bluuebunny/crossref_metadata_2025_split huggingface dataset:
Added diagnostic value of 16S rRNA gene pan-mycobacterial PCR for nontuberculous mycobacterial infections: a 10-year retrospective study
Authors: Andenmatten Simon , Opota Onya , Mazza-Stalder Jessica , Nicod Laurent , Greub Gilbert , Jaton Katia 
Published: July 2019

AbstractThe diagnosis of mycobacterial infections has been dramatically improved by the introduction of molecular methods aimed to reduce the time to diagnosis as compared with culture. The broad range pan-mycobacterial PCR can detect all the mycobacterial species directly from clinical specimens. We aimed to evaluate its usefulness and its clinical added value for the diagnosis of nontuberculous mycobacterial (NTM) infections. We performed a retrospective study (2003–2013) including 952 samples taken from 639 patients with clinical suspicion of NTM infection. The performance of smear microscopy, PCR and culture was established using clinical data to investigate discrepant results. We also compared the time to microbial diagnosis between the direct PCR and culture. The sensitivity, specificity, positive and negative predictive values of the PCR were 61.6% (53.5–69.1), 99.1% (98.2–99.6), 92.8% (85.8–96.5) and 93.4% (91.6–94.9), respectively, when considering all specimens. When considering smear-positive specimens and smear-negative specimens, the sensitivity was 81.6% and 40%, respectively. The sensitivity for pulmonary and extra-pulmonary smear-positive specimens was 85.2% versus 72.7%. The median time to identification at species level was 35 days (SD, 17.67) for culture and 6 days (SD, 2.67) for the PCR (when positive), which represents a 29-day shorter time to results (p < 0.0001). The 16S rRNA gene pan-mycobacterial PCR displays a substantial benefit in terms of time to diagnose NTM infections when compared with culture. Despite an excellent specificity, its sensitivity is yet limited in particular for smear-negative specimens, which might be improved by relying onto real-time PCRs.
Long-read sequencing in human genetics
Authors: Kraft Florian , Kurth Ingo 
Published: July 2019

Abstract
Sanger sequencing revolutionized molecular genetics 40 years ago. However, next-generation sequencing technologies became further game changers and shaped our current view on genome structure and function in health and disease. Although still at the very beginning, third-generation sequencing methods, also referred to as long-read sequencing technologies, provide exciting possibilities for studying structural variations, epigenetic modifications, or repetitive elements and complex regions of the genome. We discuss the advantages and pitfalls of current long-read sequencing methods with a focus on nanopore sequencing, summarize respective applications and provide an outlook on the potential of these novel methods.
Pragmatism and the Importance of Interdisciplinary Teams in Investigating Personality Changes Following DBS
Authors: Kubu Cynthia S. , Ford Paul J. , Wilt Joshua A. , Merner Amanda R. , Montpetite Michelle , Zeigler Jaclyn , Racine Eric 
Published: July 2019

AbstractGilbert and colleagues (2018) point out the discrepancy between the limited empirical data illustrating changes in personality (and related concepts of identity, agency, authenticity, autonomy, and self, i.e., PIAAAS) following implantation of deep brain stimulating (DBS) electrodes and the vast number of conceptual neuroethics papers implying that these changes are widespread, deleterious, and clinically significant. Their findings are reminiscent of C. P. Snow’s essay on the divide between the two cultures of the humanities (representing the conceptual publications) and the sciences (representing the empirical work). This division in the literature raises significant ethical concerns surrounding unjustified fear of personality changes in the context of DBS and negative perceptions of clinician-scientists engaged in DBS. These concerns have real world implications for funding future innovative, DBS trials aimed to reduce suffering as well as hampering true interdisciplinary scholarship. We argue that the philosophical tradition of pragmatism and the value it places on empirical inquiry, experiential knowledge, and inter-disciplinary scholarship – reflecting diverse ways of knowing – provides a framework to start to address the important questions Gilbert and colleagues raise. In particular, we highlight the importance of expert clinician knowledge in contributing to the neuroethical questions raised by Gilbert and colleagues. Finally, we provide illustrative examples of some of our interdisciplinary empirical research that demonstrate the iterative cycle of inquiry characteristic of pragmatism in which conceptual neuroethics questions have led to empirical studies whose results then raise additional conceptual questions that give rise to new empirical studies in a way that highlights the contributions of the humanities and the sciences.
Building permanence: fire outbreaks and emergent tenure security in urban Ghana
Authors: Paller Jeffrey W. 
Published: July 2019

