Miracle-dz/UniFAR-FTUs huggingface dataset:
Unambiguous Scene Text Segmentation With Referring Expression Comprehension

Text instance provides valuable information for the understanding and interpretation of natural scenes. The rich precise high-level semantics embodied in the text could be beneficial for understanding the world around us, and empower a wide range of real-world applications. While most recent visual phrase grounding approaches focus on general objects, this paper explores extracting designated texts and predicting unambiguous scene text segmentation mask, i.e., scene text segmentation from natural language descriptions (referring expressions) like orange text on a little boy in black swinging a bat. The solution of this novel problem enables accurate segmentation of scene text instances from the complex background. In our proposed framework, a unified deep network jointly models visual and linguistic information by encoding both region-level and pixel-level visual features of natural scene images into spatial feature maps, and then decode them into saliency response map of text instances. To conduct quantitative evaluations, we establish a new scene text referring expression segmentation dataset: COCO-CharRef. Experimental results demonstrate the effectiveness of the proposed framework on the text instance segmentation task. By combining image-based visual features with language-based textual explanations, our framework outperforms baselines that are derived from state-of-the-art text localization and natural language object retrieval methods on COCO-CharRef dataset.
Selective Formation of Porous Pt Nanorods for Highly Electrochemically Efficient Neural Electrode Interfaces.

The enhanced electrochemical activity of nanostructured materials is readily exploited in energy devices, but their utility in scalable and human-compatible implantable neural interfaces can significantly advance the performance of clinical and research electrodes. We utilize low-temperature selective dealloying to develop scalable and biocompatible 1D platinum nanorod (PtNR) arrays that exhibit superb electrochemical properties at various length scales, stability, and biocompatibility for high performance neurotechnologies. PtNR arrays record brain activity with cellular resolution from the cortical surfaces in birds and non-human primates. Significantly, strong modulation of surface recorded single unit activity by auditory stimuli is demonstrated in European Starling birds as well as the modulation of local field potentials in the visual cortex by light stimuli in a non-human primate, and as well as responses to electrical stimulation in mice. PtNRs record behaviorally and physiologically relevant neuronal dynamics from the surface of the brain with high spatiotemporal resolution which paves the way for less invasive brain-machine interfaces.
Molecular architecture of bacterial amyloids in Bacillus biofilms

The formation of biofilms provides structural and adaptive bacterial response to the environment. In Bacillus species, the biofilm extracellular matrix is composed of exopolysaccharides, hydrophobins, and several functional amyloid proteins. We report, using multiscale approaches such as solid‐state NMR (SSNMR), electron microscopy, X‐ray diffraction, dynamic light scattering, attenuated total reflection Fourier transform infrared (FTIR), and immune‐gold labeling, the molecular architecture of B. subtilis and pathogenic B. cereus functional amyloids. SSNMR data reveal that the major amyloid component TasA in its fibrillar amyloid form contain β‐sheet and α‐helical secondary structure, suggesting a nontypical amyloid architecture in B. subtilis. Proteinase K digestion experiments indicate the amyloid moiety is ~100 aa long, and subsequent SSNMR and FTIR signatures for B. subtilis and B. cereus TasA filaments highlight a conserved amyloid fold, albeit with substantial differences in structural polymorphism and secondary structure composition. Structural analysis and coassembly data on the accessory protein TapA in B. subtilis and its counterpart camelysin in B. cereus reveal a catalyzing effect between the functional amyloid proteins and a common structural architecture, suggesting a coassembly in the context of biofilm formation. Our findings highlight nontypical amyloid behavior of these bacterial functional amyloids, underlining structural variations between biofilms even in closely related bacterial species. —El Mammeri, N. , Hierrezuelo, J., Tolchard, J., Cámara‐Almirón, J., Caro‐Astorga, J., Álvarez‐Mena, A. , Dutour, A. , Berbon, M. , Shenoy, J., Morvan, E. , Grélard, A. , Kauffmann, B. , Lecomte, S. , de Vicente, A. , Habenstein, B. , Romero, D. , Loquet, A. Molecular architecture of bacterial amyloids in Bacillus biofilms. FASEB J. 33, 12146‐12163 (2019). www.fasebj. org
Association between cytokines and exosomes in synovial fluid of individuals with knee osteoarthritis

