Miracle-dz/UniFAR-FTUs huggingface dataset:
Biosynthetic Potentials of Metabolites and Their Hierarchical Organization

A major challenge in systems biology is to understand how complex and highly connected metabolic networks are organized. The structure of these networks is investigated here by identifying sets of metabolites that have a similar biosynthetic potential. We measure the biosynthetic potential of a particular compound by determining all metabolites than can be produced from it and, following a terminology introduced previously, call this set the scope of the compound. To identify groups of compounds with similar scopes, we apply a hierarchical clustering method. We find that compounds within the same cluster often display similar chemical structures and appear in the same metabolic pathway. For each cluster we define a consensus scope by determining a set of metabolites that is most similar to all scopes within the cluster. This allows for a generalization from scopes of single compounds to scopes of a chemical family. We observe that most of the resulting consensus scopes overlap or are fully contained in others, revealing a hierarchical ordering of metabolites according to their biosynthetic potential. Our investigations show that this hierarchy is not only determined by the chemical complexity of the metabolites, but also strongly by their biological function. As a general tendency, metabolites which are necessary for essential cellular processes exhibit a larger biosynthetic potential than those involved in secondary metabolism. A central result is that chemically very similar substances with different biological functions may differ significantly in their biosynthetic potentials. Our studies provide an important step towards understanding fundamental design principles of metabolic networks determined by the structural and functional complexity of metabolites.
DP Drillship Stationkeeping in Ice - Comparison Between Numerical Simulations and Ice Basin Tests

The present paper reports on comparisons between results from ice basin tests and numerical simulations. The tests were conducted in the model ice basin of the National Research Council Canada (NRC) in St. John’s, Newfoundland. Those tests examined the Dynamic Positioning (DP) of a vessel in managed ice conditions at a scale of 1:40. A numerical model, which was developed by the NRC over the past few years, was used to simulate ice basin test conditions. The results indicate that surge direction thrust and moments are in good agreement. The conclusions address the effects of ice channel width and floe shapes.
Ultrastructure of compatible and incompatible interactions in phloem sieve elements during the stylet penetration by cotton aphids in melon

Resistance of the melon line TGR‐1551 to the aphid Aphis gossypii is based on preventing aphids from ingesting phloem sap. In electrical penetration graphs (EPGs), this resistance has been characterized with A. gossypii showing unusually long phloem salivation periods (waveform E1) mostly followed by pathway activities (waveform C) or if followed by phloem ingestion (waveform E2), ingestion was not sustained for more than 10 min. Stylectomy with aphids on susceptible and resistant plants was performed during EPG recording while the stylet tips were phloem inserted. This was followed by dissection of the penetrated leaf section, plant tissue fixation, resin embedding, and ultrathin sectioning for transmission electron microscopic observation in order to study the resistance mechanism in the TGR. The most obvious aspect appeared to be the coagulation of phloem proteins inside the stylet canals and the punctured sieve elements. Stylets of 5 aphids per genotype were amputated during sieve element (SE) salivation (E1) and SE ingestion (E2). Cross‐sections of stylet bundles in susceptible melon plants showed that the contents of the stylet canals were totally clear and also, no coagulated phloem proteins occurred in their punctured sieve elements. In contrast, electron‐dense coagulations were found in both locations in the resistant plants. Due to calcium binding, aphid saliva has been hypothesized to play an essential role in preventing/suppressing such coagulations that cause occlusion of sieves plate and in the food canal of the aphid's stylets. Doubts about this role of E1 salivation are discussed on the basis of our results.
Best Practices for Building Trust in Virtual Business Negotiations

Virtual discussions have become a common practice in the corporate sector. This article aims to outline the most effective strategies that can be used to establish trust in virtual discussions. To achieve this goal, several techniques were employed, including direct observation, interviews with negotiators, analysis of 2,000 virtual conversations, and monitoring a company's virtual negotiations for around 24 months. Based on a thorough analysis of the content, the main findings highlighted effective strategies that can build trust in remote negotiations. These include selecting the appropriate form of virtual communication, providing multiple contact options, ensuring reliable and high-quality connections, maintaining constant accessibility, and creating an organized and conducive environment for communication, free from interruptions. This article offers a fresh perspective on virtual business negotiations that is useful to academics, negotiators, and other professionals. It presents practical strategies for establishing trust in virtual negotiations.
Monoclonal antibody-based serological methods for maize chlorotic mottle virus detection in China

