bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Side Effects after Administration of the 1st Dose of Oxford-AstraZeneca Vaccine
Authors: Singh Pramod , Faisal Abdul Rafae , Shah M. Hassaan , Saeed Ahmad , Younas Hadia , Butt Usamah Saeed , Pudasaini Sudip , Pasha Abdul Rafay , Rehman Umair 
Published: August 2022

AbstractVaccines have played a central role in minimizing new infections, the rate of hospitalizations, and the overall burden on the health sector. Fear of side-effects is the biggest and commonest reason for avoiding getting vaccinated. It is, therefore, essential to maintain the clarity and consistency of message, to support and encourage people to get vaccinated. This study aims to contribute in that regard, by registering and quantifying the early side-effects of the Oxford-AstraZeneca COVID-19 vaccine in Pakistan. This study employs a non-random cross-sectional design. Data collected from 477 participants using a structured questionnaire was used to investigate the relationship between socio-demographic characteristics and side effect profiles of the participants. Binomial Logistic Regression was used to analyze the data. Odds Ratio (OR) gives the likelihood of having a side effect versus the reference group. Significance level (α) for the probability value (p-value) is set at 0.05. Fever (30.19%) was the most commonly experienced side effect, followed closely by fatigue (22.01%). 71.11% of those with fever experienced low grade fever (99-100F) while 62.69% of body aches experienced were moderate in intensity (Grades 4-6). In general, younger people are significantly more likely (p=0.023) to experience side effects (OR-1 = 1.023: interpreted as 1.023 times increase per unit decrease in age). Similarly, they are more likely (p= 0.029) to have a headache (OR-1 =1.039). Also, they are more likely (p= 0.007) to have a body ache (OR-1 =1.038). The Oxford-AstraZeneca COVID-19 vaccine side-effects seem to be more prevalent among younger age groups, which points to increased vaccine safety among older individuals that are usually more susceptible to severe COVID-19 infection. In addition, we found a substantially reduced number of side-effects, as compared to the clinical trials, which is an encouraging indicator for vaccine safety.
Neuronal SNAP-23 scales hippocampal synaptic plasticity and memory
Authors: Huang Mengjia , Bin Na-Ryum , Rai Jayant , Ma Ke , Chow Chun Hin , Eide Sarah , Harada Hidekiyo , Xiao Jianbing , Feng Daorong , Sun Hong-Shuo , Feng Zhong-Ping , Gaisano Herbert Y. , Pessin Jeffrey E. , Monnier Philippe P. , Okamoto Kenichi , Zhang Liang , Sugita Shuzo 
Published: August 2022

SummarySoluble NSF Attachment protein REceptor (SNARE)-mediated membrane fusion plays a crucial role not only in presynaptic vesicle exocytosis but also in postsynaptic receptor delivery. The latter is considered particularly important for long-term synaptic plasticity and learning and memory, yet underlying mechanisms including the identity of the key SNARE proteins remain elusive. Here, we investigate the role of neuronal Synaptosomal-Associated Protein-23 (SNAP-23) by analyzing pyramidal-neuron specific SNAP-23 conditional knockout (cKO) mice. SNAP-23 immunostaining in postsynaptic spines was effectively decreased in the SNAP-23 cKO hippocampus. Electrophysiological analysis of SNAP-23 deficient neurons using acute hippocampal slices showed normal basal neurotransmission in CA3-CA1 synapses with unchanged AMPA and NMDA currents. Nevertheless, we found theta-burst stimulation induced long-term potentiation (LTP) was vastly diminished in SNAP-23 cKO. Moreover, unlike syntaxin-4 cKO mice in which both basal neurotransmission and LTP decrease manifested changes in a broad set of behavioral tasks, deficits of SNAP-23 cKO is more limited to spatial memory. Our data reveal that neuronal SNAP-23 is selectively crucial for synaptic plasticity and spatial memory without affecting basal glutamate receptor function.
The hologenome of Osedax frankpressi reveals the genetic interplay for the symbiotic digestion of vertebrate bone
Authors: Moggioli Giacomo , Panossian Balig , Sun Yanan , Thiel Daniel , Martín-Zamora Francisco M. , Tran Martin , Clifford Alexander M. , Goffredi Shana K. , Rimskaya-Korsakova Nadezhda , Jékelly Gáspár , Tresguerres Martin , Qian Pei-Yuan , Qiu Jian-Wen , Rouse Greg W. , Henry Lee M. , Martín-Durán José M. 
Published: August 2022

