bluuebunny/crossref_metadata_2025_split huggingface dataset:
Race and racism in the founding of the modern world order
Authors: Acharya Amitav 
Published: January 2022

Abstract
While race existed as a cultural marker in earlier history, a mutually-reinforcing link between racism, slavery and empire is a distinct product of western Europe and the US-led world order. Yet, mainstream scholarship on International Relations has obscured the question of race or worse, legitimized its exclusion in discussions of world order-building. At the same time, demand for racial equality from anti-colonial forces presented an alternative and inclusive conception of world order. The first part of this article offers a brief discussion of concepts of race, racism and world order. The next part examines how racist ideas and norms created exclusionary frameworks and approaches of world order, such as the European ‘standard of civilization’ principle. The third part looks at the role of racism in the emergence of the American-led world order, including US President Woodrow Wilson's rejection of the ‘racial equality’ principle in the League of Nations Charter, the privileging of ‘sovereign equality’ over ‘racial equality’ in the UN Charter, and the scant attention given to the link between colonialism and denial of human rights in the Universal Declaration of Human Rights. Yet, anti-colonial leaders and conferences, especially the 1955 Bandung Conference, integrated ‘national sovereignty, racialism and colonialism’, and demanded racial equality as a fundamental human right. The final part cautions against the dangers of complacency and compartmentalizing the study of race and racism, and calls instead for viewing racism as an inter-linked global challenge, hence integral to the emerging research agenda of Global International Relations.
Riemannian optimization model order reduction method for general linear port-Hamiltonian systems
Authors: Li Zi-Xue , Jiang Yao-Lin , Xu Kang-Li 
Published: January 2022

Abstract
This paper presents a Riemannian optimal model order reduction method for general linear stable port-Hamiltonian systems based on the Riemannian trust-region method. We consider the $\mathcal{H}_2$ optimal model order reduction problem of the general linear port-Hamiltonian systems. The problem is formulated as an optimization problem on the product manifold, which is composed of the set of skew symmetric matrices, the manifold of the positive definite matrices, the manifold of the positive semidefinite matrices with fixed rank and the Euclidean space. To solve the optimal problem, the Riemannian geometry of the product manifold is given. Moreover, the Riemannian gradient and the Riemannian Hessian of the objective function are derived. Furthermore, we propose the Riemannian trust-region method for the optimization problem and introduce the truncated conjugate gradient method to solve the trust-region subproblem. Finally, the numerical experiments illustrate the efficiency of the proposed method.
Random Subcomplexes and Betti Numbers of Random Edge Ideals
Authors: Dochtermann Anton , Newman Andrew 
Published: January 2022

Abstract
We study homological properties of random quadratic monomial ideals in a polynomial ring $R = {\mathbb {K}}[x_1, \dots x_n]$, utilizing methods from the Erd̋s–Rényi model of random graphs. Here, for a graph $G \sim G(n, p),$ we consider the coedge ideal $I_G$ generated by monomials corresponding to the missing edges of $G$ and study Betti numbers of $R/I_G$ as $n$ tends to infinity. Our main results involve setting the edge probability $p = p(n)$ so that asymptotically almost surely the Krull dimension of $R/I_G$ is fixed. Under these conditions, we establish various properties regarding the Betti table of $R/I_G$, including sharp bounds on regularity and projective dimension and distribution of nonzero normalized Betti numbers. These results extend work of Erman and Yang who studied such ideals in the context of conjectured phenomena in the nonvanishing of asymptotic syzygies. Along the way, we establish results regarding subcomplexes of random clique complexes as well as notions of higher-dimensional vertex $k$-connectivity that may be of independent interest.
Ceasefires and Civilian Protection Monitoring in Myanmar
Authors: Krause Jana , Kamler Erin 
Published: January 2022

