bluuebunny/crossref_metadata_2025 huggingface dataset:
primirTSS: an R package for identifying cell-specific microRNA transcription start sites
Authors: Li Pumin , Xu Qi , Hua Xu , Xie Zhongwei , Li Jie , Wang Jin
Published: March 2020

The R/Bioconductor package primirTSS is a fast and convenient tool that allows implementation of the analytical method to identify transcription start sites of microRNAs by integrating ChIP-seq data of H3K4me3 and Pol II. It further ensures the precision by employing the conservation score and sequence features. The tool showed a good performance when using H3K4me3 or Pol II Chip-seq data alone as input, which brings convenience to applications where multiple datasets are hard to acquire. This flexible package is provided with both R-programming interfaces as well as graphical web interfaces.

Availability and implementation

primirTSS is available at: http://bioconductor.org/packages/primirTSS. The documentation of the package including an accompanying tutorial was deposited at: https://bioconductor.org/packages/release/bioc/vignettes/primirTSS/inst/doc/primirTSS.html.

Contact

jwang@nju.edu.cn

Supplementary information

Supplementary data are available at Bioinformatics online.
Exploring high-dimensional biological data with sparse contrastive principal component analysis
Authors: Boileau Philippe , Hejazi Nima S , Dudoit Sandrine
Published: March 2020

Motivation

Statistical analyses of high-throughput sequencing data have re-shaped the biological sciences. In spite of myriad advances, recovering interpretable biological signal from data corrupted by technical noise remains a prevalent open problem. Several classes of procedures, among them classical dimensionality reduction techniques and others incorporating subject-matter knowledge, have provided effective advances. However, no procedure currently satisfies the dual objectives of recovering stable and relevant features simultaneously.

Results

Inspired by recent proposals for making use of control data in the removal of unwanted variation, we propose a variant of principal component analysis (PCA), sparse contrastive PCA that extracts sparse, stable, interpretable and relevant biological signal. The new methodology is compared to competing dimensionality reduction approaches through a simulation study and via analyses of several publicly available protein expression, microarray gene expression and single-cell transcriptome sequencing datasets.

Availability and implementation

A free and open-source software implementation of the methodology, the scPCA R package, is made available via the Bioconductor Project. Code for all analyses presented in this article is also available via GitHub.

Contact

philippe_boileau@berkeley.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Robust partial reference-free cell composition estimation from tissue expression
Authors: Li Ziyi , Guo Zhenxing , Cheng Ying , Jin Peng , Wu Hao
Published: March 2020

Motivation

In the analysis of high-throughput omics data from tissue samples, estimating and accounting for cell composition have been recognized as important steps. High cost, intensive labor requirements and technical limitations hinder the cell composition quantification using cell-sorting or single-cell technologies. Computational methods for cell composition estimation are available, but they are either limited by the availability of a reference panel or suffer from low accuracy.

Results

We introduce TOols for the Analysis of heterogeneouS Tissues TOAST/-P and TOAST/+P, two partial reference-free algorithms for estimating cell composition of heterogeneous tissues based on their gene expression profiles. TOAST/-P and TOAST/+P incorporate additional biological information, including cell-type-specific markers and prior knowledge of compositions, in the estimation procedure. Extensive simulation studies and real data analyses demonstrate that the proposed methods provide more accurate and robust cell composition estimation than existing methods.

Availability and implementation

The proposed methods TOAST/-P and TOAST/+P are implemented as part of the R/Bioconductor package TOAST at https://bioconductor.org/packages/TOAST.

Contact

ziyi.li@emory.edu or hao.wu@emory.edu

Supplementary information

Supplementary data are available at Bioinformatics online.
Prisoner Society in an Era of Psychoactive Substances, Organized Crime, New Drug Markets and Austerity
Authors: Gooch Kate , Treadwell James
Published: March 2020

Framed by the limited and now dated ethnographic research on the prison drug economy, this article offers new theoretical and empirical insights into how drugs challenge the social order in prisons in England and Wales. It draws on significant original and rigorous ethnographic research to argue that the ‘era of hard drugs’ has been superseded by an ‘era of new psychoactive drugs’, redefining social relations, transforming the prison illicit economy, producing new forms of prison victimization and generating far greater economic power and status for suppliers. These changes represent the complex interplay and compounding effects of broader shifts in political economy, technological advances, organized crime, prison governance and the declining legitimacy and moral performance of English and Welsh prisons.
Relationship between cortical iron and tau aggregation in Alzheimer’s disease
Authors: Spotorno Nicola , Acosta-Cabronero Julio , Stomrud Erik , Lampinen Björn , Strandberg Olof T , van Westen Danielle , Hansson Oskar
Published: March 2020

