bluuebunny/crossref_metadata_2025_split huggingface dataset:
Megakaryocyte Cytoskeletal Proteins in Platelet Biogenesis and Diseases
Authors: Mbiandjeu Serge , Balduini Alessandra , Malara Alessandro 
Published: July 2021

AbstractThrombopoiesis governs the formation of blood platelets in bone marrow by converting megakaryocytes into long, branched proplatelets on which individual platelets are assembled. The megakaryocyte cytoskeleton responds to multiple microenvironmental cues, including chemical and mechanical stimuli, sustaining the platelet shedding. During the megakaryocyte's life cycle, cytoskeletal networks organize cell shape and content, connect them physically and biochemically to the bone marrow vascular niche, and enable the release of platelets into the bloodstream. While the basic building blocks of the cytoskeleton have been studied extensively, new sets of cytoskeleton regulators have emerged as critical components of the dynamic protein network that supports platelet production. Understanding how the interaction of individual molecules of the cytoskeleton governs megakaryocyte behavior is essential to improve knowledge of platelet biogenesis and develop new therapeutic strategies for inherited thrombocytopenias caused by alterations in the cytoskeletal genes.
HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction
Authors: Notaro Marco , Frasca Marco , Petrini Alessandro , Gliozzo Jessica , Casiraghi Elena , Robinson Peter N , Valentini Giorgio 
Published: July 2021

Abstract

Motivation
Automated protein function prediction is a complex multi-class, multi-label, structured classification problem in which protein functions are organized in a controlled vocabulary, according to the Gene Ontology (GO). ‘Hierarchy-unaware’ classifiers, also known as ‘flat’ methods, predict GO terms without exploiting the inherent structure of the ontology, potentially violating the True-Path-Rule (TPR) that governs the GO, while ‘hierarchy-aware’ approaches, even if they obey the TPR, do not always show clear improvements with respect to flat methods, or do not scale well when applied to the full GO.

Results
To overcome these limitations, we propose Hierarchical Ensemble Methods for Directed Acyclic Graphs (HEMDAG), a family of highly modular hierarchical ensembles of classifiers, able to build upon any flat method and to provide ‘TPR-safe’ predictions, by leveraging a combination of isotonic regression and TPR learning strategies. Extensive experiments on synthetic and real data across several organisms firstly show that HEMDAG can be used as a general tool to improve the predictions of flat classifiers, and secondly that HEMDAG is competitive versus state-of-the-art hierarchy-aware learning methods proposed in the last CAFA international challenges.

Availability and implementation
Fully tested R code freely available at https://anaconda.org/bioconda/r-hemdag. Tutorial and documentation at https://hemdag.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
A seismic petrophysical classification study of the 2-D SEAM model using semisupervised techniques and detrended attributes
Authors: Dunham Michael W , Malcolm Alison E , Welford J Kim 
Published: July 2021

SUMMARYFor many machine learning problems, there are sufficient data to train a wide range of algorithms. However, many geoscience applications are challenged with limited training data. Seismic petrophysical classification, mapping seismic data to litho-fluid classes, is one of these examples because the training data labels are based on data gathered from wells. Supervised machine learning algorithms are prone to overfitting in scarce training data situations, but semisupervised approaches are designed for these problems because the unlabelled data are also used to inform the learning process. We adopt label propagation (LP) and self-training methods to solve this problem, because they are semisupervised methods that are conceptually simple and easy to implement. The supervised method we consider for comparison is the popular extreme gradient boosting (XGBoost) classifier. The data set we use for our study is one we generate ourselves from the SEG Advanced Modelling (SEAM) Phase 1 model. We first synthesize seismic data from this model and then perform pre-stack seismic inversion to recover seismic attributes. We formulate a classification problem using the seismic attributes as unlabelled data, with training labels from a single well. The benefit of this being a synthetic problem is that we have full control and the ability to quantitatively assess the machine learning predictions. Our initial results reveal that the inherent depth-dependent background trends of the input attributes produce artefacts in each of the machine learning predictions. We address this problem by using a simple median filter to remove these background trends. The predictions using the detrended inputs improve the performance for all three algorithms, in some cases on the order of 10 to 20 per cent. XGBoost and LP perform similarly in some situations, but our results indicate that XGBoost is rather unstable depending on the attributes used. However, LP coupled with self-training outperforms XGBoost by up to 10 per cent in some instances. Through this synthetic study, our results support the premise that semisupervised algorithms can provide more robust, generalized predictions than supervised techniques in minimal training data scenarios.
The Realization Problem for Dilation Surfaces
Authors: Wang Jane 
Published: July 2021

