Miracle-dz/UniFAR-FTUs huggingface dataset:
Chess: retargetable code generation for embedded DSP processors

This chapter introduces Chess, a retargetable code generation environment for xed-point DSP processors. Chess addresses a range of commercial as well as application-speciic processors, which are increasingly being used for embedded applications in telecommunications, speech and audio processing. Chess is based on a mixed be-havioural/structural processor representation model, which can account for many architectural peculiarities that are typical for xed-point DSP processors. In addition , the code generator is employing a number of eecient optimisation techniques. These features result in highly optimal machine code.
Polysilicon thin-film transistors using self-aligned cobalt and nickel silicide source and drain contacts

Polysilicon thin-film transistors (TFTs) with island thickness of 20 and 70 nm were fabricated with self-aligned cobalt and nickel silicide contacts to the source and drain. The silicide contacts are shown to reduce the series resistance, which limits the on-current of the device, thus significantly increasing the effective mobility in the 20-nm island devices. The mobilities of 20-nm cobalt and nickel silicided devices are similar to those with 70-nm islands, 31 versus 33 cm/sup 2//V-s, whereas the nonsilicided 20-nm devices have a mobility of only 13 cm/sup 2//V-s. The island thickness is shown to influence other device parameters affecting active matrix display driver circuit design, such as threshold voltage, leakage current, and subthreshold swing; all these parameters are improved when the island thickness is decreased.
Population control among hunter/gatherers.

Abstract This paper reaffirms that population levels in hunter/gatherers are closely tied to resource levels, although density is characteristically maintained at a fraction of carrying capacity. This is shown to be a function of physiological and cultural controls acting within the framework of natural selection between groups. Apparent differences between cultural population control mechanisms in apes and hunter/gatherers are noted, and a limited reconstruction of probable control mechanisms in Australopithecus is made. The maintenance of population control vis‐a‐vis resources is shown to be a dominant factor in natural selection. It is argued that among early hominids, at a time when pressures keeping individuals in large groups were being annulled, social traits such as extended kinship roles, ritual obligations, strict sexual division of labour, and warfare, were of selective advantage to groups adopting or elaborating them because: (a) they maintained large‐group population control mechanisms; and (.
Assembly of protein tertiary structures from secondary structures using optimized potentials

We present a simulated annealing‐based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron‐based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 Å in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 Å and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 Å. Proteins 2003;52:155–165. © 2003 Wiley‐Liss, Inc.
The Macrophage C-type Lectin Specific for Galactose/N-Acetylgalactosamine Is an Endocytic Receptor Expressed on Monocyte-derived Immature Dendritic Cells*

Lectins on antigen presenting cells are potentially involved in the antigen uptake and the cellular recognition and trafficking. Serial analysis of gene expression in monocyte-derived dendritic cells (DCs), monocytes, and macrophages revealed that 7 of the 19 C-type lectin mRNA were present in immature DCs. Two of these, the macrophage mannose receptor and the macrophage lectin specific for galactose/N-acetylgalactosamine (MGL), were found only in immature DCs, as confirmed by reverse transcriptase-PCR and flow cytometric analysis. By subcloning and sequencing the amplified mRNA, we obtained nucleotide sequences encoding seven different human MGL (hMGL) subtypes, which were apparently derived from alternatively spliced mRNA. In addition, the hMGL gene locus on human chromosome 17p13 contains one gene. A single nucleotide polymorphism was identified at a position in exon 3 that corresponds to the cytoplasmic region proximal to the transmembrane domain. Of all the splicing variants, the hMGL variant 6C was expressed at the highest levels on immature DCs from all donors tested. Immature DCs could incorporate α-GalNAc-modified soluble acrylamide polymers, and this was significantly inhibited by pretreatment of the cells with an anti-hMGL monoclonal antibody that blocks the lectin-carbohydrate interaction. We propose that hMGL is a marker of imDCs and that it functions as an endocytic receptor for glycosylated antigens.
Competition/colonization syndrome mediated by early germination in non-dispersing achenes in the heteromorphic species Crepis sancta.

