bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal feature based deep neural network for cell lineage analysis in microscopy images
Authors: Chen Siteng , Paek Andrew L. , Lasick Kathleen A. , Loganathan Suvithanandhini , Roveda Janet , Li Ao 
Published: August 2021

AbstractBackgroundTime-lapse microscopy has been widely used in biomedical experiments because it can visualize the molecular activities of living cells in real time. However, biomedical researchers are still conducting cell lineage analysis manually. Developing automatic lineage tracing algorithms is a challenging task. In the past two decades, deep neural networks (DNNs) became have shown outstanding performance on computer vision tasks. They can learn complex visual features, capture long-range temporal dependencies, and have the potential to be used for automatic cell lineage analysis.MethodsIn this study, we propose a multi-task spatio-temporal feature based deep neural network for cell lineages analysis (Cell-STN). The Cell-STN extracts spatio-temporal features from microscopy image sequences by leveraging our convolutional long short-term memory based core block. And the proposed Cell-STN utilized a task specific network to predict the cell location, the mitosis event, and the apoptosis event in a multi-task manner.ResultsWe evaluated the Cell-STN on three in-house datasets (MCF7, U2OS, and HCT116) and one public dataset (Fluo-N2DL-HeLa). For cell tracking, we used peak-wise precision, track-wise precision, end-peak precision, and spatial distance as metrics. The overall results showed the Cell-STN models outperform other state-of-the-art cell trackers. For mitosis and apoptosis tasks, we used accuracy, F1-score, temporal distance, and spatial distance as metrics. The Cell-STN models achieved the highest performance on all datasets.ConclusionThis study presented a novel DNNs approach for cell lineage analysis in microscopy images. The Cell-STN showed outstanding performance on the four datasets. Additionally, the Cell-STN required minimal training data and can be adapted to new biological event detection tasks by appending task-specific layers. This algorithm has the potential to be used in real-world biomedical research.
Validation and invalidation of SARS-CoV-2 main protease inhibitors using the Flip-GFP and Protease-Glo luciferase assays
Authors: Ma Chunlong , Tan Haozhou , Choza Juliana , Wang Yuying , Wang Jun 
Published: August 2021

AbstractSARS-CoV-2 main protease (Mpro) is one of the most extensive exploited drug targets for COVID-19. Structurally disparate compounds have been reported as Mproinhibitors, raising the question of their target specificity. To elucidate the target specificity and the cellular target engagement of the claimed Mproinhibitors, we systematically characterize their mechanism of action using the cell-free FRET assay, the thermal shift-binding assay, the cell lysate Protease-Glo luciferase assay, and the cell-based Flip-GFP assay. Collectively, our results have shown that majority of the Mproinhibitors identified from drug repurposing including ebselen, carmofur, disulfiram, and shikonin are promiscuous cysteine inhibitors that are not specific to Mpro, while chloroquine, oxytetracycline, montelukast, candesartan, and dipyridamole do not inhibit Mproin any of the assays tested. Overall, our study highlights the need of stringent hit validation at the early stage of drug discovery.Graphical abstractFlip-GFP and Protease-Glo luciferase assays, coupled with the FRET and thermal shift binding assays, were applied to validate the reported SARS-CoV-2 Mproinhibitors.
Comparing the efficiency of monofilament and traditional nets for capturing bats
Authors: Chaves-Ramírez Silvia , Castillo-Salazar Christian , Sánchez-Chavarría Mariela , Solís-Hernández Hellen , Chaverri Gloriana 
Published: August 2021

AbstractTraditional mist nets used for capturing bats have several drawbacks, particularly that they are inefficient at sampling many insectivorous species. One possible alternative is to use monofilament nets, whose netting is made of single strands of yarn instead of several as regular nets, making them less detectable. To date, no study has quantified the capture efficiency of monofilament nets compared to regular mist nets for the study of bats. Here we compare capture efficiency of monofilament and regular mist nets, focusing on bat abundance and species diversity at a lowland tropical forest in southwestern Costa Rica. During our sampling period, we captured 90 individuals and 14 species in regular nets and 125 individuals and 20 species in monofilament nets. The use of monofilament nets increased overall capture rates, but most notably for insectivorous species. Species accumulation curves indicate that samples based on regular nets are significantly underestimating species diversity, most notably as these nets fail at sampling rare species. We show that incorporating monofilament nets into bat studies offers an opportunity to expand records of different guilds and rare bat species and to improve our understanding of poorly-known bat assemblages while using a popular, relatively cheap and portable sampling method.
Vaccines alone are no silver bullets: a modeling study on the impact of efficient contact tracing on COVID-19 infection and transmission
Authors: Raja Dhesi Baha , Abdul Taib Nur Asheila , Teo Alvin Kuo Jing , Jayaraj Vivek Jason , Ting Choo-Yee 
Published: August 2021

