Miracle-dz/UniFAR-FTUs huggingface dataset:
Odorant Receptors Containing Conserved Amino Acid Sequences in Transmembrane Domain 7 Display Distinct Expression Patterns in Mammalian Tissues

Mammalian genomes are well established, and highly conserved regions within odorant receptors that are unique from other G-protein coupled receptors have been identified. Numerous functional studies have focused on specific conserved amino acids motifs; however, not all conserved motifs have been sufficiently characterized. Here, we identified a highly conserved 18 amino acid sequence motif within transmembrane domain seven (CAS-TM7) which was identified by aligning odorant receptor sequences. Next, we investigated the expression pattern and distribution of this conserved amino acid motif among a broad range of odorant receptors. To examine the localization of odorant receptor proteins, we used a sequence-specific peptide antibody against CAS-TM7 which is specific to odorant receptors across species. The specificity of this peptide antibody in recognizing odorant receptors has been confirmed in a heterologous in vitro system and a rat-based in vivo system. The CAS-TM7 odorant receptors localized with distinct patterns at each region of the olfactory epithelium; septum, endoturbinate and ectoturbinate. To our great interests, we found that the CAS-TM7 odorant receptors are primarily localized to the dorsal region of the olfactory bulb, coinciding with olfactory epithelium-based patterns. Also, these odorant receptors were ectopically expressed in the various non-olfactory tissues in an evolutionary constrained manner between human and rats. This study has characterized the expression patterns of odorant receptors containing particular amino acid motif in transmembrane domain 7, and which led to an intriguing possibility that the conserved motif of odorant receptors can play critical roles in other physiological functions as well as olfaction.
FabCode: visual programming environment for digital fabrication

In this paper, we introduce FabCode, a visual programming environment using which one can create designs that can be manufactured using digital fabrication techniques like 3D printing and laser cutting. This project is primarily about making accessible and enhancing the kinds of "thinking" that the computational medium is capable of supporting and spreading. FabCode is situated in the context of design and engineering of objects, and is based on the premise that programming 3D models for personal fabrication would enable practice of computational thinking for the same. Children will learn as they work on personally meaningful projectsbuilding, describing, printing and playing with things, and debugging and discussing their processes and outcomes. It will be a childcentered, constructionist tool for FabLabs.
In house industrial training for mechanical engineering students: A multidisciplinary approach

The integrated knowledge in the application of mechanical engineering, microprocessor and electronic sensor technologies is becoming the basic skill of a modern engineer in machinery based processes. To meet this objective, we have developed a cross-disciplinary industrial training to teach essential hard technical and soft project skills to the mechanical engineering students in mid-curriculum. Ten groups of students were selected to participate in a 150 hour program. The students were required to design and build a robot with ability to follow tracks and pick/place target blocks in specific locations. The students were trained to integrate the knowledge of computer aid design, electronics, sensor theories and motor technology to fabricate a workable robot as a major outcome of this course. On completion of the project, students competed for top robot honors by demonstrating their robots' movements and performance in pick/place to a panel of judges.
Design of a blocking-resistant anonymity system

Internet censorship is on the rise as websites around the world are increasingly blocked by government-level ﬁrewalls. Although popular anonymizing networks like Tor were originally designed to keep attackers from tracing people’s activities, many people are also using them to evade local censorship. But if the censor simply denies access to the Tor network itself, blocked users can no longer beneﬁt from the security Tor offers. Here we describe a design that builds upon the current Tor network to provide an anonymizing network that resists blocking by government-level attackers
Conserved early expression patterns of micromere specification genes in two echinoid species belonging to the orders clypeasteroida and echinoida

The micromere gene regulatory network (GRN) has been extensively examined using sea urchins belonging to the order Echinoida. To examine whether the network of Echinoida species is conserved in Scaphechinus mirabilis, an irregular echinoid of the order Clypeasteroida, the genes micro1, hesC, alx1, ets1, and delta were isolated from S. mirabilis and their expression patterns were compared with those from Hemicentrotus pulcherrimus, a species belonging to the order Echinoida. Data from this study suggest that the early GRN architecture had been largely established in a common ancestor of these two species. On the other hand, we found vegetal shifts in expression domains of some GRN members in H. pulcherrimus embryos compared to S. mirabilis embryos. Developmental Dynamics 239:3391–3403, 2010. © 2010 Wiley‐Liss, Inc.
Developmental Sequence of Chloride Cells in the Body Skin and Gills of Japanese Flounder (Paralichthys olivaceus) Larvae

