Miracle-dz/UniFAR-FTUs huggingface dataset:
Fuel Property Effects on Biodiesel

Biodiesel is an environmentally friendly alternative diesel fuel obtained from renewable resources, such as vegetable oils, animal fats, and recycled restaurant greases. It is described in ASTM standard D 6751-02 as: a fuel comprised of mono-alkyl esters of long chain fatty acids derived from vegetable oils or animal fats. Biodiesel is oxygenated, sulfur-free, biodegradable, and nontoxic. One of the attractive characteristics of biodiesel is that it does not require any significant modifications to the diesel engine, so the engine does not have to be dedicated for biodiesel. However, due to its different properties, such as a higher cetane number, lower volatility, and lower energy content, biodiesel may cause some changes in the engine performance and emissions. These different properties can effect the injection timing and the diesel combustion process causing lower power and higher oxides of nitrogen. The objective of this study was the investigation of biodiesel fuel properties such as cetane number, fuel volatility, and energy content on biodiesel combustion. The results of heat release analysis are presented from measured cylinder pressure data on a turbocharged diesel engine fueled with biodiesel from soybean oil, biodiesel from animal grease, and No. 2 diesel fuel.
Structural analysis of the subunits of the trehalose‐6‐phosphate synthase/phosphatase complex in Saccharomyces cerevisiae and their function during heat shock

Synthesis of trehalose in the yeast Saccharomyces cerevisiae is catalysed by the trehalose‐6‐phosphate (Tre6P) synthase/phosphatase complex, which is composed of at least three different subunits encoded by the genes TPS1, TPS2, and TSL1. Previous studies indicated that Tps1 and Tps2 carry the catalytic activities of trehalose synthesis, namely Tre6P synthase (Tps1) and Tre6P phosphatase (Tps2), while Tsl1 was suggested to have regulatory functions. In this study two different approaches have been used to clarify the molecular composition of the trehalose synthase complex as well as the functional role of its potential subunits. Two‐hybrid analyses of the in vivo interactions of Tps1, Tps2, Tsl1, and Tps3, a protein with high homology to Tsl1, revealed that both Tsl1 and Tps3 can interact with Tps1 and Tps2; the latter two proteins also interact with each other. In addition, trehalose metabolism upon heat shock was analysed in a set of 16 isogenic yeast strains carrying deletions of TPS1, TPS2, TSL1, and TPS3 in all possible combinations. These results not only confirm the previously suggested roles for Tps1 and Tps2, but also provide, for the first time, evidence that Tsl1 and Tps3 may share a common function with respect to regulation and/or structural stabilization of the Tre6P synthase/phosphatase complex in exponentially growing, heat‐shocked cells.
Hypothermic machine perfusion of kidneys retrieved from standard and high‐risk donors

Hypothermic machine perfusion (HMP) of kidneys is a long‐established alternative to static cold storage and has been suggested to be a better preservation method. Today, as our deceased donor profile continues to change towards higher‐risk kidneys of lower quality, we are confronted with the limits of cold storage. Interest in HMP as a preservation technique is on the rise. Furthermore, HMP also creates a window of opportunity during which to assess the viability and quality of the graft before transplantation. The technology might also provide a platform during which the graft could be actively repaired, making it particularly attractive for higher‐risk kidneys. We review the current evidence on HMP in kidney transplantation and provide an outlook for the use of the technology in the years to come.
The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters

