Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammation and short-term cardiopulmonary effects of particulate matter

Correlations between short-term exposures to urban air particulate matter (PM) and increased morbidity and mortality for various cardiopulmonary diseases have been explained by the pro-inflammatory and pro-thrombotic effects of PM. This review updates a recent one by Scapellato and Lotti () and discusses the correlations between PM exposures, inflammatory endpoints and functional changes. Panel studies and controlled exposures to PM of various sizes in either healthy individuals, asthmatics and patients with coronary heart diseases, do not provide strong evidence of an inflammatory pathophysiology of PM toxicities. Contradictory results among reviewed studies could be explained by difficulties in dissecting inflammation brought about by PM from that of the ongoing diseases. However, other mechanisms, such as neurological ones, might be more relevant and co-exist with inflammation.
Integrative radiogenomic analysis for genomic signatures in glioblastomas presenting leptomeningeal dissemination

AbstractDespite therapeutic advances, the prognosis for glioblastoma (GBM) remains poor. In particular, leptomeningeal dissemination (LMD) has a dismal prognosis. The aim of this study was to identify tumor molecular phenotype, which has a great propensity to develop LMD. Between May 2004 and December 2012, a total of 145 GBM tumor samples were obtained from data registry. A total of 20 of the 145 patients with GBM were found to develop LMD. A specialized radiologist confirmed the diagnosis of LMD on magnetic resonance imaging. To clarify the genomic signatures in GBM with LMD, we performed integrative analysis of whole transcriptome sequencing and copy number alteration in the radiological features indicating LMD phenotypes in GBM. Eleven newly diagnosed patients with GBM with LMD had worse prognosis than those without LMD (median 5.55 vs. 12.94 months, P < 0.0001). Integrating analysis using gene expression based on the change of copy number revealed that SPOCK1, EHD2, SLC2A3, and ANXA11 were highly expressed with the gain of copy number, compared with the gene expression in the non-LMD group. In addition, it was demonstrated that NME2, TMEM100, and SIVA1 were downregulated with the loss of copy number. We also found that mesenchymal subtype accounted for 50% in LMD group, whereas mesenchymal subtype consisted of 29% in non-LMD group, even though there was no statistical significance (P = 0.06). Through this radiogenomic analysis, we suggested the possibility of finding candidate genes associated with LMD and highlighted the significance of integrating approach to clarify the molecular characteristics in LMD.
Transcriptional activators enhance polyadenylation of mRNA precursors

3’ processing of mRNA precursors is frequently coupled to transcription by RNA polymerase II (RNAP II). This coupling is well known to involve the C-terminal domain of the RNAP II largest subunit, but a variety of other transcription-associated factors have also been suggested to mediate coupling. Our recent studies have provided direct evidence that transcriptional activators can enhance the efficiency of transcription-coupled 3’ processing. In this point-of-view, we discuss the mechanisms that underlie coupling, and their implications for control of alternative polyadenylation, which is emerging as a significant regulator of cell growth control.
Production of Apricot Vinegar Using an Isolated Acetobacter Strain from Iranian Apricot

