bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental factors shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench
Authors: Ma Yuewei , Ding Wenmian , Wang Yuepeng , Chen Ping , Zhou Hui , Li Xuan , Huang Yanyan , Nan Peng 
Published: January 2022

AbstractHailed as “The Fourth Pole”, the Mariana Trench is the deepest part of the ocean. The microbial diversity in it is extremely complicated, which might be caused by the unique environmental factors such as high salinity, low temperature, high hydrostatic pressure, and limited nutrition. Based on 4 seawater samples and 4 sediment samples obtained from the Mariana Trench, we isolated and fostered the microorganism clones with kinds of culture mediums and high-throughput culturing. By using the molecular identification methods based on PCR of 16S rDNA and ITS gene, 1266 bacterial strains in total were isolated and identified, which affiliated to 7 classes, 16 orders, 25 families and 36 genera in four phyla : Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Strains in genera Halomonas, Pseudoaltermonas were the dominant bacteria isolated from the samples. With Mantel tests on the sample-environmental parameter matrix, the sample-environmental organic matter diversity matrix and the sample-microbial diversity matrix, we concluded that the environmental parameters and the organic matters in the condition can shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench.
Contextual associations represented both in neural networks and human behavior
Authors: Aminoff Elissa M. , Baror Shira , Roginek Eric W. , Leeds Daniel D. 
Published: January 2022

AbstractContextual associations facilitate object recognition in human vision. However, the role of context in artificial vision remains elusive as does the characteristics that humans use to define context. We investigated whether contextually related objects (bicycle-helmet) are represented more similarly in convolutional neural networks (CNNs) used for image understanding than unrelated objects (bicycle-fork). Stimuli were of objects against a white background and consisted of a diverse set of contexts (N=73). CNN representations of contextually related objects were more similar to one another than to unrelated objects across all CNN layers. Critically, the similarity found in CNNs correlated with human behavior across three experiments assessing contextual relatedness, emerging significant only in the later layers. The results demonstrate that context is inherently represented in CNNs as a result of object recognition training, and that the representation in the later layers of the network tap into the contextual regularities that predict human behavior.
The immune synapses reveal aberrant functions of CD8 T cells during chronic HIV infection
Authors: Anikeeva Nadia , Steblyanko Maria , Kuri-Cervantes Leticia , Buggert Marcus , Betts Michael R. , Sykulev Yuri 
Published: January 2022

AbstractIt is well-established that chronic HIV infection causes persistent low-grade inflammation that induces premature aging of the immune system in HIV patient including senescence of memory and effector CD8 T cells. To uncover the reasons of gradually diminished potency of CD8 T cells from chronically HIV infected people, we have analyzed cellular morphology and dynamics of the synaptic interface followed exposure of peripheral polyclonal CD8 T cells at various differentiation stages to planar lipid bilayers. The above parameters were linked to pattern of degranulation that determines efficiency of CD8 T cells cytolytic response. We found a large fraction of naive T cells from HIV infected people developing mature synapses and demonstrating focused degranulation, a signature of a differentiated T cells. Further differentiation of aberrant naïve T cells leads to development of anomalous effector T cells undermining their capacity to control HIV and other viruses that could be contained otherwise.
The effect of mainland dynamics on data and parameter estimates in island biogeography
Authors: Lambert Joshua W. , Santos Neves Pedro , Bilderbeek Richèl J.C. , Valente Luis , Etienne Rampal S. 
Published: January 2022

