Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular and Intercellular Gene Regulatory Network Inference From Time-Course Individual RNA-Seq

Gene regulatory network (GRN) inference is an effective approach to understand the molecular mechanisms underlying biological events. Generally, GRN inference mainly targets intracellular regulatory relationships such as transcription factors and their associated targets. In multicellular organisms, there are both intracellular and intercellular regulatory mechanisms. Thus, we hypothesize that GRNs inferred from time-course individual (whole embryo) RNA-Seq during development can reveal intercellular regulatory relationships (signaling pathways) underlying the development. Here, we conducted time-course bulk RNA-Seq of individual mouse embryos during early development, followed by pseudo-time analysis and GRN inference. The results demonstrated that GRN inference from RNA-Seq with pseudo-time can be applied for individual bulk RNA-Seq similar to scRNA-Seq. Validation using an experimental-source-based database showed that our approach could significantly infer GRN for all transcription factors in the database. Furthermore, the inferred ligand-related and receptor-related downstream genes were significantly overlapped. Thus, the inferred GRN based on whole organism could include intercellular regulatory relationships, which cannot be inferred from scRNA-Seq based only on gene expression data. Overall, inferring GRN from time-course bulk RNA-Seq is an effective approach for understanding the regulatory relationships underlying biological events in multicellular organisms.
The CTPase activity of ParB acts as a timing mechanism to control the dynamics and function of prokaryotic DNA partition complexes

DNA partitioning CTPases of the ParB family mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromeric region of target DNA molecules and then spread laterally to form large nucleoprotein complexes that serve as docking points for the DNA segregation machinery. Here, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. Moreover, we solve crystal structures of ParB in the pre- and post-hydrolysis state and provide insights into the catalytic mechanism underlying nucleotide hydrolysis. The characterization of CTPase-deficient ParB variants reveals that CTP hydrolysis serves as a timing mechanism to control the sliding time of ParB. Hyperstable clamps are trapped on the DNA, leading to excessing spreading and severe chromosome segregation defects in vivo. These findings clarify the role of the ParB CTPase cycle in partition complex dynamics and function and thus complete our understanding of this prototypic CTP-dependent molecular switch.
Recurrent Somatic MAP2K1 Mutations in Papillary Thyroid Cancer and Colorectal Cancer

Mitogen-activated protein kinase kinase 1 (MAP2K1) is a dual specificity protein kinase that phosphorylates both threonine and tyrosine residues in ERK. MAP2K1 mutations have been identified in several cancers. However, their role in Middle Eastern papillary thyroid cancer (PTC) and colorectal cancer (CRC) is lacking. In this study, we evaluated the prevalence of MAP2K1 mutations in a large cohort of Middle Eastern PTC and CRC using whole-exome and Sanger sequencing technology. In the discovery cohort of 100 PTC and 100 CRC cases (comprising 50 MAPK mutant and 50 MAPK wildtype cases each), we found one MAP2K1 mutation each in PTC and CRC, both of which were MAPK wildtype. We further analyzed 286 PTC and 289 CRC MAPK wildtype cases and found three MAP2K1 mutant PTC cases and two MAP2K1 mutant CRC cases. Thus, the overall prevalence of MAP2K1 mutation in MAPK wildtype cases was 1.1% (4/336) in PTC and 0.9% (3/339) in CRC. Histopathologically, three of the four MAP2K1 mutant PTC cases were follicular variant and all four tumors were unifocal with absence of extra-thyroidal extension. All the three CRC cases harboring MAP2K1 mutation were of older age (> 50 years) and had moderately differentiated stage II/III tumors located in the left colon. In conclusion, this is the first comprehensive report of MAP2K1 somatic mutations prevalence in PTC and CRC from this ethnicity. The mutually exclusive nature of MAP2K1 and MAPK mutations suggests that each of these mutation may function as an initiating mutation driving tumorigenesis through MAPK signaling pathway.
SWAN Identification of Common Aneuploidy-Based Oncogenic Drivers