AbstractBackgroundThe computer simulation presented in this study aimed to investigate the effect of contact tracing on COVID-19 transmission and infection in the context of rising vaccination rates.MethodsThis study proposed a deterministic SEIRV model with contact tracing and vaccination components. We initialized some parameters using the Malaysian COVID-19 data to inform the model. We defined contact tracing effectiveness as the proportion of contacts of a positive case that was successfully traced and vaccination rate as the proportion of daily doses administered per population in Malaysia. Sensitivity analyses on the untraced and infectious populations were conducted. The study presented in silico findings on multiple scenarios by varying the contact tracing effectiveness and daily vaccination rates.ResultsAt a vaccination rate of 1.4%, a contact tracing with the effectiveness of 70% could delay the peak of untraced asymptomatic cases by 17 days and reduce the highest number of daily cases by 70% compared with a 30% contact tracing effectiveness. A similar trend was observed for symptomatic cases when a similar experiment setting was used. We also performed sensitivity analyses by using different combinations of contact tracing effectiveness and vaccination rates. In all scenarios, the effect of contact tracing on COVID-19 incidence persisted for both asymptomatic and symptomatic cases.ConclusionDespite testing only on two public health and social measures (PHSMs), we observed the scenario with low contact tracing and increasing vaccination rates successfully mimicked the current transmission trend in Malaysia. Hence, while vaccines are progressively rolled out, efficient contact tracing must be rapidly implemented concurrently to reach, find, test, isolate, and support the affected populations to bring the pandemic under control.
Conserved secreted effectors determine endophytic growth and multi-host plant compatibility in a vascular wilt fungus
Authors: Redkar Amey , Sabale Mugdha , Schudoma Christian , Zechmann Bernd , Gupta Yogesh K. , López-Berges Manuel S. , Venturini Giovanni , Gimenez-Ibanez Selena , Turrà David , Solano Roberto , Pietro Antonio Di 
Published: August 2021

AbstractFungal interactions with plant roots, either beneficial or detrimental, have a major impact on agriculture and ecosystems. The soil inhabiting ascomyceteFusarium oxysporum(Fo) constitutes a species complex of worldwide distribution causing vascular wilt in more than a hundred different crops. Individual isolates of the fungus exhibit host-specific pathogenicity, determined by proteinaceous effectors termed secreted in xylem (SIX). However, such isolates can also colonize roots of non-host plants asymptomatically as endophytes, or even protect them against pathogenic isolates. The molecular determinants of multi-host plant colonization are currently unknown. Here, we identified a set of fungal effectors termed ERCs (EarlyRootCompatibility effectors), which are secreted during early biotrophic growth of Fo on both host and non-host plants. In contrast to the strain-specific SIX effectors, which are encoded on accessory genomic regions, ERCs are encoded on core regions and are found across the entire Fo species complex as well as in other phytopathogens, suggesting a conserved role in fungus-plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence on the host plant and rapid activation of plant immune responses, while in a non-pathogenic isolate it led to impaired root colonization and loss of biocontrol ability. Strikingly, some ERCs also contribute to Fo infection on the non-vascular land plantMarchantia polymorpha. Our results reveal an evolutionarily conserved mechanism for multi-host colonization by root infecting fungi.
Unique Microglial Transcriptomic Signature within the Hippocampal Neurogenic Niche
Authors: Chintamen Sana , Gaur Pallavi , Vo Nicole , Bradshaw Elizabeth M. , Menon Vilas , Kernie Steven G. 
Published: August 2021

