bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malaria parasite classification framework using a novel channel squeezed and boosted CNN
Authors: Khan Saddam Hussain , Shah Najmus Saher , Nuzhat Rabia , Majid Abdul , Alquhayz Hani , Khan Asifullah 
Published: May 2022

Abstract
Malaria is a life-threatening infection that infects the red blood cells and gradually grows throughout the body. The plasmodium parasite is transmitted by a female Anopheles mosquito bite and severely affects numerous individuals within the world every year. Therefore, early detection tests are required to identify parasite-infected cells. The proposed technique exploits the learning capability of deep convolutional neural network (CNN) to distinguish the parasite-infected patients from healthy individuals using thin blood smear. In this regard, the detection is accomplished using a novel STM-SB-RENet block-based CNN that employs the idea of split–transform–merge (STM) and channel squeezing–boosting (SB) in a modified fashion. In this connection, a new convolutional block-based STM is developed, which systematically implements region and edge operations to explore the parasitic infection pattern of malaria related to region homogeneity, structural obstruction and boundary-defining features. Moreover, the diverse boosted feature maps are achieved by incorporating the new channel SB and transfer learning (TL) idea in each STM block at abstract, intermediate and target levels to capture minor contrast and texture variation between parasite-infected and normal artifacts. The malaria input images for the proposed models are initially transformed using discrete wavelet transform to generate enhanced and reduced feature space. The proposed architectures are validated using hold-out cross-validation on the National Institute of Health Malaria dataset. The proposed methods outperform training from scratch and TL-based fine-tuned existing techniques. The considerable performance (accuracy: 97.98%, sensitivity: 0.988, F-score: 0.980 and area under the curve: 0.996) of STM-SB-RENet suggests that it can be utilized to screen malaria-parasite-infected patients.
Graphical Abstract
The Development of Global Cancer Research at the United States National Cancer Institute
Authors: Parascandola Mark , Pearlman Paul C , Eldridge Linsey , Gopal Satish 
Published: May 2022

Abstract
International research and collaboration has been a part of the National Cancer Institute’s (NCI) mission since its creation in 1937. Early on, efforts were limited to international exchange of information to ensure that US cancer patients could benefit from advances in other countries. As NCI’s research grant portfolio grew in the 1950s, it included a modest number of grants to foreign institutions, primarily in the United Kingdom and Europe. In the 1960s, the development of geographic pathology, which aimed to study cancer etiology through variations in cancer incidence and risk factors, led to an increase in NCI-funded international research, including research in low- and middle-income countries. In this paper, we review key international research programs, focusing particularly on the first 50 years of NCI history. The first NCI-led overseas research programs, established in the 1960s in Ghana and Uganda, generated influential research but also struggled with logistical challenges and political instability. The 1971 National Cancer Act was followed by the creation of a number of bilateral agreements with foreign governments, including China, Japan, and Russia, to support cooperation in technology and medicine. Although these agreements were broad without specific scientific goals, they provided an important mechanism for sustained collaborations in specific areas. With the creation of the NCI Center for Global Health in 2011, NCI’s global cancer research efforts gained sustained focus. Because the global cancer burden has evolved over time, increasingly impacting low- and middle-income countries, NCI’s role in global cancer research remains more important than ever.
‘A man greatly beloved’ and Immortalized in opus sectile Powell & Sons, Monument to Robert Claudius Billing (1899)
Authors: Allen Jasmine 
Published: May 2022

Abstract
The alabaster wall monument to Robert Claudius Billing, Suffragan Bishop of Bedford, placed in the crypt of St Paul’s Cathedral, commemorates the life and service of a Victorian cleric known for his work in the overcrowded parishes of east London. Supplied by Powell and Sons, a London-based glassmaking firm that made stained glass and mosaics as well as reredoses and tablets, the monument echoes the architectural style and decoration of the iconic building in which it is placed, as well as showcasing a new vitreous mosaic material known as opus sectile that the firm innovated and marketed as suitable for both wall and floor decoration. The striking opus sectile portrait of Billing preserves an image of the deceased, and together with the accompanying epitaph demonstrates the affection and high esteem in which he was held in the Diocese of London and beyond.
No slip gravity in light of LISA standard sirens
Authors: Allahyari Alireza , Nunes Rafael C , Mota David F 
Published: May 2022