AbstractThe marine annelid Osedax has evolved a unique heterotrophic symbiosis that allows it to feed exclusively on sunken bones. Yet, the genetic and physiological principles sustaining this symbiosis are poorly understood. Here we show that Osedax frankpressi has a small, AT-rich genome shaped by extensive gene loss. While the Oceanospirillales endosymbiont of Osedax is enriched in genes for carbohydrate and nitrogen metabolism, O. frankpressi has undergone genetic changes to accommodate bone digestion, including the expansion of matrix metalloproteases, and a loss of pathways to synthesize amino acids that are abundant in collagen. Unlike other symbioses, however, innate immunity genes required to acquire and control the endosymbionts are reduced in O. frankpressi. These findings reveal Osedax has evolved an alternative genomic toolkit to bacterial symbiosis where host-symbiont co-dependence has favoured genome simplicity in the host to exploit the nutritionally unbalanced diet of bones.TeaserGenome reduction and adaptations for collagen digestion underpin the symbiosis of Osedax worms to exploit decaying bones.
AVP neurons act as the primary circadian pacesetter cells in vivo
Authors: Tsuno Yusuke , Peng Yubo , Horike Shin-ichi , Yamagata Kanato , Sugiyama Mizuki , Nakamura Takahiro J. , Daikoku Takiko , Maejima Takashi , Mieda Michihiro 
Published: August 2022

AbstractThe central circadian clock of the suprachiasmatic nucleus (SCN) is a network consisting of various neurons and glia. Individual cells have the autonomous molecular machinery of a cellular clock, but their intrinsic periods are considerably variable. Here, we show that arginine vasopressin (AVP) neurons set the ensemble period of the SCN network to control circadian behavior rhythm. Artificial lengthening of cellular periods by deleting casein kinase 1 delta (CK1δ) in the whole SCN lengthened the free-running period of behavior rhythm to an extent similar to CK1δ deletion specific to AVP neurons. In SCN slices, PER2::LUC reporter rhythms of these mice did not recapitulate the period lengthening. However, in vivo calcium rhythms of both AVP and vasoactive intestinal peptide (VIP) neurons demonstrated lengthened periods similar to the behavioral rhythm upon AVP neuron-specific CK1δ deletion. These results indicate that AVP neurons act as the primary determinant of the SCN ensemble period.
Detection of YAP1 and AR-V7 mRNA for Prostate Cancer prognosis using an ISFET Lab-On-Chip platform
Authors: Broomfield Joseph , Kalofonou Melpomeni , Pataillot-Meakin Thomas , Powell Sue M. , Moser Nicolas , Bevan Charlotte L. , Georgiou Pantelis 
Published: August 2022

AbstractProstate cancer (PCa) is the second most common cause of male cancer-related death worldwide. The gold standard of treatment for advanced PCa is androgen deprivation therapy (ADT). However, eventual failure of ADT is common and leads to lethal metastatic castration resistant PCa (mCRPC). As such, the detection of relevant biomarkers in the blood for drug resistance in mCRPC patients could lead to personalized treatment options. mRNA detection is often limited by the low specificity of qPCR assays which are restricted to specialised laboratories. Here, we present a novel reversetranscription loop-mediated isothermal amplification (RT-LAMP) assay and have demonstrated its capability for sensitive detection of AR-V7 and YAP1 RNA (3×101 RNA copies per reaction). This work presents a foundation for the detection of circulating mRNA in PCa on a non-invasive Lab-on-chip (LoC) device for use at point-of-care. This technique was implemented onto a Lab-on-Chip platform integrating an array of chemical sensors (ion-sensitive field-effect transistors - ISFETs) for real-time detection of RNA. Detection of RNA presence was achieved through the translation of chemical signals into electrical readouts. Validation of this technique was conducted with rapid detection (<15 min) of extracted RNA from prostate cancer cell lines 22Rv1s and DU145s.
In the spotlight, losing IR region: insights from euglenophytes challenge the importance of inverted repeats in the genomes of secondary plastids
Authors: Maciszewski Kacper , Fells Alicja , Karnkowska Anna 
Published: August 2022

AbstractPlastids, similarly to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids – a group which obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, riddled with losses and multiple subsequent regains of inverted ribosomal operon (rDNA) repeats, as well as independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution, and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.
Detecting Boolean Asymmetric Relationships with a Loop Counting Technique and its Implications for Analyzing Heterogeneity within Gene Expression Datasets
Authors: Zhou Haosheng , Lin Wei , Labra Sergio R. , Lipton Stuart A. , Elman Jeremy A. , Schork Nicholas J. , Rangan Aaditya V. 
Published: August 2022

