bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutralizing Immunity Against Antigenically Advanced Omicron BA.5 in Children After SARS-CoV-2 Infection
Authors: Belongia Edward A , Petrie Joshua G , Feldstein Leora R , Guan Lizheng , Halfmann Peter J , King Jennifer P , Neumann Gabriele , Pattinson David , Rolfes Melissa A , McLean Huong Q , Kawaoka Yoshihiro 
Published: December 2023

Abstract
We assessed serum neutralization of Omicron BA.5 in children following SARS-CoV-2 infection during the Delta or Omicron BA.1/BA.2 variant period. Convalescent BA.5 titers were higher following infections during the Omicron BA.1/BA.2 vs Delta variant period, and in vaccinated vs unvaccinated children. Titers against BA.5 did not differ by age group.
Heidenhain variant of Creutzfeldt-Jakob disease masquerading as neuromyelitis optica spectrum disorder: recognizing when apheresis is not the answer
Authors: Burke Olivia , Jacobs Jeremy W , Tormey Christopher A , Rinder Henry M , Figueroa Villalba Cristina A , Lee Edward S , Silva Campos Juan J , Abels Elizabeth , Yurtsever Nalan 
Published: December 2023

Abstract
The Heidenhain variant of Creutzfeld-Jakob disease (CJD) is a rare form that initially presents with visual disturbances. In early stages, the presentation can mimic neuromyelitis optica spectrum disorders (NMOSD) and lead to unnecessary treatment modalities. Herein, we describe a case of a 66-year-old man who presented with bilateral vision loss and retro-orbital discomfort. In addition to immunosuppressive therapy, he received 4 rounds of therapeutic plasma exchange after his preliminary diagnosis of NMOSD. We were surprised to note that his condition did not show improvement but deteriorated, with severe neurocognitive symptoms. Eventually, CJD was suspected, and real-time quaking-induced conversion (RT-QuIC) was performed. By the time the diagnosis of Heidenhain variant of CJD was confirmed, the patient was discharged to hospice care and died shortly after.
Impact of COVID-19 pandemic on accredited programs and graduates who sat for the American Society for Clinical Pathology Board of Certification examination: graduates’ perspective
Authors: Duzan Dana , Fong Karen , Freeman Vicki S , Goodyear Nancy , Nadder Teresa S , Spiczka Amy , Taff Teresa , Tanabe Patricia 
Published: December 2023

Abstract

Objective
Students in health profession education programs were severely affected by the COVID-19 pandemic at both didactic and clinical training levels. The purpose for this American Society for Clinical Pathology Board of Certification (ASCP BOC) study was to determine the impact of the COVID-19 pandemic on graduates. This study represents the perspectives of laboratory professional graduates who sat for the BOC certification in their respective professional disciplines.

Methods
A survey was sent to all graduates from the National Accrediting Agency for Clinical Laboratory Science (NAACLS), Accrediting Bureau of Health Education Schools (ABHES), and Commission on Accreditation of Allied Health Education Programs (CAAHEP) accredited programs who sat for the ASCP BOC examination in 2020 and 2021 to determine the impact of COVID-19 on laboratory professional graduates during the pandemic.

Results
A total of 180 graduates responded to the survey. The majority of graduates indicated that at least 1 didactic program component was shifted to an online system during the pandemic and that both clinical and nonclinical student laboratories were affected. Although program completion for most graduates was not delayed, one-third of graduates delayed taking their respective BOC exam. Due to the lack of knowledge application through practical hands-on laboratory experience in their educational programs, graduates reported feeling a lack of readiness with regards to preparing for the national certification examination as well as for employment.

