bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Polycyclic Aromatic Hydrocarbons Exposure Across Occupations Using Urinary Metabolite 1-Hydroxypyrene
Authors: Koh Dong-Hee , Park Ju-Hyun , Lee Sang-Gil , Kim Hwan-Cheol , Choi Sangjun , Jung Hyejung , Park Donguk
Published: January 2020

Objectives

Polycyclic aromatic hydrocarbons (PAHs) are well-known carcinogens causing lung and skin cancers in exposed workers. Certain occupations, such as coke production, have been associated with high PAH exposure; however, the number of occupations tested to date remains small. Here, we sought to compare PAH exposure across a wide range of occupations based on levels of 1-hydroxypyrene (1-OHP), the urinary exposure surrogate of PAHs.

Methods

We collected urine 1-OHP data from the Korean National Environmental Health Survey (KoNEHS), a nationwide biomonitoring survey. We developed a linear regression model, controlling for sex, age, smoking, and survey cycle, and obtained resulting residuals. Then, we computed the fraction of exceeding the third quartile (Q3) level of residuals for each occupation, which is employed as a relative exposure indicator across occupations.

Results

A total of 15 125 measurements derived from three cycles of KoNEHS were used for analysis. The overall geometric means (GMs) and geometric standard deviation (GSD) of urine 1-OHP levels were 0.16 µg g−1 creatinine and 3.07, respectively. Among the sub-major occupational groups, ‘construction and mining related elementary occupations’ showed the highest fraction (0.45) of exceeding the Q3 level of residuals. Among the minor occupational groups, ‘deliverers’ showed a high fraction (0.42) of exceeding the Q3 level of residuals, which indicates rapidly growing occupations to be addressed.

Conclusions

Our results provide ancillary information regarding PAH exposure across occupations, especially for occupations for which PAH exposure has not been well characterized.
netGO: R-Shiny package for network-integrated pathway enrichment analysis
Authors: Kim Jinhwan , Yoon Sora , Nam Dougu
Published: January 2020

We present an R-Shiny package, netGO, for novel network-integrated pathway enrichment analysis. The conventional Fisher’s exact test (FET) considers the extent of overlap between target genes and pathway gene-sets, while recent network-based analysis tools consider only network interactions between the two. netGO implements an intuitive framework to integrate both the overlap and networks into a single score, and adaptively resamples genes based on network degrees to assess the pathway enrichment. In benchmark tests for gene expression and genome-wide association study (GWAS) data, netGO captured the relevant gene-sets better than existing tools, especially when analyzing a small number of genes. Specifically, netGO provides user-interactive visualization of the target genes, enriched gene-set and their network interactions for both netGO and FET results for further analysis. For this visualization, we also developed a standalone R-Shiny package shinyCyJS to connect R-shiny and the JavaScript version of cytoscape.

Availability and implementation

netGO R-Shiny package is freely available from github, https://github.com/unistbig/netGO.

Supplementary information

Supplementary data are available at Bioinformatics online.
GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation
Authors: Tankhilevich Evgeny , Ish-Horowicz Jonathan , Hameed Tara , Roesch Elisabeth , Kleijn Istvan , Stumpf Michael P H , He Fei
Published: January 2020

Motivation

Approximate Bayesian computation (ABC) is an important framework within which to infer the structure and parameters of a systems biology model. It is especially suitable for biological systems with stochastic and nonlinear dynamics, for which the likelihood functions are intractable. However, the associated computational cost often limits ABC to models that are relatively quick to simulate in practice.

Results

We here present a Julia package, GpABC, that implements parameter inference and model selection for deterministic or stochastic models using (i) standard rejection ABC or sequential Monte Carlo ABC or (ii) ABC with Gaussian process emulation. The latter significantly reduces the computational cost.

Availability and implementation

https://github.com/tanhevg/GpABC.jl.
Superovulation with human chorionic gonadotropin (hCG) trigger and gonadotropin releasing hormone agonist (GnRHa) trigger differentially alter essential angiogenic factors in the endometrium in a mouse ART model†
Authors: Segal Thalia R , Amini Peyvand , Wang Junye , Peters Gregory , Skomorovska-Prokvolit Yelenna , Mainigi Monica A , Goldfarb James M , Mesiano Sam , Weinerman Rachel
Published: January 2020

Gonadotropin-releasing hormone agonists (GnRHa) are used as an alternative to human chorionic gonadotropin (hCG) to trigger ovulation and decrease the risk of ovarian hyperstimulation syndrome. GnRHa is less potent at inducing ovarian vascular endothelial growth factor (VEGF), but may also affect endometrial angiogenesis and early placental development. In this study, we explore the effect of superovulation on endometrial angiogenesis during critical periods of gestation in a mouse model. We assigned female mice to three groups: natural mating or mating following injection with equine chorionic gonadotropin and trigger with GnRHa or hCG trigger. Females were killed prior to implantation (E3.5), post-implantation (E7.5), and at midgestation (E10.5), and maternal serum, uterus, and ovaries were collected. During peri-implantation, endometrial Vegfr1 and Vegfr2 mRNA were significantly increased in the GnRHa trigger group (P < 0.02) relative to the hCG group. Vegfr1 is highly expressed in the endometrial lining and secretory glands immediately prior to implantation. At E7.5, the ectoplacental cone expression of Vegfa and its receptor, Vegfr2, was significantly higher in the hCG trigger group compared to the GnRHa group (P < 0.05). Soluble VEGFR1 and free VEGFA were much higher in the serum of mice exposed to the hCG trigger compared to GnRHa group. At midgestation, there was significantly more local Vegfa expression in the placenta of mice triggered with hCG. GnRHa and hCG triggers differentially disrupt the endometrial expression of key angiogenic factors during critical periods of mouse gestation. These results may have significant implications for placental development and neonatal outcomes following human in vitro fertilization.
The coupling apparatus of the sperm head and tail†
Authors: Wu Bingbing , Gao Hui , Liu Chao , Li Wei
Published: January 2020