Vinegar or sour wine is a product of alcoholic and subsequent acetous fermentation of sugary precursors derived from several fruits or starchy substrates. This delicious food additive and supplement contains not less than 4 grams of acetic acid in 100 cubic centimeters at 20°C. Among the large number of bacteria that are able to produce acetic acid, only few genera are used in vinegar industry most significant of which are Acetobacter and Gluconobacter. In this research we isolated and identified an Acetobacter strain from Iranian apricot, a very delicious and sensitive summer fruit to decay, we gathered from fruit's stores in Isfahan, Iran. The main culture media we used were Carr, GYC, Frateur and an industrial medium for vinegar production. We isolated this strain using a novel miniature fermentor we made at Pars Yeema Biotechnologists Co., Isfahan Science and Technology Town (ISTT), Isfahan, Iran. The microscopic examinations of isolated strain from Iranian apricot showed gram negative rods to cocobacilli. Their catalase reaction was positive and oxidase reaction was negative and could ferment ethanol to acetic acid. Also it showed an acceptable growth in 5%, 7% and 9% ethanol concentrations at 30°C using modified Carr media after 24, 48 and 96 hours incubation respectively. According to its tolerance against high concentrations of ethanol after four days incubation and its high acetic acid production, 8.53%, after 144 hours, this strain could be considered as a suitable industrial strain for a production of a new type of vinegar, apricot vinegar, with a new and delicious taste. In conclusion this is the first report of isolation and identification of an Acetobacter strain from Iranian apricot with a very good tolerance against high ethanol concentrations as well as high acetic acid productivity in an acceptable incubation period of time industrially. This strain could be used in vinegar industry to convert apricot spoilage to a beneficiary product and mentioned characteristics have made it as an amenable strain in food and agricultural biotechnology. Keywords—Acetic Acid Bacteria, Acetobacter, Fermentation, Food and Agricultural Biotechnology, Iranian Apricot, Vinegar.
Model Minimization in Markov Decision Processes

We use the notion of stochastic bisimulation homogeneity to analyze planning problems represented as Markov decision processes (MDPs). Informally, a partition of the state space for an MDP is said to be homogeneous if for each action, states in the same block have the same probability of being carried to each other block. We provide an algorithm for finding the coarsest homogeneous refinement of any partition of the state space of an MDP. The resulting partition can be used to construct a reduced MDP which is minimal in a well defined sense and can be used to solve the original MDP. Our algorithm is an adaptation of known automata minimization algorithms, and is designed to operate naturally on factored or implicit representations in which the full state space is never explicitly enumerated. We show that simple variations on this algorithm are equivalent or closely similar to several different recently published algorithms for finding optimal solutions to (partially or fully observable) factored Markov decision processes, thereby providing alternative descriptions of the methods and results regarding those algorithms.
Feed additives for swine: Fact sheets – high dietary levels of copper and zinc for young pigs, and phytase

This is the fourth in a series of peer-reviewed Practice tip articles, each including two or three fact sheets. Previous practice tips included fact sheets on acidifi ers and antibiotics in the September-October issue (J Swine Health Prod. 2009;17:270–275); on carcass modifi ers, carbohydrate-degrading enzymes, and proteases, and anthelmintics in the November-December issue (J Swine Health Prod. 2009;17:325–332); and on fl avors and mold inhibitors, mycotoxin binders, and antioxidants in the January-February issue (J Swine Health Prod. 2010;18:27–32) Future fact-sheet topics will include probiotics and prebiotics and phytogenic feed additives (phytobiotics or botanicals).
DFiant: A dataflow hardware description language

Today's dominant hardware description languages (HDLs), namely Verilog and VHDL, tightly couple design functionality with timing requirements and target device constraints. As hardware designs and device architectures became increasingly more complex, these dominant HDLs yield verbose and unportable code. To raise the level of abstraction, several high-level synthesis (HLS) tools were introduced, usually based on software languages such as C++. Unfortunately, designing with sequential software language constructs comes with a price; the designer loses the ability to control hardware construction and data scheduling, which is crucial in many design use-cases. In this paper, we introduce DFiant, a Scala-based HDL that uses the dataflow model to decouple functionality from implementation constraints. DFiant's frontend enables functional bit-accurate dataflow programming, while maintaining a complete timing-agnostic and device-agnostic code. DFiant bridges the gap between software programming and hardware construction, driving an intuitive functional object oriented code into a highperformance hardware implementation.
Five-fingered haptic interface robot: HIRO III

