bluuebunny/crossref_metadata_2025 huggingface dataset:
Eliciting and Measuring L2 Metaphoric Competence: Three Decades on from Low (1988)
Authors: O’Reilly David , Marsden Emma
Published: December 2019

In 1988 and 2006, Applied Linguistics published Low’s and Littlemore and Low’s seminal theoretical accounts of second language (L2) metaphoric competence (MC). Meanwhile, attempts to elicit metaphor-related skills/competences have been mixed. Instrumentation has varied in reliability, been limited in scope, and used arguably flawed reliability coefficients (McNeish 2018). Factor analysis, used in first language (L1) MC and other areas of L2 research (Loewen et al. 2009; Plonsky and Gonulal 2015), has not been used to explore latent L2 MC variables. To address these issues, we developed a large battery of MC tests to elicit Low/Littlemore’s constructs, administering it to 112 L1 Mandarin speakers of L2 English and 31 L1 English speakers. Data cleaning revealed some operationalization challenges, but resulting overall reliability was high and demonstrated innovative use of ordinal omega as a powerful alternative to Cronbach’s alpha, the most common instrument reliability index in L2 research (Plonsky and Derrick 2016). Exploratory factor analysis suggested four latent L2 MC variables: Productive Illocutionary MC, Metaphor Language Play, Topic/Vehicle Acceptability, and Grammatical MC, broadly supporting Low/Littlemore’s proposals.
PheGWAS: a new dimension to visualize GWAS across multiple phenotypes
Authors: George Gittu , Gan Sushrima , Huang Yu , Appleby Philip , Nar A S , Venkatesan Radha , Mohan Viswanathan , Palmer Colin N A , Doney Alex S F
Published: December 2019

Motivation

PheGWAS was developed to enhance exploration of phenome-wide pleiotropy at the genome-wide level through the efficient generation of a dynamic visualization combining Manhattan plots from GWAS with PheWAS to create a 3D ‘landscape’. Pleiotropy in sub-surface GWAS significance strata can be explored in a sectional view plotted within user defined levels. Further complexity reduction is achieved by confining to a single chromosomal section. Comprehensive genomic and phenomic coordinates can be displayed.

Results

PheGWAS is demonstrated using summary data from Global Lipids Genetics Consortium GWAS across multiple lipid traits. For single and multiple traits PheGWAS highlighted all 88 and 69 loci, respectively. Further, the genes and SNPs reported in Global Lipids Genetics Consortium were identified using additional functions implemented within PheGWAS. Not only is PheGWAS capable of identifying independent signals but also provides insights to local genetic correlation (verified using HESS) and in identifying the potential regions that share causal variants across phenotypes (verified using colocalization tests).

Availability and implementation

The PheGWAS software and code are freely available at (https://github.com/georgeg0/PheGWAS).

Supplementary information

Supplementary data are available at Bioinformatics online.
LPM: a latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations
Authors: Ming Jingsi , Wang Tao , Yang Can
Published: December 2019

Motivation

Much effort has been made toward understanding the genetic architecture of complex traits and diseases. In the past decade, fruitful GWAS findings have highlighted the important role of regulatory variants and pervasive pleiotropy. Because of the accumulation of GWAS data on a wide range of phenotypes and high-quality functional annotations in different cell types, it is timely to develop a statistical framework to explore the genetic architecture of human complex traits by integrating rich data resources.

Results

In this study, we propose a unified statistical approach, aiming to characterize relationship among complex traits, and prioritize risk variants by leveraging regulatory information collected in functional annotations. Specifically, we consider a latent probit model (LPM) to integrate summary-level GWAS data and functional annotations. The developed computational framework not only makes LPM scalable to hundreds of annotations and phenotypes but also ensures its statistically guaranteed accuracy. Through comprehensive simulation studies, we evaluated LPM’s performance and compared it with related methods. Then, we applied it to analyze 44 GWASs with 9 genic category annotations and 127 cell-type specific functional annotations. The results demonstrate the benefits of LPM and gain insights of genetic architecture of complex traits.

Availability and implementation

The LPM package, all simulation codes and real datasets in this study are available at https://github.com/mingjingsi/LPM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Human Rights and International Investment Agreements: How to Bridge the Gap?
Authors: Zhang Sheng
Published: December 2019

Although an increasing number of bilateral investment treaties (BITs) now incorporate the concept of sustainable development, direct reference to human rights is still rare and remains embryonic. A close look at the positions held by some representative groups and countries, including the European Union (EU), the USA, China, India, South Africa, and Mercosur, reveals that the reference to human rights features divergence. The divided positions held by these groups or countries reveal the difficulties of operationalizing human rights obligations into international investment rule making. Even among developed countries or economies, a consistent approach to human rights is yet to be found. Based on these observations, this article proposes a number of pragmatic solutions to bridge the gap between these divided positions. In order to synergize international investment treaty regimes on human rights, internal engagement, including the reform of BIT dispute settlement regimes, and external engagement, including dialogues among stakeholders, should be made.
Teacher Observation of Classroom Adaptation-Checklist: Measuring Children’s Social, Emotional, and Behavioral Functioning
Authors: Bradshaw Catherine P , Kush Joseph M
Published: December 2019

