Miracle-dz/UniFAR-FTUs huggingface dataset:
Design of a Novel Multiplex Real Time RT-PCR Assay for SARS-CoV-2 Detection

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 386,000 deaths globally as of June 4, 2020. In this study, we developed a novel multiplex real time reverse transcription (RT)-PCR test for detection of SARS-CoV-2, with primers designed to amplify a 108 bp target on the spike surface glycoprotein (S gene) of SARS-CoV-2 and a hydrolysis Taqman probe designed to specifically detect SARS-CoV-2. Following our design, we evaluated the Limit of detection (LOD) and clinical performance of this laboratory-developed test (LDT). A LOD study with inactivated whole virus exhibited equal performance to that seen in the modified CDC assay with a final LOD of 1,301 ± 13 genome equivalents/ml for our assay vs 1,249 ± 14 genome equivalents/ml for the modified CDC assay. In addition, a clinical evaluation with 270 nasopharyngeal (NP) swab specimens exhibited 98.5% positive percent agreement and 99.3% negative percent agreement with the modified CDC assay. The multiplex design of this assay allows the testing of 91 patients per plate, versus a maximum of 29 patients per plate on the modified CDC assay, providing the benefit of testing significantly more patients per run and saving reagents during a time when both of these parameters have been critical. Our results demonstrate that our multiplex assay performs as well as the modified CDC assay, but is more efficient and cost effective and is therefore adequate for use as a diagnostic assay and for epidemiological surveillance and clinical management of SARS-CoV-2.
EXOC1 regulates cell morphology of spermatogonia and spermatocytes in mice

Spermatogenesis requires high regulation of germ cell morphology. The spermatogonia regulates its differentiation state by its own migration. The male germ cells differentiate and mature with the formation of syncytia, failure of forming the appropriate syncytia results in the arrest of spermatogenesis at the spermatocyte stage. However, the detailed molecular mechanisms of male germ cell morphological regulation are unknown. Here, we found that EXOC1 is important for the pseudopod formation of spermatogonia and spermatocyte syncytia in mice. We found that while EXOC1 contributes to the inactivation of Rac1 in the pseudopod formation of spermatogonia, in spermatocyte syncytium formation, EXOC1 and SNAP23 cooperate with STX2. Our results showed that EXOC1 functions in concert with various cell morphology regulators in spermatogenesis. Since EXOC1 is known to bind to several cell morphogenesis factors, this study is expected to be the starting point for the discovery of many morphological regulators of male germ cells.
RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

Studying epistatic gene interactions is important in understanding genetic architecture of complex traits in organisms. However, due to an enormous number of gene combinations to be analyzed, detection of epistatic gene-gene interactions has been computationally demanding. Here, we show a simple approach RIL-StEp, specialized to Recombinant Inbred Lines (RILs), to study epistasis using single nucleotide polymorphisms (SNPs) information of the genome. We applied the method to reveal epistasis affecting rice seed hull color phenotype, and successfully identified gene pairs that presumably control seed hull color. This method has a potential to enhancing our understanding of genetic architecture of various traits.
Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm

Background and aims Diverticular disease is among the most prevalent conditions encountered by gastroenterologists, affecting ∼50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes associated with diverticular disease, utilizing the electronic health record (EHR) with Natural Language Processing (NLP). Methods We developed a NLP-enriched phenotype algorithm that incorporated colonoscopy or abdominal imaging reports to accurately identify patients with diverticulosis and diverticulitis from multicenter EHRs. We performed genome-wide association studies (GWAS) of diverticular disease in European, African and multi-ancestry participants, followed by phenome-wide association studies (PheWAS) of the risk variants to identify their potential comorbid/pleiotropic effects in the clinical phenome. For more in-depth investigation of associated clinical phenotypes, we also performed PheWAS with the previously reported 52 GWAS susceptibility variants for diverticular disease. Results Ancestry-stratified GWAS analyses confirmed the well-established associations between ARHGAP15 loci with diverticular disease in European cohorts, and found similar positive effect sizes in African cohorts but with non-significant p-values. With overall intensified GWAS signals in diverticulitis patients compared to diverticulosis patients, we found substantial genetic correlations between diverticulosis and diverticulitis, up to 0.997 in European ancestry. PheWAS analyses identified associations between the diverticular disease GWAS variants and circulatory system, genitourinary, and neoplastic EHR phenotypes. Conclusion Our multiancestry GWAS-PheWAS study demonstrated an effective use of multidimensional EHR information in disease case/control classification with NLP for more comprehensive and scalable phenotyping, and implementation of an integrative analytical pipeline to facilitate etiological investigation of a disease from a clinical perspective.
Phosphate Requirement, Photosynthesis, and Diel Cell Cycle of Scenedesmus obliquas Under Fluctuating Light

