Miracle-dz/UniFAR-FTUs huggingface dataset:
The Siderophore Iron Transporter of Candida albicans (Sit1p/Arn1p) Mediates Uptake of Ferrichrome-Type Siderophores and Is Required for Epithelial Invasion

ABSTRACT The human fungal pathogen Candida albicans contains a close homologue of yeast siderophore transporters, designated Sit1p/Arn1p. We have characterized the function of SIT1 in C. albicans by constructing sit1 deletion strains and testing their virulence and ability to utilize a range of siderophores and other iron complexes. sit1 mutant strains are defective in the uptake of ferrichrome-type siderophores including ferricrocin, ferrichrysin, ferrirubin, coprogen, and triacetylfusarinine C. A mutation of FTR1 did not impair the use of these siderophores but did affect the uptake of ferrioxamines E and B, as well as of ferric citrate, indicating that their utilization was independent of Sit1p. Hemin was a source of iron for both sit1 and ftr1 mutants, suggesting a pathway of hemin uptake distinct from that of siderophores and iron salts. Heterologous expression of SIT1 in the yeast Saccharomyces cerevisiae confirmed the function of Sit1p as a transporter for ferrichrome-type siderophores. The sit1 mutant was defective in infection of a reconstituted human epithelium as a model for human oral mucosa, while the SIT1 strain was invasive. In contrast, both sit1 and SIT1 strains were equally virulent in the mouse model of systemic infection. These results suggest that siderophore uptake by Sit1p/Arn1p is required in a specific process of C. albicans infection, namely epithelial invasion and penetration, while in the blood or within organs other sources of iron, including heme, may be used.
Eos Mediates Foxp3-Dependent Gene Silencing in CD4+ Regulatory T Cells

Treg Responses to Eos CD4+ regulatory T cells (Tregs) are critical for keeping our immune system in check: They prevent immune responses from getting out of hand and keep autoimmunity at bay. By activating the expression of some genes and turning off expression of others, the master regulatory transcription factor of Tregs, Foxp3, endows these cells with the appropriate gene expression program to mediate their suppressive effects. Pan et al. (p. 1142, published online 20 August) now demonstrate that the transcription factor Eos is selectively required for Foxp3-mediated gene suppression in mice. Genes normally suppressed by Foxp3 in Tregs remained “on” when Eos expression was suppressed, whereas genes activated by Foxp3 were unaffected. Treg function was also affected by Eos suppression. With half their genetic program disrupted, these cells resembled an intermediate between Tregs and conventional CD4+ T cells—unable to suppress immune responses properly and partially responsive to T cell–activating stimulation. A transcription factor required for gene suppression in regulatory T cells is identified. CD4+ regulatory T cells (Tregs) maintain immunological self-tolerance and immune homeostasis by suppressing aberrant or excessive immune responses. The core genetic program of Tregs and their ability to suppress pathologic immune responses depends on the transcription factor Foxp3. Despite progress in understanding mechanisms of Foxp3-dependent gene activation, the molecular mechanism of Foxp3-dependent gene repression remains largely unknown. We identified Eos, a zinc-finger transcription factor of the Ikaros family, as a critical mediator of Foxp3-dependent gene silencing in Tregs. Eos interacts directly with Foxp3 and induces chromatin modifications that result in gene silencing in Tregs. Silencing of Eos in Tregs abrogates their ability to suppress immune responses and endows them with partial effector function, thus demonstrating the critical role that Eos plays in Treg programming.
Disappearance of Nucleosome Positioning in Mitotic Chromatin in Vivo*

During mitosis, transcription is silenced and most transcription factors are displaced from their recognition sequences. By in vivo footprinting analysis, we have confirmed and extended previous studies showing loss of transcription factors from an RNA polymerase II promoter (c-FOS) and, for the first time, an RNA polymerase III promoter (U6) in HeLa cells. Because little was known about nucleosomal organization in mitotic chromosomes, we performed footprinting analysis for nucleosomes on these promoters in interphase and mitotic cells. During interphase, each of the promoters had a positioned nucleosome in the region intervening between proximal promoter elements and distal enhancer elements, but the strong nucleosome positioning disappeared during mitosis. Thus, the nucleosomal organization that appears to facilitate transcription in interphase cells may be lost in mitotic cells, and nucleosome positioning during mitosis does not seem to be a major component of the epigenetic mechanisms to mark genes for rapid reactivation after this phase.
Increased numbers of hypodense eosinophils in the blood of patients with bronchial asthma.