Abstract
Dilation surfaces, or twisted quadratic differentials, are variants of translation surfaces. In this paper, we study the question of what elements or subgroups of the mapping class group can be realized as affine automorphisms of dilation surfaces. We show that dilation surfaces can have exotic Dehn twists in their affine automorphism groups and will establish that only certain types of mapping class group elements can arise as affine automorphisms of dilation surfaces. We also generalize a construction of Thurston that constructs a translation surface from a pair of filling multicurves to dilation surfaces. This construction will give us dilation surfaces that realize a pair of Dehn multitwists in their affine automorphism groups.
Addressing overestimation and insensitivity in the 85% target for average bed occupancy
Authors: Pratt Adrian C , Wood Richard M 
Published: July 2021

Abstract

Background
An established finding suggests that, in balancing variability in patient demand and length of stay, an average bed occupancy of 85% should be targeted for acute hospital wards. The notion is that higher figures result in excessive capacity breaches, while anything lower fails to make economic use of available resources. Although concerns have previously been raised regarding the generic use of the 85% target, there has been little research interest into alternative derivations that may better represent the diverse range of conditions that exist in practice.

Objective
To quantify a continuum of average occupancy targets for use within the acute hospital setting.

Methods
Computer simulation is used to model the process of acute patient admission and discharge. Patient arrivals are assumed to be independent of one another (i.e. random) with length of stay distributions obtained through fitting to patient-level data from all of England.

Results
Target average occupancy increases with ward size, ranging from 45% to 79% for a relatively small 15-bed ward to 64–84% for a relatively large 50-bed ward. Regarding ward speciality, for a typical 25-bed ward, values range from 57–58% for Gynaecology to 67–74% for Adult Mental Health. These increase to 62–63% and 75–82%, respectively, if the tolerance on breaching capacity is relaxed from 2% to 5% of days per year.

Conclusion
An unconditional 85% target serves as an overestimate across the vast majority of settings that typically exist in practice. Hospital planners should consider ward size, speciality and capacity-breach tolerance in determining a more sensitive assessment of bed occupancy requirements. This study provides hospital planners with a means to reliably assess the operational performance and readily calculate optimal capacity requirements.
Reception and practice of diplomacy in modern Japan: power, interests, and norms
Authors: Sasaki Yuichi 
Published: July 2021

Abstract
This article re-examines Japan’s entry into international society, focusing on leading Japanese diplomats. It has been believed that Meiji leaders’ interpretation of international society and diplomacy was characterized by power-political and zero-sum thinking, and they took a realistic approach in an imperialistic system. However, the present article demonstrates that Japanese diplomacy in and after the 1890s was basically guided by interest-oriented and non–zero-sum thinking which was closely tied to the international order. Leading Japanese diplomats, who learned from their experiences in diplomacy with Western countries, understood the significance of norms as well as the importance of military power, and pursued Japan’s national interests within the rules and norms of international society. These findings offer a new image of the principles of modern Japanese diplomacy, the mechanisms of Japanese imperial expansion, and the process of the spread of norms in international society.
Driving antibiotic stewardship awareness through the minibus-taxi community across the Tshwane District, South Africa—a baseline evaluation
Authors: Mokoena Tumelo T W , Schellack Natalie , Brink Adrian J 
Published: July 2021

Abstract

Background
The minibus-taxi community plays an integral role within society, and for years this community has been neglected. Of late, studies on minibus-taxi operators’ health and their perceptions of HIV have emerged. Antibiotic resistance is a global problem and to help curb its spread studies have looked into the knowledge, attitude and perceptions amongst students and healthcare professionals, and yet little to nothing is known about the minibus-taxi community.

Objectives
To assess the knowledge and understanding of the minibus-taxi community on antibiotics and antibiotic resistance, and document indigenous antibiotic terminology used across the Tshwane District in Gauteng, South Africa.

