Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of the key characteristics of carcinogens in cancer hazard identification

Abstract Smith et al. (Env. Health Perspect. 124: 713, 2016) identified 10 key characteristics (KCs), one or more of which are commonly exhibited by established human carcinogens. The KCs reflect the properties of a cancer-causing agent, such as ‘is genotoxic,’ ‘is immunosuppressive’ or ‘modulates receptor-mediated effects,’ and are distinct from the hallmarks of cancer, which are the properties of tumors. To assess feasibility and limitations of applying the KCs to diverse agents, methods and results of mechanistic data evaluations were compiled from eight recent IARC Monograph meetings. A systematic search, screening and evaluation procedure identified a broad literature encompassing multiple KCs for most (12/16) IARC Group 1 or 2A carcinogens identified in these meetings. Five carcinogens are genotoxic and induce oxidative stress, of which pentachlorophenol, hydrazine and malathion also showed additional KCs. Four others, including welding fumes, are immunosuppressive. The overall evaluation was upgraded to Group 2A based on mechanistic data for only two agents, tetrabromobisphenol A and tetrachloroazobenzene. Both carcinogens modulate receptor-mediated effects in combination with other KCs. Fewer studies were identified for Group 2B or 3 agents, with the vast majority (17/18) showing only one or no KCs. Thus, an objective approach to identify and evaluate mechanistic studies pertinent to cancer revealed strong evidence for multiple KCs for most Group 1 or 2A carcinogens but also identified opportunities for improvement. Further development and mapping of toxicological and biomarker endpoints and pathways relevant to the KCs can advance the systematic search and evaluation of mechanistic data in carcinogen hazard identification.
Raffinose Induces Biofilm Formation by Streptococcus mutans in Low Concentrations of Sucrose by Increasing Production of Extracellular DNA and Fructan

ABSTRACT Streptococcus mutans is the primary etiological agent of dental caries and causes tooth decay by forming a firmly attached biofilm on tooth surfaces. Biofilm formation is induced by the presence of sucrose, which is a substrate for the synthesis of extracellular polysaccharides but not in the presence of oligosaccharides. Nonetheless, in this study, we found that raffinose, which is an oligosaccharide with an intestinal regulatory function and antiallergic effect, induced biofilm formation by S. mutans in a mixed culture with sucrose, which was at concentrations less than those required to induce biofilm formation directly. We analyzed the possible mechanism behind the small requirement for sucrose for biofilm formation in the presence of raffinose. Our results suggested that sucrose contributed to an increase in bacterial cell surface hydrophobicity and biofilm formation. Next, we examined how the effects of raffinose interacted with the effects of sucrose for biofilm formation. We showed that the presence of raffinose induced fructan synthesis by fructosyltransferase and aggregated extracellular DNA (eDNA, which is probably genomic DNA released from dead cells) into the biofilm. eDNA seemed to be important for biofilm formation, because the degradation of DNA by DNase I resulted in a significant reduction in biofilm formation. When assessing the role of fructan in biofilm formation, we found that fructan enhanced eDNA-dependent cell aggregation. Therefore, our results show that raffinose and sucrose have cooperative effects and that this induction of biofilm formation depends on supportive elements that mainly consist of eDNA and fructan. IMPORTANCE The sucrose-dependent mechanism of biofilm formation in Streptococcus mutans has been studied extensively. Nonetheless, the effects of carbohydrates other than sucrose are inadequately understood. Our findings concerning raffinose advance the understanding of the mechanism underlying the joint effects of sucrose and other carbohydrates on biofilm formation. Since raffinose has been reported to have positive effects on enterobacterial flora, research on the effects of raffinose on the oral flora are required prior to its use as a beneficial sugar for human health. Here, we showed that raffinose induced biofilm formation by S. mutans in low concentrations of sucrose. The induction of biofilm formation generally generates negative effects on the oral flora. Therefore, we believe that this finding will aid in the development of more effective oral care techniques to maintain oral flora health.
Fast Convolutional Sparse Coding

