bluuebunny/crossref_metadata_2025 huggingface dataset:
VIQoR: a web service for visually supervised protein inference and protein quantification
Authors: Tsiamis Vasileios , Schwämmle Veit
Published: March 2022

Motivation

In quantitative bottom-up mass spectrometry (MS)-based proteomics, the reliable estimation of protein concentration changes from peptide quantifications between different biological samples is essential. This estimation is not a single task but comprises the two processes of protein inference and protein abundance summarization. Furthermore, due to the high complexity of proteomics data and associated uncertainty about the performance of these processes, there is a demand for comprehensive visualization methods able to integrate protein with peptide quantitative data including their post-translational modifications. Hence, there is a lack of a suitable tool that provides post-identification quantitative analysis of proteins with simultaneous interactive visualization.

Results

In this article, we present VIQoR, a user-friendly web service that accepts peptide quantitative data of both labeled and label-free experiments and accomplishes the crucial components protein inference and summarization and interactive visualization modules, including the novel VIQoR plot. We implemented two different parsimonious algorithms to solve the protein inference problem, while protein summarization is facilitated by a well-established factor analysis algorithm called fast-FARMS followed by a weighted average summarization function that minimizes the effect of missing values. In addition, summarization is optimized by the so-called Global Correlation Indicator (GCI). We test the tool on three publicly available ground truth datasets and demonstrate the ability of the protein inference algorithms to handle shared peptides. We furthermore show that GCI increases the accuracy of the quantitative analysis in datasets with replicated design.

Availability and implementation

VIQoR is accessible at: http://computproteomics.bmb.sdu.dk/Apps/VIQoR/. The source code is available at: https://bitbucket.org/veitveit/viqor/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Network-based cancer heterogeneity analysis incorporating multi-view of prior information
Authors: Li Yang , Xu Shaodong , Ma Shuangge , Wu Mengyun
Published: March 2022

Motivation

Cancer genetic heterogeneity analysis has critical implications for tumour classification, response to therapy and choice of biomarkers to guide personalized cancer medicine. However, existing heterogeneity analysis based solely on molecular profiling data usually suffers from a lack of information and has limited effectiveness. Many biomedical and life sciences databases have accumulated a substantial volume of meaningful biological information. They can provide additional information beyond molecular profiling data, yet pose challenges arising from potential noise and uncertainty.

Results

In this study, we aim to develop a more effective heterogeneity analysis method with the help of prior information. A network-based penalization technique is proposed to innovatively incorporate a multi-view of prior information from multiple databases, which accommodates heterogeneity attributed to both differential genes and gene relationships. To account for the fact that the prior information might not be fully credible, we propose a weighted strategy, where the weight is determined dependent on the data and can ensure that the present model is not excessively disturbed by incorrect information. Simulation and analysis of The Cancer Genome Atlas glioblastoma multiforme data demonstrate the practical applicability of the proposed method.

Availability and implementation

R code implementing the proposed method is available at https://github.com/mengyunwu2020/PECM. The data that support the findings in this paper are openly available in TCGA (The Cancer Genome Atlas) at https://portal.gdc.cancer.gov/.

Supplementary information

Supplementary data are available at Bioinformatics online.
A Decade of Change in the Gendered Organizational Structure of Methamphetamine Markets in the American Midwest
Authors: Grundetjern Heidi
Published: March 2022

While much research has documented the gendered organization of crime markets, the variability of gender-segmentation across crime has received limited attention. Analysing interview data from a study involving two cohorts of incarcerated women who used methamphetamine in rural Missouri, USA, 40 in 2009 and 40 in 2019, this study investigates the organizational properties of markets following a shift from local methamphetamine production to imported methamphetamine, ice. Properties of the ice market include amplified uncertainty, rationality, complexity, and professionalism, as well as a shifted modus operandi with common use of violence; properties contributing to heightened exclusionary practices and gendered stereotyping. The study provides evidence to Steffensmeier’s theory of variability of gender segregation in crime markets and shows the ramifications that policy changes can have.
Delays to revascularization for patients with chronic limb-threatening ischaemia
Authors: Li Qiuju , Birmpili Panagiota , Johal Amundeep S , Waton Sam , Pherwani Arun D , Boyle Jonathan R , Cromwell David A
Published: March 2022

Background

Vascular services in England are organized into regional hub-and-spoke models, with hubs performing arterial surgery. This study examined time to revascularization for chronic limb-threatening ischaemia (CLTI) within and across different care pathways, and its association with postrevascularization outcomes.

Methods

Three inpatient and four outpatient care pathways were identified for patients with CLTI undergoing revascularization between April 2015 and March 2019 using Hospital Episode Statistics data. Differences in times from presentation to revascularization across care pathways were analysed using Cox regression. The relationship between postoperative outcomes and time to revascularization was evaluated by logistic regression.

Results

Among 16 483 patients with CLTI, 9470 had pathways starting with admission to a hub or spoke hospital, whereas 7013 (42.5 per cent) were first seen at outpatient visits. Among the inpatient pathways, patients admitted to arterial hubs had shorter times to revascularization than those admitted to spoke hospitals (median 5 (i.q.r. 2–10) versus 12 (7–19) days; P < 0.001). Shorter times to revascularization were also observed for patients presenting to outpatient clinics at arterial hubs compared with spoke hospitals (13 (6–25) versus 26 (15–35) days; P < 0.001). Within most care pathways, longer delays to revascularizsation were associated with increased risks of postoperative major amputation and in-hospital death, but the effect of delay differed across pathways.