ABSTRACT The downstream promoter element (DPE) functions cooperatively with the initiator (Inr) for the binding of TFIID in the transcription of core promoters in the absence of a TATA box. We examined the properties of sequences that can function as a DPE as well as the range of promoters that use the DPE as a core promoter element. By using an in vitro transcription assay, we identified 17 new DPE-dependent promoters and found that all possessed identical spacing between the Inr and DPE. Moreover, mutational analysis indicated that the insertion or deletion of a single nucleotide between the Inr and DPE causes a reduction in transcriptional activity and TFIID binding. To explore the range of sequences that can function as a DPE, we constructed and analyzed randomized promoter libraries. These experiments yielded the DPE functional range set, which represents sequences that contribute to or are compatible with DPE function. We then analyzed the DPE functional range set in conjunction with a Drosophila core promoter database that we compiled from 205 promoters with accurately mapped start sites. Somewhat surprisingly, the DPE sequence motif is as common as the TATA box in Drosophila promoters. There is, in addition, a striking adherence of Inr sequences to the Inr consensus in DPE-containing promoters relative to DPE-less promoters. Furthermore, statistical and biochemical analyses indicated that a G nucleotide between the Inr and DPE contributes to transcription from DPE-containing promoters. Thus, these data reveal that the DPE exhibits a strict spacing requirement yet some sequence flexibility and appears to be as widely used as the TATA box in Drosophila.
New office-based vascular interventions.

OBJECTIVE Following contemporary trend, various vascular interventions being performed in the office. We describe our office experience with radiofrequency ablation (RFA) of incompetent perforating veins (IPV) and duplex-guided balloon angioplasties of failing/nonmaturing arterio-venous fistulas (AVF). DUPLEX-GUIDED BALLOON ANGIOPLASTIES OF AVF: Eighteen patients with 20 failing arterio-venous (AV) fistulas underwent office duplex-guided balloon angioplasties. Thirteen procedures (65%) were on non-maturing fistulas and the remaining 7 (35%)--in dialyzed patients. Sheath insertion, wire and balloon passage and inflation were guided by duplex only. RFA OF IPVS We performed 25 radiofrequency ablations of 49 IPVs. Early follow-up scan confirmed total occlusion of 45 (92%) treated IPVs. Patients gender, CEAP class, perforator diameter or GSV patency did not correlate with current procedure failure. CONCLUSION Excellent duplex imaging quality and technical advances in endovascular tools allowed us safely perform AVF balloon angioplasties and RFA of IPVs in the office.
Depth Subtyping and Type Inference for Object Calculi

We present a new type system based on the notion of Split types. In this system, every method is assigned two types, namely, an update type and a select type. We show that the system of Split types is strictly more powerful than the system of recursive types and that type inference remains decidable and feasible. We include a number of interesting examples not typable with recursive types that are typable with Split types. In particular, we demonstrate that the subtyping relation needed to encode the -calculus into the Abadi and Cardelli’s &-calculus holds. We also present a polynomial-time algorithm that infers Split types and show that it is sound and complete with respect to the type system. We conclude our presentation by relating the typing power of Split types to the typing power of other systems, such as, the system of recursive types with variance annotations and the system of Self types.
Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells

Cellular differentiation entails reprogramming of the transcriptome from a pluripotent to a unipotent fate. This process was suggested to coincide with a global increase of repressive heterochromatin, which results in a reduction of transcriptional plasticity and potential. Here we report the dynamics of the transcriptome and an abundant heterochromatic histone modification, dimethylation of histone H3 at lysine 9 (H3K9me2), during neuronal differentiation of embryonic stem cells. In contrast to the prevailing model, we find H3K9me2 to occupy over 50% of chromosomal regions already in stem cells. Marked are most genomic regions that are devoid of transcription and a subgroup of histone modifications. Importantly, no global increase occurs during differentiation, but discrete local changes of H3K9me2 particularly at genic regions can be detected. Mirroring the cell fate change, many genes show altered expression upon differentiation. Quantitative sequencing of transcripts demonstrates however that the total number of active genes is equal between stem cells and several tested differentiated cell types. Together, these findings reveal high prevalence of a heterochromatic mark in stem cells and challenge the model of low abundance of epigenetic repression and resulting global basal level transcription in stem cells. This suggests that cellular differentiation entails local rather than global changes in epigenetic repression and transcriptional activity.
Simultaneously recorded single units in the frontal cortex go through sequences of discrete and stable states in monkeys performing a delayed localization task