AbstractMicroglia, the resident immune cells of the brain, are crucial in the development of the nervous system. Recent evidence demonstrates that microglia modulate adult hippocampal neurogenesis by inhibiting cell proliferation of neural precursors and survival both in vitro and in vivo, thus maintaining a balance between cell division and cell death in the neural stem cell pool. There are increasing reports suggesting these microglia found in neurogenic niches differ from their counterparts in non-neurogenic areas. Here, we present evidence that microglia in the hippocampal neurogenic niche are a specialized population that express genes known to regulate neurogenesis. By comprehensively profiling myeloid lineage cells in the hippocampus using single cell RNA-sequencing, we resolve transcriptomic differences in microglia originating from the subgranular zone. These cells have lower expression of genes associated with homeostatic microglia and increased expression of genes associated with phagocytosis. Intriguingly, this small yet distinct population expresses a gene signature with substantial overlap with previously characterized phenotypes, including disease associated microglia (DAM), a particularly unique and compelling microglial state.
Unevolved proteins from modern and prebiotic amino acids manifest distinct structural profiles
Authors: Tretyachenko Vyacheslav , Vymětal Jiří , Neuwirthová Tereza , Vondrášek Jiří , Fujishima Kosuke , Hlouchová Klára 
Published: August 2021

AbstractNatural proteins represent numerous but tiny structure/function islands in a vast ocean of possible protein sequences, most of which has not been explored by either biological evolution or research. Recent studies have suggested this uncharted sequence space possesses surprisingly high structural propensity, but development of an understanding of this phenomenon has been awaiting a systematic high-throughput approach.Here, we designed, prepared, and characterized two combinatorial protein libraries consisting of randomized proteins, each 105 residues in length. The first library constructed proteins from the entire canonical alphabet of 20 amino acids. The second library used a subset of only 10 residues (A,S,D,G,L,I,P,T,E,V) that represent a consensus view of plausibly available amino acids through prebiotic chemistry. Our study shows that compact conformations resistant to proteolysis are (i) abundant (up to 40%) in random sequence space, (ii) independent of general Hsp70 chaperone system activity, and (iii) not granted solely by “late” and complex amino acid additions. The Hsp70 chaperone system effectively increases solubility and refoldability of the canonical alphabet but has only a minor impact on the “early” library. The early alphabet proteins are inherently more soluble and refoldable, possibly assisted by the cell-like environment in which these assays were performed.Our work indicates that both early and modern amino acids are predisposed to supporting protein structure (either in forms of oligomers or globular/molten globule structures) and that protein structure may not be a unique outcome of evolution.
Cooperative Amyloid Fibre Binding and Disassembly by the Hsp70 disaggregase
Authors: Beton J. G. , Monistrol J , Wentink A , Johnston EC , Roberts AJ , Bukau B , Hoogenboom BW , Saibil HR 
Published: August 2021

SummaryAlthough amyloid fibres are highly stable protein aggregates, a specific combination of human Hsp70 system chaperones can disassemble them, including fibres formed of α-synuclein, huntingtin or Tau. Disaggregation requires the ATPase activity of the constitutively expressed Hsp70, Hsc70, together with the J domain protein DNAJB1 and the nucleotide exchange factor Apg2. Recruitment and clustering of Hsc70 on the fibrils appear to be necessary for disassembly.Here we use atomic force microscopy (AFM) to show that segments of in vitro assembled α-synuclein fibrils are first coated with chaperones and then undergo bursts of rapid, unidirectional disassembly. Cryo-electron tomography reveals fibrils with regions of densely bound chaperones extending from the fibre surface, preferentially at one end of the fibre. Sub-stoichiometric amounts of Apg2 relative to Hsc70 dramatically increase recruitment of Hsc70 to the fibres, creating localised active zones that then undergo rapid disassembly at a rate of ∼4 subunits per second.
Comprehensive analysis of mRNA poly(A) tail reveals complex and conserved regulation
Authors: Liu Yusheng , Nie Hu , Zhang Yiwei , Lu Falong , Wang Jiaqiang 
Published: August 2021