Abstract The developmental sequence of chloride cells was examined in both the body skin and gills of Japanese flounder (Paralichthys olivaceus) larvae by whole-mount immunocytochemistry using an antiserum specific for Na+,K+-ATPase. In premetamorphic larvae at 0 and 4 days after hatching (days 0 and 4), immunoreactive chloride cells were distributed only in the yolk-sac membrane and body skin. Premetamorphic larvae at days 8–18 possessed both cutaneous and branchial chloride cells. Large chloride cells in the skin of premetamorphic larvae often formed multicellular complexes, suggestive of their ion-secreting function. Cutaneous chloride cells decreased in size and density at the beginning of metamorphosis (days 21 and 24), and disappeared at the metamorphic climax (days 28 and 33). In contrast, branchial chloride cells first appeared at day 8, and increased during metamorphosis. These results indicate that the site for ion secretion in seawater may shift from cutaneous to branchial chloride cells during metamorphosis. The appearance of branchial chloride cells before the differentiation of gill lamellae suggests that the primary function of the gills during the early development is ion regulation rather than gas exchanges.
Reconstitution of Mdm2-Dependent Post-Translational Modifications of p53 in Yeast

p53 mediates cell cycle arrest or apoptosis in response to DNA damage. Its activity is subject to a tight regulation involving a multitude of post-translational modifications. The plethora of functional protein interactions of p53 at present precludes a clear understanding of regulatory principles in the p53 signaling network. To circumvent this complexity, we studied here the minimal requirements for functionally relevant p53 post-translational modifications by expressing human p53 together with its best characterized modifier Mdm2 in budding yeast. We find that expression of the human p53-Mdm2 module in yeast is sufficient to faithfully recapitulate key aspects of p53 regulation in higher eukaryotes, such as Mdm2-dependent targeting of p53 for degradation, sumoylation at lysine 386 and further regulation of this process by p14(ARF). Interestingly, sumoylation is necessary for the recruitment of p53-Mdm2 complexes to yeast nuclear bodies morphologically akin to human PML bodies. These results suggest a novel role for Mdm2 as well as for p53 sumoylation in the recruitment of p53 to nuclear bodies. The reductionist yeast model that was established and validated in this study will now allow to incrementally study simplified parts of the intricate p53 network, thus helping elucidate the core mechanisms of p53 regulation as well as test novel strategies to counteract p53 malfunctions.
Resilience and Sustainable Development: Building Adaptive Capacity in a World of Transformations

Abstract Emerging recognition of two fundamental errors under-pinning past polices for natural resource issues heralds awareness of the need for a worldwide fundamental change in thinking and in practice of environmental management. The first error has been an implicit assumption that ecosystem responses to human use are linear, predictable and controllable. The second has been an assumption that human and natural systems can be treated independently. However, evidence that has been accumulating in diverse regions all over the world suggests that natural and social systems behave in nonlinear ways, exhibit marked thresholds in their dynamics, and that social-ecological systems act as strongly coupled, complex and evolving integrated systems. This article is a summary of a report prepared on behalf of the Environmental Advisory Council to the Swedish Government, as input to the process of the World Summit on Sustainable Development (WSSD) in Johannesburg, South Africa in 26 August 4 September 2002. We use the concept of resilience—the capacity to buffer change, learn and develop—as a framework for understanding how to sustain and enhance adaptive capacity in a complex world of rapid transformations. Two useful tools for resilience-building in social-ecological systems are structured scenarios and active adaptive management. These tools require and facilitate a social context with flexible and open institutions and multi-level governance systems that allow for learning and increase adaptive capacity without foreclosing future development options.
The impact of multicast layering on network fairness

Many definitions of fairness for multicast networks assume that sessions are single-rate, requiring that each multicast session transmits data to all of its receivers at the same rate. These definitions do not account for multi-rate approaches, such as layering, that permit receiving rates within a session to be chosen independently. We identify four desirable fairness properties for multicast networks, derived from properties that hold within the max-min fair allocations of unicast networks. We extend the definition of multicast max-min fairness to networks that contain multi-rate sessions, and show that all four fairness properties hold in a multi-rate max-min fair allocation, but need not hold in a single-rate max-min fair allocation. We then show that multi-rate max-min fair rate allocations can be achieved via intra-session coordinated joins and leaves of multicast groups. However, in the absence of coordination, the resulting max-min fair rate allocation uses link bandwidth inefficiently, and does not exhibit some of the desirable fairness properties. We evaluate this inefficiency for several layered multi-rate congestion control schemes, and find that, in a protocol where the sender coordinates joins, this inefficiency has minimal impact on desirable fairness properties. Our results indicate that sender-coordinated layered protocols show promise for achieving desirable fairness properties for allocations in large-scale multicast networks.
Technology and mold design for production of hollow carbon composite parts