There is a growing need for valid measures that can be administered efficiently in school settings to assess the impact of school-based preventive interventions. The current article aimed to establish a balance among assessment efficiency, reliability, and the measurement properties of an instrument widely used to assess the impact of school-based programs, called the Teacher Observation of Classroom Adaptation-Checklist (TOCA-C). We leveraged item response theory (IRT) analyses to create a shortened, more focused checklist version of the TOCA-C that is both valid and efficient for large-scale use in schools to track students’ behavioral, social–emotional, and family factors over the course of elementary school. The sample included 17,456 children in kindergarten through grade 5 (47.7 percent female, 54.2 percent African American). IRT analyses resulted in the retention of 33 of the original 39 items comprising seven subscales: (1) Concentration Problems, (2) Aggressive/Disruptive Behavior, (3) Prosocial Behavior, (4) Emotion Regulation Problems, (5) Internalizing Problems, (6) Family Problems, and (7) Family Involvement. IRT, item difficulty estimates, and confirmatory factor analyses revealed limited evidence of bias based on gender, race, or grade; together, the findings suggested that the 33-item TOCA-C is a highly valid and reliable measure.
Measuring School Climate: Invariance across Middle and High School Students
Authors: Waasdorp Tracy Evian , Lindstrom Johnson Sarah , Shukla Kathan D , Bradshaw Catherine P
Published: December 2019

Positive school climate has been consistently associated with many desirable student outcomes in both middle and high schools. However, there has been little work comparing the perceptions across these two school settings. The U.S. Department of Education conceptualized a three-factor model for school climate consisting of safety, engagement, and environment. Drawing on data from 29,720 middle and 34,950 high school students, the fit of the three-factor model was examined for measurement invariance, to explore whether the measure functioned similarly across both middle and high schools. The results indicated measurement invariance, which suggests that practitioners and researchers can confidently compare findings across middle and high schools to inform local decision making related to school-based programming. A series of multilevel analyses also explored the extent to which perceptions of school climate differed for middle and high school students; these results generally indicated that middle school students perceived the school more favorably than high school students. Implications of these findings for social workers are considered.
Diurnal and Seasonal Activity Patterns of Drosophilid Species (Diptera: Drosophilidae) Present in Blackberry Agroecosystems With a Focus on Spotted-Wing Drosophila
Authors: Swoboda-Bhattarai Katharine A , Burrack Hannah J
Published: December 2019

Drosophilid species with different life histories have been shown to exhibit similar behavioral patterns related to locating and utilizing resources such as hosts, mates, and food sources. Drosophila suzukii (Matsumura) is an invasive species that differs from other frugivorous drosophilids in that females lay eggs in ripe and ripening fruits instead of overripe or rotten fruits. We hypothesized that there may be diurnal and/or seasonal patterns associated with the movement of drosophilid species into and out of crop fields and their attraction to fermentation-odor-based monitoring traps, and that D. suzukii would conform to similar patterns. To test these hypotheses, we deployed passive, 2-headed Malaise traps between crop fields and wooded edges to simultaneously catch flies moving into and out of crop fields. We also deployed monitoring traps with a fermentation-based bait between crop fields and wooded edges and within crop rows. Traps were deployed weekly in June–August in 2014 and 2015 at two commercial blackberry farm in Cleveland County, NC, and were checked hourly for 24 h, except during darkness. Both D. suzukii and other drosophilid species moved between crop fields and wooded edges and were attracted to monitoring traps primarily during the morning and evening hours. Whereas other drosophilids were captured in traps throughout the season, few D. suzukii were caught in traps until early to mid-July in both years and increased as the season progressed. Understanding D. suzukii movement and activity patterns is essential for the development of effective management strategies.
Whipple’s endocarditis: a case report of a blood culture-negative endocarditis
Authors: Scheurwater Miriam A , Verduin Cees M , van Dantzig Jan-Melle
Published: December 2019

Background

Whipple’s disease is caused by Tropheryma whipplei and causes a self-limiting gastrointestinal infection. The majority of the population is an asymptomatic carrier, however, in some patients, it causes an invasive infection with for example arthritis, endocarditis, or involvement of the eyes.

Case summary

This case describes a man with long-lasting complaints of progressive dyspnoea caused by heart failure due to total destruction of the aortic and mitral valve as a result of T. whipplei endocarditis, diagnosed with serum polymerase chain reaction. The patient was treated with ceftriaxone and prolonged co-trimoxazole therapy and surgical replacement of the aortic and mitral valve. He was discharged to a rehabilitation centre.