Conclusion

For patients with CLTI, time to revascularization was influenced by presentation to an arterial hub or spoke hospital. Generally, longer delays to revascularization were associated with worse outcomes, but the impact of delay differed across pathways.
Of networked lesions and lesioned networks
Authors: Gray Robert , Nachev Parashkev
Published: March 2022

This scientific commentary refers to ‘Post-stroke outcomes predicted from multivariate lesion-behaviour and lesion network mapping’ by Bowren et al. (https://doi.org/10.1093/brain/awac010).
Biallelic variants in SLC35B2 cause a novel chondrodysplasia with hypomyelinating leukodystrophy
Authors: Guasto Alessandra , Dubail Johanne , Aguilera-Albesa Sergio , Paganini Chiara , Vanhulle Catherine , Haouari Walid , Gorría-Redondo Nerea , Aznal-Sainz Elena , Boddaert Nathalie , Planas-Serra Laura , Schlüter Agatha , Vélez-Santamaría Valentina , Verdura Edgard , Bruneel Arnaud , Rossi Antonio , Huber Céline , Pujol Aurora , Cormier-Daire Valérie
Published: March 2022

Sulphated proteoglycans are essential in skeletal and brain development. Recently, pathogenic variants in genes encoding proteins involved in the proteoglycan biosynthesis have been identified in a range of chondrodysplasia associated with intellectual disability. Nevertheless, several patients remain with unidentified molecular basis. This study aimed to contribute to the deciphering of new molecular bases in patients with chondrodysplasia and neurodevelopmental disease.

Exome sequencing was performed to identify pathogenic variants in patients presenting with chondrodysplasia and intellectual disability. The pathogenic effects of the potentially causative variants were analysed by functional studies.

We identified homozygous variants (c.1218_1220del and c.1224_1225del) in SLC35B2 in two patients with pre- and postnatal growth retardation, scoliosis, severe motor and intellectual disabilities and hypomyelinating leukodystrophy. By functional analyses, we showed that the variants affect SLC35B2 mRNA expression and protein subcellular localization leading to a functional impairment of the protein. Consistent with those results, we detected proteoglycan sulphation impairment in SLC35B2 patient fibroblasts and serum.

Our data support that SLC35B2 functional impairment causes a novel syndromic chondrodysplasia with hypomyelinating leukodystrophy, most likely through a proteoglycan sulphation defect. This is the first time that SLC35B2 variants are associated with bone and brain development in human.
Viral Borders: Migration, Deceleration, and the Re-Bordering of Mobility during the COVID-19 Pandemic
Authors: De Genova Nicholas
Published: March 2022

States’ efforts to govern the COVID-19 public health emergency have been entangled with the ongoing work of producing and enforcing borders. Thus, on a global scale, the public health crisis has been converted into various spectacles of ostensible border “crisis.” Rather than seeing borders as purely a matter of control, however, it is instructive to situate the tactics of border enforcement in relation to the primacy, autonomy, and subjectivity of human mobility. If we start from the human freedom of movement and recognize border enforcement as a reaction formation, various tactics of border policing can be seen to introduce interruptions that temporarily decelerate cross-border mobilities. Compelled to revert to a kind of “standby” mode, migrants are temporarily immobilized and must find ways to convert their waiting from “dead time” into more or less productive time. Waiting to be re-activated, their mobilities remain an intractable and always potentially disruptive constitutive power.
Layer- and cell-type-specific differences in neural activity in mouse barrel cortex during a whisker detection task
Authors: Vandevelde Jens R , Yang Jenq-Wei , Albrecht Steffen , Lam Henry , Kaufmann Paul , Luhmann Heiko J , Stüttgen Maik C
Published: March 2022

To address the question which neocortical layers and cell types are important for the perception of a sensory stimulus, we performed multielectrode recordings in the barrel cortex of head-fixed mice performing a single-whisker go/no-go detection task with vibrotactile stimuli of differing intensities. We found that behavioral detection probability decreased gradually over the course of each session, which was well explained by a signal detection theory-based model that posits stable psychometric sensitivity and a variable decision criterion updated after each reinforcement, reflecting decreasing motivation. Analysis of multiunit activity demonstrated highest neurometric sensitivity in layer 4, which was achieved within only 30 ms after stimulus onset. At the level of single neurons, we observed substantial heterogeneity of neurometric sensitivity within and across layers, ranging from nonresponsiveness to approaching or even exceeding psychometric sensitivity. In all cortical layers, putative inhibitory interneurons on average proffered higher neurometric sensitivity than putative excitatory neurons. In infragranular layers, neurons increasing firing rate in response to stimulation featured higher sensitivities than neurons decreasing firing rate. Offline machine-learning-based analysis of videos of behavioral sessions showed that mice performed better when not moving, which at the neuronal level, was reflected by increased stimulus-evoked firing rates.
A promising tool: triglycerides–glucose index to stratify the risk of cardiovascular events in chronic kidney disease
Authors: Yildirim Fatma , Yildiz Abdullah B , Kanbay Mehmet
Published: March 2022

