Miracle-dz/UniFAR-FTUs huggingface dataset:
Adipocytes play an etiological role in the podocytopathy of high-fat diet-fed rats.

Obesity is a risk factor that promotes progressive kidney disease. Studies have shown that an adipocytokine imbalance contributes to impaired renal function in humans and animals, but the underlying interplay between adipocytokines and renal injury remains to be elucidated. We aimed to investigate the mechanisms linking obesity to chronic kidney disease. We assessed renal function in high-fat (HF) diet-fed and normal diet-fed rats, and the effects of preadipocyte- and adipocyte-conditioned medium on cultured podocytes. HF diet-fed and normal diet-fed Sprague Dawley rats were used to analyze the changes in plasma BUN, creatinine, urine protein and renal histology. Additionally, podocytes were incubated with preadipocyte- or adipocyte-conditioned medium to investigate the effects on podocyte morphology and protein expression. In the HF diet group, 24 h urinary protein excretion (357.5 ± 64.2 mg/day vs 115.9 ± 12.4 mg/day, P < 0.05) and the urine protein/creatinine ratio were significantly higher (1.76 ± 0.22 vs 1.09 ± 0.15, P < 0.05), increased kidney weight (3.54 ± 0.04 g vs 3.38 ± 0.04 g, P < 0.05) and the glomerular volume and podocyte effacement increased by electron microscopy. Increased renal expression of desmin and decreased renal expression of CD2AP and nephrin were also seen in the HF diet group (P < 0.05). Furthermore, we found that adipocyte-conditioned medium-treated podocytes showed increased desmin expression and decreased CD2AP and nephrin expression compared with that in preadipocyte-conditioned medium-treated controls (P < 0.05). These findings show that adipocyte-derived factor(s) can modulate renal function. Adipocyte-derived factors play an important role in obesity-related podocytopathy.
A Primary Determinant of Cap-Independent Translation Is Located in the 3′-Proximal Region of the Tomato Bushy Stunt Virus Genome

ABSTRACT Tomato bushy stunt virus (TBSV) is a positive-strand RNA virus and is the prototype member of the genus Tombusvirus. The genomes of members of this genus are not polyadenylated, and prevailing evidence supports the absence of a 5′ cap structure. Previously, a 167-nucleotide-long segment (region 3.5) located near the 3′ terminus of the TBSV genome was implicated as a determinant of translational efficiency (S.K. Oster, B. Wu and K. A. White, J. Virol. 72:5845–5851, 1998). In the present report, we provide evidence that a 3′-proximal segment of the genome, which includes region 3.5, is involved in facilitating cap-independent translation. Our results indicate that (i) a 5′ cap structure can substitute functionally for the absence of region 3.5 in viral and chimeric reporter mRNAs in vivo; (ii) deletion of region 3.5 from viral and chimeric mRNAs has no appreciable effect on message stability; (iii) region 3.5 represents part of a larger 3′ proximal element, designated as the 3′ cap-independent translational enhancer (3′CITE), that is required for proficient cap-independent translation; (iv) the 3′CITE also facilitates cap-dependent translation; (v) none of the major viral proteins are required for 3′CITE activity; and (vi) no significant 3′CITE-dependent stimulation of translation was observed when mRNAs were tested in vitro in wheat germ extract under various assay conditions. This latter property distinguishes the 3′CITE from other characterized plant viral 3′-proximal cap-independent translational enhancers. Additionally, because the 3′CITE overlaps withcis-acting replication signals, it could potentially participate in regulating the initiation of genome replication.
Personal and family history of autoimmune diabetes mellitus and susceptibility to young‐adult‐onset Hodgkin lymphoma

