Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Campylobacter jejuni Motility, Adhesion to Polystyrene Surfaces, and Invasion of INT407 Cells by Quorum-Sensing Inhibition

Campylobacter jejuni is a major foodborne pathogen, and the LuxS-mediated quorum-sensing (QS) system influences its motility, biofilm formation, invasion, host colonization, and virulence. QS therefore represents a target for the control of C. jejuni. The aim of this study was to investigate the correlation of QS inhibition with changes in C. jejuni motility, adhesion to polystyrene surfaces, and adhesion to and invasion of INT407 cells. This was achieved by studying (i) the luxS-deficient mutant and (ii) treatment of C. jejuni with 20 natural extracts as six essential oils, 11 ethanolic extracts, and three pure compounds. Compared to the wild-type, the ΔluxS mutant showed decreased motility, adhesion to polystyrene surfaces, and invasion of INT407 cells. The anti-QS effects of the treatments (n = 15/20) were assayed using Vibrio harveyi BB170 bioluminescence. Moderate positive correlation was shown between C. jejuni QS reduction and reduced motility (τ = 0.492, p = 0.024), adhesion to polystyrene surfaces (τ = 0.419, p = 0.008), and invasion (r = 0.394, p = 0.068). The best overall effect was achieved with a Sedum rosea (roseroot) extract, with 96% QS reduction, a 1.41 log (96%) decrease in adhesion to polystyrene surfaces, and an 82% decrease in invasion. We show that natural extracts can reduce motility, adhesion to polystyrene surfaces, and invasion of INT407 cells by C. jejuni through modulation of the LuxS (QS) system.
Local and systemic factors associated with marginal bone loss around dental implants: a retrospective clinical study.

OBJECTIVES The aim of this study was to determine the influence of patient-related systemic factors, local bone and intraoral factors, and implant-related factors on peri-implant marginal bone loss (MBL). METHOD AND MATERIALS The following data were collected from patients who received dental implants and were recalled for examinations at least 3 years after treatment completion: medical history, age, sex, habits, periodontal health, implant size and surface, surgical procedure, prosthesis type, implant failure, Plaque Index, and oral hygiene. MBL was investigated using both baseline and follow-up panoramic radiographs. RESULTS The study included 1,126 dental implants placed in 304 patients (185 [60.9%] women and 119 [39.1%] men). The mean age was 54.30 ± 13.52 years (range 22 to 83 years). The mean follow-up period was 58.8 ± 11.2 months. The MBL was observed in 271 (24.1%) implants, of which 160 (14.2%) were ≤ 2 mm and 111 (9.9%) were > 2 mm. Respective mean MBL values on mesial and distal sides were 0.42 ± 1.03 mm and 0.42 ± 1.02 mm. Of the implants, 19 (1.7%) were lost, leading to an implant success rate of 98.3%. Age, history of hysterectomy, history of periodontitis, oral hygiene, abrasions, smoking, implant location, implant surface, implant length, surgical procedure type, and prosthesis type were all found to be statistically significant for MBL (P < .05). Certain combinations of these factors resulted in increased MBL. CONCLUSION In the present study, local factors had more significant effects on MBL than did systemic factors, and combinations of these factors had greater effects on MBL.
Vascularization and Reperfusion of Autologous Retinal Transplant for Giant Macular Holes.

Importance Autologous retinal transplant is a recently described treatment modality for myopic and other refractory macular holes (MH). Establishment of blood supply may influence survival of a transplanted tissue. However, there are currently no reports on the vascular status of a transplanted retinal graft. Objective To report on vascularization and reperfusion of autologous retinal graft after transplant for giant MHs demonstrated by multimodal imaging. Design, Setting, Participants Two patients with giant MH (basal diameter ≥2000 μm) who underwent autologous retinal transplant at Retina-Vitreous Associates Medical Group in Los Angeles, California, in June 2018 and February 2019, respectively, were included. Main Outcomes and Measures Status of MH, Snellen visual acuity, optical coherence tomography, optical coherence tomography angiography, and fluorescein angiography findings. Results Two eyes of 2 female patients were included. The mean age was 68.5 years. Baseline visual acuity was counting fingers and 20/200, and MHs measured 3441 μm and 2387 μm, respectively. Six weeks postoperatively, MHs were closed and the superficial inner retina blood vessels within the graft appeared perfused. Optical coherence tomography and optical coherence tomography angiography demonstrated early integration of the graft into the surrounding retina and perfused graft vasculature in both patients. Fluorescein angiography confirmed perfusion of retinal graft. At the last follow-up, visual acuity was 20/200 and 20/150, respectively, the MH was closed, and the retinal grafts were perfused. Conclusions and Relevance Autologous neurosensory retinal transplant may be used for the treatment of giant MHs. Vascularization and reperfusion of the retinal graft is observed within 6 weeks of transplant. It is hypothesized that visual improvement occurs as a result of flattening of the MH rim, partial centripetal migration of MH edges during the early healing phase, and further centripetal migration in the later phase associated with the shrinkage of the retinal graft.
Information-Limiting Correlations in Large Neural Populations

