Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucan, Water Dikinase Activity Stimulates Breakdown of Starch Granules by Plastidial β-Amylases1[W][OA]

Glucan phosphorylating enzymes are required for normal mobilization of starch in leaves of Arabidopsis (Arabidopsis thaliana) and potato (Solanum tuberosum), but mechanisms underlying this dependency are unknown. Using two different activity assays, we aimed to identify starch degrading enzymes from Arabidopsis, whose activity is affected by glucan phosphorylation. Breakdown of granular starch by a protein fraction purified from leaf extracts increased approximately 2-fold if the granules were simultaneously phosphorylated by recombinant potato glucan, water dikinase (GWD). Using matrix-assisted laser-desorption ionization mass spectrometry several putative starch-related enzymes were identified in this fraction, among them β-AMYLASE1 (BAM1; At3g23920) and ISOAMYLASE3 (ISA3; At4g09020). Experiments using purified recombinant enzymes showed that BAM1 activity with granules similarly increased under conditions of simultaneous starch phosphorylation. Purified recombinant potato ISA3 (StISA3) did not attack the granular starch significantly with or without glucan phosphorylation. However, starch breakdown by a mixture of BAM1 and StISA3 was 2 times higher than that by BAM1 alone and was further enhanced in the presence of GWD and ATP. Similar to BAM1, maltose release from granular starch by purified recombinant BAM3 (At4g17090), another plastid-localized β-amylase isoform, increased 2- to 3-fold if the granules were simultaneously phosphorylated by GWD. BAM activity in turn strongly stimulated the GWD-catalyzed phosphorylation. The interdependence between the activities of GWD and BAMs offers an explanation for the severe starch excess phenotype of GWD-deficient mutants.
Adaptive fuzzy logic for focusing in optical disk player

For the nonlinear behaviors of the actuator and servo system of the optical disk player, a fuzzy control is introduced. Focus servo controls the laser beam to focus on the playing surface of the disc by vertical movement of the objective lens. The change of the distance between the objective lens and the disc must be within the allowable focus error to stay in focus. This must be maintained even with a slightly warped or uneven disc and in a portable player. This paper will observe on how the focusing is controlled in an optical disk player and will evaluate algorithm based on the model using Adaptive Fuzzy Logic.
Overview and recent developments in the medical management of paediatric uveitis

Introduction: Although rarer than its adult counterpart, non-infectious uveitis remains a significant cause of ocular morbidity in children. Owing to the chronicity of the disorder and when refractory to first-line treatment, namely corticosteroids, systemic immunosuppressive treatment may be required to control the disease. Areas covered: Following a literature search using the keywords ‘paediatric uveitis’, ‘juvenile idiopathic arthritis-associated uveitis’, ‘immunosuppression’ and ‘treatment’, we reviewed the range and effectiveness of treatments employed in the management of non-infectious, paediatric uveitis. Expert opinion: Corticosteroids (topical, periocular, intraocular or systemic) remain the initial drug of choice in ameliorating the signs and symptoms of non-infectious paediatric uveitis. Failure to control the disease and/or failure to reduce the oral dose of prednisolone at least 0.15 mg/kg within 4 weeks often requires additional immunosuppressant therapy. Methotrexate and azathioprine have shown to be effective in the management of juvenile idiopathic arthritis (JIA)-associated uveitis with the former considered the first-line corticosteroid-sparing agent. Biologic therapies are increasingly used earlier in the disease with investigators in the UK currently recruiting patients for the SYCAMORE trial evaluating the efficacy of methotrexate and adalimumab vs methotrexate alone for the treatment for JIA-associated uveitis. Until further randomised controlled trials are conducted, the use of other biologic agents should only be used with an appreciation that there are potentially unknown side-effects and that there is not a full knowledge of their efficacy.
Design of heterogeneous embedded systems using DFCharts model of computation