A strong sperm head–tail coupling apparatus (HTCA) is needed to ensure the integrity of spermatozoa during their fierce competition to fertilize the egg. A lot of HTCA-specific components have evolved to strengthen the attachment of the tail to the implantation fossa at the sperm head. Defects in HTCA formation lead to acephalic spermatozoa syndrome and pathologies of some male infertility. Recent studies have provided insights into the pathogenic molecular mechanisms of acephalic spermatozoa syndrome. Here, we summarize the proteins involved in sperm neck development and focus on their roles in the formation of HTCA. In addition, we discuss the fine structures of the sperm neck in different species from an evolutionary view, highlighting the potential conservative mechanism of HTCA formation.
Infrastructure in the Jungle: Infrastructure and Ideology in the Refugee Camps in Calais and Along the U.S.–Mexico Border
Authors: Erdener Jasmine
Published: January 2020

This article examines infrastructures as a tool for managing populations, specifically migrants and refugees, and more broadly, infrastructure as a communicative trope for social belonging and citizenship. Infrastructure emerges as a key site of ideological contestation. Refugees and their advocates argue that infrastructural breakdowns require greater investment of resources and social care. Opponents point to infrastructural breakdowns as evidence that refugees and migrants do not belong and are a drain on national resources. Through a comparative case study analysis of the refugee camp in Calais, France, and at the U.S.–Mexico border, this article argues that infrastructure and infrastructural breakdowns mediate and communicate claims to territory, political recognition, and legitimacy.
When machines think for us: the consequences for work and place
Authors: Clifton Judith , Glasmeier Amy , Gray Mia
Published: January 2020

The relationship between technology and work, and concerns about the displacement effects of technology and the organisation of work, have a long history. The last decade has seen the proliferation of academic papers, consultancy reports and news articles about the possible effects of Artificial Intelligence (AI) on work—creating visions of both utopian and dystopian workplace futures. AI has the potential to transform the demand for labour, the nature of work and operational infrastructure by solving complex problems with high efficiency and speed. However, despite hundreds of reports and studies, AI remains an enigma, a newly emerging technology, and its rate of adoption and implications for the structure of work are still only beginning to be understood. The current anxiety about labour displacement anticipates the growth and direct use of AI. Yet, in many ways, at present AI is likely being overestimated in terms of impact. Still, an increasing body of research argues the consequences for work will be highly uneven and depend on a range of factors, including place, economic activity, business culture, education levels and gender, among others. We appraise the history and the blurry boundaries around the definitions of AI. We explore the debates around the extent of job augmentation, substitution, destruction and displacement by examining the empirical basis of claims, rather than mere projections. Explorations of corporate reactions to the prospects of AI penetration, and the role of consultancies in prodding firms to embrace the technology, represent another perspective onto our inquiry. We conclude by exploring the impacts of AI changes in the quantity and quality of labour on a range of social, geographic and governmental outcomes.
Incidence, prevalence and crude survival of patients starting dialysis in Portugal (2010–16): analysis of the National Health System individual registry
Authors: de Almeida Edgar A F , Raimundo Mário , Coelho Anabela , Sá Helena
Published: January 2020

Background

The Portuguese Society of Nephrology (PSN) reported that Portugal has one of the highest incidences of dialysis in Europe. However, this claim was based on aggregated data supplied by dialysis providers, hampering comparisons between countries. In 2009, an individual registry of patients starting dialysis was set up by the Portuguese Ministry of Health. We analysed individual data of patients starting dialysis from January 2010 until December 2016.

Methods

Demography, starting treatment day, modality, regional distribution and outcomes, such as death, recovery of renal function, transfer to renal transplantation, peritoneal dialysis or conservative management, were extracted. Incidence, prevalence and survival analysis were calculated and compared with the PSN registry.

Results

Out of 19 190 registrations, 16 775 were incident patients (61.8% men). Yearly incidence of renal replacement therapy was 250, 248, 229, 239, 230, 231 and 244 per million population (p.m.p.) for 2010 to 2016, compared with 235, 224, 218, 230, 234, 225 and 239 p.m.p. reported by the PSN registry. On the other hand, prevalence increased from 998 p.m.p. in 2010 to 1286 p.m.p. in 2016, compared with 1010 p.m.p. in 2010 increasing to 1203 p.m.p. in 2016 from the PSN registry. The regions of Alentejo (122.9 p.m.p.) and the the Centre (160.8 p.m.p.) had the lowest regional incidence, while Lisbon had the highest (386 p.m.p. in 2016). Unadjusted survival analysis revealed that 93.5% of the patients were alive on the 91st day, whereas 85.2 and 78.3% were alive at 1 and 2 years, respectively. Crude survival at 7 years was 40%.

