bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Picornaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens
Authors: Andino Raul , Kirkegaard Karla , Macadam Andrew , Racaniello Vincent R , Rosenfeld Amy B 
Published: October 2023

Abstract
Picornaviruses are nonenveloped particles with a single-stranded RNA genome of positive polarity. This virus family includes poliovirus, hepatitis A virus, rhinoviruses, and Coxsackieviruses. Picornaviruses are common human pathogens, and infection can result in a spectrum of serious illnesses, including acute flaccid myelitis, severe respiratory complications, and hand-foot-mouth disease. Despite research on poliovirus establishing many fundamental principles of RNA virus biology and the first transgenic animal model of disease for infection by a human virus, picornaviruses are understudied. Existing knowledge gaps include, identification of molecules required for virus entry, understanding cellular and humoral immune responses elicited during virus infection, and establishment of immune-competent animal models of virus pathogenesis. Such knowledge is necessary for development of pan-picornavirus countermeasures. Defining enterovirus A71 and D68, human rhinovirus C, and echoviruses 29 as prototype pathogens of this virus family may provide insight into picornavirus biology needed to establish public health strategies necessary for pandemic preparedness.
Viral Prototypes for Pandemic Preparedness: The Road Ahead
Authors: Morabito Kaitlyn M , Cassetti M Cristina , DeRocco Amanda J , Deschamps Anne M , Pierson Theodore C 
Published: October 2023

AbstractThe coronavirus disease 2019 (COVID-19) pandemic demonstrated how rapidly vaccines and monoclonal antibodies (mAbs) could be deployed when the field is prepared to respond to a novel virus, serving as proof of concept that the prototype pathogen approach is feasible. This success was built upon decades of foundational research, including the characterization of protective antigens and coronavirus immunity leading to the development and validation of a generalizable vaccine approach for multiple coronaviruses. For other virus families of pandemic concern, the field is less prepared. The articles in this special issue have highlighted research gaps that need to be addressed to accelerate the development of effective vaccines and mAbs, to identify generalizable vaccine and mAb strategies, and to increase preparedness against other pandemic threats. Successful implementation of the prototype pathogen approach will require a systematic, multidisciplinary, coordinated approach with expertise and crosstalk among researchers of different virus families.
Filoviruses: Scientific Gaps and Prototype Pathogen Recommendation
Authors: Dupuy Lesley C , Spiropoulou Christina F , Towner Jonathan S , Spengler Jessica R , Sullivan Nancy J , Montgomery Joel M 
Published: October 2023

Abstract
Viruses in the family Filoviridae, including the commonly known Ebola (EBOV) and Marburg (MARV) viruses, can cause severe hemorrhagic fever in humans and nonhuman primates. Sporadic outbreaks of filovirus disease occur in sub-Saharan Africa with reported case fatality rates ranging from 25% to 90%. The high mortality and increasing frequency and magnitude of recent outbreaks along with the increased potential for spread from rural to urban areas highlight the importance of pandemic preparedness for these viruses. Despite their designation as high-priority pathogens, numerous scientific gaps exist in critical areas. In this review, these gaps and an assessment of potential prototype pathogen candidates are presented for this important virus family.
Shaping transverse-tubules: central mechanisms that play a role in the cytosol zoning for muscle contraction
Authors: Kawaguchi Kohei , Fujita Naonobu 
Published: October 2023

Abstract
A transverse-tubule (T-tubule) is an invagination of the plasma membrane penetrating deep into muscle cells. An extensive membrane network of T-tubules is crucial for rapid and synchronized signal transmission from the cell surface to the entire sarcoplasmic reticulum for Ca2+ release, leading to muscle contraction. T-tubules are also indispensable for the formation and positioning of other muscle organelles. Their structure and physiological roles are relatively well established; however, the mechanisms shaping T-tubules require further elucidation. Centronuclear myopathy (CNM), an inherited muscular disorder, accompanies structural defects in T-tubules. Membrane traffic-related genes, including MTM1 (Myotubularin 1), DNM2 (Dynamin 2), and BIN1 (Bridging Integrator-1), were identified as causative genes of CNM. In addition, causative genes for other muscle diseases are also reported to be involved in the formation and maintenance of T-tubules. This review summarizes current knowledge on the mechanisms of how T-tubule formation and maintenance is regulated.
Does Mills’ epistemology suggest a hermeneutic injustice of White Afroscepticism?
Authors: Fraser-Burgess Sheron 
Published: October 2023