Dataflow process networks have been successfully used for modeling signal processing systems which are data-dominated. In this family of models, the most popular one is synchronous dataflow (SDF). On the other hand, hierarchical concurrent finite state machines (HCFSM) have been successfully employed for control-dominated systems. Most complex embedded systems are heterogeneous, consisting of both control-dominated and data-dominated parts. In this paper, we introduce a new model of computation, called DFCharts, which targets heterogeneous embedded systems. It combines the HCFSM (with Argos semantics) and SDF models. It has a formal, operational semantics based on Boolean automata with variables.
Personalizing XML Text Search in PimenT

A growing number of text-rich XML repositories are being made available. As a result, more efforts have been deployed to provide XML full-text search that combines querying structure with complex conditions on text ranging from simple keyword search to sophisticated proximity search composed with stemming and thesaurus. However, one of the key challenges in full-text search is to match users' expectations and determine the most relevant answers to a full-text query. In this context, we propose query personalization as a way to take user profiles into account in order to customize query answers based on individual users' needs.We present PIMENT, a system that enables query personalization by query rewriting and answer ranking. PIMENT is composed of a profile repository that stores user profiles, a query customizer that rewrites user queries based on user profiles and, a ranking module to rank query answers.
Modification of hippocampal circuitry by adult neurogenesis

The adult hippocampus is one of the primary neural structures involved in memory formation. In addition to synapse‐specific modifications thought to encode information at the subcellular level, changes in the intrahippocampal neuro‐populational activity and dynamics at the circuit‐level may contribute substantively to the functional capacity of this region. Within the hippocampus, the dentate gyrus has the potential to make a preferential contribution to neural circuit modification owing to the continuous addition of new granule cell population. The integration of newborn neurons into pre‐existing circuitry is hypothesized to deliver a unique processing capacity, as opposed to merely replacing dying granule cells. Recent studies have begun to assess the impact of hippocampal neurogenesis by examining the extent to which adult‐born neurons participate in hippocampal networks, including when newborn neurons become engaged in ongoing network activity and how they modulate circuit dynamics via their unique intrinsic physiological properties. Understanding the contributions of adult neurogenesis to hippocampal function will provide new insight into the fundamental aspects of brain plasticity, which can be used to guide therapeutic interventions to replaceneural populations damaged by disease or injury. © 2012 Wiley Periodicals, Inc. Develop Neurobiol 72: 1032–1043, 2012
In Vitro Characterization of the Anti-PD-1 Antibody Nivolumab, BMS-936558, and In Vivo Toxicology in Non-Human Primates

Wang and colleagues describe the development and comprehensive preclinical characterization of nivolumab, a fully human IgG4 (S228P) anti-PD-1 receptor blocking mAb, the antitumor activity and safety profile of which has been demonstrated in human clinical trials in various solid tumors. The programmed death-1 (PD-1) receptor serves as an immunologic checkpoint, limiting bystander tissue damage and preventing the development of autoimmunity during inflammatory responses. PD-1 is expressed by activated T cells and downmodulates T-cell effector functions upon binding to its ligands, PD-L1 and PD-L2, on antigen-presenting cells. In patients with cancer, the expression of PD-1 on tumor-infiltrating lymphocytes and its interaction with the ligands on tumor and immune cells in the tumor microenvironment undermine antitumor immunity and support its rationale for PD-1 blockade in cancer immunotherapy. This report details the development and characterization of nivolumab, a fully human IgG4 (S228P) anti-PD-1 receptor-blocking monoclonal antibody. Nivolumab binds to PD-1 with high affinity and specificity, and effectively inhibits the interaction between PD-1 and its ligands. In vitro assays demonstrated the ability of nivolumab to potently enhance T-cell responses and cytokine production in the mixed lymphocyte reaction and superantigen or cytomegalovirus stimulation assays. No in vitro antibody-dependent cell-mediated or complement-dependent cytotoxicity was observed with the use of nivolumab and activated T cells as targets. Nivolumab treatment did not induce adverse immune-related events when given to cynomolgus macaques at high concentrations, independent of circulating anti-nivolumab antibodies where observed. These data provide a comprehensive preclinical characterization of nivolumab, for which antitumor activity and safety have been demonstrated in human clinical trials in various solid tumors. Cancer Immunol Res; 2(9); 846–56. ©2014 AACR.
What's new in primary bone tumors.