AbstractMany traditional methods for analyzing gene-gene relationships focus on positive and negative correlations, both of which are a kind of ‘symmetric’ relationship. Biclustering is one such technique that typically searches for subsets of genes exhibiting correlated expression among a subset of samples. However, genes can also exhibit ‘asymmetric’ relationships, such as ‘if-then’ relationships used in boolean circuits. In this paper we develop a very general method that can be used to detect biclusters within gene-expression data that involve subsets of genes which are enriched for these ‘boolean-asymmetric’ relationships (BARs). These BAR-biclusters can correspond to heterogeneity that is driven by asymmetric gene-gene interactions, e.g., reflecting regulatory effects of one gene on another, rather than more standard symmetric interactions. Unlike typical approaches that search for BARs across the entire population, BAR-biclusters can detect asymmetric interactions that only occur among a subset of samples. We apply our method to a single-cell RNA-sequencing data-set, demonstrating that the statistically-significant BAR-biclusters indeed contain additional information not present within the more traditional ‘boolean-symmetric’-biclusters. For example, the BAR-biclusters involve different subsets of cells, and highlight different gene-pathways within the data-set. Moreover, by combining the boolean-asymmetric- and boolean-symmetric-signals, one can build linear classifiers which outperform those built using only traditional boolean-symmetric signals.
Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism
Authors: Hunt Hilary , Brueggen Nico , Galle Alexander , Vanderauwera Sandy , Frohberg Claus , Fernie Alisdair R , Sonnewald Uwe , Sweetlove Lee J 
Published: August 2022

AbstractCompanion cells and sieve elements play an essential role in vascular plants and yet the details of the metabolism that underpins their function remain largely unknown. Here we construct a tissue-scale flux balance analysis (FBA) model to describe the metabolism of phloem loading in a mature Arabidopsis leaf. We explore the potential metabolic interactions between mesophyll cells, companion cells, and sieve elements based on current understanding of the physiology of phloem tissue and through the use of cell-type-specific transcriptome data as a weighting in our model. We find that companion cell chloroplasts likely play a very different role to mesophyll chloroplasts. Our model suggests that, rather than carbon capture, the most crucial function of companion cell chloroplasts is to provide photosynthetically-generated ATP to the cytosol. Additionally, our model predicts that the metabolites imported into the companion cell are not necessarily the same metabolites that are exported in phloem sap; phloem loading is more efficient if certain amino acids are synthesised in the phloem tissue. Surprisingly, in our model predictions the H+-PPiase is the more important contributor than the H+ ATPase to the energisation of the companion cell plasma membrane.
Novel adaptation supports enhanced macrophage efferocytosis in limited-oxygen environments
Authors: Wang Ya-Ting , Trzeciak Alissa , Rojas Waleska Saitz , Saavedra Pedro , Chen Yan-Ting , Chirayil Rachel , Etchegaray Jon Iker , Lucas Christopher D. , Puleston Daniel J. , Keshari Kayvan R. , Perry Justin S. A. 
Published: August 2022

SummaryApoptotic cell clearance (efferocytosis), a process essential for organismal homeostasis, is performed by phagocytes that inhabit a wide range of environments, including physiologic hypoxia. Here, we find macrophages, the predominant tissue-resident phagocyte, display enhanced efferocytosis under prolonged (chronic) physiological hypoxia, characterized by increased internalization and accelerated degradation of apoptotic cells. Analysis of mRNA and protein programs revealed that chronic physiological hypoxia induces two distinct but complimentary states in macrophages. The first, ‘primed’ state consists of concomitant induction of transcriptional and translational programs broadly associated with metabolism in apoptotic cell-naïve macrophages that persist during efferocytosis. The second, ‘poised’ state consists of transcription, but not translation, of phagocyte function programs in apoptotic cell-naïve macrophages that are subsequently translated during efferocytosis. Importantly, we discovered that both states are necessary for enhanced continual efferocytosis. Mechanistically, we find that one such ‘primed’ state consists of the efficient flux of glucose into a noncanonical pentose phosphate pathway (PPP) loop, whereby PPP-derived intermediates cycle back through the PPP to enhance production of NADPH. Furthermore, we found that PPP-derived NADPH directly supports enhanced continual efferocytosis under chronic physiological hypoxia via its role in phagolysosomal maturation and maintenance of cellular redox homeostasis. Thus, macrophages residing under chronic physiological hypoxia adopt states that both support cell fitness and ensure ability to perform essential homeostatic functions rapidly and safely.Highlights-Macrophages residing in chronic physiological hypoxia have enhanced apoptotic cell uptake and degradation-Chronic physiological hypoxia induces both primed and poised states in macrophages-Both primed and poised state programs directly support enhanced continual efferocytosis-A noncanonical PPP loop, a unique primed state, directly supports enhanced efferocytosis and maintains redox homeostasis
Species invasions shift microbial phenology in a two-decade freshwater time series
Authors: Rohwer Robin R. , Hale Riley J. , Vander Zanden M. Jake , Miller Todd R. , McMahon Katherine D. 
Published: August 2022