Conclusions

For the first time, an individual registry of patients starting dialysis in Portugal was subject to analysis and added new information about long-term survival and regional differences in the incidence and prevalence of renal replacement therapy. We were able to confirm that Portugal has one of the world’s highest incidences and prevalences of dialysis. We also demonstrate, for the first time, a striking regional difference in the incidence of dialysis and an excellent early and long-term survival of patients on dialysis. These results compare well with other European countries in terms of the dialysis efficiency.
Strengthening of banana breeding through data digitalization
Authors: Vignesh Kumar B , Backiyarani S , Chandrasekar A , Saranya S , Ramajayam D , Saraswathi M S , Durai P , Kalpana S , Uma S
Published: January 2020

Improvement of edible bananas (a triploid and sterile crop) through conventional breeding is a challenging task owing to its recalcitrant nature for seed set, prolonged crop duration. In addition, the need of huge man power at different stages of progeny development and evaluation often leads to mislabeling, poor data management and loss of vital data. All this can be overcome by the application of advanced information technology source. This ensured secure and efficient data management such as storage, retrieval and data analysis and further could assist in tracking the breeding status in real time. Thus, a user-friendly web-based banana breeding tracker (BBT) has been developed using MySQL database with Hypertext Preprocessor (PHP). This BBT works on all operating systems with access to multiple users from anywhere at any time. Quick responsive (QR) code labels can be generated by the tracker, which can be decoded using QR scanner. Also for each and every updated progress in breeding stages, a new QR code can be generated, which in turn reduce labeling errors. Moreover, the tracker has additional tools to search, sort and filter the data from the data sets for efficient retrieval and analysis. This tracker is being upgraded with phenotypic and genotypic data that will be made available in the public domain for hastening the banana improvement program.
Cohort Trends in Working Life Expectancies at Age 50 in the United States: A Register-Based Study Using Social Security Administration Data
Authors: Dudel Christian , Myrskylä Mikko
Published: January 2020

Objectives

Little is known about the length of working life, even though it is a key indicator for policy-makers. In this paper, we study how the length of working life at age 50 has developed in the United States from a cohort perspective.

Methods

We use a large longitudinal sample of U.S. Social Security register data that covers close to 1.7 million individuals of the cohorts born from 1920 to 1965. For all of these cohorts, we study the employment trajectories and working life expectancy (WLE) at age 50 by gender and nativity (native-born/foreign-born). For the cohorts with employment trajectories that are only incompletely observed, we borrow information from older cohorts to predict their WLE.

Results

The length of working life has been increasing for the native-born males and females, and the younger cohorts worked longer than the older cohorts. However, WLE might soon peak, and then stall. The gap in WLE between the native-born and the foreign-born has increased over time, although latter group might be able to catch up in the coming years.

Discussion

Our ﬁndings show that studying employment from a cohort perspective reveals crucial information about patterns of working life. The future development of the length of working life should be a major concern for policy-makers.
Refgenie: a reference genome resource manager
Authors: Stolarczyk Michał , Reuter Vincent P , Smith Jason P , Magee Neal E , Sheffield Nathan C
Published: January 2020

Background

Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.

Results

Here, we introduce refgenie, a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.

Conclusions

Refgenie streamlines sharing genome analysis resources among groups and across computing environments. Refgenie is available at https://refgenie.databio.org.
Substantive and Procedural Criminal Law Protection of Human Rights in the Law of the European Convention on Human Rights
Authors: Kamber Krešimir
Published: January 2020

This article seeks to examine and explain the interaction between the substantive and procedural aspects of criminal law protection of human rights in the law of the European Convention of Human Rights. Noting certain theoretical and conceptual lacunae that arise in this context, the article suggests the most appropriate solution for the assessment of the substantive-procedural relationship from the perspective of legal theory and the European Court of Human Rights’ case-law. It submits, in particular, that it is always necessary to examine both aspects—substantive and procedural—of the same right and that the procedural aspect should be given primacy both in terms of the order of examination and inferences to be drawn on the question of observance of human rights by states.
Nonexperimental Xenobiotics: Unintended Consequences of Intentionally Administered Substances in Terrestrial Animal Models
Authors: Perkins Scott E , Hankenson F Claire
Published: January 2020

Summary: Review of the use of nonexperimental xenobiotics in terrestrial animal models and the potential unintended consequences of these compounds, including drug-related side effects and adverse reactions.
Analysis of the susceptible-infected-susceptible epidemic dynamics in networks via the non-backtracking matrix
Authors: Masuda Naoki , Preciado Victor M , Ogura Masaki
Published: January 2020