Lipid profile management is one of the crucial components to optimize outcomes in patients with chronic kidney disease (CKD). CKD is associated with poor cardiovascular outcomes due to both a direct cardiovascular impact of CKD and the presence of metabolic comorbidities. Low-density lipoprotein cholesterol is the main target of current lipid-lowering drugs. However, the derangement of lipid metabolism in CKD is more complex. The recently described triglyceride–glucose index (TyG) is associated with cardiovascular outcomes in the general population. In recent studies, the TyG was associated with CKD progression in CKD patients and with cardiovascular death in patients on peritoneal dialysis. Quiroga et al. now show that the TyG is associated with the occurrence of major cardiovascular events in individuals free from diabetes with non-dialysis-dependent CKD.
Climbing the Wall around EU Citizenship: Has the Time Come to Align Third-Country Nationals with Intra-EU Migrants?
Authors: Weingerl Petra , Tratnik Matjaž
Published: March 2022

This article discusses legal migration in the EU, in particular labour migration. It addresses the following question: once migrant workers from non-EU countries have been admitted into the Union, should they be treated like workers from EU countries for purposes of free movement? The EU migration acquis is one of the most politically charged issues covered by the EU Treaties. As EU citizens, nationals of member states enjoy a set of free movement and political rights that can be exercised in other member states in accordance with the principle of non-discrimination on grounds of nationality affirmed in Article 18 TFEU. This principle is arguably not applicable to third-country nationals. Thus, member states are free to accord unequal treatment to third-country nationals as compared to privileged EU immigrants. The pressing question is whether it is desirable to maintain different levels of rights for third-country nationals who have been legally admitted and whose connection to the host member state does not otherwise differ from that of EU citizens who have exercised their mobility rights. To answer that question, this paper examines arguments for and against treating migrant workers from EU countries and non-EU countries equally for purposes of free movement. It will show how these arguments push in different directions depending on whether they concern the political, human, social, cultural or economic impact of such differential treatment. Our analysis strongly suggests that, on balance, there are convincing reasons for aligning the treatment of long-term resident migrant workers from non-EU countries with that of migrant workers from EU member states.
Critical Whiteness Studies and Teaching Nineteenth-Century American Literature
Authors: Murray Hannah Lauren
Published: March 2022

This article argues for implementing a Critical Whiteness studies approach to canonical White literature. After providing an overview of Critical Whiteness studies, I discuss examples from teaching nineteenth-century American literature where Critical Whiteness approaches are fruitful. Alongside widening the selection of what we teach in English departments, incorporating Critical Whiteness studies as part of decolonizing the curriculum reorients how we teach canonical White literature that remains on our syllabi and supports students to recognize continuing discourses of White supremacy today.
The development of inflammatory arthritis following SARS-CoV-2 infection: a systematic review of the literature
Authors: Chaudhry Zaira S , Nellessen Nathan , Reis Cesar , Sharip Akbar
Published: March 2022

Background

Given the widespread impact of COVID-19, it is important to explore any atypical presentations and long-term sequelae associated with this viral infection, including the precipitation of inflammatory arthritis.

Objective

To identify and summarize clinical reports of acute inflammatory arthritis associated with COVID-19.

Methods

A systematic review of the PubMed (MEDLINE), Google Scholar, and Cochrane Central databases through January 31, 2022 was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The inclusion criteria were: human subjects and English language. Data extraction and qualitative synthesis of the demographics, clinical presentations, treatments, and outcomes were performed. Quality assessment was performed using the Joanna-Briggs Institute critical appraisal tools.

Results

A total of 37 articles collectively describing the cases of 54 patients were included. The mean age was 48.2 years (6-78 years). 53.7% of patients were male and 46.3% were female. The onset of articular symptoms varied considerably, and the majority of cases were described as polyarticular (29). The classification of inflammatory arthritis in the included studies was as follows: reactive (19), post-viral (13), new-onset rheumatoid arthritis (RA) (8), crystal-proven arthropathy flare (4), acute viral (2), new-onset psoriatic arthritis (2), flare of preexisting RA (2), and other (4). Arthritis treatment regimens varied but consisted largely of NSAIDs and corticosteroids with most patients experiencing improvement or resolution of their joint symptoms.

Conclusion

There is limited low-level evidence suggesting that patients may develop acute arthritis during or after SARS-CoV-2 infection. This review highlights the need for further research to elucidate the relationship between COVID-19 and the development of inflammatory arthritis.
Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons
Authors: Zhu Peng-Peng , Hung Hui-Fang , Batchenkova Natalia , Nixon-Abell Jonathon , Henderson James , Zheng Pengli , Renvoisé Benoit , Pang Song , Xu C Shan , Saalfeld Stephan , Funke Jan , Xie Yuxiang , Svara Fabian , Hess Harald F , Blackstone Craig
Published: March 2022

