Miracle-dz/UniFAR-FTUs huggingface dataset:
Endoplasmic Reticulum Chaperones and Their Roles in the Immunogenicity of Cancer Vaccines

The endoplasmic reticulum (ER) is a major site of passage for proteins en route to other organelles, to the cell surface, and to the extracellular space. It is also the transport route for peptides generated in the cytosol by the proteasome into the ER for loading onto major histocompatibility complex class I (MHC I) molecules for eventual antigen presentation at the cell surface. Chaperones within the ER are critical for many of these processes; however, outside the ER certain of those chaperones may play important and direct roles in immune responses. In some cases, particular ER chaperones have been utilized as vaccines against tumors or infectious disease pathogens when purified from tumor tissue or recombinantly generated and loaded with antigen. In other cases, the cell surface location of ER chaperones has implications for immune responses as well as possible tumor resistance. We have produced heat-shock protein/chaperone protein-based cancer vaccines called “chaperone-rich cell lysate” (CRCL) that are conglomerates of chaperones enriched from solid tumors by an isoelectric focusing technique. These preparations have been effective against numerous murine tumors, as well as in a canine with an advanced lung carcinoma treated with autologous CRCL. We also published extensive proteomic analyses of CRCL prepared from human surgically resected tumor samples. Of note, these preparations contained at least 10 ER chaperones and a number of other residents, along with many other chaperones/heat-shock proteins. Gene ontology and network analyses utilizing these proteins essentially recapitulate the antigen presentation pathways and interconnections. In conjunction with our current knowledge of cell surface/extracellular ER chaperones, these data collectively suggest that a systems-level view may provide insight into the potent immune stimulatory activities of CRCL with an emphasis on the roles of ER components in those processes.
Māori patients' experiences and perspectives of chronic kidney disease: a New Zealand qualitative interview study

Objectives To explore and describe Māori (the indigenous people of New Zealand) patients' experiences and perspectives of chronic kidney disease (CKD), as these are largely unknown for indigenous groups with CKD. Design Face-to-face, semistructured interviews with purposive sampling and thematic analysis. Setting 3 dialysis centres in New Zealand (NZ), all of which offered all forms of dialysis modalities. Participants 13 Māori patients with CKD and who were either nearing the need for dialysis or had started dialysis within the previous 12 months. Results The Māori concepts of whakamā (disempowerment and embarrassment) and whakamana (sense of self-esteem and self-determination) provided an overarching framework for interpreting the themes identified: disempowered by delayed CKD diagnosis (resentment of late diagnosis; missed opportunities for preventive care; regret and self-blame); confronting the stigma of kidney disease (multigenerational trepidation; shame and embarrassment; fear and denial); developing and sustaining relationships to support treatment decision-making (importance of family/whānau; valuing peer support; building clinician–patient trust); and maintaining cultural identity (spiritual connection to land; and upholding inner strength/mana). Conclusions Māori patients with CKD experienced marginalisation within the NZ healthcare system due to delayed diagnosis, a focus on individuals rather than family, multigenerational fear of dialysis, and an awareness that clinicians are not aware of cultural considerations and values during decision-making. Prompt diagnosis to facilitate self-management and foster trust between patients and clinicians, involvement of family and peers in dialysis care, and acknowledging patient values could strengthen patient engagement and align decision-making with patient priorities.
A maximum-likelihood estimator to simultaneously unwrap, geocode, and fuse SAR interferograms from different viewing geometries into one digital elevation model