Haploinsufficiency drives Darwinian evolution. Siblings, while alike in many aspects, differ due to monoallelic differences inherited from each parent. In cancer, solid tumors exhibit aneuploid genetics resulting in hundreds to thousands of monoallelic gene-level copy-number alterations (CNAs) in each tumor. Aneuploidy patterns are heterogeneous, posing a challenge to identify drivers in this high-noise genetic environment. Here, we developed Shifted Weighted Annotation Network (SWAN) analysis to assess biology impacted by cumulative monoallelic changes. SWAN enables an integrated pathway-network analysis of CNAs, RNA expression, and mutations via a simple web platform. SWAN is optimized to best prioritize known and novel tumor suppressors and oncogenes, thereby identifying drivers and potential druggable vulnerabilities within cancer CNAs. Protein homeostasis, phospholipid dephosphorylation, and ion transport pathways are commonly suppressed. An atlas of CNA pathways altered in each cancer type is released. These CNA network shifts highlight new, attractive targets to exploit in solid tumors. Highlights Copy-number alteration pathways define solid tumor biology SWAN is released as an integrative point-and-click pathway analysis tool Moderate impact drivers highlighted by SWAN validated in vitro Copy-number altered pathways associate with mutations and survival
Comprehensive PAM prediction for CRISPR-Cas systems reveals evidence for spacer sharing, preferred strand targeting and conserved links with CRISPR repeats

The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. By using vast metagenomic sequence databases, we mapped one third (∼70,000) of more than 200,000 unique CRISPR spacers from a variety of microbes, and derived a catalog of more than one hundred unique PAM sequences associated with specific CRISPR subtypes. These PAMs were further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. From the curated CRISPR arrays dataset we could also deduce CRISPR subtype specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (e.g. Type I-E and Type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (i.e. Type I-A, I-B and Type III systems) prefer the coding strand and mRNA. In addition, we found large scale evidence that both CRISPR adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA- and RNA targeting of invaders, which may be effective at combating mobile genetic invaders.
Vps501, a novel vacuolar SNX-BAR protein cooperates with the SEA complex to induce autophagy

The sorting nexins (SNX), constitute a diverse family of molecules that play varied roles in membrane trafficking, cell signaling, membrane remodeling, organelle motility and autophagy. In particular, the SNX-BAR proteins, a SNX subfamily characterized by a C-terminal dimeric Bin/Amphiphysin/Rvs (BAR) lipid curvature domain and a conserved Phox-homology domain, are of great interest. In budding yeast, many SNX-BARs proteins have well-characterized endo-vacuolar trafficking roles. Phylogenetic analyses allowed us to identify an additional SNX-BAR protein, Vps501, with a novel endo-vacuolar role. We report that Vps501 uniquely localizes to the vacuolar membrane and works with the SEA complex to regulate autophagy. Furthermore, we found cells displayed a severe deficiency in starvation-induced/nonselective autophagy only when SEA complex subunits are ablated in combination with Vps501, indicating a cooperative role with the SEA complex during autophagy. Additionally, we found the SEA complex becomes destabilized in vps501Δsea1Δ cells, which resulted in aberrant TORC1 hyperactivity and misregulation of autophagy induction.
Do Jumps Matter in the Long Term? A Tale of Two Horizons

Economic scenario generators (ESGs) for equities are important components of the valuation and risk management process of life insurance and pension plans. Because the resulting liabilities are very long-lived and the short-term performance of the assets backing these liabilities may trigger important losses, it is thus a desired feature of an ESG to replicate equity returns over such horizons. In light of this horizon duality, we investigate the relevance of jumps in ESGs to replicate dynamics over different horizons and compare their performance to popular models in actuarial science. We show that jump-diffusion models cannot replicate higher moments if estimated with the maximum likelihood. Using a generalized method of moments–based approach, however, we find that simple jump-diffusion models have an excellent fit overall (moments and the entire distribution) at different timescales. We also investigate three typical applications: the value of $1 accumulated with no intermediate monitoring, a solvency analysis with frequent monitoring, and a dynamic portfolio problem. We find that jumps have long-lasting effects that are difficult to replicate otherwise, so, yes, jumps do matter in the long term.
Developing a Simulation Framework for Modeling Biomolecules in Ionic Liquids