Young‐adult‐onset (15–44 years of age) Hodgkin lymphoma (HL) is believed to arise as a consequence of late primary infection in susceptible individuals. The properties of this susceptibility remain little understood. We have previously reported an increased occurrence of HL in patients with rheumatoid arthritis and among their offspring, suggesting that susceptibility to autoimmunity might be of importance also in the pathogenesis of HL. To explore this hypothesis, we assessed the association of personal and family history of diabetes mellitus, with risk of subsequent HL in a population‐based case‐control study, including as cases all individuals diagnosed with HL above 15 years of age 1964–1999 (n=6,873) in Sweden, and matched population controls (n=12,565). First‐degree relatives of cases and controls were identified through linkage with the Multi‐generation Register. We identified discharges listing diabetes mellitus through linkage with the Inpatient Register (1964–2000). We used odds ratios (OR) as measures of relative risk. Cases with young‐adult‐onset HL were less likely to have a personal (OR=0.5, 95% CI 0.2–1.1) or family (OR=0.7, 95% CI 0.6–0.8) history of diabetes mellitus. In contrast, HL diagnosed at older ages was neither associated with a personal (OR=1.0) nor family (OR=1.0) history of diabetes mellitus. These findings suggests that characteristics of the immune system associated with conditions such as diabetes mellitus type I are of importance in the pathogenesis of young‐adult‐onset HL. © 2005 Wiley‐Liss, Inc.
Beyond Conjoint Analysis : Advances in Preference Measurement 1

We identify gaps and propose several directions for future research in preference measurement. We structure our argument around a framework that views preference measurement as comprising three inter-related components: 1) the problem that the study is ultimately intended to address; 2) the design of the preference measurement task and the data collection approach; 3) the specification and estimation of a preference model, and the conversion into action. Conjoint analysis is only one special case within this framework. We summarize cutting edge research and identify fruitful directions for future investigations pertaining to the framework’s three components and to their integration.
Track Structure in DNA Irradiated with Heavy Ions

Abstract Bowman, M. K. , Becker, D. , Sevilla, M. D. and Zimbrick, J. D. Track Structure in DNA Irradiated with Heavy Ions. Radiat. Res. 163, 447–454 (2005). The spatial properties of trapped radicals produced in heavy-ion-irradiated solid DNA at 77 K have been probed using pulsed electron paramagnetic double resonance (PELDOR or DEER) techniques. Salmon testes DNA hydrated to 12 water molecules per nucleotide was irradiated with 40Ar ions of energy 100 MeV/nucleon and LET ranging from 300 to 400 keV/μm. Irradiated samples were maintained at cryogenic temperature at all times. PELDOR measurements were made using a refocused echo detection sequence that allows dipolar interaction between trapped radicals to be observed. The EPR spectrum is attributed to electron loss/gain DNA base radicals and neutral carbon-centered radicals that likely arise from sugar damage. We find a radical concentration of 13.5 × 1018 cm−3 in the tracks and a track radius of 6.79 nm. The cross section of these tracks is 144 nm2, yielding a lineal radical density of 2.6 radicals/nm. Based on the yields determined previously for particles having calculated LET values of 300–400 keV/μm and our measured lineal density, we obtain an LET of 270 keV/μm, which is in good agreement with the calculated range of values. These measurements of radical density and spatial extent provide the first direct experimental determination of track characteristics in irradiated DNA.
Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes.

BACKGROUND A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. RESULTS While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. CONCLUSION The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry.
Relationships of brassinosteroid signaling with knox and wab1 genes on maize plant architecture

vii CHAPTER I. GENERAL INTRODUCTION . 1 I.1. Maize and the importance of plant architecture . 1 I.2. Brassinosteroids . 4 I.2. 1. Brassinosteroid signaling . 6 I.2. 2. Brassinosteroids biosynthesis . 8 I.3. knotted1-like homeobox (knox) . 11 I.4. wavy auricle in blade1 (wab1) . 14 References . 16 CHAPTER II. GENE EXPRESSION ANALYSIS OF BRASSINOSTEROID MUTANTS, BRI1-RNAI AND BIN2-RNAI, IN RELATION TO KN1-O, A KNOX MUTANT . 24 II.1. Abstract . 24 II.2. Introduction . 25 II.3. Materials and methods . 28 II.4. Results and discussion . 31 II.5. Figures and tables . 34 References . 40 CHAPTER III. GENE EXPRESSION ANALYSIS OF BRASSINOSTEROID MUTANTS, BRI1-RNAI AND BIN2-RNAI, IN RELATION TO TCP TRANSCRIPTION FACTOR, WAB1, GENE . 44 III.1. Abstract . 44 III.2. Introduction . 45 III.3. Materials and methods . 48
Optimization and Scale-up Isolation and Culture of Neonatal Porcine Islets: Potential for Clinical Application