This paper presents theory, algorithm, and results of a maximum-likelihood algorithm that is capable to fuse a number of heterogeneous synthetic aperture radar interferograms into a single digital elevation model (DEM) without the need for the critical phase-unwrapping step. The fusion process takes place in the object space, i.e., the map geometry, and considers the periodic likelihood function of each individual interferometric phase sample. The interferograms may vary regarding their radar wavelength, their baseline, their heading angle (ascending or descending), and their incidence angle. Geometric baseline error estimates and a priori knowledge from other estimates like existing DEMs are incorporated seamlessly into the estimation process. The presented approach significantly differs from the standard DEM generation method where each interferogram is first phase-unwrapped individually, then geocoded into a common map geometry, and finally averaged with DEMs generated from other interferograms. By avoiding the phase-unwrapping step, the proposed algorithm does not depend on gradients between samples and is therefore capable to reconstruct the arbitrary height of each single scatterer. Because the height of each DEM sample is determined individually, spatial propagation of phase-unwrapping errors is avoided. The algorithm is targeted to fuse an ensemble of interferometric multiangle or multibaseline observations in areas of rugged terrain or highly ambiguous data where algorithms based on phase unwrapping may fail. The algorithm is explained, and examples with real data from the Shuttle Radar Topography Mission are given. Conditions of future missions are simulated, and optimization criteria for the viewing geometry are discussed.
Cooperative Multi-Antenna Relaying in Fixed Hybrid Relay Networks

Co-operative communication using relays can achieve spatial diversity, which improves the link quality in a wireless network. In this paper, the performance of an infrastructure based multi-antenna adaptive decode-and-forward cooperative relay network in presence of a m-Nakagami fading channel using Low Density Parity check (LDPC) code has been investigated. The bit error probability (BER) and outage probability performance has been evaluated, when received signals are coherently combined at both the relays with multi-antenna and destination using Selection Combining (SC) and Maximal Ratio Combining (MRC) schemes respectively. The effects of number of relay antennas (L) and number of relays on the system performance have been studied. The impact of decoding threshold and „m‟ parameter on bit error rate (BER) and outage probability have also been evaluated. Further a tradeoff between relay antennas and number of relay is also indicated. Key-Words: Low Density Parity check (LDPC) code, Amplify and forward (AD), decode and forward (DF), adaptive decode and forward (ADF), BER, outage probability, Loglikelihood ratio (LLR), end-to-end (E2E).
Sketching intentions: comparing different metaphors for programming robots

This paper introduces a new environment for programming robots and physical computing devices---the Spatial Computing Platform (SCP)---and compares it to a text-based programming environment (the Cricket Logo). The SCP simplifies the process of constructing conditional statements that link the robot's inputs and outputs together. It does this by providing the user with a virtual canvas that they can draw rectangles on using the mouse. Each rectangle represents a range of sensor values, and specific outputs can be assigned to each rectangle. When the sensor values enter into the specified range, the outputs will turn on. We designed a study with 60 youth to compare this environment to Cricket Logo, a well-known variant of Logo designed to control robotic devices. We found that participants using the spatial computing platform were able to build programs of higher complexity and make more changes to their programs over the course of an hour-long workshop.
Agitated Behaviors in the Elderly: I. A Conceptual Review

Agitation is a significant problem for the elderly, their families, and their caretakers. Although much of the literature on agitation is pharmacologic in nature, several papers demonstrate demographic and environmental approaches to the problem. The literature review accentuates the gaps in both assessment and knowledge of the phenomenon. A conceptual framework and a rigorous methodology need to be developed for studying agitation. On these bases, research could explore the manifestations of agitation and the frequency of occurrence, predisposing factors for agitation, precipitating factors which trigger agitation, consequences of agitation for the elderly and for their caretakers, and the efficacy of alternative interventions. This paper proposes a definition of agitation and develops an initial conceptual framework in which to examine it.
Menatetrenone inhibits bone resorption partly through inhibition of PGE2 synthesis in vitro

We studied the effect of menatetrenone, a vitamin K2 homolog, on bone resorption stimulated by interleukin‐1α (IL‐1α), prostaglandin E2 (PGE2), parathyroid hormone (PTH), and 1,25‐dihydroxyvitamin D3 [1,25‐(OH)2D3]. Bone‐resorbing activity was assessed by measurement of calcium and hydroxyproline in the media and calvariae. IL‐1α (0.1–100 U/ml), 1,25‐(OH)2D3 (1010‐10−7 M), PGE2 (10−9‐10−6 M), and PTH (3 × 10−8‐3 × 10−7 M) dose dependently increased the levels of calcium and hydroxyproline in the medium. Indomethacin (10−6 M) completely inhibited bone resorption induced by IL‐1α and partially inhibited bone resorption induced by 1,25‐(OH)2D3. However, indomethacin did not affect the action of PGE2 or PTH. Menatetrenone (3 × 10−6‐3 × 10−5 M) inhibited the bone resorption induced by IL‐1α (2 U/ml), PGE2 (10−7 M), PTH (3 × 10−7 M), and 1,25‐(OH)2D3 (3 × 10−10 M) in a dose‐dependent manner. Menatetrenone also inhibited the PGE2 production stimulated by IL‐1α. These results indicate that menatetrenone may inhibit bone resorption through at least two different mechanisms; one possibly is an inhibitory effect on prostaglandin production.
Antioxidant Therapies for Alzheimer's Disease

