Miracle-dz/UniFAR-FTUs huggingface dataset:
Diffusion analysis of single particle trajectories in a Bayesian nonparametrics framework

Single particle tracking (SPT), where individual molecules are fluorescently labelled and followed over time, is an important tool that allows the spatiotemporal dynamics of subcellular biological systems to be studied at very fine temporal and spatial resolution. Mathematical models of particle motion are typically based on Brownian diffusion, reflecting the noisy environment that biomolecules inhabit. In order to study changes in particle behaviour within individual tracks, Hidden Markov models (HMM) featuring multiple diffusive states have been used as a descriptive tool for SPT data. However, such models are typically specified with an a priori defined number of particle states and it has not been clear how such assumptions have affected their outcomes. Here, we propose a method for simultaneously inferring the number of diffusive states alongside the dynamic parameters governing particle motion. Our method is an infinite HMM (iHMM) with the general framework of Bayesian nonparametric models. We directly extend previous applications of these concepts in molecular biophysics to the SPT framework and propose and test an additional constraint with the goal of accelerating convergence and reducing computational time. We test our iHMM using simulated data and apply it to a previously analyzed large SPT dataset for B cell receptor motion on the plasma membrane of B cells of the immune system.
Beyond the Motor Cortex: Theta Burst Stimulation of the Anterior Midcingulate Cortex

Intermittent Theta Burst Stimulation (TBS) applied to the left dorsolateral prefrontal cortex suppressed reward-related signaling in the anterior midcingulate cortex (aMCC), resulting in a change in goal-directed behavior. Continuous TBS had no effect. While these results are inconsistent with reported TBS effects on motor cortex, the present findings offer normative insights into the magnitude and time course of TBS-induced changes in aMCC excitability during goal-directed behavior.
uORFlight: a vehicle towards uORF-mediated translational regulation mechanisms in eukaryotes

Upstream open reading frames (uORFs) are prevalent in eukaryotic mRNAs. They act as a translational control element for precisely tuning the expression of the downstream major open reading frame (mORF) with essential cellular functionalities. uORF variation has been clearly associated with several human diseases. In contrast, natural uORF variants in plants have not ever been identified or linked with any phenotypic changes. The paucity of such evidence encouraged us to generate this database-uORFlight (http://uorflight.whu.edu.cn). It facilitates the exploration of uORF variation among different splicing models of Arabidopsis and rice genes. Most importantly, users can evaluate uORF frequency among different accessions at the population scale and find out the causal single nucleotide polymorphism (SNP) or insertion/deletion (INDEL) which can be associated with phenotypic variation through database mining or simple experiments. Such information will help to make hypotheses of uORF function in plant development or adaption to changing environments on the basis of the cognate mORF function. This database also curates plant uORF relevant literature into distinct groups. To be broadly interesting, our database expands uORF annotation into more species of fungi (Botrytis cinerea), plant (Brassica napus, Glycine max, Gossypium raimondii, Medicago truncatula, Solanum lycopersicum, Solanum tuberosum, Triticum aestivum and Zea mays), metazoan (Caenorhabditis elegans and Drosophila melanogaster) and vertebrate (Homo sapiens, Mus musculus and Danio rerio). Therefore, uORFlight will light up the runway toward how uORF genetic variation determines phenotypic diversity and advance our understanding of translational control mechanisms.
Expression of Escherichia coli araE and modified lacY genes in Campylobacter jejuni is not sufficient for arabinose transport