Abstract Background: Cytokines in synovial fluid (SF) play a crucial role in knee osteoarthritis (KOA). Exosomes are nanovesicles that are abundant in SF and carry a large quantity of signaling molecules. The purpose of this study was to evaluate the cytokine profiles of SF-derived exosomes and try to explore its biological function. Methods: Twenty-four KOA patients who were scheduled for their first intra-articular injection or knee replacement surgery were enrolled and divided into the KL1–2 group and the KL3–4 group according to the Kellgren and Lawrence (KL) classification. SF was collected from the patient’s knee for the isolation of exosomes. A multiplex cytokine assay was performed to detect the 21 cytokines in the exosomes. The SF derived-exosomes were exposed to PBMCs and chondrocytes to assess their immunomodulatory potential. Results: Exosomes were successfully extracted from the SF, with an average diameter of 92 nm. Most cytokines were detectable in the SF-derived exosomes. Twelve inflammatory cytokines and eight chemokines were elevated in the exosomes of the KL3–4 group compared to that of the KL1–2 group (p < .05). A higher number of PBMCs were chemo attracted and the proliferation of chondrocytes was restrained by the SF-derived exosomes from the KL3–4 group in comparison with the KL1–2 group (p < .05). Conclusion: Our data indicated that most cytokines in SF are not only in a free form but also associated with and enriched in exosomes. Exosomes from end-stage KOA patients have a higher level of cytokines, especially chemokines, in comparison with the cytokine profiles of the soluble SF. SF-derived exosomes recruit inflammatory cells and inhibit cartilage proliferation, thus promoting joint degeneration. These data provide a new perspective for understanding the changes in the inner environment of KOA.
Software Effort Estimation Using Adaptive Fuzzy-Neural Approach

-Software effort estimation is an important step in software development. It predicts the amount of effort and development time required to build a software system. It is one of the most important tasks and an accurate estimate is vital to the successful completion of the project. Building software effort estimation requires developing sound computational models. This paper investigates the use of fuzzy-neural systems in estimating software effort. A comparison is made with a radial basis neural network. Results obtained based on the China dataset indicates that a hybrid model that combine fuzzy inferencing with neural networks ability to learn from examples provided more accurate results than using neural networks alone.
Ascorbic acid and CoQ10 ameliorate the reproductive ability of superoxide dismutase 1-deficient female mice†

Abstract Superoxide dismutase 1 suppresses oxidative stress within cells by decreasing the levels of superoxide anions. A dysfunction of the ovary and/or an aberrant production of sex hormones are suspected causes for infertility in superoxide dismutase 1-knockout mice. We report on attempts to rescue the infertility in female knockout mice by providing two antioxidants, ascorbic acid and/or coenzyme Q10, as supplements in the drinking water of the knockout mice after weaning and on an investigation of their reproductive ability. On the first parturition, 80% of the untreated knockout mice produced smaller litter sizes compared with wild-type mice (average 2.8 vs 7.3 pups/mouse), and supplementing with these antioxidants failed to improve these litter sizes. However, in the second parturition of the knockout mice, the parturition rate was increased from 18% to 44–75% as the result of the administration of antioxidants. While plasma levels of progesterone at 7.5 days of pregnancy were essentially the same between the wild-type and knockout mice and were not changed by the supplementation of these antioxidants, sizes of corpus luteum cells, which were smaller in the knockout mouse ovaries after the first parturition, were significantly ameliorated in the knockout mouse with the administration of the antioxidants. Moreover, the impaired vasculogenesis in uterus/placenta was also improved by ascorbic acid supplementation. We thus conclude that ascorbic acid and/or coenzyme Q10 are involved in maintaining ovarian and uterus/placenta homeostasis against insults that are augmented during pregnancy and that their use might have positive effects in terms of improving female fertility. Summary sentence The results suggest that antioxidants support fertilizing ability against oxidative stress during parturition.
A pilot RCT of a school nurse delivered intervention to reduce student anxiety