AbstractCivilian ceasefire and civilian protection monitoring are often seen as innovative peacekeeping and protection mechanisms in conflict zones difficult to access for international actors. However, the literature on civilian monitoring and its impact is sparse. In many conflicts, civilians organize to protect themselves. Research into civilian agency and protection has shown that civilian capacity to self-protect and conflict conditions determine whether protective civilian agency can be effective. We analyze whether civilian protection monitoring can positively impact the protection of civilians, focusing on Myanmar, where donors have funded civilian ceasefire monitoring efforts that are inclusive of a strong civilian protection component. We argue that despite failed ceasefires in Myanmar, the nurturing of civilian monitoring networks, that is, supporting civilian capacity, had a positive—albeit limited—impact on civilian protection. Monitors adapted knowledge from international ceasefire monitoring trainings to their reality on the ground and implemented civilian protection monitoring. Yet, conflict conditions seriously limited protection monitoring and posed grave security challenges to monitors and communities. We conclude that in conflict situations where armed actors show little sensitivity to civilian preferences and commitment to respecting human rights, the need for civilian protection is high while the protective potential of civilian monitoring is limited as long as armed groups’ incentives to better protect civilians remain weak.
Streamlining statistical reproducibility: NHLBI ORCHID clinical trial results reproduction
Authors: Serret-Larmande Arnaud , Kaltman Jonathan R , Avillach Paul 
Published: January 2022

Abstract
Reproducibility in medical research has been a long-standing issue. More recently, the COVID-19 pandemic has publicly underlined this fact as the retraction of several studies reached out to general media audiences. A significant number of these retractions occurred after in-depth scrutiny of the methodology and results by the scientific community. Consequently, these retractions have undermined confidence in the peer-review process, which is not considered sufficiently reliable to generate trust in the published results. This partly stems from opacity in published results, the practical implementation of the statistical analysis often remaining undisclosed. We present a workflow that uses a combination of informatics tools to foster statistical reproducibility: an open-source programming language, Jupyter Notebook, cloud-based data repository, and an application programming interface can streamline an analysis and help to kick-start new analyses. We illustrate this principle by (1) reproducing the results of the ORCHID clinical trial, which evaluated the efficacy of hydroxychloroquine in COVID-19 patients, and (2) expanding on the analyses conducted in the original trial by investigating the association of premedication with biological laboratory results. Such workflows will be encouraged for future publications from National Heart, Lung, and Blood Institute-funded studies.
The Ṣiffīn Arbitration Agreement and statecraft in early Islamic political documents
Authors: Zein Ibrahim , El-Wakil Ahmed 
Published: January 2022

Abstract
In this article we study the different recensions of the Ṣiffīn Arbitration Agreement and classify them into six different versions. Despite the differences in length and language among them, we note that these can be traced to a source document. We then highlight the key features and terminology found in the different versions of the Ṣiffīn Arbitration Agreement and observe the striking parallels that they share with the covenants attributed to the Prophet Muḥammad. We argue that the key political actors who composed the Ṣiffīn Arbitration Agreement were in all likelihood part of the same governing and administrative body that had a hand in drafting the Covenants. The startling similarities between the Ṣiffīn Arbitration Agreement and the Covenants therefore set the foundations for a comparative method that will help us better understand statecraft in the study of early Islam’s political documents.
A retrospective study of small-pelvis radiotherapy plus image-guided brachytherapy in stage I–II non-bulky cervical squamous cell carcinoma
Authors: Yoshimoto Yuya , Murata Kazutoshi , Irie Daisuke , Ando Ken , Adachi Akiko , Aoki Hiroshi , Hirakawa Takashi , Noda Shin-ei , Nakano Takashi , Ohno Tatsuya 
Published: January 2022