To test whether spiking activity of six to eight simultaneously recorded neurons in the frontal cortex of a monkey can be characterized by a sequence of discrete and stable states, neuronal activity is analyzed by a hidden Markov model (HMM). Using the HMM method, we are able to detect distinct states of neuronal activity within which firing rates are approximately stationary. Transitions between states, as expressed by concomitant changes in the firing rates of several units, occur quite abruptly. The significance and consistency of the states are confirmed by comparison with simulated data. The detected states are specific to a monkey's response in a delayed localization task, allowing correct prediction of the response in approximately 90% of the trials. Similar predictive power is achieved by a model based simply on the response histograms (PSTH) of the units. The two models reach this predictive ability with different time courses: the PSTH model gains predictive power with a higher rate in the first second of the delay, and the HMM gains predictive power with higher rate in the next 3 sec. In this later period, conventional methods such as the PSTH cannot detect any firing rate modulations, but the HMM successfully captures transitions between distinct states that are specific to the monkey's behavioral response and occur at highly variable times from trial to trial. Our results suggest that neuronal activity in this later period is described best as transitions among distinct states that may reflect discrete steps in the monkey's mental processes.
AtKUP1: An Arabidopsis Gene Encoding High-Affinity Potassium Transport Activity

Because plants grow under many different types of soil and environmental conditions, we investigated the hypothesis that multiple pathways for K+ uptake exist in plants. We have identified a new family of potassium transporters from Arabidopsis by searching for homologous sequences among the expressed sequence tags of the GenBank database. The deduced amino acid sequences of AtKUP (for Arabidopsis thaliana K+ uptake transporter) cDNAs are highly homologous to the non-plant Kup and HAK1 potassium transporters from Escherichia coli and Schwanniomyces occidentalis, respectively. Interestingly, AtKUP1 and AtKUP2 are able to complement the potassium transport deficiency of an E. coli triple mutant. In addition, transgenic Arabidopsis suspension cells overexpressing AtKUP1 showed increased Rb+ uptake at micromolar concentrations with an apparent Km of ~22 μM, indicating that AtKUP1 encodes a high-affinity potassium uptake activity in vivo. A small, low-affinity Rb+ uptake component was also detected in AtKUP1-expressing cells. RNA gel blot analysis showed that the various members of the AtKUP family have distinct patterns of expression, with AtKUP3 transcript levels being strongly induced by K+ starvation. It is proposed that plants contain multiple potassium transporters for high-affinity uptake and that the AtKUP family may provide important components of high- and low-affinity K+ nutrition and uptake into various plant cell types.
DNA Microarray Analysis of Submandibular Glands in IgG4-Related Disease Indicates a Role for MARCO and Other Innate Immune-Related Proteins

AbstractIgG4-related disease (IgG4-RD) is a novel systemic disease entity characterized by elevated serum IgG4 and tissue infiltration of IgG4-positive plasma cells accompanied by severe fibrosis. Although recent studies demonstrated that innate immune cells including monocytes and macrophages might promote local fibrosis and IgG4 production, the pathological mechanism remains unclear. In this study, we sought to identify the disease-associated genes, especially innate immune molecules.Gene expression was analyzed by DNA microarray in submandibular glands (SMGs) from patients with IgG4-RD (n = 5), chronic sialoadenitis (CS) (n = 3), and controls (n = 3). Differentially expressed genes (DEGs) were validated by real-time polymerase chain reaction (PCR) and immunohistochemical staining in IgG4-RD (n = 18), CS (n = 4), Sjögren syndrome (n = 11), and controls (n = 10). Gene expression patterns in the 3 groups were quite different from each other by the pvclust method and principal components analysis. In IgG4-RD, 1028 upregulated genes and 692 downregulated genes were identified as DEGs (P < 0.05). Gene Ontology (GO) term analysis indicated that the upregulated DEGs in IgG4-RD encoded proteins involved in T/B cell activation and chemotaxis. PCR validated significantly higher expression of macrophage receptor with collagenous structure (MARCO), a pattern-recognition receptor, in IgG4-RD compared with the other groups (P < 0.01). Immunohistochemical analysis confirmed that the expression pattern of MARCO was similar to that of the M2 macrophage marker CD163.MARCO was identified as a disease-associated molecule in IgG4-RD by DNA microarray. Moreover, M2 macrophages might contribute to the initiation of IgG4-RD via MARCO.
Using Ontology-Driven Methods to Develop Frameworks for Tackling NLP Problems