Abstract
Charles Mills posits an epistemology of ignorance that underwrites the complicity of Whites, or people of Western European descent, as signatories of the racial contract. There is prevailing discourse about the complicity of White persons in perpetuating racism and whether they can experience epistemic injustice. In this paper, the claim to hermeneutical injustice, in particular, makes a further assertion that moral blameworthiness is mitigated for a subcategory of White Americans because of being socialized into a White-dominant culture of caste-based Afroscepticism. I argue, based on Peirce's conceptualization of doubt, as against Descartes, that Afroscepticism is a totalizing belief system predicated on a racial group-based social epistemology and maintains a settled stance of questioning the commensurate citizenship of Blacks or American descendants of slaves. These perceived social costs warrant educational interventions that can dismantle its reasoning architecture. White Afroscepticism poses a barrier to the teacher’s efforts to cultivate the democratic habitus in students; however, educator preparation that takes its existence into account can build on the standard classroom practices of critical social justice that promote equity, critical multicultural education, and critical thinking.
The paradox of epistemic ability profiling
Authors: Taylor Ashley 
Published: October 2023

Abstract
Intellectually disabled students face particular barriers to epistemic participation within schooling contexts. While negative forms of bias against intellectually disabled people play an important role in creating these barriers, this paper suggests that it is often because of the best intentions of educators and peers that intellectually disabled students are vulnerable to forms of epistemic injustice. The author outlines a form of epistemic injustice that operates through an educational practice widely regarded as serving the interests of intellectually disabled students. ‘Epistemic ability profiling’ involves the identification of the epistemic consequences of disability in the service of promoting students’ best interests, or to create opportunities for their participation in epistemic communities. Epistemic ability profiling is a double-edged sword: it is important that educators understand and attend to the ways in which differences in ability shape students’ epistemic agency, and yet epistemic ability profiling operates against the background of a conceptually ableist conceptual terrain. As a result, epistemic ability profiling runs the risk of legitimating structural forms of injustice against intellectually disabled people.
Two cases of Rapunzel syndrome in adult males
Authors: Moolamannil Mathew C , Ahmed Hanad , Devecseri Gertrud , Malam Yogeshkumar , Wilde Max , Chattopadhyay Dipankar 
Published: October 2023

Abstract
Trichobezoar are foreign bodies formed from undigested hairs that accumulate in the gastrointestinal tract and cause obstruction. Trichobezoar are usually found in the stomach but when the tail of the bezoar extends into the small intestine it is referred to as Rapunzel syndrome. Patients are usually females and have a history of psychiatric illness. However, in this study, we present two cases of Rapunzel syndrome in adult male patients that were managed with surgery. Trichobezoar should be considered in all patients with a history of psychiatric illness presenting with abdominal symptoms regardless of gender.
A case of intussusception secondary to a metastatic malignant melanoma from the nasal cavity
Authors: Ng Yuki J , Loc Leong J , Bun Kuek S , Mushtaq Sohail 
Published: October 2023

Abstract
About 5% of all intussusception are found in adults, up to 90% of these have an anatomical lesion with ~50% of them are malignant. Malignant melanoma commonly metastasizes to the small bowel; however, melanoma causing intussusception is rare. We describe a 57-year-old lady with a history of surgically treated malignant melanoma in her nasal cavity who came with an ambiguous intestinal obstruction. Computed tomography reported ileal-ileal intussusception, which was surgically removed via emergency open laparotomy and bowel resection. Intraoperatively the intussusception was 110 cm from the ileo-cecal valve with multiple palpable lymph nodes. Histopathology confirmed the origin as malignant melanoma with lymphovascular invasion. Our literature review found the mean prevalence of intussusception secondary to melanoma was 6.924% (SD ± 5.155). Minimally invasive techniques are reported non-inferior to open laparotomy. We argue that the open technique can provide informed decisions for adequate resection of affected bowel and lymphatic drainage.
Arkenstone – I. A novel method for robustly capturing high specific energy outflows in cosmological simulations
Authors: Smith Matthew C , Fielding Drummond B , Bryan Greg L , Kim Chang-Goo , Ostriker Eve C , Somerville Rachel S , Stern Jonathan , Su Kung-Yi , Weinberger Rainer , Hu Chia-Yu , Forbes John C , Hernquist Lars , Burkhart Blakesley , Li Yuan 
Published: October 2023