55 INTRODUCTION . 56 METHODS . 62 RESULTS AND DISCUSSION . 64 CONCLUSIONS . 81 IV. DESTABILIZATION OF HUMAN SERUM ALBUMIN BY IONIC LIQUIDS . 85 ABSTRACT . 85 INTRODUCTION . 86 METHODS . 89 RESULTS AND DISCUSSION . 94 CONCLUSIONS . 102 V. STRUCTURE AND FREE ENERGY OF LEUCINE LYSINE PEPTIDE AGGREGATES . 105 INTRODUCTION . 105 METHODS . 106 RESULTS AND DISCUSSION . 111 CONCLUSIONS . 114 VI. ORIENTATION OF LEUCINE LYSINE PEPTIDES AT AIR-WATER INTERFACES . 115 INTRODUCTION . 115 METHODS . 117 RESULTS AND DISCUSSION . 117 CONCLUSIONS . 124 VII. STRUCTURE OF METAL-SURFACTANT COMPLEXES IN ORGANIC SOLVENTS . 127 INTRODUCTION . 127 METHODS . 128 RESULTS AND DISCUSSION . 130 CONCLUSIONS . 136 CONTRIBUTIONS OF THIS RESEARCH . 137 BIBLIOGRAPHY . 139 SUPPORTING INFORMATION . 152 SUPPORTING INFORMATION FOR CHAPTER II . 152 SUPPORTING INFORMATION FOR CHAPTER III . 161 SUPPORTING INFORMATION FOR CHAPTER VI . 167 SUPPORTING INFORMATION FOR CHAPTER VII . 170
The dynamic interplay of PIP2 and ATP in the regulation of the KATP channel

ATP-sensitive potassium (KATP) channels couple the intracellular ATP concentration to insulin secretion. KATP channel activity is inhibited by ATP binding to the Kir6.2 tetramer and activated by phosphatidylinositol-4,5-bisphosphate (PIP2). Here, we use molecular dynamics (MD) simulation, electrophysiology and fluorescence spectroscopy to show that ATP and PIP2 occupy different binding pockets that share a single amino acid residue, K39. When both ligands are present, K39 shows a greater preference to co-ordinate with PIP2 than ATP. A neonatal diabetes mutation at K39 (K39R) increases the number of hydrogen bonds formed between K39 and PIP2, reducing ATP inhibition. We also find direct effects on nucleotide binding from mutating E179, a residue proposed to interact with PIP2. Our work suggests PIP2 and ATP interact allosterically to regulate KATP channel activity.
Fibrinogen αC-subregions critically contribute blood clot fibre growth, mechanical stability and resistance to fibrinolysis

Fibrinogen is essential for blood coagulation. The C-terminus of the fibrinogen α-chain (αC-region) is composed of an αC-domain and αC-connector. Two recombinant fibrinogen variants (α390 and α220) were produced to investigate the role of subregions in modulating clot stability and resistance to lysis. The α390 variant, truncated before the αC-domain, produced clots with a denser structure and thinner fibres. In contrast, the α220 variant, truncated at the start of the αC-connector, produced clots that were porous with short stunted fibres and visible fibre ends. These clots were mechanically weak and susceptible to lysis. Our data demonstrate differential effects for the αC-subregions in fibrin polymerisation, clot mechanical strength, and fibrinolytic susceptibility. Furthermore, we demonstrate that the αC-subregions are key for promoting longitudinal fibre growth. Together, these findings highlight critical functions of the αC-subregions in relation to clot structure and stability, with future implications for development of novel therapeutics for thrombosis.
Reinforcement alone does not explain increased reproductive isolation in sympatry