A growing body of evidence suggests that the dysregulation of neuronal iron may play a critical role in Alzheimer’s disease. Recent MRI studies have established a relationship between iron accumulation and amyloid-β aggregation. The present study provides further insight demonstrating a relationship between iron and tau accumulation using magnetic resonance-based quantitative susceptibility mapping and tau-PET in n = 236 subjects with amyloid-β pathology (from the Swedish BioFINDER-2 study). Both voxel-wise and regional analyses showed a consistent association between differences in bulk magnetic susceptibility, which can be primarily ascribed to an increase in iron content, and tau-PET signal in regions known to be affected in Alzheimer’s disease. Subsequent analyses revealed that quantitative susceptibility specifically mediates the relationship between tau-PET and cortical atrophy measures, thus suggesting a modulatory effect of iron burden on the disease process. We also found evidence suggesting the relationship between quantitative susceptibility and tau-PET is stronger in younger participants (age ≤ 65). Together, these results provide in vivo evidence of an association between iron deposition and both tau aggregation and neurodegeneration, which help advance our understanding of the role of iron dysregulation in the Alzheimer’s disease aetiology.
Heterogeneity in Brain Microstructural Development Following Preterm Birth
Authors: Dimitrova Ralica , Pietsch Maximilian , Christiaens Daan , Ciarrusta Judit , Wolfers Thomas , Batalle Dafnis , Hughes Emer , Hutter Jana , Cordero-Grande Lucilio , Price Anthony N , Chew Andrew , Falconer Shona , Vecchiato Katy , Steinweg Johannes K , Carney Olivia , Rutherford Mary A , Tournier J-Donald , Counsell Serena J , Marquand Andre F , Rueckert Daniel , Hajnal Joseph V , McAlonan Grainne , Edwards A David , O’Muircheartaigh Jonathan
Published: March 2020

Preterm-born children are at increased risk of lifelong neurodevelopmental difficulties. Group-wise analyses of magnetic resonance imaging show many differences between preterm- and term-born infants but do not reliably predict neurocognitive prognosis for individual infants. This might be due to the unrecognized heterogeneity of cerebral injury within the preterm group. This study aimed to determine whether atypical brain microstructural development following preterm birth is significantly variable between infants. Using Gaussian process regression, a technique that allows a single-individual inference, we characterized typical variation of brain microstructure using maps of fractional anisotropy and mean diffusivity in a sample of 270 term-born neonates. Then, we compared 82 preterm infants to these normative values to identify brain regions with atypical microstructure and relate observed deviations to degree of prematurity and neurocognition at 18 months. Preterm infants showed strikingly heterogeneous deviations from typical development, with little spatial overlap between infants. Greater and more extensive deviations, captured by a whole brain atypicality index, were associated with more extreme prematurity and predicted poorer cognitive and language abilities at 18 months. Brain microstructural development after preterm birth is highly variable between individual infants. This poorly understood heterogeneity likely relates to both the etiology and prognosis of brain injury.
Antiretroviral Therapy and Detection of High-grade Cervical Intraepithelial Neoplasia (CIN2+) at Post-CIN Management Follow-up Among Women Living With Human Immunodeficiency Virus: A Systematic Review and Meta-Analysis
Authors: Atemnkeng Njika , Aji Abang Desmond , de Sanjose Silvia , Mayaud Philippe , Kelly Helen
Published: March 2020

Background

We evaluated the association of antiretroviral therapy (ART), CD4+ count and human immunodeficiency virus (HIV) plasma viral load (PVL) on high-grade cervical intraepithelial neoplasia (CIN2+) detection at follow-up after CIN management among women living with HIV (WLHIV).

Methods

Medline, Embase, Global Health, and PubMed were searched from 1 January 1996 to 15 January 2020. Eligible studies investigated the association of ART, CD4+ count, or HIV PVL on histology-confirmed CIN2+ detection at follow-up. Summary estimates were obtained using random-effects meta-analyses; heterogeneity was examined using I2 statistic. PROSPERO registration: CRD42018115631.

Results

Eight studies representing 9 populations were identified, including 1452 WLHIV followed between 6 and 33 months post-CIN management. Pooled data from 8 populations (n = 1408) suggested weak evidence of a decreased risk of CIN2+ detection at follow-up among ART users compared to ART-naive women (crude odds ratio [cOR] = 0.70, 95% confidence interval [CI]: .36–1.36; I2 = 64.5%, P = .006; adjusted risk ratio [aRR] from 3 studies = 0.66, 95% CI: .20–2.24; I2 = 78.7%, P = .009). A significant association was observed in high-income countries (cOR = 0.24, 95% CI: .13–.45; I2 = 0.0%, P = .77) but not in low and middle-income countries (cOR = 1.13, 95% CI: .67–1.92; I2 = 18.8%, P = .30).

In 3 populations, ART users with HIV PVL <50 copies/ml were less likely to have CIN2+ detection at follow-up (vs ≥50 copies/mL: cOR = 0.55, 95% CI: .32–.94; I2 = 0.0%, P = .23).

There was weak evidence of decreased CIN2+ detection at follow-up among WLHIV with higher contemporary CD4+ cell counts (≥200 cells/µL vs <200 cells/µL [cOR = 0.36, 95% CI: .04–3.13; I2 = 81.3%, P = .021]) and significant evidence among women with a higher nadir CD4+ count (≥350 cells/µl vs <200 cells/µl [adjusted hazard ratio [aHR] = 0.35, 95% CI: .15–.84; I2 = 0%, P = .64]).

Conclusion

ART may reduce the risk of CIN2+ detection at follow-up; this effect is most likely enhanced by a combination of adequate HIV control and excisional CIN treatment. Our findings support recommendations of early ART and the integration of CIN2+ screening and management into HIV care.
Knowledge and Attitudes Towards Pregnancy in Females with Inflammatory Bowel Disease: An International, Multi-centre Study
Authors: Laube Robyn , Yau Yunki , Selinger Christian P , Seow Cynthia H , Thomas Amanda , Wei Chuah Sai , Hilmi Ida , Mao Ren , Ong David , Ng Siew C , Chen Wei Shu , Banerjee Rupa , Ahuja Vineet , Alharbi Othman , Leong Rupert W
Published: March 2020

Background and Aims

Poor knowledge of inflammatory bowel disease [IBD] in pregnancy underlies unwarranted voluntary childlessness [VC], and risks poorer obstetric outcomes and adverse fetal outcomes. IBD is increasing worldwide but education on IBD issues might be heterogeneous based on cultural differences and variations in models of care.