Alzheimer's disease (AD) is the most common neurodegenerative disease featuring progressive impairments in memory, cognition, and behavior and ultimately leads to death. The histopathological changes of Alzheimer's disease include neuronal and synaptic loss, formation of extracellular senile plaques and intracellular neurofibrillary tangles in brain. Multiple lines of evidence indicate that oxidative stress not only strongly participates in an early stage of Alzheimer's disease prior to cytopathology, but plays an important role in inducing and activating multiple cell signaling pathways that contribute to the lesion formations of toxic substances and then promotes the development of Alzheimer's disease. Many years of studies show that antioxidant therapies have enjoyed general success in preclinical studies. Therefore, this paper mainly focuses on the recent developments of common used antioxidant therapies for Alzheimer's disease and thus provides indications for future potential antioxidant therapeutic strategies of neurodegenerative diseases.
Stability of zeros of discrete-time multivariable systems with GSHF

This paper is concerned with the stability of zeros of the discrete-time multivariable system composed of a generalized sample hold function (GSHF), a continuous-time plant with the degrees of infinite elementary divisors being two or three, and a sampler in cascade. The properties of the limiting zeros are studied and the conditions for ensuring the stability of the limiting zeros of the discrete-time systems for sufficiently small sampling periods are derived. It is a natural extension of Liang et al.'s result for single-input-single-output systems to multivariable systems.
Hybridization and renaturation kinetics of nucleic acids.

When two DNA or RNA molecules contain sequences of nucleotides that are complementary to one another, they are able to come together to form a double helix with all of the bases paired. If both strands are DNA, the process is usually called renaturation or reassociation; if one strand is DNA and the other is RNA, the process is called hybridization. These essentially identical processes form the experimental basis for determining relatedness of nucleic acids. Renaturation and hybridization techniques have been used in thousands of papers over the past 15 years. This review is restricted to studies involving the kinetics of the renaturation and hybridization reactions. The pioneering work of Ross & Sturtevant ( 1, 2) on the kinetics of formation of helices with RNA homo polymers, Marmur & Doty (3) on the kinetics of re­ naturation of DNA [for a review, see (4)J, and Nygaard & Hall (5) on the kinetics of DNA· RNA hybridization led to the development by Britten & Kohne (6) and Wetmur & Davidson (7) of systematic frameworks for the interpretation of experi­ mental results. The literature of renaturation and hybridization kinetics in this period has been included as a subject in several reviews (8-1 1). Our emphasis is on the continued development of an integrated and quantitative understanding of the many facets of the kinetics of renaturation and hybridization of nucleic acids. A recent methods paper by Britten, Graham & Neufeld ( 12) provides complemen­ tary information for practitioners in this area of research.
Hebbian learning and spiking neurons

A correlation-based ~‘‘Hebbian’’ ! learning rule at a spike level with millisecond resolution is formulated, mathematically analyzed, and compared with learning in a firing-rate description. The relative timing of presynaptic and postsynaptic spikes influences synaptic weights via an asymmetric ‘‘learning window. ’’ A differential equation for the learning dynamics is derived under the assumption that the time scales of learning and neuronal spike dynamics can be separated. The differential equation is solved for a Poissonian neuron model with stochastic spike arrival. It is shown that correlations between input and output spikes tend to stabilize structure formation. With an appropriate choice of parameters, learning leads to an intrinsic normalization of the average weight and the output firing rate. Noise generates diffusion-like spreading of synaptic weights. @S1063-651X~99! 02804-4#
Probabilistic Rewrite Theories: Unifying Models, Logics and Tools

Probabilistic rewrite theories are proposed as a general semantic framework that uniﬁes many existing models of probabilistic systems for both discrete and continuous time and suggests new models such as probabilistic hybrid systems. Probabilistic temporal logics for existing models are likewise uniﬁed in two logics, namely P RTL and P RTL ∗ that we develop. Having a common semantic framework enables rigorously speciﬁed combinations of existing modelling and model checking tools that are based on diﬀerent models–including the P Maude interpreter that can execute ﬁnitary probabilistic rewrite theory speciﬁcations.
Characterisation of a human cell-adapted porcine endogenous retrovirus PERV-A/C.

