Miracle-dz/UniFAR-FTUs huggingface dataset:
Meta-Prism 2.0: Enabling algorithm for ultra-fast, accurate and memory-efficient search among millions of microbial community samples

Motivation Microbial community samples and sequencing data have been accumulated at a speed faster than ever, with tens of thousands of samples been sequenced each year. Mining such a huge amount of multi-source heterogeneous data is becoming more and more difficult. Among several sample mining bottlenecks, efficient and accurate search of samples is one of the most prominent: Faced with millions of samples in the data repository, traditional sample comparison and search approaches fall short in speed and accuracy. Results Here we proposed Meta-Prism 2.0, a microbial community sample search method based on smart pair-wise sample comparison, which pushed the time and memory efficiency to a new limit, without the compromise of accuracy. Based on memory-saving data structure, time-saving instruction pipeline, and boost scheme optimization, Meta-Prism 2.0 has enabled ultra-fast, accurate and memory-efficient search among millions of samples. Meta-Prism 2.0 has been put to test on several datasets, with largest containing one million samples. Results have shown that firstly, as a distance-based method, Meta-Prism 2.0 is not only faster than other distance-based methods, but also faster than unsupervised methods. Its 0.00001s per sample pair search speed, as well as 8GB memory needs for searching against one million samples, have enabled it to be the most efficient method for sample comparison. Additionally, Meta-Prism 2.0 could achieve the comparison accuracy and search precision that are comparable or better than other contemporary methods. Thirdly, Meta-Prism 2.0 can precisely identify the original biome for samples, thus enabling sample source tracking. Conclusion In summary, Meta-Prism 2.0 can perform accurate searches among millions of samples with very low memory cost and fast speed, enabling knowledge discovery from samples at a massive scale. It has changed the traditional resource-intensive sample comparison and search scheme to a cheap and effective procedure, which could be conducted by researchers everyday even on a laptop, for insightful sample search and knowledge discovery. Meta-Prism 2.0 could be accessed at: https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0.
Multifrequency electron paramagnetic resonance : theory and applications

1. Introduction 2. Multifrequency Aspects of EPR 3. Basic Theory of EPR PART A. EXPERIMENTAL 4. Spectrometers 4.1 Zero-field EPR 4.2 Low Frequency CW EPR Spectrometers 4.3 High Frequencies 4.4 Pulsed Technique 5. Multifrequency EPR: Experimental Considerations 5.1 Multiarm EPR Spectroscopy at Multiple Microwave Frequencies 5.2 Resonators for Multifrequency EPR of Spin Labels 5.3 Multi-frequency EPR Sensitivity PART B. THEORETICAL 6 First Principles Approach to Spin-Hamiltonian Parameters 7 Spin Hamiltonians and Site Symmetries for Transition Ions 8 Evaluation of Spin Hamiltonian Parameters from Multifrequency EPR Data 9 Simulation of EPR Spectra 10 Relaxation of Paramagnetic Spins 11 Molecular Motions 12 Distance Measurements: CW and Pulse Dipolar EPR PART C. APPLICATIONS 13 Determination of large Zero Field Splitting 14 Determination of non-coincident anisotrpic tensors 15 Biological Systems 16 Copper Coordination Environments 17 Multifrequency Electron Spin Relaxation Times 18 EPR Imaging 19 Multifrequency EPR Microscopy: Experimental and Theoretical Aspects 20 EPR Studies of Nano-materials 21 Single Molecule Magnets and Magnetic Quantum Tunneling 22 Multifrequency EPR of Photosynthetic Systems 23 Measurement of Superconducting Gaps 24 Dynamic Nuclear Polarization (DNP) at High Magnetic Fields 25 Chemically Induced Dynamic Nuclear Polarization and Chemically Induced Dynamic Electronic Polarization PART D. FUTURE PERSPECTIVES 26 Future Perspectives Appendix Fundamental constants and Conversion Factors used in EPR
Motor Point Stimulation in Spinal Paired Associative Stimulation can Facilitate Spinal Cord Excitability