Hereditary spastic paraplegias (HSPs) comprise a large group of inherited neurologic disorders affecting the longest corticospinal axons (SPG1–86 plus others), with shared manifestations of lower extremity spasticity and gait impairment. Common autosomal dominant HSPs are caused by mutations in genes encoding the microtubule-severing ATPase spastin (SPAST; SPG4), the membrane-bound GTPase atlastin-1 (ATL1; SPG3A) and the reticulon-like, microtubule-binding protein REEP1 (REEP1; SPG31). These proteins bind one another and function in shaping the tubular endoplasmic reticulum (ER) network. Typically, mouse models of HSPs have mild, later onset phenotypes, possibly reflecting far shorter lengths of their corticospinal axons relative to humans. Here, we have generated a robust, double mutant mouse model of HSP in which atlastin-1 is genetically modified with a K80A knock-in (KI) missense change that abolishes its GTPase activity, whereas its binding partner Reep1 is knocked out. Atl1KI/KI/Reep1−/− mice exhibit early onset and rapidly progressive declines in several motor function tests. Also, ER in mutant corticospinal axons dramatically expands transversely and periodically in a mutation dosage-dependent manner to create a ladder-like appearance, on the basis of reconstructions of focused ion beam-scanning electron microscopy datasets using machine learning-based auto-segmentation. In lockstep with changes in ER morphology, axonal mitochondria are fragmented and proportions of hypophosphorylated neurofilament H and M subunits are dramatically increased in Atl1KI/KI/Reep1−/− spinal cord. Co-occurrence of these findings links ER morphology changes to alterations in mitochondrial morphology and cytoskeletal organization. Atl1KI/KI/Reep1−/− mice represent an early onset rodent HSP model with robust behavioral and cellular readouts for testing novel therapies.
The role of institutions in the early entrepreneurial process
Authors: Bjørnskov Christian , Foss Nicolai J , Xu Tianjiao
Published: March 2022

Much entrepreneurship research has focused on explaining why some countries and regions have more entrepreneurial activity than others, and the role played in this regard by cross-national and cross-regional differences in institutions. However, this stream has not considered entrepreneurship from a process perspective that is, as a set of activities that unfold over different, discernible stages, and has therefore not examined how institutions and policies impact entrepreneurship in different stages of the process. To address this highly policy-relevant gap, we consider the role of institutions for both nascent and realized entrepreneurship, combining cross-country data of entrepreneurial nascency and start-up activity with standard measures of institutions in structural models to obtain estimates of the moderating and mediating effects of policies and institutions of different quality. Analyzing data on early entrepreneurial activities from the Global Entrepreneurship Monitor, data on new firm formation from the World Bank, and Economic Freedom of the World and Doing Business data, we find that a larger government sector leads to lower levels of both measures of entrepreneurship, while legal quality only impacts later-stage entrepreneurship. In general, the main impact of institutions lies in the later stage of entrepreneurship. We suggest that attention allocation by entrepreneurs may help explain these findings.
Searching for Signs: Developing a Handshape Taxonomy Based on Visual Similarity
Authors: Scolari Sergio , Crasborn Onno , Braviano Gilson
Published: March 2022

When designing a sign language dictionary or lexical database, a criterion that needs to be decided on is how to organize handshapes in the search-by-sign interface. Although notation systems do exist for indexing and searching sign entries, dictionaries do not often use them. This study investigates how to classify and order images of handshapes without relying on the alphabetical order of handshape names or phonological parameters. For this purpose, a cluster analysis using three variables was applied, resulting in groups based on visual similarities between handshapes. The objects in the resulting clusters were reordered based on similarity and shape gradation principles, aiming for an optimal organization with regard to Prägnanz. Ultimately, as we expect native signers to rely on the visual features of signs, the taxonomy proposed in this study makes it possible to display handshapes in a way that requires fewer metalinguistic skills to support signers’ search actions.
Age-Specific Prevalence of Anal and Cervical Human Papillomavirus Infection and High-Grade Lesions in 11 177 Women by Human Immunodeficiency Virus Status: A Collaborative Pooled Analysis of 26 Studies
Authors: Wei Feixue , Xia Ningshao , Ocampo Rebeca , Goodman Marc T , Hessol Nancy A , Grinsztejn Beatriz , Ortiz Ana P , Zhao Fanghui , Kojic Erna M , Kaul Rupert , Heard Isabelle , Morhason-Bello Imran O , Moscicki Anna-Barbara , de Pokomandy Alexandra , Palefsky Joel M , Rodrigues Luana L S , Dube Mandishora Racheal S , Ramautarsing Reshmie A , Franceschi Silvia , Godbole Sheela V , Tso Fernanda K , Menezes Lynette J , Lin Chunqing , Clifford Gary M
Published: March 2022

Background

Age-specific data on anal, and corresponding cervical, human papillomavirus (HPV) infection are needed to inform female anal cancer prevention.

Methods

We centrally reanalyzed individual-level data from 26 studies reporting HPV prevalence in paired anal and cervical samples by human immunodeficiency virus (HIV) status and age. For women with HIV (WWH) with anal high-grade squamous intraepithelial lesions or worse (HSIL+), we also investigated concurrent cervical cytopathology.

Results

In HIV-negative women, HPV16 prevalence decreased significantly with age, both at anus (4.3% at 15–24 years to 1.0% at ≥55 years; ptrend = 0.0026) and cervix (7.4% to 1.7%; ptrend < 0.0001). In WWH, HPV16 prevalence decreased with age at cervix (18.3% to 7.2%; ptrend = 0.0035) but not anus (11.5% to 13.9%; ptrend = 0.5412). Given anal HPV16 positivity, concurrent cervical HPV16 positivity also decreased with age, both in HIV-negative women (ptrend = 0.0005) and WWH (ptrend = 0.0166). Among 48 WWH with HPV16-positive anal HSIL+, 27 (56%) were cervical high-risk HPV-positive, including 8 with cervical HPV16, and 5 were cervical HSIL+.