Maize chlorotic mottle virus (MCMV) infects maize plants and causes significant losses in corn production worldwide. In this study, purified MCMV particles were used as the immunogen to produce monoclonal antibodies (MAbs) and polyclonal antibodies (PAbs). Four murine MAbs (4B8, 8C11, 6F4, and 9G1) against MCMV were obtained through the hybridoma technology. The triple antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA), dot-immunobinding assay (DIBA), and immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) using the MAb 4B8 were then developed for sensitive, specific, and rapid detection of MCMV in fields. MCMV could be detected in infected leaf crude extracts at dilutions of 1:327 680, 1:64 000, and 1:3 276 800 (w/v, g/ml) by TAS-ELISA, DIBA, and IC-RT-PCR, respectively. One hundred and sixty-one maize field samples showing virus-like symptoms and sixty-nine symptomless maize field samples from ten different provinces of China were collected and screened for the presence of MCMV using the established serological methods. A phylogenetic tree was constructed based on the full length CP genes and Chinese MCMV isolates formed one branch with Thailand isolates. The detection results demonstrated that MCMV is one of most prevalent viruses infecting maize in the Yunnan and Sichuan provinces of China.
Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the mode and strength of selection. To control for regional variation in substitution rates, the proportionate number of nonsynonymous differences (dN) is divided by the proportionate number of synonymous differences (dS). The resulting ratio (dN/dS) is a widely used indicator for functional divergence to identify particular genes that underwent positive selection. With the ever-growing amount of genome data, summary statistics like mean dN/dS allow gathering information on the mode of evolution for entire species. Both applications hinge on the assumption that dS and mean dS (∼branch length) are neutral and adequately control for variation in substitution rates across genes and across organisms, respectively. We here explore the validity of this assumption using empirical data based on whole-genome protein sequence alignments between human and 15 other vertebrate species and several simulation approaches. We find that dN/dS does not appropriately reflect the action of selection as it is strongly influenced by its denominator (dS). Particularly for closely related taxa, such as human and chimpanzee, dN/dS can be misleading and is not an unadulterated indicator of selection. Instead, we suggest that inconsistencies in the behavior of dN/dS are to be expected and highlight the idea that this behavior may be inherent to taking the ratio of two randomly distributed variables that are nonlinearly correlated. New null hypotheses will be needed to adequately handle these nonlinear dynamics.
Learning Stationary Time Series using Gaussian Processes with Nonparametric Kernels

We introduce the Gaussian Process Convolution Model (GPCM), a two-stage non-parametric generative procedure to model stationary signals as the convolution between a continuous-time white-noise process and a continuous-time linear filter drawn from Gaussian process. The GPCM is a continuous-time nonparametric-window moving average process and, conditionally, is itself a Gaussian process with a nonparametric kernel defined in a probabilistic fashion. The generative model can be equivalently considered in the frequency domain, where the power spectral density of the signal is specified using a Gaussian process. One of the main contributions of the paper is to develop a novel variational free-energy approach based on inter-domain inducing variables that efficiently learns the continuous-time linear filter and infers the driving white-noise process. In turn, this scheme provides closed-form probabilistic estimates of the covariance kernel and the noise-free signal both in denoising and prediction scenarios. Additionally, the variational inference procedure provides closed-form expressions for the approximate posterior of the spectral density given the observed data, leading to new Bayesian nonparametric approaches to spectrum estimation. The proposed GPCM is validated using synthetic and real-world signals.
Disclosures of banks’ sustainability reports, climate change and central banks: An empirical analysis with unstructured data