Sona Rusnakova1, Alexander Capka1, Ladislav Fojtl1, Milan Zaludek1, Vladimir Rusnak2 1Department of Production Engineering, Faculty of Technology, Tomas Bata University in Zlín. Nad Stranemi 4511, 760 05 Zlín. Czech Republic. E-mail: rusnakova@ft.utb. cz, capka@ft.utb. cz, fojtl@ft.utb. cz, zaludek@ft.utb. cz 2Faculty of Metallurgy and Materials Engineering, VŠB-Technical University of Ostrava, 17. listopadu 15, 708 33 Ostrava-Poruba, Czech Republic. E-mail: vladimir.rusnak@form-composite.com
Carbon cycle responses of semi‐arid ecosystems to positive asymmetry in rainfall

Recent evidence shows that warm semi‐arid ecosystems are playing a disproportionate role in the interannual variability and greening trend of the global carbon cycle given their mean lower productivity when compared with other biomes (Ahlström et al. 2015 Science, 348, 895). Using multiple observations (land‐atmosphere fluxes, biomass, streamflow and remotely sensed vegetation cover) and two state‐of‐the‐art biospheric models, we show that climate variability and extremes lead to positive or negative responses in the biosphere, depending on vegetation type. We find Australia to be a global hot spot for variability, with semi‐arid ecosystems in that country exhibiting increased carbon uptake due to both asymmetry in the interannual distribution of rainfall (extrinsic forcing), and asymmetry in the response of gross primary production (GPP) to rainfall change (intrinsic response). The latter is attributable to the pulse‐response behaviour of the drought‐adapted biota of these systems, a response that is estimated to be as much as half of that from the CO2 fertilization effect during 1990–2013. Mesic ecosystems, lacking drought‐adapted species, did not show an intrinsic asymmetric response. Our findings suggest that a future more variable climate will induce large but contrasting ecosystem responses, differing among biomes globally, independent of changes in mean precipitation alone. The most significant changes are occurring in the extensive arid and semi‐arid regions, and we suggest that the reported increased carbon uptake in response to asymmetric responses might be contributing to the observed greening trends there.
How Many Colors to Identify Regulatory T Cells in Humans

+ T cells can also express these markers. The number of parameters that can be scored simultaneously by multicolor flow cytometry has increased dramatically, through the development of new fluorescent dyes and tandems, providing a variety of excitation and emission spectra. Although a more polychromatic immunophenotyping generally corresponds to a more detailed Treg definition, most additional markers that are currently proposed for Treg identification are often expressed by activated conventional CD4 + T cells. Moreover, these analyses are both expensive and time consuming. Exploring typical Treg functions, i. e. , anergy and suppressive capability with the intent to enumerate Tregs is difficult because of factors like Treg isolation, culture conditions, and the variable contamination of non-Treg populations in the assays. Functional assays are also cumbersome to set up and time consuming. We describe a simple flow cytometric assay that is based on the notion that Foxp3 and interleukin-2 expression is essentially mutually exclusive in Tregs.
Direct voltage control strategies for variable-speed permanent magnet synchronous generator system

Two direct voltage control (DVC) strategies for the permanent magnet synchronous generator (PMSG) system are proposed and comparatively studied in this paper. The strategies are especially utilized in variable-speed applications, in order to stabilize the PWM rectifier output voltage on the dc bus. One of the DVC strategies uses hysteresis control (HC) of the dc bus voltage to determine the PWM signals, while the other uses PI control of the dc bus voltage together with the space vector modulation (SVM) to determine the PWM signals. The former strategy exhibits simplicity in both theory and implementation, whilst the latter has better performance on the output dc voltage. Both strategies are analyzed with MATLAB/Simulink and verified by experiments with a laboratory test bench.
Automatically Tuned Collective Communications

The performance of the MPI's collective communications is critical in most MPI-based applications. A general algorithm for a given collective communication operation may not give good performance on all systems due to the differences in architectures, network parameters and the storage capacity of the underlying MPI implementation. In this paper, we discuss an approach in which the collective communications are tuned for a given system by conducting a series of experiments on the system. We also discuss a dynamic topology method that uses the tuned static topology shape, but re-orders the logical addresses to compensate for changing run time variations. A series of experiments were conducted comparing our tuned collective communication operations to various native vendor MPI implementations. The use of the tuned collective communications resulted in about 30%-650% improvement in performance over the native MPI implelementations.
Impact of wheelchair acquisition on social participation