Discussion

Tropheryma whipplei is one of the possible microorganisms classified as causing blood culture-negative endocarditis, with predominantly afebrile patients that do not fulfil the Dukes criteria, which makes it difficult to diagnose. Polymerase chain reaction is the cornerstone of the diagnosis. It requires long-term antibiotic treatment up to 12 months. It is recommended by the European Society of Cardiology to discuss treatment in an Endocarditis Team because Whipple’s endocarditis has only rarely been described in the literature previously. Whipple’s endocarditis has high mortality and relapse rates.
Novel mutations in malonyl-CoA-acyl carrier protein transacylase provoke autosomal recessive optic neuropathy
Authors: Li Huiping , Yuan Shiqin , Minegishi Yuriko , Suga Akiko , Yoshitake Kazutoshi , Sheng Xunlun , Ye Jianping , Smith Stuart , Bunkoczi Gabor , Yamamoto Megumi , Iwata Takeshi
Published: December 2019

Inherited optic neuropathies are rare eye diseases of optic nerve dysfunction that present in various genetic forms. Previously, mutation in three genes encoding mitochondrial proteins has been implicated in autosomal recessive forms of optic atrophy that involve progressive degeneration of optic nerve and retinal ganglion cells (RGC). Using whole exome analysis, a novel double homozygous mutation p.L81R and pR212W in malonyl CoA-acyl carrier protein transacylase (MCAT), a mitochondrial protein involved in fatty acid biosynthesis, has now been identified as responsible for an autosomal recessive optic neuropathy from a Chinese consanguineous family. MCAT is expressed in RGC that are rich in mitochondria. The disease variants lead to structurally unstable MCAT protein with significantly reduced intracellular expression. RGC-specific knockdown of Mcat in mice, lead to an attenuated retinal neurofiber layer, that resembles the phenotype of optic neuropathy. These results indicated that MCAT plays an essential role in mitochondrial function and maintenance of RGC axons, while novel MCAT p.L81R and p.R212W mutations can lead to optic neuropathy.
Antipsychotic Polypharmacy: A Dirty Little Secret or a Fashion?
Authors: Lin Shih-Ku
Published: December 2019

The term polypharmacy was originally coined to refer to problems related to multiple drug consumption and excessive drug use during the treatment of a disease or disorder. In the treatment of schizophrenia, polypharmacy usually refers to the simultaneous use of 2 or more antipsychotic medications or combined (adjunct) medications such as mood stabilizers, antidepressants, anxiolytics, or hypnotics in addition to single or multiple antipsychotics. Two decades ago, antipsychotic polypharmacy was criticized as being more expensive, having unproven efficacy, and causing more side effects. However, in recent years, antipsychotic polypharmacy has become more or less acceptable in the views of clinical practitioners and academic researchers. Results from recent reviews have suggested that the common practice of antipsychotic polypharmacy lacks double-blind or high-quality evidence of efficacy, except for negative symptom reduction with aripiprazole augmentation. We reviewed some representative studies that enrolled large numbers of patients and compared antipsychotic polypharmacy and monotherapy during the past decade. The results revealed that a certain proportion of select patients can benefit from antipsychotic polypharmacy without further negative consequences. Because most of the current treatment guidelines from different countries and organizations prefer monotherapy and discourage all antipsychotic polypharmacy, guidelines regarding the use of antipsychotic polypharmacy in clinical practice should be revised. On the basis of the findings of 2 large-scale studies from Asia and Europe, we also suggest ideal rates of various maintenance treatments of schizophrenia, which are as follows: antipsychotic polypharmacy, 30%; combined mood stabilizer, 15%; combined antidepressant, 10%; combined anxiolytics, 30%; and combined hypnotic, 10%.
Correlation of mRNA delivery timing and protein expression in lipid-based transfection
Authors: Reiser A , Woschée D , Mehrotra N , Krzysztoń R , Strey H H , Rädler J O
Published: December 2019

Non-viral gene delivery is constrained by the dwell time that most synthetic nucleic acid nanocarriers spend inside endosomal compartments. In order to overcome this endosomal-release bottleneck, methods are required that measure nanocarrier uptake kinetics and transfection efficiency simultaneously. Here, we employ live-cell imaging on single-cell arrays (LISCA) to study the delivery-time distribution of lipid-based mRNA complexes under varied serum conditions. By fitting a translation-maturation model to hundreds of individual eGFP reporter fluorescence time courses, the protein expression onset times and the expression rates after transfection are determined. Using this approach, we find that delivery timing and protein expression rates are not intrinsically correlated at the single-cell level, even though population-averaged values of both parameters conjointly change as a function of increasing external serum protein fraction. Lipofectamine-mediated delivery showed decreased transfection efficiency and longer delivery times with increasing serum protein concentration. This is in contrast to ionizable lipid nanoparticle (i-LNP)-mediated transfer, which showed increased efficiency and faster uptake in the presence of serum. In conclusion, the interdependences of single-cell expression rates and onset timing provide additional clues on uptake and release mechanisms, which are useful for improving nucleic acid delivery.
Phenotypic chemical and mutant screening of zebrafish larvae using an on-demand response to electric stimulation
Authors: Khalili Arezoo , Peimani Amir Reza , Safarian Nickie , Youssef Khaled , Zoidl Georg , Rezai Pouya
Published: December 2019