Conclusions

Age-specific shifts in HPV16 prevalence from cervix to anus suggest that HPV infections in the anus persist longer, or occur later in life, than in the cervix, particularly in WWH. This is an important consideration when assessing the utility of cervical screening results to stratify anal cancer risk.
‘Moral’ Determinations in WTO Law: Lessons from the Seals Dispute
Authors: Czapnik Ben
Published: March 2022

This article develops a conceptual framework for understanding the ambiguous concept of public morals in World Trade Organization (WTO) law. It reviews the jurisprudence and literature to suggest there are four main options for operationalizing this concept in a legal test. If WTO adjudicators opt for an empirical approach, they can test whether a certain belief is genuinely held within the regulator’s society (unilateralism) or whether it is shared more broadly by the global community (externalism). If WTO adjudicators prefer a ‘moral’ approach, they can interrogate the content of the regulator’s measure (normative inquiry) or whether it addresses a moral issue (meta-ethical inquiry). Each of these approaches suffers from important weaknesses. WTO adjudicators have taken an equivocal approach: they make amorphous statements alluding to all four approaches but do not settle on a clear public morals legal test. In Seals, they went further by establishing an equivocal characterization of the European Union’s (EU) policy objective, which failed to clarify what the EU’s seal products ban sought to achieve or even whether it was based on objective rational considerations. This use of fallacious reasoning by dispute bodies has important implications for WTO law with respect to indeterminacy, transparency, and judicial activism.
The ‘Aramaic Substrate’ Hypothesis in the Levant Revisited
Authors: Pat-El Naʾama , Stokes Phillip W
Published: March 2022

Aramaic was the lingua franca in the Levant in the millennium prior to the Muslim conquests. The exact nature of the spread of Arabic and the specifics of language shift in the Middle East are not yet well understood. Many scholars assume that Arabic primarily spread in the immediate aftermath of the Muslim conquest. The common opinion is that in the new empire, Arabic was learnt imperfectly by speakers of other languages, and the resulting dialects bear the marks of those underlying languages (Versteegh 2012). Specifically, in the Levant and parts of Mesopotamia that language was Aramaic. Several features of the colloquial dialects of the Levant and Mesopotamia were argued to be a result of an Aramaic substrate. In this paper we concentrate on the alleged Aramaic substrate in the modern Arabic dialects of the Levant, where information about the Arabic dialects is more complete, and draw attention to a number of methodological flaws in the scholarly work supporting this hypothesis. We show that some core ‘Aramaic’ features in Levantine Arabic are unlikely to originate from Aramaic. We further argue that the evidence is not consistent with a rapid and imperfect language shift, which resulted in substrate influence, but rather with a prolonged period of contact between bilingual populations, which resulted in the expected transference of specialized lexical items, but almost no grammatical features.
Association of rs5742612 Polymorphism in the Promoter Region of IGF1 Gene with Nonalcoholic Fatty Liver Disease: A Case-Control Study
Authors: Nobakht Hossein , Mahmoudi Touraj , Rezamand Gholamreza , Tabaeian Seidamir Pasha , Jeddi Golnaz , Asadi Asadollah , Farahani Hamid , Dabiri Reza , Mansour-Ghanaei Fariborz , Kaboli Seyed Alireza , Derakhshan Faramarz , Zali Mohammad Reza
Published: March 2022

Objective

Nonalcoholic fatty liver disease (NAFLD) is an emerging global chronic liver disease encompassing a wide spectrum of disorders ranging from simple steatosis to nonalcoholic steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Considering the strong association between NAFLD and insulin resistance, and the vital role of insulin-like growth factor 1 (IGF1) in IR, we hypothesized that IGF1 gene polymorphism might be associated with NAFLD.

Methods

A total of 302 subjects, including 149 patients with biopsy-proven NAFLD and 153 controls, were enrolled in this case-control study. All the subjects were genotyped for the rs5742612 polymorphism of the IGF1 gene using the polymerase chain reaction-restriction fragment length polymorphism method.

Results

The distribution of IGF1 rs5742612 genotypes and alleles differed significantly between the cases with NAFLD and controls. The IGF1 rs5742612 CC genotype compared with the TT genotype or the TT+TC genotype occurred more frequently in the cases than the controls and the differences remained significant after adjustment for confounding factors such as age and body mass index (P = .011, OR = 2.71, 95%CI = 1.16-5.85; and P = .032, OR = 2.29, 95% CI = 1.10-5.24, respectively).