BACKGROUND AND AIMS The competition-colonization trade-off theory postulates that the competitive and colonizing abilities of organisms are negatively related; this trade-off has been proposed as a major force in the maintenance of diversity. In plants, the competition-colonization trade-off is often considered to result from variation in resource partitioning, thus generating heavy competitive (non-dispersing) seeds and light (dispersing) non-competitive seeds. Here, the possibility is explored that early germination provides a competitive advantage, thus mediating competitive interactions. METHODS Using eight populations of the heterocarpic species Crepis sancta (Asteraceae), the possibility was tested that dispersing and non-dispersing achenes differ in germination timing, and the impact of early germination on individual fitness components was analysed in the context of intraspecific competition. To evaluate whether seed reserve varies among achene types, endosperm size was also measured by analysing photographs of cross-sections taken under a binocular microscope. KEY RESULTS AND CONCLUSIONS The results show that non-dispersing achenes germinated 4 d earlier (on average) than dispersing achenes. It is also shown that early germination provides a positive advantage for the survival and final biomass of individuals, a pattern that was consistent over the eight populations and independent of achene type. Dispersing and non-dispersing achenes did not differ in terms of seed reserve (endosperm size). It is proposed that germination phenology may mediate the competition-colonization trade-off in Crepis sancta and the evolutionary significance of this phenomenon is discussed.
Modulation of pursuit eye movements by stimulation of cortical areas MT and MST.

1. Many cells in the superior temporal sulcus (STS) of the monkey that represent the foveal region of the visual field discharge during pursuit eye movements. Damage to these areas produces a deficit in the maintenance of pursuit eye movements when the target towards the side of the brain with the lesion. In the present experiments, we electrically stimulated these areas to better localize and understand the mechanisms underlying this directional pursuit deficit. 2. Monkeys were trained to pursue a moving target using a step-ramp task in which the target first stepped to an eccentric position and then moved smoothly across the screen. Trains of stimulation were applied after the monkey had begun to pursue the target to study stimulation effects of maintenance of pursuit. 3. Stimulation during pursuit frequently produced eye acceleration toward the side of the brain stimulated. Eye speed increased during pursuit toward the side stimulated and decreased during pursuit away from the side stimulated. This increase in velocity toward the side of the brain where stimulation presumably activated cells is consistent with the decrease in pursuit velocity toward the side of the brain after cells were removed by chemical lesions. 4. The increase or decrease in pursuit speed following stimulation produced a slip of the target on the retina. The pursuit system seemed to be insensitive to this slip during the period of stimulation, however, since the effect of stimulation during pursuit of a stabilized image (open-loop condition) was similar to that resulting from stimulation under normal pursuit conditions (closed-loop). This insensitivity to visual motion during stimulation suggests that the stimulation substitutes for that visual input. 5. The separation of eye and target position that resulted from stimulation did produce catch-up saccades. This provides added evidence that alteration of middle temporal area (MT) and medial superior temporal area (MST) modifies visual-motion but not visual-position information. 6. Stimulation that produced eye acceleration during pursuit produced only a slight effect during fixation of a stationary target. The effectiveness of the stimulation also increased as the speed of the pursuit increased between 5 and 25 degrees/s. These observations, which show that pursuit velocity altered the effect of stimulation, suggest that the stimulation acted on visual motion processing before information about the pursuit movement itself is incorporated. Since this stimulation produces directional pursuit effects, we hypothesize that the directional bias for pursuit originates in the visual signal conveyed to the pursuit system. (ABSTRACT TRUNCATED AT 400 WORDS)
Broken Hill lead-zinc-silver deposit

The deposit is at lat 31 degrees 58'S, long 141 degrees 28'E in NSW, on the Broken Hill (SH 54-15) 1:250 000 scale and the Broken Hill (7134) 1:100 000 scale map sheets. It is one of the richest accumulations of lead, zinc and silver in the world. Mining by the Broken Hill Proprietary Company Limited began in 1883 and continues today in the Southern Operations of Pasminco Mining - Broken Hill. This paper documents results of significant research work and mine exploration that has taken place at both the North Mine and Southern Operations since the description by Mackenzie and Davies (1990).
Towards Smart Grid system validation: Integrating the SmartEST and the SESA laboratories

The evolution of the European electrical energy system has been in progress for several years now. During this process the complexity of the overall power system has been continuously increasing. Installing new components and concepts into the interrelated infrastructure is getting more complicated as their impacts are hard to predict. Moreover, the energy system is a critical infrastructure that cannot be jeopardized by components with unclear behavior. Thus, new approaches have to be tested and validated in complex, large-scale co-simulations. In this paper an integration of two different laboratory infrastructures is introduced that enables such co-simulation analysis. On the one hand, the SmartEST laboratory in Austria is focusing on distributed energy resources, power electronic components as well as their integration issues. The SESA laboratory in Germany, on the other hand, addresses mainly hard- and software simulation integration.
PhoP/PhoQ: macrophage‐specific modulators of Salmonella virulence?