We investigated the density of blood eosinophils from patients with asthma using polyvinylpyrrolidone-coated silica gel (Percoll) discontinuous density gradient centrifugation of peripheral blood leukocytes. Ten patients with allergic asthma, 10 normal subjects, and 2 patients with the hypereosinophilic syndrome (HES) were studied. The density distribution profiles of eosinophils from normal subjects showed: (1) peaks at densities of 1.085 to 1.090 g/ml and (2) inflection points or nadirs near 1.082 g/ml, below which only 10% of eosinophils were found. On the basis of these results, we divided eosinophils into 2 subpopulations: normodense (greater than 1.082 g/ml) and hypodense (less than 1.082 g/ml). Densities of eosinophils from patients with asthma and HES peaked at 1.083 and 1.076 g/ml (mean values), respectively, significantly lighter than eosinophils from normal donors (p less than 0.005 and p less than 0.001, respectively). The proportions of hypodense eosinophils in patients with asthma and HES were 35 and 95%, respectively, and were significantly greater than that in normal donors (p less than 0.002 and p less than 0.001, respectively). The density distribution profiles of a normal subject were stable over time, but those of asthmatic patients varied with time. For the 22 participants, there was a positive correlation between log-transformed blood eosinophil counts and the percentage of hypodense eosinophils (r = +0.86, p less than 0.001). Similarly, for 15 of them, plasma eosinophil granule major basic protein correlated with the numbers of peripheral blood eosinophils (r = +0.92, p less than 0.0005) and hypodense eosinophils (r = +0.92, p less than 0.0005). Thus, a portion of the eosinophils in asthmatic patients and most of the eosinophils in patients with HES are hypodense. (ABSTRACT TRUNCATED AT 250 WORDS)
Eliminating the Synthesis of Mature Lamin A Reduces Disease Phenotypes in Mice Carrying a Hutchinson-Gilford Progeria Syndrome Allele*

Hutchinson-Gilford progeria syndrome is caused by the synthesis of a mutant form of prelamin A, which is generally called progerin. Progerin is targeted to the nuclear rim, where it interferes with the integrity of the nuclear lamina, causes misshapen cell nuclei, and leads to multiple aging-like disease phenotypes. We created a gene-targeted allele yielding exclusively progerin (LmnaHG) and found that heterozygous mice (LmnaHG/+) exhibit many phenotypes of progeria. In this study, we tested the hypothesis that the phenotypes elicited by the LmnaHG allele might be modulated by compositional changes in the nuclear lamina. To explore this hypothesis, we bred mice harboring one LmnaHG allele and one LmnaLCO allele (a mutant allele that produces lamin C but no lamin A). We then compared the phenotypes of LmnaHG/LCO mice (which produce progerin and lamin C) with littermate LmnaHG/+ mice (which produce lamin A, lamin C, and progerin). LmnaHG/LCO mice exhibited improved body weight curves (p < 0.0001), reduced numbers of spontaneous rib fractures (p < 0.0001), and improved survival (p < 0.0001). In addition, LmnaHG/LCO fibroblasts had fewer misshapen nuclei than LmnaHG/+ fibroblasts (p < 0.0001). A likely explanation for these differences was uncovered; the amount of progerin in LmnaHG/LCO fibroblasts and tissues was lower than in LmnaHG/+ fibroblasts and tissues. These studies suggest that compositional changes in the nuclear lamina can influence both the steady-state levels of progerin and the severity of progeria-like disease phenotypes.
IBRS: An Iterative Background Reconstruction and Suppression Framework for Hyperspectral Target Detection