Conclusion
The study results showed the pandemic greatly impacted the education experience and readiness for the ASCP BOC examinations for graduates. Factors such as the absence of in-person learning and hands-on experience—both crucial aspects in laboratory training—and the ripple effects as a result of the pandemic, such as job loss, financial constraints, and health concerns, contributed to the decreased quality of education for graduates.
Du Fu’s conspicuous negativity and Li Bai’s hidden positivity: a sentiment comparison and exploration
Authors: Meng Yingying , Wan Yuwei , Kit Chunyu 
Published: December 2023

Abstract
In the studies of classical Chinese poetry, the comparison between Li Bai and Du Fu is an everlasting topic, yielding many qualitative interpretations, among which a widely known but disputable one is Li’s positivity versus Du’s negativity. With the development of digital means, distant reading has become possible, and the sentiment issue can be further explored in quantitative ways. This research conducts a corpus-based sentiment comparison of Li and Du with a self-constructed sentiment dictionary. The Complete Collection of Tang Poems is used as a representative of Tang poets, and sentiment comparisons are made at the levels of poems, verses, and characters, as well as key characters extracted with the log-likelihood measure. Analyses show that (1) among Tang poets, Du is more negative at all of the above textual levels, while Li is only more positive at the key character level, proving the importance of key characters in readers’ perception of sentiment; (2) Li and Du both stand out among Tang poets with a negative depiction of the dark reality and a positive expression of grand ideals; and (3) Li’s positivity is largely embodied in his depictions of color, light, and temperature, while Du’s negativity is closely related to his psychological description. To conclude, this research has not only determined the sentiment difference between Li and Du but also located its sources in texts with a novel key character-based sentiment analysis approach.
Keywords:
AI-assisted super-resolution cosmological simulations III: time evolution
Authors: Zhang Xiaowen , Lachance Patrick , Ni Yueying , Li Yin , Croft Rupert A C , Matteo Tiziana Di , Bird Simeon , Feng Yu 
Published: December 2023

ABSTRACT
In this work, we extend our recently developed super-resolution (SR) model for cosmological simulations to produce fully time-consistent evolving representations of the particle phase-space distribution. We employ a style-based constrained generative adversarial network (StyleGAN), where the changing cosmic time is an input style parameter to the network. The matter power spectrum and halo mass function agree well with results from high-resolution N-body simulations over the full trained redshift range (10 ≤ z ≤ 0). Furthermore, we assess the temporal consistency of our SR model by constructing halo merger trees. We examine progenitors, descendants, and mass growth along the tree branches. All statistical indicators demonstrate the ability of our SR model to generate satisfactory high-resolution simulations based on low-resolution inputs.
Mapping out the parameter space for photoevaporation and core-powered mass-loss
Authors: Owen James E , Schlichting Hilke E 
Published: December 2023

ABSTRACT
Understanding atmospheric escape in close-in exoplanets is critical to interpreting their evolution. We map out the parameter space over which photoevaporation and core-powered mass-loss dominate atmospheric escape. Generally, the transition between the two regimes is determined by the location of the Bondi radius (i.e. the sonic point of core-powered outflow) relative to the penetration depth of extreme ultra-violet (XUV) photons. Photoevaporation dominates the loss when the XUV penetration depth lies inside the Bondi radius (RXUV &lt; RB) and core-powered mass-loss when XUV radiation is absorbed higher up in the flow (RB &lt; RXUV). The transition between the two regimes occurs at a roughly constant ratio of the planet’s radius to its Bondi radius, with the exact value depending logarithmically on planetary and stellar properties. In general, core-powered mass-loss dominates for lower gravity planets with higher equilibrium temperatures, and photoevaporation dominates for higher gravity planets with lower equilibrium temperatures. However, planets can transition between these two mass-loss regimes during their evolution, and core-powered mass-loss can ‘enhance’ photoevaporation over a significant region of parameter space. Interestingly, a planet that is ultimately stripped by core-powered mass-loss has likely only ever experienced core-powered mass-loss. In contrast, a planet that is ultimately stripped by photoevaporation could have experienced an early phase of core-powered mass-loss. Applying our results to the observed super-Earth population suggests that it contains significant fractions of planets where each mechanism controlled the final removal of the H/He envelope, although photoevaporation appears to be responsible for the final carving of the exoplanet radius valley.
Estimating photometric redshift from mock flux for CSST survey by using weighted Random Forest
Authors: Lu Junhao , Luo Zhijian , Chen Zhu , Fu Liping , Du Wei , Gong Yan , Li Yicheng , Meng Xian-Min , Tang Zhirui , Zhang Shaohua , Shu Chenggang , Zhou Xingchen , Fan Zuhui 
Published: December 2023