ABSTRACT
Standard sirens (SS) are the gravitational wave analogue of the astronomical standard candles, and can provide powerful information about the dynamics of the Universe up to very high z values. In this work, we generate three mock SS catalogues based on the merger of massive black hole binaries which are expected to be observed in the LISA operating frequency band. Then, we perform an analysis to test modifications of general relativity (GR) inspired by the no slip gravity framework. We find that in the best scenarios, we can constrain the free parameters which quantify deviations from GR to 21 per cent accuracy, while the Hubble parameter can be simultaneously fit to 6 per cent accuracy. In combination with CMB information, we find a 15 per cent accuracy on the modified gravity free parameters and 0.7 per cent accuracy on the Hubble parameter. The SS events at very large cosmological distances to be observed in LISA band will provide a unique way to test nature of gravity, but in the context of the analysis performed here, it will not be possible to distinguish the no slip gravity from GR.
BUDDI-MaNGA II: the star-formation histories of bulges and discs of S0s
Authors: Johnston Evelyn J , Häußler Boris , Jegatheesan Keerthana , Fraser-McKelvie Amelia , Coccato Lodovico , Cortesi Arianna , Jaffé Yara , Galaz Gaspar , Mora Marcelo , Ordenes-Briceño Yasna 
Published: May 2022

ABSTRACT
Many processes have been proposed to explain the quenching of star formation in spiral galaxies and their transformation into S0s. These processes affect the bulge and disc in different ways, and so by isolating the bulge and disc spectra, we can look for these characteristic signatures. In this work, we used buddi to cleanly extract the spectra of the bulges and discs of 78 S0 galaxies in the MaNGA Survey. We compared the luminosity and mass weighted stellar populations of the bulges and discs, finding that bulges are generally older and more metal rich than their discs. When considering the mass and environment of each galaxy, we found that the galaxy stellar mass plays a more significant role on the formation of the bulges. Bulges in galaxies with masses $\ge 10^{10}\, {\rm M}_\odot$ built up the majority of their mass rapidly early in their lifetimes, while those in lower mass galaxies formed over more extended time-scales and more recently. No clear difference was found in the formation or quenching processes of the discs as a function of galaxy environment. We conclude that more massive S0 galaxies formed through an inside-out scenario, where the bulge formed first and evolved passively while the disc underwent a more extended period of star formation. In lower mass S0s, the bulges and discs either formed together from the same material, or through an outside-in scenario. Our results therefore imply multiple formation mechanisms for S0 galaxies, the pathway of which is chiefly determined by a galaxy’s current stellar mass.
Constraints on interacting dark energy models from time-delay cosmography with seven lensed quasars
Authors: Wang Ling-Feng , Zhang Jie-Hao , He Dong-Ze , Zhang Jing-Fei , Zhang Xin 
Published: May 2022