Paired associative stimulation at the spinal cord (spinal PAS) has been shown to increase muscle force and dexterity by strengthening the corticomuscular connection, through spike timing dependent plasticity. Typically, transcranial magnetic stimulation (TMS) and transcutaneous peripheral nerve electrical stimulation (PNS) are often used in spinal PAS. PNS targets superficial nerve branches, by which the number of applicable muscles is limited. Alternatively, a muscle can be activated by positioning the stimulation electrode on the “motor point” (MPS), which is the most sensitive location of a muscle to electrical stimulation. Although this can increase the number of applicable muscles for spinal PAS, nobody has tested whether MPS can be used for the spinal PAS to date. Here we investigated the feasibility of using MPS instead of PNS for spinal PAS. Ten healthy male individuals (26.0 ± 3.5 yrs) received spinal PAS on two separate days with different stimulation timings expected to induce (1) facilitation of corticospinal excitability (REAL) or (2) no effect (CONTROL) on the soleus. The motor evoked potentials (MEP) response curve in the soleus was measured prior to the spinal PAS, immediately after (0 min) and at 10, 20, 30 min post-intervention as a measure of corticospinal excitability. The post-intervention MEP response curve areas were larger in the REAL condition than the CONTROL conditions. Further, the post-intervention MEP response curve areas were significantly larger than pre-intervention in the REAL condition but not in the CONTROL condition. We conclude that MPS can facilitate corticospinal excitability through spinal PAS.
AbaM Regulates Quorum Sensing, Biofilm Formation, and Virulence in Acinetobacter baumannii

Acinetobacter baumannii is a multiantibiotic-resistant pathogen of global health care importance. Understanding Acinetobacter virulence gene regulation could aid the development of novel anti-infective strategies. ABSTRACT Acinetobacter baumannii possesses a single divergent luxR/luxRI-type quorum-sensing (QS) locus named abaR/abaI. This locus also contains a third gene located between abaR and abaI, which we term abaM, that codes for an uncharacterized member of the RsaM protein family known to regulate N-acylhomoserine lactone (AHL)-dependent QS in other beta- and gammaproteobacteria. Here, we show that disruption of abaM via a T26 insertion in A. baumannii strain AB5075 resulted in increased production of N-(3-hydroxydodecanoyl)-l-homoserine lactone and enhanced surface motility and biofilm formation. In contrast to the wild type and the abaI::T26 mutant, the virulence of the abaM::T26 mutant was completely attenuated in a Galleria mellonella infection model. Transcriptomic analysis of the abaM::T26 mutant revealed that AbaM differentially regulates at least 76 genes, including the csu pilus operon and the acinetin 505 lipopeptide biosynthetic operon, that are involved in surface adherence, biofilm formation and virulence. A comparison of the wild type, abaM::T26 and abaI::T26 transcriptomes, indicates that AbaM regulates ∼21% of the QS regulon including the csu operon. Moreover, the QS genes (abaI and abaR) were among the most upregulated in the abaM::T26 mutant. A. baumannii lux-based abaM reporter gene fusions revealed that abaM expression is positively regulated by QS but negatively autoregulated. Overall, the data presented in this work demonstrates that AbaM plays a central role in regulating A. baumannii QS, virulence, surface motility, and biofilm formation. IMPORTANCE Acinetobacter baumannii is a multiantibiotic-resistant pathogen of global health care importance. Understanding Acinetobacter virulence gene regulation could aid the development of novel anti-infective strategies. In A. baumannii, the abaR and abaI genes that code for the receptor and synthase components of an N-acylhomoserine (AHL) lactone-dependent quorum sensing system (QS) are separated by abaM. Here, we show that although mutation of abaM increased AHL production, surface motility, and biofilm development, it resulted in the attenuation of virulence. AbaM was found to control both QS-dependent and QS-independent genes. The significance of this work lies in the identification of AbaM, an RsaM ortholog known to control virulence in plant pathogens, as a modulator of virulence in a human pathogen.
Clinical Positioning of the IAP Antagonist Tolinapant (ASTX660) in Colorectal Cancer