Behavioral responses of zebrafish larvae to environmental cues are important functional readouts that should be evoked on-demand and studied phenotypically in behavioral, genetical and developmental investigations. Very recently, it was shown that zebrafish larvae execute a voluntary and oriented movement toward the positive electrode of an electric field along a microchannel. Phenotypic characterization of this response was not feasible due to larva’s rapid movement along the channel. To overcome this challenge, a microfluidic device was introduced to partially immobilize the larva’s head while leaving its mid-body and tail unrestrained in a chamber to image motor behaviors in response to electric stimulation, hence achieving quantitative phenotyping of the electrically evoked movement in zebrafish larvae. The effect of electric current on the tail-beat frequency and response duration of 5–7 days postfertilization zebrafish larvae was studied. Investigations were also performed on zebrafish exposed to neurotoxin 6-hydroxydopamine and larvae carrying a pannexin1a (panx1a) gene knockout, as a proof of principle applications to demonstrate on-demand movement behavior screening in chemical and mutant assays. We demonstrated for the first time that 6-hydroxydopamine leads to electric response impairment, levodopa treatment rescues the response and panx1a is involved in the electrically evoked movement of zebrafish larvae. We envision that our technique is broadly applicable as a screening tool to quantitatively examine zebrafish larvae’s movements in response to physical and chemical stimulations in investigations of Parkinson’s and other neurodegenerative diseases, and as a tool to combine recent advances in genome engineering of model organisms to uncover the biology of electric response.
‘An indefatigable intermediary’
Authors: Rowlands Eliot W
Published: December 2019

At a time when museum curatorship in America was in its infancy, Harold Woodbury Parsons (1882–1967) scouted and negotiated for outstanding works of art for the cash-rich Cleveland Museum of Art, which opened to the public in 1916. As its European representative (1925–41), he acquired such masterworks as the Stroganoff Ivory, El Greco’s Holy Family with St Mary Magdalen, and the Warren tondo by Filippino Lippi, all during the late 1920s. During a lifetime’s work in the art market, in which he worked for private collectors and other museums, this was his most important achievement. What he acquired for the Cleveland Museum is vividly recounted in the art agent’s correspondence, until now, almost entirely unpublished. After moving to Rome in 1910, Parsons first served as ‘an indefatigable intermediary’ in the world market for antiquities. Later, with the blessing of Edward Waldo Forbes and Paul J. Sachs – director and assistant director, respectively, of Harvard’s Fogg Art Museum – and with a host of European contacts, he was able to ‘gun for’ art for an ever expanding number of clients.
Oral Leukoplakia and Risk of Progression to Oral Cancer: A Population-Based Cohort Study
Authors: Chaturvedi Anil K , Udaltsova Natalia , Engels Eric A , Katzel Jed A , Yanik Elizabeth L , Katki Hormuzd A , Lingen Mark W , Silverberg Michael J
Published: December 2019

Background

The optimal clinical management of oral precancer remains uncertain. We investigated the natural history of oral leukoplakia, the most common oral precancerous lesion, to estimate the relative and absolute risks of progression to cancer, the predictive accuracy of a clinician’s decision to biopsy a leukoplakia vis-à-vis progression, and histopathologic predictors of progression.

Methods

We conducted a retrospective cohort study (1996–2012) of patients with oral leukoplakia (n = 4886), identified using electronic medical records within Kaiser Permanente Northern California. Among patients with leukoplakia who received a biopsy (n = 1888), we conducted a case-cohort study to investigate histopathologic predictors of progression. Analyses included indirect standardization and unweighted or weighted Cox regression.

Results

Compared with the overall Kaiser Permanente Northern California population, oral cancer incidence was substantially elevated in oral leukoplakia patients (standardized incidence ratio = 40.8, 95% confidence interval [CI] = 34.8 to 47.6; n = 161 cancers over 22 582 person-years). Biopsied leukoplakias had a higher oral cancer risk compared with those that were not biopsied (adjusted hazard ratio = 2.38, 95% CI = 1.73 to 3.28). However, to identify a prevalent or incident oral cancer, the biopsy decision had low sensitivity (59.6%), low specificity (62.1%), and moderate positive–predictive value (5.1%). Risk of progression to oral cancer statistically significantly increased with the grade of dysplasia; 5-year competing risk-adjusted absolute risks were: leukoplakia overall = 3.3%, 95% CI = 2.7% to 3.9%; no dysplasia = 2.2%, 95% CI = 1.5% to 3.1%; mild-dysplasia = 11.9%, 95% CI = 7.1% to 18.1%; moderate-dysplasia = 8.7%, 95% CI = 3.2% to 17.9%; and severe dysplasia = 32.2%, 95% CI = 8.1%–60.0%. Yet 39.6% of cancers arose from biopsied leukoplakias without dysplasia.