AbstractNon-templated poly(A) tails are added to the 3′-end of most mRNAs, which have important roles in post-transcriptional regulation1–3. Recent studies have revealed that poly(A) tails are not composed purely of A residues, but also contain U, C and G residues internally and at their 3′-ends4–6, revealing new levels of complexity. However, no method is able to analyze these internal and terminal non-A residues simultaneously. Here, we developed a new method called unbiased capture of 3-terminal followed by full-length RNA sequencing (UCTF-seq) which captures RNA 3′-ends by direct 3′ adaptor ligation and rRNA removal by CRISPR/Cas9. This method allows simultaneous evaluation of the poly(A) tail length and 5′-end, internal, and 3′-end non- A residues together with the full-length cDNA for a transcript. Applying this method, we achieved the first complete transcriptome-wide 3′ tail map of mRNA within the nuclear and cytoplasmic compartments of mammalian cells, uncovering differences in poly(A) tail length and non-A residues between these two mRNA populations. A survey of diverse eukaryotic species revealed the conservation of a subset of poly(A) tails containing consecutive U residues in the internal positions, whereas those with consecutive C or G residues were of much lower abundance. Together, we established the first method to be able to comprehensively analyze poly(A) tail 5′-end, internal and 3′-end non-A residues in addition to the length simultaneously, and reveal the first complete mRNA 3′ tail map, providing rich insights into the regulatory roles of poly(A) tails.
Maternal mRNA deadenylation is defective in in vitro matured mouse and human oocytes
Authors: Liu Yusheng , Tao Wenrong , Zhang Yiwei , Nie Hu , Hou Zhenzhen , Zhang Jingye , Yang Zhen , Wang Jiaqiang , Lu Falong , Wu Keliang 
Published: August 2021

AbstractOocyte in vitro maturation is a technique of assisted reproductive technology that was first introduced in patients with polycystic ovarian syndrome and is now used in most fertility clinics. Thousands of genes show abnormally high expression in in vitro maturated metaphase II (in vitro MII) oocytes compared with in vivo maturated metaphase II (in vivo MII) oocytes in bovines, mice, and humans1-3. However, the underlying mechanisms of this abnormal expression are still poorly understood. In this study, we use PAIso-seq1 to reveal a transcriptome-wide expression profile of full-length transcripts containing entire poly(A) tails in in vivo and in vitro matured mouse and human oocytes. Our results indicate that more genes are up-regulated than down-regulated in in vitro MII oocytes in both mice and humans. Furthermore, we demonstrate that the observed increase in maternal mRNA abundance is caused by impaired deadenylation in in vitro MII oocytes in both mice and humans. We also found that the cytoplasmic polyadenylation of dormant Btg4 and Cnot7 mRNAs, which encode key components of deadenylation machinery, is impaired in in vitro MII oocytes in mice and humans respectively, likely contributing to reduced translation and impaired global maternal mRNA deadenylation. Our findings highlight that impaired maternal mRNA deadenylation is a definite molecular defect in in vitro MII oocytes in both mice and humans. The findings here offer a new criterion for evaluating the quality of in vitro MII oocytes and a potential direction for improving in vitro maturation by fixing the dysregulated maternal mRNA deadenylation.
A novel post-developmental role of the Hox genes underlies normal adult behaviour
Authors: Raouf Issa A. , Alonso Claudio R. 
Published: August 2021

ABSTRACTThe molecular mechanisms underlying the stability of mature neurons and neural circuits are poorly understood. Here we explore this problem and discover that the Hox genes are a component of the genetic programme that maintains normal neural function in adult Drosophila. We show that post-developmental downregulation of the Hox gene Ultrabithorax (Ubx) in adult neurons leads to substantial anomalies in flight. Mapping the cellular basis of these effects reveals that Ubx is required within a subset of dopaminergic neurons, and cell circuitry analyses and optogenetics allow us to link these dopaminergic neurons to flight control. Functional imaging experiments show that Ubx is necessary for normal dopaminergic activity, and neuron-specific RNA-sequencing defines two previously uncharacterised ion channel-encoding genes as potential mediators of Ubx behavioural roles. Our study thus reveals a novel role of the Hox system in controlling adult behaviour and neural function.
Exo1-protected DNA nicks direct crossover formation in meiosis
Authors: Gioia Michael , Payero Lisette , Pannafino Gianno , Chen Jun Jie , Salim Sagar , Fajith Ghanim , Farnaz Amamah F. , Momoh Sherikat , Scotland Michelle , Raghavan Vandana , Manhart Carol , Shinohara Akira , Nishant K.T. , Alani Eric 
Published: August 2021