The effect of light fluctuation (0.06 Hz) on P requirement, photosynthesis, and the diel cell-division cycle was investigated in Scenedesmus obliquus in a chemostat under a 12 h day: 12 h night cycle. P requirement was much less under oscillating than under constant daylight of the same photon flux density. However, cell chlorophyll a was significantly higher, indicating an increased N requirement. There was little difference in photosynthetic efficiency (the slope of the photosynthesis–light regression) between oscillating and constant light, but photosynthetic capacity was higher in fluctuating light. Cell C was also higher. A strong diel rhythmicity in steady-state cell numbers was observed with little phase difference between oscillating and constant light. Although steady-state cell numbers under P limitation were significantly higher under fluctuating light, there was no difference in instantaneous growth rates and their diel distribution. At a dilution rate of 0.6∙d−1, cell death occurred at an ave.
YAP and β-catenin co-operate to drive oncogenesis in basal breast cancer

Targeting cancer stem cells (CSCs) can serve as an effective approach toward limiting resistance to therapies and the development of metastases in many forms of cancer. While basal breast cancers encompass cells with CSC features, rational therapies remain poorly established. Here, we show that receptor tyrosine kinase Met signalling promotes the activity of the Hippo component YAP in basal breast cancer. Further analysis revealed enhanced YAP activity within the CSC population. Using both genetic and pharmaceutical approaches, we show that interfering with YAP activity delays basal cancer formation, prevents luminal to basal trans-differentiation and reduces CSC survival. Gene expression analysis of YAP knock-out mammary glands revealed a strong decrease in β-catenin target genes in basal breast cancer, suggesting that YAP is required for nuclear β-catenin activity. Mechanistically, we find that nuclear YAP interacts and overlaps with β-catenin and TEAD4 at common gene regulatory elements. Analysis of proteomic data from primary breast cancer patients identified a significant upregulation of the YAP activity signature in basal compared to other breast cancers, suggesting that YAP activity is limited to basal types. Our findings demonstrate that in basal breast cancers, β-catenin activity is dependent on YAP signalling and controls the CSC program. These findings suggest that targeting the YAP/TEAD4/β-catenin complex offers a potential therapeutic strategy for eradicating CSCs in basal (triple-negative) breast cancers.
The mRNA translation landscape in the synaptic neuropil

To form and modify synaptic connections and store information, neurons continuously remodel their proteomes. The impressive length of dendrites and axons imposes unique logistical challenges to maintain synaptic proteins at locations remote from the transcription source (the nucleus). The discovery of thousands of mRNAs near synapses suggested that neurons overcome distance and gain autonomy by producing proteins locally1. It is not known, however if, how and when localized mRNAs are translated into protein. To investigate the translational landscape in neuronal subregions, we performed simultaneous RNA-seq and Ribo-seq from microdissected rodent brain slices to identify and quantify the transcriptome and translatome in cell bodies as well as dendrites and axons (neuropil). More than 4800 transcripts were translated in synaptic regions. Thousands of transcripts were differentially translated between somatic and synaptic regions, with scaffold and signaling molecules mostly arising from local sources. Furthermore, specific mRNA features were identified that regulate the efficiency of mRNA translation. The findings overturn the view that local translation is a minor source of synaptic protein2 and indicate that on-site translational control is an important mechanism to control synaptic strength.
Nitric oxide, KATP channels and endothelin-1 modulate brain pericyte function, vascular tone and neurovascular coupling

Neurotransmitter-mediated signaling correlates strongly to changes in cerebral blood flow (CBF), and functional neuroimaging relies on the robust coupling between activity and CBF, i.e. neurovascular coupling (NVC). We here reveal that key endothelial signaling molecules, nitric oxide (eNO) and endothelin-1 (ET1), modulate pericyte contractility and that pericyte ATP-sensitive potassium (KATP) channels interact with endothelial factors to modulate vascular tone and NVC. We show that NVC requires local synthesis of cGMP, but not NO derived from endothelial cells. The potent endothelial vasoconstrictor ET1 contracted pericytes by IP3 receptor mediated Ca2+ release and blocked NVC. In comparison, pericyte KATP channel openers increased the diameter of capillaries by deactivation of L-type Ca2+ channels while KATP blockers shortened the NVC response. All vasoactive stimuli produced the largest diameter changes at the first capillary that branches off from the penetrating arteriole. Our results reveal that three different signaling pathways mediate the effects of NO, ET1 and KATP channels on brain pericytes and capillary blood flow by mechanisms similar to vascular smooth muscle despite great differences in morphology.
Comparative Modeling of CDK9 Inhibitors to Explore Selectivity and Structure-Activity Relationships

