bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying the best PCR enzyme for library amplification in NGS
Authors: Quail Michael A. , Corton Craig , Uphill James , Keane Jacqueline , Gu Yong 
Published: April 2024

Background. PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods []. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimized NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short-read Illumina library preparation and long fragment amplification ahead of long-read sequencing.
We tested over 20 different hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) ‘Equinox’ and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR-free datasets. We also test a range of enzymes for long-read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4 kb, respectively.
The enzymes of choice for short-read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) ‘Equinox’ and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long-read sequencing.
Ascorbate depletion increases quiescence and self-renewal potential in hematopoietic stem cells and multipotent progenitors
Authors: Comazzetto Stefano , Cassidy Daniel L. , DeVilbiss Andrew W. , Jeffery Elise C. , Ottesen Bethany R. , Reyes Amanda R. , Muh Sarah , Mathews Thomas P. , Chen Brandon , Zhao Zhiyu , Morrison Sean J. 
Published: April 2024

ABSTRACTAscorbate (vitamin C) limits hematopoietic stem cell (HSC) function and suppresses leukemia development by promoting the function of the Tet2 tumor suppressor. In humans, ascorbate is obtained from the diet while in mice it is synthesized in the liver. In this study, we show that deletion of the Slc23a2 ascorbate transporter severely depleted ascorbate from hematopoietic cells.Slc23a2deficiency increased HSC reconstituting potential and self-renewal potential upon transplantation into irradiated mice.Slc23a2deficiency also increased the reconstituting and self-renewal potential of multipotent hematopoietic progenitors (MPPs), conferring the ability to long-term reconstitute irradiated mice.Slc23a2-deficient HSCs and MPPs divided much less frequently than control HSCs and MPPs. Increased self-renewal and reconstituting potential were observed particularly in quiescentSlc23a2-deficient HSCs and MPPs. The effect ofSlc23a2deficiency on MPP self-renewal was not mediated by reduced Tet2 function. Ascorbate thus regulates quiescence and restricts self-renewal potential in HSCs and MPPs such that ascorbate depletion confers MPPs with long-term self-renewal potential.KEY POINTSDeletion of the ascorbate transporter, Slc23a2, increases quiescence and self-renewal potential in HSCs and multipotent progenitorsAscorbate depletion is sufficient to confer long-term self-renewal potential upon multipotent hematopoietic progenitors
Taxonomic Revision and Identification Keys for the Giant Honey Bees
Authors: Kitnya Nyaton , Brockmann Axel , Otis Gard W. 
Published: April 2024

AbstractThe taxonomy and phylogeny of the giant honey bees (Apis; subgenusMegapis) are still controversial and unresolved. The species boundaries within the subgenus are unclear and some species that are recognized on the basis of genetic differences lack supporting morphological characters. Two species are now well accepted:Apis dorsataF. of tropical regions of Asia andApis laboriosaSmith that inhabits the foothills of Himalaya and neighboring mountain ranges. In addition, researchers have suggested that the two allopatric populations of giant honey bees that inhabit Sulawesi, Indonesia (A. binghamiCockerell) and the oceanic Philippine islands (A. breviligulaMaa) as well as the South Indian form also deserve species status. We conducted a taxonomic study based on morphological characters ofMegapisfrom throughout Asia. Our study confirms thatApis laboriosais a distinct species based on numerous morphological characters. Moreover,A. dorsataof mainland Asia differs from the two island taxa based on coloration, ocellus size, and the spacing of compound eyes and ocelli. We found no evidence thatbreviligulaof the Philippines has a distinctively short tongue, and report only one minor character (the shape of sternum 5) that differed statistically between bees from Sulawesi and the Philippines. We conclude that the bees from these islands represent a single morphological species,A. binghami, with two subspecies,A. b. binghamiandA. b. breviligula.Apis dorsatafrom the Andaman Islands are smaller than but conspecific with those of mainland Asia. We found no morphological autapomorphies in the giant honey bees of southern India known to differ in mtDNA fromA. dorsatafrom elsewhere in mainland Asia. We provide a taxonomic keys to workers and drones within the subgenusMegapis.
Distinct Type 1 Immune Networks Underlie the Severity of Restrictive Lung Disease after COVID-19
Authors: Canderan Glenda , Muehling Lyndsey M. , Kadl Alexandra , Ladd Shay , Bonham Catherine , Cross Claire E. , Lima Sierra M. , Yin Xihui , Sturek Jeffrey M. , Wilson Jeffrey M. , Keshavarz Behnam , Bryant Naomi , Murphy Deborah D. , Cheon In Su , McNamara Coleen A. , Sun Jie , Utz Paul J. , Dolatshahi Sepideh , Irish Jonathan M. , Woodfolk Judith A. 
Published: April 2024