AbstractFire outbreaks are common sources of anxiety and insecurity in informal settlements, but they can also provide new opportunities for claim making and governance of urban space. This article examines how a series of four fires in Accra, Ghana – three of which took place in its largest squatter settlement – offered new opportunities to experiment with governance, or a new way for residents and leaders to imagine and construct the future. Empirically, I document how, in the process of reconstruction, residents redrew property lines and reshaped social relations. They did this through the emergent political action I call building permanence, or a physical claim to the urban space one inhabits, as well as a new existential state of being and living in environs that will last and remain unharmed. The article offers a possible way towards achieving more secure tenure beyond formalization and infrastructure upgrades, and focuses attention on how institutions change in the context of daily life after a moment of crisis.
Molecular screening of traditional rice varieties using tsv1-linked simple sequence repeat markers
Authors: Caguiat X. G. I. 
Published: July 2019

AbstractGenebanks offer vast amounts of traditional germplasm with potential sources of novel genes against biotic and abiotic stresses. In order to utilize the germplasm in rice breeding programmes, there should be a fast screening approach such as the use of molecular markers. Thus, the current study aimed to evaluate the use of tsv1 resistance-linked simple sequence repeat markers (SSR) for the preliminary screening of Philippine traditional rice germplasm against rice tungro spherical virus (RTSV). The tsv1 resistance-linked SSR markers consisted of two to four repeat motifs with 5–24 base repeats. Expected sizes ranged from 123 to 465 base pairs (bp) with polymorphism information content ranging from 0.23 to 0.73. Genetic analysis showed six major clusters at 50%: Clusters A, B and C had individual accessions, Cluster D had three accessions, Cluster E had 55 and Cluster F had 42 accessions. The study showed the germplasm with alleles linked to tsv1 but should be validated in the future with induced screening. In general, the material consisted of selected germplasm showing the presence of alleles linked to the tsv1 gene. These rice accessions could be a source of resistance to RTSV following further validation. Furthermore, molecular markers provide a useful tool to accelerate the screening of genetic resources for biotic and abiotic stress tolerance.
Evaluation of Ethical Analyses in Seven Reports from the European Network for Health Technology Assessment
Authors: Ekmekci Perihan Elif , Güner Müberra Devrim 
Published: July 2019

AbstractObjectivesEthics has been considered among the core domains of health technology assessment (HTA), but there are still disputes regarding ethical analysis. This study aimed to examine full final reports of the European Network for Health Technology Assessment (EUnetHTA) in terms of their compliance with the ethical methodology and ethical perspective of the HTA Core Model®.MethodsThe study examines seven full final HTA reports of EUnetHTA written based on the methodology proposed in the HTA Core Model®. The reports were analyzed using the following parameters: competency of the person/group who conducted ethical analysis, assessment elements, and the methodology of ethical analysis.ResultsThe results show that, although the HTA Core Model® helped to standardize the final reports of the assessment, there are still concerns regarding the competency of the ethical analysis team, the perspectives on the purpose of ethical analysis, data sources and viewpoints of various stakeholders, use of ethical analysis methodology, and the evaluation of the ethical appropriateness of the entire HTA process.ConclusionsThe HTA Core Model® helped to standardize the final reports on the HTA; however, not all issues with the content and outcomes were solved. The lack of expertise in ethics and insufficiency of the teams regarding ethical analysis are other existing problems. This study also demonstrated that stakeholder viewpoints in general and patient perspectives, in particular, have been overlooked in the HTA process.
The ecology of prelinguistic vocal learning: parents simplify the structure of their speech in response to babbling
Authors: ELMLINGER Steven L. , SCHWADE Jennifer A. , GOLDSTEIN Michael H. 
Published: July 2019