Methods

Consecutive female IBD subjects aged 18–45 years were prospectively recruited from two dedicated IBD-pregnancy clinics, two multidisciplinary IBD clinics and nine general gastroenterology clinics. Subjects completed the validated CCPKnow [score 0–17] with questions on demographics, medical history and pregnancy knowledge. The primary outcome was knowledge per clinic-type and per geographical region.

Results

Surveys were completed by 717 subjects from 13 hospitals across ten countries. Dedicated IBD-pregnancy clinics had the highest knowledge, followed by multidisciplinary IBD clinics then general IBD clinics (median CCPKnow 10.0 [IQR: 8.0–11.0], 8.0 [IQR: 5.0–10.5] and 4.0 [IQR:2.0–6.0]; p < 0.001). Median CCPKnow scores in Western, Asian and Middle Eastern clinics were 9.0, 5.0 and 3.0 respectively [p < 0.001]. Dedicated IBD-pregnancy clinics, IBD support organization membership, childbearing after IBD diagnosis and employment independently predicted greater knowledge. Patient perception of disease severity [r = −0.18, p < 0.01] and consideration of VC [r = −0.89, p = 0.031] negatively correlated with CCPKnow score. The overall VC rate was 15.0% [95% CI: 12.2–18.2]. VC subjects had significantly lower pregnancy-specific IBD knowledge than non-VC subjects (median CCPKnow 4.0 [IQR: 2.0–6.0] and 6.0 [IQR: 3.0–9.0] respectively; p < 0.001). Pregnancy-specific IBD knowledge and dedicated IBD-pregnancy clinic attendance were significant negative predictors of VC.

Conclusions

In this large international study we identified predictors of pregnancy-specific IBD knowledge. Dedicated IBD-pregnancy clinics had the greatest IBD-related pregnancy knowledge and lowest VC rates, reflecting the benefits of pre-conception counselling.
Inflammatory Bowel Disease: A Nationwide Study of Hip Fracture and Mortality Risk After Hip Fracture
Authors: Bartko Johann , Reichardt Berthold , Kocijan Roland , Klaushofer Klaus , Zwerina Jochen , Behanova Martina
Published: March 2020

Background and Aims

With rising rates of inflammatory bowel diseases [IBD] in older adults, management of comorbidities such as osteoporosis is becoming increasingly important. Hip fracture [HF] is the most serious consequence of low bone mineral quality and is associated with excess risk of mortality. For older IBD patients, there are only limited data available. Therefore, we aimed to assess the association of IBD with HF, and all-cause mortality risk after HF, among IBD patients older than 50 years.

Methods

In a national database-registered case-control study, 56 821 HF cases aged ≥50 years, and 113 718 age-, sex- and region-matched non-hip-fracture controls, were analysed between 2012 and 2016. A history of IBD was assessed from data from Austrian social health insurance funds. Logistic regression and Cox proportional multivariate models were used to test the association of IBD with HF and post-hip fracture mortality risk.

Results

A total of 531 patients were identified with IBD (25.0% men, mean age 81.2 years, standard deviation [SD] 9.7). Analysis, adjusted for anti-osteoporotic treatment, use of glucocorticoids, and selected medications, showed that IBD patients had an increased odds of HF (odds ratio [[OR] 2.22, 95% confidence interval [CI] 1.86–2.64). Patients with Crohn’s disease [CD] revealed a higher HF odds in contrast to patients with ulcerative colitis [OR 2.91, 95% CI 2.17–3.89 and OR 1.89, 95% CI 1.52–2.35, respectively]. Overall mortality risk after HF was higher among female CD patients [HR 1.75, 95% CI 1.28–2.41] than in the general population.

Conclusions

IBD was strongly associated with HF in older patients. Post-hip fracture mortality risk was elevated particularly in women with CD.
Association of post-diagnosis cardiorespiratory fitness with cause-specific mortality in cancer
Authors: Groarke John D , Payne David L , Claggett Brian , Mehra Mandeep R , Gong Jingyi , Caron Jesse , Mahmood Syed S , Hainer Jon , Neilan Tomas G , Partridge Ann H , Di Carli Marcelo , Jones Lee W , Nohria Anju
Published: March 2020

Aims 

The prognostic importance of post-diagnosis assessment of cardiorespiratory fitness (CRF) in cancer patients is not well established. We sought to examine the association between CRF and mortality in cancer patients.

Methods and results 

This was a single-centre cohort analysis of 1632 patients (58% male; 64 ± 12 years) with adult-onset cancer who were clinically referred for exercise treadmill testing a median of 7 [interquartile range (IQR): 3–12] years after primary diagnosis. Cardiorespiratory fitness was defined as peak metabolic equivalents (METs) achieved during standard Bruce protocol and categorized by tertiles. The association between CRF and all-cause and cause-specific mortality was assessed using multivariable Cox proportional hazard models adjusting for important covariates. Median follow-up was 4.6 (IQR: 2.6–7.0) years; a total of 411 deaths (229, 50, and 132 all-cause, cardiovascular (CV), and cancer related, respectively) occurred during this period. Compared with low CRF (range: 1.9–7.6 METs), the adjusted hazard ratio (HR) for all-cause mortality was 0.38 [95% confidence interval (CI): 0.28–0.52] for intermediate CRF (range: 7.7–10.6 METs) and 0.17 (95% CI: 0.11–0.27) for high CRF (range: 10.7–22.0 METs). The corresponding HRs were 0.40 (95% CI: 0.19–0.86) and 0.41 (95% CI: 0.16–1.05) for CV mortality and 0.40 (95% CI: 0.26–0.60) and 0.16 (95% CI: 0.09–0.28) for cancer mortality, respectively. The adjusted risk of all-cause, CV, and cancer mortality decreased by 26%, 14%, and 25%, respectively with each one MET increment in CRF.