ABSTRACT
Accurate estimation of photometric redshifts (photo-z) is crucial in studies of both galaxy evolution and cosmology using current and future large sky surveys. In this study, we employ Random Forest (RF), a machine learning algorithm, to estimate photo-z and investigate the systematic uncertainties affecting the results. Using galaxy flux and colour as input features, we construct a mapping between input features and redshift by using a training set of simulated data, generated from the Hubble Space Telescope Advanced Camera for Surveys (HST-ACS) and COSMOS catalogue, with the expected instrumental effects of the planned China Space Station Telescope (CSST). To improve the accuracy and confidence of predictions, we incorporate inverse variance weighting and perturb the catalogue using input feature errors. Our results show that weighted RF can achieve a photo-z accuracy of $\rm \sigma _{NMAD}=0.025$ and an outlier fraction of $\rm \eta =2.045\ \hbox{per cent}$, significantly better than the values of $\rm \sigma _{NMAD}=0.043$ and $\rm \eta =6.45\ \hbox{per cent}$ obtained by the widely used Easy and Accurate Zphot from Yale (EAZY) software, which uses template-fitting method. Furthermore, we have calculated the importance of each input feature for different redshift ranges and found that the most important input features reflect the approximate position of the break features in galaxy spectra, demonstrating the algorithm’s ability to extract physical information from data. Additionally, we have established confidence indices and error bars for each prediction value based on the shape of the redshift probability distribution function, suggesting that screening sources with high confidence can further reduce the outlier fraction.
Internal shocks hydrodynamics: the collision of two cold shells in detail
Authors: Rahaman Sk Minhajur , Granot Jonathan , Beniamini Paz 
Published: December 2023

ABSTRACT
Emission in many astrophysical transients originates from a shocked fluid. A central engine typically produces an outflow with varying speeds, leading to internal collisions within the outflow at finite distances from the source. Each such collision produces a pair of forward and reverse shocks with the two shocked regions separated by a contact discontinuity (CD). As a useful approximation, we consider the head-on collision between two cold and uniform shells (a slower leading shell and a faster trailing shell) of finite radial width, and study the dynamics of shock propagation in planar geometry. We find significant differences between the forward and reverse shocks, in terms of their strength, internal energy production efficiency, and the time it takes for the shocks to sweep through the respective shells. We consider the subsequent propagation of rarefaction waves in the shocked regions and explore the cases where these waves can catch up with the shock fronts and thereby limit the internal energy dissipation. We demonstrate the importance of energy transfer from the trailing to leading shell through pdV work across the CD. We outline the parameter space regions relevant for models of different transients,e.g. Gamma-ray burst internal shock model, fast radio burst blast wave model, Giant flare due to magnetars, and superluminous supernovae ejecta. We find that the reverse shock likely dominates the internal energy production for many astrophysical transients.
Exploration of faint X-ray and radio sources in the massive globular cluster M14: a UV-bright counterpart to Nova Ophiuchus 1938
Authors: Zhao Yue , D’Antona Francesca , Milone Antonino P , Heinke Craig , Zhao Jiaqi , Lugger Phyllis , Cohn Haldan 
Published: December 2023