AbstractWhat is the function of babbling in language learning? We examined the structure of parental speech as a function of contingency on infants’ non-cry prelinguistic vocalizations. We analyzed several acoustic and linguistic measures of caregivers’ speech. Contingent speech was less lexically diverse and shorter in utterance length than non-contingent speech. We also found that the lexical diversity of contingent parental speech only predicted infant vocal maturity. These findings illustrate a new form of influence infants have over their ambient language in everyday learning environments. By vocalizing, infants catalyze the production of simplified, more easily learnable language from caregivers.
The semantics and pragmatics of Norwegian sentence-internal jo
Authors: Berthelin Signe Rix , Borthen Kaja 
Published: July 2019

AbstractThe paper proposes a refined analysis of the semantics and pragmatics of the Norwegian non-truth-conditional adverbjo‘after all, of course’. According to the literature,joindicates that the proposition is ‘given’ in some sense or other. Based on new empirical investigations, we argue that the Relevance-theoretic notion mutual manifestness (Sperber &amp; Wilson 1986/1995, Blass 2000) accurately captures the givenness aspect ofjo, and we demonstrate through authentic examples what it means for a proposition to be mutually manifest. In addition to mutual manifestness,josignals that the proposition is a premise for deriving a conclusion. The conclusion often – but not always – opposes someone’s view. We argue that the frequent opposition interpretations are a consequence of the nature of the procedures encoded byjo. In addition to clarifying the semantic and pragmatic properties ofjo, the paper sheds light on the Relevance-theoretic notion procedural semantics as well as illustrating its usefulness in the study of pragmatic particles.
Middlemen: good for resources and fishermen?
Authors: Thủy Phạm Thị Thanh , Flaaten Ola , Skonhoft Anders 
Published: July 2019

AbstractThis paper studies the role of middlemen in open-access fisheries and how the organization of the supply chains affects resource exploitation and the level and distribution of economic rent. Imperfect competition among middlemen can help ensure that fish stocks are not depleted, which is typically the case in open-access fisheries with competitive markets. Middlemen with market power can also induce higher economic rent for the supply chain in total, but these rents mainly benefit the middlemen. The supply chains of inshore anchovy and offshore skipjack tuna fisheries in Vietnam are used as empirical examples. The analysis shows that in the anchovy supply chain, the middlemen have insignificant market power and the stock is being overexploited. In the skipjack tuna supply chain, the middlemen have oligopsony power and the stock is higher than the level that produces maximum sustainable yield.
CHARACTERIZING O-MINIMAL GROUPS IN TAME EXPANSIONS OF O-MINIMAL STRUCTURES
Authors: Eleftheriou Pantelis E. 
Published: July 2019

AbstractWe establish the first global results for groups definable in tame expansions of o-minimal structures. Let
${\mathcal{N}}$
be an expansion of an o-minimal structure
${\mathcal{M}}$
that admits a good dimension theory. The setting includes dense pairs of o-minimal structures, expansions of
${\mathcal{M}}$
by a Mann group, or by a subgroup of an elliptic curve, or a dense independent set. We prove: (1) a Weil’s group chunk theorem that guarantees a definable group with an o-minimal group chunk is o-minimal, (2) a full characterization of those definable groups that are o-minimal as those groups that have maximal dimension; namely, their dimension equals the dimension of their topological closure, (3) as an application, if
${\mathcal{N}}$
expands
${\mathcal{M}}$
by a dense independent set, then every definable group is o-minimal.
A Square Deal in Lake County: Anderson v. Mathews (1917), California Indian Communities, and Indian Citizenship
Authors: Schneider Khal 
Published: July 2019

AbstractIn 1917, California's Supreme Court upheld the Eastern Pomo man Ethan Anderson's right to vote. The court recognized that Anderson lived and worked like his white neighbors and, most importantly, did not live in “tribal relations” and was subject to local jurisdiction. But Anderson, his lawyers, the opposing counsel, and the court never denied that he was a member of an Indian community. In fact, local authorities and the federal government had long acknowledged that Indian communities existed in Lake County, and they had both legitimized small Indian community landholdings as the homes of self-sufficient Indian laborers. Now, as Indian citizenship seemed to signal to local and federal authorities more claims on the state, both denied responsibility for those communities. Although citizenship seemed to stand as the categorical opposite of “Indians, not taxed,” Anderson's vindicated voting rights was not an end point of a successful program of assimilation, but one aspect of Indians’ ongoing pursuit of community security through their engagements with local and federal authorities.
Cognitive behavioural therapy for worry in young individuals with at-risk mental states: a preliminary investigation
Authors: Pozza Andrea , Domenichetti Sandro , Dèttore Davide 
Published: July 2019