ABSTRACT
Arkenstone is a new model for multiphase, stellar feedback-driven galactic winds designed for inclusion in coarse resolution cosmological simulations. In this first paper of a series, we describe the features that allow Arkenstone to properly treat high specific energy wind components and demonstrate them using idealized non-cosmological simulations of a galaxy with a realistic circumgalactic medium (CGM), using the arepo code. Hot, fast gas phases with low mass loadings are predicted to dominate the energy content of multiphase outflows. In order to treat the huge dynamic range of spatial scales involved in cosmological galaxy formation at feasible computational expense, cosmological volume simulations typically employ a Lagrangian code or else use adaptive mesh refinement with a quasi-Lagrangian refinement strategy. However, it is difficult to inject a high specific energy wind in a Lagrangian scheme without incurring artificial burstiness. Additionally, the low densities inherent to this type of flow result in poor spatial resolution. Arkenstone addresses these issues with a novel scheme for coupling energy into the transition region between the interstellar medium (ISM) and the CGM, while also providing refinement at the base of the wind. Without our improvements, we show that poor spatial resolution near the sonic point of a hot, fast outflow leads to an underestimation of gas acceleration as the wind propagates. We explore the different mechanisms by which low and high specific energy winds can regulate the star formation rate of galaxies. In future work, we will demonstrate other aspects of the Arkenstone model.
CNN photometric redshifts in the SDSS at r ≤ 20
Authors: Treyer M , Ait Ouahmed R , Pasquet J , Arnouts S , Bertin E , Fouchez D 
Published: October 2023

ABSTRACT
We release photometric redshifts, reaching ∼0.7, for ∼14M galaxies at r ≤ 20 in the 11 500 deg2 of the SDSS north and south Galactic caps. These estimates were inferred from a convolution neural network (CNN) trained on ugriz stamp images of galaxies labelled with a spectroscopic redshift from the SDSS, GAMA, and BOSS surveys. Representative training sets of ∼370k galaxies were constructed from the much larger combined spectroscopic data to limit biases, particularly those arising from the over-representation of luminous red galaxies. The CNN outputs a redshift classification that offers all the benefits of a well-behaved PDF, with a width efficiently signalling unreliable estimates due to poor photometry or stellar sources. The dispersion, mean bias, and rate of catastrophic failures of the median point estimate are of order σMAD = 0.014, &lt;Δznorm&gt;=0.0015, $\eta (|\Delta z_{\rm norm}|\gt 0.05)=4{{\, \rm per\ cent}}$ on a representative test sample at r &lt; 19.8, outperforming currently published estimates. The distributions in narrow intervals of magnitudes of the redshifts inferred for the photometric sample are in good agreement with the results of tomographic analyses. The inferred redshifts also match the photometric redshifts of the redMaPPer galaxy clusters for the probable cluster members.
A Kpc-scale radio polarization study of PG BL Lacs with the uGMRT
Authors: Baghel Janhavi , Kharb P , Hovatta T , Gulati S , Lindfors E , S. Silpa 
Published: October 2023