Conclusions

The modest accuracy of the decision to biopsy a leukoplakia vis-à-vis presence or eventual development of oral cancer highlights the need for routine biopsy of all leukoplakias regardless of visual or clinical impression. Leukoplakia patients, particularly those with dysplasia, need to be closely monitored for signs of early cancer.
Narratives and International Reconciliation
Authors: Lind Jennifer
Published: December 2019

In relations between Japan and South Korea, as well as between other former adversaries, observers frequently argue that “history stands in the way” of better relations. They expect that hostile historical narratives will prevent leaders from pursuing potentially advantageous cooperation. To evaluate this claim, in this article I define narratives and their elements, noting that they range from more hostile to more friendly. I outline and theoretically develop two perspectives: the view of history as an obstacle, and a view more optimistic about the potential for cooperation and narrative transformation. Evidence from Franco-German relations after World War II, as well as other cases across time and space, supports the latter, more optimistic, view. Finally, I hypothesize different strategic and domestic conditions that make cooperation and narrative change more or less likely. Ultimately, I argue that observers have exaggerated the constraining power of narratives and thus underestimated the potential for cooperation between former enemies. This has important implications for relations between longtime rivals all over the world, and particularly in East Asia, where a conventional wisdom expects historical memories to impede balancing against China's rise.
Species turnover drives grassland community to phylogenetic clustering over long-term grazing disturbance
Authors: Zhu Juntao , Zhang Yangjian , Wang Wenfeng , Yang Xian , Chen Ning , Shen Ruonan , Wang Li , Jiang Lin
Published: December 2019

Aims

Grazing exerts profound effects on grassland ecosystem service and functions by regulating species composition and diversity, and structuring community assembly worldwide. However, adaptions of phylogenetic diversity and phylogenetic community structure to long-term grazing disturbance remain poorly studied, especially for ecosystems distributed in extreme environments.

Methods

Here, we conducted an experiment with multigrazing intensities to explore the impacts of grazing disturbance on plant phylogenetic diversity and community structure in an alpine grassland of the Tibetan Plateau.

Important Findings

Grazing disturbance enriched plant species richness (SR), and stimulated species turnover from regional species pool, consequently changing community species composition. Under low intensities, grazing exerted no obvious effects on phylogenetic diversity and community structure, whereas communities changed from overdispersion to clustering under high grazing intensity. High grazing intensity resulted in stronger environmental filtering, which consequently selected those species with high resilience to grazing disturbance. The observed clustering structure was associated with the colonizing species which were closely related to resident species, and locally extinct species, and distantly related to residents. At the plant functional trait level, high grazing intensity increased species colonization largely by altering the effect of root depth on species colonization compared to light grazing. Our results highlight that solely utilization of SR and diversity cannot fully represent grassland communities responses to grazing. The effects of species turnover on community phylogenetic diversity and structure are entailed to be explored in the future grazing studies.
Natural selection on flower size in invasive Cytisus scoparius along an elevation gradient
Authors: Bode Robert Frederick , Dufresne Catherine
Published: December 2019

Aims

Established invasive plant species have more diverse gene pools than single populations in their home range. This genetic and often phenotypic variation allows for natural selection to act and produce rapid adaptations as an invasive species interacts with other members of the community. For an invasive flowering plant, interactions with pollinators may lead to adaptations to a heterogeneous pollinator community. The variation in the pollinator community in the invaded range is similar to variation in the native range, suggesting that adaptations may mirror patterns seen in the home range. In this study, we investigated variation in flower size in Cytisus scoparius, an invasive leguminous shrub, along an elevation gradient.

Methods

This study took place in the Capitol State Forest in Washington State. We measured flower widths and the proportion of visited flowers, using 10 plants per field site. Sites were located along an elevation gradient and were visited three times to measure phenological variation on a per-plant basis.

Important Findings

We saw positive selection for flower size, albeit without a distinct pattern of higher selection at higher elevations. The pattern of natural selection could be seen both in terms of pollinator visitation rates and in seed production. We also found that the largest contributor to changes in seed production was not elevation or flower size but management practices.
Enhancement of membrane lipid peroxidation in lung cancer cells irradiated with monoenergetic X-rays at the K-shell resonance absorption peak of phosphorus
Authors: Maezawa Hiroshi , Indo Hiroko P , Usami Noriko , Majima Hideyuki J , Ito Hiromu , Ohnishi Ken , Kobayashi Katsumi
Published: December 2019

The aim of this study was to determine whether membrane lipid peroxidation in mammalian cells is enhanced by X-ray irradiation at the K-shell resonance absorption peak of phosphorus. A549 and wild-type p53-transfected H1299 (H1299/wtp53) cell lines derived from human lung carcinoma were irradiated with monoenergetic X-rays at 2.153 keV, the phosphorus K-shell resonance absorption peak, or those at 2.147 or 2.160 keV, which are off peaks. Immunofluorescence staining for 4-hydroxy-2-nonenal (HNE), a lipid peroxidation product, was used as marker for protein modification. In both cell lines, the HNE production was significantly enhanced after irradiation at 2.153 keV compared to sham-irradiation. The enhancement (E) was calculated as the ratio of the fluorescence intensity of irradiated cells to that of sham-irradiated cells. In both the cell lines, E2.153 was significantly larger than E2.147 and no significant difference between E2.147 and E2.160 was observed. The extra enhancement at 2.153 keV was possibly caused by energy transition within the phosphorus K-shell resonance absorption. Our results indicate that membrane lipid peroxidation in cells is enhanced by the Auger effect after irradiation at the K-shell resonance absorption peak of phosphorus rather than by the photoelectric effect of the constituent atoms in the membrane lipid at 2.147 keV.
Living in Permanent Temporariness: The Multigenerational Ordeal of Living under Germany’s Toleration Status
Authors: Tize Carola
Published: December 2019

