bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of baleen whales in the New York Bight, 1998–2017: insights from opportunistic data
Authors: Chou Emily , Rekdahl Melinda L. , Kopelman Arthur H. , Brown Danielle M. , Sieswerda Paul L. , DiGiovanni Robert A. , Rosenbaum Howard C. 
Published: November 2022

AbstractThe New York Bight is undergoing rapid anthropogenic change amidst an apparent increase in baleen whale sightings. Though survey efforts have increased in recent years, the lack of published knowledge on baleen whale occurrence prior to these efforts impedes effective assessments of distributional or behavioural shifts due to increasing human activities. Here we synthesize opportunistic sightings of baleen whales from 1998–2017, which represent the majority of sightings data prior to recent survey efforts, and which are largely unpublished. Humpback and fin whales were the most commonly sighted species, followed by North Atlantic right whales and North Atlantic minke whales. Important behaviours such as feeding and nursing were observed, and most species (including North Atlantic right whales) were seen during all seasons. Baleen whales overlapped with multiple anthropogenic use areas, and all species, but of particular importance North Atlantic right whales, were sighted outside the spatial and temporal bounds of the Seasonal Management Areas for North Atlantic right whales. These opportunistic data are vital for providing a baseline and context of baleen whales in the New York Bight prior to broad-scale efforts and facilitate interpretation of current and future observations and trends, which can more accurately inform effective management and mitigation efforts.
The 0161 rap gap: the marginalisation of Black rap musicians in Manchester's live music scene
Authors: Reisner Latoya , Rymajdo Kamila 
Published: November 2022

AbstractFocusing on Manchester, the largest city in the north of England, this paper explores why and how Black rap practitioners have been excluded from performing and promoting rap music in its city centre during the last 20 years. Discussing the intersecting factors of policing of venues and racial bias and class stigma among Manchester's venue owners and promoters, while also scrutinising the city's neoliberal urban expansion and gentrification, the paper analyses the ways in which Black rappers and practitioners have been marginalised but also how they have attempted to resist and overcome these conditions. Drawing on cultural studies, critical race theory and urban geography, while employing qualitative research methods of in-depth interviews, this paper builds on existing research on the marginalisation of Black rap musicians and promoters. It builds on and moves beyond the scholarly emphasis on the policing of rap genres in London to argue that discrimination faced by Black rap practitioners extends far outside the capital and is part of a wider problem of racial capitalism of which policing is but one agent.
Doors, privacy and the public sphere: a conceptual discussion on the spatial structure of early modern Istanbul
Authors: Şavk Serkan 
Published: November 2022

AbstractThe aim of this article is to offer a new conceptual framework for the study of various spaces in Istanbul during the seventeenth and the eighteenth centuries. I contend that rather than the sharp distinction manifested with the public–private dichotomy, we need to focus on gradations of privacy. I offer qāpū and bāb as two new concepts borrowed from the period's own repertoire for representing the macro and micro ends of the spatial gradation. Theoretically, I draw on George Simmel's definition of doors as the interfaces of spatial formation.
Children’s Perspectives on Fairness and Inclusivity in the Classroom
Authors: Kaufman Elise Marie , Killen Melanie 
Published: November 2022

AbstractSchool represents an important context for children’s social, moral, and identity development. Research indicates that supportive teacher-student relationships are significantly related to positive student academic achievement. Unfortunately, teacher bias as well as peer exclusion based on group identity (gender, race, ethnicity, and nationality) pervade many school contexts. The presence of these biases in the classroom is negatively related to students’ academic development, especially for children who are minoritized and marginalized. Very little research has connected teacher bias and children’s reasoning about bias and inequalities in the classroom context. The classroom is a complex environment in which to examine children’s social and moral reasoning about bias, given teachers’ position of authority which often includes power, status, and prestige. We propose that understanding both teacher bias and peer intergroup exclusion are essential for promoting more fair classrooms. This paper reviews foundational theory as well as the social reasoning developmental model as a framework for studying how children think about fairness and bias in the classroom context. We then discuss current research on children’s social-cognitive and moral capacities, particularly in the contexts of societal inequality and social inclusion or exclusion. Finally, this article proposes new directions for research to promote fairness and inclusivity in schools and suggests how these new lines of research might inform school-based interventions.
Weed detection to weed recognition: reviewing 50 years of research to identify constraints and opportunities for large-scale cropping systems
Authors: Coleman Guy R.Y. , Bender Asher , Hu Kun , Sharpe Shaun M. , Schumann Arnold W. , Wang Zhiyong , Bagavathiannan Muthukumar V. , Boyd Nathan S. , Walsh Michael J. 
Published: November 2022