We study the stochastic susceptible-infected-susceptible model of epidemic processes on finite directed and weighted networks with arbitrary structure. We present a new lower bound on the exponential rate at which the probabilities of nodes being infected decay over time. This bound is directly related to the leading eigenvalue of a matrix that depends on the non-backtracking and incidence matrices of the network. The dimension of this matrix is $N+M$, where $N$ and $M$ are the number of nodes and edges, respectively. We show that this new lower bound improves on an existing bound corresponding to the so-called quenched mean-field theory. Although the bound obtained from a recently developed second-order moment-closure technique requires the computation of the leading eigenvalue of an $N^2\times N^2$ matrix, we illustrate in our numerical simulations that the new bound is tighter, while being computationally less expensive for sparse networks. We also present the expression for the corresponding epidemic threshold in terms of the adjacency matrix of the line graph and the non-backtracking matrix of the given network.
Inhibition of Amebic Cysteine Proteases Blocks Amebic Trogocytosis but Not Phagocytosis
Authors: Gilmartin Allissia A , Ralston Katherine S , Petri William A
Published: January 2020

Background

Entamoeba histolytica kills human cells by ingesting fragments of live cells until the cell eventually dies, a process termed amebic trogocytosis. In a previous study, we showed that acidified amebic lysosomes are required for both amebic trogocytosis and phagocytosis, as well as cell killing.

Methods

Amebic cysteine proteases (CPs) were inhibited using an irreversible inhibitor, E-64d.

Results

Interfering with amebic CPs decreased amebic trogocytosis and amebic cytotoxicity but did not impair phagocytosis.

Conclusions

We show that amebic CPs are required for amebic trogocytosis and cell killing but not phagocytosis. These data suggest that amebic CPs play a distinct role in amebic trogocytosis and cell killing.
Genocide in Sudan as Colonial Ecology
Authors: Wise Louise
Published: January 2020

This article presents a novel theoretical and empirical account of the genesis and constitution of genocide in Sudan. To do so, it brings developments in critical genocide studies, notably the colonial and international “turns” and renewed attention to the scholarship of Lemkin, into dialogue with theoretical arguments about processual ontologies, complexity theory, and assemblage thinking. The latter provide a conceptual vocabulary to rethink the kind of ontological phenomenon that genocide constitutes. Rather than a discrete outcome or temporally and geographically bounded “event,” genocide in Sudan is seen as a heterogeneous, process-based, systemic entity. Challenging conventional genocide models generally and dominant narratives about Sudan specifically, the article argues that genocide in Sudan should be conceptualized as an historical internal frontier-based pattern that is constituted by three intersecting colonial forms: postcolonialism, internal colonialism, and neocolonialism. In doing so, it suggests a new way of thinking about the genocide-colonialism nexus. Tracing these three colonialisms, genocide appears not as an aberrant breakdown, violent outburst, or top-down ideological “master plan.” Neither is it a single, linearly unfolding process. Rather, it is emergent from a colonial ecology, its logic and potentiality imbricated with, and incipient within, a temporally and geographically expansive web of actors, processes, structures, relations, discourses, practices, and global forces.
In Search of Normality for Vitamin K1: Establishing Age-Dependent Reference Intervals in the Danish Population
Authors: Boegh Andersen Ida , Brasen Claus Lohman , Schmedes Anne , Brandslund Ivan , Madsen Jonna Skov
Published: January 2020

Background

A growing body of evidence suggests that vitamin K has beneficial effects on human health, especially cardiovascular and bone health. Vitamin K1 (phylloquinone), the predominant form of vitamin K in blood, is regarded as an indicator of vitamin K status, but to our knowledge no reference intervals (RIs) have been established for vitamin K1.

Methods

In this population-based study, vitamin K1 was measured in serum from 3808 Caucasian individuals without diabetes from 26 to 78 years of age. The need for gender- and age-partitioned vitamin K1 reference intervals was evaluated using Lahti’s method, and exclusion criteria were defined to obtain as healthy a study group as possible. The excluded subgroups were tested for differences in mean serum vitamin K1 levels. Serum vitamin K1 levels were quantified using an in-house newly developed, validated, and highly sensitive online SPE-LC-MS/MS method with a limit of quantitation of (LOQ) 0.05 nmol/L.

Results

The reference interval for serum vitamin K1 was 0.22 to 3.95 nmol/L for individuals aged 26 to 44 years and 0.35 to 3.70 nmol/L for individuals aged 45 to 78. Similar age-specific reference intervals were established for vitamin K1-triglyceride ratio being 0.20 to 3.16 and 0.31 to 3.44, respectively. No significant difference was found between genders. Serum vitamin K1 was detectable in all serum samples. Individuals with known comorbidity were found to have significantly lower serum vitamin K1 compared to those without comorbidity. Current smokers had lower serum vitamin K1 compared to nonsmokers.

