Miracle-dz/UniFAR-FTUs huggingface dataset:
easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application

Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it is extensible to other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.
Electrophysiological correlates of perceptual prediction error are attenuated in dyslexia

A perceptual adaptation deficit often accompanies reading difficulty in dyslexia, manifesting in poor perceptual learning of consistent stimuli and reduced neurophysiological adaptation to stimulus repetition. However, it is not known how adaptation deficits relate to differences in feedforward or feedback processes in the brain. Here we used electroencephalography (EEG) to interrogate the feedforward and feedback contributions to neural adaptation as adults with and without dyslexia viewed pairs of faces and words in a paradigm that manipulated whether there was a high probability of stimulus repetition versus a high probability of stimulus change. We measured three neural dependent variables: expectation (the difference between prestimulus EEG power with and without the expectation of stimulus repetition), feedforward repetition (the difference between event-related potentials (ERPs) evoked by an expected change and an unexpected repetition), and feedback-mediated prediction error (the difference between ERPs evoked by an unexpected change and an expected repetition). Expectation significantly modulated prestimulus theta- and alpha-band EEG in both groups. Unexpected repetitions of words, but not faces, also led to significant feedforward repetition effects in the ERPs of both groups. However, neural prediction error when an unexpected change occurred instead of an expected repetition was significantly weaker in dyslexia than the control group for both faces and words. These results suggest that the neural and perceptual adaptation deficits observed in dyslexia reflect the failure to effectively integrate perceptual predictions with feedforward sensory processing. In addition to reducing perceptual efficiency, the attenuation of neural prediction error signals would also be deleterious to the wide range of perceptual and procedural learning abilities that are critical for developing accurate and fluent reading skills.
Yet another mitochondrial genome of the Pacific cupped oyster: the published mitogenome of Alectryonella plicatula (Ostreinae) is based on a misidentified Magallana gigas (Crassostreinae)

The recently published mitochondrial genome of the fingerprint oyster Alectryonella plicatula (Gmelin, 1791) with GenBank accession number MW143047 was resolved in an unexpected phylogenetic position, as sister to the Pacific cupped oyster Magallana gigas (Thunberg, 1793) and share with this species three typical gene duplications that represent robust synapomorphies of the Magallana clade. In this study, we verified the identity of MW143047 using direct comparisons of single gene sequences, DNA barcoding and phylogenetic analyses. BLAST searches using each of the 12 protein coding genes and rRNA genes extracted from MW143047 as query retrieved M. gigas as best hit with 100% sequence identity. MW143047 is nested within the clade formed by M. gigas sequences, with virtually no difference between their terminal branch lengths, both in the cox1 gene tree (based on 3639 sequences) and in the 16S gene tree (based on 1839 sequences), as well as in the Maximum Likelihood mitogenomic tree based on concatenated sequence of 12 PCGs. Our findings suggest that the original specimen used for mitogenome sequencing was misidentified and represents an individual of M. gigas. This study reinforces the notion that morphological shell analysis alone is not sufficient for oyster identification, not even at high taxonomic ranks such as subfamilies. While it is well established that morphological identification of oysters should be validated by molecular data, this study emphasizes that also molecular data should be taxonomically validated by means of DNA barcoding and phylogenetic analyses. The implications of the publication of taxonomically misidentified sequences and mitogenomes are discussed.
Engineering 3D Vascularized Adipose Tissue Construct using a Decellularized Lung Matrix

Critically sized defects in subcutaneous white adipose tissue result in extensive disfigurement and dysfunction and remain a reconstructive challenge for surgeons; as larger defect sizes are correlated with higher rates of complications and failure due to insufficient vascularization following implantation. Our study demonstrates for the first-time a method to engineer perfusable, pre-vascularized, high-density adipose grafts that combine patient-derived adipose cells with a decellularized lung matrix (DLM). The lung is one of the most vascularized organs with high flow, low resistance, and a large blood-alveolar interface separated by a thin basement membrane. For our work, the large volume capacity within the alveolar compartment was repurposed for high-density adipose cell filling, while the acellular vascular bed provided efficient graft perfusion throughout. Both adipocytes and hASCs were successfully delivered and remained in the alveolar space even after weeks of culture. While adipose derived cells maintained their morphology and functionality in both static and perfusion DLM cultures, perfusion culture offered enhanced outcomes over static culture. Furthermore, we demonstrate that endothelial cells seamlessly integrate into the acellular vascular tree of the DLM with adipocytes. These results support that the DLM is a unique platform for creating vascularized adipose tissue grafts for large defect filling.
A binocular synaptic network supports interocular response alignment in visual cortical neurons