Conclusion

For the first time, this study uncovered that the IGF1 rs5742612 CC genotype compared with the TT genotype or the TT+TC genotype had a 2.71-fold or 2.29-fold increased risk for NAFLD, respectively.
The GMRT archive atomic gas survey – I. Survey definition, methodology, and initial results from the pilot sample
Authors: Biswas Prerana , Patra Narendra Nath , Roy Nirupam , Rashid Md
Published: March 2022

Interferometric observations of H i in galaxies have played a pivotal role in studies of nearby galaxies. Compared to single-dish observations, they provide resolved distributions of gas in galaxies with unprecedented resolution. Several extensive H i surveys of nearby galaxies have been performed in the past; however, most of them consist of less than 100 galaxies due to individual efforts. On the other hand, the present-day archives of radio telescopes include data for at least several hundred galaxies. To utilize these data sets to their full potential, we construct a sample including all galaxies observed by the Giant Metrewave Radio Telescope in H i. This results in a total of 515 galaxies, the largest sample to date. We intend to analyse all the data uniformly and carry out different exciting science. As a pilot project, we analyse data from 11 galaxies and present the data products in this paper. We further investigate the neutral interstellar medium in these galaxies and extract cold and warm phases using a multi-Gaussian decomposition method. This pilot project assures the quality of the data, which will enable us to perform critical science investigations using the full sample.
Submillimetre galaxies in two massive protoclusters at z = 2.24: witnessing the enrichment of extreme starbursts in the outskirts of HAE density peaks
Authors: Zhang Yuheng , Zheng Xian Zhong , Shi Dong Dong , Gao Yu , Dannerbauer Helmut , An Fang Xia , Shu Xinwen , Gao Zhen-Kai , Wang Wei-Hao , Wang Xin , Cai Zheng , Fan Xiaohui , Fang Min , Pan Zhizheng , Liu Wenhao , Tan Qinghua , Qin Jianbo , Ren Jian , Qiao Man , Wen Run , Liu Shuang
Published: March 2022

Submillimetre galaxies represent a rapid growth phase of both star formation and massive galaxies. Mapping SMGs in galaxy protoclusters provides key insights into where and how these extreme starbursts take place in connections with the assembly of the large-scale structure in the early Universe. We search for SMGs at 850 $\rm{\mu m}$ using JCMT/SCUBA-2 in two massive protoclusters at z = 2.24, BOSS1244 and BOSS1542, and detect 43 and 54 sources with S850 > 4 mJy at the 4σ level within an effective area of 264 arcmin2, respectively. We construct the intrinsic number counts and find that the abundance of SMGs is 2.0 ± 0.3 and 2.1 ± 0.2 times that of the general fields, confirming that BOSS1244 and BOSS1542 contain a higher fraction of dusty galaxies with strongly enhanced star formation. The volume densities of the SMGs are estimated to be ∼15–30 times the average, significantly higher than the overdensity factor (∼6) traced by H α emission-line galaxies (HAEs). More importantly, we discover a prominent offset between the spatial distributions of the two populations in these two protoclusters – SMGs are mostly located around the high-density regions of HAEs, and few are seen inside these regions. This finding may have revealed for the first time the occurrence of violent star formation enhancement in the outskirts of the HAE density peaks, likely driven by the boosting of gas supplies and/or starburst triggering events. Meanwhile, the lack of SMGs inside the most overdense regions at z ∼ 2 implies a transition to the environment disfavouring extreme starbursts.
Multiwavelength campaign on the Super-Eddington NLS1 RX J0134.2-4258 – I. Peculiar X-ray spectra and variability
Authors: Jin Chichuan , Done Chris , Ward Martin , Panessa Francesca , Liu Bo , Liu Heyang
Published: March 2022

We have conducted a new long-term multiwavelength campaign on one of the most super-Eddington narrow-line Seyfert 1s (NLS1s) known, namely RX J0134.2-4258. In this first paper, we report deep simultaneous X-ray observations performed by XMM–Newton and NuSTAR on 2019 December 19, during which RX J0134.2-4258 was fortuitously at one of its lowest X-ray flux states. However, there is a clear rise above 4 keV which implies that the intrinsic source flux may be higher. The X-ray spectra observed between 1996 and 2019 show drastic variability, probably due to complex, variable absorption along the line of sight. Unusually, the soft X-ray excess appears extremely weak in all these spectra, even when the hard X-ray spectrum has a steep slope of Γ ≃ 2.2. We explore the spectral-timing properties of the new (low X-ray flux) and archival (high X-ray flux) XMM–Newton data, fitting their time-average, rms, and lag spectra simultaneously. The variability spectra indicate the presence of a very weak soft X-ray Comptonization component, whose shape is similar to the soft excess in normal super-Eddington NLS1s, but with flux relative to the power law which is lower by more than one order of magnitude. Above 4 keV the low-flux data are dominated by a different component, which lags with respect to the lower energy emission. This is consistent with an origin of reflection or partial covering absorption from low ionization material located within 100 Rg. We interpret this as further indication of the presence of a clumpy disc wind.
RNAspider: a webserver to analyze entanglements in RNA 3D structures
Authors: Luwanski Kamil , Hlushchenko Vladyslav , Popenda Mariusz , Zok Tomasz , Sarzynska Joanna , Martsich Daniil , Szachniuk Marta , Antczak Maciej
Published: March 2022