ABSTRACT
Measurements of time-delay cosmography of lensed quasars can provide an independent probe to explore the expansion history of the late-time Universe. In this paper, we employ the time-delay cosmography measurements from seven lenses (here abbreviated as the TD data) to constrain interacting dark energy (IDE) models. We mainly focus on the scenario of vacuum energy (with w = −1) interacting with cold dark matter, and consider four typical cases of the interaction form Q. When the TD data alone are employed, we find that the IDE models with Q ∝ ρde seem to have an advantage in relieving the H0 tension between the cosmic microwave background (CMB) and TD data. When the TD data are added to the CMB+BAO+SN+H0 data, we find that (i) the coupling parameter β in all the considered IDE models is positive within 1σ range, implying a mild preference for the case of cold dark matter decaying into dark energy; (ii) the IDE model with Q = βH0ρc slightly relieves the S8 tension, but the other considered IDE models further aggravate this tension; (iii) the Akaike information criteria of the IDE models with Q ∝ ρc are lower than that of the ΛCDM model, indicating that these IDE models are more preferred by the current mainstream data. We conclude that the considered IDE models have their own different advantages when the TD data are employed, and none of them can achieve good scores in all aspects.
High time resolution search for prompt radio emission from the long GRB 210419A with the Murchison Widefield Array
Authors: Tian J , Anderson G E , Hancock P J , Miller-Jones J C A , Sokolowski M , Swainston N A , Rowlinson A , Williams A , Kaplan D L , Hurley-Walker N , Morgan J , Bhat N D R , Ung D , Tingay S , Bannister K W , Bell M E , Meyers B W , Walker M 
Published: May 2022

ABSTRACT
We present a low-frequency (170–200 MHz) search for prompt radio emission associated with the long GRB 210419A using the rapid-response mode of the Murchison Widefield Array (MWA), triggering observations with the Voltage Capture System for the first time. The MWA began observing GRB 210419A within 89 s of its detection by Swift, enabling us to capture any dispersion delayed signal emitted by this gamma-ray burst (GRB) for a typical range of redshifts. We conducted a standard single pulse search with a temporal and spectral resolution of $100\, \mu$s and 10 kHz over a broad range of dispersion measures from 1 to $5000\, \text{pc}\, \text{cm}^{-3}$, but none were detected. However, fluence upper limits of 77–224 Jy ms derived over a pulse width of 0.5–10 ms and a redshift of 0.6 &lt; z &lt; 4 are some of the most stringent at low radio frequencies. We compared these fluence limits to the GRB jet–interstellar medium interaction model, placing constraints on the fraction of magnetic energy (ϵB ≲ [0.05–0.1]). We also searched for signals during the X-ray flaring activity of GRB 210419A on minute time-scales in the image domain and found no emission, resulting in an intensity upper limit of $0.57\, \text{Jy}\, \text{beam}^{-1}$, corresponding to a constraint of ϵB ≲ 10−3. Our non-detection could imply that GRB 210419A was at a high redshift, there was not enough magnetic energy for low-frequency emission, or the radio waves did not escape from the GRB environment.
Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids
Authors: Coluzzi Charles , Garcillán-Barcia Maria Pilar , de la Cruz Fernando , Rocha Eduardo P.C. 
Published: May 2022

Abstract
Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.
Evidence for TET-mediated DNA demethylation as an epigenetic alteration in cumulus granulosa cells of women with polycystic ovary syndrome
Authors: Sagvekar Pooja , Shinde Gayatri , Mangoli Vijay , Desai Sadhana K , Mukherjee Srabani 
Published: May 2022

Abstract
Peripheral and tissue-specific alterations in global DNA methylation (5-methylcytosine (5mC)) and DNA hydroxymethylation (5-hydroxymethylcytosine (5hmC)) profiles have been identified as both biomarkers for disease prediction and as hallmarks of dysregulated localized gene networks. Global and gene-specific epigenetic alterations in the 5mC profiles have shown widespread implications in the etiology of polycystic ovary syndrome (PCOS). However, there has been no study in PCOS that integrates the quantification of 5mC and 5hmC signatures alongside the expression levels of DNA methylating and demethylating enzymes as respective indicators of methylation and demethylation pathways. Having previously shown that the 5mC signatures are not substantially altered in PCOS, we assessed the global 5hmC levels in peripheral blood leukocytes and cumulus granulosa cells (CGCs) of 40 controls and 40 women with PCOS. This analysis revealed higher 5hmC levels in CGCs of PCOS women, indicating a more dominant demethylation pathway. Furthermore, we assessed the transcript and protein expression levels of DNA demethylating and methylating enzymes, i.e. ten-eleven translocation methylcytosine dioxygenases (TET1, TET2, TET3) and DNA methyltransferases (DNMT1, DNMT3A and DNMT3B), respectively, in CGCs. The relative transcript and protein expression levels of all three TETs were found to be higher in women with PCOS, and the TET mRNA expression profiles were positively correlated with 5hmC levels in CGCs. Also, all three DNMT genes showed altered transcript expression in PCOS, although only the downregulated DNMT3A transcript was correlated with decreasing 5mC levels. At the protein level, the expression of DNMT1 (maintenance methylation enzyme) was higher, while that of DNMT3A (de novo methylation enzyme) was found to be lower in PCOS compared to controls. Overall, these results indicate that DNA methylation changes in CGCs of PCOS women may arise partly due to intrinsic alterations in the transcriptional regulation of TETs and DNMT3A.
Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation
Authors: Micic Jelena , Rodríguez-Galán Olga , Babiano Reyes , Fitzgerald Fiona , Fernández-Fernández José , Zhang Yunyang , Gao Ning , Woolford John L , de la Cruz Jesús 
Published: May 2022

