Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic Engineering of Valine- and Isoleucine-Derived Glucosinolates in Arabidopsis Expressing CYP79D2 from Cassava

Glucosinolates are amino acid-derived natural products that, upon hydrolysis, typically release isothiocyanates with a wide range of biological activities. Glucosinolates play a role in plant defense as attractants and deterrents against herbivores and pathogens. A key step in glucosinolate biosynthesis is the conversion of amino acids to the corresponding aldoximes, which is catalyzed by cytochromes P450 belonging to the CYP79 family. Expression of CYP79D2 from cassava (Manihot esculenta Crantz.) in Arabidopsis resulted in the production of valine (Val)- and isoleucine-derived glucosinolates not normally found in this ecotype. The transgenic lines showed no morphological phenotype, and the level of endogenous glucosinolates was not affected. The novel glucosinolates were shown to constitute up to 35% of the total glucosinolate content in mature rosette leaves and up to 48% in old leaves. Furthermore, at increased concentrations of these glucosinolates, the proportion of Val-derived glucosinolates decreased. As the isothiocyanates produced from the Val- and isoleucine-derived glucosinolates are volatile, metabolically engineered plants producing these glucosinolates have acquired novel properties with great potential for improvement of resistance to herbivorous insects and for biofumigation.
Narrative after traumatic brain injury: A comparison of monologic and jointly-produced discourse

Primary objective: To investigate the effects of a familiar communication partner on the production of narrative after traumatic brain injury (TBI). Method: Ten participants with TBI were matched with 10 control participants for sex, age, and education. Participants independently retold a story from a picture sequence and also retold a video segment with a friend to a researcher. The resulting discourse was analyzed for productivity, cohesion, story grammar, informational content and exchange structure. Results: There was a significant difference between participants with and without TBI for all measures in the monologic narrative. In the jointly-produced narrative, there was no significant difference in performance and participation between individuals with TBI and control participants. Participants with TBI demonstrated a significant improvement between the monologic and the jointly-produced task in story grammar and informational content. Conclusions: The natural scaffolding provided by the friends of participants with TBI in a meaningful narrative task facilitated competent participation in and production of narrative. These findings indicate an avenue for training everyday communication partners in supporting narrative skills after TBI, and for the use of jointly-produced narrative as an additional assessment tool to create a holistic view of everyday skills.
Acid phosphatase activity of virulent and avirulent clones of Leishmania donovani promastigotes

Virulent and avirulent clones of Leishmania donovani promastigotes were examined for their acid phosphatase activity. The acid phosphatase activity of whole-cell lysates of virulent clones was 1.5 to 2.0 times higher than that of avirulent clones. Pellet fractions (260,000 x g, 30 min) from sonicated promastigotes of a virulent clone and an avirulent clone contained 60 and 40% of the total enzyme activity, respectively. Membrane-bound acid phosphatase was extracted with Triton X-100 from the pellet. This membrane-bound phosphatase activity was 2.4-fold higher in virulent organisms than in avirulent organisms. The membrane acid phosphatase exhibited two distinct bands on polyacrylamide gels stained for enzyme activity. One diffuse, faster-migrating band showed identical electrophoretic mobility in both virulent and avirulent clones, although a higher enzymatic activity was observed with the extract from virulent cells. In contrast, a slower-migrating band was different between the two clones in the mobility. These results suggest that membrane-bound acid phosphatase was quantitatively and qualitatively different between virulent and avirulent promastigotes of L. donovani. In addition, virulent cells produced a relatively high level of acid phosphatase throughout the growth in culture.
Chitosan and chitosan sulfate have opposing effects on collagen–fibroblast interactions