Conclusion 

Cardiorespiratory fitness is a strong, independent predictor of all-cause, CV, and cancer mortality, even after adjustment for important clinical covariates in patients with certain cancers.
Aging Endocrine and Metabolic Phenotypes Are Programmed by Mother’s Age at Conception in a Sex-Dependent Fashion in the Rat
Authors: Zambrano Elena , Reyes-Castro Luis A , Rodríguez-González Guadalupe L , Chavira Roberto , Nathanielsz Peter W
Published: March 2020

Programming of offspring life-course health by maternal nutrition and stress are well studied. At postnatal day 850, we evaluated male and female steroid levels and metabolism in aged offspring of primigravid sister rats bred at 70, 90, 150, or 300 days’ life. At 850 days life, male offspring corticosterone was similar regardless of maternal age. Female corticosterone was highest in offspring of 70- and 300-day mothers. Serum dehydroepiandrosterone:corticosterone was lowest in both sexes of offspring of 70- and 300-day mothers. Male and female fat depots were smaller in offspring of 150- than 70- and 90-day mothers. Insulin, glucose, and homeostatic model assessment were similar in all male offspring but higher in female offspring of 70-day mothers than other ages. We conclude, maternal age affects offspring aging in an offspring sex-dependent manner and merits consideration in designing and interpreting programming studies.
What will it cost to prevent violence against women and girls in low- and middle-income countries? Evidence from Ghana, Kenya, Pakistan, Rwanda, South Africa and Zambia
Authors: Torres-Rueda Sergio , Ferrari Giulia , Orangi Stacey , Hitimana Regis , Daviaud Emmanuelle , Tawiah Theresa , Prah Rebecca Kyerewaa Dwommoh , Karmaliani Rozina , Kapapa Eleonah , Barasa Edwine , Jewkes Rachel , Vassall Anna
Published: March 2020

Violence against women and girls (VAWG) is a global problem with profound consequences. Although there is a growing body of evidence on the effectiveness of VAWG prevention interventions, economic data are scarce. We carried out a cross-country study to examine the costs of VAWG prevention interventions in low- and middle-income countries. We collected primary cost data on six different pilot VAWG prevention interventions in six countries: Ghana, Kenya, Pakistan, Rwanda, South Africa and Zambia. The interventions varied in their delivery platforms, target populations, settings and theories of change. We adopted a micro-costing methodology. We calculated total costs and a number of unit costs common across interventions (e.g. cost per beneficiary reached). We used the pilot-level cost data to model the expected total costs and unit costs of five interventions scaled up to the national level. Total costs of the pilots varied between ∼US $208 000 in a small group intervention in South Africa to US $2 788 000 in a couples and community-based intervention in Rwanda. Staff costs were the largest cost input across all interventions; consequently, total costs were sensitive to staff time use and salaries. The cost per beneficiary reached in the pilots ranged from ∼US $4 in a community-based intervention in Ghana to US $1324 for one-to-one counselling in Zambia. When scaled up to the national level, total costs ranged from US $32 million in Ghana to US $168 million in Pakistan. Cost per beneficiary reached at scale decreased for all interventions compared to the pilots, except for school-based interventions due to differences in student density per school between the pilot and the national average. The costs of delivering VAWG prevention vary greatly due to differences in the geographical reach, number of intervention components and the complexity of adapting the intervention to the country. Cost-effectiveness analyses are necessary to determine the value for money of interventions.
Clinical and Analytical Impact of Moving from Jaffe to Enzymatic Serum Creatinine Methodology
Authors: Syme Neil R , Stevens Kathryn , Stirling Catherine , McMillan Donald C , Talwar Dinesh
Published: March 2020

Background

Identification and monitoring of chronic kidney disease (CKD) requires accurate quantification of serum creatinine. The poor specificity of Jaffe creatinine methods is well documented, and guidelines recommend enzymatic methodology. We describe our experience of moving from Jaffe to enzymatic creatinine methodology. We present comparison of >5000 paired Jaffe and enzymatic creatinine results, examine interferences, and attempt to assess clinical consequences of changing methodology.

Methods

Overall, 5303 serum samples received for routine creatinine measurement were analyzed using Jaffe and enzymatic methods with an Abbott Architect autoanalyzer. Associated results for glucose, total bilirubin, triglycerides, total protein, and hemolytic, icteric, and lipemic indexes were extracted from the laboratory database. CKD staging was estimated for each sample to assess potential clinical effects.

Results

The methods correlated well (r = 0.996) and showed good agreement (Passing-Bablok fit, y = 0.935x + 0.074). Paired analysis, however, showed significant differences (P < 0.001), and approximately 20% of results differed by more than ±10%. Multivariate analysis demonstrated independent associations between difference in creatinine results, glucose (P < 0.0001), and hemolytic index (P = 0.009). Glucose demonstrated positive interference in the Jaffe method, and hemolysis produced negative interference in the enzymatic method. Little or no association was observed with other analytes. CKD staging differed in 4% of samples.