Understanding the neural code requires understanding how populations of neurons code information. Theoretical models predict that information may be limited by correlated noise in large neural populations. Nevertheless, analyses based on tens of neurons have failed to find evidence of saturation. Moreover, some studies have shown that noise correlations can be very small, and therefore may not affect information coding. Understanding the neural code requires understanding how populations of neurons code information. Theoretical models predict that information may be limited by correlated noise in large neural populations. Nevertheless, analyses based on tens of neurons have failed to find evidence of saturation. Moreover, some studies have shown that noise correlations can be very small, and therefore may not affect information coding. To determine whether information-limiting correlations exist, we implanted eight Utah arrays in prefrontal cortex (PFC; area 46) of two male macaque monkeys, recording >500 neurons simultaneously. We estimated information in PFC about saccades as a function of ensemble size. Noise correlations were, on average, small (∼10−3). However, information scaled strongly sublinearly with ensemble size. After shuffling trials, destroying noise correlations, information was a linear function of ensemble size. Thus, we provide evidence for the existence of information-limiting noise correlations in large populations of PFC neurons. SIGNIFICANCE STATEMENT Recent theoretical work has shown that even small correlations can limit information if they are “differential correlations,” which are difficult to measure directly. However, they can be detected through decoding analyses on recordings from a large number of neurons over a large number of trials. We have achieved both by collecting neural activity in dorsal-lateral prefrontal cortex of macaques using eight microelectrode arrays (768 electrodes), from which we were able to compute accurate information estimates. We show, for the first time, strong evidence for information-limiting correlations. Despite pairwise correlations being small (on the order of 10−3), they affect information coding in populations on the order of 100 s of neurons.
An Accurate and Efficient Voting Scheme for a Maximally All-Inlier 3D Correspondence Set

We present a highly accurate and efficient, yet simple, two-stage voting scheme for distinguishing inlier 3D correspondences by densely assessing and ranking their local and global geometric consistencies. The strength of the proposed method stems from both the novel idea of post-validated voting set, as well as single-point superimposition transforms, which are computationally cheap and avoid rotational ambiguities. Using a well-known dataset consisting of various 3D models and numerous scenes that include different occlusion rates, the proposed scheme is evaluated against state-of-the-art 3D voting schemes, in terms of both the correspondence PR (precision–recall) AUC (area under curve), and the execution time. A total of 374 experiments were conducted for each method, which involved a combination of four models, 50 scenes, and two down-samplings. The proposed scheme outperforms the state-of-the-art 3D voting schemes in terms of both accuracy and speed. Quantitatively, the proposed scheme scores <inline-formula><tex-math notation="LaTeX">$97.0\% \pm 12.9\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>97</mml:mn><mml:mo>. </mml:mo><mml:mn>0</mml:mn><mml:mo>%</mml:mo><mml:mo>±</mml:mo><mml:mn>12</mml:mn><mml:mo>. </mml:mo><mml:mn>9</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="sahloul-ieq1-2963980.gif"/></alternatives></inline-formula> on the PR AUC metric, averaged over all of the experiments, while the two state-of-the-art schemes score <inline-formula><tex-math notation="LaTeX">$74.2\% \pm 22.2\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>74</mml:mn><mml:mo>. </mml:mo><mml:mn>2</mml:mn><mml:mo>%</mml:mo><mml:mo>±</mml:mo><mml:mn>22</mml:mn><mml:mo>. </mml:mo><mml:mn>2</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="sahloul-ieq2-2963980.gif"/></alternatives></inline-formula> and <inline-formula><tex-math notation="LaTeX">$78.3\% \pm 26.4\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>78</mml:mn><mml:mo>. </mml:mo><mml:mn>3</mml:mn><mml:mo>%</mml:mo><mml:mo>±</mml:mo><mml:mn>26</mml:mn><mml:mo>. </mml:mo><mml:mn>4</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="sahloul-ieq3-2963980.gif"/></alternatives></inline-formula>. Furthermore, the proposed scheme requires only <inline-formula><tex-math notation="LaTeX">$24.1\% \pm 6.0\%$</tex-math><alternatives><mml:math><mml:mrow><mml:mn>24</mml:mn><mml:mo>. </mml:mo><mml:mn>1</mml:mn><mml:mo>%</mml:mo><mml:mo>±</mml:mo><mml:mn>6</mml:mn><mml:mo>. </mml:mo><mml:mn>0</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><inline-graphic xlink:href="sahloul-ieq4-2963980.gif"/></alternatives></inline-formula> of the time consumed by the fastest state-of-the-art scheme. The proposed voting scheme also demonstrates high robustness against occlusions and scarce inliers.
Longitudinal trajectory of Amyloid‐related hippocampal subfield atrophy in nondemented elderly