Soon after injury, hyaluronan is prominent in granulation tissue. As hyaluronan wanes, sulfated glycosaminoglycans predominate. The temporal relationship between the transition from unsulfated to sulfated glycosaminoglycans and the phenotypic changes in fibroblasts in the wound bed suggest that these two events are interrelated. This possibility was investigated using chitosan and its sulfated product as model compounds. The ability of cultured human foreskin fibroblasts to bind and to contract lattices of collagen, collagen–chitosan, and collagen–chitosan sulfate was determined. Fibroblast adherence to substrates after 24 hours was determined by the MTT assay at A570. Adherence to the collagen–chitosan substrate was markedly reduced (mean A570± SD; 0.16 ± 0.05, n = 6) (p < 0.01) compared to collagen alone (0.92 ± 0.04) or to collagen–chitosan sulfate (0.84 ± 0.05). Kinetics of contraction of lattices by enmeshed fibroblasts was determined by planimetric measurements, 0–48 hours after loosening the lattices. Contraction of the collagen–chitosan lattices (n = 5) was less at all time points than for the other two lattices. After 48 hours, the collagen– chitosan lattices contracted significantly (p < 0.01) less (30.0%± 4.4) compared to collagen alone (66.9%± 4.7) and collagen–chitosan sulfate (71.6%± 7.7). Scanning electron microscopy of the acellular lattices showed fibers of the collagen–chitosan mixture to be the thickest and with altered organization. These results show that chitosan sulfation markedly enhances fibroblast adhesion and promotes contraction of a collagen lattice compared to the unsulfated material. By analogy to the in vivo sequence of hyaluronan followed by sulfated glycosaminoglycans in wounds, the results suggest that glycosaminoglycan sulfation may be a contributing signal for phenotypic transformation during wound healing.
Thermoregulation of the Escherichia coli O157:H7 pO157 ecf operon and lipid A myristoyl transferase activity involves intrinsically curved DNA

Escherichia coli O157:H7 survives in diverse environments from the ruminant gastrointestinal tract to cool nutrient‐dilute water. We hypothesized that the gene regulation required for this flexibility includes intrinsically curved DNA that responds to environmental changes. Three intrinsically curved DNAs were cloned from the E. coli O157:H7 virulence plasmid (pO157), sequenced and designated Bent 1 through Bent 3 (BNT1, BNT2 and BNT3). Compared to BNT1 and BNT3, BNT2 had characteristics typical of intrinsically curved DNA including electrophoretic gel retardation at 4°C, six partially phased adenine:thymine tracts and transcriptional activation. BNT2::lacZ operon fusions showed that BNT2 activated transcription at 24°C compared to 37°C and was partially repressed by a bacterial nucleoid‐associated protein H‐NS. BNT2 regulated the E. coli attaching and effacing gene‐positive conserved fragments 1–4 (ecf1–4) that are conserved in Shiga toxin‐producing E. coli associated with human disease. Experimental analyses showed that ecf1–4 formed an operon. ecf1, 2 and 3 encoded putative proteins associated with bacterial surface polysaccharide biosynthesis and invasion and ecf4 complemented a chromosomal deletion of lpxM encoding lipid A myristoyl transferase. Mass spectrometric analysis of lipid A from ecf and lpxM single and double mutants showed that myristoylation was altered at lower temperature.
Utilization of RFID analytics in assessing student engagement

The teaching and learning methods are increasingly adopting educational data mining approaches. This ever-changing landscape has allowed management to use educational data for strategic decision-making, offered students with relevant information to improve academic performance, and provided teachers with data on learners' behavior for effective teaching. To assess academically at-risk students, teachers need to gain valuable insights on student engagement, which includes class attendance, library and computer laboratory access, and use of other learning resources so that they can tailor the learning needs of students. Data analytics is used to examine student engagement inside and outside the classroom and predict learning trends. The popularity of Internet of Things and the convergence of RFID, Wireless Sensor Networks, Big Data, and Cloud Computing have enabled organizations to implement innovative information systems; however, their integrative potential has not been thoroughly explored. Having an RFID in combination with data analytics will provide various academic stakeholders valuable and critical information as regards students' learning behavior. Therefore, this paper reviews current trends of RFID in education and discusses opportunities of data analytics integration. Moreover, this paper also presents a conceptual framework of a basic RFID Analytic System that can be used in assessing student engagement.
Improving Incident Detection Effectiveness in Vehicular Networks: Methodology and Evaluation