AbstractThe past 50 yr of advances in weed recognition technologies have poised site-specific weed control (SSWC) on the cusp of requisite performance for large-scale production systems. The technology offers improved management of diverse weed morphology over highly variable background environments. SSWC enables the use of nonselective weed control options, such as lasers and electrical weeding, as feasible in-crop selective alternatives to herbicides by targeting individual weeds. This review looks at the progress made over this half-century of research and its implications for future weed recognition and control efforts; summarizing advances in computer vision techniques and the most recent deep convolutional neural network (CNN) approaches to weed recognition. The first use of CNNs for plant identification in 2015 began an era of rapid improvement in algorithm performance on larger and more diverse datasets. These performance gains and subsequent research have shown that the variability of large-scale cropping systems is best managed by deep learning for in-crop weed recognition. The benefits of deep learning and improved accessibility to open-source software and hardware tools has been evident in the adoption of these tools by weed researchers and the increased popularity of CNN-based weed recognition research. The field of machine learning holds substantial promise for weed control, especially the implementation of truly integrated weed management strategies. Whereas previous approaches sought to reduce environmental variability or manage it with advanced algorithms, research in deep learning architectures suggests that large-scale, multi-modal approaches are the future for weed recognition.
Geometric-phase intraocular lenses with multifocality
Authors: Lee Seungmin , Park Gayeon , Kim Seonho , Ryu Yeonghwa , Yoon Jae Woong , Hwang Ho Sik , Song In Seok , Lee Chang Sun , Song Seok Ho 
Published: November 2022

AbstractWe demonstrate a new type of multifocal and extended depth of focus (EDOF) intraocular lenses (IOLs) embedding μm-thin geometric phase (GP) lens layers. As an emerging approach for lens phase design, the GP modulated IOLs outperform conventional diffractive IOLs in multifocality while completely avoiding the clinically undesirable demand for additional surface patterns to standard monofocal IOL designs. The number of foci and light splitting ratio of the GP IOLs are adjusted by changing the number of stacked GP layers and the thickness of each layer. Bifocal and trifocal GP IOLs are fabricated by radial alignment of anisotropic orientation in UV-curable liquid crystal polymers. After characterizing the defocus image and modulation transfer function of the GP IOLs, it is expected that GP IOLs will alleviate the most common problems associated with multifocal and EDOF IOLs, blurred vision and photic phenomena caused by light scattering and posterior capsule opacification.
Ultrasonically actuated neural probes for reduced trauma and inflammation in mouse brain
Authors: Chen Po-Cheng , Young Catharine G. , Schaffer Chris B. , Lal Amit 
Published: November 2022

AbstractElectrical neural recordings measured using direct electrical interfaces with neural tissue suffer from a short lifespan because the signal strength decreases over time. The inflammatory response to the inserted microprobe can create insulating tissue over the electrical interfaces, reducing the recorded signal below noise levels. One of the factors contributing to this inflammatory response is the tissue damage caused during probe insertion. Here, we explore the use of ultrasonic actuation of the neural probe during insertion to minimize tissue damage in mice. Silicon neural microprobes were designed and fabricated with integrated electrical recording sites and piezoelectric transducers. The microprobes were actuated at ultrasonic frequencies using integrated piezoelectric transducers. The microprobes were inserted into mouse brains under a glass window over the brain surface to image the tissue surrounding the probe using two-photon microscopy. The mechanical force required to penetrate the tissue was reduced by a factor of 2–3 when the microprobe was driven at ultrasonic frequencies. Tissue histology at the probe insertion site showed a reduced area of damage and decreased microglia counts with increasing ultrasonic actuation of the probes. Two-photon imaging of the microprobe over weeks demonstrated stabilization of the inflammatory response. Recording of electrical signals from neurons over time suggests that microprobes inserted using ultrasound have a higher signal-to-noise ratio over an extended time period.
Cholinergic basal forebrain degeneration due to sleep-disordered breathing exacerbates pathology in a mouse model of Alzheimer’s disease
Authors: Qian Lei , Rawashdeh Oliver , Kasas Leda , Milne Michael R. , Garner Nicholas , Sankorrakul Kornraviya , Marks Nicola , Dean Matthew W. , Kim Pu Reum , Sharma Aanchal , Bellingham Mark C. , Coulson Elizabeth J. 
Published: November 2022

AbstractAlthough epidemiological studies indicate that sleep-disordered breathing (SDB) such as obstructive sleep apnea is a strong risk factor for the development of Alzheimer’s disease (AD), the mechanisms of the risk remain unclear. Here we developed a method of modeling SDB in mice that replicates key features of the human condition: altered breathing during sleep, sleep disruption, moderate hypoxemia, and cognitive impairment. When we induced SDB in a familial AD model, the mice displayed exacerbation of cognitive impairment and the pathological features of AD, including increased levels of amyloid-beta and inflammatory markers, as well as selective degeneration of cholinergic basal forebrain neurons. These pathological features were not induced by chronic hypoxia or sleep disruption alone. Our results also revealed that the cholinergic neurodegeneration was mediated by the accumulation of nuclear hypoxia inducible factor 1 alpha. Furthermore, restoring blood oxygen levels during sleep to prevent hypoxia prevented the pathological changes induced by the SDB. These findings suggest a signaling mechanism whereby SDB induces cholinergic basal forebrain degeneration.
Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level
Authors: Sefer Anna , Kallis Eleni , Eilert Tobias , Röcker Carlheinz , Kolesnikova Olga , Neuhaus David , Eustermann Sebastian , Michaelis Jens 
Published: November 2022