Conclusions

Differences between Jaffe and enzymatic serum creatinine results exceed the recommended 5% target for a significant proportion of samples, particularly at concentrations <1.13 mg/dL (100 µmol/L). Both glucose and hemolysis contribute to the variance in results. Although the clinical impact of these differences seems small, laboratories should continue moving toward enzymatic creatinine estimation to ensure the best estimate of renal function.
Effects of dietary supplementation with exogenous catalase on growth performance, oxidative stress, and hepatic apoptosis in weaned piglets challenged with lipopolysaccharide
Authors: Li Yang , Zhao Xilun , Jiang Xuemei , Chen Ling , Hong Liang , Zhuo Yong , Lin Yan , Fang Zhengfeng , Che Lianqiang , Feng Bin , Xu Shengyu , Li Jian , Wu De
Published: March 2020

Two experiments were conducted to investigate the effects of exogenous catalase (CAT) in the diet of weaned piglets on growth performance, oxidative capacity, and hepatic apoptosis after challenge with lipopolysaccharide (LPS). In experiment 1, 72 weaned piglets [Duroc × Landrace × Yorkshire, 6.90 ± 0.01 kg body weight (BW), 21 d of age] were randomly assigned to be fed either a basal diet (CON group) or a basal diet supplemented with 2,000 mg/kg CAT (CAT group; dietary CAT activity, 120 U/kg) for 35 d. Blood samples were collected on day 21 and day 35. At the end of this experiment, 12 pigs were selected from each of the CON and CAT groups, and six pigs were injected with LPS (50 μg/kg BW), while the remaining six pigs were injected with an equal amount of sterile saline, resulting in a 2 × 2 factorial arrangement of treatments (experiment 2). Blood samples and rectal temperature data were collected 0 and 4 h after challenge, and liver samples were obtained after evisceration. The gain-to-feed ratio was higher (P < 0.05) in piglets in the CAT group than in those in the CON group from day 1 to 35. Catalase and total superoxide dismutase (T-SOD) activities were higher (P < 0.05), whereas malondialdehyde (MDA) concentrations were lower (P < 0.05), in piglets in the CAT group than in those in the CON group at day 35. During challenge, rectal temperature and liver MDA and H2O2 concentrations increased significantly (P < 0.05), whereas plasma CAT and glutathione peroxidase (GSH-Px) activities and liver CAT activity decreased markedly (P < 0.05), in LPS-challenged piglets 4 h post-challenge. Increased CAT activity and decreased MDA concentration were observed in the plasma and liver of piglets in the CAT group 4 h post-challenge (P < 0.05). Dietary CAT supplementation markedly suppressed the LPS-induced decrease in plasma GSH-Px activity and liver CAT activity to levels observed in the CON group (P < 0.05) as well as significantly decreasing the concentration and mRNA expression of caspase-3 and caspase-9 (P < 0.05). LPS-induced liver injury was also attenuated by dietary CAT supplementation, as demonstrated by a decrease in liver caspase-3 mRNA expression (P < 0.05). Overall, dietary supplementation with 2,000 mg/kg exogenous CAT (dietary CAT activity, 120 U/kg) improves growth performance and has a beneficial effect on antioxidant capacity in weaned piglets; alleviates oxidative stress and reduces liver damage by suppressing hepatic apoptosis in LPS-challenged piglets.
Human capital portability and international student migration
Authors: Arenas Andreu
Published: March 2020

This article examines how human capital portability frictions affect the quantity and the quality of international student migration (ISM). Using administrative data on college enrolment in Spain, it evaluates a reform that lifted the requirement to take the Spanish end-of-high-school exam for foreign students from a subset of countries. The reform increased student migration from treated countries by 50%, compared to migration from control countries. Post-reform migrants have lower predicted test scores but still outperform native students. The results suggest that multilateral diploma recognitions can significantly increase ISM without large costs in student migrant quality, and with positive effects on average student quality.
When Curry met Abel
Authors: Tapia-Navarro Manuel Eduardo , Estrada-González Luis
Published: March 2020

Based on his Inclosure Schema and the Principle of Uniform Solution (PUS), Priest has argued that Curry’s paradox belongs to a different family of paradoxes than the Liar. Pleitz (2015, The Logica Yearbook 2014, pp. 233–248) argued that Curry’s paradox shares the same structure as the other paradoxes and proposed a scheme of which the Inclosure Schema is a particular case and he criticizes Priest’s position by pointing out that applying the PUS implies the use of a paraconsistent logic that does not validate Contraction, but that this can hardly seen as uniform. In this paper, we will develop some further reasons to defend Pleitz’ thesis that Curry’s paradox belongs to the same family as the rest of the self-referential paradoxes & using the idea that conditionals are generalized negations. However, we will not follow Pleitz in considering doubtful that there is a uniform solution for the paradoxes in a paraconsistent spirit. We will argue that the paraconsistent strategies can be seen as special cases of the strategy of restricting Detachment and that the latter uniformly blocks all the connective-involving self-referential paradoxes, including Curry’s.
Combined sleeve lobectomy for centrally located primary lung cancer and lung cancer with hilar lymph node metastasis
Authors: Tsukioka Takuma , Izumi Nobuhiro , Komatsu Hiroaki , Inoue Hidetoshi , Miyamoto Hikaru , Ito Ryuichi , Kimura Takuya , Nishiyama Noritoshi
Published: March 2020

Background

Centrally located lung cancer or metastatic hilar lymph nodes can invade the airway and other hilar structures, and they must be removed to achieve complete resection.

Methods

We retrospectively assessed the clinical course of 47 patients with centrally located lung cancer or metastatic hilar lymph nodes who underwent sleeve lobectomy from January 2010 to December 2017.