Introduction Unlike Escherichia coli , Campylobacter jejuni is unable to import a range of sugars, including arabinose, which makes common expression vectors, such as pBAD33, non-functional in these bacteria. Aim The aim of this study was to investigate whether the E. coli transporters AraE and modified LacY (LacYA177C) would enable C. jejuni to uptake arabinose. Methodology and Results The respective genes of E. coli were constitutively expressed in C. jejuni strain 11168H after integration into the chromosome via homologous recombination. Vectors carrying these genes also contained a reporter gene, gfp, under the control of the arabinose-inducible promoter, pBAD. These constructs were verified in E. coli by demonstrating the induction of gfp in the presence of arabinose. Integration of the genes into one of the rRNA gene clusters was verified by PCR and genome sequencing. The latter also confirmed that the inserted gene clusters contained no mutations. Expression of the gfp gene in the presence of arabinose inducer was monitored using fluorescence microscopy of colonies and fluorimetry using both whole cells and lysates. Conclusion The results demonstrated the inability of C. jejuni to use arabinose transporters, which are fully functional in E. coli , suggesting a remarkable difference in the physiology of these bacteria.
Isolation of Cadmium and Lead Tolerant Plant Growth Promoting Rhizobacteria: Lysinibacillus varians and Pseudomonas putida from Indian Agricultural Soil

ABSTRACT Cadmium and lead tolerant plant growth promoting rhizobacteria can be an eco-friendly option for reclamation of metal-contaminated soil and mitigation of heavy metal stress for phytostimulation to develop sustainable agriculture. Novel heavy metal tolerant PGPR strain isolation is prerequisite in practical scale. The present study was to isolate, characterize and identify cadmium and lead tolerant PGPR strains. Some potent multi heavy metal tolerant PGPRs were isolated from rhizospheric soil contaminated with industrial, sewage or agrochemical waste and two most promising strains were identified as Lysinibacillus varians strain KUBM17 and Pseudomonas putida strain KUBM18 on the basis of 16S rDNA sequencing. These two strains were exhibiting a high degree of Cd and Pb tolerant ability with bioaccumulatory properties to remove Cd and Pb from the medium which was evidenced by AAS study. Furthermore, L. varians strain KUBM17 and P. putida strain KUBM18 showed very promising PGP traits such as ammonia production, IAA production (20–22 µg/ml), Nitrogen fixation, phosphate solubilization (55–515 ppm) and siderophore production (14–40 nmole) capability together with biocontrol properties with survival ability under different agro-climatic conditions. These PGPR isolates improved the early radish plant growth under cadmium and lead stress condition. So, KUBM 17 and KUBM 18 might be concerned as PGPR-biofertilizer in heavy metal-contaminated agricultural soil.
MicroRNA 145 enhances chemosensitivity of glioblastoma stem cells to demethoxycurcumin

Background: The presence of glioma stem cells (GSCs) is thought to be a key factor responsible for development of the incurable glioblastoma multiforme (GBM). GSCs are often displayed during chemotherapy resistance, except for demethoxycurcumin (DMC), a component of curcumin, which has been previously confirmed to inhibit GSCs proliferation and induce apoptosis. Purpose: The objective of this study was to identify the main mechanism underlying anti-GSCs resistance by DMC. Patients and methods: qRT-PCR was used to determine the expression of miR-145 in glioma patients and GSCs, and GSCs were transfected with miR-145 overexpressed vectors. Then, functional analyses (in vitro and in vivo) were performed to confirm the role of miR-145 and DMC in GSCs. Finally, related proteins were tested by immunohistochemistry and Western blot. Results: miR-145 was atypically low-expressed miRNA in GSCs, and could enhance GSC chemosensitivity to DMC both in vitro and in vivo. Upregulation of miR-145 in GSCs resulted in increased cell growth inhibition and apoptosis to DMC. Further research on the mechanism demonstrated that the combined effects of miR-145 and DMC were involved in the miR-145/SOX2-Wnt/β-catenin pathway. Overexpression of SOX2 reduced GSC resistance to growth inhibition by miR-145+ DMC treatment. Conclusion: Our data strongly support an important role for miR-145 in enhancing GSC chemosensitivity to DMC by targeting the SOX2-Wnt/β-catenin axis.
In vivo Neutralization of Pro-inflammatory Cytokines During Secondary Streptococcus pneumoniae Infection Post Influenza A Virus Infection

