Miracle-dz/UniFAR-FTUs huggingface dataset:
The endosomal proteome of macrophage and dendritic cells

The essential roles of the endovacuolar system in health and disease call for the development of new tools allowing a better understanding of the complex molecular machinery involved in endocytic processes. We took advantage of the floating properties of small latex beads (sLB) on a discontinuous sucrose gradient to isolate highly purified endosomes following internalization of small latex beads in J774 macrophages and bone marrow‐derived dendritic cells (DC). We particularly focused on the isolation of macrophages early endosomes and late endosomes/lysosomes (LE/LYS) as well as the isolation of LE/LYS from immature and lipopolysaccharide‐activated (mature) DC. We subsequently performed a comparative analysis of their respective protein contents by MS. As expected, proteins already known to localize to the early endosomes were enriched in the earliest fraction of J774 endosomes, while proteins known to accumulate later in the process, such as hydrolases, were significantly enriched in the LE/LYS preparations. We next compared the LE/LYS protein contents of immature DC and mature DC, which are known to undergo massive reorganization leading to potent immune activation. The differences between the protein contents of endocytic organelles from macrophages and DC were underlined by focusing on previously poorly characterized biochemical pathways, which could have an unexpected but important role in the endosomal functions of these highly relevant immune cell types.
Sonic Hedgehog Stimulates Proliferation of Human Periodontal Ligament Stem Cells

Regulation of cell renewal in the periodontium is a critical cell function that has not been clarified. Sonic hedgehog (Shh) is a secreted signaling molecule that plays a key role during development and adult tissue homeostasis. In the present study, we have analyzed the role played by Shh in human periodontal ligament stem cell (HPLSC) proliferation. HPLSC were isolated with anti-STRO-1 antibodies. Shh increased the expression of GLI1 and PTC-1 and selectively stimulated cell proliferation in STRO-1(+) derived from adult periodontal ligament. Shh components were localized to primary cilia in STRO-1(+) cells after Shh stimulation. STRO-1(+) also expressed Shh, suggesting an autocrine-regulated phenomenon. Thus, we propose that Shh plays a critical role in the regulation of cell proliferation in STRO-1(+)/HPLSC.
Ultrasound imaging of milk ejection in the breast of lactating women.

OBJECTIVE Currently, the methods for assessing milk ejection in women include serial sampling of plasma oxytocin and measurement of intraductal pressure, both of which are invasive and may induce stress. We hypothesized that milk ejection would cause an increase in milk-duct diameter that could be observed noninvasively with ultrasound, and this could be used to investigate the physiology of milk ejection in women. METHODS One milk duct was scanned in the unsuckled breast in 2 groups of mothers: group BB (n = 21) for the beginning of a breastfeed and group EB (n = 24) for the entire breastfeed. A duct also was monitored for a 5-minute period on 2 separate days in the absence of factors that may induce milk ejection in group EB to provide a baseline duct diameter. Milk intake at a breastfeed was measured by test weighing. RESULTS A significant increase in milk-duct diameter was observed when milk ejection was sensed and/or the infant changed its swallowing pattern in both groups. Multiple increases and decreases (mean: 2.5 per breastfeed; standard deviation: 1.5; n = 62) in duct diameter occurred in group EB. Duct diameter remained relatively stable between breastfeeds (coefficient of variation: 1.4%-8.3%). Infant milk intake was positively related to the number of milk ejections (r2 =.365; n = 57). CONCLUSIONS Ultrasound is an objective, noninvasive technique for detecting milk ejection by observing an increase in milk-duct diameter. However, this technique requires an experienced ultrasonographer, adequate imaging time, and surroundings conducive to breastfeeding. Multiple milk ejections were common during breastfeeding, although they were not sensed by mothers. The number of milk ejections influenced the amount of milk the infant consumed.
Combination of Fixed and Mobile Cameras for Automatic Pedestrian Detection

Pedestrian detection in the surroundings of a vehicle is highly desirable to avoid dangerous traffic situations. Typical vision-based pedestrian detection algorithms on mobile cameras suffer from the lack of a-priori knowledge on the object to be detected. The variability in the shape, pose, color distribution, and behavior affect the robustness of the detection process. A novel vision-based system is proposed to detect pedestrians with a single mobile camera collaborating with a fixed camera observing the same scene. Nowadays, a large number of fixed cameras are installed in major cities. This work presents how features extracted from those fixed cameras can be used to detect pedestrians with mobile cameras present in the same scene. The proposed system outperforms state-of-the-art single frame pedestrian detectors using a feature-based classification framework. In addition, the system can be generalized to any object of interest. Any object detected by a fixed camera, can be detected with a mobile camera.
Comment on “In Vitro Effects of Bisphenol A β-D-Glucuronide (BPA-G) on Adipogenesis in Human and Murine Preadipocytes”