Advances in experimental and computational techniques enable the exploration of large and complex RNA 3D structures. These, in turn, reveal previously unstudied properties and motifs not characteristic for small molecules with simple architectures. Examples include entanglements of structural elements in RNA molecules and knot-like folds discovered, among others, in the genomes of RNA viruses. Recently, we presented the first classification of entanglements, determined by their topology and the type of entangled structural elements. Here, we introduce RNAspider – a web server to automatically identify, classify, and visualize primary and higher-order entanglements in RNA tertiary structures. The program applies to evaluate RNA 3D models obtained experimentally or by computational prediction. It supports the analysis of uncommon topologies in the pseudoknotted RNA structures. RNAspider is implemented as a publicly available tool with a user-friendly interface and can be freely accessed at https://rnaspider.cs.put.poznan.pl/.
Non-State Actors and Atrocity Crimes
Authors: Ümit Üngör Uğur
Published: March 2022

This chapter examines the involvement of non-state actors (NSAs) in atrocity crimes, focusing on four exemplary cases from four different continental and national contexts, which demonstrate a broad range of atrocity crimes: the Irish Republican Army, the Islamic State, the Lord’s Resistance Army, and the Mexican drug cartel the Zetas. It argues that NSAs in various conflicts can be roughly divided into rebel groups and terrorist groups, and that virtually all have been involved in atrocity crimes, but in different forms, purposes, and contexts. The chapter conceptualizes NSAs and violence, examines the four cases, synthesizes their similarities and differences, and finally concludes, setting an agenda for future research.
The Dionysian Corpus
Authors: Regina Suchla Beate
Published: March 2022

The so-called Corpus Dionysiacum Areopagiticum is a collection of four philosophical-theological treatises and ten Epistulae. These texts were originally written in Greek and come from an author whom the manuscripts of the corpus call Dionysius Areopagita, bishop of Athens. Yet, this apostolic Dionysius is not the true author of these texts; the true author is unknown and must have written these texts between ad 482/485 and 518/528 in or nearby Caesarea. The Corpus stems back to an early critical edition. The editor included variant readings, and added the prologue and the scholia of John of Scythopolis and three smaller texts of John Philoponus to his edition, which strengthened the assumption of Dionysiusʼ authenticity, and which supported the reception, tradition, and transmission of the Dionysian works.
Dionysius in Albertus Magnus and his Student Thomas Aquinas
Authors: Hankey Wayne J.
Published: March 2022

The first part of this essay considers how and why Albert constructed, and Aquinas acquired, Dionysian Peripateticism. The second part examines how Aquinas, for whom the Areopagite remained a quasi-biblical authority, later came to identify him as a Platonist. Aquinas had been initiated by Albert into the congruence of Dionysius and Aristotle when he was his student. Aquinas was his scribe when Albert exposited the Dionysian corpus and began to comment on Aristotle. Albert’s philosophical theology continued to shift so that a Greek apophatic Dionysius, matched with Aristotelian philosophy in the Arabic Neoplatonic–Peripatetic medium in which it was received, provided the system within which his Latin Augustinianism is situated. Aquinas labelled Augustine as a Platonist. Without knowing what he was doing, Albert separated Dionysius from Proclus. In virtue of Moerbeke’s translations of the Greek commentators and the Elements of Theology, when Aquinas compared Proclus with the Liber de causis and the Dionysian corpus, he was able to construct a more complete and accurate history of Platonism. He continued his teacher’s endeavour to save Greek Christian apophatism within the limits set by the condemnation of 1241. Aquinas’ characteristic doctrines used the logical means Albert invented, but his more strongly kataphatic results still preserved the apophaticism, which, for Albert and Aquinas, Dionysius and Aristotle shared.
Dionysius the Areopagite and Nicholas of Cusa
Authors: Kobusch Theo
Published: March 2022

Nicholas of Cusa (Cusanus) attributes three of his most important principles to Dionysius the Areopagite: Complicatio-explicatio, Docta ignorantia, and Non-aliud. According to Nicholas, God is the Complicatio, the unfolding of all being, he is, in an intellectual way, complicating everything and, at the same time, the ‘cancelled’.

Perhaps the most important thing about docta ignorantia is that it is a reflexive knowledge in the Socratic sense. He makes it clear that the scholastic thesis of transcendentalities as the first principles of reality and as the first known reveals a one-sided view of things. For the One, both the transcendental One of the scholastic and the One of the Neoplatonic tradition, appears to be different from the non-one. As it cannot lead to the first origin of everything, because that is not opposed to anything, this is why he calls it the non-other. The non-other is thus that which precedes everything that establishes it, but in such a way that it is at the same time present in it, even if it is contradictorily opposed to it.
Dionysius the Areopagite and the New Testament
Authors: Constas Maximos
Published: March 2022

Modern scholarship has shown only minimal interest in the use of the New Testament in the corpus of writings attributed to Dionysius the Areopagite. The reason for this neglect is the long-standing focus on the relationship of these writings to later Neoplatonism, and in particular to the writings of the Athenian philosopher Proclus. Dionysius was indebted to Neoplatonic philosophy, but he was equally indebted to the sacred Scriptures of Christianity, which he cites more than 1500 times, and which informs his theology much more deeply than has been previously recognized. This chapter argues that two of the major treatises in the corpus, On the Divine Names and On the Celestial Hierarchy, are hermeneutical guides to the biblical language for God and the angels, respectively. Moreover, the rites described in On the Ecclesiastical Hierarchy are based directly on Scripture, while two of the author’s seven reputedly lost works, Theological Outlines and Symbolic Theology, were likewise concerned with questions of biblical revelation and the anthropomorphic forms attributed to God in Scripture. The chapter begins with a general survey of Christian Scripture in the Dionysian corpus, after which it focuses on the New Testament, including the place of the New Testament in Dionysios’ understanding of the Eucharistic synaxis, and the relationship of Dionysian theology to the theology of Paul.
Robert Grosseteste, Translator of Dionysius
Authors: Lawell Declan
Published: March 2022

