Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring the Upper End of the Initial Mass Function with Supernovae

Supernovae arise from progenitor stars occupying the upper end of the initial mass function. Their extreme brightness allows individual massive stars to be detected at cosmic distances, lending supernovae great potential as tracers of the upper end of the IMF and its evolution. Exploiting this potential requires progress in many areas of supernova science. These include understanding the progenitor masses that produce various types of supernovae and accurately characterizing the supernova outburst and the environment in which it was produced. I present some preliminary work identifying the environmental conditions that produce the most luminous supernovae, believed to arise from stars with masses greater than 100 M_sun. I illustrate that the presence of these extreme supernovae in small star-forming dwarfs can be used to test our understanding of the upper end of the IMF.
Improving T-DNA Transfer to Tamarix hispida by Adding Chemical Compounds During Agrobacterium tumefaciens Culture

Agrobacterium tumefaciens-mediated gene transfer is the most commonly used method for plant genetic engineering. However, during the period of A. tumefaciens culture, the effects of Agrobacterium culture before inoculation on genetic transformation are poorly understood. In the present study, we investigated the factors that affect the genetic transformation efficiency during Agrobacterium culture using Tamarix hispida as transgenic plant material. Agrobacterium treatment with spermidine (Spe), azacitidine (5-AzaC), dithiothreitol (DTT), or acetosyringone (AS) alone all significantly improved the efficiency of T-DNA transfer. Treatment with 5-AzaC reduced DNA methylation in Agrobacterium to induce the expression of virulence (vir) family genes, including virA, virB1, virC1, virD2, virD4 virE2, and virG. Spe treatment significantly induced the expression of all the studied genes, including virA, virB1, virC1, virD1, virD2, virD4, virE2, and virG. DTT treatment decreased reactive oxygen species accumulation. AS treatment activated the expression of the genes virA, virB1, virC1, virD1, virD2, virD4 and virG. All these effects resulted in increased T-DNA transfer. Additionally, combined Spe, 5-AzaC, DTT, and AS treatment improve Agrobacterium infection to a greater extent compared with their use alone, increasing T-DNA transfer by more than 8-fold relative to no treatment. Therefore, to improve genetic transformation, pretreatment of Agrobacterium during the culture period is important for improving genetic transformation efficiency.
Identification of an Essential Cis-Element Near the Transcription Start Site for Transcriptional Activation of the Proliferating Cell Nuclear Antigen Gene (*)

Interleukin 2 (IL-2) stimulates T lymphocyte proliferation and induces the expression of proliferating cell nuclear antigen (PCNA), a processivity factor for DNA polymerase . Previously, deletion analysis suggested cis-element(s) in the proximal region of the PCNA promoter (−40 to +143) are required for IL-2 induction in cloned T lymphocytes. The sequence 5′-TTGCGGGC-3′ located at +10 to +17 is similar to the E2F consensus binding site and is required for optimal PCNA promoter activity. In IL-2-stimulated T cells, nuclear proteins are induced to bind to this sequence as demonstrated using electrophoretic mobility shift assay (EMSA), competition EMSA, and methylation interference analysis. A 180-kDa polypeptide was detected by UV cross-linking to bind specifically to the PCNA E2F-like sequence. Our data indicate that the protein bound to the PCNA E2F-like site is not one of the transcription factor E2F proteins. Our results demonstrate that the E2F-like sequence and the protein(s) binding to it are required for optimal PCNA promoter activity and IL-2 induction of PCNA expression.
Exome-wide association study identifies four novel loci for systemic lupus erythematosus in Han Chinese population

Objectives Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of considerable genetic predisposition. Genome-wide association studies have identified tens of common variants for SLE. However, the majority of them reside in non-coding sequences. The contributions of coding variants have not yet been systematically evaluated. Methods We performed a large-scale exome-wide study in 5004 SLE cases and 8179 healthy controls in a Han Chinese population using a custom exome array, and then genotyped 32 variants with suggestive evidence in an independent cohort of 13 246 samples. We further explored the regulatory effect of one novel non-coding single nucleotide polymorphism (SNP) in ex vivo experiments. Results We discovered four novel SLE gene regions (LCT, TPCN2, AHNAK2 and TNFRSF13B) encompassing three novel missense variants (XP_016859577.1:p.Asn1639Ser, XP_016859577.1:p.Val219Phe and XP_005267356.1:p.Thr4664Ala) and two non-coding variants (rs10750836 and rs4792801) with genome-wide significance (pmeta <5.00×10−8). These variants are enriched in several chromatin states of primary B cells. The novel intergenic variant rs10750836 exhibited an expression quantitative trait locus effect on the TPCN2 gene in immune cells. Clones containing this novel SNP exhibited gene promoter activity for TPCN2 (P=1.38×10−3) whose expression level was reduced significantly in patients with SLE (P<2.53×10−2) and was suggested to be further modulated by rs10750836 in CD19+ B cells (P=7.57×10−5) in ex vivo experiments. Conclusions This study identified three novel coding variants and four new susceptibility gene regions for SLE. The results provide insights into the biological mechanism of SLE.
Improving Auditory Warning Design: Quantifying and Predicting the Effects of Different Warning Parameters on Perceived Urgency