With the development of hyperspectral imaging technology and detection algorithm research, hyperspectral target detection has become indispensable in the field of target recognition and reconnaissance. But limited by the complex distribution of land covers and the difficulties to distinguish spectral characteristics between the target and its surroundings, existing target detection algorithms may still be insufficient on identifying target spectrum and suppressing background spectra. In this paper, we propose a novel iterative background reconstruction and suppression framework for hyperspectral target detection. By means of iteratively integrating the dictionary training algorithm with sparse-coding method to estimate the background training dictionary and its corresponding sparse representation, hyperspectral imagery (HSI) dataset is purified into background subspace matrix. Then, we add the constructed background suppression regularization term on the constrained energy minimization model to form the framework as a linearly background constrained optimization filter model. The optimal solution is then solved by a convex optimization interior-point method and improved by an iteratively reweighting method to achieve the goal of separating the target and the background. The proposed algorithm is applied to two synthetic hyperspectral datasets and two real-HSI datasets; the experimental results show that our algorithm performs a superior detection result compared to other classical hyperspectral target detection algorithms. It also provides a fresheye idea to integrate a variety of theoretical algorithms to explore the way of constructing and solving target detection model.
The Future of Linguistics and Lexicographers: Will there be Lexicographers in the year 3000?

Lexicography has been a respected tradition of scientific pursuit since the eighteenth century.Will the science of lexicography survive into the third millennium? I will discuss what present ­day computational linguistics can offer the lexicographer in the lexicographic task. I will show that the data can be purified in clearer and clearer forms through approximate linguistics. I will then speculate about what aspects of the lexicographic task can be automated, what tasks remain incumbent on humans, and wonder whether a new vision of the lexicon will • emerge .
Extension of the Common Information Model With a Catalog of Topologies

This paper presents an extension of the Common Information Model (CIM) with a catalog of topologies, in other words with a catalog of bays, for distribution networks. This extension has been realized by defining an additional set of metadata for cataloguing equipment containers. The extended CIM was tested on real distribution networks. Performance metrics of the model, taken into account at the time of evaluation were: the size of the CIM/XML (eXtensible Markup Language) document containing exported data about the network, and the speed of processing the topological connectivity of the network in advanced Distribution Management System (DMS) applications. According to the test results, incorporating the catalog of bays may significantly boost the performance of CIM based solutions without jeopardizing CIM compatibility
Sentiment lexicon adaptation with context and semantics for the social web

Sentiment analysis over social streams offers governments and organisations a fast and effective way to monitor the publics' feelings towards policies, brands, business, etc. General purpose sentiment lexicons have been used to compute sentiment from social streams, since they are simple and effective. They calculate the overall sentiment of texts by using a general collection of words, with predetermined sentiment orientation and strength. However, words' sentiment often vary with the contexts in which they appear, and new words might be encountered that are not covered by the lexicon, particularly in social media environments where content emerges and changes rapidly and constantly. In this paper, we propose a lexicon adaptation approach that uses contextual as well as semantic information extracted from DBPedia to update the words' weighted sentiment orientations and to add new words to the lexicon. We evaluate our approach on three different Twitter datasets, and show that enriching the lexicon with contextual and semantic information improves sentiment computation by 3.4% in average accuracy, and by 2.8% in average F1 measure.
Measurements of storm and nonstorm circulation in the northern Adriatic: October 2002 Through April 2003

[1] Fifteen bottom-mounted Acoustic Doppler Current Profilers were deployed from October 2002 through April 2003 in the northern Adriatic Sea. Average transport from the portion of the Western Adriatic Current (WAC) along the Italian slope was 0.1470 ± 0.0043 Sv, punctuated by bursts of more than twice that amount during storm events. Monthly means were calculated with times of strong wind-driven circulation excluded. These suggest a 2002/2003 seasonal separation consisting of October, December through February, and March through April. An extreme Po River flood influenced November conditions making seasonal categorization difficult. October generally had more kinetic energy and more vertical structure than other months, and near-inertial waves were more frequent in April and October. The Eastern Adriatic Current (EAC)/WAC (i.e. inflow/outflow) system was clearly present in the means for all months. The cyclonic gyre north of the Po River was present October through February. Generally, in the WAC, over 50% of kinetic energy came from vertically uniform monthly mean flows. Elsewhere, eddy kinetic energy was stronger than mean kinetic energy with 10–40% contributions for vertically uniform monthly mean flows, 40–60% for vertically uniform monthly varying flows, and 10–30% for vertically varying monthly varying flows. Mean currents for bora storms indicate enhancement of the EAC/WAC and the cyclonic northern gyre, a shift toward Kvarner Bay in EAC direction, a circulation null point south of the Po, and double-gyre bifurcation of flow at Istria. Strengthening of both the EAC and WAC also occurs during sirocco storms.
Static Optimization of Data Integration Plans in Global Information Systems