Abstract
Cognitive behavioural therapy (CBT) is a first-line strategy in reducing or delaying risk of transition to psychosis among young individuals with at-risk mental states (ARMS). However, there is little knowledge about its effects on other outcomes associated with ARMS. No study on CBT for ARMS has assessed worry, an important process associated with this condition. The present study investigated changes in worry at immediate post-treatment and 14-month follow-up after CBT for young individuals with ARMS seeking psychiatric care in mental health services. Thirty-seven young individuals (mean age = 26 years, SD = 6.07; 22.20% female) seeking psychiatric care in mental health services and classified as reporting ARMS through the Comprehensive Assessment of At-Risk Mental States were included. The Positive And Negative Syndrome Scales (PANSS) and Penn State Worry Questionnaire (PSWQ) were administered at baseline, post-treatment, and follow-up. CBT consisted of 30 weekly individual 1-hour sessions based on a validated CBT for ARMS manual enriched with components targeting worry [psychoeducation, problem-solving, (meta)cognitive restructuring, behavioural experiments]. Seven participants (18.91%) at follow-up had cumulatively made transition to psychosis. Repeated measures ANOVA with post-hoc pairwise comparisons showed significant changes in PSWQ scores from baseline to post-treatment and from baseline to follow-up; PSWQ scores remained stable from post-treatment to follow-up. This is the first study investigating changes in worry after CBT for ARMS, which appears to be a promising strategy also for this outcome. Future research with a larger sample size and control group may determine whether changes in worry are also associated with reduced transition risk.

Key learning aims

(1)
To understand CBT evidence and procedures for young individuals with ARMS.

(2)
To reflect on the current limitations in the literature on CBT for ARMS.

(3)
To understand the importance and clinical implications of assessing worry in ARMS.

(4)
To focus on changes in worry as an outcome after CBT for ARMS.

(5)
To reflect on future research directions on the role of worry in CBT for ARMS.
Male-Dominated Occupations, Employment Status, and Suicidal Behaviors Among Australian Men
Authors: Milner Allison J. , Shields Marissa , Currier Dianne , King Tania L. 
Published: July 2019

Abstract. Background: Suicide rates are higher among unemployed men as well as those employed in male-dominated occupations such as construction. There has been less research on whether these patterns are similar for suicide ideation and attempt. Aims: In a cohort of 13,892 Australian males, this study examined the relationship between employment status and occupational gender ratio on reported thoughts of suicide and suicide attempts. Method: Men reporting suicide ideation or attempts at Wave 1 were removed from the sample. Logistic regression was used to examine Wave 1 employment status and occupational gender ratio and Wave 2 reported suicide ideation and attempts, controlling for confounders (measured in Wave 1). We conducted a sensitivity analysis controlling for mental health status. Results: Those who were unemployed or not in the labor force had elevated rates of suicide ideation (unemployed OR = 1.91, 95% CI [1.30, 2.82], p = .001; not in the labor force OR = 1.68, 95% CI [1.09, 2.60], p = .020). Those who were not in the labor force had greater odds of attempts ( OR = 2.32, 95% CI [1.05, 5.12], p = .037). There was no association between occupational gender ratio and suicide ideation or attempt. Limitations: We only had single item measures of ideation and attempts. Conclusion: There is a need for further investigation into risk factors for suicide among males, both when they are in and out of employment.
Quantifying the Effect of Irrigation on Nonlocal Aspects of the Atmosphere
Authors: Nauert C. J. , Ancell B. C. 
Published: July 2019