Malignant tumors of the musculoskeletal system can be aggressive, with a high chance of systemic spread. Much of the basic science research regarding sarcoma focuses on molecular pathways and the identification of targets of systemic therapy. Chemotherapy continues to evolve, with targeted agents playing a larger role in the management of tumors. Radiation therapy also continues to evolve, with high-precision radiation techniques being used in many centers throughout the world. Researchers are focusing on identifying the potential benefit of these techniques with regard to local control and lessening of wound complications. The purpose of this article is to present some of the advances in the treatment of malignant musculoskeletal tumors that were reported from August 2013 through October 2014. Chondrosarcoma remains principally a surgically treated disease; chemotherapy and radiation have not proven to be effective in local or distant control. Many researchers are trying to understand the basis of chondrosarcoma, in an effort to identify systemic targets. The role of the transcription factor ETV5 in the development of chondrosarcoma has been elucidated through a study by Mak et al., who found that miR-145 (microRNA-145) was expressed at an abnormally low level, leading to increased expression of SOX-91. SOX-9 induces the expression of ETV5 and subsequently MMP-2 (matrix metalloproteinase-2), which has been linked to the pathophysiology of chondrosarcoma. Studies have shown that miR-145 is an important inhibitor of cell growth, and its underexpression is thought to play a role in cancer development2,3. Osteoclasts have been shown to play an important role in the pathophysiology of cancers including chondrosarcoma. A recent study by Otero et al. demonstrated that osteoclasts affect the ability of chondrosarcoma to invade bone4. This invasion was partially halted by the administration of zoledronic acid, which inhibits osteoclast function. No invasion …
Disseminated Fusariosis Occurring in Two Patients Despite Posaconazole Prophylaxis

ABSTRACT Posaconazole is widely used for prophylaxis against invasive fungal infections in patients undergoing myeloablative therapy. Disseminated fusariosis is a serious invasive mold infection in such patients. Preclinical and clinical studies indicate activity of posaconazole against Fusarium. We describe two cases of disseminated fusariosis that occurred despite posaconazole prophylaxis.
Chip Formation Characteristics in High-Speed Machining of Hardened AISI1045 Steel

Analyzing mechanism of the chip formation is a significant way to understand the metal cutting process better. The characterization of serrated chip formation in high speed machining of hardened AISI1045 steel is investigated with the aid of optical microscopy and micro-hardness measurement in this paper. The chip morphology evolving from continuous one to serrated one with the cutting speed increasing from 100-1500m/min is observed. Compared with the continuous chip pattern, serrated chip has its particular characterization parameters. The characteristics of serration degree and the segmentation frequency of the serrated chip are presented. The micro-hardness at the adiabatic shear band of serrated chip is then measured. The results show that the serration degree and segmentation frequency of serrated chip have a tendency of enhancement with the cutting speed increasing. The micro-hardness along the adiabatic shear band increases with the cutting speed increasing due to severe strain hardening. With a critical speed at about 100-200m/min, micro-hardness decreases from the tool-chip interface to the free surface of the chip.
Role of Interaction and Nucleoside Diphosphate Kinase B in Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator Function by cAMP-Dependent Protein Kinase A

Cystic fibrosis results from mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), a cAMP-dependent protein kinase A (PKA) and ATP-regulated chloride channel. Here, we demonstrate that nucleoside diphosphate kinase B (NDPK-B, NM23-H2) forms a functional complex with CFTR. In airway epithelia forskolin/IBMX significantly increases NDPK-B co-localisation with CFTR whereas PKA inhibitors attenuate complex formation. Furthermore, an NDPK-B derived peptide (but not its NDPK-A equivalent) disrupts the NDPK-B/CFTR complex in vitro (19-mers comprising amino acids 36-54 from NDPK-B or NDPK-A). Overlay (Far-Western) and Surface Plasmon Resonance (SPR) analysis both demonstrate that NDPK-B binds CFTR within its first nucleotide binding domain (NBD1, CFTR amino acids 351-727). Analysis of chloride currents reflective of CFTR or outwardly rectifying chloride channels (ORCC, DIDS-sensitive) showed that the 19-mer NDPK-B peptide (but not its NDPK-A equivalent) reduced both chloride conductances. Additionally, the NDPK-B (but not NDPK-A) peptide also attenuated acetylcholine-induced intestinal short circuit currents. In silico analysis of the NBD1/NDPK-B complex reveals an extended interaction surface between the two proteins. This binding zone is also target of the 19-mer NDPK-B peptide, thus confirming its capability to disrupt NDPK-B/CFTR complex. We propose that NDPK-B forms part of the complex that controls chloride currents in epithelia.
Partition Sort Revisited: Reconfirming the Robustness in Average Case and much more!