In this paper, we present the meta-tooling framework named TAISim that can be used both as a developer‟s tool for creating NLP systems and as a NLP learning environment, which allows helping students to construct NLP systems by example in a flexible way. TAISim enables the end user to combine different components of a typical NLP system in order to tackle specific NLP problems. We use ontology-engineering methods to accumulate meta-knowledge about the system construction and about users‟ activities to control the process of development and using the NLP system. Thanks to ontologydriven methods TAISim can be modified and enriched with additional information resources and program modules by means of a high-level interface. Additionally, we demonstrate how the using of meta-ontology helps us to improve TAISim to tackle ontology design automation problems.
The development and maintenance of human visceral pain hypersensitivity is dependent on the N-methyl-D-aspartate receptor.

BACKGROUND & AIMS Visceral hypersensitivity is a common feature of functional gastrointestinal disorders. One speculated mechanism is an activity-dependent increase in spinal cord neuronal excitability (central sensitization), which is dependent on activation of the N-methyl-D-aspartate (NMDA) receptor. Our aims were to determine whether the development and maintenance of human visceral hypersensitivity is NMDA receptor mediated. METHODS Healthy subjects were studied using a randomized, double-blind, placebo-controlled, crossover design. Pain thresholds to electrical stimulation were determined both in the proximal esophagus and in the foot (control) before and after a 30-minute distal esophageal infusion of 0.15 mol/L HCl acid. Ketamine (NMDA receptor antagonist) or saline (vehicle) was given intravenously either prior to or following acid infusion, and pain thresholds were measured for the following 120 minutes. Protocol 1: In 6 subjects, the effect of ketamine in the esophagus was assessed without acid infusion. Protocol 2: In 14 subjects, ketamine was given prior to esophageal acid. Protocol 3: In 12 subjects, ketamine was given after esophageal acid. RESULTS Protocol 1: In the absence of esophageal acid, ketamine had no effect on either esophageal or foot pain thresholds (area-under-the-curve, [AUC] P = 0.36 esophagus, P = 0.34 foot, ANOVA) within 30 minutes of cessation of the infusion. Protocol 2: Acid-induced esophageal hypersensitivity was prevented by ketamine (AUC, P < 0.0001, ANOVA) without affecting foot pain thresholds (AUC, P = 0.06, ANOVA). Protocol 3: Ketamine delivered after acid reversed the induction of esophageal hypersensitivity induced by acid (AUC, P < 0.0001, ANOVA). CONCLUSIONS The induction and maintenance of acid-induced esophageal hypersensitivity is prevented and reversed by ketamine. This finding strongly indicates that central sensitization is a mechanism of visceral hypersensitivity.
On the Polynomial Parity Argument Complexity of the Combinatorial Nullstellensatz