An overt pro-inflammatory immune response is a key factor contributing to lethal pneumococcal infection in an influenza pre-infected host and represents a potential target for therapeutic intervention. However, there is a paucity of knowledge about the level of contribution of individual cytokines. Based on the predictions of our previous mathematical modeling approach, the potential benefit of IFN-γ- and/or IL-6-specific antibody-mediated cytokine neutralization was explored in C57BL/6 mice infected with the influenza A/PR/8/34 strain, which were subsequently infected with the Streptococcus pneumoniae strain TIGR4 on day 7 post influenza. While single IL-6 neutralization had no effect on respiratory bacterial clearance, single IFN-γ neutralization enhanced local bacterial clearance in the lungs. Concomitant neutralization of IFN-γ and IL-6 significantly reduced the degree of pneumonia as well as bacteremia compared to the control group, indicating a positive effect for the host during secondary bacterial infection. The results of our model-driven experimental study reveal that the predicted therapeutic value of IFN-γ and IL-6 neutralization in secondary pneumococcal infection following influenza infection is tightly dependent on the experimental protocol while at the same time paving the way toward the development of effective immune therapies.
Moisture content calculations for 1000-hour timelag fuels

Techniques to calculate 1000-hour timelag fuel moistures were developed from the­ ory of water movement in wood. The 1000-hour timelag fuel moisture is computed from mean daily temperatures and humidities and precipitation duration. Comparison of calculated and ob­ served fuel moistures showed good agreement. Techniques to determine the seasonal starting value of the 1000-hour timelag fuel moisture are based on monthly climatological summaries. The seasonal starting value calculation was made from a least squares regression equation. FOREST SCI. 27:19-26. ADDITIONAL
Functional Localization of the Frontal Eye Fields in the Common Marmoset Using Microstimulation

The frontal eye field (FEF) is a critical region for the deployment of overt and covert spatial attention. Although investigations in the macaque continue to provide insight into the neural underpinnings of the FEF, due to its location within a sulcus, the macaque FEF is virtually inaccessible to electrophysiological techniques such as high-density and laminar recordings. With a largely lissencephalic cortex, the common marmoset (Callithrix jacchus) is a promising alternative primate model for studying FEF microcircuitry. Putative homologies have been established with the macaque FEF on the basis of cytoarchitecture and connectivity; however, physiological investigation in awake, behaving marmosets is necessary to physiologically locate this area. Here, we addressed this gap using intracortical microstimulation in a broad range of frontal cortical areas in three adult marmosets (two males, one female). We implanted marmosets with 96-channel Utah arrays and applied microstimulation trains while they freely viewed video clips. We evoked short-latency fixed vector saccades at low currents (<50 μA) in areas 45, 8aV, 8C, and 6DR. We observed a topography of saccade direction and amplitude consistent with findings in macaques and humans: small saccades in ventrolateral FEF and large saccades combined with contralateral neck and shoulder movements encoded in dorsomedial FEF. Our data provide compelling evidence supporting homology between marmoset and macaque FEF and suggest that the marmoset is a useful primate model for investigating FEF microcircuitry and its contributions to oculomotor and cognitive functions. SIGNIFICANCE STATEMENT The frontal eye field (FEF) is a critical cortical region for overt and covert spatial attention. The microcircuitry of this area remains poorly understood because in the macaque, the most commonly used model, it is embedded within a sulcus and is inaccessible to modern electrophysiological and imaging techniques. The common marmoset is a promising alternative primate model due to its lissencephalic cortex and potential for genetic manipulation. However, evidence for homologous cortical areas in this model remains limited and unclear. Here, we applied microstimulation in frontal cortical areas in marmosets to physiologically identify FEF. Our results provide compelling evidence for an FEF in the marmoset and suggest that the marmoset is a useful model for investigating FEF microcircuitry.
Broodmate aggression and life history variation in accipitrid birds of prey