In this paper a comprehensive and efficient incident detection approach is proposed, that uses probabilistic network and processing methodologies to exploit spatial and temporal correlations and dependencies in vehicular networks. The proposed approach, based on principal component analysis, provides an integrated way of effectively processing and organizing accumulated spatiotemporal information from a variety of different locations, vehicles and sources, and therefore allows for the development of enhanced and efficient transportation systems. The performance and operational effectiveness of our proposed incident detection methodology is achieved via modelling and simulation under various scenarios.
Autonomous behavior control architecture of entertainment humanoid robot SDR-4X

In this paper we describe the autonomous behavior control architecture of SDR-4X, which serves to integrate multi-modal recognition and motion control technologies. We overview the entire software architecture of SDR-4X, which is composed of perception, short and long term memory, behavior control, and motion control parts. Regarding autonomous behavior control, we further focus on issues such as spontaneous behavior generation using a homeostasis regulation mechanism, and a behavior control/selection mechanism with tree-structured situated behavior modules. In the autonomous behavior control architecture, we achieve three basic requirements, which are the concurrent evaluation of the situation of each behavior module, concurrent execution of multiple behavior modules, and preemption (behavior interruption/resume capability). Using the autonomous behavior control architecture described, we demonstrate that SDR-4X can spontaneously and passively interact with a human.
A Knowledge Engineering Methodology for Resource Monitoring in the Industrial Domain

Abstract In industrial production, the efficient use of resources is becoming increasingly important due to the rising prices of resources and ecological awareness. A resource monitoring system can observe the individual resource consumption of the devices in an industrial plant to detect excessive resource consumption while considering context information such as the process steps or varying energy costs. A systematic approach for the semantic integration of relevant information is a key requirement to infer reliable monitoring states of the devices. Recent research explores how future industrial plants may use decentralized autonomous devices. To integrate such autonomous devices in a monitoring system, semantic models are required that describe the devices and their data, thus we need knowledge-based approaches. To date, the research on knowledge-based systems in the industrial domain has tended to focus on application-specific solutions rather than on generic solutions that integrate knowledge of multiple sources. In this paper, we introduce a knowledge-engineering methodology to build a generic, reusable resource monitoring system for industrial plants which includes multiple knowledge sources. This approach can also be used to develop knowledge-based systems for other applications such as diagnostic or prognostic systems.
A novel CRIg‐targeted complement inhibitor protects cells from complement damage

The inappropriate activation of complement may contribute to various immune diseases. The alternative pathway (AP) predominates during complement activation regardless of the initiating pathways. Hence, the main AP regulator factor H (FH) holds great potential as an attractive therapeutic intervention. In addition, complement receptor of the immunoglobulin superfamily (CRIg) has been demonstrated to inhibit AP and, more notably, still specifically binds to C3b/iC3b. We thus developed novel CRIg‐targeted complement inhibitors by connecting the functional domains of CRIg and FH, which we termed CRIg‐FH and CRIg‐L‐FH. CRIg‐L‐FH, slightly more potent than CRIg‐FH, considerably inhibited both AP‐ and also classical pathway (CP)‐mediated hemolysis and successfully eliminated the deposition of C3b/iC3b. Kinetic analysis further revealed that the binding affinity constant (KD) of CRIg/FH was in the micromolar range, consistent with its long‐lasting binding to complement‐attacked cells. CRIg‐L‐FH efficiently protected aberrant erythrocytes of patients with paroxysmal nocturnal hemoglobinuria (PNH) from AP‐and CP‐mediated complement damage (IC50 was 22.43 and 64.69 nM, respectively). Moreover, CRIg‐L‐FH was found to inhibit complement activation induced by the anti‐Thy1 antibody in a mesangiopro‐liferative glomerulonephritis (MPGN) rat model. Hence, CRIg‐L‐FH protects glomerular mesangial cells (GMCs) from complement‐mediated injury and proliferative lesions. These findings strongly suggest that CRIg/FH is a potential therapeutic drug candidate for a range of complement‐mediated diseases. —Qiao, Q. , Teng, X. , Wang, N. , Lu, R. , Guo, L. , Zhang, X. , Du, Y. , Wang, W. , Chen, S. , Wu, Q. , He, G. , Wang, Y. , and Hu, W. , A novel CRIg‐targeted complement inhibitor protects cells from complement damage. FASEB J. 28, 4986–4999 (2014). www.fasebj. org
Hypothetical Double‐Helical Poly(A) Formation in a Cell and Its Possible Biological Significance