AbstractThe variable etiology of persistent breathlessness after COVID-19 have confounded efforts to decipher the immunopathology of lung sequelae. Here, we analyzed hundreds of cellular and molecular features in the context of discrete pulmonary phenotypes to define the systemic immune landscape of post-COVID lung disease. Cluster analysis of lung physiology measures highlighted two phenotypes of restrictive lung disease that differed by their impaired diffusion and severity of fibrosis. Machine learning revealed marked CCR5+CD95+ CD8+ T-cell perturbations in mild-to-moderate lung disease, but attenuated T-cell responses hallmarked by elevated CXCL13 in more severe disease. Distinct sets of cells, mediators, and autoantibodies distinguished each restrictive phenotype, and differed from those of patients without significant lung involvement. These differences were reflected in divergent T-cell-based type 1 networks according to severity of lung disease. Our findings, which provide an immunological basis for active lung injury versus advanced disease after COVID-19, might offer new targets for treatment.
Comparative analysis of serological assays and sero-surveillance for SARS-CoV-2 exposure in US cattle
Authors: Ramasamy Santhamani , Qureshi Meysoon , Mukherjee Swastidipa , Mahajan Sonalika , LaBella Lindsey Cecelia , Chothe Shubhada , Jakka Padmaja , Gontu Abhinay , Misra Sougat , Surendran-Nair Meera , Nissly Ruth H. , Kuchipudi Suresh V. 
Published: April 2024

AbstractCoronavirus disease-2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to pose a significant threat to public health globally. Notably, SARS-CoV-2 demonstrates a unique capacity to infect various non-human animal species, documented in captive and free-living animals. However, experimental studies revealed low susceptibility of domestic cattle (Bos taurus) to ancestral B.1 lineage SARS-CoV-2 infection, with limited viral replication and seroconversion. Despite the emergence of viral variants with potentially altered host tropism, recent experimental findings indicate greater permissiveness of cattle to SARS-CoV-2 Delta variant infection compared to other variants, though with limited seroconversion and no clear evidence of transmission. While some studies detected SARS-CoV-2 antibodies in cattle in Italy and Germany, there is no evidence of natural SARS-CoV-2 infection in cattle from the United States or elsewhere. Since serological tests have inherent problems of false positives and negatives, we conducted a comprehensive assessment of multiple serological assays on over 600 cattle serum samples, including pre-pandemic and pandemic cattle sera. We found that SARS-CoV-2 pseudovirus neutralization assays with a luciferase reporter system can produce false positive results, and care must be taken to interpret serological diagnosis using these assays. We found no serological evidence of natural SARS-CoV-2 infection or transmission among cattle in the USA. Hence, it is critical to develop more reliable serological assays tailored to accurately detect SARS-CoV-2 antibodies in cattle populations and rigorously evaluate diagnostic tools. This study underscores the importance of robust evaluation when employing serological assays for SARS-CoV-2 detection in cattle populations.
Mosquito immune cells enhance dengue and Zika virus dissemination inAedes aegypti
Authors: Hall David R. , Johnson Rebecca M. , Kwon Hyeogsun , Ferdous Zannatul , Laredo-Tiscareño S. Viridiana , Blitvich Bradley J. , Brackney Doug E. , Smith Ryan C. 
Published: April 2024

