Miracle-dz/UniFAR-FTUs huggingface dataset:
Antigenic Properties and Processing Requirements of 65-Kilodalton Mannoprotein, a Major Antigen Target of Anti-Candida Human T-Cell Response, as Disclosed by Specific Human T-Cell Clones

ABSTRACT T-cell-mediated immunity is known to play a central role in the host response to Candida albicans. T-cell clones are useful tools for the exact identification of fungal T-cell epitopes and the processing requirements of C. albicans antigens. We isolated human T-cell clones from an HLA-DRB1*1101 healthy donor by using an antigenic extract (MP-F2) of the fungus. Specific clones were T-cell receptor α/β and CD4+/CD8−and showed a T-helper type 1 cytokine profile (production of gamma interferon and not interleukin-4). The large majority of these clones recognized both the natural (highly glycosylated) and the recombinant (nonglycosylated) 65-kDa mannoprotein (MP65), an MP-F2 minor constituent that was confirmed to be an immunodominant antigen of the human T-cell response. Surprisingly, most of the clones recognized two synthetic peptides of different MP65 regions. However, the peptides shared the amino acid motif IXSXIXXL, which may be envisaged as a motif sequence representing the minimal epitope recognized by these clones. Three clones recognized natural and pronase-treated MP65 but did not detect nonglycosylated, recombinant MP65 or the peptides, suggesting a possible role for polysaccharides in T-cell recognition ofC. albicans. Finally, lymphoblastoid B-cell lines were efficient antigen-presenting cells (APC) for recombinant MP65 and peptides but failed to present natural, glycosylated antigens, suggesting that nonprofessional APC might be defective in processing highly glycosylated yeast proteins. In conclusion, this study provides the first characterization of C. albicans-specific human T-cell clones and provides new clues for the definition of the cellular immune response against C. albicans.
Characterization of Blast Furnace Sludge for Clayey Ceramic Fabrication

Operation in an integrated steel making plant, such as the processing of iron ore by blast furnace result in several wastes that need to be conveniently disposed to avoid environmental pollution. In the case of sludge wastes, a feasible solution is their addition to clayey ceramics. The objective of this work was then to characterize a steel making plant waste was subjected to mineralogical, chemical and physical tests. The combustion gases: CO, CO2, NO and SO2 from thermal emission were analyzed. It was found that the blast furnace sludge has a high content of both iron and carbon. Its combustion generates enough heat to sensibly contribute to the firing of the ceramic, which is an energetical advantage associated with the sludge waste addition. The gas emission was monitored and, for relatively small addition of waste, no harm is apparently caused to the environment.
Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1

The diverse forms of protein phosphatase 1 in vivo result from the association of its catalytic subunit (PP1c) with different regulatory subunits, one of which is the G‐subunit (GM) that targets PP1c to glycogen particles in muscle. Here we report the structure, at 3.0 Å resolution, of PP1c in complex with a 13 residue peptide (GM[63–75]) of GM. The residues in GM[63–75] that interact with PP1c are those in the Arg/Lys–Val/Ile–Xaa–Phe motif that is present in almost every other identified mammalian PP1‐binding subunit. Disrupting this motif in the GM[63–75] peptide and the M110[1–38] peptide (which mimics the myofibrillar targeting M110 subunit in stimulating the dephosphorylation of myosin) prevents these peptides from interacting with PP1. A short peptide from the PP1‐binding protein p53BP2 that contains the RVXF motif also interacts with PP1c. These findings identify a recognition site on PP1c, invariant from yeast to humans, for a critical structural motif on regulatory subunits. This explains why the binding of PP1 to its regulatory subunits is mutually exclusive, and suggests a novel approach for identifying the functions of PP1‐binding proteins whose roles are unknown.
Aloe vera: Nature's soothing healer to periodontal disease

Background: Recent interest and advances in the field of alternative medicine has promoted the use of various herbal and natural products for multiple uses in the field of medicine. Aloe vera is one such product exhibiting multiple benefits and has gained considerable importance in clinical research. This clinical study focuses on Aloe vera and highlights its property when used as a medicament in the periodontal pocket. Materials and Methods: A total number of 15 subjects were evaluated for clinical parameters like plaque index, gingival index, probing pocket depth at baseline, followed by scaling and root planing (SRP). Test site comprised of SRP followed by intra-pocket placement of Aloe vera gel, which was compared with the control site in which only SRP was done, and clinical parameters were compared between the two sites at one month and three months from baseline. Results: Results exhibited encouraging findings in clinical parameters of the role of Aloe vera gel as a drug for local delivery. Conclusion: We conclude that subgingival administration of Aloe vera gel results in improvement of periodontal condition. Aloe vera gel can be used as a local drug delivery system in periodontal pockets.
Phylogeography and evolution in matsutake and close allies inferred by analyses of ITS sequences and AFLPs