Inhibitors of apoptosis proteins (IAPs) are intracellular proteins, with important roles in regulating cell death, inflammation, and immunity. Here, we examined the clinical and therapeutic relevance of IAPs in colorectal cancer. We found that elevated expression of cIAP1 and cIAP2 (but not XIAP) significantly correlated with poor prognosis in patients with microsatellite stable (MSS) stage III colorectal cancer treated with 5-fluorouracil (5FU)–based adjuvant chemotherapy, suggesting their involvement in promoting chemoresistance. A novel IAP antagonist tolinapant (ASTX660) potently and rapidly downregulated cIAP1 in colorectal cancer models, demonstrating its robust on-target efficacy. In cells co-cultured with TNFα to mimic an inflammatory tumor microenvironment, tolinapant induced caspase-8–dependent apoptosis in colorectal cancer cell line models; however, the extent of apoptosis was limited because of inhibition by the caspase-8 paralogs FLIP and, unexpectedly, caspase-10. Importantly, tolinapant-induced apoptosis was augmented by FOLFOX in human colorectal cancer and murine organoid models in vitro and in vivo, due (at least in part) to FOLFOX-induced downregulation of class I histone deacetylases (HDAC), leading to acetylation of the FLIP-binding partner Ku70 and downregulation of FLIP. Moreover, the effects of FOLFOX could be phenocopied using the clinically relevant class I HDAC inhibitor, entinostat, which also induced acetylation of Ku70 and FLIP downregulation. Further analyses revealed that caspase-8 knockout RIPK3-positive colorectal cancer models were sensitive to tolinapant-induced necroptosis, an effect that could be exploited in caspase-8–proficient models using the clinically relevant caspase inhibitor emricasan. Our study provides evidence for immediate clinical exploration of tolinapant in combination with FOLFOX in poor prognosis MSS colorectal cancer with elevated cIAP1/2 expression.
Insomnia in Chinese College Students With Internet Addiction: Prevalence and Associated Clinical Correlates

Background: Internet addiction (IA) has gained more and more attention for its negative impact on the subjects' study and daily life. However, in a large sample, there is little research on the association between IA and insomnia in Chinese college students. This study aimed to investigate the prevalence of insomnia and its related risk factors among Chinese college students with IA. Methods: A cross-sectional design was used to investigate 627 Chinese college students with IA. Each student completed a survey on demographic data, Internet addiction (Revised Chinese Internet Addiction Scale), depression (Self-Rating Depression Scale), insomnia (Athens Insomnia Scale), anxiety (Self-Rating Anxiety Scale), and suicidal behavior. Binary logistic regression analysis was employed to adjust for confounding factors. Results: The prevalence of insomnia among students with IA was 54.86%. Compared with IA students without insomnia, IA students with insomnia were more likely to be younger, smoking, drinking, have anxiety, depression, suicidal ideations, suicide plans, and suicide attempts (all p < 0.05). Moreover, drinking [OR, 1.664; 95% confidence interval (CI), 1.139–2.431; p = 0.008], anxiety (OR, 2.321; 95% CI, 1.116–4.826; p = 0.024), and suicidal ideation (OR, 1.942; 95% CI:1.295–2.911; p = 0.001) were independently associated with insomnia in IA students. Conclusions: Insomnia is very common in Chinese IA students. Drinking, anxiety, and suicidal ideation are independently correlated with insomnia. This study provides valuable evidence for school counselors and clinical professionals to assess Internet addiction, insomnia, and suicide risk.
The centriolar satellite protein Cfap53/Ccdc11 facilitates the formation of the first zygotic microtubule organizing center in the zebrafish embryo

In embryos from most animal species a zygotic centrosome is assembled by the centriole derived from the sperm cell and pericentriolar proteins present in the oocyte. This zygotic centrosome acts as a microtubule organizing center (MTOC) to assemble the mitotic spindle in the first and all subsequent cell divisions. As MTOC formation has been studied mainly in adult cells, very little is known about the formation of the first zygotic MTOC. Here we find that zebrafish (Danio rerio) embryos lacking maternal or paternal Cfap53, a centriolar satellite protein, arrest during the first cell cycle due to a failure in proper formation of the mitotic spindle. During the first cell cycle Cfap53 co-localizes with γ-tubulin and other centrosomal and centriolar satellite proteins to the very large MTOC. Furthermore, we find that γ-tubulin localization to the MTOC is impaired in the absence of Cfap53 or when the microtubule network is disrupted. Based on these results we propose a model in which maternal and paternal Cfap53 participates in the organization of the first zygotic MTOC of the embryo. Once the zygotic MTOC is formed, Cfap53 is dispensable for MTOC formation and integrity in subsequent cell divisions.
Strategic Energy Management Model in A Cement Plant in Indonesia