ABSTRACT
Using a 12 ks archival Chandra X-ray Observatory ACIS-S observation on the massive globular cluster (GC) M14, we detect a total of 7 faint X-ray sources within its half-light radius at a $0.5{\small --}7\, \mathrm{keV}$ depth of $2.5\times 10^{31}\, \mathrm{erg s^{-1}}$. We cross-match the X-ray source positions with a catalogue of the Very Large Array radio point sources and a Hubble Space Telescope (HST) UV/optical/near-IR photometry catalogue, revealing radio counterparts to 2 and HST counterparts to 6 of the X-ray sources. In addition, we also identify a radio source with the recently discovered millisecond pulsar PSR 1737−0314A. The brightest X-ray source, CX1, appears to be consistent with the nominal position of the classic nova Ophiuchi 1938 (Oph 1938), and both Oph 1938 and CX1 are consistent with a UV-bright variable HST counterpart, which we argue to be the source of the nova eruption in 1938. This makes Oph 1938 the second classic nova recovered in a Galactic GC since Nova T Scorpii in M80. CX2 is consistent with the steep-spectrum radio source VLA8, which unambiguously matches a faint blue source; the steepness of VLA8 is suggestive of a pulsar nature, possibly a transitional millisecond pulsar with a late K dwarf companion, though an active galactic nucleus (AGN) cannot be ruled out. The other counterparts to the X-ray sources are all suggestive of chromospherically active binaries or background AGNs, so their nature requires further membership information.
Performance of Topology Tests under Extreme Selection Bias
Authors: Markowski Etai , Susko Edward 
Published: December 2023

AbstractTree tests like the Kishino–Hasegawa (KH) test and chi-square test suffer a selection bias that tests like the Shimodaira–Hasegawa (SH) test and approximately unbiased test were intended to correct. We investigate tree-testing performance in the presence of severe selection bias. The SH test is found to be very conservative and, surprisingly, its uncorrected analog, the KH test has low Type I error even in the presence of extreme selection bias, leading to a recommendation that the SH test be abandoned. A chi-square test is found to usually behave well and but to require correction in extreme cases. We show how topology testing procedures can be used to get support values for splits and compare the likelihood-based support values to the approximate likelihood ratio test (aLRT) support values. We find that the aLRT support values are reasonable even in settings with severe selection bias that they were not designed for. We also show how they can be used to construct tests of topologies and, in doing so, point out a multiple comparisons issue that should be considered when looking at support values for splits.
PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation
Authors: Hu Mengwen , Yeh Yu-Han , Maezawa So , Nakagawa Toshinori , Yoshida Shosei , Namekawa Satoshi H 
Published: December 2023

Abstract
Spermatogonial stem cells functionality reside in the slow-cycling and heterogeneous undifferentiated spermatogonia cell population. This pool of cells supports lifelong fertility in adult males by balancing self-renewal and differentiation to produce haploid gametes. However, the molecular mechanisms underpinning long-term stemness of undifferentiated spermatogonia during adulthood remain unclear. Here, we discover that an epigenetic regulator, Polycomb repressive complex 1 (PRC1), shields adult undifferentiated spermatogonia from differentiation, maintains slow cycling, and directs commitment to differentiation during steady-state spermatogenesis in adults. We show that PRC2-mediated H3K27me3 is an epigenetic hallmark of adult undifferentiated spermatogonia. Indeed, spermatogonial differentiation is accompanied by a global loss of H3K27me3. Disruption of PRC1 impairs global H3K27me3 deposition, leading to precocious spermatogonial differentiation. Therefore, PRC1 directs PRC2-H3K27me3 deposition to maintain the self-renewing state of undifferentiated spermatogonia. Importantly, in contrast to its role in other tissue stem cells, PRC1 negatively regulates the cell cycle to maintain slow cycling of undifferentiated spermatogonia. Our findings have implications for how epigenetic regulators can be tuned to regulate the stem cell potential, cell cycle and differentiation to ensure lifelong fertility in adult males.
piRNA generation is associated with the pioneer round of translation in stem cells
Authors: Allikka Parambil Sudheesh , Li Danyan , Zelko Michael , Poulet Axel , van Wolfswinkel Josien C 
Published: December 2023