Sparse coding has become an increasingly popular method in learning and vision for a variety of classification, reconstruction and coding tasks. The canonical approach intrinsically assumes independence between observations during learning. For many natural signals however, sparse coding is applied to sub-elements ( i.e. patches) of the signal, where such an assumption is invalid. Convolutional sparse coding explicitly models local interactions through the convolution operator, however the resulting optimization problem is considerably more complex than traditional sparse coding. In this paper, we draw upon ideas from signal processing and Augmented Lagrange Methods (ALMs) to produce a fast algorithm with globally optimal sub problems and super-linear convergence.
Is bronchial thermoplasty cost‐effective as treatment for problematic asthma patients? Singapore's perspective on a global model

Bronchial thermoplasty (BT) has been shown to be effective at reducing asthma exacerbations and improving asthma control for patients with severe persistent asthma but it is also expensive. Evidence on its cost‐effectiveness is limited and inconclusive. In this study, we aim to evaluate the incremental cost‐effectiveness of BT combined with optimized asthma therapy (BT‐OAT) relative to OAT for difficult‐to‐treat and severe asthma patients in Singapore, and to provide a general framework for determining BT's cost‐effectiveness in other healthcare settings.
Neonatal mouse intervertebral discs heal with restored function following herniation injury

Adult intervertebral discs (IVDs) have poor endogenous healing capacity, because of their challenging microenvironment and complex mechanical demands, which can result in painful IVD herniation. There are no regenerative strategies available to improve IVD healing and restore its function. Neonatal mice are excellent models of mammalian regeneration, but there are no studies of the regenerative capacity of neonatal IVDs. In this study, we developed a neonatal model of improved IVD healing to inform repair strategies after herniation. In vivo puncture injuries were performed to simulate herniation with complete annulus fibrosus (AF) tears in caudal IVDs of neonatal (postnatal d 5) and adult (4–6 mo) Scleraxis green fluorescent protein (ScxGFP) mice. Acute and long‐term healing responses were assessed with histologic, radiologic, and biomechanical measurements. Neonates underwent accelerated IVD healing compared to adults with functional restoration and enhanced structural repair after herniation. A population of ScxGFP− cells identified in the neonatal repair site may be associated with this improved healing and warrants future investigation. In summary, function of neonatal IVDs was restored after herniation injury, whereas that of adult discs was not. This improved healing response is likely driven by multiple mechanisms that may include differences in mechanical loading and available repair cells during growth. —Torre, O. M. , Das, R. , Berenblum, R. E. , Huang, A.H. , Iatridis, J. C. Neonatal mouse intervertebral discs heal with restored function following herniation injury. FASEB J. 32, 4753–4762 (2018). www.fasebj. org
Mutation in TDRD9 causes non-obstructive azoospermia in infertile men

Background Azoospermia is diagnosed when sperm cells are completely absent in the ejaculate even after centrifugation. It is identified in approximately 1% of all men and in 10%–20% of infertile males. Non-obstructive azoospermia (NOA) is characterised by the absence of sperm due to either a Sertoli cell-only pattern, maturation arrest, hypospermatogenesis or mixed patterns. NOA is a severe form of male infertility, with limited treatment options and low fertility success rates. In the majority of patients, the cause for NOA is not known and mutations in only a few genes were shown to be causative. Aim We investigated the cause of maturation arrest in five azoospermic infertile men of a large consanguineous Bedouin family. Methods and results Using whole genome genotyping and exome sequencing we identified a 4 bp deletion frameshift mutation in TDRD9 as the causative mutation with a Lod Score of 3.42. We demonstrate that the mutation results in a frameshift as well as exon skipping. Immunofluorescent staining with anti-TDRD9 antibody directed towards the N terminus demonstrated the presence of the protein in testicular biopsies of patients with an intracellular distribution comparable to a control biopsy. The mutation does not cause female infertility. Conclusion This is the first report of a recessive deleterious mutation in TDRD9 in humans. The clinical phenotype recapitulates that observed in the Tdrd9 knockout mice where this gene was demonstrated to participate in long interspersed element-1 retrotransposon silencing. If this function is preserved in human, our data underscore the importance of maintaining DNA stability in the human male germ line.
Understanding human motion and gestures for underwater human–robot collaboration