Climate change will impact the economy in the long term but also in the medium run potentially affecting financial stability and the whole economic system (Nyambuu & Semmler, 2023). Some studies suggested that climate change may hit financial actors even if there are few studies related to the role of banks’ sustainability disclosure and central banks’ mandates. This paper examines the sustainability reports disclosures of the banks listed on the FTSE Italia All-Share Italian Stock Exchange for the year 2021–2020. It applies five kinds of multivariate techniques on unstructured data using Iramuteq (www.iramuteq.org) and SAS Viya (www.sas.com). The article tries to assess how and whether banks are disclosing transition and physical risk, and how and whether they conducted scenario analysis through the lens of the Task Force on Climate-related Financial Disclosures (TCFD) framework. Even though banks provided environmental, social, and governance (ESG) disclosure, they paid scant attention to furnishing climate change information to market and central banks, and to prioritize their complying with international frameworks. The article addresses the main research gap in the literature review and focuses on the role of disclosures and central banks’ mandates, sustainability data gap and solutions through machine learning, analysis of deep uncertainty for monetary policy, and the use of scenario analysis when it is impossible to apply deterministic or probabilistic approaches and text mining for central banks in the context of unstructured data.
Telomere protein RAP1 levels are affected by cellular aging and oxidative stress

Telomeres are important for maintaining the integrity of the genome through the action of the shelterin complex. Previous studies indicted that the length of the telomere did not have an effect on the amount of the shelterin subunits; however, those experiments were performed using immortalized cells with stable telomere lengths. The interest of the present study was to observe how decreasing telomere lengths over successive generations would affect the shelterin subunits. As neonatal human dermal fibroblasts aged and their telomeres became shorter, the levels of the telomere-binding protein telomeric repeat factor 2 (TRF2) decreased significantly. By contrast, the levels of one of its binding partners, repressor/activator protein 1 (RAP1), decreased to a lesser extent than would be expected from the decrease in TRF2. Other subunits, TERF1-interacting nuclear factor 2 and protection of telomeres protein 1, remained stable. The decrease in RAP1 in the older cells occurred in the nuclear and cytoplasmic fractions. Hydrogen peroxide (H2O2) stress was used as an artificial means of aging in the cells, and this resulted in RAP1 levels decreasing, but the effect was only observed in the nuclear portion. Similar results were obtained using U251 glioblastoma cells treated with H2O2 or grown in serum-depleted medium. The present findings indicate that TRF2 and RAP1 levels decrease as fibroblasts naturally age. RAP1 remains more stable compared to TRF2. RAP1 also responds to oxidative stress, but the response is different to that observed in aging.
Altered regional blood flow distribution in Mas-deficient mice

Background: We have recently shown that the acute infusion of angiotensin-(1–7) [Ang-(1-7)] or chronic increase in plasma Ang-(1-7) produces important changes in regional blood flow in rats. Methods: To further assess whether these changes are related to Mas, in this study hemodynamic measurements were performed in Ang-(1-7) receptor Mas knockout C57BL/6 (Mas-KO) mice and age-matched wild type (WT) control mice, using fluorescent microspheres. Results: Mean arterial pressure in urethane-anesthetized Mas-KO mice (12–16 weeks old) did not differ from that in WT mice (79 ± 2 and 80 ± 2 mmHg respectively). However, pronounced differences were observed in other hemodynamic measurements. Mas-KO mice exhibited a significant decrease in stroke volume (0.03 ± 0.01 versus 0.05 ± 0.01 ml/beat in WT) and decreased cardiac index (0.81 ± 0.08 versus 1.24 ± 0.24 ml/min/g in WT). Strikingly, Mas-KO mice exhibited a marked increase in vascular resistance and a decrease in blood flow in the kidney, lung, adrenal gland, mesentery, spleen and brown fat tissue. The decrease in blood flow ranged from 34% (spleen) to 55% (brown fat tissue). Conclusion: These results suggest that the Ang-(1-7)/Mas axis plays an important role in regional and systemic hemodynamic adjustments in mice.
A Robust Image Alignment Algorithm for Video Stabilization Purposes