This survey of the work of Robert Grosseteste as translator of Dionysius demonstrates that he was capable of improving on both the readings and the renderings of his predecessors in Latin. At the same time, this thirteenth-century philosopher, scholar, and Bishop of Lincoln shares with Sarracenus and Aquinas a belief that the summit of perfection for souls is the intellectual or speculative contemplation of God, and therefore adapts his renderings to this theory, in contrast to Thomas Gallus, for whom love supersedes reason in the last stages of the ascent to the ineffable. Grosseteste is notable also for the fact that, after learning Greek in his later years, he produced his own translations into Latin of the works of Dionysius.
Transcriptomic Dissection of Allotetraploid Rapeseed (Brassica napus L.) in Responses to Nitrate and Ammonium Regimes and Functional Analysis of BnaA2.Gln1;4 in Arabidopsis
Authors: Zhou Ting , Wu Pengjia , Yue Caipeng , Huang Jinyong , Zhang Zhenhua , Hua Yingpeng
Published: March 2022

Plant roots acquire nitrogen predominantly as two inorganic forms, nitrate (NO3−) and ammonium (NH4+), to which plants respond differentially. Rapeseed (Brassica napus L.) is an important oil-crop species with very low nitrogen-use efficiency (NUE), the regulatory mechanism of which was elusive due to the vastness and complexity of the rapeseed genome. In this study, a comparative transcriptomic analysis was performed to investigate the differential signatures of nitrogen-starved rapeseed in responses to NO3− and NH4+ treatments and to identify the key genes regulating rapeseed NUE. The two nitrogen sources differentially affected the shoot and root transcriptome profiles, including those of genome-wide nitrogen transporter and transcription factor (TF)-related genes. Differential expression profiling showed that BnaA6.NRT2;1 and BnaA7.AMT1;3 might be the core transporters responsible for efficient NO3− and NH4+ uptake, respectively; the TF genes responsive to inorganic nitrogen, specifically responding to NO3−, and specifically responsive to NH4+ were also identified. The genes which were commonly and most significantly affected by both NO3− and NH4+ treatments were related to glutamine metabolism. Among the glutamine synthetase (GS) family genes, we found BnaA2.Gln1;4, significantly responsive to low-nitrogen conditions and showed higher transcription abundance and GS activity in the leaf veins, flower sepals, root cortex and stele, silique petiole and stem tissues. These characters were significantly different from those of AtGln1;4. The heterologous overexpression of BnaA2.Gln1;4 in Arabidopsis increased plant biomass, NUE, GS activity and total amino acid concentrations under both sufficient- and low-nitrogen conditions. Overall, this study provided novel information about the genes involved in the adaptation to different nitrogen regimes and identified some promising candidate genes for enhancing NUE in rapeseed.
Elevations in adipocytokines and mortality in rheumatoid arthritis
Authors: Baker Joshua F , England Bryant R , George Michael D , Wysham Katherine , Johnson Tate , Kunkel Gary , Sauer Brian , Hamilton Bartlett C , Hunter Carlos D , Duryee Michael J , Monach Paul , Kerr Gail , Reimold Andreas , Xiao Rui , Thiele Geoff M , Mikuls Ted R
Published: March 2022

Objectives

This study assessed whether circulating levels of adiponectin and leptin are associated with higher mortality in patients with RA.

Methods

Participants were adults from the Veterans Affairs RA Registry. Adipokines and inflammatory cytokines were measured as part of a multi-analyte panel on banked serum at enrolment. Dates and causes of death were derived from the Corporate Data Warehouse and the National Death Index. Covariates were derived from medical record, biorepository and registry databases. Multivariable Cox proportional hazard models evaluated associations between biomarkers and all-cause and cause-specific mortality.

Results

A total of 2583 participants were included. Higher adiponectin levels were associated with older age, male sex, white race, lower BMI, autoantibody seropositivity, radiographic damage, longer disease duration, prednisone use and osteoporosis. Higher adiponectin concentrations were also associated with higher levels of inflammatory cytokines but not higher disease activity at enrolment. Leptin was primarily associated with greater BMI and comorbidity. The highest quartile of adiponectin (vs lowest quartile) was associated with higher all-cause mortality [hazard ratio (HR): 1.46 (95% CI: 1.11, 1.93), P = 0.009] and higher cardiovascular mortality [HR: 1.85 (95% CI: 1.24, 2.75), P = 0.003], after accounting for covariates. Higher leptin levels were also associated with greater all-cause and cancer mortality.

Conclusions

Elevations in adipokines are associated with age, BMI, comorbidity and severe disease features in RA and independently predict early death. Associations between adiponectin and inflammatory cytokines support the hypothesis that chronic subclinical inflammation promotes metabolic changes that drive elevations in adipokines and yield adverse health outcomes.