Methods
A semi-structured questionnaire was adopted from WHO, translated into commonly spoken languages and administered to 83 minibus-taxi community members: 27 minibus-taxi operators and 56 commuters. A convenience sampling method was utilized in selecting the minibus-taxi ranks and routes. The questionnaire was later adapted to the minibus-taxi community’s busy lifestyle and a section added to document antibiotic terms.

Results
Seventy-one percent (n = 59) of the participants knew the importance of taking antibiotics as directed, while 64% (n = 53) believed it’s correct to share antibiotics. Seventy-five percent (n = 62) thought antibiotic resistance occurred in the human body. One misconception noted was that the minibus-taxi community thought antibiotics treated cold/flu and fever. Over 80% of the community were unfamiliar with antibiotic terminology.

Conclusions
Several misconceptions were documented amongst the minibus-taxi community and, whilst highlighting the linguistic barriers for the term antibiotic resistance, we identified several enablers for public awareness and empowerment. Further studies are required to define appropriate indigenous terms for future educational antibiotic campaigns.
Characterization and Phylogenetic Analysis of the Mitochondrial Genome Sequence ofNisia fuliginosa(Hemiptera: Fulgoroidea: Meenoplidae)
Authors: Lv Sha-Sha , Zhang Yu-Jie , Gong Nian , Chen Xiang-Sheng 
Published: July 2021

AbstractWe explored characterization of the mitochondrial genome (mitogenome or mtGenome) and phylogenetic analysis between 32 Fulgoroid species by sequencing and analyzing the mitogenome of Nisia fuliginosa Yang and Hu, 1985 (Hemiptera: Fulgoroidea: Meenoplidae), thereby making it the first determined mitogenome from the family Meenoplidae. The mitogenome was found to be 15,754 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, two ribosomal RNA genes (rRNAs), and a control region. All PCGs started with typical ATN codons, except for nad1, which used GTG as the start codon. Canonical TAA termination codons were found in 10 PCGs and the remaining three genes (cox2, nad6, and nad1) had incomplete stop codons T. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnC, trnV, and trnS1. Additionally, we compared the AT and GC skews of 13 PCGs of 32 Fulgoroidea mitogenomes, on the L-strand, the AT and GC skews were negative and positive, respectively. However, on the H-strand, the AT skew could be positive or negative and the GC skew was always negative. Phylogenetic results showed that the eight families of Fulgoroidea were divided into two large groups. Delphacidae formed a monophyletic group sister to a clade comprising Meenoplidae and other six families (Fulgoridae, Ricaniidae, Flatidae, Issidae, Caliscelidae, and Achilidae). Meenoplidae was located near the clade of Delphacidae, and Fulgoridae was located near the clade of Meenoplidae. Furthermore, Caliscelidae, Issidae, Ricaniidae, and Flatidae are closely related and they collectively formed a sister group to Achilidae.
Validity of skeletal muscle mass index measurements for assessing sarcopenia in patients with gynecological cancer
Authors: Yamada Ryutaro , Tsuruta Tomohiko , Todo Yukiharu , Kurosu Hiroyuki , Minowa Kaoru , Minobe Shinichiro , Matsumiya Hiroko , Kato Hidenori , Mori Yoichi , Osanai Toshihisa 
Published: July 2021

Abstract

Background
The current study investigated an optimal method for using CT scan in detection of low skeletal muscle mass quantity (SMQ).

Methods
In total, 82 consecutive patients with gynecological cancers were examined using computed tomography (CT) and dual-energy X-ray absorptiometry (DEXA) before treatment. Low SMQ was defined as a DEXA-based skeletal muscle mass index (SMI) of &lt;5.40 kg/m2. Furthermore, CT-based SMI values were measured by six evaluators, and each evaluator measured SMI values two times for each subject. The first SMI value and the average SMI value were used for analyses. Receiver operating characteristic (ROC) analyses were performed to evaluate the performance of CT-based SMI measurements for detecting low SMQ. Interobserver agreement was assessed using the intraclass correlation coefficient (ICC).