In this paper, we present a number of robust methodologies for an underwater robot to visually detect, follow, and interact with a diver for collaborative task execution. We design and develop two autonomous diver‐following algorithms, the first of which utilizes both spatial‐ and frequency‐domain features pertaining to human swimming patterns to visually track a diver. The second algorithm uses a convolutional neural network‐based model for robust tracking‐by‐detection. In addition, we propose a hand gesture‐based human–robot communication framework that is syntactically simpler and computationally more efficient than the existing grammar‐based frameworks. In the proposed interaction framework, deep visual detectors are used to provide accurate hand gesture recognition; subsequently, a finite‐state machine performs robust and efficient gesture‐to‐instruction mapping. The distinguishing feature of this framework is that it can be easily adopted by divers for communicating with underwater robots without using artificial markers or requiring memorization of complex language rules. Furthermore, we validate the performance and effectiveness of the proposed methodologies through a number of field experiments in closed‐ and open‐water environments. Finally, we perform a user interaction study to demonstrate the usability benefits of our proposed interaction framework compared to the existing methods.
Entropy redistribution controls allostery in a metalloregulatory protein

Significance The immune system limits nutrient availability and releases highly reactive toxic molecules to control bacterial infections. Successful pathogens resist these host effects by using regulatory proteins that “sense” diverse environmental stressors and alter the transcription of genes required to mount an adaptive response. We demonstrate here that these regulatory proteins are capable of sensing a specific stressor in a process that relies nearly exclusively on a redistribution of atomic motions to regulate gene transcription. This work provides insights into how nature exploits a simple molecular scaffold that relies on changes in atomic motions to evolve new adaptive responses to a wide range of environmental stimuli. Allosteric communication between two ligand-binding sites in a protein is a central aspect of biological regulation that remains mechanistically unclear. Here we show that perturbations in equilibrium picosecond–nanosecond motions impact zinc (Zn)-induced allosteric inhibition of DNA binding by the Zn efflux repressor CzrA (chromosomal zinc-regulated repressor). DNA binding leads to an unanticipated increase in methyl side-chain flexibility and thus stabilizes the complex entropically; Zn binding redistributes these motions, inhibiting formation of the DNA complex by restricting coupled fast motions and concerted slower motions. Allosterically impaired CzrA mutants are characterized by distinct nonnative fast internal dynamics “fingerprints” upon Zn binding, and DNA binding is weakly regulated. We demonstrate the predictive power of the wild-type dynamics fingerprint to identify key residues in dynamics-driven allostery. We propose that driving forces arising from dynamics can be harnessed by nature to evolve new allosteric ligand specificities in a compact molecular scaffold.
Identification of Antigenic Glycans from Schistosoma mansoni by Using a Shotgun Egg Glycan Microarray

ABSTRACT Infection of mammals by the parasitic helminth Schistosoma mansoni induces antibodies to glycan antigens in worms and eggs, but the differential nature of the immune response among infected mammals is poorly understood. To better define these responses, we used a shotgun glycomics approach in which N-glycans from schistosome egg glycoproteins were prepared, derivatized, separated, and used to generate an egg shotgun glycan microarray. This array was interrogated with sera from infected mice, rhesus monkeys, and humans and with glycan-binding proteins and antibodies to gather information about the structures of antigenic glycans, which also were analyzed by mass spectrometry. A major glycan antigen targeted by IgG from different infected species is the FLDNF epitope [Fucα3GalNAcβ4(Fucα3)GlcNAc-R], which is also recognized by the IgG monoclonal antibody F2D2. The FLDNF antigen is expressed by all life stages of the parasite in mammalian hosts, and F2D2 can kill schistosomula in vitro in a complement-dependent manner. Different antisera also recognized other glycan determinants, including core β-xylose and highly fucosylated glycans. Thus, the natural shotgun glycan microarray of schistosome eggs is useful in identifying antigenic glycans and in developing new anti-glycan reagents that may have diagnostic applications and contribute to developing new vaccines against schistosomiasis.
The Microstructure of Weld Overlay Ni-Base Alloy Deposited on Carbon Steel by CMT Method