Comparative studies of reproductive isolation (RI) by Coyne and Orr (1, 2) and others indicate a significant role for reinforcing natural selection in Drosophila speciation. The reinforcement hypothesis predicts increased prezygotic, but not postzygotic, RI between sympatric species pairs in response to maladaptive hybridization. We revisit this hypothesis and others using additional Drosophila, Lepidopteran, and toad (Bufo) data. In contrast to the predictions of reinforcement, we find increased premating and postzygotic RI between sympatric Drosophila species, including between recently diverged species pairs, as defined by Coyne and Orr (1) and others (i.e., DNei < 0.5). However, at slightly lower divergence thresholds increased postzygotic RI in sympatry is not statistically significant, while increased premating RI is, generally in agreement with the predictions of reinforcement. While premating data are unavailable, postzygotic RI is also increased between sympatric Lepidopteran and toad (Bufo) species. We find only modest support for “concordant asymmetries” in premating and postzygotic RI between sympatric Drosophila, described by others as uniquely supporting reinforcement. Finally, the proportion of geographic range overlap shared by species is positively associated with the magnitude of premating RI as predicted by reinforcement, but it is also positively associated with postzygotic RI, which cannot be explained by reinforcement. Taken together, our results demonstrate that comparisons of premating and postzygotic RI in sympatry depend greatly on divergence time, and suggest that fusion, extinction, and/or other mechanisms must combine with reinforcement to generate these patterns. Significance Statement Understanding mechanisms underlying the origin of species remains a central goal of biology. By combining laboratory estimates of premating and postzygotic reproductive isolation (RI) with phylogenetic hypotheses, geographic range data, and genetic divergence estimates, the fundamental meta-analyses of Coyne and Orr provided compelling support that reinforcement contributes significantly to Drosophila speciation. Using additional Drosophila data, we demonstrate increased premating and postzygotic RI in sympatry. Postzygotic RI is also increased in sympatry between Lepidopteran and toad species. We also find only modest support for patterns previously described as uniquely supporting reinforcement. Together, our analyses demonstrate that comparisons of premating and postzygotic RI depend on divergence time, and suggest that fusion, extinction, and/or other mechanisms combine with reinforcement to produce these patterns.
High-Resolution Simulation of Polar Lows over Norwegian and Barents Seas Using the COSMO-CLM and ICON Models for the 2019–2020 Cold Season

The lack of meteorological observations at high latitudes and the small size and relatively short lifetime of polar lows (PLs) constitute a problem in the simulation and prediction of these phenomena by numerical models. On the other hand, PLs, which are rapidly developing, can lead to such extreme weather events as stormy waves, strong winds, the icing of ships, and snowfalls with low visibility, which can influence communication along the Arctic seas. This article is devoted to studying the possibility of the numerical simulation and prediction of polar lows by different model configurations and resolutions. The results of the numerical experiments for the Norwegian and Barents seas with grid spacings of 6.5 and 2 km using the ICON-Ru configurations of the ICON (ICOsahedral Nonhydrostatic) model and with a grid spacing of 6.5 km using the COSMO-CLM (Climate Limited-area Modeling) configuration of the COSMO (COnsortium for Small-scale MOdelling) model are presented for the cold season of 2019–2020. All the used model configurations demonstrated the possibility of the realistic simulation of polar lows. The ICON model showed slightly more accurate results for the analyzed cases. The best results showed runs with lead times of less than a day.
SEPARATION OF FISCHER-TROPSCH WAX FROM CATALYST BY SUPERCRITICAL EXTRACTION

The objective of this research project was to evaluate the potential of supercritical fluid (SCF) extraction for the recovery and fractionation of the wax product from the slurry bubble column (SBC) reactor of the Fischer-Tropsch (F-T) process. The wax, comprised mostly of branched and linear alkanes with a broad molecular weight distribution up to C{sub 100}, is to be extracted with a hydrocarbon solvent that has a critical temperature near the operating temperature of the SBC reactor, i.e., 200-300 C. Aspen Plus{trademark} was used to perform process simulation studies on the proposed extraction process, with Redlich-Kwong-Soave (RKS) being used for the thermodynamic property model. In summary, we have made comprehensive VLE measurements for short alkane + long alkane systems over a wide range of pressures and temperatures, dramatically increasing the amount of high-quality data available for these simple, yet highly relevant systems. In addition, our work has demonstrated that, surprisingly, no current thermodynamic model can adequately predict VLE behavior for these systems. Thus, process simulations (such as those for our proposed SCF extraction process) that incorporate these systems can currently only give results that are qualitative at best. Although significant progress has been made in the past decade, more experimental and theoretical work remain to be done before the phase equilibria of asymmetric alkane mixtures can be predicted with confidence.
Effect of Alloying Elements on the Mechanical Properties of Mo3Si

