bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duration of Exposure Among Close Contacts of Patients With Infectious Tuberculosis and Risk of Latent Tuberculosis Infection
Authors: Reichler Mary R , Khan Awal , Yuan Yan , Chen Bin , McAuley James , Mangura Bonita , Sterling Timothy R ,   Tuberculosis Epidemiologic Studies Consortium Task Order 2 Team, Bakhtawar I , LeDoux C , McAuley J , Beison J , Fitzgerald M , Naus M , Nakajima M , Schluger N , Hirsch-Moverman Y , Moran J , Blumberg H , Tapia J , Singha L , Hershfeld E , Roche B , Mangura B , Sevilla A , Sterling T , Chavez-Lindell T , Maruri F , Dorman S , Cronin W , Munk E , Khan A , Yuan Y , Chen B , Yan F , Shen Y , Zhao H , Zhang H , Bessler P , Fagley M , Reichler M , Reichler M , Sterling T , Tapia J , Hirsch C , Luo C , Bakhtawar I , LeDoux C , McAuley J , Beison J , Fitzgerald M , Naus M , Nakajima M , Schluger N , Hirsch-Moverman Y , Moran J , Blumberg H , Tapia J , Singha L , Hershfeld E , Roche B , Mangura B , Sevilla A , Sterling T , Chavez-Lindell T , Maruri F , Dorman S , Cronin W , Munk E , Khan A , Yuan Y , Chen B , Yan F , Shen Y , Zhao H , Zhang H , Bessler P , Fagley M , Reichler M , Reichler M , Sterling T , Tapia J , Hirsch C , Luo C 
Published: January 2020

Abstract

Background
Predictors of latent tuberculosis infection (LTBI) among close contacts of persons with infectious tuberculosis (TB) are incompletely understood, particularly the number of exposure hours.

Methods
We prospectively enrolled adult patients with culture-confirmed pulmonary TB and their close contacts at 9 health departments in the United States and Canada. Patients with TB were interviewed and close contacts were interviewed and screened for TB and LTBI during contact investigations.

Results
LTBI was diagnosed in 1390 (46%) of 3040 contacts, including 624 (31%) of 2027 US/Canadian-born and 766 (76%) of 1013 non-US/Canadian-born contacts. In multivariable analysis, age ≥5 years, male sex, non-US/Canadian birth, smear-positive index patient, and shared bedroom with an index patient (P &lt; .001 for each), as well as exposure to &gt;1 index patient (P &lt; .05), were associated with LTBI diagnosis. LTBI prevalence increased with increasing exposure duration, with an incremental prevalence increase of 8.2% per 250 exposure hours (P &lt; .0001). For contacts with &lt;250 exposure hours, no difference in prevalence was observed per 50 exposure hours (P = .63).

Conclusions
Hours of exposure to a patient with infectious TB is an important LTBI predictor, with a possible risk threshold of 250 hours. More exposures, closer exposure proximity, and more extensive index patient disease were additional LTBI predictors.
Into the wild: new yeast genomes from natural environments and new tools for their analysis
Authors: Libkind D , Peris D , Cubillos F A , Steenwyk J L , Opulente D A , Langdon Q K , Rokas A , Hittinger C T 
Published: January 2020

ABSTRACTGenomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
Extensive Genomic Rearrangements along with Distinct Mobilome and TALome are Associated with Extreme Pathotypes of a Rice Pathogen
Authors: Kaur Amandeep , Bansal Kanika , Patil Prabhu B 
Published: January 2020

Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a serious pathogen of rice which displays tremendous interstrain variation. The emergence of highly-virulent strains of Xoo is a major threat to rice cultivation. Evolutionary insights into genome dynamics of highly virulent strains as compared with the less-virulent ones are crucial for understanding the molecular basis of exceptional success of Xoo as a highly evolved plant pathogen. In the present study, we report complete genome sequence of Xoo strains with extreme-virulent pathotypes (XVPs) characterized based on their reaction toward ten resistance (Xa) genes. One strain, IXO1088, can overcome resistance mediated by all the ten resistance genes while the other strain IXO704 cannot overcome any of them. Interestingly, our investigation revealed that XVPs display dramatic variation in the genome structure with numerous rearrangements/inversions. Moreover, XVPs also possess distinct transposon content and prophage elements that may provide genomic flux required for the acquisition of novel gene cassettes and structural changes in the genome. Interestingly, analysis of transcription activator-like effector proteins, which are major virulence determinants of Xanthomonas pathogen show marked variation in the transcription activator-like effector content and DNA binding domain of tal genes. Overall, the present study indicates the possible role of mobilomes and repetitive elements in major structural and sequence alterations, which may be leading to the emergence of novel and extreme pathotypes. The knowledge and resource of XVPs will be invaluable in the further systematic understanding of evolution and management of variant pathotypes of Xoo.
Surgical and endovascular treatment of a bilateral deep femoral artery aneurysm
Authors: Okugi Satoshi , Watanabe Kazumasa , Kunii Yoshifumi , Koide Masaaki 
Published: January 2020

Abstract
We report the rare case of a 68-year-old man with a bilateral deep femoral artery aneurysm. Right-sided rupture was treated via plug embolization of the right deep femoral artery and ligation. In the following year, Viabahn® stent grafts were placed in the left superficial femoral artery to relieve occlusion and in the left deep femoral artery to treat the left aneurysm. The postoperative course of the patient was uneventful.
Robust stabilization of non-linear non-autonomous control systems with periodic linear approximation
Authors: Slyn’ko V I , Tunç Cemil , Bivziuk V O 
Published: January 2020

AbstractThe paper deals with the problem of stabilizing the equilibrium states of a family of non-linear non-autonomous systems. It is assumed that the nominal system is a linear controlled system with periodic coefficients. For the nominal controlled system, a new method for constructing a Lyapunov function in the quadratic form with a variable matrix is proposed. This matrix is defined as an approximate solution of the Lyapunov matrix differential equation in the form of a piecewise exponential function based on partial sums of a W. Magnus series. A stabilizing control in the form of a linear feedback with a piecewise constant periodic matrix is constructed. This control simultaneously stabilizes the considered family of systems. The estimates of the domain of attraction of an asymptotically stable equilibrium state of a closed-loop system that are common for all systems are obtained. A numerical example is given.
Genus One Cobordisms Between Torus Knots
Authors: Feller Peter , Park JungHwan 
Published: January 2020

Abstract
We determine the pairs of torus knots that have a genus one cobordism between them, with one notable exception. This is done by combining obstructions using $\nu ^+$ from the Heegaard Floer knot complex and explicit constructions of cobordisms. As an application, we determine the pairs of torus knots related by a single crossing change. Also, we determine the pairs of Thurston–Bennequin number maximizing Legendrian torus knots that have a genus one exact Lagrangian cobordism, with one exception.
A comparative study between real-time PCR and loop-mediated isothermal amplification to detect carbapenemase and/or ESBL genes in Enterobacteriaceae directly from bronchoalveolar lavage fluid samples
Authors: Vergara A , Moreno-Morales J , Roca I , Pitart C , Kostyanev T , Rodriguez-Baño J , Goossens H , Marco F , Vila J 
Published: January 2020

Abstract

Objectives
To evaluate and compare the efficacy of real-time PCR (Xpert Carba-R) and loop-mediated isothermal amplification (Eazyplex® SuperBug CRE) for detecting carbapenemase carriage in Enterobacteriaceae directly from bronchoalveolar lavage (BAL).