Global information systems provide its users with a centralized and transparent view of many heterogeneous and distributed sources of data. The requests to access data at a central site are decomposed and processed at the remote sites and the results are returned back to a central site. A data integration component of the system processes data retrieved and transmitted from the remote sites accordingly to the earlier prepared data
THE SMOOTH MUSCLE CELL

These studies have examined the ability of smooth muscle cells from developing aorta of the prepubertal rat to utilize amino acids in the synthesis and secretion of connective tissue proteins. Prepubertal rats, previously given either an alcohol carrier or estradiol-17-beta, were each given an intravenous injection of proline-3H. The animals were sacrificed after 15 and 30 min, and 4 hr. Light and electron microscope radioautographs of the aortic smooth muscle and of the myometrial cells demonstrated that the aortic cells, in both groups of animals, and the myometrial cells, in the estrogen-stimulated animals, took up the proline and rapidly secreted it in both collagen and elastic fibers within 4 hr. In contrast, the myometrial cells of the nonstimulated animal took up relatively small amounts of proline and retained most of the amino acid within the cells. Electron microscope radioautographs demonstrated that the organelles involved in this activity were the rough endoplasmic reticulum and Golgi complex together with peripheral elements, presumed to be small vesicles. These studies have demonstrated that the smooth muscle cells of the developing aorta and of the estrogen-stimulated myometrium have a capacity to synthesize and secrete proteins associated with the extracellular connective tissue matrix.
Preconditioning and Postinsult Therapies for Perinatal Hypoxic–Ischemic Injury at Term

Perinatal hypoxic–ischemic encephalopathy can be a devastating complication of childbirth. Herein, the authors review the pathophysiology of hypoxic–ischemic encephalopathy and the current status of neuroprotective strategies to ameliorate the injury centering on four themes: (1) monitoring in the perinatal period, (2) rapid identification of affected neonates to allow timely institution of therapy, (3) preconditioning therapy (a therapeutic that reduces the brain vulnerability) before hypoxic–ischemic encephalopathy, and (4) prompt institution of postinsult therapies to ameliorate the evolving injury. Recent clinical trials have demonstrated the significant benefit for hypothermic therapy in the postnatal period; furthermore, there is accumulating preclinical evidence that adjunctive therapies can enhance hypothermic neuroprotection. Advances in the understanding of preconditioning may lead to the administration of neuroprotective agents earlier during childbirth. Although most of these neuroprotective strategies have not yet entered clinical practice, there is a significant hope that further developments will enhance hypothermic neuroprotection.
High-efficiency and flat-gain Doherty type transmitter using a 180-degree hybrid-combiner

It is well-known that the isolation provided by a hybrid combiner defeats the active load-modulation mechanism between the carrier and peaking power amplifiers in a Doherty transmitter. In this paper, a hybrid combiner is used in combination with a lattice network to combine the carrier and peaking amplifiers in order to manage load modulation between them. Both amplifiers have a driver stage. The driver of the peaking amplifier is tuned and biased so that the efficiency at 6-dB backoff power is peaked. The prototype exhibits an efficiency at peak power of 80.5% and an efficiency at 6-dB back-off of 70.5%. Alternatively, the transmitter can be optimized for flat AM-AM characteristics scarifying efficiency enhancement at back-off power.
The analysis and practice of the human-computer interaction course system in Stanford University