This paper presents the design and characteristics of a five-fingered haptic interface robot: HIRO III. The aim of the paper is to provide a high-precision force representation at the five human fingertips. HIRO III consists of a 15-degree-of-freedom (DOF) haptic hand, a 6 DOF interface arm and a control system. The haptic interface, which consists of a robot arm and hand, can be used in a large workspace and can provide multipoint contact between the user and a virtual environment. However, the following problems peculiar to a multi-DOF robot have resulted: a backlash, a large amount of friction, many motors, and many sensors. In order to solve these problems, a new mechanism and a wire-saving control system have been designed and developed. Furthermore, experiments in both free space and constraint space have been carried out. In comparison with the previous HIRO, the force errors in free space and in constraint space have been reduced to 30% and 57%, respectively. These results show a high-precision force representation and the great potential of HIRO III.
Simultaneous rotation and translation movement for four omnidirectional wheels holonomic mobile robot

Navigation and positioning is the main system for a mobile robot. Holonomicity in the field of robotic has becoming more and more important as it allow the mobile robot to do translation and rotation movements. Although many research had done to overcome the poor motion stability and trajectory motion using three omnidirectional wheels, they may have stability problems due to triangular contact area with the ground and the payload they carry. Thus, to increase the movement efficiency of the holonomic mobile robot, simultaneous translation and rotation movements for four omnidirectional wheels holonomic mobile robot was introduced. To create the system for the movement, a methodology is laid out in this paper. A kinematic analysis was done on the movement of the holonomic mobile robot. The algorithm of the kinematic movement of the mobile robot then was developed. A test grid was carry out to test the navigation algorithm of the system and the result is within the acceptable range. This algorithm would allow the holonomic mobile robot to do translation and rotation movements either simultaneously or independently.
Quantification of Grain Boundary Mediated Plasticity Mechanisms in Nanocrystalline Metals

Nanocrystalline metals have been a topic of great discussion over recent years due to their exceptional strengths and novel grain boundary-mediated deformation mechanisms. Their microstructures are known to evolve through dynamic processes such as grain boundary migration and grain rotation, but how the collective interaction of these mechanisms alter the microstructure on a larger scale is not completely understood. In this thesis, we present coupled atomistic modeling and experimental tasks that aim to understand how the grain structure, grain boundaries, and associated grain boundary network change during nanocrystalline plasticity. Due to the complex three-dimensional nature of these mechanisms and the limited spatial and temporal resolution of current in-situ experimental techniques, we turn to atomistic modeling to help understand the dynamics by which these mechanisms unfold. In order to provide a quantitative analysis of this behavior, we develop a tool which fully characterizes nanocrystalline microstructures in atomistic models and subsequently tracks their evolution during molecular dynamics simulations. We then use this algorithm to quantitatively track grain structure and boundary network evolution in plastically deformed nanocrystalline Al, finding that higher testing temperature and smaller average grain size results in increased evolution of grain structure with evidence of larger scale changes to the grain boundary network also taking place. This prompts us to extend our analysis technique to include full characterization of grain boundary networks and rigorous topographical feature identification. We then employ this tool on simulations of Al subject to monotonic tension, cycling loading, and simple annealing, and find that each case results in different evolution of the grain boundary network. Finally, our computational work is complemented synergistically by experimental analyses which track surface microstructure evolution during sliding wear of nanocrystalline Ni-W thin films. These experiments track the development of a surface grain growth layer which evolves through grain boundary mediated plasticity and we are able to make direct connections between this evolution and that which was observed in our simulation work. All of the findings of this thesis are a direct result of the dynamic and collective nature by which nanocrystalline materials deform.
Dynamic modeling of engine combustion system using approximated kernel method

Recently, modeling methods using dynamic measurement data have attracted much attention in the automotive industry. A mathematical model of the gasoline engine is constructed in order to express and predict its transient response during running. Since in the modeling process, we need to handle an extremely large data set, the computational cost increases accordingly. In this paper, we apply the approximated kernel method to combustion modeling in the gasoline engine. An approximation of the kernel reduces the computational cost and enables us to handle a large data set. In addition, a strategy for setting tunable parameters is proposed by analyzing their effect on the model accuracy. The effectiveness of the approach is illustrated by constructing a combustion model using experimental data.
New Applications of FIB: a 3D Look into the Past throughout the Ultrastructure of Fossil Plant Cuticles