The effects of four parameters (speed, fundamental frequency, repetition units, and inharmonicity) on perceived urgency were scaled using an application of Stevens's power law. From the exponents obtained, equal units of urgency change were calculated for three parameters. The units were combined in a set of stimuli, and the order of urgency was predicted. The obtained and predicted orders of urgency were highly correlated. The results also showed that even when equalized by psychophysical techniques, some parameters contribute more to perceived urgency than do others. This may be attributable to the different types of parameters scaled or the proportion of the usable range of each parameter that represents a unit change in urgency. The implication of the work for the design and improvement of auditory warnings is discussed.
Probabilistic modeling for segmentation in magnetic resonance images of the human brain

This thesis deals with the fully automatic generation of sem antic annotations for medical imaging data by means of medical image segmentation and labe ling. In particular, we focus on the segmentation of the human brain and related stru ctures from magnetic resonance imaging (MRI) data. We present three novel probabilis tic methods from the field of database-guided knowledge-based medical image segment ation. We apply each of our methods to one of three MRI segmentation scenarios: 1) 3-D MRI b rain tissue classification and intensity non-uniformity correction, 2) pediat ric brain cancer segmentation in multi-spectral 3-D MRI, and 3) 3-D MRI anatomical brain struct ure segmentation. All the newly developed methods make use of domain knowledge enc od d by probabilistic boosting-trees (PBT), which is a recent machine learning tec hnique. For all the methods we present uniform probabilistic formalisms that group the methods into the broader context of probabilistic modeling for the purpose of image s egmentation. We show by comparison with other methods from the literature that in al l the scenarios our newly developed algorithms in most cases give more accurate results and have a lower computational cost. Evaluation on publicly available benchmarking data s ets ensures reliable comparability of our results to those of other current and future met hods. We also document the participation of one of our methods in the ongoing online cau date segmentation challenge (www.cause07.org), where we rank among the top five methods f or this particular segmentation scenario.
Analysis of Protein Transport to Lysosomes

Lysosomes are terminal degradative organelles that are found in all higher eukaryotic cells. The biogenesis of lysosomes involves the transport of various acid hydrolases and transmembrane glycoproteins from their site of synthesis in the endoplasmic reticulum through the biosynthetic and endocytic pathways. Protein transport to lysosomes can be studied by a combination of techniques based on the separation of intracellular organelles. Percoll density gradient centrifugation has long been the method of choice for separating lysosomes from other organelles in cell homogenates, and accordingly, this unit describes protocols for obtaining reasonably pure lysosomal fractions from mammalian cells using Percoll density gradient separation.
Linear and ellipsoidal pattern separation : theoretical aspects and experimental analysis

This thesis deals with a pattern classification problem, which geometrically implies data separation in some Euclidean feature space. The task is to infer a classifier (a separating surface) from a set or sequence of observations. This classifier would later be used to discern observations of different types. In this work, the classification problem is viewed from the perspective of the optimization theory: we suggest an optimization problem for the learning model and adapt optimization algorithms for this problem to solve the learning problem. The aim of this research is twofold, so this thesis can be split into two self-contained parts because it deals with two different type of classifiers each in a different learning setting. The first part deals with linear classification in the online learning setting and includes analysis of existing polynomial-time algorithms: the ellipsoid algorithm and the perceptron rescaling algorithm. We establish that they are based on different types of the same space dilation technique, and derive the parametric version of the latter algorithm, which allows to improve its complexity bound and exploit some extra information about the problem. We also interpret some results from the information-based complexity theory to the optimization model to suggest tight lower bounds on the learning complexity of this family of problems. To conclude this study, we experimentally test both algorithms on the positive semidefinite constraint satisfaction problem. Numerical results confirm our conjectures on the behaviour of the algorithms when the dimension of the problem grows. In the second part, we shift our focus from linear to ellipsoidal classifiers, which form a subset of second-order decision surfaces, and tackle a pattern separation problem with two concentric ellipsoids where the inner encloses one class (which is normally our class of interest, if we have one) and the outer excludes inputs of the other class(es). The classification problem leads to semidefinite program, which allows us to harness the efficient interior-point algorithms for solving it. This part includes analysis of the maximal separation ratio algorithm
Molar-incisor hypomineralisation: prevalence and defect characteristics in Iraqi children.