Conclusion

Age-dependent reference intervals were established for serum vitamin K1 and vitamin K1-triglyceride ratio in a well-defined, healthy Caucasian population. Lower serum vitamin K1 levels were found in individuals with known comorbidity, suggesting an association between serum vitamin K1 and disease status. Further studies are needed to determine an optimal serum vitamin K1 level.
Lack of interactive effects between diet composition and acid addition with drying method on amino acid digestibility values in porcine ileal digesta
Authors: Kerr Brian J , Curry Shelby M , Ramirez Brett C
Published: January 2020

Two experiments were conducted to determine the effect of oven drying (OD) or freeze drying (FD) on apparent ileal digestibility (AID) of AA in diets fed to pigs. In experiment 1, 15 barrows (88.4 ± 6.4 kg) were allotted to either a corn starch–soybean meal (CST), potato starch–soybean meal (PST), or corn–soybean meal (CSBM) diet, over 2 collection periods. Following collection, samples were pooled within pig and subdivided into either OD or FD, resulting in 10 observations per diet by drying-method combination. In experiment 2, 11 barrows (63.3 ± 3.8 kg) were fed a CST diet, and, following collection, samples were pooled within pig and subdivided and either adjusted to pH 4 or remain unadjusted. Subsets of these samples were then subdivided to be either FD or OD, resulting in 11 observations per pH level by drying-method combination. OD was accomplished by drying samples in a forced air oven at either 100 °C (experiment 1) or 75 °C (experiment 2). In experiment 1, there was no diet type by drying-method interactions noted for any of the AA (P > 0.10).OD resulted in a higher AID of AA compared with samples which were FD (P ≤ 0.10), for all AA except for Gly and Tyr. Averaged across all AA, AID of AA was 3.3% greater if the sample was OD compared with FD. Differences in AID of AA among the 3 diets were noted for all AA (P ≤ 0.07), except for Cys (P = 0.33), due to the fact that CST and PST diets only contained soybean meal (SBM) as an AA-providing ingredient while the CSBM diet contained both corn and SBM. Pigs fed the PST diet had greater SID for all AA compared with pigs fed the CST diet (P ≤ 0.05), except for His, Lys, Cys, and Glu. In experiment 2, there were no pH-adjustment by drying-method interactions noted on AID for any of the AA (P > 0.10). Adjusting ileal digesta to a pH of 4.0 had little effect on AID for most of the AA, except for a lowered AID of Arg, His, Lys, Trp, and Ser (P ≤ 0.10). OD resulted in a higher AID for all AA (P ≤ 0.09) except for Ile, Thr, Val, Ala, Asp, Glu, and Gly. Averaged across all AA, the increase in AID of AA was 1.7% greater if the sample was OD compared with FD. On average, OD of ileal digesta resulted in a 2.5% greater estimate of AID of AA compared with samples that were FD, and was not diet-, pH-, or AA-dependent. Because the majority of the data on AA digestibility are based on FD, a bias factor may be necessary to adjust AA digestibility data obtained on an OD-basis relative to an FD-basis for use in feed formulation.
Characteristics and outcomes of RET-rearranged Korean non-small cell lung cancer patients in real-world practice
Authors: Lee Jiyun , Ku Bo Mi , Shim Joon Ho , La Choi Yoon , Sun Jong-Mu , Lee Se-Hoon , Ahn Jin Seok , Park Keunchil , Ahn Myung-Ju
Published: January 2020

Objective

Since the first discovery of rearranged during transfection (RET) fusion in lung adenocarcinoma in 2011, two tyrosine kinase inhibitors, namely vandetanib and cabozantinib, are currently available. Despite favorable outcomes in systemic control, the intracranial therapeutic response remains insufficient. In this study, the clinical characteristics and outcomes of non-small cell lung cancer (NSCLC) patients with RET rearrangements were analyzed.

Methods

Patients with NSCLC harboring RET fusion who received treatment between January 2006 and January 2018 were analyzed. RET rearrangement was identified by FISH or NGS.

Results

A total of 59 patients were identified. About half of the patients were female (47.5%) and never smokers (50.9%). Most patients had adenocarcinoma (89.8%). A total of 17 patients (28.8%) had an intracranial lesion at the initial diagnosis of stage IV disease, and 11 additional patients (18.6%) developed intracranial metastases during follow-up. The median time to development of intracranial metastases was 19.0 months (95% CI: 9.6–28.5), resulting in a >60% cumulative incidence of brain metastasis at 24 months. The systemic efficacy of pemetrexed-based regimens was favorable with progression-free survival of 9.0 (95% CI: 6.9–11.2) and OS of 24.1 (95% CI: 15.2–33.0) months. The median progression-free survival for vandetanib and immunotherapy was 2.9 (95% CI: 2.0–3.8) and 2.1 (95% CI: 1.6–2.6) months, respectively.

Conclusions

Given the likelihood of RET-rearranged NSCLC progressing to intracranial metastases and the absence of apparent clinical benefit of currently available targeted or immunotherapeutic agents, development of novel treatment with higher selectivity and better penetration of the blood–brain barrier remains a priority.
Disparities of National Lung Cancer Screening Guidelines in the US Population
Authors: Han Summer S , Chow Eric , ten Haaf Kevin , Toumazis Iakovos , Cao Pianpian , Bastani Mehrad , Tammemagi Martin , Jeon Jihyoun , Feuer Eric J , Meza Rafael , Plevritis Sylvia K
Published: January 2020

Background

Current US Preventive Services Task Force (USPSTF) lung cancer screening guidelines are based on smoking history and age (55–80 years). These guidelines may miss those at higher risk, even at lower exposures of smoking or younger ages, because of other risk factors such as race, family history, or comorbidity. In this study, we characterized the demographic and clinical profiles of those selected by risk-based screening criteria but were missed by USPSTF guidelines in younger (50–54 years) and older (71–80 years) age groups.