Aiming at the design of Human-Computer Interaction (HCI) course system in software engineering, the HCI course system in Stanford University and the teaching practice details of related courses are analysed and studied. We sum up nearly five-years of teaching experience, propose a theoretical knowledge system of three levels in HCI, and build up a suitable road to reform and practice the course system.
Appendage-Mediated Surface Adherence of Sulfolobus solfataricus

ABSTRACT Attachment of microorganisms to surfaces is a prerequisite for colonization and biofilm formation. The hyperthermophilic crenarchaeote Sulfolobus solfataricus was able to attach to a variety of surfaces, such as glass, mica, pyrite, and carbon-coated gold grids. Deletion mutant analysis showed that for initial attachment the presence of flagella and pili is essential. Attached cells produced extracellular polysaccharides containing mannose, galactose, and N-acetylglucosamine. Genes possibly involved in the production of the extracellular polysaccharides were identified.
Antimicrobial Resistance in Campylobacter

To the Editor: Iovine and Blaser (1) write, "This therapeutic use [of enrofloxacin] was withdrawn (2) but is now under appeal" and "Despite the restrictions on enrofloxacin use, emergence of fluoroquinolone-resistant Campylobacter species, with poultry as an important source, has been documented in the United States… Therefore, our conclusion remains: use of enrofloxacin in poultry materially contributed to increase in human infection by fluoroquinolone-resistant Campylobacter species. " These claims propagate the following important errors. First, the therapeutic use of enrofloxacin was not withdrawn. Judge Davidson's order to withdraw the approval was an initial decision, to which exceptions were filed in 2004. A final decision rests with the US Food and Drug Administration Commissioner. Second, poultry has not been identified as an important source of fluoroquinolone resistance in human Campylobacter isolates. The raw data of the cited Smith et al. article (3) indicate a nonsignificant negative association between chicken consumption and fluoroquinolone resistance in human isolates. Substantial resistance levels in Northern Hemisphere countries with and without enrofloxacin use, which occurred well before fluoroquinolones were ever used in animals (3–5), also suggest that attribution of such resistance to enrofloxacin is simplistic. Finally, rational decision-making is based on probable future consequences of a decision, not past history or causes of the current situation. Iovine and Blaser's claim, "Thus the decision to withdraw therapeutic use of enrofloxacin (3) was warranted," is not implied, even if enrofloxacin use caused the emergence of fluoroquinolone resistance. If withdrawing enrofloxacin increases campylobacteriosis from airsacculitis-positive chickens, withdrawal may greatly harm human health. A rational withdrawal decision cannot be justified. In summary, Iovine and Blaser's view that enrofloxacin should be banned is not supported by the data that they have cited or by principles of sound risk management and decision-making.
Invasive Aspergillosis in Solid Organ Transplant Recipients

This chapter discusses the current status and evolving trends in the epidemiology, risk factors, diagnostic laboratory assays, and the approach to antifungal prophylaxis and treatment of invasive aspergillosis in Solid Organ Transplant (SOT) recipients. Most invasive fungal infections in these high-risk patients occur within the first month posttransplant; the median time to onset of invasive aspergillosis after renal replacement therapy and retransplantation was 13 and 28 days, respectively, in one study. Other factors associated with invasive aspergillosis in liver transplant recipients include transplantation for fulminate hepatic failure, cytomegalovirus (CMV) infection, and prolonged intensive care unit stay. A retrospective survey documented invasive pulmonary aspergillosis in 7.5% (19/251) of lung transplant recipients, of whom 47% (9/19) had disseminated aspergillosis. In a survey of antifungal prophylactic strategies in lung transplant units in the United States, aerosolized amphotericin B was the most frequently employed antifungal prophylactic agent. In order of preference, the prophylactic agents used in lung transplant centers in this study were inhaled amphotericin B (61%), itraconazole (46%), parenteral amphotericin formulations (25%), and fluconazole (21%); many centers used more than one agent. Preemptive therapy, where antifungal prophylaxis is directed towards lung transplant recipients colonized with Aspergillus spp. immediately before or within 6 to 9 months after transplantation, is another approach to the prevention of invasive aspergillosis in lung transplant recipients.