Results
In total, 23 patients (28.0%) were diagnosed with low skeletal muscle mass. All areas under the curve (AUC) values from twelve (six evaluators × two measurements) ROC curves were within the range of 0.8–0.9. AUC values based on a single measurement and those based on two measurements were almost the same. The ICC was 0.828 (95% CI 0.777–0.874, P &lt; 0.001) when using a single measurement value and increased to 0.959 (95% CI 0.944–0.971, P &lt; 0.001) when using the average of the two measurements.

Conclusions
A single measurement CT-based SMI efficiently identified patients with low SMQ in a daily clinical setting. The reliability of SMI measurements might be further improved by using a mean value of two measurements compared with the use of a single measurement value.
Carbon flux around leaf-cytosolic glyceraldehyde-3-phosphate dehydrogenase introduces a 13C signal in plant glucose
Authors: Wieloch Thomas , Werner Roland Anton , Schleucher Jürgen 
Published: July 2021

Abstract
Within the plant and Earth sciences, stable isotope analysis is a versatile tool conveying information (inter alia) about plant physiological and paleoclimate variability across scales. Here, we identify a 13C signal (i.e. systematic 13C/12C variation) at tree-ring glucose C-4 and report an experimentally testable theory on its origin. We propose the signal is introduced by glyceraldehyde-3-phosphate dehydrogenases in the cytosol of leaves. It conveys two kinds of (potentially convoluted) information: (i) commitment of glyceraldehyde 3-phosphate to 3-phosphoglycerate versus fructose 1,6-bisphosphate metabolism; and (ii) the contribution of non-phosphorylating versus phosphorylating glyceraldehyde-3-phosphate dehydrogenase to catalysing the glyceraldehyde 3-phosphate to 3-phosphoglycerate forward reaction of glycolysis. The theory is supported by 13C fractionation modelling. Modelling results provide the first evidence in support of the cytosolic oxidation–reduction (COR) cycle, a carbon-neutral mechanism supplying NADPH at the expense of ATP and NADH, which may help to maintain leaf-cytosolic redox balances. In line with expectations related to COR cycling, we found a positive correlation between air vapour pressure deficit and 13C discrimination at glucose C-4. Overall, 13C-4 signal analysis may enable an improved understanding of leaf carbon and energy metabolism.
Mesophyll conductance in two cultivars of wheat grown in glacial to super-elevated CO2 concentrations
Authors: Jahan Eisrat , Thomson Peter C , Tissue David T 
Published: July 2021

Abstract
Mesophyll conductance (gm) is an important factor limiting photosynthesis. However, gm response to long-term growth in variable [CO2] is not well understood, particularly in crop plants. Here, we grew two cultivars of wheat (Halberd and Cranbrook), known to differ in gm under current environmental conditions, in four [CO2] treatments: glacial (206 μmol mol−1), pre-industrial (344 μmol mol−1), current ambient (489 μmol mol−1), and super-elevated (1085 μmol mol−1), and two water treatments (well-watered and moderate water limitation), to develop an evolutionary and future climate perspective on gm control of photosynthesis and water-use efficiency (WUE). In the two wheat genotypes, gm increased with rising [CO2] from glacial to ambient [CO2], but declined at super-elevated [CO2]. The responses of gm to different growth [CO2] also depend on water stress; however, the specific mechanism of gm response to [CO2] remains unclear. Although gm and gm/gsc (mesophyll conductance/stomatal conductance) were strongly associated with the variability of photosynthetic rates (A) and WUE, we found that plants with higher gm may increase A without increasing gsc, which increased WUE. These results may be useful to inform plant breeding programmes and cultivar selection for Australian wheat under future environmental conditions.
‘United through our values’? Expressing unity through value-talk after terrorism in France and Norway
Authors: Ezzati Rojan Tordhol 
Published: July 2021