Matsutake are commercially important ectomycorrhizal basidiomycetes in the genus Tricholoma. Despite their importance, the systematics of this species complex have remained elusive and little is known about their origin and biogeography. Using DNA analyses on a worldwide sample of matsutake, we present here the first comprehensive definition of natural groupings in this species complex. We infer patterns of migration and propose Eocene origins for the group in western North America by a transfer from an angiosperm-associated ancestor to an increasingly specialized conifer symbiont. From these origins, matsutake appear to have followed migratory routes parallel to those of coniferous hosts. Patterns of vicariance between eastern North America and eastern Asia are resolved and their origins are suggested to stem from migration through Beringia. Using an analysis of genetic dissimilarity and geographical distance, we reject both the possibility that migration into Europe and Asia occurred through Atlantic bridges and the connection between matsutake populations in the Mahgrebi Mountains and those from Europe. Instead, African and European matsutake appear to be the most recent ends of a westward expansion of the domain of these fungi from North America.
Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

Significance Quantitative understanding of how coupled binding and folding occurs for intrinsically disordered molecular recognition element (MoRE) critical for function is still challenging. By developing an integrated approach, we provided physical quantification of folding and binding energy landscapes of a MoRE at atomistic level. Our predictions are in remarkable agreements with the experiments, and lead to the recognition mechanism via conformational selection, followed by induced folding. We provided an explanation for the underlying connections among “downhill folding,” “molten globule,” and “intrinsic disorder. ” We proposed a “kinetic divide-and-conquer” mechanism to understand the high specificity without high affinity in intrinsic disordered protein binding. Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding–binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between “downhill folding,” “molten globule,” and “intrinsic disorder” in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a “kinetic divide-and-conquer” strategy that confers them high specificity without high affinity.
NO–&bgr;-catenin crosstalk modulates primitive streak formation prior to embryonic stem cell osteogenic differentiation

Summary Nitric oxide (NO) has been shown to play a crucial role in bone formation in vivo. We sought to determine the temporal effect of NO on murine embryonic stem cells (ESCs) under culture conditions that promote osteogenesis. Expression profiles of NO pathway members and osteoblast-specific markers were analyzed using appropriate assays. We found that NO was supportive of osteogenesis specifically during an early phase of in vitro development (days 3–5). Furthermore, ESCs stably overexpressing the inducible NO synthase showed accelerated and enhanced osteogenesis in vitro and in bone explant cultures. To determine the role of NO in early lineage commitment, a stage in ESC differentiation equivalent to primitive streak formation in vivo, ESCs were transfected with a T-brachyury–GFP reporter. Expression levels of T-brachyury and one of its upstream regulators, &bgr;-catenin, the major effector in the canonical Wnt pathway, were responsive to NO levels in differentiating primitive streak-like cells. Our results indicate that NO may be involved in early differentiation through regulation of &bgr;-catenin and T-brachyury, controlling the specification of primitive-streak-like cells, which may continue through differentiation to later become osteoblasts.
Oscillating Positive Airway Pressure Versus CPAP for the Treatment of Obstructive Sleep Apnea

Although continuous positive airway pressure (CPAP) is the most effective therapy for obstructive sleep apnea (OSA), it is not always well tolerated by the patients. Previous physiological studies showed that pressure oscillations applied to the pharynx could activate upper airway muscles, but it is not clear whether these pressure oscillations could be tolerated during sleep in OSA patients. The aim of this study was to assess the tolerance of oscillating positive airway pressure (O-PAP) (a CPAP device delivering high-frequency pressure oscillations to the upper airway) compared to CPAP. Fourteen OSA patients currently on CPAP [age 59.9 ± 10.1 years old, BMI 34.8 ± 7.2 kg/m2, initial apnea–hypopnea index (AHI): 58.7 ± 25.2 events/h] used O-PAP or CPAP on two consecutive nights under polysomnography, in a single-blind randomized crossover design to assess sleep quality. A subtherapeutic pressure (70% of the optimal titrated pressure) was applied in both conditions and the residual AHI with each technique was also compared. There was no difference in measured or perceived sleep quality between the two treatment modalities (sleep efficiency 90.0% versus 88.1%, p = 0.54). Despite the small sample, we also found a trend toward a decrease in residual respiratory events with O-PAP compared to CPAP (median AHI 14.3 versus 20.5/h, p = 0.194). The good tolerance of O-PAP and the positive trend toward a reduction in residual AHI should stimulate further research on the effects of O-PAP in OSA patients.
Influence of deep brain stimulation and levodopa on sensory signs in Parkinson's disease