ABSTRACT
We present here uGMRT band 4 (∼650 MHz) polarization images of 8 BL Lac objects belonging to the Palomar-Green (PG) ‘blazar’ sample. A large fraction of the sources ($\sim 63~{{\ \rm per\ cent}}$) reveal core-halo radio structures with most of the polarization detected in the inner core-jet regions. PG1101 + 385 and PG2254 + 075 exhibit a ‘spine-sheath structure’ in polarization. The core-halo and ‘spine-sheath’ structures are consistent with the Unified Scheme suggestion that BL Lacs are the pole-on beamed counterparts of Fanaroff–Riley (FR) type I radio galaxies. PG1418 + 546 and PG0851 + 203 (OJ287) show the presence of terminal hotspots similar to FR type II radio galaxies. They were also found to be low-spectrally peaked BL Lacs, supportive of the ‘blazar envelope’ scenario for BL Lacs and quasars. Fractional polarization ranges from 1 to 13 per cent in the cores and 2 to 26 per cent in the inner jets/lobes of the sample BL Lacs. Compared to the varied radio morphology of quasars from the PG ‘blazar’ sample, the BL Lacs appear to be less diverse. A comparison of the inferred core magnetic (B-) field structures on arcsec- (kpc-) scales w.r.t. the Very Long Baseline Interferometry jet direction does not reveal any preferred orientation, suggesting that if large-scale ordered B-fields exist, they do so on scales smaller than probed by the current observations. However, the presence of polarized emission on arcsec-scales suggests that any mixing of thermal plasma with the synchrotron emitting plasma is insufficient to fully depolarize the emission via the internal depolarization process.
CAPOS: the bulge Cluster APOgee Survey IV elemental abundances of the bulge globular cluster NGC 6558
Authors: González-Díaz Danilo , Fernández-Trincado José G , Villanova Sandro , Geisler Doug , Barbuy Beatriz , Minniti Dante , Beers Timothy C , Moni Bidin Christian , Mauro Francesco , Muñoz Cesar , Tang Baitian , Soto Mario , Monachesi Antonela , Lane Richard R , Frelijj Heinz 
Published: October 2023

ABSTRACT
This study presents the results concerning six red giant stars members of the globular cluster NGC 6558. Our analysis utilized high-resolution near-infrared spectra obtained through the CAPOS initiative (the APOgee Survey of Clusters in the Galactic Bulge), which focuses on surveying clusters within the Galactic Bulge, as a component of the Apache Point Observatory Galactic Evolution Experiment II survey (APOGEE-2). We employ the Brussels Automatic Code for Characterizing High accUracy Spectra (BACCHUS) code to provide line-by-line elemental-abundances for Fe-peak (Fe, Ni), α-(O, Mg, Si, Ca, Ti), light-(C, N), odd-Z (Al), and the s-process element (Ce) for the four stars with high-signal-to-noise ratios. This is the first reliable measure of the CNO abundances for NGC 6558. Our analysis yields a mean metallicity for NGC 6558 of 〈[Fe/H]〉 = −1.15 ± 0.08, with no evidence for a metallicity spread. We find a Solar Ni abundance, 〈[Ni/Fe]〉 ∼ +0.01, and a moderate enhancement of α-elements, ranging between +0.16 and &lt;+0.42, and a slight enhancement of the s-process element 〈[Ce/Fe]〉 ∼ +0.19. We also found low levels of 〈[Al/Fe]〉 ∼ +0.09, but with a strong enrichment of nitrogen, [N/Fe] &gt; +0.99, along with a low level of carbon, [C/Fe] &lt; −0.12. This behaviour of Nitrogen-Carbon is a typical chemical signature for the presence of multiple stellar populations in virtually all GCs; this is the first time that it is reported in NGC 6558. We also observed a remarkable consistency in the behaviour of all the chemical species compared to the other CAPOS bulge GCs of the same metallicity.
From images to features: unbiased morphology classification via variational auto-encoders and domain adaptation
Authors: Xu Quanfeng , Shen Shiyin , de Souza Rafael S , Chen Mi , Ye Renhao , She Yumei , Chen Zhu , Ishida Emille E O , Krone-Martins Alberto , Durgesh Rupesh 
Published: October 2023