Abstract
Much insight has been gained on how stem cells maintain genomic integrity, but less attention has been paid to how they maintain their transcriptome. Here, we report that the PIWI protein SMEDWI-1 plays a role in the filtering of dysfunctional transcripts from the transcriptome of planarian stem cells. SMEDWI-1 accomplishes this through association with the ribosomes during the pioneer round of translation, and processing of poorly translated transcripts into piRNAs. This results in the removal of such transcripts from the cytoplasmic pool and at the same time creates a dynamic pool of small RNAs for post-transcriptional surveillance through the piRNA pathway. Loss of SMEDWI-1 results in elevated levels of several non-coding transcripts, including rRNAs, snRNAs and pseudogene mRNAs, while reducing levels of several coding transcripts. In the absence of SMEDWI-1, stem cell colonies are delayed in their expansion and a higher fraction of descendants exit the stem cell state, indicating that this transcriptomic sanitation mediated by SMEDWI-1 is essential to maintain stem cell health. This study presents a new model for the function of PIWI proteins in stem cell maintenance, that complements their role in transposon repression, and proposes a new biogenesis pathway for piRNAs in stem cells.
Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen
Authors: Badet Thomas , Tralamazza Sabina Moser , Feurtey Alice , Croll Daniel 
Published: December 2023

Abstract
Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate the spread of the pathogenicity-associated Styx element across five species that last diverged ∼11 000 years ago. We show that the element likely originated in the Zymoseptoria fungal pathogen genus and underwent multiple independent reactivation events. Using a global 900-genome panel of the wheat pathogen Zymoseptoria tritici, we assess Styx copy number variation and identify renewed transposition activity in Oceania and South America. We show that the element can mobilize to create additional Styx copies in a four-generation pedigree. Importantly, we find that new copies of the element are not affected by genomic defenses suggesting minimal control against the element. Styx copies are preferentially located in recombination breakpoints and likely triggered multiple types of large chromosomal rearrangements. Taken together, we establish the origin, diversification and reactivation of a highly active TE with likely major consequences for chromosomal integrity and the expression of disease.
Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae
Authors: Yu Lifang , Marchisio Mario Andrea 
Published: December 2023

Abstract
New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal transcriptional activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.
Acetylation of xenogeneic silencer H-NS regulates biofilm development through the nitrogen homeostasis regulator in Shewanella
Authors: Liu Xiaoxiao , Li Jun , Zhang Zhixuan , He Yizhou , Wang Mingfang , Zhao Yunhu , Lin Shituan , Liu Tianlang , Liao Yiwen , Zhang Ni , Yuan Kaixuan , Ling Yong , Liu Ziyao , Chen Xiaozhong , Chen Zhe , Chen Ran , Wang Xiaoxue , Gu Bing 
Published: December 2023

Abstract
Adjusting intracellular metabolic pathways and adopting suitable live state such as biofilms, are crucial for bacteria to survive environmental changes. Although substantial progress has been made in understanding how the histone-like nucleoid-structuring (H-NS) protein modulates the expression of the genes involved in biofilm formation, the precise modification that the H-NS protein undergoes to alter its DNA binding activity is still largely uncharacterized. This study revealed that acetylation of H-NS at Lys19 inhibits biofilm development in Shewanella oneidensis MR-1 by downregulating the expression of glutamine synthetase, a critical enzyme in glutamine synthesis. We further found that nitrogen starvation, a likely condition in biofilm development, induces deacetylation of H-NS and the trimerization of nitrogen assimilation regulator GlnB. The acetylated H-NS strain exhibits significantly lower cellular glutamine concentration, emphasizing the requirement of H-NS deacetylation in Shewanella biofilm development. Moreover, we discovered in vivo that the activation of glutamine biosynthesis pathway and the concurrent suppression of the arginine synthesis pathway during both pellicle and attached biofilms development, further suggesting the importance of fine tune nitrogen assimilation by H-NS acetylation in Shewanella. In summary, posttranslational modification of H-NS endows Shewanella with the ability to respond to environmental needs by adjusting the intracellular metabolism pathways.