ABSTRACTIn most sexually reproducing organisms crossing over between chromosome homologs during meiosis is critical for the viability of haploid gametes. Most crossovers that form in meiosis in budding yeast result from the biased resolution of double Holliday Junction (dHJ) intermediates. This dHJ resolution step involves the actions Rad2/XPG family nuclease Exo1 and the Mlh1-Mlh3 mismatch repair endonuclease. At present little is known about how these factors act in meiosis at the molecular level. Here we show that Exo1 promotes meiotic crossing over by protecting DNA nicks from ligation. We found that structural elements in Exo1 required for interactions with DNA, such as bending of DNA during nick/flap recognition, are critical for its role in crossing over. Consistent with these observations, meiotic expression of the Rad2/XPG family member Rad27 partially rescued the crossover defect inexo1null mutants, and meiotic overexpression of Cdc9 ligase specifically reduced the crossover levels ofexo1DNA binding mutants to levels approaching theexo1null. In addition, our work identified a role for Exo1 in crossover interference that appears independent of its resection activity. Together, these studies provide experimental evidence for Exo1-protected nicks being critical for the formation of meiotic crossovers and their distribution.
Adipocyte-Specific Ablation Of PU.1 Promotes Energy Expenditure and Ameliorates Metabolic Syndrome In Aging Mice
Authors: Chen Keyun , De Angulo Alejandra , Guo Xin , More Aditya , Ochsner Scott A. , Lopez Eduardo , Saul David , Pang Weijun , Sun Yuxiang , McKenna Neil J. , Tong Qiang 
Published: August 2021

ABSTRACTObjectiveAlthough PU.1/Spi1 is known as a master regulator for macrophage development and function, we have reported previously that it is also expressed in adipocytes and is transcriptionally induced in obesity. Here, we investigated the role of adipocyte PU.1 in the development of age-associated metabolic syndrome.MethodsWe generated mice with adipocyte specific PU.1 knockout, assessed metabolic changes in young and aged PU.1fl/fl(control) and AdipoqCre PU.1fl/fl(aPU.1KO) mice, including body weight, body composition, energy expenditure and glucose homeostasis. We also performed transcriptional analyses using RNA-Sequencing of adipocytes from these mice.ResultsaPU.1KO mice have elevated energy expenditure at a young age and decreased adiposity and increased insulin sensitivity in later life. Corroborating these observations, transcriptional network analysis indicated the existence of validated, aPU.1-modulated regulatory hubs that direct inflammatory and thermogenic gene expression programs.ConclusionsOur data provide evidence for a previously uncharacterized role of PU.1 in the development of age-associated obesity and insulin resistance.
Constructing Tumor Immune Microenvironment and Identifying the Immune-Related Prognostic Signatures in Colorectal Cancer Using Multi-omics Data
Authors: Zhang Shuai , Lv Jiali , Fan Bingbing , Fan Zhe , Li Chunxia , Gu Bingbing , Yu Wenhao , Zhang Tao 
Published: August 2021

ABSTRACTBackgroundThe tumor immune microenvironment (TIME) plays a key role in occurrence, progression and prognosis of colorectal cancer (CRC). However, the genetic and epigenetic alterations and potential mechanisms in the TIME of CRC are still unclear.MethodsWe investigated the immune-related differences in three types of genetic or epigenetic alterations (gene expression, somatic mutation, and DNA methylation) and considered the potential roles that these alterations have in the immune response and the immune-related biological processes by analyzing the multi-omics data from The Cancer Genome Atlas (TCGA) portal. Additionally, a four-step method based on LASSO regression and Cox regression was used to construct the prognostic prediction model. Cross validation was performed to validate the model.ResultsA total of 1,745 differentially expressed genes, 178 differentially mutated genes and 1,961 differentially methylation probes were identified between the high-immunity group and the low-immunity group. We retained 15 genetic and epigenetic variables after using LASSO regression and Cox regression. For the prognostic predictions on the TCGA profiles, the performance of the model with 1-year, 3-year, and 5-year areas under the curve (AUCs) equal to 0.861, 0.797, and 0.875. Finally, the overall risk score model was constructed based on genetic, epigenetic, demographic and clinical characteristics, which comprised 18 variables and achieved a high degree of accuracy on the 1-year (AUC = 0.865), 3-year (AUC = 0.839), and 5-year (AUC = 0.914) survival predictions. Kaplan-Meier survival analysis demonstrated that the overall survival of the high-risk group was significantly poorer compared with the low-risk group. Prognostic nomogram, calibration plot and cross validation showed excellent predictive performance.ConclusionsOur study provides a new clue to explore the TIME of CRC patients in genetic and epigenetic aspects. Meanwhile, the prognostic model also has clinical prognostic value and may provide new indicators for the treatment of CRC patients.