Abstract
We herein report a retrospective analysis of the efficacy of a combination therapy of pelvic irradiation that excluded the common iliac lymph nodes region and image-guided brachytherapy (IGBT) for non-bulky (≤4 cm) cervical cancer. Thirty-three patients with stage I–II cervical squamous cell carcinoma (≤4 cm) and without pelvic/para-aortic lymphadenopathy who were treated with definitive radiotherapy alone between February 2009 and September 2016 were included. The radiotherapy consisted of CT-based small-pelvis irradiation (whole pelvis minus common iliac lymph node area) of 20 Gy/10 fractions followed by pelvic irradiation with a midline block of 30 Gy/15 fractions and IGBT of 24 Gy/4 fractions (6 Gy/fraction for high-risk [HR] clinical target volume [CTV] D90%). In-room computed tomography (CT) imaging with applicator insertion was used for brachytherapy planning, with physical examinations and diagnostic magnetic resonance imaging (MRI) also being referred to for determination of HR CTV. Over a median follow-up of 60.5 months (range, 7–89), two patients developed distant recurrence and one developed local and distant recurrence. Two patients died from cervical cancer, one from hepatocellular carcinoma and one from non-cancerous disease. The 2/5-year local control (LC), progression-free survival (PFS) and overall survival (OS) rates were 100%/96.7%, 93.8%/90.6% and 93.9%/93.9%, respectively. No pelvic/para-aortic lymph node recurrence was observed. There were no late complications of grade 3 or higher in the small bowel, large bowel/rectum, or bladder. Our results suggest that a combination therapy of IGBT plus small-pelvis irradiation excluding common iliac lymph nodes provides reasonable clinical outcomes and can be a treatment option in non-bulky (≤4 cm) cervical squamous cell carcinoma.
BEBOP II: sensitivity to sub-Saturn circumbinary planets using radial-velocities
Authors: Standing Matthew R , Triaud Amaury H M J , Faria João P , Martin David V , Boisse Isabelle , Correia Alexandre C M , Deleuil Magali , Dransfield Georgina , Gillon Michaël , Hébrard Guillaume , Hellier Coel , Kunovac Vedad , Maxted Pierre F L , Mardling Rosemary , Santerne Alexandre , Sairam Lalitha , Udry. Stéphane 
Published: January 2022

ABSTRACT
BEBOP is a radial-velocity survey that monitors a sample of single-lined eclipsing binaries, in search of circumbinary planets by using high-resolution spectrographs. Here, we describe and test the methods we use to identify planetary signals within the BEBOP data and establish how we quantify our sensitivity to circumbinary planets by producing detection limits. This process is made easier and more robust by using a diffusive nested sampler. In the process of testing our methods, we notice that contrary to popular wisdom, assuming circular orbits in calculating detection limits for a radial-velocity survey provides overoptimistic detection limits by up to $40{{\ \rm per\ cent}}$ in semi-amplitude with implications for all radial-velocity surveys. We perform example analyses using three BEBOP targets from our Southern HARPS survey. We demonstrate for the first time a repeated ability to reach a residual root mean squared scatter of $3\, \rm m\, s^{-1}$ (after removing the binary signal), and find that we are sensitive to circumbinary planets with masses down to that of Neptune and Saturn, for orbital periods up to $1000\, \rm d$.
Is FRB 191001 embedded in a supernova remnant?
Authors: Kundu Esha 
Published: January 2022

ABSTRACT
Fast radio burst (FRB) 191001 is localized at the spiral arm of a highly star-forming galaxy with an observed dispersion measure (DM) of 507 $\mbox{pc cm$^{-3}$}$. Subtracting the contributions of the intergalactic medium and our Milky Way Galaxy from the total DM, one gets an excess of around 200 $\mbox{pc cm$^{-3}$}$, which may have been contributed by the host galaxy of the FRB. It is found in this work that the position of FRB 191001 is consistent with the distribution of supernovae (SNe) in the spiral arm of their parent galaxies. If this event is indeed due to an SN explosion, then, from the analysis of the SN contributions to the excess DM, a core-collapse (CC) channel is preferred over a thermonuclear runaway. For the CC explosion, depending on the density of the surrounding medium, the age of the central engine that powers the radio burst is within a couple of years to a few decades. However, the observed rotation measure of FRB 191001 does not confirm the fact that the radio burst has passed through the remnant of a young SN.
RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics
Authors: Biedenbänder Thomas , de Jesus Vanessa , Schmidt-Dengler Martina , Helm Mark , Corzilius Björn , Fürtig Boris 
Published: January 2022

AbstractA plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA’s secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates.
The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium
Authors: Chan Ngai Ting , Huang Junfeng , Ma Gui , Zeng Hao , Donahue Kristine , Wang Yidan , Li Lingjun , Xu Wei 
Published: January 2022