Hippocampal atrophy and abnormal β‐Amyloid (Aβ) deposition are established markers of Alzheimer's disease (AD). Nonetheless, longitudinal trajectory of Aβ‐associated hippocampal subfield atrophy prior to dementia remains unclear. We hypothesized that elevated Aβ correlated with longitudinal subfield atrophy selectively in no cognitive impairment (NCI), spreading to other subfields in mild cognitive impairment (MCI). We analyzed data from two independent longitudinal cohorts of nondemented elderly, including global PET‐Aβ in AD‐vulnerable cortical regions and longitudinal subfield volumes quantified with a novel auto‐segmentation method (FreeSurfer v.6.0). Moreover, we investigated associations of Aβ‐related progressive subfield atrophy with memory decline. Across both datasets, we found a converging pattern that higher Aβ correlated with faster CA1 volume decline in NCI. This pattern spread to other hippocampal subfields in MCI group, correlating with memory decline. Our results for the first time suggest a longitudinal focal‐to‐widespread trajectory of Aβ‐associated hippocampal subfield atrophy over disease progression in nondemented elderly.
Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing

Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.
Pediatric Pulmonology

Funding information Chiesi Farmaceutici S.p.A Abstract Background: Nasal continuous positive airway pressure support (nCPAP) is the standard of care for prematurely born infants at risk of neonatal respiratory distress syndrome (nRDS). However, nasal intermittent positive pressure ventilation (NIPPV) may be an alternative to nCPAP in babies requiring surfactant, and in conjunction with surfactant nebulization, it could theoretically reduce the need for invasive mechanical ventilation. We compared lung deposition of nebulized poractant in newborn piglets supported by nCPAP or NIPPV. Methods: Twenty‐five sedated newborn piglets (1.2‐2.2 kg) received either nCPAP (3 cmH2O, n = 12) or NIPPV (3 cmH2O positive end expiratory pressure+3 cmH2O inspiratory pressure, n = 13) via custom‐made nasal prongs (FiO2 0.4, Servo‐i ventilator). Piglets received 200mg kg of technetium‐99m‐surfactant mixture continuously nebulized with a customized eFlow‐Neos investigational vibrating‐ membrane nebulizer system. Blood gases were taken immediately before, during, and after nebulization. The deposition was estimated by gamma scintigraphy. Results: Mean surfactant deposition in the lungs was 15.9 ± 11.9% [8.3, 23.5] (mean ± SD [95% CI]) in the nCPAP group and 21.6 ± 10% [15.6, 27.6] in the NIPPV group (P = .20). Respiratory rates were similar in both groups. Minute volume was 489 ± 203 [360, 617] in the nCPAP group and 780 ± 239 [636, 924] mL kg min in the NIPPV group (P = .009). Blood gases were comparable in both groups. Conclusion: Irrespective of the noninvasive ventilatory support mode used, relatively high lung deposition rates of surfactant were achieved with nebulization. The amounts of deposited surfactant might suffice to elicit a pulmonary function improvement in the context of nRDS.
Chloride Resistance of Portland Cement-Based Mortar Incorporating High Aluminate Cement and Calcium Carbonate

Whether chloride resistance is highly influenced by chloride binding capacity remains unknown. In this study, the chloride resistance of Portland cement-based mortar incorporating aluminate cement and calcium carbonate was investigated considering the chloride binding capacity, pore structures and chloride diffusion coefficient from non-steady state chloride migration and natural chloride diffusion. The cement hydrates were investigated using X-ray diffraction and thermogravimetric analysis. The chloride binding capacity was evaluated based on the chloride adsorption from the solutions using the adsorption isotherm. The aluminate cement, as an available alumina source, can stimulate the formulation of layered double hydroxides, which in turn can increase the chloride binding capacity. The results of mercury intrusion porosimetry show that non-substituted (control) and substituted (only aluminate cement) specimens have capillary pore volume 8.9 vol % and 8.2 vol %, respectively. However, the specimen substituted with aluminate cement and calcium carbonate shows a higher capillary volume (12.9 vol %), which correlates with the chloride diffusion coefficient. Although the specimen substituted with calcium carbonate has a higher chloride binding capacity than the control, it does not necessarily affect the decrease in the chloride diffusion coefficient. The capillary pore volume can affect not only the chloride diffusion but also the chloride adsorption.
Machine learning models for identifying preterm infants at risk of cerebral hemorrhage