In the visual system, signals from the two eyes are combined to form a coherent representation through the convergence of synaptic input populations onto individual cortical neurons. As individual synapses originate from either monocular (representing one eye) or binocular (representing both eyes) cortical networks, it has been unclear how these inputs are integrated coherently. Here, we imaged dendritic spines on layer 2/3 binocular cells in ferret visual cortex with in vivo two-photon microscopy to examine how monocular and binocular synaptic networks contribute to the interocular alignment of orientation tuning. We found that binocular synapses varied in degree of ‘congruency’, namely response correlation between left and right eye visual stimulation. Binocular congruent inputs were functionally distinct from binocular noncongruent and monocular inputs, exhibiting greater tuning selectivity and connection specificity. Using correlative light and electron microscopy, we found no difference in ultrastructural anatomy and instead, observed strength in numbers using a simple model simulating aggregate synaptic input. This model demonstrated a predominate contribution of binocular congruent inputs in sculpting somatic orientation preference and interocular response alignment. Our study suggests that, in layer 2/3 cortical neurons, a binocular network is responsible for forming a coherent representation in individual neurons through recurrent intracortical interactions.
Parvalbumin interneuron dendrites enhance gamma oscillations

Dendrites are important determinants of the input-output relationship of single neurons, but their role in network computations is not well understood. Here, we used a combination of dendritic patch-clamp recordings and in silico modeling to determine how dendrites of parvalbumin (PV)-expressing basket cells contribute to network oscillations in the gamma frequency band. Simultaneous soma-dendrite recordings from PV basket cells in the dentate gyrus revealed that the slope, or gain, of the dendritic input-output relationship is exceptionally low, thereby reducing the cell’s sensitivity to changes in its input. By simulating gamma oscillations in detailed network models, we demonstrate that the low gain is key to increase spike synchrony in PV neuron assemblies when cells are driven by spatially and temporally heterogeneous synaptic input. These results highlight the role of dendritic computations in synchronized network oscillations.
SPIKE-TRIGGERED INTRASPINAL MICROSTIMULATION IMPROVES MOTOR PERFORMANCE IN AN AMBULATORY RAT MODEL OF SPINAL CORD INJURY

The purpose of this study was to determine if spike-triggered intraspinal microstimulation (ISMS) results in improved motor performance in an ambulatory rat model of spinal cord injury (SCI). Experiments were carried out in adult male Sprague Dawley rats with 175 kdyn moderate T8 contusion injury. Rats were randomly assigned to one of two groups: Control or Activity Dependent Stimulation (ADS) therapy. Four weeks post-SCI, all rats were implanted with a recording electrode in the left hindlimb motor cortex and a fine-wire, custom-made stimulating electrode in the contralateral lumbar spinal cord. Intracortical and intraspinal microstimulation were used to find sites of similar hip representation areas, which were paired together for ADS therapy. In the ADS therapy group, spike-stimulus conditioning was administered for 4 hours/day, 4 days/week, for 4 weeks via a tethered cable in a testing chamber. During therapy sessions, single-unit spikes were discriminated in real time in the hindlimb motor cortex and used to trigger stimulation in the spinal cord ventral horn. The optimal stimulus intensity (50% ISMS movement threshold) and spike-stimulus delay (10ms) determined in preliminary anesthetized preparations were used during ADS. Control rats were similarly implanted with electrodes but did not receive stimulation therapy. Motor performances of each rat were evaluated before SCI contusion, once a week post-SCI for four weeks (prior to electrode implantation), and once a week post-conditioning for four weeks. Behavioral testing included BBB scoring, Ledged Beam walking, Horizontal Ladder walking, treadmill kinematics via the DigiGait and TreadScan system, and open field walking using OptiTrack kinematic analysis. BBB scores were significantly improved in ADS rats compared to Control rats after 1 week of therapy. In the ADS therapy rats, BBB scores were significantly improved after two weeks of ADS therapy when compared to pre-therapy. Foot fault scores on the Horizontal Ladder were significantly lower in ADS rats compared to pre-therapy ADS and Control rats after 1 week of therapy and returned to pre-injury measures after three weeks of ADS therapy. The Ledged Beam test and kinematic analysis using the DigiGait and TreadScan system showed deficits after SCI in both ADS and Control rats but there were no significant differences between groups after 4 weeks of ADS therapy. These results show that activity dependent stimulation after spinal cord injury using spike-triggered ISMS enhances behavioral recovery of locomotor function as measured by the BBB score and the Horizontal Ladder task.
Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs

Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Prior studies showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of TF spacing alterations resulting from naturally occurring insertions and deletions (InDels) has not been systematically analyzed. To address this question, we first characterized the genome-wide spacing relationships of 75 TFs in K562 cells as determined by ChIP-sequencing. We found a dominant pattern of a relaxed range of spacing between collaborative factors, including 46 TFs exclusively exhibiting relaxed spacing with their binding partners. Next, we exploited millions of InDels provided by genetically diverse mouse strains and human individuals to investigate the effects of altered spacing on TF binding and local histone acetylation. Spacing alterations resulting from naturally occurring InDels are generally tolerated in comparison to genetic variants directly affecting TF binding sites. A remarkable range of tolerance was further established for PU.1 and C/EBPβ, which exhibit relaxed spacing, by introducing synthetic spacing alterations ranging from 5-bp increase to >30-bp decrease using CRISPR/Cas9 mutagenesis. These findings provide implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation.
Rapid label-free identification of pathogenic bacteria species from a minute quantity 1 exploiting three-dimensional quantitative phase imaging and artificial neural network

The healthcare industry is in dire need for rapid microbial identification techniques. Microbial infection is a major 27 healthcare issue with significant prevalence and mortality, which can be treated effectively during the early stages 28 using appropriate antibiotics. However, determining the appropriate antibiotics for the treatment of the early stages 29 of infection remains a challenge, mainly due to the lack of rapid microbial identification techniques. Conventional 30 culture-based identification and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy are 31 the gold standard methods, but the sample amplification process is extremely time-consuming. Here, we propose 32 an identification framework that can be used to measure minute quantities of microbes by incorporating artificial 33 neural networks with three-dimensional quantitative phase imaging. We aimed to accurately identify the species 34 of bacterial bloodstream infection pathogens based on a single colony-forming unit of the bacteria. The successful 35 distinction between a total of 19 species, with the accuracy of 99.9% when ten bacteria were measured, suggests 36 that our framework can serve as an effective advisory tool for clinicians during the initial antibiotic prescription. at single CFU level was verified in a comparative experiment. Our proposed framework was compared with two other approaches utilizing the 2D equivalent
Differential excretion of urinary complement fragments in kidney diseases: a potential link to complement activation?

Defective Complement activation has been associated with various types of kidney disease. This led to the hypothesis that specific urine complement fragments may be associated with kidney disease etiologies, and disease progression may be reflected by changes in these complement fragments. Therefore, we investigated the occurrence of complement fragments in urine, their association with kidney function and disease etiology. Mass spectrometry based peptidomics data from the Human Urinary Proteome/Peptidome Database were extracted and the distribution of complement peptides in the different kidney disease etiologies and controls was investigated. All datasets where information on disease/health status was available and at least one complement peptide could be detected were included (n=16027). Twenty-three different urinary peptides derived from complement proteins could be identified, originating from the complement proteins C3, C4 and CFB. For most C3-derived peptides an inverse association with eGFR was observed, while the majority of peptides derived from CFB demonstrated positive association with eGFR. Highest levels of significant C3 excretion relative to controls were seen in minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), membranous glomerulonephritis (MGN), lupus nephritis (LN), diabetic kidney disease (DKD), IgAN, membranoproliferative glomerulonephritis (MPGN), and C3-glomerulonephritis. In conclusion, several peptides derived from the complement proteins C3, C4 and Factor B are significantly associated with specific kidney disease etiologies. These peptides may depict disease-specific complement activation, as well as damage to the glomerular basement membrane. Further investigation of these complement peptides may provide additional insight into disease pathophysiology and could possibly guide therapeutic decisions, especially when targeting complement factors.
Disease-modifying therapies for T1 hypointense lesions (Black Holes) volume in patients with multiple sclerosis: Protocol for a systematic review and meta-analysis

Rationale: A major part of diagnosis and follow-up in patients with multiple sclerosis is based on MRI evaluations. As T1-hypointense lesions represent neural destruction or axonal loss and anticipate irreversible disability in the patients, evaluation of the effects of Disease-modifying therapies (DMTs) on the volume of black holes seems necessary. Objectives: To evaluate the effects of FDA approved disease-modifying therapies (DMTs) on T1 hypointense lesions (Black Holes) volume in patients with multiple sclerosis (MS) Data sources: We will search MEDLINE (through Ovid), Embase, and CENTRAL. We will not consider any timeframe, language, or geographical restrictions. Methods: We will include only randomized controlled trials (RCTs) that have evaluated the effects of DMTs on black holes mean volume in adult patients diagnosed with any phenotype of multiple sclerosis (MS) in comparison to the placebo, routine care, or no treatment regimen. We will assess the risk of bias in the primary studies using the Revised Cochrane risk-of-bias tool for randomized trials (RoB2). Data will be synthesized based on the random-effects model and results will be plotted on a forest plot. Heterogeneity will be assessed using I2 statistics. If feasible, we will also perform subgroup analyses for each DMT. Funding: This study is not funded. Registration: PROSPERO submission ID: 262883.
Seasonal relationships between foliar moisture content, heat content and biochemistry of lodgepole line and big sagebrush foliage