The regulation of gene expression by the two‐component regulatory system PhoP/PhoQ is necessary for Salmonella typhimurium survival within macro‐phages, defensin resistance, acid resistance, and murine typhoid fever pathogenesis. Salmonella experience multiple environments during mammalian infection and survival requires tightly regulated gene expression. Alter phagocytosis by macrophages, signal transduction by PhoQ results in the transcription of QhoP‐activated genes (pags) encoding proteins essential to bacterial survival and virulence. One such gene, pagC, encodes an envelope protein with amino acid similarity to an epithelial cell invasion protein of Yersina enterocolitica, Ail, and a bacteriophage λ outer membrane protein, Lom. The PhoP and PhoQ proteins can also repress the synthesis of proteins, encoded by phoP repressed genes (prgs), when pags are maximally expressed. If prgs encode receptors for toxic compounds, prg repression may protect the cell within macrophages when pag expression is most necessary. At least one prg locus, prgH, is required for full S. typhimurium mouse virulence. Within the macrophage, different environments may stimulate a switch from pag to prg expression that is necessary to Salmonella survival, prg expression may also be necessary for surviving non‐macrophage environments. Study of the PhoP regulon should lead to the discovery of new virulence factors, increase knowledge of how gene regulation is essential to bacterial virulence, and perhaps lead to the development of better vaccines for typhoid fever.
Zopiclone Increases the Arousal Threshold without Impairing Genioglossus Activity in Obstructive Sleep Apnea.

STUDY OBJECTIVES To determine the effects of the nonbenzodiazepine sedative zopiclone on the threshold to arousal with increasing respiratory effort and genioglossus muscle activity and to examine potential physiological factors mediating disparate effects of zopiclone on obstructive sleep apnea (OSA) severity between patients. METHODS Twelve patients with OSA (apnea-hypopnea index = 41 ± 8 events/h) were studied during 2 single night sleep studies conducted approximately 1 w apart after receiving 7.5 mg of zopiclone or placebo according to a double-blind, placebo-controlled, randomized, crossover design. The respiratory arousal threshold (epiglottic pressure immediately prior to arousal during naturally occurring respiratory events), genioglossus activity and its responsiveness to pharyngeal pressure during respiratory events, and markers of OSA severity were compared between conditions. Genioglossus movement patterns and upper airway anatomy were also assessed via magnetic resonance imaging in a subset of participants (n = 7) during wakefulness. RESULTS Zopiclone increased the respiratory arousal threshold versus placebo (-31.8 ± 5.6 versus -26.4 ± 4.6 cmH2O, P = 0.02) without impairing genioglossus muscle activity or its responsiveness to negative pharyngeal pressure during respiratory events (-0.56 ± 0.2 versus -0.44 ± 0.1 %max/-cmH2O, P = 0.48). There was substantial interindividual variability in the changes in OSA severity with zopiclone explained, at least in part, by differences in pathophysiological characteristics including body mass index, arousal threshold, and genioglossus movement patterns. CONCLUSIONS In a group of patients with predominantly severe OSA, zopiclone increased the arousal threshold without reducing genioglossus muscle activity or its responsiveness to negative pharyngeal pressure. These properties may be beneficial in some patients with OSA with certain pathophysiological characteristics but may worsen hypoxemia in others. CLINICAL TRIAL REGISTRATION Australian New Zealand Clinical Trials Registry, http://www.anzctr. org.au, trial ID: ACTRN12614000364673.
The Ins and Outs of DNA Fingerprinting the Infectious Fungi

SUMMARY DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.
A milestone for hepatitis C virus research: a virus generated in cell culture is fully viable in vivo.

Chronic hepatitis C virus (HCV) infection is a leading cause of end-stage liver disease in the United States, and the Centers for Disease Control has predicted that ≈10,000 Americans die annually from this disease. Since the discovery of HCV in 1989, basic research on this important pathogen has been difficult because of the lack of a robust cell-culture system. Thus, the recent development of a cell culture resulting in production of significant levels of infectious virus particles (1–3) will without doubt lead to rapid progress in our understanding of the HCV viral life cycle and, it is hoped, development of better therapies. The development of molecular clones of strain H77 (genotype 1a) infectious for chimpanzees in 1997 was an important initial advance, but these clones and subsequent infectious clones of other genotype strains did not produce viruses in cell culture (4–7). Another critical advance was the development of subgenomic replicons in 1999 that permitted studies of RNA replication (8). Efficient replication, however, depended on adaptive mutations (9, 10). In 2003, Kato et al. (11) observed that the WT JFH1 strain of HCV, belonging to genotype 2a, replicated to high levels in the replicon system. Subsequently, in 2005, Wakita and coworkers (2) demonstrated that RNA transcripts from the full-length JFH1 genome could produce viruses in a human liver hepatoma cell line (Huh-7 cells), and it was demonstrated by Chisari and coworkers (3) that this system could be developed to generate relatively high titers of HCV. In a different approach, Rice and coworkers (1) developed a chimeric genome in which the structural genes (C, E1, and E2), p7, and NS2 from an infectious clone of another genotype 2a strain (strain HC-J6) (6) were inserted into the subgenomic replicon of the JFH1 strain and demonstrated that RNA transcripts from this full-length chimeric genome could produce relatively high titers of HCV. In the current issue of PNAS, a study by Lindenbach et al. (12) demonstrated that chimeric J6/JFH1 viruses generated in vitro were fully viable also in vivo, as tested in chimpanzees and in SCID-uPA mice with human liver grafts, and that virus recovered from infected animals efficiently infected naive Huh-7 cells. An overview of this important study is shown in Fig. 1. Therefore, it appears that not only has a cell-culture system been developed for HCV, but this system produces viruses that are biologically relevant.
Realtime estimation of the degree of market efficiency using variable weighted Sample Entropy