AbstractUnderstanding macroevolution on islands requires knowledge of the closest relatives of is-land species on the mainland. The evolutionary relationships between island and mainland species can be reconstructed using phylogenies, to which models can be fitted to understand the dynamical processes of colonisation and diversification. But how much information on the mainland is needed to gain insight into macroevolution on islands? Here we first test whether species turnover on the mainland and incomplete mainland sampling leave recognis-able signatures in community phylogenetic data. We find predictable phylogenetic patterns: colonisation times become older and the perceived proportion of endemic species increases as mainland turnover and incomplete knowledge increase. We then analyse the influence of these factors on the inference performance of the island biogeography model DAISIE, a whole-island community phylogenetic model that assumes that mainland species do not diversify, and that the mainland is fully sampled in the phylogeny. We find that colonisation and diversification rate are estimated with little bias in the presence of mainland extinction and incomplete sampling. By contrast, the rate of anagenesis is overestimated under high levels of mainland extinction and incomplete sampling, because these increase the perceived level of island endemism. We conclude that community-wide phylogenetic and endemism datasets of island species carry a signature of mainland extinction and sampling. The ro-bustness of parameter estimates suggests that island diversification and colonisation can be studied even with limited knowledge of mainland dynamics.
The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies
Authors: Prakash Shruthy Priya , Chandrasekar Vaidheki , Subramanian Selvi , Ummar Rahamatthunnisha 
Published: January 2022

ABSTRACTBanana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.
Rab35 Governs Apicobasal Polarity Through Regulation of Actin Dynamics During Sprouting Angiogenesis
Authors: Francis Caitlin R. , Kincross Hayle , Kushner Erich J. 
Published: January 2022

ABSTRACTIn early blood vessel development, trafficking programs, such as those using Rab GTPases, are tasked with delivering vesicular cargo with high spatiotemporal accuracy. However, the function of many Rab trafficking proteins remain ill-defined in endothelial tissue; therefore, their relevance to blood vessel development is unknown. Rab35 has been shown to play an enigmatic role in cellular behaviors which differs greatly between tissue-type and organism. Importantly, Rab35 has never been characterized for its potential contribution in sprouting angiogenesis; thus, our goal was to map Rab35’s primary function in angiogenesis. Our results demonstrate that Rab35 is critical for sprout formation; in its absence apicobasal polarity is entirely lost in vitro and in vivo. To determine mechanism, we systematically explored established Rab35 effectors and show that none are operative in endothelial cells. However, we find that Rab35 partners with DENNd1c, an evolutionarily divergent guanine exchange factor, to localize to actin. Here, Rab35 regulates actin polymerization, which is required to setup proper apicobasal polarity during sprout formation. Our findings establish that Rab35 is a potent regulator of actin architecture during blood vessel development.
RefZ and Noc act synthetically to prevent aberrant divisions during Bacillus subtilis sporulation
Authors: Miller Allyssa K. , Herman Jennifer K. 
Published: January 2022

ABSTRACTDuring sporulation, Bacillus subtilis undergoes an atypical cell division that requires overriding mechanisms which protect chromosomes from damage and ensure inheritance by daughter cells. Instead of assembling between segregated chromosomes at midcell, the FtsZ-ring (Z-ring) coalesces polarly, directing division over one chromosome. The DNA-binding protein RefZ facilitates the timely assembly of polar Z-rings and partially defines the region of chromosome initially captured in the forespore. RefZ binds to motifs (RBMs) located proximal to the origin of replication (oriC). Although refZ and the RBMs are conserved across the Bacillus genus, a refZ deletion mutant sporulates with wildtype efficiency, so the functional significance of RefZ during sporulation remains unclear. To further investigate RefZ function, we performed a candidate-based screen for synthetic sporulation defects by combining ΔrefZ with deletions of genes previously implicated in FtsZ regulation and/or chromosome capture. Combining ΔrefZ with deletions of ezrA, sepF, parA, or minD did not detectably affect sporulation. In contrast, a ΔrefZ Δnoc mutant exhibited a sporulation defect, revealing a genetic interaction between RefZ and Noc. Using reporters of sporulation progression, we determined the ΔrefZ Δnoc mutant exhibited sporulation delays after Spo0A activation but prior to late sporulation, with a subset of cells failing to divide polarly or activate the first forespore-specific sigma factor, SigF. The ΔrefZ Δnoc mutant also exhibited extensive dysregulation of cell division, producing cells with extra, misplaced, or otherwise aberrant septa. Our results reveal a previously unknown epistatic relationship that suggests refZ and noc contribute synthetically to regulating cell division and supporting spore development.IMPORTANCEThe DNA-binding protein RefZ and its binding sites (RBMs) are conserved in sequence and location on the chromosome across the Bacillus genus and contribute to the timing of polar FtsZ-ring assembly during sporulation. Only a small number of non-coding and non-regulatory DNA motifs are known to be conserved in chromosomal position in bacteria, suggesting there is strong selective pressure for their maintenance; however a refZ deletion mutant sporulates efficiently, providing no clues as to their functional significance. Here we find that in the absence of the nucleoid occlusion factor Noc, deletion of refZ results in a sporulation defect characterized by developmental delays and aberrant divisions.
Bat Red Blood Cells express Nucleic Acid Sensing Receptors and bind RNA and DNA
Authors: Lam LK Metthew , Dobkin Jane , Eckart Kaitlyn A. , Gereg Ian , DiSalvo Andrew , Nolder Amber , Anis Eman , Ellis Julie C. , Turner Greg , Mangalmurti Nilam S. 
Published: January 2022