Ni-base alloys, like Inconel 625, exhibit a high temperature corrosion and oxidation resistance. For this reason, these alloys are typically used as a one of the most important coating material and can be applied in a different environments and elements of devices having various applications. In this work, Inconel 625 was deposited onto a carbon steel P235GH by Cold Metal Transfer method. Due to the segregation of Ni, Cr, Nb and Mo elements the Inconel 625 weld overlays cladded on boiler pipes P235GH obtained the dendritic structure, with the formation of a second phases at the end of solidification. The presence of γ (with high dislocation density), the Laves and (Nb,Ti)C phases was revealed by means of TEM examinations. The multipoint EDS analysis confirmed the presence of low Fe concentration in the Inconel 625 alloy coatings. The concentration profiles of Ni, Cr, Mo and Nb performed across the dendritic structure showed segregation of these elements.
Contributions of Charged Residues in Structurally Dynamic Capsid Surface Loops to Rous Sarcoma Virus Assembly

ABSTRACT Extensive studies of orthoretroviral capsids have shown that many regions of the CA protein play unique roles at different points in the virus life cycle. The N-terminal domain (NTD) flexible-loop (FL) region is one such example: exposed on the outer capsid surface, it has been implicated in Gag-mediated particle assembly, capsid maturation, and early replication events. We have now defined the contributions of charged residues in the FL region of the Rous sarcoma virus (RSV) CA to particle assembly. Effects of mutations on assembly were assessed in vivo and in vitro and analyzed in light of new RSV Gag lattice models. Virus replication was strongly dependent on the preservation of charge at a few critical positions in Gag-Gag interfaces. In particular, a cluster of charges at the beginning of FL contributes to an extensive electrostatic network that is important for robust Gag assembly and subsequent capsid maturation. Second-site suppressor analysis suggests that one of these charged residues, D87, has distal influence on interhexamer interactions involving helix α7. Overall, the tolerance of FL to most mutations is consistent with current models of Gag lattice structures. However, the results support the interpretation that virus evolution has achieved a charge distribution across the capsid surface that (i) permits the packing of NTD domains in the outer layer of the Gag shell, (ii) directs the maturational rearrangements of the NTDs that yield a functional core structure, and (iii) supports capsid function during the early stages of virus infection. IMPORTANCE The production of infectious retrovirus particles is a complex process, a choreography of protein and nucleic acid that occurs in two distinct stages: formation and release from the cell of an immature particle followed by an extracellular maturation phase during which the virion proteins and nucleic acids undergo major rearrangements that activate the infectious potential of the virion. This study examines the contributions of charged amino acids on the surface of the Rous sarcoma virus capsid protein in the assembly of appropriately formed immature particles and the maturational transitions that create a functional virion. The results provide important biological evidence in support of recent structural models of the RSV immature virions and further suggest that immature particle assembly and virion maturation are controlled by an extensive network of electrostatic interactions and long-range communication across the capsid surface.
Phytochemical and antioxidant properties of some Cassia species

Abstract In this study, the antioxidant activity of aqueous and ethanol extracts of four plants from the genus Cassia were evaluated by various antioxidant assays, including ferric reducing antioxidant power (FRAP), DPPH free radical scavenging, metal chelating activity, phosphomolybdenum reducing power, hydrogen peroxide radical scavenging, hydroxyl radical scavenging, deoxyribose degradation and β-carotene bleaching assay. The various antioxidant activities were compared to standard antioxidant such as ascorbic acid. All the extracts showed antioxidant activity in the tested methods. Among the four species, Cassia auriculata has been found to possess highest activity in most of the tested models. In addition to the antioxidant activity, the total phenolics and flavonoids were measured in the extracts. The ethanolic extract exhibited highest phenolics and flavonoid contents and had also shown potent antioxidant activity in comparison to the aqueous extracts. The possible antioxidant mechanism of the ethanol extract can be due to its hydrogen or electron donating and direct free radical scavenging properties. Hence, the ethanol extract represents a source of potential antioxidants that could be used in pharmaceutical industries.
The Novelty in Fabrication of Poly Vinyl Alcohol/κ-Carrageenan Hydrogel with Lactobacillus bulgaricus Extract as Anti-inflammatory Wound Dressing Agent