Recently, the complex features of financial time series have been studied using a variety of methods developed in econophysics. These analyses of extensive financial data have empirically pointed to the breakdown of the efficient market hypothesis (EMI), in particular the weak-form of EMI. Sample entropy (SampEn) can be used to quantify the randomness in the time series. In the financial time series analysis, the SampEn can quantify the degree of market efficiency. In this paper, we investigated the degree of market efficiency of the US market and Asian market around the epoch of Black Monday and Asian Currency Crisis respectively by using variable weighted SampEn algorithm.
CD40-CD40 Ligand Interaction between Dendritic Cells and CD8+ T Cells Is Needed to Stimulate Maximal T Cell Responses in the Absence of CD4+ T Cell Help1

Stimulation of CD40 on APCs through CD40L expressed on helper CD4+ T cells activates and “licenses” the APCs to prime CD8+ T cell responses. Although other stimuli, such as TLR agonists, can also activate APCs, it is unclear to what extent they can replace the signals provided by CD40-CD40L interactions. In this study, we used an adoptive transfer system to re-examine the role of CD40 in the priming of naive CD8+ T cells. We find an ∼50% reduction in expansion and cytokine production in TCR-transgenic T cells in the absence of CD40 on all APCs, and on dendritic cells in particular. Moreover, CD40-deficient and CD40L-deficient mice fail to develop endogenous CTL responses after immunization. Surprisingly, the role for CD40 and CD40L are observed even in the absence of CD4+ T cells; in this situation, the CD8+ T cell itself provides CD40L. Furthermore, we show that although TLR stimulation improves T cell responses, it cannot fully substitute for CD40. Altogether, these results reveal a direct and unique role for CD40L on CD8+ T cells interacting with CD40 on APCs that affects the magnitude and quality of CD8+ T cell responses.
COMPARISON OF THE EFFECT OF APOMORPHINE AND l‐DOPA ON SERUM GROWTH HORMONE LEVELS IN NORMAL MEN

Apomorphine hydrochloride (0.75 mg s.c.) has been compared with l‐dopa (500 mg p.o.) in their effects on growth hormone secretion in a double blind cross‐over study involving nine healthy men. Apomorphine increased serum GH levels above 10 ng/ml in all nine subjects 30–60 min after injection. In contrast, only six of these subjects showed a similar elevation with l‐dopa and in only three had the level increased above 6 ng/ml by 60 min. One subject failed to respond to l‐dopa and in two others the peak was less than 6 ng/ml. GH levels were significantly higher at 30, 45 and 60 min following apomorphine than following l‐dopa. Apomorphine‐induced GH release was not related to changes in serum cortisol or blood sugar. Benztropine mesylate (1 mg i.m.) had no effect on apomorphine‐induced GH release. These results suggest: (a) apomorphine may have advantages over l‐dopa as a provocative agent to assess GH secretory capacity; (b) a dopaminergic mechanism subserves GH secretion; (c) cholinergic mechanisms do not antagonize dopaminergic‐related GH release.
Fast and guaranteed C compilation onto the PACT-XPP/spl trade/ reconfigurable computing platform

We introduce the XPP-VC high-level compiler, which maps C programs to the coarse-grained XPP architecture. XPP-VC's main feature is the integration of pipeline vectorization and temporal partitioning techniques. The former provides high-throughput inner loop computations and the later allows the compilation of large programs or the use of fewer XPP processing elements. Although the preliminary results are very encouraging, improvements on the generation of configurations are still required. The evaluation we have conducted shows that only a few seconds are required to generate, from algorithms in C, the binaries to program the XPP. To our knowledge this compilation performance is unmatched by any other compiler targeting reconfigurable architectures. Moreover the compiler still achieves high-performance implementations. Since the XPP is delivered as an IP core or device to be coupled to a host processor, a future version of XPP-VC will consider co-compilation, i.e., compilation to hybrid microprocessor/XPP architectures.