Toleration status (temporary suspension of deportation) has been Germany’s hesitant answer to providing humanitarian relief for Palestinians escaping the dismal conditions of refugee camps and the civil war in Lebanon in the late 1980s and early 1990s. At the same time, the status has subjected families to years, even decades, of insecurity and uncertainty through constant threats of deportation and restrictions on work, travel and higher education. Based on 19 months of ethnographic research, the article shows the story of one family during their 16 years on toleration status and their experiences after gaining permanent residency. The family’s experiences illuminate the insecurity and uncertainty large communities on toleration status in Berlin-Neukölln experienced, all sharing the fate of constantly wavering between hope, fear and disillusionment. Their struggles also show how the permanent temporariness of long-term toleration status affects both the parents who fled the conflict and their children, most of whom were born and raised in Germany. I argue that toleration status limits the capabilities of children stuck in the stagnant realities of their family’s insecure status, along the lines of gender and birth order. Moreover, toleration status as a multigenerational ordeal persists long after the legal insecurity has ended.
An intrathoracic mass behind severe immunodeficiency: a case report of Good’s syndrome and large type AB thymoma
Authors: Thuraisingam Amalan
Published: December 2019

A large solitary intrathoracic mass was identified in a patient with concurrent immunodeficiency. The patient was found to have a type AB thymoma and was diagnosed with Good’s syndrome. A case report demonstrates the importance of timely surgical intervention for this rare syndrome.
A rare case of a digital papillary carcinoma of the hand with secondary conservative management
Authors: Khan Rabeet , Irri Renu , Katsarma Effie
Published: December 2019

A digital papillary carcinoma (DPC) is a cancer of the sweat glands which develops on the digits of the hands and feet. With an incidence of 0.08 per 1 000 000 people/year, it is often initially misdiagnosed as a simple ganglion although it has a significant risk of metastasis. Histological analysis is beneficial in the formal diagnosis of DPCs. In this report, we present a rare case of DPC affecting the palm of the hand, rather than the more commonly reported DPC of the digits. We discuss the management strategy utilized in this case and the various prognostic considerations taken into account when deciding on an amputation versus local excision surgical approach. All cases of DPC require regular follow up imaging for early detection of recurrence or new metastases to maximize prognosis.
Freeing Ahasuerus, Haman, and Mordechai: Liberating the Oppressor in the Book of Esther
Authors: Flanders Denise
Published: December 2019

The approach taken in this essay proceeds from the assumption that the biblical text of Esther reflects a patriarchal ideology and it is largely the males in the story who wield the power. However, instead of examining the negative consequences for the female characters and how the patriarchal system forces them to operate, I look to the male characters to see how they fare in the system of patriarchy which they undoubtedly inhabit. In the first part of the essay, I consider the call issued by womanist and liberation theologians from traditionally marginalized communities for the need for liberation of both the oppressed and the oppressors from systems of oppression. In the second part of the essay, I respond to this call via an analysis of the book of Esther. First, I examine four different actions or attitudes that characterize the men in the story. Second, I observe some places where their power clearly brings them loss. Third, I argue that the destructive attitudes, actions, and relationships of the men in the story demonstrate their own need for liberation from the oppressive system of patriarchy from which they supposedly benefit.
The Radio Scream from black holes at Cosmic Dawn: a semi-analytic model for the impact of radio-loud black holes on the 21 cm global signal
Authors: Ewall-Wice Aaron , Chang Tzu-Ching , Lazio T Joseph W
Published: December 2019

We use a semi-analytic model to explore the potential impact of a brief and violent period of radio-loud accretion on to black holes (The Radio Scream) during the Cosmic Dawn on the H i hyperfine 21 cm signal. We find that radio emission from supermassive black hole seeds can impact the global 21 cm signal at the level of tens to hundreds of per cent provided that they were as radio loud as $z$ ≈ 1 black holes and obscured by gas with column depths of NH ≳ 1023 cm−2. We determine plausible sets of parameters that reproduce some of the striking features of the EDGES absorption feature including its depth, timing, and side steepness while producing radio/X-ray backgrounds and source counts that are consistent with published limits. Scenarios yielding a dramatic 21 cm signature also predict large populations of ∼$\mu$Jy point sources that will be detectable in future deep surveys from the Square Kilometer Array (SKA). Thus, 21 cm measurements, complemented by deep point-source surveys, have the potential to constrain optimistic scenarios where supermassive black hole progenitors were radio loud.
Pulsar candidate selection using pseudo-nearest centroid neighbour classifier
Authors: Xiao Jiangping , Li Xiangru , Lin Haitao , Qiu Kaibin
Published: December 2019