To examine the effects of levodopa (L‐dopa) and deep brain stimulation of the subthalamic nucleus (STN‐DBS) on sensory symptoms and signs in Parkinson's disease (PD). Seventeen patients with PD were included. (1) Presence of sensory symptoms and (2) effects of L‐dopa and STN‐DBS on sensory symptoms and signs [assessed by quantitative sensory testing (QST)] were examined 6 months after starting STN‐DBS. In addition, in 12 of these patients, presence of sensory symptoms prior and post STN‐DBS was compared. Pain was most frequently nociceptive. In about 30–40%, pain and sensory symptoms were associated with PD motor symptoms. In most of these cases, pain responded to L‐dopa. Intensity of pain was reduced post STN‐DBS compared to pre STN‐DBS. L‐Dopa had no influence on detection thresholds, whereas STN‐DBS improved thermal detection thresholds. However, thermal and mechanical pain thresholds were uninfluenced by L‐dopa or STN‐DBS. Although some patients reported an improvement of pain with STN‐DBS or L‐dopa, objectively pain sensitivity as assessed by QST was not altered by STN‐DBS or L‐dopa suggesting that there is no evidence for a direct modulation of central pain processing by L‐dopa or STN‐DBS. © 2010 Movement Disorder Society
Phosphatidylinositol 3,5-bisphosphate is involved in methylglyoxal-induced activation of the Mpk1 mitogen-activated protein kinase cascade in Saccharomyces cerevisiae

Methylglyoxal (MG) is a natural metabolite derived from glycolysis, and this 2-oxoaldehyde has been implicated in some diseases including diabetes. However, the physiological significance of MG for cellular functions is yet to be fully elucidated. We previously reported that MG activates the Mpk1 (MAPK) cascade in the yeast Saccharomyces cerevisiae. To gain further insights into the cellular functions and responses to MG, we herein screened yeast-deletion mutant collections for susceptibility to MG. We found that mutants defective in the synthesis of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) are more susceptible to MG. PtdIns(3,5)P2 levels increased following MG treatment, and vacuolar morphology concomitantly changed to a single swollen shape. MG activated the Pkc1–Mpk1 MAPK cascade in which a small GTPase Rho1 plays a crucial role, and the MG-induced phosphorylation of Mpk1 was impaired in mutants defective in the PtdIns(3,5)P2 biosynthetic pathway. Of note, heat shock-induced stress also provoked Mpk1 phosphorylation in a Rho1-dependent manner; however, PtdIns(3,5)P2 was dispensable for the heat shock-stimulated activation of this signaling pathway. Our results suggest that PtdIns(3,5)P2 is specifically involved in the MG-induced activation of the Mpk1 MAPK cascade and in the cellular adaptation to MG-induced stress.
Strong Instability of Standing Waves for the Nonlinear Klein-Gordon Equation and the Klein-Gordon-Zakharov System

The orbital instability of ground state standing waves $e^{i\omega t}\phi_{\omega}(x)$ for the nonlinear Klein–Gordon equation has been known in the domain of all frequencies ω for the supercritical case and for frequencies strictly less than a critical frequency $\omega_c$ in the subcritical case. We prove the strong instability of ground state standing waves for the entire domain above. For the case when the frequency is equal to the critical frequency $\omega_c$ we prove strong instability for all radially symmetric standing waves $e^{i\omega_c t}\varphi(x)$. We prove similar strong instability results for the Klein–Gordon–Zakharov system.
Domain Ontology Construction from Biomedical Text

NLM's Unified Medical Language System (UMLS) is a very large ontology of biomedical and health data. In order to be used effectively for knowledge processing, it needs to be customized to a specific domain. In this paper, we present techniques to automatically discover domain-specific concepts, discover relationships between these concepts, build a context map from these relationships, link these domain concepts with the best- matching concept identifiers in UMLS using our context map and UMLS concept trees, and finally assign categories to the discovered relationships. This specific domain ontology of terms and relationships using evidential information can serve as a basis for applications in analysis, reasoning and discovery of new relationships. We have automatically built an ontology for the Nuclear Cardiology domain as a testbed for our techniques.
The effect of octreotide, an analog of somatostatin, on bleomycin-induced interstitial pulmonary fibrosis in rats