BACKGROUND Porcine endogenous retroviruses (PERVs) pose a potential risk for xenotransplantation using pig cells, tissues or organs. A special threat comes from viruses generated by recombination between human-tropic PERV-A and ecotropic PERV-C. Serial passages of a recombinant PERV-A/C on human 293 cells resulted in increased infectious titers and a multimerization of transcription factor binding sites in the viral long terminal repeat (LTR). In contrast to the LTR, the sequence of the env gene did not change, indicating that the LTR represents the determinant of high infectivity. MATERIAL/METHODS The virus was further propagated on human cells and characterized by different methods (titration, sequencing, infection experiments, electron microscopy). RESULTS Further propagation on human 293 cells resulted in deletions and mutations in the LTR. In contrast to low-titer viruses, the high-titer virus was infectious for cells from non-human primates including chimpanzees. Scanning electron microscopy revealed clustering of budding virions at the cell surface of infected human cells and transmission electron microscopy indicated that the virus infects them via receptor-mediated endocytosis. CONCLUSIONS After propagation of PERV on human cells without selection pressure, viruses with different LTR were generated. High titer PERV was shown to infect cells from non-human primates. The experiments performed here simulate the situation in vivo and give an extended characterization of human cell-adapted PERVs.
Comparative effectiveness of a one-year follow-up of thoracic medial branch blocks in management of chronic thoracic pain: a randomized, double-blind active controlled trial.

BACKGROUND Thoracic facet joints have been implicated as the source of chronic pain in the mid back or upper back in 34% to 42% of patients when the modified criteria of the International Association for the Study of Pain (IASP) is utilized. Various therapeutic techniques utilized in managing chronic thoracic pain of facet joint origin include intraarticular injections, medial branch blocks, and radiofrequency neurotomy of thoracic medial branch nerves. STUDY DESIGN A randomized, double-blind, active controlled trial. SETTING A private practice, interventional pain management setting, and a specialty referral center setting in the United States. OBJECTIVE To determine the clinical effectiveness of therapeutic local anesthetic medial branch blocks with or without steroid in managing chronic function-limiting mid back or upper back pain of facet joint origin. METHODS The study was performed in an interventional pain management private practice, a tertiary referral center, in the United States. A total of 100 participants were included, with 50 participants in each of the local anesthetic and steroid groups. All of the participants met the diagnostic criteria of thoracic facet joint pain by means of comparative, controlled diagnostic blocks and the inclusion criteria. Group I participants received thoracic medial branch blocks with bupivacaine, whereas Group II participants received thoracic medial branch blocks with bupivacaine and non-particulate betamethasone. OUTCOMES ASSESSMENT Outcomes measures included numeric rating scores (NRS), Oswestry Disability Index (ODI), opioid intake, and return to work status at baseline, 3 months, 6 months, and 12 months. Significant pain relief was defined as >/= 50% pain relief and/or a positive change in ODI scores. RESULTS In Group I and Group II 90% of participants showed significant pain relief and functional improvement at 12 months. The majority of the participants experienced significant pain relief of 47.2 ± 10.1 weeks in Group I and 46.3 ± 8.4 weeks in Group II, requiring approximately 3.5 treatments per year with an average relief of 15.8 ± 10.5 in Group I and 13.6 ± 3.6 weeks in Group II per episode of treatment. LIMITATIONS Study limitations include the lack of a placebo group. CONCLUSIONS Therapeutic thoracic medial branch blocks, with or without steroid, may provide a management option for chronic function-limiting mid back or upper back pain of facet joint origin. CLINICAL TRIAL NCT00355706.
Making Ecopreneurs: Developing Sustainable Entrepreneurship