Arguments are presented in favor of capability of poly(A)‐tracts of cellular RNA to form double helices in vivo. It is suggested that formation of the double helix in the mRNA poly(A) tail provides the basis for such processes as polyadenylation termination, PAB I synthesis autoregulation, and stabilization of ARE‐containing mRNA by ELAV‐like proteins.
An adaptive control architecture for cyber-physical system security in the face of sensor and actuator attacks and exogenous stochastic disturbances

In this paper, we propose a novel adaptive control architecture for addressing security and safety in cyber-physical systems subject to exogenous disturbances. Specifically, we develop an adaptive controller for time-invariant, state-dependent adversarial sensor and actuator attacks in the face of stochastic exogenous disturbances. We show that the proposed controller guarantees uniform ultimate boundedness of the closed-loop dynamical system in a mean-square sense. We further discuss the practicality of the proposed approach and provide a numerical example involving the lateral directional dynamics of an aircraft to illustrate the efficacy of the proposed adaptive control architecture.
Biomechanical effects of environmental and engineered particles on human airway smooth muscle cells

The past decade has seen significant increases in combustion-generated ambient particles, which contain a nanosized fraction (less than 100 nm), and even greater increases have occurred in engineered nanoparticles (NPs) propelled by the booming nanotechnology industry. Although inhalation of these particulates has become a public health concern, human health effects and mechanisms of action for NPs are not well understood. Focusing on the human airway smooth muscle cell, here we show that the cellular mechanical function is altered by particulate exposure in a manner that is dependent upon particle material, size and dose. We used Alamar Blue assay to measure cell viability and optical magnetic twisting cytometry to measure cell stiffness and agonist-induced contractility. The eight particle species fell into four categories, based on their respective effect on cell viability and on mechanical function. Cell viability was impaired and cell contractility was decreased by (i) zinc oxide (40–100 nm and less than 44 μm) and copper(II) oxide (less than 50 nm); cell contractility was decreased by (ii) fluorescent polystyrene spheres (40 nm), increased by (iii) welding fumes and unchanged by (iv) diesel exhaust particles, titanium dioxide (25 nm) and copper(II) oxide (less than 5 μm), although in none of these cases was cell viability impaired. Treatment with hydrogen peroxide up to 500 μM did not alter viability or cell mechanics, suggesting that the particle effects are unlikely to be mediated by particle-generated reactive oxygen species. Our results highlight the susceptibility of cellular mechanical function to particulate exposures and suggest that direct exposure of the airway smooth muscle cells to particulates may initiate or aggravate respiratory diseases.
Self‐care burden, stress appraisal, and mood among persons receiving radiotherapy

This study was undertaken to describe the self-care burden (SCB) of persons receiving radiation as outpatients, to identify factors contributing to SCB, and to test a model of the effects of SCB, symptom distress, and appraisal of illness on mood. The subjects were 72 adults with cancer who had been in treatment an average of 4 weeks. Fatigue was reported to be the most distressing symptom. Among health deviation self-care tasks, coming for treatment was the most demanding, and self-treatment, such as administering medications, was the most difficult. Universal self-care activities most disrupted by treatment were social and recreational activities. Path analysis revealed that dependency was the primary predictor of health deviation SCB, while symptom distress was the best predictor of universal SCB. Universal SCB and family hardiness were the best predictors of appraisal scores. Symptom distress and somatic mood were highly correlated, suggesting collinearity between these factors. Four variables—appraisal, symptom distress, family hardiness, and health deviation SCB—explained 55% of the variance in affective mood scores. Theoretical and clinical implications are discussed.
EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures

UNLABELLED SiteHound uses Molecular Interaction Fields (MIFs) produced by EasyMIFs to identify protein structure regions that show a high propensity for interaction with ligands. The type of binding site identified depends on the probe atom used in the MIF calculation. The input to EasyMIFs is a PDB file of a protein structure; the output MIF serves as input to SiteHound, which in turn produces a list of putative binding sites. Extensive testing of SiteHound for the detection of binding sites for drug-like molecules and phosphorylated ligands has been carried out. AVAILABILITY EasyMIFs and SiteHound executables for Linux, Mac OS X, and MS Windows operating systems are freely available for download from http://sitehound.sanchezlab. org/download.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The mitochondrial outer membrane protein MDI promotes local protein synthesis and mtDNA replication

Early embryonic development features rapid nuclear DNA replication cycles, but lacks mtDNA replication. To meet the high‐energy demands of embryogenesis, mature oocytes are furnished with vast amounts of mitochondria and mtDNA. However, the cellular machinery driving massive mtDNA replication in ovaries remains unknown. Here, we describe a Drosophila AKAP protein, MDI that recruits a translation stimulator, La‐related protein (Larp), to the mitochondrial outer membrane in ovaries. The MDI‐Larp complex promotes the synthesis of a subset of nuclear‐encoded mitochondrial proteins by cytosolic ribosomes on the mitochondrial surface. MDI‐Larp's targets include mtDNA replication factors, mitochondrial ribosomal proteins, and electron‐transport chain subunits. Lack of MDI abolishes mtDNA replication in ovaries, which leads to mtDNA deficiency in mature eggs. Targeting Larp to the mitochondrial outer membrane independently of MDI restores local protein synthesis and rescues the phenotypes of mdi mutant flies. Our work suggests that a selective translational boost by the MDI‐Larp complex on the outer mitochondrial membrane might be essential for mtDNA replication and mitochondrial biogenesis during oogenesis.
The use of cell culture platforms to identify novel markers of bone and dentin resorption.

OBJECTIVES 1) To test the hypothesis that there would be proteomic differences in the composition of exosomes isolated from osteoclasts and odontoclasts and 2) to determine the clinical usefulness of these in vitro biomarker candidates. MATERIALS AND METHODS Mouse bone marrow-derived precursors were cultured on either dentin or bone slices and allowed to mature and begin resorption. Exosomes were isolated from cell culture media and characterized by mass spectrometry. The proteomic data obtained from this in vitro study were compared with the data obtained from human samples in our previous work. RESULTS There was a difference in the proteomic composition of exosomes from osteoclasts and odontoclasts. A total of 40 exosomal proteins were only present in osteoclast media, whereas six unique exosomal proteins were identified in odontoclast supernatants. Approximately 50% of exosomal proteins released by clastic cells in vitro can be found in oral fluids. CONCLUSION Our data suggest that the mineralized matrix type plays a role in the final phenotypic characteristics of mouse clastic cells. Many in vitro biomarker candidates of bone and dentin resorption can also be found in human oral fluids, thus indicating that this approach may be a viable alternative in biomarker discovery.
Ovarian cystectomy for a dermoid cyst with the new single-port robotic system

Abstract We report a 27 year-old patient with a dermoid cyst who underwent robotic single port transumbilical ovarian cystectomy. She was operated through a 2 cm long single midline umbilical incision using a new platform from Intuitive Surgical. The operative time was 45 minutes and the docking time was 15 minutes. Ovarian cystectomy using the da Vinci single-port system is feasible and effective. This new semi-rigid robotic surgery platform may increase access to the potential advantages of single-site surgery. Robotic systems designed specifically for single port approach have the potential of alleviating several of the limitations associated with traditional laparoscopic single-site surgery.