BACKGROUND. Little prevalence data relating to molar incisor hypomineralisation (MIH) exist for Middle East populations. AIM. To evaluate the prevalence and the clinical features of MIH in school-aged children residing in Mosul City, Iraq. DESIGN. A cluster sample of 823 7- to 9-year-old children had their first permanent molars and incisors (index teeth) evaluated using the European Academy of Paediatric Dentistry (EAPD) criteria for MIH. The examinations were conducted at schools by a calibrated examiner. RESULTS. Of the children examined, 177 (21.5%) had hypomineralisation defects in at least one index tooth, 153 (18.6%) had at least one affected first molar or first molars and incisors and were considered as having MIH. The most commonly affected teeth were maxillary molars. Demarcated creamy white opacities were the most frequent lesion type. Dental restorations and tooth extraction because of MIH were uncommon. Children with three or more affected teeth were 3.7 times more likely to have enamel breakdown when compared with those children having only one or two affected teeth. CONCLUSIONS. Molar incisor hypomineralisation was common amongst Iraqi children. Demarcated opacities were more prevalent than breakdown. The severity of the lesions increased with the number of affected teeth. The more severe the defect, the greater the involved tooth surface area.
Muscle glycogen storage after different amounts of carbohydrate ingestion.

The purpose of this study was to determine whether the rate of muscle glycogen storage could be enhanced during the initial 4-h period postexercise by substantially increasing the amount of the carbohydrate consumed. Eight subjects cycled for 2 h on three separate occasions to deplete their muscle glycogen stores. Immediately and 2 h after exercise they consumed either 0 (P), 1.5 (L), or 3.0 g glucose/kg body wt (H) from a 50% glucose polymer solution. Blood samples were drawn from an antecubital vein before exercise, during exercise, and throughout recovery. Muscle biopsies were taken from the vastus lateralis immediately, 2 h, and 4 h after exercise. Blood glucose and insulin declined significantly during exercise in each of the three treatments. They remained below the preexercise concentrations during recovery in the P treatment but increased significantly above the preexercise concentrations during the L and H treatments. By the end of the 4 h-recovery period, blood glucose and insulin were still significantly above the preexercise concentrations in both treatments. Muscle glycogen storage was significantly increased above the basal rate (P, 0.5 mumol.g wet wt-1.h-1) after ingestion of either glucose polymer supplement. The rates of muscle glycogen storage, however, were not different between the L and H treatments during the first 2 h (L, 5.2 +/- 0.9 vs. H, 5.8 +/- 0.7 mumol.g wet wt-1.h-1) or the second 2 h of recovery (L, 4.0 +/- 0.9 vs. H, 4.5 +/- 0.6 mumol.g wet wt-1. h-1). (ABSTRACT TRUNCATED AT 250 WORDS)
An adaptive control scheme for real-time media streaming over wireless networks

Real time video streaming over wireless networks is not trivial because of the two characteristics of the wireless networks - (1) smaller bandwidth and (2) unreliable transmission media. An adaptive real-time video streaming scheme that uses the layered video technique is proposed. Two attributes that are used to determine the network situation and then adjust the sending rate accordingly are loss rate and round trip time (RTT). Since the unreliable media cause of packet loss in the wireless environment is rate-independent, a method that can separate the rate-independent loss from the congestion loss is needed. We use inter-arrival time between two received packets to identify if an out of order packet was received in time to do the packet loss separating. When a congestion situation is determined, the sending rate of the sender is dropped down one layer; when an unloaded situation is determined, the sending rate of the sender is raised up one layer. In this way, the adaptive real-time video streaming can be achieved for wireless networks.
Interaction analysis–based information modeling of complex electromechanical systems in the processing industry

Information modeling for complex electromechanical systems in the processing industry is the foundation for system vulnerability analysis, failure propagation mechanism, and fault root cause tracing driven by data analysis. Focusing on the difficulties in information modeling for complex electromechanical systems, a new approach based on interaction analysis and a general framework for information modeling of complex electromechanical systems are proposed. First, the basic structures of the information model are defined based on monitoring data. Second, an improved symbolic transfer entropy method with procedures for optimizing the number of symbols, phase space reconstruction, binary encoding, and decimal decoding are proposed to detect the interaction direction and quantify the interaction strength between different monitoring variables. Third, some optional methods are introduced to simplify and modify models. Finally, a directed-weighted information model for a specific complex electromechanical system is constructed based on information flow. An actual information modeling application of a complex electromechanical system is used to demonstrate the proposed method and compare it with existing methods. This new approach can handle general information modeling problems and overcome the drawbacks of existing methods since all the monitoring variables are used to improve integrity of the model, and prior knowledge about the physical structure and key points’ selection are not required. A unique and complete information model is obtained regardless of the choice of the initial variable. Thus, the proposed method can be flexibly and effectively used in information modeling for complex electromechanical systems in the processing industry and formulate the foundation of system vulnerability analysis, failure propagation mechanism, and fault root cause tracing methodology, as well as other engineering applications.
A study of transition mechanism in knowledge creation based on organizational learning