Molybdenum silicides are attractive high-temperature structural materials because of their excellent thermal stability and outstanding oxidation resistance at high temperatures. First-principles calculations were employed to investigate the effect of alloying elements (Cr, Nb, V, W, Al, Ga, and Ge) on the mechanical properties of Mo3Si. The structural stabilities of doped Mo3Si were calculated, showing that the Pm-3n structure was stable at the investigated low-doping concentration. The calculated elastic constants have also evaluated some essential mechanical properties of doped Mo3Si. Cr- and V-doping decreased the elastic modulus, while Al- and Nb-doping slightly increased the shear and Young’s modulus of Mo3Si. Furthermore, V-, Al- and Nb-doping decreased the B/G and Poisson ratio, suggesting that these elements could form strong covalent bonds, and decrease shear deformation and alloy ductility. Based on the three-dimensional contours and two-dimensional projection of the elastic modulus, Cr- and V-doping exhibited a significant influence on the anisotropy of the shear and Young’s modulus. According to charge density and density of states, the electronic structures of alloyed Mo3Si were further analyzed to reveal the doping effects.
A gas chromatographic‐based headspace biochemical oxygen demand test

The 5‐day biochemical oxygen demand (BOD5) test is an established tool for measuring the concentration of biodegradable organic matter in wastewater effluents. Unfortunately, the BOD test is time consuming, labor intensive, and, due to the dilution of the wastewater, takes a relatively long time to complete. A few years ago a headspace BOD (HBOD) test was developed that avoided the need to dilute wastewater samples. A disadvantage of the original HBOD test was that the sample had to be transferred from the HBOD tube to another vessel for a dissolved oxygen measurement. This study demonstrates that it is possible to conduct HBOD tests using a gas chromatograph to measure oxygen utilization in the sealed tube and that a 3‐day HBOD provides a reliable estimate of the BOD5. The HBOD3 values measured for primary and secondary clarifier effluents from an activated sludge plant were 114 and 23 mg/L; BOD5 measurements were 116 and 24 mg/L. Changes in headspace volumes did not significantly change the HBODs. Secondary settled wastewater had a HBOD5 of 83 ± 3 mg/L (mean ± SD) for headspace volumes of 10–20 mL (36–71%) in a 28‐mL tube. The HBOD5 was also constant (84 ± 6 mg/L) when samples were diluted 20–60% using BOD dilution water at a fixed headspace volume of 8 mL in HBOD tubes. Nitrification increased the HBOD of nondiluted wastewaters after 4 days, although nitrification appeared to be sufficiently inhibited using a standard nitrification inhibitor. A calibration test for the HBOD was developed using a 300‐mg/L glucose and glutamic acid (GGA, 50% each) solution and secondary clarifier wastewater that provided HBOD3 values similar to those obtained in the analogous BOD5 test. It is argued that the simpler procedures, added precision of GC‐based protocols, and more rapid exertion of oxygen demand make the HBOD test superior to the conventional BOD test.
“I’m not like others”: stigma navigation by people who inject drugs in Vietnam

Abstract Background People who inject drugs are subjected to great stigmatization in many parts of the world. How they deal with stigma is closely linked to how stigma means to them. Understanding the strategies individuals employ to cope with these negative attitudes and what resources they mobilize in this process gives useful insights for clinical work and policy development. Methods We conducted 12 months of field observation in 2017 and 2018 and 54 in-depth interviews with people who inject drugs in Haiphong, Vietnam. Grounded theory underpinned our sampling and data analysis. Results The strategies participants used to manage stigma were both information and tension management. Many participants not only concealed their drug use but actively cultivated a pro-social image based on Vietnamese cultural virtues such as selflessness, hard work or harmonious living with others. Participants withdrew from social relationships to distance themselves from the stereotype of a money-begging drug user. They used techniques of neutralization to emphasize their good character and reframe their drug-related issues in a different light in order to negotiate their social status with their interlocutors. Conclusion People who inject drugs endorse the same social values and aspirations as nonusers. A good support structure and resources could help them to cope more effectively with stigma.