Wildland fires propagate by liberating energy contained within living and senescent plant biomass. The maximum amount of energy that can be generated by burning a given plant part can be quantified and is generally referred to as its heat content (HC). Many studies have examined heat content of wildland fuels but studies examining the seasonal variation in foliar HC among vegetation types are severely lacking. We collected foliage samples bi-weekly for five months from two common species in the western USA: lodgepole pine (Pinus contorta Douglas ex Loudon) and big sagebrush (Artemisia tridentata Nutt). We measured HC, live fuel moisture content (LFMC) and biochemical components in the leaf dry mass. Our results showed that HC increased for both species, coinciding with LFMC decrease during the growing season. Measured HC values were higher than the constant value in standard fuel models. Lasso regression models identified biochemical components for explaining temporal HC and LFMC variation in lodgepole pine (HC: R2adj = 0.55, root mean square error (RMSE) = 0.35; LFMC: R2adj = 0.84, RMSE = 10.79), sagebrush (HC: R2adj = 0.90, RMSE = 0.13; LFMC: R2adj = 0.96, RMSE = 7.66) and combined data from both species (HC: R2adj = 0.77, RMSE = 0.33; LFMC: R2adj = 0.61, RMSE = 19.75). These results demonstrated the seasonal change in HC and LFMC resulted from temporal biochemical composition variation in dry mass. This new knowledge about HC seasonal change will ultimately lead to improved predictions of wildland fire spread and intensity.
Buffalo Sperm Surface Proteome Pro ling Reveals an Intricate Relationship Between Innate Immunity and Reproduction

Vipul Batra National Dairy Research Institute Vanya Bhushan National Dairy Research Institute Syed Ali National Dairy Research Institute Parul Sarwalia National Dairy Research Institute Subhash Solanki National Dairy Research Institute Arumugam Kumaresan National Dairy Research Institute Rakesh Kumar National Dairy Research Institute Tirtha Datta (  tirthadatta@gmail.com ) National Dairy Research Institute
Heuristic Search for Approximating One Matrix in Terms of Another Matrix

We study the approximation of a target matrix in terms of several selected columns of another matrix, sometimes called "a dictionary". This approximation problem arises in various domains, such as signal processing, computer vision, and machine learning. An optimal column selection algorithm for the special case where the target matrix has only one column is known since the 1970's, but most previously proposed column selection algorithms for the general case are greedy. We propose the first nontrivial optimal algorithm for the general case, using a heuristic search setting similar to the classical A* algorithm. We also propose practical sub-optimal algorithms in a setting similar to the classical Weighted A* algorithm. Experimental results show that our sub-optimal algorithms compare favorably with the current state-of-the-art greedy algorithms. They also provide bounds on how close their solutions are to the optimal solution.
News in Bone Modeling for Customized Hybrid Biological Prostheses Development

Corresponding Author: Florian Ion Tiberiu Petrescu IFToMM, ARoTMM, Bucharest Polytechnic University, Bucharest, Romania Email: tiberiuflorianion@gmail.com Abstract: The complex biomechanics and morphologies of the femur proximal epiphysis are presented. The nature and fine morphology of the femur head and its structural behavior have been investigated. Isotropic and orthotropic trabecular structures have been associated with oriented compression and tensioned areas of the femur head FEM models. These isotropic/orthotropic trabecular morphologies and their allocations govern the stress and strain distribution in the overall proximal femur region. Finite element models of the femur biofidel were developed using a specific combination of segmentation with computed tomography and solid modeling tools capable of representing bone physiology and structural behavior. This biofidel Finite Element (FEM) model is used to evaluate the change in the physiological distribution of stress in the femoral prosthesis and to evaluate the new design criteria for biopsy. The use of femur proper biofidel modeling while enabling the explanation of physiological stress distribution elucidates the critical mechanical role of the trabecular bone that should be accounted for in the design new innovative more “biologic” prosthetic system. Biomimetics, biomechanics and tissue engineering are three multidisciplinary fields that have been considered in this research to achieve the goal of improving the reliability of prosthetic implants. The authors took these studies to gather the untapped potential of such advanced materials and design technologies by developing finite models of Biofidel elements capable of correctly mimicking the biomechanical behavior of the femur.