AbstractSingle-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1’s multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1’s N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.
HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex
Authors: Leisegang Matthias S. , Bains Jasleen Kaur , Seredinski Sandra , Oo James A. , Krause Nina M. , Kuo Chao-Chung , Günther Stefan , Sentürk Cetin Nevcin , Warwick Timothy , Cao Can , Boos Frederike , Izquierdo Ponce Judit , Haydar Shaza , Bednarz Rebecca , Valasarajan Chanil , Fuhrmann Dominik C. , Preussner Jens , Looso Mario , Pullamsetti Soni S. , Schulz Marcel H. , Jonker Hendrik R. A. , Richter Christian , Rezende Flávia , Gilsbach Ralf , Pflüger-Müller Beatrice , Wittig Ilka , Grummt Ingrid , Ribarska Teodora , Costa Ivan G. , Schwalbe Harald , Brandes Ralf P. 
Published: November 2022

AbstractDNA:DNA:RNA triplexes that are formed through Hoogsteen base-pairing of the RNA in the major groove of the DNA duplex have been observed in vitro, but the extent to which these interactions occur in cells and how they impact cellular functions remains elusive. Using a combination of bioinformatic techniques, RNA/DNA pulldown and biophysical studies, we set out to identify functionally important DNA:DNA:RNA triplex-forming long non-coding RNAs (lncRNA) in human endothelial cells. The lncRNA HIF1α-AS1 was retrieved as a top hit. Endogenous HIF1α-AS1 reduces the expression of numerous genes, including EPH Receptor A2 and Adrenomedullin through DNA:DNA:RNA triplex formation by acting as an adapter for the repressive human silencing hub complex (HUSH). Moreover, the oxygen-sensitive HIF1α-AS1 is down-regulated in pulmonary hypertension and loss-of-function approaches not only result in gene de-repression but also enhance angiogenic capacity. As exemplified here with HIF1α-AS1, DNA:DNA:RNA triplex formation is a functionally important mechanism of trans-acting gene expression control.
Barium content of Archaean continental crust reveals the onset of subduction was not global
Authors: Huang Guangyu , Mitchell Ross N. , Palin Richard M. , Spencer Christopher J. , Guo Jinghui 
Published: November 2022

AbstractEarth’s earliest continental crust is dominated by tonalite–trondhjemite–granodiorite (TTG) suites, making these rocks key to unlocking the global geodynamic regime operating during the Archaean (4.0–2.5 billion years ago [Ga]). The tectonic setting of TTG magmatism is controversial, with hypotheses arguing both for and against subduction. Here we conduct petrological modeling over a range of pressure–temperature conditions relevant to the Archaean geothermal gradient. Using an average enriched Archaean basaltic source composition, we predict Ba concentrations in TTG suites, which is difficult to increase after magma generated in the source. The results indicate only low geothermal gradients corresponding to hot subduction zones produce Ba-rich TTG, thus Ba represents a proxy for the onset of subduction. We then identify statistically significant increases in the Ba contents of TTG suites worldwide as recording the diachronous onset of subduction from regional at 4 Ga to globally complete sometime after 2.7 Ga.
Endothelial dysfunction markers and immune response indices in cosmonauts’ blood after long-duration space flights
Authors: Kuzichkin D. S. , Nichiporuk I. A. , Zhuravleva O. A. , Markin A. A. , Rykova M. P. , Zhuravleva T. V. , Sadova A. A. , Kutko O. V. , Shmarov V. A. , Ponomarev S. A. 
Published: November 2022