The main purpose of this article is to develop a proper method with theory of energy level transition combined with organizational learning for analyzing knowledge creation in firms. For this purpose, guided by knowledge-based view and knowledge creation process, as well as energy level theory in physics, we address the relationship between organizational learning and knowledge creation and propose a set of important concept combining transition with “organizational learning-knowledge creation” process. We further build a transition model of knowledge creation based on organizational learning. The vital implication of the model is the 3 stages embedded in it. Hence we discuss each stage in detail. This kind of research encourages the belief that there is a transition mechanism in knowledge creation process in firms, based on organizational learning. The framework used in this article could provide references for studies in knowledge creation, organizational learning, as well as “knowledge creation-organizational learning” process inside and outside firms.
The use of spiral loops in serological and virological micro-methods.

For commemoration of 50th anniversary of foundation of this journal, an article of historical interest, and of general importance is reprinted in the present volume accompanied by current editorial notes. On 6 June 1955 an article was submitted for publication by Gyula Takatsy M.D., senior virologist at State Institute of Public Health, Budapest, initiating a new era - the era of microtechniques - in microbiology and other fields of natural science. The article with reference 1955, 3: 191-202 together with current editorial notes appear below.
Fast full-wave analysis of a cylindrical antenna using a single integral with an exact kernel

This paper presents a fast approach in the method-of-moments (MoM) analysis so as to obtain the nonuniform current distributions of cylindrical antennas with electrically large radii. An oblique incident field in its general form and a delta-gap source are considered in the formulation of nonuniform current distributions. In the Galerkin's MoM procedure, the Fourier cosine series is considered as the entire domain basis function series. In this formulation, the kernel is represented by a series of weighted spherical Hankel functions of the second kind and the convergence of this series is fast. As the result, the computation time is short. The Mathematica package is used to obtain and plot the current distributions along the cylindrical antennas.
Free hydroxyl groups are not required for endotoxic activity of lipid A

Previous studies demonstrated that lipid A from Salmonella abortusequi loses its B-cell mitogenicity for murine spleen cells as a result of the introduction of succinyl residues on hydroxyl groups and that the inactivated lipid A specifically antagonizes the mitogenicity of endotoxin. Hypothesizing that the hydroxyl groups are essential both for its biological activity and for producing nontoxic preparations having antagonistic activity, I tested the role of the hydroxyl groups in its activities by using well-characterized biologically active lipid A preparations synthesized chemically (Escherichia coli and Salmonella types 506 and 516, respectively) by the introduction of either succinyl or acetyl residues at the hydroxyl groups of each of these lipid A preparations. However, the biological activities of neither lipid A preparation were reduced at all after succinylation; in fact, succinylated 516 became much more potent than the original molecule with respect to most activities tested, i.e., lethal toxicity, Limulus gelation activity, and the induction of tumor necrosis factor release. On the other hand, when the hydroxyl groups were replaced with acetyl residues, the lethality and tumor necrosis factor-inducing activity of both lipid A preparations were decreased, whereas their Limulus gelation activity was increased. Mitogenicity was not affected much by the chemical modifications of either lipid A preparation. These findings indicate that although the residues introduced into the free hydroxyl groups of lipid A modulate its activities, the hydroxyl groups in lipid A need not exist in free form.
INSAR imagery of surface currents, wave fields, and fronts

The authors demonstrate the ability of interferometric radar imagery to determine both relative and absolute surface velocities in the open ocean. Absolute phase calibration is accomplished by noting the azimuthal displacement of range-travelling targets-demonstrating for the first time that under favourable circumstances phase calibration can be achieved in open-ocean in the absence of ground truth. The high resolution of radar imagery permits observation of sharp velocity discontinuities, e.g. the Gulf Stream boundary and the wave field. The recent SIR-C/X-SAR shuttle missions dramatically emphasize the experimental and observational aspects of space-based radar. The combination of absolute velocities, high spatial resolution, and wide-area coverage suggest that interferometric radar imagery can provide a unique and powerful aid both for studies of global circulation patterns and detailed analysis of slope/shelf water interactions with ocean currents. In particular, the authors employ this measurement of the surface currents and wave field near a velocity front to help refine and bound results of their modeling of calculated radar images of the front. The results of this paper are compared with available ground truth. >