As it is well known, every material respond in a different way to the ion beam; therefore, the methodology we developed for the previously cited palynological specimens could not be directly applied. In particular, we found out that the use of water vapour-enhanced milling (SCE, Selective Carbon Etching), which would normally speed up the milling process in organic materials, result in the formation of large columnar structures inside the trench (Figs 1a, b). X-ray analysis revealed them to be mostly composed of Ga, which rules out redeposition of milled material as an explanation. A detailed study was therefore carried out to determine the best experimental conditions.
International Journal of Behavioral Nutrition and Physical Activity Home Grocery Delivery Improves the Household Food Environments of Behavioral Weight Loss Participants: Results of an 8-week Pilot Study

Background: Household food availability is consistently linked to dietary intake; yet behavioral weight control treatment includes only minimal instruction on how to change the home environment to support dietary goals. This pilot study examined whether it is feasible to change the household food environments of behavioral weight loss participants through the use of a commercially available grocery home delivery service.
The potential for ductility enhancement from surface and interface dislocation sources in NiAl

Limited ductility and toughness of NiAl and related aluminides near room temperature pose major problems in their potential application as structural materials. An analysis of these problems is presented as part of a review of the flow and fracture behavior of binary NiAl. Following this discussion is a demonstration that conditions of elastic and plastic constraint associated with phase boundaries afforded by surface films, internal lamellae, or precipitates may introduce sufficient densities of mobile dislocations to enhance the ductility of NiAl-based materials by significant amounts. Examples of this behavior are presented for several model materials, including 001- and 123-oriented single crystals of oxide-coated NiAl, directionally solidified beta-gamma-prime (Ni70Al30) and beta-gamma (Ni50Fe30Al20) in situ composites, and several NiAl/precipitate systems. The nature of the resulting dislocation substructures and the effects of several materials variables are described.
Disseminated Tumor Cells in Prostate Cancer Patients after Radical Prostatectomy and without Evidence of Disease Predicts Biochemical Recurrence

Purpose: Men with apparently localized prostate cancer often relapse years after radical prostatectomy. We sought to determine if epithelial-like cells identified from bone marrow in patients after radical prostatectomy, commonly called disseminated tumor cells (DTC), were associated with biochemical recurrence. Experimental Design: We obtained bone marrow aspirates from 569 men prior to radical prostatectomy and from 34 healthy men with prostate-specific antigens <2.5 ng/mL to establish a comparison group. Additionally, an analytic cohort consisting of 98 patients with no evidence of disease (NED) after radical prostatectomy was established to evaluate the relationship between DTC and biochemical recurrence. Epithelial cells in the bone marrow were detected by magnetic bead enrichment with antibodies to CD45 and CD61 (negative selection) followed by antibodies to human epithelial antigen (positive selection) and confirmation with FITC-labeled anti-BerEP4 antibody. Results: DTC were present in 72% (408 of 569) of patients prior to radical prostatectomy. There was no correlation with pathologic stage, Gleason grade, or preoperative prostate-specific antigens. Three of 34 controls (8.8%) had DTC present. In patients with NED after radical prostatectomy, DTC were present in 56 of 98 (57%). DTC were detected in 12 of 14 (86%) NED patients after radical prostatectomy who subsequently suffered biochemical recurrence. The presence of DTC in NED patients was an independent predictor of recurrence (hazard ratio 6.9; 95% confidence interval, 1.03-45.9). Conclusions: Approximately 70% of men undergoing radical prostatectomy had DTC detected in their bone marrow prior to surgery, suggesting that these cells escape early in the disease. Although preoperative DTC status does not correlate with pathologic risk factors, persistence of DTC after radical prostatectomy in NED patients was an independent predictor of recurrence.
Activity of Voriconazole Combined with Neutrophils or Monocytes against Aspergillus fumigatus: Effects of Granulocyte Colony-Stimulating Factor and Granulocyte-Macrophage Colony-Stimulating Factor