AbstractSpace flight factors are known to cause a malfunction in the human immune system and lead to damage to blood vessels. The hemostatic function of endothelium during space missions and its interaction with human immunity has not been determined so far. In this work, we investigated the markers of endothelial activation and damage (plasma concentrations of soluble thrombomodulin fraction (sTM), von Willebrand factor (vWF), highly sensitive C-reactive protein (hs-CRP)), as well as the level of D-dimer and compared them to the immunological parameters characterizing the state of human humoral and cellular immunity. The immune status of long-duration ISS crewmembers was assessed by whole-blood testing, and comprehensive postflight immune assessment included the analysis of leukocyte distribution. Flow cytometry was applied to determine the absolute counts and the percentage of lymphocyte subsets: B cells (CD19+), T cells (CD3+, CD3+CD4+, CD3+CD8+), NK cells (CD3−CD16+CD56+, CD11b+CD56+), and activated subsets (CD3+CD25+ and CD3+HLA-DR+). The in vitro basal cytokine production was investigated in whole blood cell culture. The cytokines IFN-gamma, IL-1-beta, IL-4, IL-6, IL-10, IL-18, and TNF-alpha were measured in plasma and the 24-h supernatants by a sensitive enzyme-linked immunosorbent assay. A significant increase in the plasma levels of vWF and hs-CRP and a decrease in the concentration of sTM after spaceflights were detected. Divergent changes in the parameters characterizing the state of the immune system were observed. We propose that the changes revealed may lead to an increase in the procoagulant activity of blood plasma, suppression of protein C activation and thrombin inhibition, as well as to an increase in the adhesive-aggregate potential of platelets, especially in case of changes in the rheological characteristics of blood flow during re-adaptation to ground conditions. We also speculate that the immune system might play an important role in vessel damage during long-duration missions.
Histone H2B.8 compacts flowering plant sperm through chromatin phase separation
Authors: Buttress Toby , He Shengbo , Wang Liang , Zhou Shaoli , Saalbach Gerhard , Vickers Martin , Li Guohong , Li Pilong , Feng Xiaoqi 
Published: November 2022

AbstractSperm chromatin is typically transformed by protamines into a compact and transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines, yet they have small, transcriptionally active nuclei with chromatin condensed through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8 causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression in somatic cells produces smaller nuclei with aggregated chromatin. This result demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates transcriptionally inactive AT-rich chromatin into phase-separated condensates, which facilitates nuclear compaction without reducing transcription. Reciprocal crosses show that mutation of h2b.8 reduces male transmission, which suggests that H2B.8-mediated sperm compaction is important for fertility. Altogether, our results reveal a new mechanism of nuclear compaction through global aggregation of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation of flowering plants that achieves nuclear condensation compatible with active transcription.
Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells
Authors: Nguyenla Xammy , Wehri Eddie , Van Dis Erik , Biering Scott B. , Yamashiro Livia H. , Zhu Chi , Stroumza Julien , Dugast-Darzacq Claire , Graham Thomas G. W. , Wang Xuanting , Jockusch Steffen , Tao Chuanjuan , Chien Minchen , Xie Wei , Patel Dinshaw J. , Meyer Cindy , Garzia Aitor , Tuschl Thomas , Russo James J. , Ju Jingyue , Näär Anders M. , Stanley Sarah , Schaletzky Julia 
Published: November 2022

AbstractSARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy is only moderate, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. This identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir’s apparent potency > 25-fold. We report that HCV NS5A inhibitors act on the SARS-CoV-2 exonuclease proofreader, providing a possible explanation for the synergy observed with nucleoside analog remdesivir. FDA-approved Hepatitis C therapeutics Epclusa® (velpatasvir/sofosbuvir) and Zepatier® (elbasvir/grazoprevir) could be further optimized to achieve potency and pharmacokinetic properties that support clinical evaluation in combination with remdesivir.
Seasonal variations of the airborne microbial assemblages of the Seoul subway, South Korea from 16S and ITS gene profiles with chemical analysis
Authors: Hassan Zohaib Ul , Cho Hana , Park Changwoo , Yim Yong-Hyeon , Kim Seil 
Published: November 2022

AbstractIn this study, we determined the seasonal airborne microbial diversity profiles at SMRT stations by sequencing the 16S rRNA and ITS. Particulate matter samples were collected from air purifiers installed in the platform area of the SMRT subway stations. Three stations that included the most crowded one were selected for the sampling. The sampling was done at each season during 2019. After extracting the total DNA from all seasonal samples, PCR was performed with Illumina overhang adapter primers for the V3–V4 region of the 16S rRNA gene and ITS2 region of the ITS gene. The amplified products were further purified, and sequencing libraries were made. Sequencing was carried with the Illumina Miseq Sequencing system (Illumina, USA) followed by in-depth diversity analyses. The elemental composition of the particulate matter samples collected from the different subway stations were obtained using a WD-XRF spectrometer. The SMRT microbiome showed extensive taxonomic diversity with the most common bacterial genera at the subway stations associated with the skin. Overall, the stations included in this study harbored different phylogenetic communities based onα- and β-diversity comparisons. Microbial assemblages also varied depending upon the season in which the samples were taken and the station. Major elements present at the subway stations were from aerosols generated between wheels and brake cushions and between the catenaries and the pantographs. This study shows that the microbial composition of the SMRT subway stations comes from a diverse combination of environmental and human sources, the season and the lifestyle of commuters.