The complexity class PPA consists of NP-search problems which are reducible to the parity principle in undirected graphs. It contains a wide variety of interesting problems from graph theory, combinatorics, algebra and number theory, but only a few of these are known to be complete in the class. Before this work, the known complete problems were all discretizations or combinatorial analogues of topological fixed point theorems. Here we prove the PPA-completeness of two problems of radically different style. They are PPA-Circuit CNSS and PPA-Circuit Chevalley, related respectively to the Combinatorial Nullstellensatz and to the Chevalley-Warning Theorem over the two elements field GF(2). The input of these problems contain PPA-circuits which are arithmetic circuits with special symmetric properties that assure that the polynomials computed by them have always an even number of zeros. In the proof of the result we relate the multilinear degree of the polynomials to the parity of the maximal parse subcircuits that compute monomials with maximal multilinear degree, and we show that the maximal parse subcircuits of a PPA-circuit can be paired in polynomial time.
Episodic non-Markov localization: Reasoning about short-term and long-term features

Markov localization and its variants are widely used for localization of mobile robots. These methods assume Markov independence of observations, implying that observations made by a robot correspond to a static map. However, in real human environments, observations include occlusions due to unmapped objects like chairs and tables, and dynamic objects like humans. We introduce an episodic non-Markov localization algorithm that maintains estimates of the belief over the trajectory of the robot while explicitly reasoning about observations and their correlations arising from unmapped static objects, moving objects, as well as objects from the static map. Observations are classified as arising from long-term features, short-term features, or dynamic features, which correspond to mapped objects, unmapped static objects, and unmapped dynamic objects respectively. By detecting time steps along the robot's trajectory where unmapped observations prior to such time steps are unrelated to those afterwards, non-Markov localization limits the history of observations and pose estimates to “episodes” over which the belief is computed. We demonstrate non-Markov localization in challenging real world indoor and outdoor environments over multiple datasets, comparing it with alternative state-of-the-art approaches, showing it to be robust as well as accurate.
Input—Output Approach to Control for Fuzzy Markov Jump Systems With Time-Varying Delays and Uncertain Packet Dropout Rate

This paper is concerned with H∞ control problem for a class of discrete-time Takagi-Sugeno fuzzy Markov jump systems with time-varying delays under unreliable communication links. It is assumed that the data transmission between the plant and the controller are subject to randomly occurred packet dropouts satisfying Bernoulli distribution and the dropout rate is uncertain. Based on a fuzzy-basis-dependent and mode-dependent Lyapunov function, the existence conditions of the desired H∞ state-feedback controllers are derived by employing the scaled small gain theorem such that the closed-loop system is stochastically stable and achieves a guaranteed H∞ performance. The gains of the controllers are constructed by solving a set of linear matrix inequalities. Finally, a practical example of robot arm is provided to illustrate the performance of the proposed approach.
Flammability and thermal behavior of polypropylene composites containing dihydrogen phosphate anion‐intercalated layered double hydroxides

Dihydrogen phosphate anion-intercalated layered double hydroxides (M-LDHs) was prepared by modification of Mg-Al-CO32− layered double hydroxides (LDHs) with anion exchange procedure. The structure of the M-LDHs was characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and transmission electron microscope (TEM). Polypropylene (PP)/LDHs and PP/M-LDHs composites were prepared by melt compounding. The morphology of PP composites was investigated by TEM and XRD, which demonstrated that M-LDHs could be well dispersed in PP matrix to form a nano-scale exfoliated structure. Thermogravimetric analysis showed that thermal stability of PP composites was improved by the presence of LDHs and M-LDHs. The flammability of PP composites was characterized by limited oxygen index, vertical burning test (UL-94), FTIR, and cone calorimeter test, and the result showed the fire performance were significantly improved after the addition of LDHs and/or M-LDHs which can remarkably decrease the heat release rate, total heat release, and the fire performance index. It was proposed that the lamellar structure of LDHs can block the heat, dilute the flammable gases and decrease the temperature, while the replaced H2PO4− into LDHs molecules can enhance the charred layer formation during burning procedure. Inductively coupled plasma mass spectrometer analysis showed that most phosphorus remained in the char layer, suggesting the replaced H2PO4− in LDHs molecules mainly function in the condensed phase. POLYM. COMPOS. , 36:2230–2237, 2015. © 2014 Society of Plastics Engineers