A typical characteristic of the pulsar candidate classification task is the class imbalance between true pulsars and false candidates. This imbalance has negative effects on traditional classification methods. In this study, we introduce a strategy using a scatter matrix-based class separability measure to estimate the harmfulness of class imbalance on pulsar candidate classification. The measure quantitatively describes the damage of the imbalanced situations on the pulsar candidate classification problem and provides some priori information to guide us to select an appropriate data processing method and to construct an effective classifier. After that, we present a non-parametric data exploration technique, a pseudo-nearest centroid neighbour classifier (PNCN), to identify credible pulsar candidates from pulsar survey data sets. The PNCN algorithm can effectively resolve the class imbalance problem and is applicable to data streams. The proposed algorithm is tested on High Time Resolution Universe Pulsar Survey (HTRU) 2 (obtained by an analysis of HTRU Medium Latitude data) and LOTAAS 1 (obtained from the LOFAR Tied-Array All-Sky Survey). The experimental results show that the proposed classifier can excellently identify the pulsars with high performance: the precision and the recall on HTRU 2 are 92.3 per cent and 83.1 per cent, and those on LOTAAS 1 are 97.4 per cent and 95.6 per cent, respectively; the false positive rate (FPR) on HTRU 2 is 0.7 per cent, on LOTAAS 1 is 0.03 per cent, which is an order of magnitude lower than the corresponding FPR obtained in Lyon et al. (2016) and Tan et al. (2018).
The importance of Hall effect on the magnetized thin accretion disc
Authors: Ghasemnezhad Maryam
Published: December 2019

To study the role of Hall effect on the structure of accretion disc, we have considered a toroidal magnetic field in our paper. To study the vertical structure of the disc, we have written a set of magnetohydrodynamic (MHD) equations in the spherical coordinates (r, θ, ϕ) based on the two assumptions of axisymmetric and steady state. Also, we employed the self-similar solutions in the radial direction to obtain the structure of the disc in the θ-direction. We have solved a set of ordinary differential equations in the θ-coordinate with symmetrical boundary conditions in the equatorial plane. In order to describe the behaviour of Hall effect, we introduced the ΛH parameter that was called the dimensionless Hall Elsasser number. The strength of the Hall effect is measured by the inverse of dimensionless Hall Elsasser number. We have shown that the strong Hall effect decreases the accretion rate or infall velocity and size of inflow part. It has also been found the Hall effect is maximum in the equatorial plane and gets the value close to zero near the boundary, and it has the antidiffusive nature. The results display that the strong Hall effect makes the standard accretion sub-Keplerian disc becomes thinner. Our solutions have shown the Hall effect leads to transport magnetic flux outward in the upper layer of the disc and it produces outflows in the surface of the disc.
The EDGE–CALIFA survey: using optical extinction to probe the spatially resolved distribution of gas in nearby galaxies
Authors: Barrera-Ballesteros Jorge K , Utomo Dyas , Bolatto Alberto D , Sánchez Sebastián F , Vogel Stuart N , Wong Tony , Levy Rebecca C , Colombo Dario , Kalinova Veselina , Teuben Peter , García-Benito Rubén , Husemann Bernd , Mast Damián , Blitz Leo
Published: December 2019

We present an empirical relation between the cold gas surface density (Σgas) and the optical extinction (AV) in a sample of 103 galaxies from the Extragalactic Database for Galaxy Evolution (EDGE) survey. This survey provides CARMA interferometric CO observations for 126 galaxies included in the Calar Alto Legacy Integral Field Area (CALIFA) survey. The matched, spatially resolved nature of these data sets allows us to derive the Σgas–AV relation on global, radial, and kpc (spaxel) scales. We determine AV from the Balmer decrement (H α/H β). We find that the best fit for this relation is $\Sigma _{\rm gas}\,(\rm {M_\odot \,pc}^{-2}) \sim 26 \times {\rm \mathit{ A}_\mathit{ V}} \,(\rm mag)$, and that it does not depend on the spatial scale used for the fit. However, the scatter in the fits increases as we probe smaller spatial scales, reflecting the complex relative spatial distributions of stars, gas, and dust. We investigate the Σgas/AV ratio on radial and spaxel scales as a function of $\mathrm{EW(H\,\alpha)}$. We find that at larger values of $\mathrm{EW({H\,\alpha })}$ (i.e. actively star-forming regions) this ratio tends to converge to twice the value expected for a foreground dust screen geometry (∼30 $\mathrm{M_{\odot } \, pc^{-2} \, mag^{-1}}$). On radial scales, we do not find a significant relation between the Σgas/AV ratio and the ionized gas metallicity. We contrast our estimates of Σgas using AV with compilations in the literature of the gas fraction on global and radial scales as well as with well-known scaling relations such as the radial star formation law and the Σgas–Σ* relation. These tests show that optical extinction is a reliable proxy for estimating Σgas in the absence of direct sub/millimeter observations of the cold gas.
magritte, a modern software library for 3D radiative transfer: I. Non-LTE atomic and molecular line modelling
Authors: De Ceuster Frederik , Homan Ward , Yates Jeremy , Decin Leen , Boyle Peter , Hetherington James
Published: December 2019