Methods

We used data from the National Health Interview Survey, the CISNET Smoking History Generator, and results of logistic prediction models to simulate lifetime lung cancer risk-factor data for 100 000 individuals in the 1950–1960 birth cohorts. We calculated age-specific 6-year lung cancer risk for each individual from ages 50 to 90 years using the PLCOm2012 model and evaluated age-specific screening eligibility by USPSTF guidelines and by risk-based criteria (varying thresholds between 1.3% and 2.5%).

Results

In the 1950 birth cohort, 5.4% would have been ineligible for screening by USPSTF criteria in their younger ages but eligible based on risk-based criteria. Similarly, 10.4% of the cohort would be ineligible for screening by USPSTF in older ages. Notably, high proportions of blacks were ineligible for screening by USPSTF criteria at younger (15.6%) and older (14.2%) ages, which were statistically significantly greater than those of whites (4.8% and 10.8%, respectively; P < .001). Similar results were observed with other risk thresholds and for the 1960 cohort.

Conclusions

Further consideration is needed to incorporate comprehensive risk factors, including race and ethnicity, into lung cancer screening to reduce potential racial disparities.
Selection of patients with left breast cancer for IMRT with deep inspiration breath-hold technique
Authors: CHANG Chih-Shen , CHEN Chia-Hsin , LIU Kuo-Chi , HO Chia-Sheng , CHEN Miao-Fen
Published: January 2020

The deep inspiration breath-hold (DIBH) technique has been utilized to reduce the cardiac dose in left-sided breast cancer (BC) patients undergoing radiotherapy. Further investigation of the parameters for selecting which patients will benefit most from DIBH is essential. We performed dosimetric comparisons for 21 patients with left-sided BC who had both computed tomography (CT)-based free-breathing (FB) and DIBH plans. The doses to the heart and left anterior descending artery (LAD) and any reduction due to the DIBH technique were analysed. Based on CTFB plans, dosimetric analysis revealed that the irradiation doses to the heart and LAD were significantly correlated with the target volume, the ipsilateral lung volume (ILV) and the total lung volume (TLV). When patients had an ILV ≥ 950 cm3 or a TLV ≥ 2200 cm3, the irradiation doses to the heart and LAD were significantly decreased. Furthermore, the reduction in the mean heart dose (MHD) was correlated to the difference in lung volume between FB and DIBH. The difference in ILV between DIBH and FB of 1.8 indicated that the patients obtained more benefit from the DIBH technique. The data suggest that lung volume (ILV and TLV) measured on a CT-simulation scan and the difference between FB and DIBH could be utilized to help select patients for DIBH.
Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis
Authors: Tsogtbaatar Enkhtuul , Cocuron Jean-Christophe , Alonso Ana Paula
Published: January 2020

Pennycress (Thlaspi arvense L.) accumulates oil up to 35% of the total seed biomass, and its overall fatty acid composition is suitable for aviation fuel. However, for this plant to become economically viable, its oil production needs to be improved. In vivo culture conditions that resemble the development of pennycress embryos in planta were developed based on the composition of the liquid endosperm. Then, substrate uptake rates and biomass accumulation were measured from cultured pennycress embryos, revealing a biosynthetic efficiency of 93%, which is one of the highest in comparison with other oilseeds to date. Additionally, the ratio of carbon in oil to CO2 indicated that non-conventional pathways are likely to be responsible for such a high carbon conversion efficiency. To identify the reactions enabling this phenomenon, parallel labeling experiments with 13C-labeled substrates were conducted in pennycress embryos. The main findings of these labeling experiments include: (i) the occurrence of the oxidative reactions of the pentose phosphate pathway in the cytosol; (ii) the reversibility of isocitrate dehydrogenase; (iii) the operation of the plastidic NADP-dependent malic enzyme; and (iv) the refixation of CO2 by Rubisco. These reactions are key providers of carbon and reductant for fatty acid synthesis and elongation.
Evolving Populations in Biofilms Contain More Persistent Plasmids
Authors: Stalder Thibault , Cornwell Brandon , Lacroix Jared , Kohler Bethel , Dixon Seth , Yano Hirokazu , Kerr Ben , Forney Larry J , Top Eva M
Published: January 2020

Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid–bacteria coevolution is solely based on studies done in well-mixed liquid cultures, even though biofilms represent the main way of bacterial life on Earth and are responsible for most infections. The spatial structure and the heterogeneity provided by biofilms are known to lead to increased genetic diversity as compared with well-mixed liquids. Therefore, we expect that growth in this complex environment could affect the evolutionary trajectories of plasmid–host dyads. We experimentally evolved Shewanella oneidensis MR-1 with plasmid pBP136Gm in biofilms and chemostats and sequenced the genomes of clones and populations. Biofilm populations not only maintained a higher diversity of mutations than chemostat populations but contained a few clones with markedly more persistent plasmids that evolved via multiple distinct trajectories. These included the acquisition of a putative toxin–antitoxin transposon by the plasmid and chromosomal mutations. Some of these genetic changes resulted in loss of plasmid transferability or decrease in plasmid cost. Growth in chemostats led to a higher proportion of variants with decreased plasmid persistence, a phenomenon not detected in biofilms. We suggest that the presence of more stable plasmid–host dyads in biofilms reflects higher genetic diversity and possibly unknown selection pressures. Overall, this study underscores the importance of the mode of growth in the evolution of antibiotic-resistant bacteria.
The impact of comorbid chronic kidney disease and diabetes on health-related quality-of-life: a 12-year community cohort study
Authors: Wyld Melanie L R , Morton Rachael L , Aouad Leyla , Magliano Dianna , Polkinghorne Kevan R , Chadban Steve
Published: January 2020