Results

The invaded structure other than the airway was the pulmonary artery in 21 patients, chest wall in 3, esophageal muscular wall in 2, vagus nerve in 2, pericardium in 2, left atrium in 1, phrenic nerve in 1 and superior vena cava in 1. Twenty-four patients were treated with sleeve lobectomy alone (simple sleeve lobectomy), and 23 patients were treated with sleeve lobectomy with additional methods (combined sleeve lobectomy). Adverse events occurred in 10 patients (48%) in the simple sleeve lobectomy group and 7 patients (30%) in the combined sleeve lobectomy group. During the follow-up period, 15 patients developed recurrent disease and 12 patients died. Patients in the combined sleeve lobectomy group had significantly shorter overall survival (P = 0.004) and disease-free survival periods (P = 0.013). Combined sleeve lobectomy was a significantly poor prognostic factor in the univariate and multivariate analyses. Patients who underwent sleeve lobectomy with an additional method other than angioplasty had a significantly poorer prognosis. However, no patient developed recurrent disease in the hilar area.

Conclusions

Combined sleeve lobectomy has acceptable adverse events and good local controllability. However, combined sleeve lobectomy is associated with a significantly poorer prognosis than simple sleeve lobectomy in terms of overall survival and disease-free survival.
Stochastic calibration of radio interferometers
Authors: Yatawatta Sarod
Published: March 2020

With ever-increasing data rates produced by modern radio telescopes like LOFAR and future telescopes like the SKA, many data-processing steps are overwhelmed by the amount of data that needs to be handled using limited compute resources. Calibration is one such operation that dominates the overall data processing computational cost; none the less, it is an essential operation to reach many science goals. Calibration algorithms do exist that scale well with the number of stations of an array and the number of directions being calibrated. However, the remaining bottleneck is the raw data volume, which scales with the number of baselines, and which is proportional to the square of the number of stations. We propose a ‘stochastic’ calibration strategy where we read only in a mini-batch of data for obtaining calibration solutions, as opposed to reading the full batch of data being calibrated. None the less, we obtain solutions that are valid for the full batch of data. Normally, data need to be averaged before calibration is performed to accommodate the data in size-limited compute memory. Stochastic calibration overcomes the need for data averaging before any calibration can be performed, and offers many advantages, including: enabling the mitigation of faint radio frequency interference; better removal of strong celestial sources from the data; and better detection and spatial localization of fast radio transients.
SuperCLASS – II. Photometric redshifts and characteristics of spatially resolved μJy radio sources
Authors: Manning Sinclaire M , Casey Caitlin M , Hung Chao-Ling , Battye Richard , Brown Michael L , Jackson Neal , Abdalla Filipe , Chapman Scott , Demetroullas Constantinos , Drew Patrick , Hales Christopher A , Harrison Ian , Riseley Christopher J , Sanders David B , Watson Robert A
Published: March 2020

We present optical and near-infrared imaging covering a ∼1.53 deg2 region in the Super-Cluster Assisted Shear Survey (SuperCLASS) field, which aims to make the first robust weak lensing measurement at radio wavelengths. We derive photometric redshifts for ≈176 000 sources down to $i^\prime _{\rm AB}\sim 24$ and present photometric redshifts for 1.4 GHz expanded Multi-Element Radio Linked Interferometer Network (e-MERLIN) and Karl G. Jansky Very Large Array (VLA) detected radio sources found in the central 0.26 deg2. We compile an initial catalogue of 149 radio sources brighter than S1.4 > 75 μJy and find their photometric redshifts span 0 < zphot < 4 with radio luminosities between 1021 and 1025 W Hz−1, with medians of $\langle z \rangle \, =0.55$ and $\langle L_{1.4}\rangle \, =1.9\times 10^{23}$ W Hz−1, respectively. We find 95 per cent of the μJy radio source sample (141/149) have spectral energy distributions (SEDs) best fit by star-forming templates while 5 per cent (8/149) are better fit by active galactic nuclei (AGN). Spectral indices are calculated for sources with radio observations from the VLA and Giant Metrewave Radio Telescope (GMRT) at 325 MHz, with an average spectral slope of α = 0.59 ± 0.04. Using the full photometric redshift catalogue, we construct a density map at the redshift of the known galaxy clusters, z = 0.20 ± 0.08. Four of the five clusters are prominently detected at $\gt 7\, \sigma$ in the density map and we confirm the photometric redshifts are consistent with previously measured spectra from a few galaxies at the cluster centres.
Isotopologues of dense gas tracers in nearby infrared bright galaxies
Authors: Li Fei , Wang Junzhi , Fang Min , Li Shanghuo , Zhang Zhi-Yu , Gao Yu , Kong Minzhi
Published: March 2020

We present 1 and 3 mm observations of the 13C- and 15N-bearing isotopologues of dense gas tracers towards eight nearby infrared-bright galaxies. With the Institut de Radioastronomie Millimétrique 30-m telescope, we observed the J  = 1–0 transitions of H13CN, HC15N, H13CO+, HN13C, and H15NC towards M 82, NGC 3079, IC 694, Mrk 231, and NGC 6240. The J  = 3–2 transition of H13CN was obtained in M 82, NGC 3079, NGC 3504, NGC 4418, NGC 6240, and NGC 6946, using the 10-m Submillimeter Telescope (SMT). We report the first detections of HN13C J  = 1–0 and H13CN J  = 3–2 in M 82, and H13CN J  = 3–2 in NGC 6240 and NGC 3079. We find different line profiles between the J  = 1–0 and 3–2 transitions of H13CN in both M 82 and NGC 3079. The optical depths of HCN show significant variations among the sample, indicating that dense gas masses estimated from the line luminosities of HCN J  = 1–0 and 3–2 should be treated with caution for individual galaxies. Optical depth of HCN J  = 3–2 is found to be higher than that of HCN J  = 1–0 in M 82, NGC 3079, NGC 4418, and NGC 6240, which indicates that ground state transitions of dense gas tracers might better trace the star-forming gas than the high-J transitions. Based on the H13CN/HC15N line ratios, with the double-isotopic method, low 14N/15N abundance ratios of 120 and 140 are found in NGC 3079 and Mrk 231, respectively.
2MASS J15460752−6258042: a mid-M dwarf hosting a prolonged accretion disc
Authors: Lee Jinhee , Song Inseok , Murphy Simon
Published: March 2020