In our previous work there was some indication that Partition Sort could be having a more robust average case O(nlogn) complexity than the popular Quick Sort. In our first study in this paper, we reconfirm this through computer experiments for inputs from Cauchy distribution for which expectation theoretically does not exist. Additionally, the algorithm is found to be sensitive to parameters of the input probability distribution demanding further investigation on parameterized complexity. The results on this algorithm for Binomial inputs in our second study are very encouraging in that direction.
Wired Smart Home: Energy metering, security, and emergency issues

This paper discusses the specific area of M2M applications - Wired Smart Home. It contains the overview of requirements to Wired Smart Home in the scope of energy metering, security, and emergency communications. We consider ETSI activities on M2M standardization, Open Metering System specification, and Emergency Communications. In the field of software issues, we offer a newer web tool - Web Intents as a modern enhancement of M2M middleware. Also, the experience in Wired Smart Home implementation is given.
The Early Revascularization of Membranous Bone

The experimental finding that membranous onlay bone grafts maintain volume and viability to a greater extent than do endochondral grafts may be related to the more rapid vascularization of membranous bone. Microangiographic techniques were used to study the rates of vascularization of membranous and endochondral bone grafts in adult white New Zealand rabbits at 1, 3, 7, 14, and 21 days after bone grafting. Vascularization patterns were quantified microscopically using a modified point-counting technique. At 3 days, membranous bone grafts demonstrated vessel ingrowth from both soft tissue and host bone. Little ingrowth was seen in endochondral grafts. By day 7, 2.5 vessels per square were indentified entering membranous grafts, while an average of 0.6 vessels per square were counted for endochondral bone grafts. At day 14, there was an average of greater than 20 vessels per square for membranous grafts versus 1.8 for their endochondral counterparts. At 21 days, the endochondral grafts demonstrated persistent avascular central areas not seen in membranous grafts. Membranous onlay bone grafts in the rabbit are more rapidly vascularized than endochondral grafts. This factor may affect the greater volume maintenance seen in experimental membranous grafts.
Robust Regulation Adaptation in Multi-Agent Systems

Adaptive organisation-centred multi-agent systems can dynamically modify their organisational components to better accomplish their goals. Our research line proposes an abstract distributed architecture (2-LAMA) to endow an organisation with adaptation capabilities. This article focuses on regulation-adaptation based on a machine learning approach, in which adaptation is learned by applying a tailored case-based reasoning method. We evaluate the robustness of the system when it is populated by non compliant agents. The evaluation is performed in a peer-to-peer sharing network scenario. Results show that our proposal significantly improves system performance and can cope with regulation violators without incorporating any specific regulation-compliance enforcement mechanisms.
The Role of Geographical Slant in Virtual Environment Navigation