Cyclin-dependent kinase 9 (CDK9) plays a key role in transcription elongation, and more recently it was also identified as the molecular target of a series of diaminothiazole compounds that reverse epigenetic silencing in a phenotypic assay. To better understand the structural basis underlying these compounds’ activity and selectivity, we developed a comparative modeling approach that we describe herein. Briefly, this approach draws upon the strong structural conservation across the active conformation of all protein kinases, and their shared pattern of interactions with Type I inhibitors. Because of this, we hypothesized that the large collection of inhibitor/kinase structures available in the Protein Data Bank (PDB) would enable accurate modeling of this diaminothiazole series in complex with each CDK family member. We apply this new comparative modeling pipeline to build each of these structural models, and then demonstrate that these models provide retrospective rationale for the structure-activity relationships that ultimately guided optimization to the lead diaminothiazole compound MC180295 (14e). We then solved the crystal structure of the 14e/CDK9 complex, and found the resulting structure to be in excellent agreement with our corresponding comparative model. Finally, inspired by these models, we demonstrate how structural changes to 14e can be used to rationally tune this compound’s selectivity profile. With the emergence of CDK9 as a promising target for therapeutic intervention in cancer, we anticipate that comparative modeling can provide a valuable tool to guide optimization of potency and selectivity of new inhibitors targeting this kinase.
Speech perception under the tent: A domain-general predictive role for the cerebellum

The role of the cerebellum in speech perception remains a mystery. Given its uniform architecture, we tested the hypothesis that it implements a domain-general mechanism whose role in speech is determined by connectivity. We collated all neuroimaging studies reporting cerebellar activity in the Neurosynth database (n = 8,206). From this set, we found all studies involving passive speech and sound perception (n = 72, 64% speech, 12.5% sounds, 12.5% music, and 11% tones) and speech production and articulation (n = 175). Standard and coactivation neuroimaging meta-analyses were used to compare cerebellar and associated cortical activations between passive perception and production. We found distinct regions of perception-and production-related activity in the cerebellum and regions of perception-production overlap. Each of these regions had distinct patterns of cortico-cerebellar connectivity. To test for domain generality versus specificity, we identified all psychological and task-related terms in the Neurosynth database that predicted activity in cerebellar regions associated with passive perception and production. Regions in the cerebellum activated by speech perception were associated with domain-general terms related to prediction. One hallmark of predictive processing is metabolic savings (i.e., decreases in neural activity when events are predicted). To test the hypothesis that the cerebellum plays a predictive role in speech perception, we examined cortical activation between studies reporting cerebellar activation and those without cerebellar activation during speech perception. When the cerebellum was active during speech perception there was far less cortical activation than when it was inactive. The results suggest that the cerebellum implements a domain-general mechanism related to prediction during speech perception.
Requirement for NF-κB in osteoclast and B-cell development

NF-κB is a family of related, dimeric transcription factors that are readily activated in cells by signals associated with stress or pathogens. These factors are critical to host defense, as demonstrated previously with mice deficient in individual subunits of NF-κB. We have generated mice deficient in both the p50 and p52 subunits of NF-κB to reveal critical functions that may be shared by these two highly homologous proteins. We now demonstrate that unlike the respective single knockout mice, the p50/p52 double knockout mice fail to generate mature osteoclasts and B cells, apparently because of defects that track with these lineages in adoptive transfer experiments. Furthermore, these mice present markedly impaired thymic and splenic architectures and impaired macrophage functions. The blocks in osteoclast and B-cell maturation were unexpected. Lack of mature osteoclasts caused severe osteopetrosis, a family of diseases characterized by impaired osteoclastic bone resorption. These findings now establish critical roles for NF-κB in development and expand its repertoire of roles in the physiology of differentiated hematopoietic cells.
Decomposing metabolite set activity levels with PALS

