention strategies aimed at prevalence reduction. We find that dairy farms are the main drivers of BVD persistence in Italy, and any control strategy targeting these farms would lead to significantly higher prevalence reduction, with respect to targeting other production compartments. Our multiscale metapopulation model is a simple yet effective tool for studying BVD dispersion and persistence at country level, and is a good instrument for testing targeted strategies aimed at the containment or elimination of this disease. Furthermore, it can readily be applied to any national market for which cattle movement data is available.
Spotiton: New Features and Applications
Authors: Dandey Venkata P. , Wei Hui , Zhang Zhening , Tan Yong Zi , Acharya Priyamvada , Eng Edward T. , Rice William J. , Kahn Peter A. , Potter Clinton S. , Carragher Bridget 
Published: December 2017

AbstractWe present an update describing new features and applications of Spotiton, a novel instrument for vitrifying samples for cryoEM. We have used Spotiton to prepare several test specimens that can be reconstructed using routine single particle analysis to ~3 Å resolution, indicating that the process has no apparent deleterious effect on the sample integrity. The system is now in routine and continuous use in our lab and has been used to successfully vitrify a wide variety of samples.