Background

Quality-of-life is an essential outcome for clinical care. Both chronic kidney disease (CKD) and diabetes have been associated with poorer quality-of-life. The combined impact of having both diseases is less well understood. As diabetes is the most common cause of CKD, it is imperative that we deepen our understanding of their joint impact.

Methods

This was a prospective, longitudinal cohort study of community-based Australians aged ≥25 years who participated in the Australian Diabetes, Obesity and Lifestyle study. Quality-of-life was measured by physical component summary (PCS) and mental component summary sub-scores of the Short Form (36) Health Survey. Univariate and multivariate linear mixed effect regressions were performed.

Results

Of the 11 081 participants with quality-of-life measurements at baseline, 1112 had CKD, 1001 had diabetes and of these 271 had both. Of the 1112 with CKD 421 had Stage 1, 314 had Stage 2, 346 had Stage 3 and 31 had Stages 4/5. Adjusted linear mixed effect models showed baseline PCS was lower for those with both CKD and diabetes compared with either disease alone (P < 0.001). Longitudinal analysis demonstrated a more rapid decline in PCS in those with both diseases.

Conclusions

The combination of CKD and diabetes has a powerful adverse impact on quality-of-life, and participants with both diseases had significantly poorer quality-of-life than those with one condition.
Empathy: An Integral Model in Clinical Social Work
Authors: Clark Arthur J , Butler Carrie M
Published: January 2020

Empathy has held a vital and enduring standing in the theory and practice of clinical social work. Defining and conceptualizing empathy is a continuing challenge in social work and across the human services. A multitude of definitions of empathy exist in the therapeutic literature, creating confusion relating to research findings and treatment processes. Recent trends emphasize an overarching and expansive way of conceiving empathic understanding in the therapeutic relationship and informing treatment practice. Multiple perspectives of empathy facilitate a broad and wide-ranging engagement of the practitioner and the client in the therapeutic process. With significant implications for clinical social workers, an integral model capitalizes on the engagement of empathy from multiple ways of knowing: subjective, objective, and interpersonal. Numerous clinical examples illustrate applications of the tripartite model in social work practice. The integral empathy model is amenable to research and training across therapeutic contexts in social work and related fields.
Spectral differentiation of oak wilt from foliar fungal disease and drought is correlated with physiological changes
Authors: Fallon Beth , Yang Anna , Lapadat Cathleen , Armour Isabella , Juzwik Jennifer , Montgomery Rebecca A , Cavender-Bares Jeannine
Published: January 2020

Hyperspectral reflectance tools have been used to detect multiple pathogens in agricultural settings and single sources of infection or broad declines in forest stands. However, differentiation of any one disease from other sources of tree stress is integral for stand and landscape-level applications in mixed species systems. We tested the ability of spectral models to differentiate oak wilt, a fatal disease in oaks caused by Bretziella fagacearum ``Bretz'', from among other mechanisms of decline. We subjected greenhouse-grown oak seedlings (Quercus ellipsoidalis ``E.J. Hill'' and Quercus macrocarpa ``Michx.'') to chronic drought or inoculation with the oak wilt fungus or bur oak blight fungus (Tubakia iowensis ``T.C. Harr. & D. McNew''). We measured leaf and canopy spectroscopic reflectance (400–2400 nm) and instantaneous photosynthetic and stomatal conductance rates, then used partial least-squares discriminant analysis to predict treatment from hyperspectral data. We detected oak wilt before symptom appearance, and classified the disease with high accuracy in symptomatic leaves. Classification accuracy from spectra increased with declines in photosynthetic function in oak wilt-inoculated plants. Wavelengths diagnostic of oak wilt were only found in non-visible spectral regions and are associated with water status, non-structural carbohydrates and photosynthetic mechanisms. We show that hyperspectral models can differentiate oak wilt from other causes of tree decline and that detection is correlated with biological mechanisms of oak wilt infection and disease progression. We also show that within the canopy, symptom heterogeneity can reduce detection, but that symptomatic leaves and tree canopies are suitable for highly accurate diagnosis. Remote application of hyperspectral tools can be used for specific detection of disease across a multi-species forest stand exhibiting multiple stress symptoms.
Effect of initial gravimetric water content and cyclic wetting-drying on soil-water characteristic curves of disintegrated carbonaceous mudstone
Authors: Zeng Ling , Li Fan , Liu Jie , Gao Qianfeng , Bian Hanbing
Published: January 2020