Today, many people in the world without any (or with little) knowledge about video recording, thanks to the widespread use of mobile devices (personal digital assistants, mobile phones, etc.), take videos. However, the unwanted movements of their hands typically blur and introduce disturbing jerkiness in the recorded sequences. Many video stabilization techniques have been hence developed with different performances but only fast strategies can be implemented on embedded devices. A fundamental issue is the overall robustness with respect to different scene contents (indoor, outdoor, etc.) and conditions (illumination changes, moving objects, etc.). In this paper, we propose a fast and robust image alignment algorithm for video stabilization purposes. Our contribution is twofold: a fast and accurate block-based local motion estimator together with a robust alignment algorithm based on voting. Experimental results confirm the effectiveness of both local and global motion estimators.
Colonic J-pouch decreases bowel frequency by improving the evacuation ratio.

BACKGROUND/AIMS To compare the functional outcome of ultra-low anterior resection for rectal cancer with colonic J-pouch reconstruction with that of straight reconstruction. METHODOLOGY Twenty-three patients who underwent ultra-low anterior resection with or without J-pouch reconstruction underwent bowel transit study, videodefecography, and answered a questionnaire survey 4 months and 1 year after surgery. Eleven healthy subjects underwent similar testing as controls. RESULTS Patients with a J-pouch had less frequent stools than patients with straight reconstruction 4 months after surgery (p<0.05), but the two groups were similar at 1 year. Bowel transit time was similar at both study points. The evacuation ratio was higher after J-pouch than straight reconstruction 4 months after surgery (p<0.05). However, the ratio improved in the straight group, and no difference existed at 1 year. Colonic contraction was seen only near the anastomosis 4 months after surgery, but the contraction proximal to the anastomosis improved over the next 8 months. CONCLUSIONS J-pouch reconstruction facilitates evacuation by improving the evacuation ratio. Although straight anastomosis caused excessive stool frequency 4 months after surgery, colonic function continued to improve and was comparable with J-pouch and straight reconstruction 1 year after surgery because the contraction ratio proximal to the anastomosis improved.
Evaluation of Outflow Structures In Vivo after the Phacocanaloplasty

Purpose. To evaluate the in vivo changes in Schlemm's canal (SC) and the trabecular meshwork (TM) in patients with primary open-angle glaucoma (POAG) after phacocanaloplasty using anterior segment optical coherence tomography (AS-OCT). Methods. Ten eyes of nine patients with POAG (6 men and 3 women) who underwent phacocanaloplasty. Preoperative and postoperative visual acuity (VA), intraocular pressure (IOP), and use of glaucoma medications were evaluated. The main outcome measures were the area of SC and TM thickness assessed using AS-OCT before and 12 months after surgery. Results. We found statistically significant reduction in IOP (from 26.4 (8.6) mmHg to 12.9 (2.5) (p < 0.05) mmHg), increase in VA from 0.7 (0.4) to 0.9 (0.2), and decrease in glaucoma medication from 2.6 (1.2) to 1.1 (1.3) at 12 months postoperatively. There was a significant increase in the SC area (3081.7 (842.8) μm2 versus 5098.8 (1190.5) μm2, p < 0.001) and a decrease in mean TM thickness (91.2 (18.6) μm versus 81.3 (15.1) μm, p = 0.001) after surgery. We found negative correlations between SC area and IOP before surgery (r = −0.67, p = 0.03) and also between SC area before and IOP reduction 12 months after the phacocanaloplasty (r = −0.80, p = 0.005). Conclusions. Our results showed statistically significant dilation of SC area and reduction of TM thickness after phacocanaloplasty in POAG patients. The degree of SC expansion was related to the IOP decrease.
Learning directed acyclic graphs based on sparsest permutations