The goal of this study was to evaluate the feasibility and impact of brief school-nurse-administered interventions for reducing anxiety. Thirty school nurses in Connecticut and Maryland were randomly assigned to deliver the Child Anxiety Learning Modules (CALM; n = 14) or CALM–Relaxation only (CALM-R; n = 16). Students (N = 54) were ages 5–12 (M age = 8; 84.9% White; 68.5% female) with elevated anxiety symptoms and/or anxiety disorders. Feasibility was assessed based on recruitment, retention, attendance, training and intervention satisfaction, and intervention adherence. Multiple informants, including independent evaluators (IEs), completed measures of clinical improvement at postintervention and at a 3-month follow-up. Of nurses in CALM and CALM-R, 62% and 81%, respectively, enrolled a student and completed an average of 6 sessions. Youth retention was 85% and 94% in CALM and CALM-R, respectively. Training and intervention satisfaction were high. At postintervention and follow-up, youth in both groups showed significant reductions in anxiety and related symptoms and improvements in functioning. Within-group effect sizes were medium to large, and between-group effect sizes were small. Task shifting responsibility for delivering brief mental health interventions to school nurses is feasible and shows promise for reducing anxiety and related impairment. This approach may also be integrated within a response to intervention model used in schools. Public Health Significance: Brief school-nurse-administered anxiety reduction interventions were shown to be feasible and had a positive impact on student anxiety and related impairment highlighting that school nurses can be an important school resource.
Neonatal Diet Impacts Bioregional Microbiota Composition in Piglets Fed Human Breast Milk or Infant Formula.

BACKGROUND Early infant diet influences postnatal gut microbial development, which in turn can modulate the developing immune system. OBJECTIVES The aim of this study was to characterize diet-specific bioregional microbiota differences in piglets fed either human breast milk (HM) or infant formula. METHODS Male piglets (White Dutch Landrace Duroc) were raised on HM or cow milk formula (MF) from postnatal day (PND) 2 to PND 21 and weaned to an ad libitum diet until PND 51. Piglets were euthanized on either PND 21 or PND 51, and the gastrointestinal contents were collected for 16s RNA sequencing. Data were analyzed using the Quantitative Insight into Microbial Ecology. Diversity measurements (Chao1 and Shannon) and the Wald test were used to determine relative abundance. RESULTS At PND 21, the ileal luminal region of HM-fed piglets showed lower Chao1 operational taxonomic unit diversity, while Shannon diversity was lower in cecal, proximal colon (PC), and distal colon (DC) luminal regions, relative to MF-fed piglets. In addition, at PND 51, the HM-fed piglets had lower genera diversity within the jejunum, ileum, PC, and DC luminal regions, relative to MF-fed piglets. At PND 21, Turicibacter was 4- to 5-fold lower in the HM-fed piglets' ileal, cecal, PC, and DC luminal regions, relative to the MF-fed piglets. Campylobacter is 3- to 6-fold higher in HM-fed piglets duodenal, ileal, cecal, PC, and DC luminal regions, in comparison to MF-fed piglets. Furthermore, the large intestine (cecum, PC, and rectum) luminal region of HM-fed piglets showed 4- to 7-fold higher genera that belong to class Bacteroidia, in comparison to MF-fed piglets at PND 21. In addition, at PND 51 distal colon lumen of HM-fed piglets showed 1.5-fold higher genera from class Bacteroidia than the MF-fed piglets. CONCLUSIONS In the large intestinal regions (cecum, PC, and rectum), MF diet alters microbiota composition, relative to HM diet, with sustained effects after weaning from the neonatal diet. These microbiota changes could impact immune system and health outcomes later in life.
Long noncoding RNA GAS5 silencing inhibits the expression of KCNQ3 by sponging miR‐135a‐5p to prevent the progression of epilepsy