AbstractIn the immediate aftermath of terrorism, references to ‘our values’ as a source of unity become a substantial part of public discourse. Leaders, the media, and the public emphasize ‘values’ to express that ‘we’ are united across ethnic, religious, and political differences. This article comparatively examines formulations of ‘we’, ‘us’, and ‘them’ with reference to ‘values’ (i.e. value-talk) after terror attacks in France (November 2015) and Norway (July 2011). To access speech, events, and symbols as they were unfolding, the analysis draws on the first week of national television news following these attacks. Whereas the terrorists in France were self-proclaimers of an Islamic State, the terrorist in Norway was a self-proclaimed defender of the Christian civilization. The central place of a value-based unity—regardless of the terrorists’ ethnicity and motivations—contrasts with the otherwise common idea expressed in public debate that ‘values’ embody a fundamental divide between ‘natives’ and immigrant populations. This article argues that scholarship on values, in migration studies and beyond, reifies the much-repeated assumption in public debate that there is a value-based divide between groups of people. By examining expressions of unity in contexts of conflict, the analysis untangles the dynamic and flexible ‘groupness’ articulated through value-talk. Analytical attention to this variability, I argue, better reflects the widespread attention to cultural complexities in migration studies. Through the study of value-talk in the immediate aftermath of terrorism, the article explores some of the dimensions of how and when unity is mobilized in societies marked by migration-related diversity.
High eccentricities and high masses characterize gravitational-wave captures in galactic nuclei as seen by Earth-based detectors
Authors: Gondán László , Kocsis Bence 
Published: July 2021

ABSTRACT
The emission of gravitational waves (GWs) during single–single close encounters in galactic nuclei (GNs) leads to the formation and rapid merger of highly eccentric stellar-mass black hole (BH) binaries. The distinct distribution of physical parameters makes it possible to statistically distinguish this source population from others. Previous studies determined the expected binary parameter distribution for this source population in single GNs. Here, we take into account the effects of dynamical friction, post-Newtonian corrections, and observational bias to determine the detected sources’ parameter distributions from all GNs in the Universe. We find that the total binary mass distribution of detected mergers is strongly tilted towards higher masses. The distribution of initial peak GW frequency is remarkably high between 1 and 70 Hz, $\sim \! 50{{\ \rm per\ cent}}$ of GW capture sources form above 10 Hz with e ≳ 0.95. The eccentricity when first entering the LIGO/Virgo/KAGRA band satisfies $e_{\rm 10\, Hz}\gt 0.1$ for over $92{{\ \rm per\ cent}}$ of sources and $e_{\rm 10\, Hz}\gt 0.8$ for more than half of the sources. At the point when the pericentre reaches 10GM/c2 the eccentricity satisfies e10M &gt; 0.1 for over $\sim \! 70{{\ \rm per\ cent}}$ of the sources, making single–single GW capture events in GNs the most eccentric source population among the currently known stellar-mass binary BH merger channels in our Universe. We identify correlations between total mass, mass ratio, source detection distance, and eccentricities $e_{\rm 10\, Hz}$ and e10M. The recently measured source parameters of GW190521 lie close to the peak of the theoretical distributions and the estimated escape speed of the host environment is $\sim \! 7.5\times 10^3\!-\!1.2\times 10^4\, \rm km\, s^{-1}$, making this source a candidate for this astrophysical merger channel.
Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data
Authors: Nakajima Natsu , Hayashi Tomoatsu , Fujiki Katsunori , Shirahige Katsuhiko , Akiyama Tetsu , Akutsu Tatsuya , Nakato Ryuichiro 
Published: July 2021

AbstractSingle-cell RNA-seq (scRNA-seq) can be used to characterize cellular heterogeneity in thousands of cells. The reconstruction of a gene network based on coexpression patterns is a fundamental task in scRNA-seq analyses, and the mutual exclusivity of gene expression can be critical for understanding such heterogeneity. Here, we propose an approach for detecting communities from a genetic network constructed on the basis of coexpression properties. The community-based comparison of multiple coexpression networks enables the identification of functionally related gene clusters that cannot be fully captured through differential gene expression-based analysis. We also developed a novel metric referred to as the exclusively expressed index (EEI) that identifies mutually exclusive gene pairs from sparse scRNA-seq data. EEI quantifies and ranks the exclusive expression levels of all gene pairs from binary expression patterns while maintaining robustness against a low sequencing depth. We applied our methods to glioblastoma scRNA-seq data and found that gene communities were partially conserved after serum stimulation despite a considerable number of differentially expressed genes. We also demonstrate that the identification of mutually exclusive gene sets with EEI can improve the sensitivity of capturing cellular heterogeneity. Our methods complement existing approaches and provide new biological insights, even for a large, sparse dataset, in the single-cell analysis field.