A cement plant was required to provide consistency of its energy performance through energy system implementation and a third-party certification. However, the plant has not an energy system in place to answer the quick demand apart from routine energy measurement. Energy design and implementation of management system (EDIM) based on ISO 50001: 2018 and the Pearce II and Robinson's strategic management model is then made and implemented to answer the problem. The ISO model contributes much on operational risks whilst the second emphasizes on strategic ones. The study applies qualitative method through interactions with 2 energy experts in strategic and management system and 3 plant staff dealing with energy and management system. Interview, notetaking and written comments are done to get themes of the issues. The investigation results in that the EDIM model has fully met requirements of the ISO 50001 as well as the strategic management model. It has provided adequate implementable framework and easily applied to attain energy performance indicators. Problems, though, are emerged during implementation due to separated strategic actions with operational practices including use of new energy-management terms asking for longer time to be comprehended. In conclusion, consistent energy performance in current business situation can be assured through the model consisting of strategic and operational components.
Advanced applications of NMR to organometallic chemistry

Selective Excitation and Selective Detection in 2? 9Si NMR (E. Kupce & B. Wrackmeyer). Two--Dimensional 1? 3C--Metal Nuclei Correlation (S. Berger, et al.). Two--dimensional 1? H--1? 19Sn Proton Detected Correlation Spectroscopy in Coordination Chemistry of Hypervalent Organotin Compounds (F. Kayser, et al.). Indirect Nuclear 1? 19Sn--X Spin--Spin Coupling (B. Wrackmeyer). Solid State NMR Applications in Organotin and Organolead Chemistry (A. Sebald). Solid State NMR Investigations of Metal Carbonyl Complexes (S. Aime, et al.). High Pressure NMR in Organometallic Chemistry (U. Frey, et al.). Multinuclear NMR Spectroscopy in Supercritical Fluids (M. Waugh & G. Lawless). High Resolution 6? ,7? Li NMR of Organolithium Compounds (H. Gunther). Metal NMR of Organovanadium, --Niobium and --Tantalum Compounds (D. Rehder & D. Rodewald). NMR of Metallic Nuclei in Clusters (P. Granger). 1? 71Yb NMR Spectroscopy (J. Keates & G. Lawless). Index.
Temporospatial Flavonoids Metabolism Variation in Ginkgo biloba Leaves

Ginkgo (Ginkgo biloba L.) is a high-value medicinal tree species characterized by its flavonoids beneficial effects that are abundant in leaves. We performed a temporospatial comprehensive transcriptome and metabolome dynamics analyses of clonally propagated Ginkgo plants at four developmental stages (time: May to August) across three different environments (space) to unravel leaves flavonoids biosynthesis variation. Principal component analysis revealed clear gene expression separation across samples from different environments and leaf-developmental stages. We found that flavonoid-related metabolism was more active in the early stage of leaf development, and the content of total flavonoid glycosides and the expression of some genes in flavonoid biosynthesis pathway peaked in May. We also constructed a co-expression regulation network and identified eight GbMYBs and combining with other TF genes (3 GbERFs, 1 GbbHLH, and 1 GbTrihelix) positively regulated the expression of multiple structural genes in the flavonoid biosynthesis pathway. We found that part of these GbTFs (Gb_11316, Gb_32143, and Gb_00128) expressions was negatively correlated with mean minimum temperature and mean relative humidity, while positively correlated with sunshine duration. This study increased our understanding of the molecular mechanisms of flavonoids biosynthesis in Ginkgo leaves and provided insight into the proper production and management of Ginkgo commercial plantations.
COVID-19 Pandemic and Psychiatric Symptoms: The Impact on Parkinson's Disease in the Elderly