Epilepsy is one of the most common neurological disorders in humans. Recently, long noncoding RNAs (lncRNAs) have been reported to be important players in neurological diseases. Herein, this study aimed to examine the effect of lncRNA GAS5 on the occurrence of epilepsy in rat and cell models of epileptic seizure. The expression of lncRNA GAS5 was measured in the established rat and cell models. The binding sites between lncRNA GAS5 and miR‐135a‐5p, as well as those between miR‐135a‐5p and 3′ untranslated region of KCNQ3 were predicted by miRDB and Targetscan, separately, followed by verification using dual‐luciferase reporter gene assay. The expression of miR‐135a‐5p was measured in response to the overexpression of lncRNA GAS5. The mRNA and protein levels of KCNQ3 were examined in response to overexpression of miR‐135a‐5p. Next, the latency of epilepsy and frequency of epileptic seizures were assessed in rats injected with Lv‐shGAS5 and Lv‐miR‐135a‐5p in epileptic seizure model. In the rat and cell models, lncRNA GAS5 was highly expressed when epileptic seizure was induced. The expression of miR‐135a‐5p was decreased by overexpression of lncRNA GAS5. Meanwhile, the mRNA and protein levels of KCNQ3 were decreased in response to knockdown of miR‐135a‐5p. After the treatment of Lv‐shGAS5 and Lv‐miR‐135a‐5p, the average latent period of epilepsy was prolonged and the frequency of seizures was decreased. The key findings of the present study provide evidence emphasizing that lncRNA GAS5 functions as a competitive endogenous RNA of miR‐135a‐5p to increase expression of KCNQ3, and lncRNA GAS5 silencing inhibited the occurrence and progression of epilepsy.
Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Dublin Isolates

Salmonella enterica serovar Dublin, which can cause enteritis and systemic infections in humans, has been associated with antimicrobial resistance. Here, we report draft genome sequences of seven multidrug-resistant S. Dublin isolates from human samples. These sequences will contribute to an understanding of pathogenesis and resistance determinants in this serovar. ABSTRACT Salmonella enterica serovar Dublin, which can cause enteritis and systemic infections in humans, has been associated with antimicrobial resistance. Here, we report draft genome sequences of seven multidrug-resistant S. Dublin isolates from human samples. These sequences will contribute to an understanding of pathogenesis and resistance determinants in this serovar.
Inhibition of UCH-L1 Deubiquitinating Activity with Two Forms of LDN-57444 Has Anti-Invasive Effects in Metastatic Carcinoma Cells

Normally ubiquitin C-terminal hydrolase L1 (UCH-L1) is expressed in the central nervous and reproductive systems of adults, but its de novo expression has been detected in many human cancers. There is a growing body of evidence that UCH-L1 de-ubiquitinating (DUB) activity plays a major pro-metastatic role in certain carcinomas. Here we tested anti-metastatic effects of the small-molecule inhibitor of UCH-L1 DUB activity, LDN-57444, in cell lines from advanced oral squamous cell carcinoma (OSCC) as well as invasive nasopharyngeal (NP) cell lines expressing the major pro-metastatic gene product of Epstein–Barr virus (EBV) tumor virus, LMP1. To overcome the limited aqueous solubility of LDN-57444 we developed a nanoparticle formulation of LDN-57444 by incorporation of the compound in polyoxazoline micellear nanoparticles (LDN-POx). LDN-POx nanoparticles were equal in effects as the native compound in vitro. Our results demonstrate that inhibition of UCH-L1 DUB activity with LDN or LDN-POx inhibits secretion of exosomes and reduces levels of the pro-metastatic factor in exosomal fractions. Both forms of UCH-L1 DUB inhibitor suppress motility of metastatic squamous carcinoma cells as well as nasopharyngeal cells expressing EBV pro-metastatic Latent membrane protein 1 (LMP1) in physiological assays. Moreover, treatment with LDN and LDN-POx resulted in reduced levels of pro-metastatic markers, a decrease of carcinoma cell adhesion, as well as inhibition of extra-cellular vesicle (ECV)-mediated transfer of viral invasive factor LMP1. We suggest that soluble inhibitors of UCH-L1 such as LDN-POx offer potential forms of treatment for invasive carcinomas including EBV-positive malignancies.
The P429L loss of function mutation of the human glycine transporter 2 associated with hyperekplexia