Boucher et al. reported that treatment of 3T3L1 preadipocytes with 10 μM bisphenol A β-D-glucuronide (BPA-G) induced a significant increase in lipid accumulation, in mRNA expression of the adipogenic markers sterol regulatory element binding factor 1 (SREBF1) and lipoprotein lipase (LPL), and in protein levels of LPL, aP2, and adipsin. They concluded that their study was the first to show that BPA-G induced adipocyte differentiation and was not simply an inactive metabolite. To justify the relevance of their 10-µM effective BPA-G concentration, they claimed that this tested concentration was within the range found in human fluids. To support their statement, they cited Harthe et al. (2012), who reported an average BPA-G concentration of 4.64 µg/L in human urine samples but wrongly converted this figure to a urine concentration of 11.5 µM (their effective in vitro concentration) rather than to the correct figure of 11.5 nM, i.e., a value 1,000 times lower. Apart from this error, it should be stressed that the plasma concentration and not the urine concentration is the driving concentration to explain any systemic effect. As the estimated ratio of total BPA (sum of BPA and its metabolites) concentration between serum and urine was less than 0.045 (Teeguarden et al. 2013), it can be concluded that the 10-µM in vitro effective BPA-G concentration was several orders of magnitude higher than what would be expected to be measured in the general population. Nevertheless, the fact that such high in vitro BPA-G displayed an estrogenic action merits some attention and was not totally unexpected. It should be recognized that BPA-G can be back-converted to BPA (aglycone) thanks to the ubiquitous presence of β-glucuronidases in many organs and bodily fluids (Sperker et al. 1997). Such a deconjugation process was reported to account for the estrogenic effect of soy isoflavone glucuronides on breast cancer cell lines (Islam et al. 2015). The likelihood that such a mechanism underlies the effects of BPA-G is supported by the ex vivo demonstration that BPA-G is readily converted back to its parent compound in ovine gonads, BPA conjugation–deconjugation cycling favoring BPA-G hydrolysis (Corbel et al. 2015). Nishikawa et al. (2010) also observed deconjugation of BPA-G in fetal liver cells, suggesting that BPA-G can enter cells and that endogenous glucuronidases may convert BPA-G to its aglycone form, about 5% of BPA-G being reactivated after 2 hours. More generally, the lack of stability of BPA-G in the presence of rodent fetal tissue homogenates has been reported (Waechter et al. 2007). Thus, it can be hypothesized that BPA-G deconjugation by the preadipocytes could result in sufficiently high residual BPA concentrations to trigger the effects reported by Boucher et al. This issue could be easily explored by analyzing the extracellular medium and the intracellular BPA content of preadipocyte cells after 48 hours of exposure.
Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp. , and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.
Rapid screening of natural products for antimycobacterial activity by using luciferase-expressing strains of Mycobacterium bovis BCG and Mycobacterium intracellulare

The object of this study was to investigate the ability of a rapid luciferase assay to detect antimycobacterial activity in plant extracts. Recombinant strains of Mycobacterium bovis BCG (rBCG) and Mycobacterium intracellulare expressing firefly luciferase were used as the test organisms. Assays were conducted in a 96-well minitube format under biosafety level 2 conditions. Control and test wells were sampled immediately after inoculation and after 3 (recombinant M. intracellulare) and 5 (rBCG) days of incubation to measure luminescence with a microplate luminometer, and the relative change in luminescence was calculated as a percentage of control values. As an alternative test method, Alamar blue was added after 12 days of incubation, and changes in color were read visually. A total of 480 extracts were tested. Sixteen extracts were active against rBCG, and of those, seven were also active against recombinant M. intracellulare. With activity defined as a relative change in luminescence of < or = 1% (i.e., > or = 99% inhibition) and a persistence of blue color after addition of Alamar blue, there was 99.0% agreement between the two methods. Our results suggest that the luciferase assay is rapid and accurate and has the potential to greatly accelerate the evaluation of antimycobacterial activity in plant extracts in vitro. With this method, it is possible to screen a large number of samples in a short period of time.
Adaptation of a Gaussia princeps Luciferase reporter system in Candida albicans for in vivo detection in the Galleria mellonella infection model