AbstractIrrigation‐induced effects on weather have been studied for several decades using observations and numerical weather prediction models. However, few have ventured to investigate nonlocal, downstream effects on convective weather produced during the passage of strongly forced synoptic systems, or as we refer to as high‐impact weather. One reason for this discrepancy is the influence of chaos seeding (Ancell et al., 2018, https://doi.org/10.1175/BAMS‐D‐17‐0129.1) from the model physics in areas where precipitation or convection are occurring, causing unrealistic changes in precipitation far downstream in a matter of hours. The effects of chaos seeding have made it difficult to distinguish what downstream weather modifications are irrigation‐induced feedbacks and what are products of chaos seeding itself—a distinction at the center of this work. The authors investigate whether atmospheric perturbations produced by land‐surface feedbacks from local irrigation in the Texas Panhandle can significantly modify downstream atmospheric structure on time and space scales across days and thousands of kilometers using the Advanced Research Weather Research and Forecasting Model Version 3.5.1. Irrigation is represented by perturbing the grid point variable of soil moisture with an ensemble of 75 members per 9 case studies for 96‐hr simulations, with 25 members representing unrealistic perturbations applied in New York accounting for chaos seeding. The authors find irrigation influences downstream and nonlocally elsewhere beyond the modification of chaos seeding, with effects shown in three of nine cases amid precipitation shifts occurring around cyclone, dryline, and cold front tracks with changes of 50 mm or more.
Spatial‐Temporal Assessment of Environmental Factors Related to Dengue Outbreaks in São Paulo, Brazil
Authors: Ogashawara I. , Li L. , Moreno‐Madriñán M. J. 
Published: July 2019

AbstractDengue fever, a disease caused by a vector‐borne flavivirus, is endemic to tropical countries, but its occurrence has been reported worldwide. This study aimed to understand important factors contributing to the spatial and temporal patterns of dengue occurrence in São Paulo, the largest municipality of Brazil. The temporal assessment of dengue occurrence covered the 2011–2016 time period and was based on climatological data, such as the El Niño indices and time series statistical tools such as the continuous wavelet transformation. The spatial assessment used Landsat 8 data for years 2014–2016 to estimate land surface temperature and normalized indices for vegetation, urban areas, and leaf water. Results from a cross correlation for the temporal analysis found a relationship between the sea surface temperature anomalies index and the number of reported dengue cases in São Paulo (r = 0.5) with a lag of +29 (weeks) between the climatic event and the response on the dengue incidence. This relationship, initially nonlinear, became linear after correcting for the lag period. For the spatial assessment, the linear stepwise regression model detected a low relationship between dengue incidence and minimum surface temperature (r = 0.357) and no relationship with other environmental parameters. The poor relationship might be due to confounding effects of socioeconomic factors as these seem to influence the spatial dynamics of dengue incidence. More testing is needed to validate these methods in other locations. Nevertheless, we presented possible tools to be used for the improvement of dengue control programs.
Injection‐Induced Propagation and Coalescence of Preexisting Fractures in Granite Under Triaxial Stress
Authors: Ye Zhi , Ghassemi Ahmad 
Published: July 2019

AbstractThe dilatant shear slip of preexisting fractures/faults by injection at pressures below the minimum in situ stress has been recognized as an important permeability creation mechanism during reservoir stimulation. However, interconnected fracture network generation through the propagation and coalescence of preexisting fractures during shear stimulation has been rarely studied through laboratory experiments. To examine permeability enhancement through the propagation and coalescence of preexisting fractures, we conducted novel triaxial‐injection experiments under representative crustal stress conditions on cylindrical granite samples containing single or double preexisting fracture(s)/flaw(s). In the sample with a single fracture, SW‐1, new cracks propagated from the preexisting fracture due to injection. In the sample with two fractures, SW‐2, a highly conductive fracture network was created by the coalescence of newly formed cracks with preexisting fractures. As a result, the equivalent permeability of the sample was enhanced by 17 to 35 times. Both tensile wing cracks and shear and/or mixed‐mode secondary cracks were detected from the scanning electron microscope images of the tested samples. Our results suggest that in addition to dilatant shear slip, propagation and coalescence of preexisting fractures significantly contribute to reservoir permeability creation during low injection pressure stimulation in fractured rocks. Although the experiments focused on reservoir stimulation, the results have relevance to crustal permeability evolution and induced seismicity.