Methods
Negative BAL samples were spiked with 21 well-characterized carbapenemase-producing Enterobacteriaceae strains to a final concentration of 102–104 cfu/mL. Xpert Carba-R (Cepheid, Sunnyvale, CA, USA), which detects five targets (blaKPC, blaNDM, blaVIM, blaOXA-48 and blaIMP-1), and the Eazyplex® SuperBug CRE system (Amplex-Diagnostics GmbH, Germany), which detects seven genes (blaKPC, blaNDM, blaVIM, blaOXA-48, blaOXA-181, blaCTXM-1 and blaCTXM-9), were evaluated for the detection of these genes directly from BAL samples.

Results
Xpert Carba-R showed 100% agreement with carbapenemase characterization by PCR and sequencing for all final bacteria concentrations. Eazyplex® SuperBug CRE showed 100%, 80% and 27% agreement with PCR and sequencing when testing 104, 103 and 102 cfu/mL, respectively. False negative results for Eazyplex® SuperBug CRE matched the highest cycle threshold values for Xpert Carba-R. Hands-on time for both assays was about 15 min, but Eazyplex® SuperBug CRE results were available within 30 min, whereas Xpert Carba-R took around 50 min.

Conclusions
We here describe the successful use of two commercial diagnostic tests, Xpert Carba-R and Eazyplex® SuperBug CRE, to detect bacterial carbapenem resistance genes directly in lower respiratory tract samples. Our results could be used as proof-of-concept data for validation of these tests for this indication.
Population Bottlenecks Strongly Influence the Evolutionary Trajectory to Fluoroquinolone Resistance in Escherichia coli
Authors: Garoff Linnéa , Pietsch Franziska , Huseby Douglas L , Lilja Tua , Brandis Gerrit , Hughes Diarmaid 
Published: January 2020

Abstract
Experimental evolution is a powerful tool to study genetic trajectories to antibiotic resistance under selection. A confounding factor is that outcomes may be heavily influenced by the choice of experimental parameters. For practical purposes (minimizing culture volumes), most experimental evolution studies with bacteria use transmission bottleneck sizes of 5 × 106 cfu. We currently have a poor understanding of how the choice of transmission bottleneck size affects the accumulation of deleterious versus high-fitness mutations when resistance requires multiple mutations, and how this relates outcome to clinical resistance. We addressed this using experimental evolution of resistance to ciprofloxacin in Escherichia coli. Populations were passaged with three different transmission bottlenecks, including single cell (to maximize genetic drift) and bottlenecks spanning the reciprocal of the frequency of drug target mutations (108 and 1010). The 1010 bottlenecks selected overwhelmingly mutations in drug target genes, and the resulting genotypes corresponded closely to those found in resistant clinical isolates. In contrast, both the 108 and single-cell bottlenecks selected mutations in three different gene classes: 1) drug targets, 2) efflux pump repressors, and 3) transcription-translation genes, including many mutations with low fitness. Accordingly, bottlenecks smaller than the average nucleotide substitution rate significantly altered the experimental outcome away from genotypes observed in resistant clinical isolates. These data could be applied in designing experimental evolution studies to increase their predictive power and to explore the interplay between different environmental conditions, where transmission bottlenecks might vary, and resulting evolutionary trajectories.
Double-Tonic Complexes in Rock Music
Authors: Nobile Drew 
Published: January 2020

Abstract
Most analysts consider a song either to be in a single key or to exhibit competition or ambiguity among multiple possible keys. This article proposes an alternative in which two keys combine to create a coherent, stable tonality. I adapt Robert Bailey’s concept of the “double-tonic complex” to demonstrate that in many rock songs, relative major and minor keys coexist with neither superior to the other and no conflict between them. These songs are not quite in two keys at once, but rather each component key represents a different incarnation of a single, more abstract tonality encompassing them both. The prolonged generative tonic of such a structure is a four-note sonority built from the union of the two tonic triads; this sonority often—but not always—appears as a surface chord at structurally important moments.
Options Trading Costs Are Lower than You Think
Authors: Muravyev Dmitriy , Pearson Neil D 
Published: January 2020