ABSTRACT Voriconazole (VCZ) was tested for antifungal activity againstAspergillus fumigatus hyphae alone or in combination with neutrophils or monocytes. Antifungal activity was measured as percent inhibition of hyphal growth in assays using the dye MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] or XTT [2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide]. With both assays, VCZ inhibited hyphal growth at concentrations of <1 μg/ml and was almost as active as amphotericin B. VCZ (0.6 μg/ml) was sporicidal, as was amphotericin B (0.4 μg/ml). With both the MTT and XTT assays, neutrophils alone inhibited hyphae; when combined with VCZ, there was additive activity. Both granulocyte colony-stimulating factor- and granulocyte-macrophage colony-stimulating factor (GM-CSF)-treated polymorphonuclear neutrophils (PMN) had enhanced inhibition of hyphal growth. Moreover, such treatment of PMN also enhanced the collaboration of PMN with VCZ. Monocytes inhibited hyphal growth. When VCZ was combined with monocytes or monocytes were treated with GM-CSF, inhibition was significantly increased, to similar levels. However, the combination of VCZ with GM-CSF treatment of monocytes did not significantly increase the high-level inhibition by monocytes with either agent alone.
Role of Protein Kinase Cα in Regulation of [Ca2+]I and Force in Human Myometrium

Recent findings implicate protein kinase C in regulation of contraction of uterine muscle (myometrium). However, the role of protein kinase C isoforms in myometrial contraction remains uncertain. Therefore, this study examined protein kinase Cα's role in regulation of contraction and intracellular calcium concentration ([Ca2+]I) of myometrium from term pregnant women. The authors demonstrated that protein kinase Cα inhibitor Go6976 decreased the amplitude of potassium chloride—induced myometrial contractions in a time-dependent manner. The treatment of the myometrial strips with protein kinase Cα—specific antisense oligodeoxynucleotides decreased the potassium chloride—induced contraction and [Ca2+]I response to 39.3% + 6.8% and 50.0% + 3.3%, respectively, compared to control. The sense oligonucleotides treatment did not significantly change the potassium chloride responses (89.8% + 6.8% and 93.9% + 4.5% of the control for the contraction and [Ca2+]I, respectively). These data, coupled with the observation that protein kinase Cα levels are elevated in the pregnant myometrium, suggest the involvement of protein kinase Cα in regulation of human uterine contraction.
Breadcrumbs: efficient context sensitivity for dynamic bug detection analyses

Calling context--the set of active methods on the stack--is critical for understanding the dynamic behavior of large programs. Dynamic program analysis tools, however, are almost exclusively context insensitive because of the prohibitive cost of representing calling contexts at run time. Deployable dynamic analyses, in particular, have been limited to reporting only static program locations. This paper presents Breadcrumbs, an efficient technique for recording and reporting dynamic calling contexts. It builds on an existing technique for computing a compact (one word) encoding of each calling context that client analyses can use in place of a program location. The key feature of our system is a search algorithm that can reconstruct a calling context from its encoding using only a static call graph and a small amount of dynamic information collected at cold (infrequently executed) callsites. Breadcrumbs requires no offline training or program modifications, and handles all language features, including dynamic class loading. We use Breadcrumbs to add context sensitivity to two dynamic analyses: a data-race detector and an analysis for diagnosing null pointer exceptions. On average, it adds 10% to 20% runtime overhead, depending on a tunable parameter that controls how much dynamic information is collected. Collecting less information lowers the overhead, but can result in a search space explosion. In some cases this causes reconstruction to fail, but in most cases Breadcrumbs >produces non-trivial calling contexts that have the potential to significantly improve both the precision of the analyses and the quality of the bug reports.