One challenge that must be overcome to allow transplantation of neonatal porcine islets (NPIs) to become a clinical reality is defining a reproducible and scalable protocol for the efficient preparation of therapeutic quantities of clinical grade NPIs. In our standard protocol, we routinely isolate NPIs from a maximum of four pancreases, requiring tissue culture in 16 Petri dishes (four per pancreas) in Ham's F10 and bovine serum albumin (BSA). We have now developed a scalable and technically simpler protocol that allows us to isolate NPIs from a minimum of 12 pancreases at a time by employing automated tissue chopping, collagenase digestion in a single vessel, and tissue culture/media changes in 75% fewer Petri dishes. For culture, BSA is replaced with human serum albumin and supplemented with Z-VAD-FMK general caspase inhibitor and a protease inhibitor cocktail. The caspase inhibitor was added to the media for only the first 90 min of culture. NPIs isolated using the scalable protocol had significantly more cellular insulin recovered (56.9 ± 1.4 μg) when compared to the standard protocol (15.0 ± 0.5 μg; p < 0.05). Compared to our standard protocol, recovery of β-cells (6.0 × 106 ± 0.2 vs. 10.0 × 106 ± 0.4; p < 0.05) and islet equivalents (35,135 ± 186 vs. 41,810 ± 226; p < 0.05) was significantly higher using the scalable protocol. During a static glucose stimulation assay, the SI of islets isolated by the standard protocol were significantly lower than the scale-up protocol (4.3 ± 0.2 vs. 5.5 ± 0.1; p < 0.05). Mice transplanted with NPIs using the scalable protocol had significantly lower blood glucose levels than the mice that receiving NPIs from the standard protocol (p < 0.01) and responded significantly better to a glucose tolerance test. Based on the above findings, this improved simpler scalable protocol is a significantly more efficient means for preparing therapeutic quantities of clinical grade NPIs.
Importance of the Inter-Electrode Distance for the Electrochemical Synthesis of Magnetite Nanoparticles: Synthesis, Characterization, Computational Modelling, and Cytotoxicity

Magnetite (Fe3O4) nanoparticles, are promising inorganic nanomaterials for future biomedical applications due to their low toxicity and unique magnetic properties. However, the synthesis of these particles can often be expensive, energy intensive, and non-scalable, requiring the addition of surfactants to stabilize the material to control the particle size and avoid agglomeration. We wish to report a simple, green, surfactant-free electrochemical synthesis of these materials using a closed aqueous system at ambient temperature. Particle diameter, between 19 and 33 nm, was controlled by simply modifying the distance between the electrodes. These magnetite nanoparticles were then fully characterized using both spectroscopy and microscopy. Vibrational magnetometry indicates that as the size of the particle decreases, the magnetic hysteretic gap decreases, although for samples below 25 nm no inter-sample difference was observed. To support this experimental data, we carried out a Density Functional Theory (DFT) analysis of magnetite containing more than three iron atoms in the cluster, an essential proposition as magnetite contains three distinct iron species. These calculations were used to support the experimental observations, and closely reproduced both the experimental IR spectrum, and the XRD pattern. In vitro cytotoxicity assays showed dose responsive behavior for the nanoparticles, and demonstrated that they are non-toxic at clinically relevant concentrations; below 200 μg/mL we observed no toxicity in a 48-hour standard assay. This work represents the first DFT based simulation of this detailed magnetite cluster, and demonstrates that this sustainable synthetic method is capable of producing nanomaterials with a physical and biological profile that might make them suitable for biomedical applications. [DOI: 10.1380/ejssnt.2017. 31]
Five-Repetition Sit-to-Stand Test: Usefulness for Older Patients in a Home-Care Setting