AbstractRed blood cells (RBCs) demonstrate immunomodulatory capabilities through the expression of nucleic acid sensors. However, little is known about bat RBCs, and no studies have examined the immune function of bat erythrocytes. Here we show that bat RBCs express the nucleic acid-sensing Toll-like receptors TLR7 and TLR9 and bind the nucleic acid ligands, single-stranded RNA, and CpG DNA. Collectively, these data suggest that, like human RBCs, bat erythrocytes possess immune function and may be reservoirs for nucleic acids. These findings provide unique insight into bat immunity and may uncover potential mechanisms by which virulent pathogens in humans are concealed in bats.
OrganoID: a versatile deep learning platform for tracking and analysis of single-organoid dynamics
Authors: Matthews Jonathan , Schuster Brooke , Kashaf Sara Saheb , Liu Ping , Ben-Yishay Rakefet , Ishay-Ronen Dana , Shen Le , Weber Christopher , Bielski Margaret , Kupfer Sonia S. , Bilgic Mustafa , Rzhetsky Andrey , Tay Savaş 
Published: January 2022

ABSTRACTOrganoids have immense potential as ex vivo disease models for drug discovery and personalized drug screening. Dynamic changes in individual organoid morphology, number, and size can indicate important drug responses, however these metrics are difficult and labor-intensive to obtain for high-throughput image datasets. Here, we present OrganoID, a robust image analysis platform that automatically recognizes, labels, and tracks single organoids, pixel-by-pixel, in brightfield and phase-contrast microscopy experiments. The platform was trained on images of pancreatic cancer organoids and validated on separate images of pancreatic, lung, colon, and adenoid cystic carcinoma organoids, which showed excellent agreement with manual measurements of organoid count (96%) and size (95%) without any parameter adjustments. Single-organoid tracking accuracy remained above 89% over a four-day time-lapse microscopy study. Automated single-organoid morphology analysis of a chemotherapy dose-response experiment identified decreased organoid circularity as an important morphological feature reflecting drug response. OrganoID enables straightforward, detailed, and accurate image analysis to accelerate the use of organoids in high-throughput, data-intensive biomedical applications.
Multifunctional properties of Nej1XLF C-terminus promote end-joining and impact DNA double-strand break repair pathway choice
Authors: Mojumdar Aditya , Adam Nancy , Cobb Jennifer 
Published: January 2022

