Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of the compensatory reserve measurement in an emergency department trauma population

The Compensatory Reserve Measurement (CRM) is a novel method used to provide early assessment of shock based on arterial wave form morphology changes. We hypothesized that (1) CRM would be significantly lower in those trauma patients who received life‐saving interventions compared with those not receiving interventions, and (2) CRM in patients who received interventions would recover after the intervention was performed.
An atlas of the Norway spruce needle seasonal transcriptome

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 – June 30), cell walls, organelles etc. were formed, and this developmental program heavily influenced the transcriptome, explained by over represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February) and spring (March-April), where over represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools. Significance statement The development of Norway spruce needles and their annual cycle of biochemical activities (photosynthesis in the summer, adaptation and survival of the harsh boreal winter) is not well understood. We use deep RNA sequencing to profile the transcriptome over the season, and show how the dataset could be used to give information about “what needles do” over the year, and are here making the dataset available for the scientific community. Graphical abstract
VirB4- and VirD4-Like ATPases, Components of a Putative Type 4C Secretion System in Clostridioides difficile

C. difficile is a Gram-positive, anaerobic, spore-forming bacterium that causes life-threatening colitis in humans. Major virulence factors of the microorganism include the toxins TcdA, TcdB, and CDT. ABSTRACT The type 4 secretion system (T4SS) represents a bacterial nanomachine capable of trans-cell wall transportation of proteins and DNA and has attracted intense interest due to its roles in the pathogenesis of infectious diseases. In the current investigation, we uncovered three distinct gene clusters in Clostridioides difficile strain 630 encoding proteins structurally related to components of the VirB4/D4 type 4C secretion system from Streptococcus suis strain 05ZYH33 and located within sequences of conjugative transposons (CTn). Phylogenic analysis revealed that VirB4- and VirD4-like proteins of the CTn4 locus, on the one hand, and those of the CTn2 and CTn5 loci, on the other hand, fit into separate clades, suggesting specific roles of identified secretion system variants in the physiology of C. difficile. Our further study on VirB4- and VirD4-like products encoded by CTn4 revealed that both proteins possess Mg2+-dependent ATPase activity, form oligomers (most likely hexamers) in aqueous solutions, and rely on potassium but not sodium ions for the highest catalytic rate. VirD4 binds nonspecifically to DNA and RNA. The DNA-binding activity of VirD4 strongly decreased with the W241A variant. Mutations in the nucleotide sequences encoding presumable Walker A and Walker B motifs decreased the stability of the oligomers and significantly but not completely attenuated the enzymatic activity of VirB4. In VirD4, substitutions of amino acid residues in the peptides reminiscent of Walker structural motifs neither attenuated the enzymatic activity of the protein nor influenced the oligomerization state of the ATPase. IMPORTANCE C. difficile is a Gram-positive, anaerobic, spore-forming bacterium that causes life-threatening colitis in humans. Major virulence factors of the microorganism include the toxins TcdA, TcdB, and CDT. However, other bacterial products, including a type 4C secretion system, have been hypothesized to contribute to the pathogenesis of the infection and are considered possible virulence factors of C. difficile. In the current paper, we describe the structural organization of putative T4SS machinery in C. difficile and characterize its VirB4- and VirD4-like components. Our studies, in addition to its significance for basic science, can potentially aid the development of antivirulence drugs suitable for the treatment of C. difficile infection.
Formins play important role in Leishmania physiology by acting as cytosolic actin bundlers

Formins are a highly conserved eukaryotic family of proteins that regulate actin dynamics. They play important physiological roles in cell adhesion, motility, vesicular trafficking and cytokinesis. Although sequence analysis of Trypanosomatida genomes predicted multiple formin-encoding genes, none of them are functionally characterized yet. We report here experimental identification and functional characterization of two constitutively expressed formins from the trypanosomatid protozoa Leishmania major viz. LmForminA and LmForminB. These formins exhibited irregular cytosolic distribution that co-localized with actin patches. Co-sedimentation assay and surface plasmon resonance confirmed that purified LmForminA and B FH2 domains can bind actin, albeit with differential affinity. Interestingly, both LmForminA and B FH2 domains were found to be actin bundlers as revealed by low-speed co-sedimentation assay and TIRF microscopy. LmForminA and B also had actin-nucleating activities, which was abolished by mutating their conserved Ile residue crucial for actin assembly. The Ile-mutant formins, however, retained their actin binding and bundling properties. Treatment of Leishmania cells with formin inhibitor SMIFH2 severely perturbed parasite growth and morphology indicating that Lmformins are physiologically important and may be considered as novel drug targets.
Assessment of Health Hazard of Metal Concentration in Groundwater of Bangladesh