Purpose. Efficient mobility could be a prerequisite to carrying out many daily activities and social roles (social participation). The aim of this study was to assess the impact of wheelchair acquisition on social participation. Methods. Single group pre/post design where the intervention was the acquisition of a wheelchair paid for by the provincial government. Data were collected retrospectively from the participants' medical files. Individuals were excluded if they received an assistive device other than a wheelchair or contacted the centre only for wheelchair repairs. Social participation was measured using the Reintegration to Normal Living Index (RNLI) questionnaire. Results. The sample (n = 42) had a mean age of 64.2 ± 18.5 years, and 50% of them (n = 21) did not have a wheelchair before the intervention. The total RNLI scores pre- (46.9/100 ± 24.7) and post-acquisition (29.7/100 ± 18.5) showed a significant improvement in participation (p < 0.001). No difference was found between those who had their first wheelchair (n = 21) compared with replacement. Single-item analysis of the RNLI showed a significant difference for 5 of the 11 items. Age and diagnosis were significantly correlated (p < 0.05) with some of the items. Conclusion. Social participation improved significantly following wheelchair acquisition although confounding variables may have contributed to this improvement.
Creating and Using Domain-specific Ontologies for Terminological Applications

Huge volumes of scientific databases and text collections are constantly becoming available, but their usefulness is at present hampered by their lack of uniformity and structure. There is therefore an overwhelming need for tools to facilitate the processing and discovery of technical terminology, in order to make processing of these resources more efficient. Both NLP and statistical techniques can provide such tools, but they would benefit greatly from the availability of suitable lexical resources. While information resources do exist in some areas of terminology, these are not designed for linguistic use. In this paper, we investigate how one such resource, the UMLS, is used for terminological acquisition in the TRUCKS system, and how other domain-specific resources might be adapted or created for terminological applications.
Bacterial Identification Using 16S rDNA Gene Sequencing and Antibiogram Analysis on Biofield Treated Pseudomonas fluorescens

Biofield therapies have been reported to improve the quality of life as compared to other energy medicine. The aim of the study was to evaluate the impact of Mr. Trivedi’s biofield energy treatment on Pseudomonas fluorescens (P. fluorescens) for antimicrobial sensitivity, minimum inhibitory concentration (MIC), biochemical reactions, and biotype number. P. fluorescens cells were procured from MicroBioLogics Inc., USA in sealed packs bearing the American Type Culture Collection (ATCC 49838) number and divided in control and treated group. The effect was evaluated on day 10, and 159 after biofield treatment in lyophilized state. Further study was performed on day 5, 10, and 15 after retreatment on day 159 in revived state as per study design. All experimental parameters were studied using automated MicroScan Walk-Away® system. The 16S rDNA sequencing was carried out to correlate the phylogenetic relationship of P. fluorescens with other bacterial species after treatment. The results showed improved sensitivities and decreased MIC value of aztreonam, cefepime, moxifloxacin, and tetracycline in revived and lyophilized treated sample with respect to the control. Arginine, cetrimide, kanamycin, and glucose showed altered biochemical reactions after biofield treatment with respect to control. Biotype numbers were altered along with species in lyophilized as well as in revived group. Based on nucleotides homology and phylogenetic analysis using 16S rDNA gene sequencing, treated sample was detected to be Pseudomonas entomophila (GenBank Accession Number: AY907566) with 96% identity of gene sequencing data, which was nearest homolog species to P. fluorescens (Accession No. EF672049). These findings suggest that Mr. Trivedi’s unique biofield treatment has the capability to alter changes in pathogenic P. fluorescens even in the lyophilized storage condition and can be used to modify the sensitivity of microbes against antimicrobials.
The effect of curcumin (turmeric) on Alzheimer's disease: An overview

This paper discusses the effects of curcumin on patients with Alzheimer's disease (AD). Curcumin (Turmeric), an ancient Indian herb used in curry powder, has been extensively studied in modern medicine and Indian systems of medicine for the treatment of various medical conditions, including cystic fibrosis, haemorrhoids, gastric ulcer, colon cancer, breast cancer, atherosclerosis, liver diseases and arthritis. It has been used in various types of treatments for dementia and traumatic brain injury. Curcumin also has a potential role in the prevention and treatment of AD. Curcumin as an antioxidant, anti-inflammatory and lipophilic action improves the cognitive functions in patients with AD. A growing body of evidence indicates that oxidative stress, free radicals, beta amyloid, cerebral deregulation caused by bio-metal toxicity and abnormal inflammatory reactions contribute to the key event in Alzheimer's disease pathology. Due to various effects of curcumin, such as decreased Beta-amyloid plaques, delayed degradation of neurons, metal-chelation, anti-inflammatory, antioxidant and decreased microglia formation, the overall memory in patients with AD has improved. This paper reviews the various mechanisms of actions of curcumin in AD and pathology.
High Abundances of Potentially Active Ammonia-Oxidizing Bacteria and Archaea in Oligotrophic, High-Altitude Lakes of the Sierra Nevada, California, USA

Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems—and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 9 high-altitude lakes (2289–3160 m) in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA) genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate) were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r2 = 0.32, p<0.1), whereas AOA abundance was inversely correlated with lake elevation (r2 = 0.43, p<0.05). We also measured low rates of ammonia oxidation—indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.