The usefulness of the five-repetition sit-to-stand (FRSTS) test was assessed with older patients in a home-care setting. Records of 45 patients (≥ 65 years old) were examined for information on FRSTS test performance. 5 patients were excluded. 23 patients were unable to complete the test. For the 17 able to complete the FRSTS test, the time required was statistically significantly greater than age-stratified norms. For patients treated in a home-care setting, inability to complete the FRSTS test clearly underscores the test's limitations and the need for alternatives.
Hash Tree Indexing for Fast SPARQL Query in Large Scale RDF Data Management Systems

In the past decade, the volume of RDF (Resource Description Framework, which is a standard model for data interchange on the Web) data has grown enormously, and many RDF datasets (e.g., Wikipedia) have reached up to billions of triples. As a result, efﬁcient management of this huge RDF data has become a tremedous challenge. In this paper, we present HTStore, a hash tree based system for fast storing and accessing large scale RDF data. The design of HTStore has three salient features. First, the compact design can effectively reduce the size of the indexes. Second, HTStore utilizes the hash function to signiﬁcantly reduce the query time. Third, the proposed hash tree structure can easily adapt to the changes in data volume (e.g., data expansion). The experimental results demonstrate that the proposed system can improve the query efﬁciency up to 21.3% compared with the representative RDF data management systems.
Covalent Modification of Human P-glycoprotein Mutants Containing a Single Cysteine in Either Nucleotide-binding Fold Abolishes Drug-stimulated ATPase Activity (*)

The ATPase activity of P-glycoprotein is inactivated by N-ethylmaleimide (NEM), which is postulated to modify cysteine residues within either of the homology A consensus sequences for nucleotide binding (GNSGCGKS and GSSGCGKS, respectively) (Al-Shawi, M. K., Urbatsch, I. L., and Senior, A. E.(1994) J. Biol. Chem. 269, 8986-8992). To test this postulate as well as determine the contribution of either nucleotide-binding domain to function, a Cys-less mutant was constructed, and then a single cysteine residue was reintroduced back into each nucleotide-binding consensus sequence. We then tested the sensitivity of the ATPase activity of each mutant to covalent modification by NEM. It was found that covalent modification of a single cysteine residue within either nucleotide-binding consensus sequence (Cys-431 and Cys-1074, respectively) with NEM inhibited drug-stimulated ATPase activity of P-glycoprotein. The concentrations of NEM required for half-maximal inactivation of ATPase activity were 7 and 35 μM for mutants Cys-431 and Cys-1074, respectively. In both cases, inactivation of ATPase activity by NEM was prevented by ATP. These results suggest that both nucleotide-binding domains may need to bind ATP to couple drug binding to ATPase activity.
Graph-based approach for software allocation in automotive networked embedded systems: A partition-and-map algorithm

Complex automotive networked embedded systems require novel algorithms for exploring different design decisions at early stages of the design flow. The problem of allocating the software components on electronic control units lies at the core of these design decisions. This paper formalizes this allocation problem using graph theory. The proposed formalism allows the designer to use a wide variety of graph-theoretic optimization algorithms, which are capable of minimizing more than one criterion simultaneously. The proposed algorithm is then shown, by means of numerical examples, to give the same answer as mathematical optimization but is 15 times faster in computation time.
Non-Gaussian multivariate adaptive AR estimation using the super exponential algorithm

We formulate as a deconvolution problem the causal/noncausal non-Gaussian multichannel autoregressive (AR) parameter estimation problem. The super exponential algorithm presented in a paper by Shalvi and Weinstein (1993) is generalized to the vector case. We present an adaptive implementation that is very attractive since it is higher order statistics (HOS) based but does not present the high computational complexity of methods proposed up to now.
Significant Qualitative Differences Exist between Thyrotropin and Prolactin Secretory Dynamics Induced by Pituitary Cell Swelling