Glycine transporter 2 (GlyT2) mutations across the entire sequence have been shown to represent the presynaptic component of the neurological disease hyperekplexia. Dominant, recessive and compound heterozygous mutations have been identified, most of them leading to impaired glycine uptake. Here, we identified a novel loss of function mutation of the GlyT2 resulting from an amino acid exchange of proline 429 to leucine in a family with both parents being heterozygous carriers. A homozygous child suffered from severe neuromotor deficits. We characterised the GlyT2P429L variant at the molecular, cellular and protein level. Functionality was determined by glycine uptake assays. Homology modelling revealed that the mutation localises to α‐helix 5, presumably disrupting the integrity of this α‐helix. GlyT2P429L shows protein trafficking through various intracellular compartments to the cellular surface. However, the protein expression at the whole cell level was significantly reduced. Although present at the cellular surface, GlyT2P429L demonstrated a loss of protein function. Coexpression of the mutant with the wild‐type protein, reflecting the situation in the parents, did not affect transporter function, thus explaining their non‐symptomatic phenotype. Nevertheless, when the mutant was expressed in excess compared with the wild‐type protein, glycine uptake was significantly reduced. Thus, these data demonstrate that the proline residue at position 429 is structurally important for the correct formation of α‐helix 5. The failure in functionality of the mutated GlyT2 is most probably due to structural changes localised in close proximity to the sodium‐binding site of the transporter.
Placental Image Analysis using Coupled Diffusion-Weighted and Multi-Echo T2 MRI and a Multi-Compartment Model

Current popular methods of ow and uid measurement are confounded by the interaction of relaxation and perfusion characteristics which are rarely simultaneously considered. To address this shortcoming we propose a new multi-compartment model for the tissue signal in MRI and apply this to placenta imaging data. Motivated by the different flow characteristics across the placenta, a three compartment model comprising fast and slowly circulating uid pools and a tissue pool is fitted to overlapping multi-echo T2 relaxometry and an intra-voxel incoherent motion diffusion acquisition with low b-values. The new model is supported by a modified image acquisition to enable successful model fitting, but this acquisition is clinically practical; we implemented the acquisition on a standard 1.5T clinical system with acquisition taking less than 20 minutes with 26 slices. This is particularly important for placenta image acquisition. We test this combined acquisition and model-fitting routine on simulated data and show parametric maps for a placenta dataset.
Volumetric and shear processes in crystalline rock approaching faulting

Significance The dynamics of brittle deformation prior to macroscopic instability is critical to faulting events. This study provides direct high-resolution information on this process obtained using X-ray microtomography and digital volume correlation analysis of evolving microfractures and deformation fields in laboratory fracturing experiments. Brittle failure results from the dynamic coupling between microfracture growth, opening, shear, coalescence, and closing. The evolving microfracture volume and size distributions increase as powers of the differential stress, as the differential stress approached the failure level. The results highlight the key roles that seismic and aseismic off-fault cracking play in the preparation process leading to large brittle shear rupture events. Understanding the approach to faulting in continental rocks is critical for identifying processes leading to fracturing in geomaterials and the preparation process of large earthquakes. In situ dynamic X-ray imaging and digital volume correlation analysis of a crystalline rock core, under a constant confining pressure of 25 MPa, are used to elucidate the initiation, growth, and coalescence of microfractures leading to macroscopic failure as the axial compressive stress is increased. Following an initial elastic deformation, microfractures develop in the solid, and with increasing differential stress, the damage pervades the rock volume. The creation of new microfractures is accompanied by propagation, opening, and closing of existing microfractures, leading to the emergence of damage indices that increase as powers of the differential stress when approaching failure. A strong spatial correlation is observed between microscale zones with large positive and negative volumetric strains, microscale zones with shears of opposite senses, and microscale zones with high volumetric and shear strains. These correlations are attributed to microfracture interactions mediated by the heterogeneous stress field. The rock fails macroscopically as the microfractures coalesce and form a geometrically complex 3D volume that spans the rock sample. At the onset of failure, more than 70% of the damage volume is connected in a large fracture cluster that evolves into a fault zone. In the context of crustal faulting dynamics, these results suggest that evolving rock damage around existing locked or future main faults influences the localization process that culminates in large brittle rupture events.