For the past 10 years, mini-host models and in particular the greater wax moth Galleria mellonella have tended to become a surrogate for murine models of fungal infection mainly due to cost, ethical constraints and ease of use. Thus, methods to better assess the fungal pathogenesis in G. mellonella need to be developed. In this study, we implemented the detection of Candida albicans cells expressing the Gaussia princeps luciferase in its cell wall in infected larvae of G. mellonella. We demonstrated that detection and quantification of luminescence in the pulp of infected larvae is a reliable method to perform drug efficacy and C. albicans virulence assays as compared to fungal burden assay. Since the linearity of the bioluminescent signal, as compared to the CFU counts, has a correlation of R2 = 0.62 and that this method is twice faster and less labor intensive than classical fungal burden assays, it could be applied to large scale studies. We next visualized and followed C. albicans infection in living G. mellonella larvae using a non-toxic and water-soluble coelenterazine formulation and a CCD camera that is commonly used for chemoluminescence signal detection. This work allowed us to follow for the first time C. albicans course of infection in G. mellonella during 4 days.
Integrin-dependent interaction of lipid rafts with the actin cytoskeleton in activated human platelets

Dynamic connections between actin filaments and the plasma membrane are crucial for the regulation of blood platelet functions. Protein complexes associated with αIIbβ3 integrin-based cytoskeleton structures are known to play a role in these processes. However, mechanisms involving lateral organizations of the plasma membrane remain to be investigated. Here, we demonstrate that a large fraction of platelet lipid rafts specifically associates with the actin cytoskeleton upon activation. This association was inhibited by antagonists of fibrinogen-αIIbβ3 binding and did not occur in type I Glanzman's thrombasthenic platelets. The raft-cytoskeleton interaction is a reversible process correlating with the intensity and stability of platelet aggregation. Although only a minor fraction of αIIbβ3 was recovered in rafts upon activation, this integrin specifically upregulated the level of PtdIns(4,5)P2 in membrane microdomains and induced the recruitment of several actin-modulating proteins known to directly or indirectly interact with this lipid. Controlled disruption of rafts did not affect αIIbβ3-mediated platelet aggregation in response to high concentrations of thrombin but significantly inhibited fibrin clot retraction. We propose that rafts participate in the organization of membrane-cytoskeleton interactions where αIIbβ3-mediated tension forces apply during the late phase of platelet activation.
Changes in movement characteristics of the spastic upper extremity after botulinum toxin injection.

OBJECTIVE To examine the longitudinal effects of botulinum toxin injection on movement characteristics of the spastic upper extremity in children by using motor control testing (MCT) techniques and standard clinical measures. DESIGN Open-label clinical trial. SETTING Motor control laboratory at an academic medical center. PARTICIPANTS A convenience sample of 9 subjects (5 boys, 4 girls; age range, 7-16 y) with cerebral injury (stroke or cerebral palsy) and asymmetric upper-extremity function because of spasticity. Eight subjects had right-sided involvement. INTERVENTIONS Botulinum toxin injection to the involved upper extremity, involving elbow, wrist, and finger flexors, depending on clinical presentation. MAIN OUTCOME MEASURES Clinical measures included range of motion (ROM), the Ashworth Scale, FIM trade mark instrument, Pediatric Evaluation of Disability Inventory, portions of the Bruininks-Oseretsky Test of Motor Proficiency, and the Purdue pegboard. MCT consisted of visually guided reaching, bilateral finger-to-nose movements, hand tapping, and isometric pinch force tasks. Kinematic assessments were made before and at 2, 4, 6, 12, 18, and 24 weeks after botulinum toxin injection. RESULTS All subjects had increased ROM and decreased Ashworth values throughout the testing period. In motor control tasks, improvement typically occurred earlier in the least complex movements, such as hand tapping, with 6 of 9 subjects showing a maximum, although transient, unilateral tapping speed by 6 weeks. A similar time course was observed for pinch force tasks. Improvement in more complex, forward-reaching tasks occurred much later (week 12 or later) or did not occur at all. As with the hand tasks, improved reach performance declined toward the end of the testing period. All subject showed minimal or no improvement in bilateral finger-to-nose movements. Neither maximum changes in ROM or Ashworth values correlated with improvements in functional elbow extension during sit and reach tasks, with 3 subjects with normal active ROM showing late onset or no change in reach. CONCLUSIONS Although botulinum toxin reduced tone and increased ROM of the spastic upper extremity, the time course and degree of motor improvement appears to depend on the complexity of the task. Future research should focus on the value of adjunct therapy, such as task-specific training, in addition to botulinum toxin treatments to facilitate functional improvement of the spastic upper extremity.
The Neurotrophin Receptors TrkA and TrkB are Inhibitory for Neurite Outgrowth