Abstract
During translation, nascent polypeptide chains travel from the peptidyl transferase center through the nascent polypeptide exit tunnel (NPET) to emerge from 60S subunits. The NPET includes portions of five of the six 25S/5.8S rRNA domains and ribosomal proteins uL4, uL22, and eL39. Internal loops of uL4 and uL22 form the constriction sites of the NPET and are important for both assembly and function of ribosomes. Here, we investigated the roles of eL39 in tunnel construction, 60S biogenesis, and protein synthesis. We show that eL39 is important for proper protein folding during translation. Consistent with a delay in processing of 27S and 7S pre-rRNAs, eL39 functions in pre-60S assembly during middle nucleolar stages. Our biochemical assays suggest the presence of eL39 in particles at these stages, although it is not visualized in them by cryo-electron microscopy. This indicates that eL39 takes part in assembly even when it is not fully accommodated into the body of pre-60S particles. eL39 is also important for later steps of assembly, rotation of the 5S ribonucleoprotein complex, likely through long range rRNA interactions. Finally, our data strongly suggest the presence of alternative pathways of ribosome assembly, previously observed in the biogenesis of bacterial ribosomal subunits.
Mutations compensating for the fitness cost of rifampicin resistance inEscherichia coliexert pleiotropic effect on RNA polymerase catalysis
Authors: Kurepina Natalia , Chudaev Maxim , Kreiswirth Barry N , Nikiforov Vadim , Mustaev Arkady 
Published: May 2022

AbstractThe spread of drug-resistant bacteria represents one of the most significant medical problems of our time. Bacterial fitness loss associated with drug resistance can be counteracted by acquisition of secondary mutations, thereby enhancing the virulence of such bacteria. Antibiotic rifampicin (Rif) targets cellular RNA polymerase (RNAP). It is potent broad spectrum drug used for treatment of bacterial infections. We have investigated the compensatory mechanism of the secondary mutations alleviating Rif resistance (Rifr) on biochemical, structural and fitness indices. We find that substitutions in RNAP genes compensating for the growth defect caused by βQ513P and βT563P Rifr mutations significantly enhanced bacterial relative growth rate. By assaying RNAP purified from these strains, we show that compensatory mutations directly stimulated basal transcriptional machinery (2–9-fold) significantly improving promoter clearance step of the transcription pathway as well as elongation rate. Molecular modeling suggests that compensatory mutations affect transcript retention, substrate loading, and nucleotidyl transfer catalysis. Strikingly, one of the identified compensatory substitutions represents mutation conferring rifampicin resistance on its own. This finding reveals an evolutionary process that creates more virulent species by simultaneously improving the fitness and augmenting bacterial drug resistance.
Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of endogenously tagged genes in Drosophila ovarian somatic sheath cells)
Authors: Meng Qingcai , Stoyko Daniel , Andrews Celine Marlin , Konstantinidou Parthena , Genzor Pavol , O Timothy , Elchert Alexandra R , Benner Leif , Sobti Sushil , Katz Esther Y , Haase Astrid D 
Published: May 2022