Abstract
Conventional estimates of the costs of taking liquidity in options markets are large. Nonetheless, options trading volume is high. We resolve this puzzle by showing that options price changes are predictable at high frequency, and many traders time executions by buying (selling) when the option fair value is close to the ask (bid). Effective spreads of traders who time executions are less than 40% of the size of conventional measures, and the overall average effective spread is one-quarter smaller than conventional estimates. Price impact measures are also affected. These findings alter conclusions about the after-cost profitability of options trading strategies.
Financial Inclusion, Human Capital, and Wealth Accumulation: Evidence from the Freedman’s Savings Bank
Authors: Stein Luke C D , Yannelis Constantine 
Published: January 2020

Abstract
This paper studies how access to financial services among a previously unbanked group affects human capital, labor market, and wealth outcomes. We use novel data from the Freedman’s Savings Bank—created following the American Civil War to serve free Blacks—employing an instrumental variables strategy exploiting the staggered rollout of bank branches. Families with accounts are more likely to have children in school, be literate, work, and have higher occupational income, business ownership, and real estate wealth. Placebo effects are not present using planned but unbuilt branches, or for Whites, suggesting significant positive effects of financial inclusion.
The last chance to pass the ball: investigating the role of temporal expectation and motor resonance in processing temporal errors in motor actions
Authors: Pedullà Ludovico , Gervasoni Elisa , Bisio Ambra , Biggio Monica , Ruggeri Piero , Avanzino Laura , Bove Marco 
Published: January 2020

Abstract
Humans can acquire information on others’ motor outputs (action prediction) and intentions (action understanding) according to their individual motor repertoire and to the detected gesture’s features (e.g. temporal patterns). We aimed at dissociating between action prediction and action understanding abilities in soccer players and novices observing soccer action videos including correct timing pass (CTP) or delayed pass (DP). First, we used an occluding paradigm to evaluate participants’ ability to predict the correct time to pass the ball. Although soccer players showed reduced reaction times, all subjects showed a similar pattern of performance: during DP observation, responses appeared delayed with respect to the other conditions but anticipated with respect to the observed DP. In a separate experiment, we investigated the ability to recognize CTP vs DP and the modulation of primary motor cortex (M1) excitability associated to video observation. Only soccer players showed selective modulation of M1 according to the plausibility of the observed action, with increased excitability during the observation of the CTP and in a phase preceding the DP. In conclusion, action prediction ability seems to be independent from the individual motor repertoire. By contrast, only subjects with previously acquired sensorimotor skills are able to infer the observed action’s long-term intention.
Prospect patents, data markets, and the commons in data-driven medicine: Openness and the political economy of intellectual property rights
Authors: Sideri Katerina 
Published: January 2020

Abstract
Scholars who point to political influences and the regulatory function of patent courts in the USA have long questioned the courts’ subjective interpretation of what ‘things’ can be claimed as inventions. The present article sheds light on a different but related facet: the role of the courts in regulating knowledge production. I argue that the recent cases decided by the US Supreme Court and the Federal Circuit, which made diagnostics and software very difficult to patent and which attracted criticism for a wealth of different reasons, are fine case studies of the current debate over the proper role of the state in regulating the marketplace and knowledge production in the emerging information economy. The article explains that these patents are prospect patents that may be used by a monopolist to collect data that everybody else needs in order to compete effectively. As such, they raise familiar concerns about failure of coordination emerging as a result of a monopolist controlling a resource such as datasets that others need and cannot replicate. In effect, the courts regulated the market, primarily focusing on ensuring the free flow of data in the emerging marketplace very much in the spirit of the ‘free the data’ language in various policy initiatives, yet at the same time with an eye to boost downstream innovation. In doing so, these decisions essentially endorse practices of personal information processing which constitute a new type of public domain: a source of raw materials which are there for the taking and which have become most important inputs to commercial activity. From this vantage point of view, the legal interpretation of the private and the shared legitimizes a model of data extraction from individuals, the raw material of information capitalism, that will fuel the next generation of data-intensive therapeutics in the field of data-driven medicine.
Mapping and Analysis of US State and Urban Local Sodium Reduction Laws
Authors: Sloan Arielle A. , Keane Thomas , Pettie Jennifer Rutledge , Bhuiya Aunima R. , Taylor Lauren N. , Bates Marlana , Bernard Stephanie , Akinleye Fahruk , Gilchrist Siobhan 
Published: January 2020

Context:
Excessive sodium consumption contributes to high blood pressure, which is a risk factor for cardiovascular disease.