To investigate the possibility that the neurotrophin tyrosine kinase receptors are also recognition molecules by virtue of their immunoglobulin‐like domains, the ability of TrkA and TrkB to influence neurite outgrowth was tested in vitro. Cell monolayers of fibroblasts transfected to express either the TrkA or TrkB receptor reduced neurite outgrowth of phaeochromocytoma PC12 cells by 50–60% when compared to mock transfected fibroblasts or fibroblasts transfected with the epidermal growth factor receptor. Neurite outgrowth from cerebellar neurons was inhibited by 30–40% on these substrates. When a recombinantly expressed fragment of TrkA comprising the two immunoglobulin‐like domains was coated as a substrate in combination with poly‐L‐lysine and laminin, neurite outgrowth was inhibited in a dose‐dependent manner. This inhibition of neurite outgrowth was not mediated via an interaction with laminin as there is no specific binding of the TrkA fragment to laminin. The adhesion of cell bodies to this substrate was not affected by the immunoglobulin‐like domains. These observations suggest that the mammalian neurotrophin receptors not only influence neurite outgrowth by neurotrophin triggered activation of the receptor, but also by cell surface recognition processes conveyed by the immunoglobulin‐like domains.
Increased Patient Enrollment to a Randomized Surgical Trial Through Equipoise Polling of an Expert Surgeon Panel

Objective: To determine whether patients who learned the views of an expert surgeons’ panel's assessment of equipoise between 2 alternative operative treatments had increased likelihood of consenting to randomization. Background: Difficulty obtaining patient consent to randomization is an important barrier to conducting surgical randomized clinical trials, the gold standard for generating clinical evidence. Methods: Observational study of the rate of patient acceptance of randomization within a 5-center randomized clinical trial comparing lumbar spinal decompression versus lumbar spinal decompression plus instrumented fusion for patients with symptomatic grade I degenerative lumbar spondylolisthesis with spinal stenosis. Eligible patients were enrolled in the trial and then asked to accept randomization. A panel of 10 expert spine surgeons was formed to review clinical information and images for individual patients to provide an assessment of suitability for randomization. The expert panel vote was disclosed to the patient by the patient's surgeon before the patient decided whether to accept randomization or not. Results: Randomization acceptance among eligible patients without expert panel review was 40% (19/48) compared with 81% (47/58) among patients undergoing expert panel review (P < 0.001). Among expert-reviewed patients, randomization acceptance was 95% when all experts or all except 1 voted for randomization, 75% when 2 experts voted against randomization, and 20% with 3 or 4 votes against (P < 0.001 for trend). Conclusions: Patients provided with an expert panel's assessment of their own suitability for randomization were twice as likely to agree to randomization compared with patients receiving only their own surgeon's recommendation.
Optimization of Shared Autonomy Vehicle Control Architectures for Swarm Operations

The need for greater capacity in automotive transportation (in the midst of constrained resources) and the convergence of key technologies from multiple domains may eventually produce the emergence of a “swarm” concept of operations. The swarm, which is a collection of vehicles traveling at high speeds and in close proximity, will require technology and management techniques to ensure safe, efficient, and reliable vehicle interactions. We propose a shared autonomy control approach, in which the strengths of both human drivers and machines are employed in concert for this management. Building from a fuzzy logic control implementation, optimal architectures for shared autonomy addressing differing classes of drivers (represented by the driver's response time) are developed through a genetic-algorithm-based search for preferred fuzzy rules. Additionally, a form of “phase transition” from a safe to an unsafe swarm architecture as the amount of sensor capability is varied uncovers key insights on the required technology to enable successful shared autonomy for swarm operations.
Construction of a Functional CMP-Sialic Acid Biosynthesis Pathway in Arabidopsis1[OA]

Previous studies have reported that plants contain negligible amounts of free or protein-bound N-acetylneuraminic acid (Neu5Ac). This is a major disadvantage for the use of plants as a biopharmaceutical expression system, since N-glycans with terminal Neu5Ac residues are important for the biological activities and half-lives of recombinant therapeutic glycoproteins in humans. For the synthesis of Neu5Ac-containing N-glycans, plants have to acquire the ability to synthesize Neu5Ac and its nucleotide-activated derivative, cytidine monophospho-N-acetylneuraminic acid. In this study, we have generated transgenic Arabidopsis (Arabidopsis thaliana) plants expressing three key enzymes of the mammalian Neu5Ac biosynthesis pathway: UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase, N-acetylneuraminic acid phosphate synthase, and CMP-N-acetylneuraminic acid synthetase. Simultaneous expression of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase and N-acetylneuraminic acid phosphate synthase resulted in the generation of significant Neu5Ac amounts (1,275 nmol g−1 fresh weight in leaves) in planta, which could be further converted to cytidine monophospho-N-acetylneuraminic acid (2.4 nmol g−1 fresh weight in leaves) by coexpression of CMP-N-acetylneuraminic acid synthetase. These findings are a major step toward the production of Neu5Ac-containing glycoproteins in plants.