Background: The coronavirus disease 2019 (COVID-19) pandemic represents a condition of increased vulnerability and frailty for elderly patients with Parkinson's disease (PD). Social isolation may worsen the burden of the disease and specifically exacerbate psychiatric symptoms, often comorbid with PD. This study aimed at identifying risk/protective factors associated with subjective worsening of psychiatric symptomatology during the COVID-19 outbreak in a sample of individuals with PD aged 65 years or older. Methods: Patients with PD routinely followed at the outpatient clinic of Gemelli University Hospital, Rome, were assessed for subjective worsening of psychiatric symptoms through a dedicated telephone survey, after Italy COVID-19 lockdown. Patients' medical records were reviewed to collect sociodemographic and clinical data, including lifetime psychiatric symptoms and pharmacological treatment. Results: Overall, 134 individuals were assessed and 101 (75.4%) reported lifetime psychiatric symptoms. Among those, 23 (22.8%) presented with subjective worsening of psychiatric symptomatology during the COVID-19 outbreak. In this group, the most frequent symptom was depression (82.6%), followed by insomnia (52.2%). Subjective worsening of neurological symptoms (Wald = 24.03, df = 1, p = 0.001) and lifetime irritability (Wald = 6.35, df = 1, p = 0.020), together with younger age (Wald = 5.06, df = 1, p = 0.038) and female sex (Wald = 9.07 df = 1, p = 0.007), resulted as specific risk factors for ingravescence of psychiatric presentation. Lifetime pre-existing delusions, having received antipsychotics, and not having received mood stabilizer were also associated with subjective worsening of psychiatric symptomatology due to the COVID-19 pandemic. Conclusions: Individuals with PD and lifetime history of psychiatric symptoms may be exposed to increased vulnerability to the stressful effect of COVID-19 outbreak. Interventions aimed at reducing irritability and mood instability might have an indirect effect on the health of patients with PD during the COVID-19 pandemic.
Early Uncertainty Quantification for an Improved Decision Support Modeling Workflow: A Streamflow Reliability and Water Quality Example

Effective decision making for resource management is often supported by combining predictive models with uncertainty analyses. This combination allows quantitative assessment of management strategy effectiveness and risk. Typically, history matching is undertaken to increase the reliability of model forecasts. However, the question of whether the potential benefit of history matching will be realized, or outweigh its cost, is seldom asked. History matching adds complexity to the modeling effort, as information from historical system observations must be appropriately blended with the prior characterization of the system. Consequently, the cost of history matching is often significant. When it is not implemented appropriately, history matching can corrupt model forecasts. Additionally, the available data may offer little decision-relevant information, particularly where data and forecasts are of different types, or represent very different stress regimes. In this paper, we present a decision support modeling workflow where early quantification of model uncertainty guides ongoing model design and deployment decisions. This includes providing justification for undertaking (or forgoing) history matching, so that unnecessary modeling costs can be avoided and model performance can be improved. The workflow is demonstrated using a regional-scale modeling case study in the Wairarapa Valley (New Zealand), where assessments of stream depletion and nitrate-nitrogen contamination risks are used to support water-use and land-use management decisions. The probability of management success/failure is assessed by comparing the proximity of model forecast probability distributions to ecologically motivated decision thresholds. This study highlights several important insights that can be gained by undertaking early uncertainty quantification, including: i) validation of the prior numerical characterization of the system, in terms of its consistency with historical observations; ii) validation of model design or indication of areas of model shortcomings; iii) evaluation of the relative proximity of management decision thresholds to forecast probability distributions, providing a justifiable basis for stopping modeling.
Large-Scale Analysis of Circulating Amino Acids and Gene Expression in Relation to Abdominal Obesity

Background Circulating branched-chain amino acid (BCAA) levels are increased in obesity. One hypothesis explaining this phenomenon is downregulated catabolism in adipose tissue. Glutamate is a byproduct of this pathway and was found to be positively associated with central fat accumulation. We assessed the association between circulating glutamate and abdominal obesity, and how it relates to gene expression pathways in abdominal fat depots and cell types. Methods We used logistic regression to assess the odds of presenting abdominal obesity with varying circulating glutamate in 4,665 individuals from the TwinsUK cohort. We also compared glutamate levels in twin pairs discordant for abdominal obesity. We accessed gene expression profiles of adipose tissue and cells across depots derived from independent cohorts for phenotype, differential expression and pathway analysis. Results Individuals in the 5th quintile of circulating glutamate had a 7-fold increase in the risk of presenting abdominal obesity compared to those in the 1st quintile. This risk was greater than that associated with being in the 5th quintile of either BCAAs. Twins with abdominal obesity had significantly higher glutamate levels than their leaner co-twins. Most genes of the BCAA catabolism pathway were more expressed in the stromal vascular fraction (SVF) compared to adipocytes and associated with abdominal obesity in both men and women. Among the top pathways to be upregulated in visceral SVF was the glutamate receptor signaling pathway. Conclusion Glutamate is a potential biomarker of abdominal fat accumulation. Differences in gene expression across adipose tissue depots and cell types reflect this association.