We consider the problem of learning a Bayesian network or directed acyclic graph (DAG) model from observational data. A number of constraint-based, score-based and hybrid algorithms have been developed for this purpose. For constraint-based methods, statistical consistency guarantees typically rely on the faithfulness assumption, which has been show to be restrictive especially for graphs with cycles in the skeleton. However, there is only limited work on consistency guarantees for score-based and hybrid algorithms and it has been unclear whether consistency guarantees can be proven under weaker conditions than the faithfulness assumption. In this paper, we propose the sparsest permutation (SP) algorithm. This algorithm is based on finding the causal ordering of the variables that yields the sparsest DAG. We prove that this new score-based method is consistent under strictly weaker conditions than the faithfulness assumption. We also demonstrate through simulations on small DAGs that the SP algorithm compares favorably to the constraint-based PC and SGS algorithms as well as the score-based Greedy Equivalence Search and hybrid Max-Min Hill-Climbing method. In the Gaussian setting, we prove that our algorithm boils down to finding the permutation of the variables with sparsest Cholesky decomposition for the inverse covariance matrix. Using this connection, we show that in the oracle setting, where the true covariance matrix is known, the SP algorithm is in fact equivalent to $\ell_0$-penalized maximum likelihood estimation.
Are You Talking to a Machine? Dataset and Methods for Multilingual Image Question

In this paper, we present the mQA model, which is able to answer questions about the content of an image. The answer can be a sentence, a phrase or a single word. Our model contains four components: a Long Short-Term Memory (LSTM) to extract the question representation, a Convolutional Neural Network (CNN) to extract the visual representation, an LSTM for storing the linguistic context in an answer, and a fusing component to combine the information from the first three components and generate the answer. We construct a Freestyle Multilingual Image Question Answering (FM-IQA) dataset to train and evaluate our mQA model. It contains over 150,000 images and 310,000 freestyle Chinese question-answer pairs and their English translations. The quality of the generated answers of our mQA model on this dataset is evaluated by human judges through a Turing Test. Specifically, we mix the answers provided by humans and our model. The human judges need to distinguish our model from the human. They will also provide a score (i.e. 0, 1, 2, the larger the better) indicating the quality of the answer. We propose strategies to monitor the quality of this evaluation process. The experiments show that in 64.7% of cases, the human judges cannot distinguish our model from humans. The average score is 1.454 (1.918 for human). The details of this work, including the FM-IQA dataset, can be found on the project page: this http URL
Bayesian multimodel estimation of global terrestrial latent heat flux from eddy covariance, meteorological, and satellite observations

Accurate estimation of the satellite‐based global terrestrial latent heat flux (LE) at high spatial and temporal scales remains a major challenge. In this study, we introduce a Bayesian model averaging (BMA) method to improve satellite‐based global terrestrial LE estimation by merging five process‐based algorithms. These are the Moderate Resolution Imaging Spectroradiometer (MODIS) LE product algorithm, the revised remote‐sensing‐based Penman‐Monteith LE algorithm, the Priestley‐Taylor‐based LE algorithm, the modified satellite‐based Priestley‐Taylor LE algorithm, and the semi‐empirical Penman LE algorithm. We validated the BMA method using data for 2000–2009 and by comparison with a simple model averaging (SA) method and five process‐based algorithms. Validation data were collected for 240 globally distributed eddy covariance tower sites provided by FLUXNET projects. The validation results demonstrate that the five process‐based algorithms used have variable uncertainty and the BMA method enhances the daily LE estimates, with smaller root mean square errors (RMSEs) than the SA method and the individual algorithms driven by tower‐specific meteorology and Modern Era Retrospective Analysis for Research and Applications (MERRA) meteorological data provided by the NASA Global Modeling and Assimilation Office (GMAO), respectively. The average RMSE for the BMA method driven by daily tower‐specific meteorology decreased by more than 5 W/m2 for crop and grass sites, and by more than 6 W/m2 for forest, shrub, and savanna sites. The average coefficients of determination (R2) increased by approximately 0.05 for most sites. To test the BMA method for regional mapping, we applied it for MODIS data and GMAO‐MERRA meteorology to map annual global terrestrial LE averaged over 2001–2004 for spatial resolution of 0.05°. The BMA method provides a basis for generating a long‐term global terrestrial LE product for characterizing global energy, hydrological, and carbon cycles.