AbstractCTR9 is the scaffold subunit in polymerase-associated factor complex (PAFc), a multifunctional complex employed in multiple steps of RNA Polymerase II (RNAPII)-mediated transcription. CTR9/PAFc is well known as an evolutionarily conserved elongation factor that regulates gene activation via coupling with histone modifications enzymes. However, little is known about its function to restrain repressive histone markers. Using inducible and stable CTR9 knockdown breast cancer cell lines, we discovered that the H3K27me3 levels are strictly controlled by CTR9. Quantitative profiling of histone modifications revealed a striking increase of H3K27me3 levels upon loss of CTR9. Moreover, loss of CTR9 leads to genome-wide expansion of H3K27me3, as well as increased recruitment of PRC2 on chromatin, which can be reversed by CTR9 restoration. Further, CTR9 depletion triggers a PRC2 subtype switch from the less active PRC2.2, to the more active PRC2.1 with higher methyltransferase activity. As a consequence, CTR9 depletion generates vulnerability that renders breast cancer cells hypersensitive to PRC2 inhibitors. Our findings that CTR9 demarcates PRC2-mediated H3K27me3 levels and genomic distribution provide a unique mechanism that explains the transition from transcriptionally active chromatin states to repressive chromatin states and sheds light on the biological functions of CTR9 in development and cancer.
FILER: a framework for harmonizing and querying large-scale functional genomics knowledge
Authors: Kuksa Pavel P , Leung Yuk Yee , Gangadharan Prabhakaran , Katanic Zivadin , Kleidermacher Lauren , Amlie-Wolf Alexandre , Lee Chien-Yueh , Qu Liming , Greenfest-Allen Emily , Valladares Otto , Wang Li-San 
Published: January 2022

ABSTRACT
Querying massive functional genomic and annotation data collections, linking and summarizing the query results across data sources/data types are important steps in high-throughput genomic and genetic analytical workflows. However, these steps are made difficult by the heterogeneity and breadth of data sources, experimental assays, biological conditions/tissues/cell types and file formats. FILER (FunctIonaL gEnomics Repository) is a framework for querying large-scale genomics knowledge with a large, curated integrated catalog of harmonized functional genomic and annotation data coupled with a scalable genomic search and querying interface. FILER uniquely provides: (i) streamlined access to &gt;50 000 harmonized, annotated genomic datasets across &gt;20 integrated data sources, &gt;1100 tissues/cell types and &gt;20 experimental assays; (ii) a scalable genomic querying interface; and (iii) ability to analyze and annotate user’s experimental data. This rich resource spans &gt;17 billion GRCh37/hg19 and GRCh38/hg38 genomic records. Our benchmark querying 7 × 109 hg19 FILER records shows FILER is highly scalable, with a sub-linear 32-fold increase in querying time when increasing the number of queries 1000-fold from 1000 to 1 000 000 intervals. Together, these features facilitate reproducible research and streamline integrating/querying large-scale genomic data within analyses/workflows. FILER can be deployed on cloud or local servers (https://bitbucket.org/wanglab-upenn/FILER) for integration with custom pipelines and is freely available (https://lisanwanglab.org/FILER).
Matching anticancer compounds and tumor cell lines by neural networks with ranking loss
Authors: Prasse Paul , Iversen Pascal , Lienhard Matthias , Thedinga Kristina , Bauer Chris , Herwig Ralf , Scheffer Tobias 
Published: January 2022

ABSTRACT
Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drug components that are likely to achieve the highest efficacy for a cancer cell line at hand at a therapeutic dose. State of the art drug sensitivity models use regression techniques to predict the inhibitory concentration of a drug for a tumor cell line. This regression objective is not directly aligned with either of these principal goals of drug sensitivity models: We argue that drug sensitivity modeling should be seen as a ranking problem with an optimization criterion that quantifies a drug’s inhibitory capacity for the cancer cell line at hand relative to its toxicity for healthy cells. We derive an extension to the well-established drug sensitivity regression model PaccMann that employs a ranking loss and focuses on the ratio of inhibitory concentration and therapeutic dosage range. We find that the ranking extension significantly enhances the model’s capability to identify the most effective anticancer drugs for unseen tumor cell profiles based in on in-vitro data.
Egg consumption and risks of all-cause and cause-specific mortality: a dose–response meta-analysis of prospective cohort studies
Authors: Yang Peng-Fei , Wang Chun-Rui , Hao Fa-Bao , Peng Yang , Wu Jing-Jing , Sun Wei-Ping , Hu Jie-Jun , Zhong Guo-Chao 
Published: January 2022