The study was to assess health hazard of metal concentation in groundwater of Bangladesh for drinking purposes. A number of 13 deep tube wells were selected purposively for collecting groundwater samples from the different sampling location of the study area. The study was carried out by laboratory analysis of chemical parameters which were analyzed by ion Chromatograph (IC) and atomic absorption spectrophotometer methods (AAS). The result shown that the concentration of iron and manganese were found to be more than permissible limit according to Bangladesh and WHO standard. The descriptive statistics revealed that most of the heavy metal concentrations like As, Cd, Fe and Mn were found to be range from 0.00 to 0.02 mg/l, 0.00 to 0.20 mg/l, 0.11 to 24.20 mg/l, 0.06 to 16.00 mg/l respectively within accessible limit for drinking Original Research Article Islam et al.; ACSj, 5(1): 41-49, 2015; Article no.ACSj. 2015.006 42 according to Bangladesh and WHO standard except some water sampling locations were exceed the permissible limits. Pearson correlation matrix results were depicted that a strong positive correlation between the parameters such as Na + and SO4 2and K + and NH3 while low negative correlation were existed between Dissolved Oxygen and Mn + . From the analysis of result, it suggests that using groundwater for drinking purposes in the study area is slightly detrimental to human health hazard and thier surrouding environment.
Spectral Clustering Reveals Different Profiles of Central Sensitization in Women with Carpal Tunnel Syndrome

Identification of subgroups of patients with chronic pain provides meaningful insights into the characteristics of a specific population, helping to identify individuals at risk of chronification and to determine appropriate therapeutic strategies. This paper proposes the use of spectral clustering (SC) to distinguish subgroups (clusters) of individuals with carpal tunnel syndrome (CTS), making use of the obtained patient profiling to argue about potential management implications. SC is a powerful algorithm that builds a similarity graph among the data points (the patients), and tries to find the subsets of points that are strongly connected among themselves, but weakly connected to others. It was chosen due to its advantages with respect to other simpler clustering techniques, such as k-means, and the fact that it has been successfully applied to similar problems. Clinical (age, duration of symptoms, pain intensity, function, and symptom severity), psycho-physical (pressure pain thresholds—PPTs—over the three main nerve trunks of the upper extremity, cervical spine, carpal tunnel, and tibialis anterior), psychological (depressive levels), and motor (pinch tip grip force) variables were collected in 208 women with clinical/electromyographic diagnosis of CTS, whose symptoms usually started unilaterally but eventually evolved into bilateral symmetry. SC was used to identify clusters of patients without any previous assumptions, yielding three clusters. Patients in cluster 1 exhibited worse clinical features, higher widespread pressure pain hyperalgesia, higher depressive levels, and lower pinch tip grip force than the other two. Patients in cluster 2 showed higher generalized thermal pain hyperalgesia than the other two. Cluster 0 showed less hypersensitivity to pressure and thermal pain, less severe clinical features, and more normal motor output (tip grip force). The presence of subgroups of individuals with different altered nociceptive processing (one group being more sensitive to pressure pain and another group more sensitive to thermal pain) could lead to different therapeutic programs.
Structuring and Controlling the Knowledge for the Software User Support

The research aims to create a smart user Support Assistant LAVA – a solution providing context sensitive and user experience aware support to a user of a software product. The solution is based on machine learning and search in a two-level distributed knowledge store. LAVA model focuses on providing user on a mouse click with a content relevant to a current context. LAVA uses context transferred from the supported product to instantly show a FAQ list of items used and/or positively rated by other users in the same context. Full-text search and a topic hierarchy are provided as well to cover as many of cases as possible given the content available currently in the Knowledge base. Main design ideas of the LAVA model are presented in the article including the calculation of ranges and creation of ranged context-sensitive FAQs, customizing the full-text search, organizing the topic hierarchy and integrating with the Service desk. The article covers as well the main considerations on how the LAVA model should be implemented in a successful solution, and a description of method to evaluate the model performance.
Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond. (Algorithmes ensemblistes et combinatoire analytique en Bioinformatique des ARN)