Abstract Aggressive sibling competition for parental food resources is relatively infrequent in animals but highly prevalent and extreme among certain bird families, particularly accipitrid raptors (Accipitriformes). Intense broodmate aggression within this group is associated with a suite of traits including a large adult size, small broods, low provisioning rates, and slow development. In this study, we apply phylogenetic comparative analyses to assess the relative importance of several behavioral, morphological, life history, and ecological variables as predictors of the intensity of broodmate aggression in 65 species of accipitrid raptors. We show that intensity of aggression increases in species with lower parental effort (small clutch size and low provisioning rates), while size effects (adult body mass and length of nestling period) are unimportant. Intense aggression is more closely related to a slow life history pace (high adult survival coupled with a restrained parental effort), rather than a by‐product of allometry or food limitation. Consideration of several ecological variables affecting prey abundance and availability reveals that certain lifestyles (e.g., breeding in aseasonal habitats or hunting for more agile prey) may slow a species’ life history pace and favor the evolution of intense broodmate aggression.
Usefulness of Haemoglobin Level Combined with CAMI-STEMI Score for Predicting MACCE in Patients with Acute ST-Elevation Myocardial Infarction after PCI

Anaemia and high haemoglobin levels are common in ST elevation myocardial infarction (STEMI) patients, but the effect of the haemoglobin level on the prognosis of STEMI patients remains in dispute. This study aimed to evaluate the prognostic value of the haemoglobin level combined with the CAMI-STEMI score in STEMI patients after percutaneous coronary intervention (PCI). We included 360 STEMI patients who underwent PCI. The patients were divided into 3 groups according to the first haemoglobin value after PCI. Clinical characteristics and the incidence of major adverse cardiovascular and cerebral events (MACCE) during the follow-up period were recorded. The incidence of MACCE in the 3 groups increased with a decrease in the haemoglobin level. Multivariate regression analysis showed that the CAMI-STEMI score was an independent predictor of MACCE incidence at 30 days after PCI and that anaemia was an independent predictor of MACCE incidence at 6 months and 1 year after PCI. A high haemoglobin level was an independent predictor of MACCE incidence at 1 year after PCI. The area under receiver operating characteristic curves (AUCs) of the haemoglobin level, CAMI-STEMI score, and haemoglobin level combined with CAMI-STEMI score predicting the occurrence of MACCE in STEMI patients within 30 days after PCI were 0.604, 0.614, and 0.639, respectively. In conclusion, The CAMI-STEMI score was an independent predictor of MACCE incidence at 30 days after PCI. The haemoglobin level combined with the CAMI-STEMI score improved the predictive value of MACCE in STEMI patients within 30 days after PCI. Trial Registration. This trial was a prospective cohort study and registered with ChiCTR-ROC-17011542.
Chicken or Egg: Is Clonal Hematopoiesis Primarily Caused by Genetic or Epigenetic Aberrations?

Hematopoietic malignancies, including multiple myeloma, are associated with characteristic mutations and genetic instabilities that drive malignant transformation. On the other hand, tumor formation is also associated with drastic epigenetic aberrations, which can impact the genetic sequence. Therefore, the question arises if malignant transformation is primarily caused by genetic or epigenetic events. The tight connection of these processes becomes obvious by the fact that in several malignancies, as well as in age-related clonal hematopoiesis, mutations are particularly observed in epigenetic writers such as DNMT3A and TET2. On the other hand, specific epigenetic aberrations, so-called “epimutations,” can mimic genomic mutations. In contrast to the genetic sequence, which remains relatively stable throughout life, the epigenome notoriously undergoes drastic changes in normal hematopoietic development and aging. It is conceivable that such epigenetic reorganization, e.g., in 3D chromatin conformation, paves the way for secondary chromosomal instabilities, which then result in tumor-specific genomic changes that further trigger disease progression. This scenario might explain the occurrence of tumor-specific mutations particularly in the elderly. Taken together, the causality dilemma is difficult to solve because genetic and epigenetic aberrations are interlinked during disease development. A better understanding of how the chromatin structure or 3D nuclear organization can evoke specific mutations might provide new perspectives for prevention, early diagnostics, and targeted therapy.
In vivo monitoring of hepatic glycolipid distribution of n-6 ∕ n-3 in jugular-vein-cannulated rats as a nutritional research model for monogastric animal