AbstractInvasive species impart abrupt changes on ecosystems, but their impacts on microbial communities are often overlooked. We paired a 20-year freshwater microbial community time series with zooplankton and phytoplankton counts, rich environmental data, and a 6-year cyanotoxin time series. We observed strong microbial phenological patterns that were disrupted by the invasions of spiny water flea (Bythotrephes cederströmii) and zebra mussels (Dreissena polymorpha). First, we detected shifts inCyanobacteriaphenology. After the spiny water flea invasion,Cyanobacteriadominance crept earlier into clearwater; and after the zebra mussel invasion,Cyanobacteriaabundance crept even earlier into the diatom-dominated spring. During summer, the spiny water flea invasion sparked a cascade of shifting diversity where zooplankton diversity decreased andCyanobacteriadiversity increased. Second, we detected shifts in cyanotoxin phenology. After the zebra mussel invasion, microcystin increased in early summer and the duration of toxin production increased by over a month. Third, we observed shifts in heterotrophic bacteria phenology. TheBacteroidotaphylum and members of the acINanopelagicaleslineage were differentially more abundant. The proportion of the bacterial community that changed also differed by season; the spring and clearwater bacterial communities changed most following the spiny water flea invasion that lessened clearwater duration and intensity, while the diverse summer bacterial community changed least following the zebra mussel invasion despite the observed shifts in diversity and toxicity during summer. These long-term invasion-mediated shifts in microbial phenology demonstrate the interconnectedness of microbes with the broader food web, and their susceptibility to long-term environmental change.Significance StatementMicrobial communities are typically studied as part of the microbial loop, separately from the broader food web. Using a two-decade freshwater time series, we explored whether two species invasions that shifted the metazoan food web (spiny water flea and zebra mussels) also impacted the microbial communities. We looked for seasonal responses because the microbial communities had strong seasonal patterns. We discovered thatCyanobacteriaincreased early in the year, andCyanobacteriadiversity increased in the summer. Cyanotoxins also increased, along with the duration of toxin production. In the heterotrophic bacterial community, some organisms changed consistently within lineages and seasons while others diverged. These findings illustrate the importance of seasonal context, and highlight the interconnectedness of bacteria with the broader food web.
Collective polarization dynamics in gonococcal colonies
Authors: Hennes Marc , Bender Niklas , Cronenberg Tom , Welker Anton , Maier Berenike 
Published: August 2022

AbstractMembrane potential in bacterial systems has been shown to be dynamic and tightly related to survivability at the single cell level. However, little is known about spatio-temporal patterns of membrane potential in bacterial colonies and biofilms. Here, we discovered a switch from uncorrelated to collective dynamics within colonies formed by the human pathogen Neisseria gonorrhoeae. In freshly assembled colonies, polarization is heterogeneous with instances of transient and uncorrelated hyper- or depolarization of individual cells. As colonies reach a critical size, the polarization behaviour switches to collective dynamics: A hyperpolarized shell forms at the centre, travels radially outward, and halts several micrometres from the colony periphery. Once the shell has passed, we detect an influx of potassium correlated with depolarisation. Transient hyperpolarization also demarks the transition from volume to surface growth. By combining simulations and the use of an alternative electron acceptor for the respiratory chain, we provide strong evidence that local oxygen gradients shape the collective polarization dynamics. Finally, we show that within the hyperpolarized shell, tolerance against aminoglycoside antibiotics but not against β-lactam antibiotics is increased, suggesting that depolarization instantaneously protects cells, while the protective effect of growth arrest does not set in immediately. These findings highlight that the polarization pattern can demark the differentiation into distinct subpopulations with different growth rates and antibiotic tolerance.Significance statementAt the level of single bacteria, membrane potential is surprisingly dynamic and transient hyperpolarization has been associated with increased death rate. Yet, little is known about the spatiotemporal dynamics of membrane polarization during biofilm development. Here, we reveal a discrete transition from uncorrelated to collective polarization dynamics within spherical colonies. Suddenly, a shell of hyperpolarized cells forms at the colony centre and hyperpolarization travels radially outward. In the wake of this shell, bacteria depolarize, reduce their growth rate, and become tolerant against antibiotics, indicating the onset of habitat diversity. Single cell live imaging and modelling link hyperpolarization to an oxygen gradient formed within the colonies. We anticipate that dynamical polarization patterns are tightly connected to biofilm differentiation in various bacterial species.