AbstractMosquito-borne viruses cause more than 400 million annual infections and place over half of the world’s population at risk. Despite this importance, the mechanisms by which arboviruses infect the mosquito host and disseminate to tissues required for transmission are not well understood. Here, we provide evidence that mosquito immune cells, known as hemocytes, play an integral role in the dissemination of dengue virus (DENV) and Zika virus (ZIKV) in the mosquitoAedes aegypti. We establish that phagocytic hemocytes are a focal point for virus infection and demonstrate that these immune cell populations facilitate virus dissemination to the ovaries and salivary glands. Additional transfer experiments confirm that virus-infected hemocytes confer a virus infection to non-infected mosquitoes more efficiently than free virus in acellular hemolymph, revealing that hemocytes are an important tropism to enhance virus dissemination in the mosquito host. These data support a “trojan horse” model of virus dissemination where infected hemocytes transport virus through the hemolymph to deliver virus to mosquito tissues required for transmission and parallels vertebrate systems where immune cell populations promote virus dissemination to secondary sites of infection. In summary, this study significantly advances our understanding of virus infection dynamics in mosquitoes and highlights conserved roles of immune cells in virus dissemination across vertebrate and invertebrate systems.
Multi-scale phenotyping of senescence-related changes in roots ofRapeseedin response to nitrogen deficiency
Authors: James Maxence , Masclaux-Daubresse Céline , Balliau Thierry , Marmagne Anne , Chardon Fabien , Trouverie Jacques , Etienne Philippe 
Published: April 2024

ABSTRACTSenescence related markers have been widely studied in leaves in many plant species. Root senescence is more difficult to characterize. The existence of two different root organs inB. napus,with a taproot that appear to be specifically dedicated to the storage and remobilization of nutrients, offered the possibility of analysing the temporality of the changes linked to aging, based on the degradation of the taproot reserves. Microscopic and biochemical analyses showed that taproot plays an important role in carbon and nitrogen storage as reflected by the large quantities of starch and proteins present at early development stages. The proteomic study associated to the description of biochemical, morphological and anatomic changes provides a comprehensive picture of the main events occurring in the taproot and in the lateral roots with aging. Master modifications as protein and cell wall degradation, amino acid catabolism versus synthesis, nucleic acid degradation are presented and senescence related markers specific or not of the root types were identified. Comparison with Arabidopsis public data facilitated the identification of markers common to root and leaf senescence. The analysis of protease changes provides a list of candidates that may play a role in nitrogen and carbohydrate remobilization from taproot to the shoot and flowering organs and that would deserve attention for further functional analyses.
Within-host genetic diversity of SARS-CoV-2 across animal species
Authors: Naderi Sana , Sagan Selena M. , Shapiro B. Jesse 
Published: April 2024

AbstractInfectious disease transmission to different host species makes eradication very challenging and expands the diversity of evolutionary trajectories taken by the pathogen. Since the beginning of the ongoing COVID-19 pandemic, SARS-CoV-2 has been transmitted from humans to many different animal species, within which viral variants of concern could potentially evolve. Previously, using available whole genome consensus sequences of SARS-CoV-2 from four commonly sampled animals (mink, deer, cat, and dog) we inferred similar numbers of transmission events from humans to each animal species. Using a genome-wide association study (GWAS), we identified 26 single nucleotide variants (SNVs) that tend to occur in deer – more than any other animal – suggesting a high rate of viral adaptation to deer. The reasons for this rapid adaptive evolution remain unclear, but within-host evolution – the ultimate source of the viral diversity that transmits globally – could provide clues. Here we quantify intra-host SARS-CoV-2 genetic diversity across animal species and show that deer harbor more intra-host SNVs (iSNVs) than other animals, providing a larger pool of genetic diversity for natural selection to act upon. Mixed infections involving more than one viral lineage are unlikely to explain the higher diversity within deer. Rather, a combination of higher mutation rates, longer infections, and species-specific selective pressures are likely explanations. Combined with extensive deer-to-deer transmission, the high levels of within-deer viral diversity help explain the apparent rapid adaptation of SARS-CoV-2 to deer.
Saccadic compression of time as a marker for Developmental Dyslexia
Authors: Domenici Nicola , Tonelli Alessia , Ponente Cristina , Gori Monica 
Published: April 2024