Material barrier properties to microbes are an important issue in many pharmaceutical applications like wound dressings. A wide range of biomaterials has been used to manage the chronic inflamed wounds. Eight hydrogel membranes of poly vinyl alcohol (PVA) with κ-carrageenan (KC) and Lactobacillus bulgaricus extract (LAB) have been prepared by using freeze–thawing technique. To evaluate the membranes efficiency as wound dressing agents, various tests have been done like gel fraction, swelling behavior, mechanical properties, etc. The antibacterial activities of the prepared membranes were tested against the antibiotic-resistant bacterial isolates. In addition, the safety usage of the prepared hydrogel was checked on human dermal fibroblast cells. The anti-inflammatory properties of the prepared hydrogel on LPS-PBMC cell inflammatory model were quantified using enzyme-linked immunosorbent assay (ELISA) and real-time polymerase chain reaction (RT-qPCR). The analysis data of TGA, SEM, gel fraction, and swelling behavior showed changes in properties of prepared PVA\KC\LAB hydrogel membrane than pure PVA hydrogel membrane. The antibacterial activities of the prepared membranes augmented in LAB extract-prepared membranes. Out of the eight used hydrogel membranes, the PVAKC4 hydrogel membrane is the safest one on fibroblast cellular proliferation with a maximum proliferation percentage 97.3%. Also, all the used hydrogel membrane showed abilities to reduce the concentration of IL-2 and IL-8 compared with both negative and positive control. In addition, almost all the prepared hydrogel membrane showed variable abilities to downregulate the expression of TNF-α gene with superior effect of hydrogel membrane KC1. PVA/KC/LAB extract hydrogel membrane may be a promising material for wound dressing application and could accelerate the healing process of the chronic wound because of its antimicrobial and anti-inflammatory properties.
Inactivation of mTORC1 Signaling in Osterix‐Expressing Cells Impairs B‐cell Differentiation

Osteoblasts provide a microenvironmental niche for B‐cell commitment and maturation in the bone marrow (BM). Any abnormity of osteoblasts function may result in the defect of B lymphopoiesis. Signaling from mechanistic target of rapamycin complex 1 (mTORC1) has been implicated in regulating the expansion and differentiation of osteoblasts. Thus, we raise a hypothesis that mTORC1 signaling in osteoblasts plays a vital role in B‐cell development. Inactivation of mTORC1 in osterix‐expressing cells (mainly osteoblast lineage) through Osx‐Cre‐directed deletion of Raptor (an mTORC1‐specific component) resulted in a reduction in the total B‐cell population in the BM, which was due to a block in early B‐cell development from the pro‐B to pre‐B cell stage. Further mechanistic studies revealed that this defect was the result of reduction of interleukin‐7 (IL‐7) expression in osterix‐expressing immature osteoblasts, which caused the abnormality of IL‐7/Stat5 signaling in early B lymphocytes, leading to an increased apoptosis of pre‐B plus immature B cells. In vitro and in vivo studies demonstrated that the addition of exogenous IL‐7 partially restored B lymphopoiesis in the BM of Raptor mutant mice. Furthermore, total BM cells cultured in conditioned media from Raptor null immature osteoblasts or media with anti‐IL‐7 neutralizing antibody failed to differentiate into pre‐B and immature B cells, indicating that inactivation of mTORC1 in immature osteoblast cannot fully support normal B‐cell development. Taken together, these findings demonstrate a novel role for mTORC1 in the regulation of bone marrow environments that support B‐cell differentiation via regulating IL‐7 expression. © 2017 American Society for Bone and Mineral Research.