Radiative transfer is a key component in almost all astrophysical and cosmological simulations. We present magritte: a modern open-source software library for 3D radiative transfer. It uses a deterministic ray-tracer and formal solver, i.e. it computes the radiation field by tracing rays through the model and solving the radiative transfer equation in its second-order form along a fixed set of rays originating from each point. magritte can handle structured and unstructured input meshes, as well as smoothed-particle hydrodynamics (SPH) particle data. In this first paper, we describe the numerical implementation, semi-analytic tests and cross-code benchmarks for the non-LTE line radiative transfer module of magritte. This module uses the radiative transfer solver to self-consistently determine the populations of the quantized energy levels of atoms and molecules using an accelerated Lambda iteration (ALI) scheme. We compare magritte with the established radiative transfer solvers ratran (1D) and lime (3D) on the van Zadelhoff benchmark and present a first application to a simple Keplerian disc model. Comparing with lime, we conclude that magritte produces more accurate and more precise results, especially at high optical depth, and that it is faster.
Amino acetaldehyde conformers: structure and spectroscopic properties
Authors: Redondo Pilar , Sanz-Novo Miguel , Largo Antonio , Barrientos Carmen
Published: December 2019

We present a computational study of the different conformers of amino acetaldehyde. This molecule is a precursor of glycine and also an isomer of the detected molecules acetaldehyde and methylformamide. In addition, a previous theoretical result shows that amino acetaldehyde could be formed from the gas phase reaction of formamide with CH$_{5}^{+}$. Different computational approaches, going from density functional theory (DFT) to coupled cluster (CC) calculations, are employed for the characterization of the amino acetaldehyde conformers. We locate four low-lying conformation on the singlet potential energy surface (PES), two with a synperiplanar arrangement of the carboxylic oxygen atom and the NH2 group, and the other two conformers with an anticlinal disposition. All levels of theory predict the conformer with a synperiplanar arrangement and the H atoms of the NH2 group pointing in the direction of the oxygen, denoted as in-sp-amino acetaldehyde, as the most stable. The viability of the interconversion processes between the four conformers in space is analysed. Relevant spectroscopic parameters to rotational spectroscopy with ‘spectroscopic’ accuracy at the composite level are reported. Vibrational frequencies and infrared intensities are also computed at the CC with single and double excitations (CCSD) level including anharmonic corrections. This information could help in the experimental characterization of amino acetaldehyde that could be considered as a good candidate molecule to be searched for in space.
On the survival of cool clouds in the circumgalactic medium
Authors: Li Zhihui , Hopkins Philip F , Squire Jonathan , Hummels Cameron
Published: December 2019

We explore the survival of cool clouds in multiphase circumgalactic media. We revisit the ‘cloud-crushing problem’ in a large survey of simulations including radiative cooling, self-shielding, self-gravity, magnetic fields, and anisotropic Braginskii conduction and viscosity (with saturation). We explore a wide range of parameters including cloud size, velocity, ambient temperature and density, and a variety of magnetic field configurations and cloud turbulence. We find that realistic magnetic fields and turbulence have weaker effects on cloud survival; the most important physics is radiative cooling and conduction. Self-gravity and self-shielding are important for clouds that are initially Jeans-unstable, but largely irrelevant otherwise. Non-self-gravitating, realistically magnetized clouds separate into four regimes: (1) at low column densities, clouds evaporate rapidly via conduction; (2) a ‘failed pressure confinement’ regime, where the ambient hot gas cools too rapidly to provide pressure confinement for the cloud; (3) an ‘infinitely long-lived’ regime, in which the cloud lifetime becomes longer than the cooling time of gas swept up in the leading bow shock, so the cloud begins to accrete and grow; and (4) a ‘classical cloud destruction’ regime, where clouds are eventually destroyed by instabilities. In the final regime, the cloud lifetime can exceed the naive cloud-crushing time owing to conduction-induced compression. However, small and/or slow-moving clouds can also evaporate more rapidly than the cloud-crushing time. We develop simple analytic models that explain the simulated cloud destruction times in this regime.
Determining the primordial helium abundance and UV background using fluorescent emission in star-free dark matter haloes
Authors: Sykes Calvin , Fumagalli Michele , Cooke Ryan , Theuns Tom
Published: December 2019

Observational measures of the primordial helium mass fraction, YP, are of interest for cosmology and fundamental particle physics. Current measures obtained from ${\text{H}\, \small {II}}$ regions agree with the Standard Model prediction to approximately 1 per cent precision, although these determinations may be affected by systematic uncertainties. This possibility can only be tested by independently measuring the helium abundance in new ways. Here, we propose a novel method to obtain a measurement of YP using hydrogen and helium recombination line emission from REionization-Limited HI Clouds (RELHICs): pristine, gas-rich but star-free low-mass dark matter haloes whose existence is predicted by hydrodynamical simulations. Although expected to be uncommon and intrinsically faint in emission, the primordial composition and simple physical properties of these objects make them an ideal laboratory to determine YP. We present radiative transfer simulations to demonstrate the effectiveness of this approach, finding that a comparison of the emission in H and He lines, either via their volumetric emissivities, or integrated properties such as the surface brightness and total flux, may be used to infer YP. Furthermore, we show that RELHICs can be used to provide an entirely novel constraint on the spectral slope of the ultraviolet background, and discuss the possibility of measuring this slope and the primordial helium abundance simultaneously.