SummaryAbout 10% of the world’s population is dyslexic, experiencing reading impairments unrelated to cognitive deterioration. Due to its impact, identifying the mechanisms subtending dyslexia is paramount. However, while most research focused on the eye movements’ phenomenology, none investigated their perceptual, transient consequences. In fact, it has been shown that rapid eye movements (i.e., saccades) are accompanied by temporary distortions of space and time. Such distortions have been linked to the receptive fields’ predictive remapping, which anticipates the movement and compensates for the gaze’s displacement. Here, we demonstrate that dyslexic children show reduced flexibility in modulating temporal information around the saccadic onset. Moreover, accuracy oscillations within the delta band, phase-locked to the saccade’s onset, preceded transient temporal compression in typical readers. Conversely, no oscillatory behavior was observed in dyslexic participants, suggesting that the absence of transient temporal distortions originated from the mismatch between the anticipatory remapping and the saccadic onset.
Low Blood Levels of Selenium, Selenoprotein P and GPx3 are Associated with Accelerated Biological Aging: Results from the Berlin Aging Study II (BASE-II)
Authors: Vetter Valentin Max , Demircan Kamil , Homann Jan , Chillon Thilo Samson , Mülleder Michael , Shomroni Orr , Steinhagen-Thiessen Elisabeth , Ralser Markus , Lill Christina M. , Bertram Lars , Schomburg Lutz , Demuth Ilja 
Published: April 2024

AbstractIntroductionBiological age reflects inter-individual differences in biological function and capacity beyond chronological age. Biological age can be estimated by DNA methylation age (DNAmA) and its deviation from chronological age, DNAmA acceleration (DNAmAA). Low levels of serum selenium, selenoprotein P (SELENOP), and the selenocysteine-containing glutathione peroxidase 3 (GPx3) are associated with adverse health outcomes and selenium supplementation is discussed as an anti-aging intervention.MethodsIn this study we analyzed 1,568 older participants from the Berlin Aging Study II (mean age +/− SD: 68.8 +/− 3.7 years, 51% women). DNAmA was estimated from genome-wide DNA methylation data using the Horvath, GrimAge, and DunedinPACE algorithms. Serum selenium levels were measured by total reflection X-ray fluorescence (TXRF) spectroscopy. SELENOP was measured by ELISA and GPx3 was derived from a larger set of mass spectrometry proteomics data.ResultsParticipants with deficient serum selenium levels (<90μg/L) had a higher rate of biological aging (DunedinPACE, p=0.01, n=865). This association remained statistically significant after adjustment for age, sex, BMI, smoking, and genetic ancestry (β=-0.02, SE=0.01, 95%CI: - 0.034 to −0.004, n=757). Compared to the highest quartile, participants in the lowest quartile of SELENOP levels showed an accelerated biological aging rate (DunedinPACE, β=-0.03, SE=0.01, 95%CI: −0.051 to −0.008, n=740, fully adjusted model). Similarly, after adjustment for covariates, accelerated biological age was found in participants within the lowest GPx3 quartile compared to participants in the fourth quartile (DunedinPACE, p=<0.001 and GrimAge, p<0.001).ConclusionOur study suggests that low levels of selenium biomarkers are associated with accelerated biological aging measured as DNAmA. This effect was not substantially changed after adjustment for known covariates.
The use and impact of surveillance-based technology initiatives in inpatient and acute mental health settings: A systematic review
Authors: Griffiths Jessica L. , Saunders Katherine R. K. , Foye Una , Greenburgh Anna , Regan Ciara , Cooper Ruth E. , Powell Rose , Thomas Ellen , Brennan Geoff , Rojas-Garcia Antonio , Lloyd-Evans Brynmor , Johnson Sonia , Simpson Alan 
Published: April 2024