We have investigated the role of geographical slant in simple navigation and spatial memory tasks, using a computer graphics town called \Hexatown" (Gillner & Mallot 1998). This environment was a hexagonal grid of streets with landmarks placed in each angle between two streets. The whole environment could be slanted by an angle of 4 . Three slant conditions were used: at: no slant; slanted NW: slant direction 30 Northwest with respect to some arbitrarily chosen \North"; slanted NE: slant direction 30 Northeast. Twelve subjects participated in each condition. Images were projected on a 180 half cylindrical projection-screen. Subjects could interact with the virtual environment by pedaling with force-feedback on a bicycle simulator (translation) or by hitting buttons (discrete rotations in 60 steps). Subjects explored the environment by searching 15 routes to various goals presented to them as pictures. After learning, spatial memory was accessed by three tasks, using an across subjects design: (i) pointing from various positions to the learned goals (19 pointings per subject); (ii) choosing the more elevated of two landmarks from memory in a forced choice paradigm; (iii) drawing a sketch map of the environment. The number of navigation errors (wrong motion decisions with respect to the goal) was strongly reduced (p < 0:001) in the slanted conditions. Furthermore, subjects were able to point to currently invisible targets in virtual environments. Adding a geographical slant improves this performance. Signi cant di erences (circular F-test) of the mean angular deviations between the \ at" and the two \slanted" conditions were found. There was also a signi cant di erence between the two slanted conditions (p < 0:01). We conclude that geographical slant plays a role either in the construction of a spatial memory, or in its readout, or in both.
Apheresis research–more abstracts should be published as full manuscripts to provide more evidence for clinical practice guidelines

High‐quality evidence to support clinical practice is lacking in apheresis medicine compared to other therapeutic modalities. A potential source of evidence comes from the abstracts submitted to the Annual Meetings of the American Society for Apheresis (ASFA). Therefore, the goal of this study is to determine the proportion of abstracts from the 2005 to 2012 ASFA Annual Meetings that subsequently became PubMed‐indexed publications. Furthermore, we sought to determine the factor(s) that were associated with the likelihood of abstracts to be published as full manuscripts. During the 8‐year study period, 684 abstracts were available for analysis (median: 82/year, range: 64–118). Most abstracts (74%) were from US institutions, and 67% of first authors were affiliated with academic centers. There were more abstracts (64%) on therapeutic versus donor apheresis (20%) and cellular therapy (16%). Overall, 16% of the abstracts have been published in PubMed‐indexed journals, with a median time of 17 months from the ASFA Annual Meeting (range: 1–96 months). Abstracts whose first authors were affiliated with academic institutions were 3.14 times more likely to have been published than abstracts with ones affiliated with an apheresis organization and/or a community hospital. However, neither the first author's location nor the type of apheresis procedure significantly affected the publication rate after adjusting for other covariates. In conclusion, the rate of publication is low and authors should be encouraged to follow their presentations at the meeting with peer‐reviewed manuscripts. This change is essential to provide more published evidence for future apheresis practice guidelines. J. Clin. Apheresis 31:353–358, 2016. © 2015 Wiley Periodicals, Inc.
Novel Dynamic Bioreactor and PEGDA Hydrogel Scaffolds forInvestigation and Engineering of Aortic Valve Tissues

Tissue engineered heart valves (TEHV) will allow clinicians to have a highquality prosthesis for patients that could eliminate many drawbacks of currently available treatments. Although there is great promise for TEHV, the field is still in its infancy; proper scaffolding materials and dynamic culture regimens that produce TEHV suitable for implantation in the aortic valve (A V) position have not yet been identified. Novel systems to apply biomechanical stimuli to developing engineered tissues and materials development and characterization will be necessary to progress towards an aortic TEHV. This thesis work aimed to address these issues in a parallel manner. The thesis begins by describing the design and physical characterization of a bioreactor system capable of both AV organ culture and biomechanical conditioning of engineered A V tissues. This work demonstrated that the newly developed bioreactor system allows A V to be cultured dynamically in a simple system that scales to accommodate varying sample sizes. Evaluation of this bioreactor system showed that dynamic culture of A V maintained normal tissue phenotype for durations of up to seven days, which is to-date the longest ex vivo maintenance of normal A V tissue phenotype in a dynamic bioreactor system. This thesis work also investigated the suitability ofpoly(ethylene glycol) diacrylate hydro gels to be used as a TEHV scaffold. These studies showed that flexural stiffness of the resulting scaffolds could be modulated by varying the formulation parameters chosen, and that valvular interstitial cells embedded and cultured within these gels (also containing incorporated bioactive moieties) maintained expression of several characteristic phenotypic markers. The thesis also describes studies in which advanced