Intracerebral hemorrhage in preterm infants is a major cause of brain damage and cerebral palsy. The pathogenesis of cerebral hemorrhage is multifactorial. Among the risk factors are impaired cerebral autoregulation, infections, and coagulation disorders. Machine learning methods allow the identification of combinations of clinical factors to best differentiate preterm infants with intra-cerebral bleeding and the development of models for patients at risk of cerebral hemorrhage. In the current study, a Random Forest approach is applied to develop such models for extremely and very preterm infants (23–30 weeks gestation) based on data collected from a cohort of 229 individuals. The constructed models exhibit good prediction accuracy and might be used in clinical practice to reduce the risk of cerebral bleeding in prematurity.
Selection for psychosocial treatment for youth at clinical high risk for psychosis based on the North American Prodrome Longitudinal Study individualized risk calculator

Recent findings suggest that family‐focused therapy (FFT) is effective for individuals at clinical high‐risk for psychosis (CHR‐P). As outcomes of CHR‐P individuals are quite varied, certain psychosocial interventions may be differentially effective in subgroups. The present study examined change in positive symptoms for CHR‐P individuals at different levels of predicted risk for conversion to psychosis who received either FFT, a brief form of family education termed enhanced care (EC) or treatment as usual.
A Review on the Partial and Complete Dissolution and Fractionation of Wood and Lignocelluloses Using Imidazolium Ionic Liquids

Ionic liquids have shown great potential in the last two decades as solvents, catalysts, reaction media, additives, lubricants, and in many applications such as electrochemical systems, hydrometallurgy, chromatography, CO2 capture, etc. As solvents, the unlimited combinations of cations and anions have given ionic liquids a remarkably wide range of solvation power covering a variety of organic and inorganic materials. Ionic liquids are also considered “green” solvents due to their negligible vapor pressure, which means no emission of volatile organic compounds. Due to these interesting properties, ionic liquids have been explored as promising solvents for the dissolution and fractionation of wood and cellulose for biofuel production, pulping, extraction of nanocellulose, and for processing all-wood and all-cellulose composites. This review describes, at first, the potential of ionic liquids and the impact of the cation/anion combination on their physiochemical properties and on their solvation power and selectivity to wood polymers. It also elaborates on how the dissolution conditions influence these parameters. It then discusses the different approaches, which are followed for the homogeneous and heterogeneous dissolution and fractionation of wood and cellulose using ionic liquids and categorize them based on the target application. It finally highlights the challenges of using ionic liquids for wood and cellulose dissolution and processing, including side reactions, viscosity, recyclability, and price.
Isolation and Characterization of Mammalian Otic Progenitor Cells that Can Differentiate into Both Sensory Epithelial and Neuronal Cell Lineages

The mammalian inner ear mediates hearing and balance and during development generates both cochleo‐vestibular ganglion neurons and sensory epithelial receptor cells, that is, hair cells and support cells. Cell marking experiments have shown that both hair cells and support cells can originate from a common progenitor. Here, we demonstrate the lineage potential of individual otic epithelial cell clones using three cell lines established by a combination of limiting dilution and gene‐marking techniques from an embryonic day 12 (E12) rat otocyst. Cell‐type specific marker analyses of these clonal lines under proliferation and differentiation culture conditions demonstrate that during differentiation immature cell markers (Nanog and Nestin) were downregulated and hair cell (Myosin VIIa and Math1), support cell (p27Kip1 and cytokeratin) and neuronal cell (NF‐H and NeuroD) markers were upregulated. Our results suggest that the otic epithelium of the E12 mammalian inner ear possess multipotent progenitor cells able to generate cell types of both sensory epithelial and neural cell lineages when cultured under a differentiation culture condition. Understanding the molecular mechanisms of proliferation and differentiation of multipotent otic progenitor cells may provide insights that could contribute to the development of a novel cell therapy with a potential to initiate or stimulate the sensorineural repair of damaged inner ear sensory receptors. Anat Rec, 303:451–460, 2020. © 2019 American Association for Anatomy
Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom

Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. Some obvious correlations were found between dominant viral species and host biomass. Functional analysis indicated some functional genes had dramatic response in algal-associated viral assemblages, especially the CAZyme encoding genes. This work expands the existing knowledge of algal-associated viruses by characterizing viral composition and function across a complete algal bloom cycle. Our data provide supporting evidence that viruses participate in dinoflagellate bloom dynamics under natural conditions.