ABSTRACTA DNA double strand break (DSB) is primarily repaired by one of two canonical pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). NHEJ requires no or minimal end processing for ligation, whereas HR requires 5’ end resection followed by a search for homology. The main event that determines the mode of repair is the initiation of 5’ resection because if resection starts, then NHEJ cannot occur. Nej1 is a canonical NHEJ factor that functions at the cross-roads of repair pathway choice and prior to its function in stimulating Dnl4 ligase. Nej1 competes with Dna2, inhibiting its recruitment to DSBs and thereby inhibiting resection. The highly conserved C-terminal region (CTR) of Nej1 (330-338) is important for two events that drive NHEJ, stimulating ligation and inhibiting resection, but it is dispensable for end-bridging. By combining nej1 point mutants with nuclease-dead dna2-1, we find that Nej1-F335 is essential for end-joining whereas V338 promotes NHEJ indirectly through inhibiting Dna2-mediated resection.HighlightsNej1 C-terminus is critical for repair pathway choice.The KKRK region of Nej1 is important for interactions with ssDNA and dsDNA.Nej1-F335 and V338 are key residues for end-joining and inhibition of resection at DSB.Nej1-mediated end-bridging is not sufficient for end-joining repair.
A biphasic Deep Semi-supervised framework for Suptype Classification and biomarker discovery
Authors: Le Hoang , Nguyen Van-Minh , Nguyen Quang-Huy , Le Duc-Hau 
Published: January 2022

ABSTRACTTo take full advantage of the unprecedented development of -omics technologies and generate further biological insights into human disease, it is a pressing need to develop novel computational methods for integrative analysis of multi-omics data. Here we proposed a biphasic Deep Semi-supervised multi-omics integration framework for Subtype Classification and biomarker discovery, DeepSSC. In phase 1, each denoising autoencoder was used to extract a compact representation for each -omics data, and then they were concatenated and put into a feed-forward neural network for subtype classification. In phase 2, our Biomarker Gene Identification procedure leveraged that neural network classifier to render subtype-specific important biomarkers. We also validated our given results on independent dataset. We demonstrated that DeepSSC exhibited better performance over other state-of-the-art techniques concerning classification tasks. As a result, DeepSSC successfully detected well-known biomarkers and hinted at novel candidates from different -omics data types related to the investigated biomedical problems.
The bladder microbiome, metabolome, cytokines, and phenotypes in patients with systemic lupus erythematosus
Authors: Liu Fengping , Du Jingjie , Zhai Qixiao , Hu Jialin , Miller Aaron W. , Ren Tianli , Feng Yangkun , Jiang Peng , Hu Lei , Sheng Jiayi , Gu Chaoqun , Yan Ren , Lv Longxian , Wolfe Alan J. , Feng Ninghan 
Published: January 2022

AbstractBackground and aimsEmerging studies reveal a unique bacterial community in the human bladder, with alteration of composition associated to disease states. Systemic lupus erythematosus (SLE) is a complex autoimmune disease that is characterized by frequent impairment of the kidney. Here, we explored the bladder microbiome, metabolome, and cytokine profiles in SLE patients, as well as correlations between microbiome and metabolome, cytokines, and disease profiles.Methods and materialsWe recruited a cohort of 50 SLE patients and 50 individually matched asymptomatic controls. We used transurethral catheterization to collect urine samples, 16S rRNA gene sequencing to profile bladder microbiomes, and LC-MS/MS to perform untargeted metabolomic profiling.ResultsCompared to controls, SLE patients possessed a unique bladder microbial community and increased alpha diversity. These differences were accompanied by differences in urinary metabolomes, cytokines, and patients’ disease profiles. The SLE-enriched genera, including Bacteroides, were positively correlated with several SLE-enriched metabolites, including olopatadine. The SLE-depleted genera, such as Pseudomonas, were negatively correlated to SLE-depleted cytokines, including IL-8. Alteration of the bladder microbiome was associated with disease profile. For example, the genera Megamonas and Phocaeicola were negatively correlated with serum complement C3, and Streptococcus was positively correlated with IgG.ConclusionsOur present study reveals associations between the bladder microbiome and the urinary metabolome, cytokines, and disease phenotypes. Our results could help identify biomarkers for SLE.
Efficacy, Practicality, Intimal Health, and Sustainability of Menstrual Cups use among Undergraduate Medical Students: a cross-sectional study
Authors: Lobascz Brenda Czekalski , de França Reis Maria Beatriz , e Tiburcio Mendes Gabriella de Perez Monteiro , de Oliveira Cruz Danillo Christian , Ferreira Damaceno Maria Jose Caetano , Sartorao Filho Carlos Izaias 
Published: January 2022