Dynamic Programming (DP) is one of the foremost algorithmic tool for solving combinatorial problems in bioinformatics. This popularity stems from historical reasons, and from the remarkable robustness of DP to changes in the parameters of the objective function. However, the design of dynamic programming schemes is often tedious and error-prone for the kind of intricate objective functions that naturally arise in real-life applications. Accordingly, multiple frameworks and languages have been proposed over the past decades to abstract dynamic programming and ease the task of implementing a DP scheme. In this Habilitation à Diriger des Recherches, we describe a complementary line of research, which relies on a deep-rooted connection between combinatorics and dynamic programming. Indeed, the decomposition schemes that can be found at the core of dynamic programming algorithms can very frequently be reinterpreted as enumeration principles. While this parallel is not strict, and requires some conditions to be met, it enables an exchange of ideas between the fields of Bioinformatics and Enumerative Combinatorics that both motivates new analyses for search space of combinatorial problems, and opens to new applications in Bioinformatics and allows the formulation of novel biological questions. Disclaimer: Temporary version, currently under review, use at your own risk.
VIREO @ TRECVid 2021 Ad-hoc Video Search

In this paper, we summarize our submitted runs and results for Ad-hoc Video Search (AVS) task at TRECVid 2021 [1]. Ad-hoc Video Search (AVS): We applied three video search systems for AVS: two extended dual-task models trained with a novel unlikelihood loss or with additional phrase concepts, and an enhanced dual encoding model with advanced video features. The unlikelihood model addresses contrary relationships between concepts to prevent embedding features from being interpreted with opposite concepts simultaneously, such as "outdoors" and "indoors". The phrase model extends the concept bank of dual-task model [2] with phrases such that the visual embedding can be interpreted with both words and phrases. The enhanced dual encoding model [3] appends video network input with two advanced deep features extracted from SlowFast [4] and Swin-Transformer [5]. We submitted four automatic runs and four manual runs for both the main task and progress subtask. Besides, we also submitted one novelty run for the main task. We brieﬂy summarize our runs as follows:
Hybrid Embedding via Cross-Layer Random Walks on Multiplex Networks

Node embedding aims to encode network nodes as a set of low-dimensional vectors while preserving certain structural properties of the network. In recent years, extensive studies have been conducted to preserve network communities, i.e., structural proximity of network nodes. However, few of them have focused on preserving the structural equivalence of network nodes, which describes the similarity of structural roles between network nodes. In this paper, we focus on a hybrid network embedding problem of how to flexibly and simultaneously preserve both structural proximity and equivalence. Here, we introduce the concept of graphlet degree vector (GDV) to describe structure roles of network nodes, and further measure structural equivalence based on their similarity. Specifically, we capture both structural proximity and equivalence by building a multiplex network, where both unsupervised and semi-supervised cross-layer random walk (CL-Walk) methods are implemented. By carrying out experiments on both synthetic and real-world datasets, we evaluate the performance of the proposed CL-Walk methods for the tasks of node clustering, node classification, and label prediction. The experimental results indicate that the CL-Walk method outperforms several state-of-the-art methods when both structural proximity and structural equivalence are relevant to specific network analytic task.
A Robust State of Charge Estimation Approach Based on Nonlinear Battery Cell Model for Lithium-Ion Batteries in Electric Vehicles

This study proposes a robust SOC estimation scheme for lithium-ion batteries in commercialized electric vehicles: pure electric vehicles and hybrid electric vehicles. Development of a nonlinear-model-based robust SOC estimation method and comprehensive performance comparison with the existing SOC estimation methods under the two kinds of operating scenarios are considered. The features of the results of this study are summarized as follows: a) a robust SOC estimator is designed to deal with the model uncertainty and parameter variation, b) an analysis of asymptotic stability of the proposed robust SOC estimator is provided and c) a comprehensive analysis was performed not only on the different aging levels of battery cells but also on the different operational conditions of the electrified vehicles. The effectiveness of the proposed SOC estimation method was experimentally verified using two 18 650 cylindrical battery cells with different degradation levels. The proposed SOC estimation scheme ensures considerable accuracy under both pure electric vehicle operating mode and hybrid vehicle operating mode even if the battery cell is aged.
Transition from Discrete to Continuous Media: The Impact of Symmetry Changes on Asymptotic Behavior of Waves