ABSTRACT
We present a novel approach for the dimensionality reduction of galaxy images by leveraging a combination of variational auto-encoders (VAEs) and domain adaptation (DA). We demonstrate the effectiveness of this approach using a sample of low-redshift galaxies with detailed morphological type labels from the Galaxy Zoo Dark Energy Camera Legacy Survey (DECaLS) project. We show that 40-dimensional latent variables can effectively reproduce most morphological features in galaxy images. To further validate the effectiveness of our approach, we utilized a classical random forest classifier on the 40-dimensional latent variables to make detailed morphology feature classifications. This approach performs similar to a direct neural network application on galaxy images. We further enhance our model by tuning the VAE network via DA using galaxies in the overlapping footprint of DECaLS and Beijing-Arizona Sky Survey + Mayall z-band Legacy Survey, enabling the unbiased application of our model to galaxy images in both surveys. We observed that DA led to even better morphological feature extraction and classification performance. Overall, this combination of VAE and DA can be applied to achieve image dimensionality reduction, defect image identification, and morphology classification in large optical surveys.
Rad53 regulates the lifetime of Rdh54 at homologous recombination intermediates
Authors: Hu Jingyi , Ferlez Bryan , Dau Jennifer , Crickard J Brooks 
Published: October 2023

Abstract
Rdh54 is a conserved DNA translocase that participates in homologous recombination (HR), DNA checkpoint adaptation, and chromosome segregation. Saccharomyces cerevisiae Rdh54 is a known target of the Mec1/Rad53 signaling axis, which globally protects genome integrity during DNA metabolism. While phosphorylation of DNA repair proteins by Mec1/Rad53 is critical for HR progression little is known about how specific post translational modifications alter HR reactions. Phosphorylation of Rdh54 is linked to protection of genomic integrity but the consequences of modification remain poorly understood. Here, we demonstrate that phosphorylation of the Rdh54 C-terminus by the effector kinase Rad53 regulates Rdh54 clustering activity as revealed by single molecule imaging. This stems from phosphorylation dependent and independent interactions between Rdh54 and Rad53. Genetic assays reveal that loss of phosphorylation leads to phenotypic changes resulting in loss-of-heterozygosity (LOH) outcomes. Our data highlight Rad53 as a key regulator of HR intermediates through activation and attenuation of Rdh54 motor function.
Sea-ATI unravels novel vocabularies of plant active cistrome
Authors: Wen Chenjin , Yuan Zhen , Zhang Xiaotian , Chen Hao , Luo Lin , Li Wanying , Li Tian , Ma Nana , Mao Fei , Lin Dongmei , Lin Zhanxi , Lin Chentao , Xu Tongda , Lü Peitao , Lin Juncheng , Zhu Fangjie 
Published: October 2023

Abstract
The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants.
mtFociCounter for automated single-cell mitochondrial nucleoid quantification and reproducible foci analysis
Authors: Rey Timo , Tábara Luis Carlos , Prudent Julien , Minczuk Michal 
Published: October 2023

Abstract
Mitochondrial DNA (mtDNA) encodes the core subunits for OXPHOS, essential in near-all eukaryotes. Packed into distinct foci (nucleoids) inside mitochondria, the number of mtDNA copies differs between cell-types and is affected in several human diseases. Currently, common protocols estimate per-cell mtDNA-molecule numbers by sequencing or qPCR from bulk samples. However, this does not allow insight into cell-to-cell heterogeneity and can mask phenotypical sub-populations. Here, we present mtFociCounter, a single-cell image analysis tool for reproducible quantification of nucleoids and other foci. mtFociCounter is a light-weight, open-source freeware and overcomes current limitations to reproducible single-cell analysis of mitochondrial foci. We demonstrate its use by analysing 2165 single fibroblasts, and observe a large cell-to-cell heterogeneity in nucleoid numbers. In addition, mtFociCounter quantifies mitochondrial content and our results show good correlation (R = 0.90) between nucleoid number and mitochondrial area, and we find nucleoid density is less variable than nucleoid numbers in wild-type cells. Finally, we demonstrate mtFociCounter readily detects differences in foci-numbers upon sample treatment, and applies to Mitochondrial RNA Granules and superresolution microscopy. mtFociCounter provides a versatile solution to reproducibly quantify cellular foci in single cells and our results highlight the importance of accounting for cell-to-cell variance and mitochondrial context in mitochondrial foci analysis.