AbstractContextCurrent dietary guidelines recommend eggs as a part of a healthy diet. However, whether egg consumption is associated with risk of mortality remains controversial. Moreover, the dose-response association of egg consumption with risk of mortality has not been determined.ObjectiveTo determine the potential dose-response association of egg consumption with risk of mortality in the general population.Data SourcesThe PubMed and Embase databases were searched for publications meeting eligibility criteria through November 2021.Data ExtractionRequired data were extracted by 1 reviewer and then checked for accuracy by another reviewer. A random-effects dose-response meta-regression model was used to calculate the pooled risk estimates. A restricted cubic spline model was used to test nonlinearity. The certainty of evidence was assessed using the GRADE system.Data AnalysisNineteen prospective cohort studies, involving 1 737 893 participants, were included. The pooled hazard ratios for an increase of 1 egg/d were 1.08 (95%CI, 1.01–1.15) for all-cause mortality, 1.07 (95%CI, 0.97–1.18) for cardiovascular disease–caused mortality, and 1.16 (95%CI, 1.04–1.30) for cancer-caused mortality. The certainty of evidence for these observations was rated as very low. Nonlinear dose-response associations were found for egg consumption and all-cause, cardiovascular disease–caused, and cancer-caused mortality. Moreover, the positive association between egg consumption and all-cause mortality was more pronounced in studies with adjustment for blood cholesterol-related covariates than those without (Pinteraction = 0.011).ConclusionsGreater amount of egg consumption confers higher risks of death from all causes, cardiovascular disease, and canc er in a nonlinear dose-response pattern. These findings should be treated with caution and need to be confirmed by future studies.
Comparison of the Clinical Outcomes of Patients With Positive Xpert Carba-R Tests for Carbapenemase-Producing Enterobacterales According to Culture Positivity
Authors: Seo Hyeonji , Lee Jeong-Young , Ryu Seung Hee , Kwak Sun Hee , Kim Eun Ok , Bae Seongman , Kim Min Jae , Chong Yong Pil , Kim Sung-Han , Lee Sang-Oh , Choi Sang-Ho , Sung Heungsup , Kim Mi-Na , Kim Yang Soo , Jung Jiwon 
Published: January 2022

Abstract

Background
We aimed to compare the clinical outcomes of patients with positive Xpert Carba-R assay results for carbapenemase-producing Enterobacterales (CPE) according to CPE culture positivity.

Methods
We retrospectively collected data for patients with positive CPE (positive Xpert Carba-R or culture) who underwent both tests from August 2018 to March 2021 in a 2700-bed tertiary referral hospital in Seoul, South Korea. We compared the clinical outcomes of patients positive for Xpert Carba-R according to whether they were positive (XPCP) or negative (XPCN) for CPE culture.

Results
Of 322 patients with CPE who underwent both Xpert Carba-R and culture, 313 (97%) were positive for Xpert Carba-R for CPE. Of these, 87 (28%) were XPCN, and 226 (72%) were XPCP. XPCN patients were less likely to have a history of previous antibiotic use (75.9% vs 90.3%; P = .001) and to have Klebsiella pneumoniae carbapenemase (21.8% vs 48.9%; P &lt; .001). None of the XPCN patients developed infection from colonization within 6 months, whereas 13.4% (29/216) of the XPCP patients did (P &lt; .001). XPCN patients had lower transmission rates than XPCP patients (3.0% [9/305] vs 6.3% [37/592]; P = .03). There was no significant difference in CPE clearance from positive culture results between XPCN and XPCP patients (40.0% [8/20] vs 26.7% [55/206]; P = .21).

Conclusions
Our study suggests that XPCN patients had lower rates of both infection and transmission than XPCP patients. The Xpert Carba-R assay is clinically useful not only for rapid identification of CPE but also for predicting risks of infection and transmission when performed along with culture.