Abstract The metabolic distribution via blood from liver of glycerolipids by omega-6 to omega-3 fatty acid (n-6 / n-3) ratio in monogastric animal nutrition is very important. In vivo monitoring technique using jugular-vein-cannulated rats as a nutritional model for monogastric animal can yield important insights into animal nutrition. This study was conducted to determine the effect of different n-6 / n-3 ratios (71:1, 4:1, 15:1, 30:1) on metabolic distribution of glycerolipids newly synthesized and secreted in the liver of the rats and explore the mechanism involved. Regarding 14CO2 released from oxidation of glycerolipid metabolism, it was the highest (22.5 %) in groups with a n-6 / n-3 ratio of 4:1 (P<0.05). The control group showed the highest total glycerolipid level, followed by the 30:1, 15:1, and 4:1 groups in order (P<0.05). When secreted triacylglycerol level of each group was compared with that of the control group, the 4:1, 15:1, and 30:1 groups were decreased by 36.3 %, 20.9 %, and 13.3 %, respectively (P<0.05). Regarding the distribution of phospholipid against total glycerolipid compared to the control group, the 4:1, 15:1, and 30:1 groups were 1.38, 1.29, and 1.17 times higher, respectively (P<0.05). In the comparison of 14CO2 emission against total glycerolipid compared with the control group, the 4:1, 15:1, and 30:1 groups were 1.61, 1.52, and 1.29 times higher, respectively (P<0.05). These results demonstrate that a dietary n-6 / n-3 fatty acid ratio of 4:1 could significantly decrease harmful lipid levels in the blood by controlling the mechanism of metabolic distribution via blood from triglyceride and phospholipid newly synthesized in the liver of cannulated rat.
What Do Editors Maximize? Evidence from Four Leading Economics Journals

We study editorial decision-making using anonymized submission data for four leading economics journals: the Journal of the European Economics Association, the Quarterly Journal of Economics, the Review of Economic Studies, and the Review of Economics and Statistics. We match papers to the publication records of authors at the time of submission and to subsequent Google Scholar citations. To guide our analysis we develop a benchmark model in which editors maximize the expected quality of accepted papers and citations are unbiased measures of quality. We then generalize the model to allow different quality thresholds for different papers, and systematic gaps between citations and quality. Empirically, we find that referee recommendations are strong predictors of citations, and that editors follow the recommendations quite closely. Holding constant the referees' evaluations, however, papers by highly-published authors get more citations, suggesting that referees impose a higher bar for these authors, or that prolific authors are over-cited. Editors only partially offset the referees' opinions, effectively discounting the citations of more prolific authors in their revise and resubmit decisions by up to 80%. To disentangle the two explanations for this discounting, we conduct a survey of specialists, asking them for their preferred relative citation counts for matched pairs of papers. The responses show no indication that prolific authors are over-cited and thus suggest that referees and editors seek to support less prolific authors.
Coaxial Cable Equalization Techniques at 50-110 Gbps

Next generation communication systems are reaching 110Gbps rates. At these frequencies, the skin effect and dielectric loss of copper cables cause inter-symbol interference (ISI) and frequency dependent loss, severely limiting the channel bandwidth. In this thesis, different methods for alleviating ISI are explored. The design of the critical blocks of an adaptive channel equalizer with up to two times oversampling are presented. The circuits were fabricated in a 0. 13μm SiGe BiCMOS technology. The linear, adaptive equalizer operates up to 70Gbps and its measured S-parameters exhibit a single-ended peak gain of 12.2dB at 52GHz, allowing for 31dB of peaking between DC and 52GHz. Equalization is demonstrated experimentally at 59Gbps for a cable loss of 17.9dB. These results make it the fastest receive equalizer published to date. A retiming flip-flop operating between 72 and 118 GHz, the highest reported in silicon, is also designed and characterized, showing less than 500-fs jitter.