AbstractBackgroundThe use of surveillance technologies is becoming increasingly common in inpatient mental health settings, commonly justified as efforts to improve safety and cost-effectiveness. However, the use of these technologies has been questioned in light of limited research conducted and the sensitivities, ethical concerns and potential harms of surveillance. This systematic review aims to: 1) map how surveillance technologies have been employed in inpatient mental health settings, 2) identify any best practice guidance, 3) explore how they are experienced by patients, staff and carers, and 4) examine evidence regarding their impact.MethodsWe searched five academic databases (Embase, MEDLINE, PsycInfo, PubMed and Scopus), one grey literature database (HMIC) and two pre-print servers (medRxiv and PsyArXiv) to identify relevant papers published up to 18/09/2023. We also conducted backwards and forwards citation tracking and contacted experts to identify relevant literature. Quality was assessed using the Mixed Methods Appraisal Tool. Data were synthesised using a narrative approach.ResultsA total of 27 studies were identified as meeting the inclusion criteria. Included studies reported on CCTV/video monitoring (n = 13), Vision-Based Patient Monitoring and Management (VBPMM) (n = 6), Body Worn Cameras (BWCs) (n = 4), GPS electronic monitoring (n = 2) and wearable sensors (n = 2). Twelve papers (44.4%) were rated as low quality, five (18.5%) medium quality, and ten (37.0%) high quality. Five studies (18.5%) declared a conflict of interest. We identified minimal best practice guidance. Qualitative findings indicate that patient, staff and carer perceptions and experiences of surveillance technologies are mixed and complex. Quantitative findings regarding the impact of surveillance on outcomes such as self-harm, violence, aggression, care quality and cost-effectiveness were inconsistent or weak.DiscussionThere is currently insufficient evidence to suggest that surveillance technologies in inpatient mental health settings are achieving the outcomes they are employed to achieve, such as improving safety and reducing costs. The studies were generally of low methodological quality, lacked lived experience involvement, and a substantial proportion (18.5%) declared conflicts of interest. Further independent coproduced research is needed to more comprehensively evaluate the impact of surveillance technologies in inpatient settings, including harms and benefits. If surveillance technologies are to be implemented, it will be important to engage all key stakeholders in the development of policies, procedures and best practice guidance to regulate their use, with a particular emphasis on prioritising the perspectives of patients.
Human Saposin B Ligand Binding and Presentation to α-Galactosidase A
Authors: Sawyer Thomas K. , Aral Efecan , Staros James V. , Bobst Cedric E. , Garman Scott C. 
Published: April 2024

ABSTRACTSphingolipid activator protein B (saposin B; SapB) is an essential activator of globotriaosylceramide (Gb3) catabolism by α-galactosidase A. However, the manner by which SapB stimulates α-galactosidase A activity remains unknown. To uncover the molecular mechanism of SapB presenting Gb3 to α-galactosidase A, we subjected the fluorescent substrate globotriaosylceramide-nitrobenzoxidazole (Gb3-NBD) to a series of biochemical and structural assays involving SapB. First, we showed that SapB stably binds Gb3-NBD using a fluorescence equilibrium binding assay, isolates Gb3-NBD from micelles, and facilitates α-galactosidase A cleavage of Gb3-NBDin vitro. Second, we crystallized SapB in the presence of Gb3-NBD and validated the ligand-bound assembly. Third, we captured transient interactions between SapB and α-galactosidase A by chemical cross-linking. Finally, we determined the crystal structure of SapB bound to α-galactosidase A. These findings establish general principles for molecular recognition in saposin:hydrolase complexes and highlight the utility of NBD reporter lipids in saposin biochemistry and structural biology.
Ais: streamlining segmentation of cryo-electron tomography datasets
Authors: Last Mart G.F. , Abendstein Leoni , Voortman Lenard M. , Sharp Thomas H. 
Published: April 2024

AbstractSegmentation is a critical data processing step in many applications of cryo-electron tomography. Downstream analyses, such as subtomogram averaging, are often based on segmentation results, and are thus critically dependent on the availability of open-source software for accurate as well as high-throughput tomogram segmentation. There is a need for more user-friendly, flexible and comprehensive segmentation software that offers an insightful overview of all steps involved in preparing automated segmentations. Here, we present Ais: a dedicated tomogram segmentation package that is geared towards both high performance and accessibility, available atgithub.com/bionanopatterning/Ais. In this report, we demonstrate two common processing steps that can be greatly accelerated with Ais: particle picking for subtomogram averaging, and generating many-feature segmentations of cellular architecture based onin situtomography data. Featuring comprehensive annotation, segmentation, and rendering functionality, as well as an open repository for trained models at aiscryoet.org, we hope that Ais will help accelerate research and dissemination of data involving cryoET.