We report the discovery of the oldest (∼55 Myr) mid-M type star known to host ongoing accretion. 2MASS J15460752–6258042 (2M1546, spectral type M5, 59.2 pc) shows spectroscopic signs of accretion such as strong H α, He i, and [O i] emission lines, from which we estimate an accretion rate of ∼10−10 M⊙ yr−1. Considering the clearly detected infrared excess in all WISE bands, the shape of its spectral energy distribution (SED) and its age, we believe that the star is surrounded by a transitional disc, clearly with some gas still present at inner radii. The position and kinematics of the star from Gaia DR2 and our own radial-velocity measurements suggest membership in the nearby ∼55 Myr-old Argus moving group. At only 59 pc from Earth, 2M1546 is one of the nearest accreting mid-M dwarfs, making it an ideal target for studying the upper limit on the lifetimes of gas-rich discs around low-mass stars.
Accurate mass estimates from the proper motions of dispersion-supported galaxies
Authors: Lazar Alexandres , Bullock James S
Published: March 2020

We derive a new mass estimator that relies on internal proper motion measurements of dispersion-supported stellar systems, one that is distinct and complementary to existing estimators for line-of-sight velocities. Starting with the spherical Jeans equation, we show that there exists a radius where the mass enclosed depends only on the projected tangential velocity dispersion, assuming that the anisotropy profile slowly varies. This is well-approximated at the radius where the log-slope of the stellar tracer profile is −2: r−2. The associated mass is $M(r_{-2}) = 2 G^{-1} \langle \sigma _{\mathcal {T}}^{2}\rangle ^{*} r_{-2}$ and the circular velocity is $V^{2}({r_{-2}}) = 2\langle \sigma _{\mathcal {T}}^{2}\rangle ^{*}$. For a Plummer profile r−2 ≃ 4Re/5. Importantly, r−2 is smaller than the characteristic radius for line-of-sight velocities derived by Wolf et al. Together, the two estimators can constrain the mass profiles of dispersion-supported galaxies. We illustrate its applicability using published proper motion measurements of dwarf galaxies Draco and Sculptor, and find that they are consistent with inhabiting cuspy NFW subhaloes of the kind predicted in CDM but we cannot rule out a core. We test our combined mass estimators against previously published, non-spherical cosmological dwarf galaxy simulations done in both cold dark matter (CDM; naturally cuspy profile) and self-interacting dark matter (SIDM; cored profile). For CDM, the estimates for the dynamic rotation curves are found to be accurate to $10\rm { per\, cent}$ while SIDM are accurate to $15\rm { per\, cent}$. Unfortunately, this level of accuracy is not good enough to measure slopes at the level required to distinguish between cusps and cores of the type predicted in viable SIDM models without stronger priors. However, we find that this provides good enough accuracy to distinguish between the normalization differences predicted at small radii (r ≃ r−2 < rcore) for interesting SIDM models. As the number of galaxies with internal proper motions increases, mass estimators of this kind will enable valuable constraints on SIDM and CDM models.
Spectroscopic analysis of accretion/ejection signatures in the Herbig Ae/Be stars HD 261941 and V590 Mon
Authors: Moura T , Alencar S H P , Sousa A P , Alecian E , Lebreton Y
Published: March 2020

Herbig Ae/Be (HAeBe) stars are the intermediate-mass analogues of low-mass T Tauri stars. Both groups may present signs of accretion, outflow, and IR excess related to the presence of circumstellar discs. Magnetospheric accretion models are generally used to describe accreting T Tauri stars, which are known to have magnetic fields strong enough to truncate their inner discs and form accretion funnels. Since few HAeBe stars have had magnetic fields detected, they may accrete through a different mechanism. Our goal is to analyse the morphology and variability of emission lines that are formed in the circumstellar environment of HAeBe stars and use them as tools to understand the physics of the accretion/ejection processes in these systems. We analyse high-resolution (R ∼ 47 000) UVES/ESO spectra of two HAeBe stars – HD 261941 (HAe) and V590 Mon (HBe) that are members of the young (∼3 Myr) NGC 2264 stellar cluster and present indications of sufficient circumstellar material for accretion and ejection processes to occur. We determine stellar parameters with synthetic spectra, and also analyse and classify circumstellar lines such as H α, H β, and He i λ5875.7, according to their morphologies. We model the H α mean line profile, using a hybrid Magnetohydrodynamics (MHD) model that includes a stellar magnetosphere and a disc wind, and find signatures of magnetically driven outflow and accretion in HD 261941, while the H α line of V590Mon seems to originate predominantly in a disc wind.
Contribution of starburst nuclei to the diffuse gamma-ray and neutrino flux
Authors: Peretti Enrico , Blasi Pasquale , Aharonian Felix , Morlino Giovanni , Cristofari Pierre
Published: March 2020