Abstract
The combination of genome-editing and epitope tagging provides a powerful strategy to study proteins with high affinity and specificity while preserving their physiological expression patterns. However, stably modifying endogenous genes in cells that do not allow for clonal selection has been challenging. Here, we present a simple and fast strategy to generate stable, endogenously tagged alleles in a non-transformed cell culture model. At the example of piwi in Drosophila ovarian somatic sheath cells, we show that this strategy enables the generation of an N-terminally tagged protein that emulates the expression level and subcellular localization of the wild type protein and forms functional Piwi–piRNA complexes. We further present a concise workflow to establish endogenously N-terminally and C-terminally tagged proteins, and knockout alleles through rapid selection of cell pools in fly and human models.
Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly
Authors: Kasiliauskaite Aiste , Kubicek Karel , Klumpler Tomas , Zanova Martina , Zapletal David , Koutna Eliska , Novacek Jiri , Stefl Richard 
Published: May 2022

Abstract
Transcription elongation factor Spt6 associates with RNA polymerase II (Pol II) and acts as a histone chaperone, which promotes the reassembly of nucleosomes following the passage of Pol II. The precise mechanism of nucleosome reassembly mediated by Spt6 remains unclear. In this study, we used a hybrid approach combining cryo-electron microscopy and small-angle X-ray scattering to visualize the architecture of Spt6 from Saccharomyces cerevisiae. The reconstructed overall architecture of Spt6 reveals not only the core of Spt6, but also its flexible N- and C-termini, which are critical for Spt6’s function. We found that the acidic N-terminal region of Spt6 prevents the binding of Spt6 not only to the Pol II CTD and Pol II CTD-linker, but also to pre-formed intact nucleosomes and nucleosomal DNA. The N-terminal region of Spt6 self-associates with the tSH2 domain and the core of Spt6 and thus controls binding to Pol II and nucleosomes. Furthermore, we found that Spt6 promotes the assembly of nucleosomes in vitro. These data indicate that the cooperation between the intrinsically disordered and structured regions of Spt6 regulates nucleosome and Pol II CTD binding, and also nucleosome assembly.
USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation
Authors: Rong Yan , Zhu Ye-Zhang , Yu Jia-li , Wu Yun-Wen , Ji Shu-Yan , Zhou Yong , Jiang Yu , Jin Jin , Fan Heng-Yu , Shen Li , Sha Qian-Qian 
Published: May 2022

Abstract
Maternal-to-zygotic transition (MZT) is the first and key step in the control of animal development and intimately related to changes in chromatin structure and histone modifications. H2AK119ub1, an important epigenetic modification in regulating chromatin configuration and function, is primarily catalyzed by PRC1 and contributes to resistance to transcriptional reprogramming in mouse embryos. In this study, the genome-wide dynamic distribution of H2AK119ub1 during MZT in mice was investigated using chromosome immunoprecipitation and sequencing. The results indicated that H2AK119ub1 accumulated in fully grown oocytes and was enriched at the TSSs of maternal genes, but was promptly declined after meiotic resumption at genome-wide including the TSSs of early zygotic genes, by a previously unidentified mechanism. Genetic evidences indicated that ubiquitin-specific peptidase 16 (USP16) is the major deubiquitinase for H2AK119ub1 in mouse oocytes. Conditional knockout of Usp16 in oocytes did not impair their survival, growth, or meiotic maturation. However, oocytes lacking USP16 have defects when undergoing zygotic genome activation or gaining developmental competence after fertilization, potentially associated with high levels of maternal H2AK119ub1 deposition on the zygotic genomes. Taken together, H2AK119ub1 level is declined during oocyte maturation by an USP16-dependent mechanism, which ensures zygotic genome reprogramming and transcriptional activation of essential early zygotic genes.