This paper is devoted to comparing the asymptotics of a solution, describing the wave motion of a discrete lattice and its continuous approximations. The transition from a discrete medium to a continuous one changes the symmetry of the system. The influence of this change on the asymptotic behavior of waves is of great interest. For the discrete case, Schrödinger’s analytical solution of the initial-value problem for the Lagrange lattice is used. Various continuous approximations are proposed to approximate the lattice. They are based on Debye’s concept of quasicontinuum. The asymptotics of the initial motion and the behavior of the systems in the vicinity of the quasifront and at large times are compared. The approximations of phase and group velocities is analyzed. The merits and limitations of the described approaches are discussed.
Trade Exports Predict Regional Ballast Water Discharge by Ships in San Francisco Bay

Biological invasions often result from transfers of organisms during trade activities. In coastal ecosystems, commercial ships are a dominant source of species transfers globally, and ships’ ballast water (BW) is a major focus of biosecurity management and policy to reduce invasions. While trade drives shipping patterns, diverse vessel types and behaviors exist such that the quantitative relationship between trade and BW dynamics is still poorly resolved, limiting both science and management. Here, we evaluated a new method to predict BW discharge using trade data, by explicitly considering known BW practices according to vessel and commodity type. Specifically, we estimated the relationship between tonnage of overseas exports and BW discharge volume for San Francisco Bay (SFB), California, as a model system to demonstrate this approach. Using extensive datasets on shipborne exports and BW discharge, we (a) evaluated spatial and temporal patterns across nearly 20 ports in this estuary from 2006 to 2014 and (b) developed a predictive model to estimate overseas BW discharge volume from foreign export tonnage for the whole estuary. Although vessel arrivals in SFB remained nearly constant from 2006 to 2014, associated tonnage of exported commodities more than doubled and BW discharge more than tripled. Increased BW volume resulted from increased frequency and per capita discharge of bulk carriers from Asia and tankers from western Central America and Hawaii, reflecting shifts in direction of commodity movement. The top 11 export commodities (59% of total export tonnage) were transported on bulk carriers or tankers. In a multivariate linear model, annual tonnage of these top 11 export commodities by vessel type were strong predictors of total bay-wide overseas BW discharge (adjusted R2 = 0.92), creating the potential to estimate past or future BW delivery in SFB. Bulk export tonnage provides valuable insights into BW flux, since most BW discharge to ports is driven by trade of bulk commodities and the behavior of bulk and tank ships. BW discharge data are unavailable for many regions and time periods, whereas trade data are widely available and can provide a reliable proxy estimate of BW volume and geographic source, which are both critical to evaluate invasion risk.
Marine Organisms as a Rich Source of Biologically Active Peptides

Oceanic environments are one of the largest sources of bioactive molecules, due to the high degree of biodiversity and the innumerable ecological relationships established between macro and microorganisms found in the different ecosystems of these complex environments. Marine organisms are being studied increasingly because they are considered important producers of biologically active peptides. Peptides extracted from marine sources have different functions and structures, when compared to peptides isolated from terrestrial sources, considering the different adaptive pressures undergone by these organisms throughout the evolutionary process. Most bioactive compounds isolated from marine environments are obtained from symbiont microorganisms. Of these microorganisms, bacteria are an important source of bioactive peptides, isolated by metagenomic studies from complex gene networks expressed under marine conditions. Several peptides have been shown to have biotechnological properties such as antimicrobial, antitumor, antihypertensive, anticoagulant, anti-fouling, and antioxidant activity and can be used in the pharmaceutical and food industries. This review article aims to provide an overview of peptides of biotechnological importance, isolated from different phyla of marine organisms, examining the relationship between structure and function of some of these peptides, as well as the ways of extracting, purifying and prospecting new peptides by traditional methods of isolation or sequence analysis in databases. It also intends to list the peptides that are already being produced and used by the industry, in its various branches, and their current state in the market and in clinical tests.
Investigating Post-translational Modifications in Neuropsychiatric Disease: The Next Frontier in Human Post-mortem Brain Research

Gene expression and translation have been extensively studied in human post-mortem brain tissue from subjects with psychiatric disease. Post-translational modifications (PTMs) have received less attention despite their implication by unbiased genetic studies and importance in regulating neuronal and circuit function. Here we review the rationale for studying PTMs in psychiatric disease, recent findings in human post-mortem tissue, the required controls for these types of studies, and highlight the emerging mass spectrometry approaches transforming this research direction.