Contents: Introduction, Michael Schaper Part 1 Concepts: Understanding the green entrepreneur, Michael Schaper Sustainability entrepreneurship: charting a field in emergence, Bradley D. Parrish and Fiona Tilley The making of the ecopreneur, Robert Isaak Beyond the visionary champion: testing a typology of green entrepreneurs, Liz Walley, David Taylor and Karen Greig A framework and typology of ecopreneurship: leading bioneers and environmental managers to ecopreneurship, Stefan Schaltegger Little acorns in action: green entrepreneurship and New Zealand micro-enterprises, Anne de Bruin and Kate Lewis An insider's experiences with environmental entrepreneurship, Lassi Linnanen. Part 2 Contexts and Conditions: Ecopreneurship in India: a review of key drivers and policy environment, Astad Pastakia Sustainability in the start-up process, JA rgen Freimann, Sandra Marxen and Hildegard Schick How venture capital can help build ecopreneurship, Anastasia R. O'Rourke Offsetting the disadvantages of smallness: promoting green entrepreneurs through Industry clusters, Elya Tagar and Chris Cocklin Ecopreneurship, corporate citizenship and sustainable decision-making, David A. Holloway The competitive strategies of ecopreneurs:striving for market leadership by promoting sustainability, Holger Petersen. Part 3 Cases: Entrepreneurship and sustainable tourism: the global gypsies approach, Jim Macbeth and Yamini Narayanan Promoting sustainability, building networks: a green entrepreneur in Mexico, Gabrielle Kruks-Wisner Sustainable harvest international: expanding ecopreneur expertise, Jill A. Kammermeyer and Margaret J. Naumes Sustainability entrepreneurship: organizational innovation at NativeEnergy, Bradley D. Parrish The Mimosa Project, Kumba Jallow. Index.
Regulated expression of foreign genes fused to lac: control by glucose levels in growth medium.

Expression of cloned genes from the E. coli lac promoter has been used by many investigators to produce a variety of foreign or mutant gene products. The commonly used expression plasmids are the pUC series of plasmids, or derivatives thereof (1). The expression of genes cloned downstream of the lac promoter can be conveniently induced by addition of j3-isopropylthiogalactoside (IPTG), however, in the absence of inducer there is a basal level of expression from this promoter (2). It is this 'leakiness' which has limited the utility ofthis cloning strategy when the cloned gene product may be lethal to the cell. This is unfortunate because many of the initial cloning steps are carried out in this plasmid type and procedures for rapid sequencing of these plasmids are available. We coli gene for translation the inherent 'leakiness' of lac by growing the transformed cells harboring the recombinant pUC plasmid in the presence of small amounts of glucose. The plasmid pDD1 contains the gene for IF3 under the control of lac in pUC 19. Overnight cultures of JM107-transformed cells were inoculated into 250 mL of L broth in the presence or absence of glucose, grown at 37°C to OD600 = 0.9 and subsequently induced for three hours with 0.4 mM IPTG. Cells were harvested after induction and analyzed for IF3 production by immunoblotting. When the initial growth is carried out in the presence of 0.4% glucose induction by IPTG is inhibited (lane 2). In contrast, cultures grown in lower concentrations of glucose (0.05%-0.1%) can yield maximal overproduction of
Immunological Mechanisms in Glomerulonephritis

Glomerulonephritis is not a single disease, but a group of diseases. Examination of renal biopsies has shown a wide variety of histological lesions associated with the syndromes of nephritis (Brewer, 1964) and now the clinical progress of ' many patients, with or without treatment, can be predicted with some accuracy from the biopsy appearances (Hardwicke et al., 1967). The capacity of the glomerulus to respond to noxious stimuli is clearly limited and the very high proportion of the cardiac output it receives makes it particularly susceptible to circulating pathogenic influences. Until aetiological factors can be positively identified we must bear in mind two points:
Learning bagged models of dynamic systems

In this paper, we present an ensemble learning method for modeling dynamic systems. The method is a combination of the bagging approach to ensemble learning and the approach of inductive process modeling of dynamic systems. We illustrate the use of the proposed method on the task of modeling phytoplankton growth in Lake Bled.