Objectives:
To (1) identify state and urban local laws addressing adult or general population sodium consumption in foods and beverages and (2) align findings to a previously published evidence classification review, the Centers for Disease Control and Prevention Sodium Quality and Impact of Component (QuIC) evidence assessment.

Design:
Systematic collection of sodium reduction laws from all 50 states, the 20 most populous counties in the United States, and the 20 most populous cities in the United States, including Washington, District of Columbia, effective on January 1, 2019. Relevant laws were assigned to 1 or more of 6 interventions: (1) provision of sodium information in restaurants or at point of purchase; (2) consumer incentives to purchase lower sodium foods; and provision of lower sodium offerings in (3) workplaces, (4) vending machines, (5) institutional meal services, and (6) grocery, corner, and convenience stores. The researchers used Westlaw, local policy databases or city Web sites, and general nutrition policy databases to identify relevant laws.

Results:
Thirty-nine sodium reduction laws and 10 state laws preempting localities from enacting sodium reduction laws were identified. Sodium reduction laws were more common in local jurisdictions and in the Western United States. Sodium reduction laws addressing meal services (n = 17), workplaces (n = 12), labeling (n = 13), and vending machines (n = 11) were more common, while those addressing grocery stores (n = 2) or consumer incentives (n = 6) were less common. Laws with high QuIC evidence classifications were generally more common than laws with low QuIC evidence classifications.

Conclusions:
The distribution of sodium laws in the US differed by region, QuIC classification, and jurisdiction type, indicating influence from public health and nonpublic health factors. Ongoing research is warranted to determine how the strength of public health evidence evolves over time and how those changes correlate with uptake of sodium reduction law.
Putting Policy Into Practice: School-Level Compliance With and Implementation of State Concussion Laws
Authors: Sullivan Lindsay , Harvey Hosea H. , Smith Gary A. , Yang Jingzhen 
Published: January 2020

Context:Each year, approximately 2 million US children 18 years or younger sustain a concussion, a type of mild traumatic brain injury (TBI). Concussions can have detrimental effects on physical, cognitive, emotional, or sleep health.Policy:Between 2009 and 2014, all 50 US states and Washington, District of Columbia, enacted state concussion laws aimed to increase awareness about concussion and reduce the prevalence and severity of this injury. Most state laws include the following core tenets: (1) immediate removal from play after an actual or suspected concussion; (2) medical clearance before an athlete can return to play (RTP); and (3) concussion education for athletes, parents, and coaches.Implementation:State concussion laws allow for substantial interpretation at the school level, resulting in considerable variation in the content of school written concussion policies and the level of implementation of state law requirements at the school level.Evaluation:We assessed the degree of high school written concussion policy compliance with the respective state law and examined the relationship between concussion policy compliance and school-level implementation of concussion laws. Seventy-one school officials completed a semistructured telephone interview and submitted their school's written concussion policy. Of the 71 policies analyzed, most complied with the removal-from-play, RTP, and concussion education tenets (90.1%, 97.2%, and 76.1%, respectively). The majority of participants reported that their school implemented the removal-from-play (91.5%), RTP (93.0%), and concussion education (80.6%) tenets well or very well. No significant relationships were found between researcher-rated school policy compliance and school-reported implementation of state law requirements at the school level.Discussion:Our findings suggest that most participating schools complied with their state concussion law and implemented law requirements well or very well. Future studies should identify facilitators and barriers to the implementation of state concussion laws at the school level.