ABSTRACTIntroductionWomen need effective, safe, and affordable menstrual hygiene products. The menstrual cup is an alternative method.ObjectiveTo identify the prevalence of menstrual cups among the medical students and the independent variables associated with their use adherence.Methodsa cross-sectional study with an online survey applied to regularly matriculate women from FEMA Medical School in January 2021.ResultsOf 277 women, 164 participated. The mean age was 22.26 (SD 3.21). 136 preferred external pads, 60 internal pads, 28 menstrual cups, and 11 did not use. Using a 1-10 scale, price, efficacy, sustain, practice, intimal health status, hygiene, and importance of internal genitalia integrity were questioned. 37 (22,56%) women related the use of menstrual cups in the last year. Using any method to reduce menstruation had an odds ratio adjusted of 0.310 (95%CI 0.122-0.787). Concern about the environmental biodegradation had ORadj of 6.369 (95%CI 1.372-29.562); Intimal Health, ORadj of 1.996 (95%CI 1.183-3.368); internal genital integrity, ORadj of 0.824 (95%CI 0.682-0.995), for menstrual cups use.Conclusionwomen using a method to reduce their menstrual flow, concerning about biodegradation, concerning with intimal health, and with no concerns about manipulating their genitalia were significant independent factors for the adherence of menstrual cups.
The effectiveness of psychological interventions for anxiety in the perinatal period: A systematic review and meta-analysis
Authors: Clinkscales Natalie , Golds Lisa , Berlouis Katherine , MacBeth Angus 
Published: January 2022

AbstractBackgroundAnxiety disorders are a relatively common occurring mental health issue during pregnancy and the perinatal period. There is evidence that untreated perinatal anxiety is a risk factor for adverse outcomes for mother and infant. Despite their potential acceptability to users, psychological interventions research for this population is still in its infancy. This systematic review and meta-analysis aimed to comprehensively evaluate the evidence of the effectiveness of psychological interventions for reducing perinatal anxiety.MethodThis review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Databases searched included EMBASE, MEDLINE, PsychINFO, MIDIRS, CINAHL and the Cochrane Library. Search terms included: Psychological Therapy, Perinatal Period, Antenatal, Postnatal, Anxiety, Obsessive Compulsive Disorder and Phobia.ResultsThe search strategy identified 2,025 studies. A total of 21 studies published between 2004 and 2021 fulfilled inclusion criteria. Of those, 17 were included in the meta-analysis. Overall results indicated that psychological interventions were more effective than control conditions in reducing symptoms of perinatal anxiety with a medium post treatment effect size. Significant effect sizes were also identified for online, face-to-face, group and guided self-help treatment modalities.LimitationsA small sample of studies are represented and limited to articles published in English. The review was unable to draw specific conclusions about what works (i.e. therapeutic modality/delivery) for whom (i.e. specific diagnoses) due to purposefully broad inclusion criteria. The longer-term effects of psychological interventions for perinatal anxiety and infant outcomes could not be established.ConclusionsThis review demonstrates that psychological interventions are effective in reducing symptoms of both anxiety and comorbid anxiety and depression in the antenatal and postnatal periods. The results also demonstrate the efficacy of delivering such interventions in multiple settings, including online, and in group format. Further research is required to optimise treatment delivery to individual needs.