In nuclei of starburst galaxies (SBGs), the combination of an enhanced rate of supernova explosions and a high gas density suggests that cosmic rays (CRs) can be efficiently produced, and that most of them lose their energy before escaping these regions, resulting in a large flux of secondary products, including neutrinos. Although the flux inferred from an individual starburst region is expected to be well below the sensitivity of current neutrino telescopes, such sources may provide a substantial contribution to the diffuse neutrino flux measured by IceCube. Here, we compute the gamma-ray and neutrino flux due to SBGs based on a physical model of CR transport in a starburst nucleus, and accounting for the redshift evolution of the number density of starburst sources as inferred from recent measurements of the star formation rate. The model accounts for gamma-ray absorption both inside the sources and in the intergalactic medium. The latter process is responsible for electromagnetic cascades, which also contribute to the diffuse gamma-ray background at lower energies. The conditions for acceleration of CR protons up to energies exceeding $\sim 10 \, \rm PeV$ in starburst regions, necessary for the production of PeV neutrinos, are investigated in a critical way. We show that starburst nuclei can account for the diffuse neutrino flux above $\sim 200 \, \rm TeV$, thereby producing $\lesssim 40 {\rm { per\, cent}}$ of the extragalactic diffuse gamma-ray background. Below $\sim 200 \, \rm TeV$, the flux from starburst appears to be somewhat lower than the observed one, where both the Galactic contribution and the flux of atmospheric neutrinos may account for the difference.
Secular changes in the orbits of the quadruple system VW LMi
Authors: Pribulla T , Puha E , Borkovits T , Budaj J , Garai Z , Guenther E , Hambálek L , Komžík R , Kundra E , Szabó Gy M , Vaňko M
Published: March 2020

VW LMi is the tightest known quadruple system with 2 + 2 hierarchy. It consists of a W UMa-type eclipsing binary (P12 = 0.477 55 d) and another detached non-eclipsing binary (P34 = 7.93 d) orbiting around a common centre of mass in about P1234 = 355 d. We present new observations of the system extending the time baseline to study long-term perturbations in the system and to improve orbital elements. The multidataset modelling of the system (four radial-velocity curves for the components and the timing data) clearly showed an apsidal motion in the non-eclipsing binary at a rate of 4.6 deg yr−1, but no other perturbations. This is consistent with the nearly co-planarity of the outer, 355-d orbit, and the 7.93-d orbit of the non-eclipsing binary. Extensive N-body simulations enabled us to constrain the mutual inclination of the non-eclipsing binary and the outer orbits to j34–1234 < 10 deg.
Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts
Authors: Rolland Jonathan , Schluter Dolph , Romiguier Jonathan
Published: March 2020

Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.
Establishment of an in vitro placental barrier model cultured under physiologically relevant oxygen levels
Authors: Wong Michael K , Li Edward W , Adam Mohamed , Selvaganapathy Ponnambalam R , Raha Sandeep
Published: March 2020

The human placental barrier facilitates many key functions during pregnancy, most notably the exchange of all substances between the mother and fetus. However, preclinical models of the placental barrier often lacked the multiple cell layers, syncytialization of the trophoblast cells and the low oxygen levels that are present within the body. Therefore, we aimed to design and develop an in vitro model of the placental barrier that would reinstate these factors and enable improved investigations of barrier function. BeWo placental trophoblastic cells and human umbilical vein endothelial cells were co-cultured on contralateral sides of an extracellular matrix-coated transwell insert to establish a multilayered barrier. Epidermal growth factor and forskolin led to significantly increased multi-nucleation of the BeWo cell layer and increased biochemical markers of syncytial fusion, for example syncytin-1 and hCGβ. Our in vitro placental barrier possessed size-specific permeability, with 4000-Da molecules experiencing greater transport and a lower apparent permeability coefficient than 70 000-Da molecules. We further demonstrated that the BeWo layer had greater resistance to smaller molecules compared to the endothelial layer. Chronic, physiologically low oxygen exposure (3–8%) increased the expression of hypoxia-inducible factor 1α and syncytin-1, further increased multi-nucleation of the BeWo cell layer and decreased barrier permeability only against smaller molecules (457 Da/4000 Da). In conclusion, we built a novel in vitro co-culture model of the placental barrier that possessed size-specific permeability and could function under physiologically low oxygen levels. Importantly, this will enable future researchers to better study the maternal–fetal transport of nutrients and drugs during pregnancy.
CAMIO: a transgenic CRISPR pipeline to create diverse targeted genome deletions in Drosophila
Authors: Chen Hui-Min , Marques Jorge Garcia , Sugino Ken , Wei Dingjun , Miyares Rosa Linda , Lee Tzumin
Published: March 2020

The genome is the blueprint for an organism. Interrogating the genome, especially locating critical cis-regulatory elements, requires deletion analysis. This is conventionally performed using synthetic constructs, making it cumbersome and non-physiological. Thus, we created Cas9-mediated Arrayed Mutagenesis of Individual Offspring (CAMIO) to achieve comprehensive analysis of a targeted region of native DNA. CAMIO utilizes CRISPR that is spatially restricted to generate independent deletions in the intact Drosophila genome. Controlled by recombination, a single guide RNA is stochastically chosen from a set targeting a specific DNA region. Combining two sets increases variability, leading to either indels at 1–2 target sites or inter-target deletions. Cas9 restriction to male germ cells elicits autonomous double-strand-break repair, consequently creating offspring with diverse mutations. Thus, from a single population cross, we can obtain a deletion matrix covering a large expanse of DNA at both coarse and fine resolution. We demonstrate the ease and power of CAMIO by mapping 5′UTR sequences crucial for chinmo's post-transcriptional regulation.