The soil-water characteristic curve (SWCC) is often used to estimate unsaturated soil properties (e.g. strength, permeability, volume change, solute and thermal diffusivity). The SWCC of soil samples is significantly affected by cyclic wetting-drying. To examine how water content and cyclic wetting-drying affect the SWCC of disintegrated carbonaceous mudstone (DCM), SWCC tests were implemented using a pressure-plate apparatus. In addition, SWCC models for DCM considering the initial gravimetric water content and cyclic wetting-drying were developed. The test results showed that the volumetric water content (θ) of the DCM first decreased rapidly and then became stable as matric suction (s) increased. The initial water content affected the SWCC by altering the pore structure of the DCM. For a given number of wetting-drying cycles, the higher the initial water content, the higher the stabilized θ. At a given s value, θ decreased as the number of wetting-drying cycles increased, which suggests that cyclic wetting-drying reduces the water-holding capacity of DCM. The Gardner model for DCM was constructed considering initial water content and cyclic wetting-drying, and was effective at describing and predicting the SWCC model for DCM.
Development of a Rapid Approach for Detecting Sharp Eyespot Resistance in Seedling-Stage Wheat and Its Application in Chinese Wheat Cultivars
Authors: Ren Yan , Yu Peng-Bo , Wang Yue , Hou Wei-Xiu , Yang Xia , Fan Jia-Lin , Wu Xiao-Hui , Lv Xia-Lei , Zhang Ning , Zhao Lei , Dong Zhong-Dong , Chen Feng
Published: January 2020

Sharp eyespot, caused by Rhizoctonia cerealis, has become one of the most severe diseases affecting global wheat production in recent decades. Quick and efficient screening methods are required to accelerate the development of cultivars for sharp eyespot resistance in wheat breeding. Here, a two-step colonized wheat kernels (TSCWK) method for the inoculation and classification of sharp eyespot resistance in seedlings was established in a greenhouse. After preliminary verification of the reliability of the method in two replicates, 196 wheat cultivars were assessed for sharp eyespot resistance, and significant correlations were identified among the four replicates (r = 0.78 to 0.84; P < 0.01). Furthermore, the 196 cultivars were scored for sharp eyespot resistance at the milk-ripe stage using traditional toothpick inoculation in the field. Correlation and linear regression analysis showed that the application of this approach at the seedling stage showed good consistency with the traditional field method. Moreover, the scoring of 442 cultivars using the TSCWK method indicated that most cultivars from the Huanghuai valley were susceptible to R. cerealis, suggesting an urgent need to improve sharp eyespot resistance in this region. Additionally, the relative resistance index of sharp eyespot decreased in the surveyed cultivars of the region with time. This study offers a rapid and effective approach for the identification of wheat sharp eyespot resistance and provides valuable germplasm for improving sharp eyespot resistance in wheat breeding.
Society for Developmental and Behavioral Pediatrics Clinical Practice Guideline for the Assessment and Treatment of Children and Adolescents with Complex Attention-Deficit/Hyperactivity Disorder
Authors: Barbaresi William J. , Campbell Lisa , Diekroger Elizabeth A. , Froehlich Tanya E. , Liu Yi Hui , O'Malley Eva , Pelham William E. , Power Thomas J. , Zinner Samuel H. , Chan Eugenia
Published: January 2020

Attention-deficit/hyperactivity disorder (ADHD) is the most common childhood neurodevelopmental disorder and is associated with an array of coexisting conditions that complicate diagnostic assessment and treatment. ADHD and its coexisting conditions may impact function across multiple settings (home, school, peers, community), placing the affected child or adolescent at risk for adverse health and psychosocial outcomes in adulthood. Current practice guidelines focus on the treatment of ADHD in the primary care setting. The Society for Developmental and Behavioral Pediatrics has developed this practice guideline to facilitate integrated, interprofessional assessment and treatment of children and adolescents with “complex ADHD” defined by age (<4 years or presentation at age >12 years), presence of coexisting conditions, moderate to severe functional impairment, diagnostic uncertainty, or inadequate response to treatment.
Urbanization without isolation: the absence of genetic structure among cities and forests in the tiny acorn ant
Temnothorax nylanderi
Authors: Khimoun A. , Doums C. , Molet M. , Kaufmann B. , Peronnet R. , Eyer P. A. , Mona S.
Published: January 2020

Urban alteration of neutral and adaptive evolutionary processes is still underexplored. Using a genome-wide SNP dataset, we investigated (i) urban-induced modifications of population demography, genetic diversity and population structure and (ii) signature of divergent selection between urban and forest populations in the ant species,
Temnothorax nylanderi.
Our results did not reveal an impact of urbanization on neutral processes since we observed: (i) analogous genetic diversity among paired urban/forest sites and two control populations; (ii) weak population genetic structure explained neither by habitat (urban versus forest) nor by geography; (iii) a remarkably similar demographic history across populations with an ancestral growth followed by a recent decline, regardless of their current habitat or geographical location. The micro-geographical home range of ants may explain their resilience to urbanization. Finally, we detected 19 candidate loci discriminating urban/forest populations and associated with core cellular components, molecular function or biological process. Two of these loci were associated with a gene ontology term that was previously found to belong to a module of co-expressed genes related to caste phenotype. These results call for transcriptomics analyses to identify genes associated with ant social traits and to infer their potential role in urban adaptation.