Motivation Related metabolites can be grouped into metabolite sets in many ways. Examples of these include the grouping of metabolites through their participation in a series of chemical reactions (forming metabolic pathways); or based on fragmentation spectral similarities and shared chemical substructures. Understanding how such metabolite sets change across samples can be incredibly useful in the interpretation and understanding of complex metabolomics data. However many of the available tools suitable for the enrichment analysis of metabolite sets are based on simple methods that badly handle the missing features inherent in untargeted metabolomics measurements and can be difficult to integrate into existing applications. Results We present PALS (Pathway Activity Level Scoring), a Python library, command-line tool and Web application that performs the ranking of significantly-changing metabolite sets over different experimental conditions. As example applications, PALS is used to analyse metabolites grouped as pathways and by common MS-MS fragmentation structures. A comparison of PALS with two other commonly used methods (ORA and GSEA) is also given, and reveals that PALS is more robust to missing peaks and noisy data than the alternatives. We report results from using PALS to analyse pathways from a study of Human African Trypanosomiasis. Finally, we also report how PALS used tandem MS fragmentation structures to reveal enriched metabolite sets between clades in Rhamnaceae plant data, and on American Gut Project data. Availability PALS is freely available from our project Web site at https://pals.glasgowcompbio. org/. It can be imported as a Python library, run as a stand-alone tool or used as a web application.
Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS

In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells, transforming our understanding of cellular diversity and function. However, the field lacks an accessible method to screen and sort droplets based on cellular phenotype upstream of genetic analysis, particularly for large and complex cells. To meet this need, we developed Dropception, a robust, easy-to-use workflow for precise single-cell encapsulation into picoliter-scale double emulsion droplets compatible with high-throughput phenotyping via fluorescence-activated cell sorting (FACS). We demonstrate the capabilities of this method by encapsulating five standardized mammalian cell lines of varying size and morphology as well as a heterogeneous cell mixture of a whole dissociated flatworm (5 - 25 μm in diameter) within highly monodisperse double emulsions (35 μm in diameter). We optimize for preferential encapsulation of single cells with extremely low multiple-cell loading events (<2% of cell-containing droplets), thereby allowing direct linkage of cellular phenotype to genotype. Across all cell lines, cell loading efficiency approaches the theoretical limit with no observable bias by cell size. FACS measurements reveal the ability to discriminate empty droplets from those containing cells with good agreement to single-cell occupancies quantified via microscopy, establishing robust droplet screening at single-cell resolution. High-throughput FACS phenotyping of cellular picoreactors has the potential to shift the landscape of single-cell droplet microfluidics by expanding the repertoire of current nucleic acid droplet assays to include functional screening. ABSTRACT FIGURE
Differential activity and expression of human 5β-reductase (AKR1D1) splice variants

Steroid hormones, including glucocorticoids and androgens, exert a wide variety of effects in the body across almost all tissues. The steroid A-ring 5β-reductase (AKR1D1) is expressed in human liver and testes, and three splice variants have been identified (AKR1D1-001, AKR1D1-002, AKR1D1-006). Amongst these, AKR1D1-002 is the best described; it modulates steroid hormone availability and catalyses an important step in bile acid synthesis. However, specific activity and expression of AKR1D1-001 and AKR1D1-006 are unknown. AKR1D1-002, AKR1D1-001 and AKR1D1-006 were measured in human liver biopsies and human hepatoma cell lines by qPCR. Three-dimensional (3D) structures of AKR1D1 variants were determined using in silico approaches. AKR1D1 variants were over-expressed in HEK293 cells, and successful overexpression confirmed by qPCR and western blotting. Steroid hormone clearance was measured by mass spectrometry and ELISA, and steroid receptor activation determined by luciferase reporter assays. AKR1D1-002 and AKR1D1-001 are expressed in human liver, and only AKR1D1-006 is expressed in human testes. Following over-expression in HEK293 cells, AKR1D1-001 and AKR1D1-006 protein levels were lower than AKR1D1-002, but significantly increased following treatment with the proteasomal inhibitor, MG-132. AKR1D1-002 efficiently metabolised glucocorticoids and androgens and decreased receptor activation. AKR1D1-001 and AKR1D1-006 poorly metabolised dexamethasone, but neither protein metabolised cortisol, prednisolone or testosterone. We have demonstrated the differential expression and role of AKR1D1 splice variants to regulate steroid hormone clearance and receptor activation. AKR1D1-002 is the predominant functional protein in steroidogenic and metabolic tissues. In addition, AKR1D1-001 and AKR1D1-006 may have a limited role in the regulation of synthetic glucocorticoid action.