Abstract Cell swelling produced by a variety of techniques is a potent stimulus intensity-related inducer of an immediate secretory burst of thyroid-stimulating hormone (TSH) and prolaction (PRL) secretion from anterior pituitary cells. A 2-min “square wave” exposure to either hyposmolarity or isotonic urea induced stimulus intensity-correlated TSH and PRL secretory bursts peaking within 3 min, but the PRL zenith occurred 1 min later than that of TSH. With continuous exposure to these stimuli, TSH secretion rapidly decreased and remained only slightly above the unstimulated rate after 5 min. PRL secretion fell to and remained below the unstimulated level after 10 min. After stopping the stimulus, another secretory burst (“off” response) occurred with PRL, but not with TSH. A progressive “ramp” increase in stimulus intensity over 18 min induced a corresponding gradual increase in TSH secretion; there was a progressive depression, rather than increase, in PRL secretion during the stimulus ramp, with an off response secretory burst when the stimulus was discontinued. Removal of extracellular Ca2+ or addition of verapamil to the medium did not alter the dynamics of hyposmolarity-induced TSH secretion, but markedly altered those of PRL secretion; there was no off response PRL secretion and a hyposmolar ramp induced a corresponding gradual increase in PRL secretion, with a return to baseline after removing the stimulus. The dramatic qualitative differences in the response of the thyrotroph and lactotroph may reflect differences between the cell types in the size of secretory vesicles, membrane potential, the mechanism of exocytosis, and/or the role of Ca2+ influx across the plasmalemma.
High-Performance $\lambda \sim 8.6~\mu {\rm m}$  Quantum Cascade Lasers With Single Phonon-Continuum Depopulation Structures

We report high performance λ~8.6 μm m quantum cascade lasers based on 5 quantum well single phonon-continuum (SPC) depopulation scheme, grown by metal organic vapor-phase epitaxy. Devices with SPC depopulation structures exhibit high device performances in pulsed and continuous wave (CW) operation due to a large dipole matrix element (3.0 nm) and short depopulation time (0.22 ps). A 4 mm-long, 8 μm-wide, high reflective (HR)-coated buried-hetero-structure laser with 33 cascade stages, for active region, demonstrates a high output power of 313 mW, a threshold current density of 1.35 kA/cm2, and slope efficiency of 547 mW/A at 30°C in CW operation. The maximum CW lasing temperature of the device is observed to be 120°C. Furthermore, by using a higher number of cascade stages (N=70) in a 4 mm-long, 22 m-wide, HR-coated ridge laser, a high peak power of 6.3 W is obtained together with a high wall-plug efficiency (WPE) of 10.8%, a slope efficiency of 2.7 W/A, and a threshold current density of 0.76 kA/cm2 in pulsed operation at 300 K. The measured WPE of over 10% at room temperature is close to the theoretical values.
New Diagnostic Tool for Robotic Psychology and Robotherapy Studies

Robotic psychology and robotherapy as a new research area employs a systematic approach in studying psycho-physiological, psychological, and social aspects of person-robot communication. An analysis of the mechanisms underlying different forms of computer-mediated behavior requires both an adequate methodology and research tools. In the proposed article we discuss the concept, basic principles, structure, and contents of the newly designed Person-Robot Complex Interactive Scale (PRCIS), proposed for the purpose of investigating psychological specifics and therapeutic potentials of multilevel person-robot interactions. Assuming that human-robot communication has symbolic meaning, each interactive pattern evaluated via the newly developed scale is assigned certain psychological value associated with the person's past life experiences, likes and dislikes, emotional, cognitive, and behavioral traits or states. PRCIS includes (1) assessment of a person's individual style of communication with the robotic creature based on direct observations; (2) the participant's evaluation of his/her new experiences with an interactive robot and evaluation of its features, advantages and disadvantages, as well as past experiences with modern technology; and (3) the instructor's overall evaluation of the session.
Single-mode tapered optical fiber for temperature sensor based on multimode interference

A temperature sensor using a single-mode tapered fiber coated by thermo-sensitive material is presented. It works on the multimode interference influenced by the small change of the ambient refractive index. To better understand the tapered optical fiber, simulations that change parameters such as the taper waist diameter and the ambient refractive index are performed using RSOFT BeamPROP. It is illustrated that optical losses vary with the ambient refractive index, and reduce diameter within a certain range can increase the sensitivity. In our experiment, with the high thermo-sensitive coefficient of material, a good temperature sensing result was achieved. The range of temperature measured is from ∼20°C to 80°C. The results show that the temperature sensor has high temperature sensitivity and good repeatability.