In this study, octreotide (OCT), a synthetic somatostatin analog, was tested for its beneficial effects in the prevention of interstitial pulmonary fibrosis (IPF) induced by bleomycin (BLM) in rats by histological examination and by evaluating tissue OH-proline levels. Thirty male Wistar rats were divided randomly into three groups: group I: intratracheal (i.t.) BLM (7.5 mg/kg, single dose) + saline solution [0.9% NaCl, subcutaneously (s.c.), once-daily for 7 days]; group II: i.t. BLM (7.5 mg/kg, single dose) + OCT acetate (82.5 µg/kg, s.c., once-daily for 7 days); and the control group. At the end of the 7 days, lung tissues were excised and examined by histopathological methods. Levels of tissue hydroxyproline (OH-proline) were determined. BLM administration resulted in prominent histopathologic findings, such as diffuse alveolar damage and interstitial pulmonary fibrosis, as well as a significant increase in OH-proline level, as compared to controls. OCT application explicitly attenuated the histopathologic changes to a significant extent. OCT decreased paranchymal fibrosis and structural deformities in BLM-induced lung fibrosis. These results suggest that OCT administration to rats with BLM-induced IPF has a protective effect. Further studies are necessary to reveal the molecular mechanism(s) of OCT-induced protective effect.
Choosing a genome browser for a Model Organism Database: surveying the Maize community

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb. org/
Peer-to-Peer 3D Streaming

Virtual worlds have become very popular in recent years, with trends toward larger worlds and more user-generated content. The growth of 3D content in virtual worlds will make real-time content streaming (or 3D streaming) increasingly attractive for developers. To meet the demands of a large user base while lowering costs, peer-to-peer (P2P) content delivery holds the promise for a paradigm shift in how future virtual worlds will be deployed and used. The authors define both the problem and solution spaces for P2P 3D streaming - by outlining its requirements and challenges - and categorize existing proposals.
Heartburn is More Likely to Recur after Toupet Fundoplication than Nissen Fundoplication

Toupet (270°) fundoplication is commonly recommended for patients with gastroesophageal reflux (GER) and esophageal dysmotility. However, Toupet fundoplication may be less effective at protecting against reflux than Nissen (360°) fundoplication. We therefore compared the effectiveness and durability of both types of fundoplication as a function of preoperative esophageal motility. From January 1992 through January 1998, 669 patients with GER underwent laparoscopic fundoplication (78 Toupet, 591 Nissen). Patients scored heartburn, regurgitation, and dysphagia preoperatively, and at 6 weeks and 1 year postoperatively, using a 0 (“none”) to 3 (“severe”) scale. We compared symptom scores (Wilcoxon rank sum test) and redo fundoplication rates (Fisher exact test) in Toupet and Nissen patients. We also performed subgroup analyses on 81 patients with impaired esophageal motility (mean peristaltic amplitude, <30 mm Hg or peristalsis <70% of wet swallows) and 588 patients with normal esophageal motility. Toupet and Nissen patients reported similar preoperative heartburn, regurgitation, and dysphagia. At 6 weeks after operation, heartburn and regurgitation were similarly improved in both groups, but dysphagia was more prevalent among Nissen patients. After 1 year, heartburn and regurgitation were re-emerging in Toupet patients, and dysphagia was again similar between groups. Patients with impaired motility who have Nissen fundoplication are no more likely to suffer persistent dysphagia than their counterparts who have Toupet fundoplication. In addition, patients with normal motility are more likely to develop symptom recurrence after Toupet fundoplication than Nissen fundoplication, with no distinction in dysphagia rates. We conclude that since Toupet patients suffer more heartburn recurrence than Nissen patients, with similar dysphagia, selective use of Toupet fundoplication requires further study.
Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus

Nosocomial infection rates due to antibiotic-resistant bacteriae, e.g., methicillin-resistant Staphylococcus aureus (MRSA) remain high in most countries. Screening for MRSA carriage followed by barrier precautions for documented carriers (so-called screen and isolate (S&I)) has been successful in some, but not all settings. Moreover, different strategies have been proposed, but comparative studies determining their relative effects and costs are not available. We, therefore, used a mathematical model to evaluate the effect and costs of different S&I strategies and to identify the critical parameters for this outcome. The dynamic stochastic simulation model consists of 3 hospitals with general wards and intensive care units (ICUs) and incorporates readmission of carriers of MRSA. Patient flow between ICUs and wards was based on real observations. Baseline prevalence of MRSA was set at 20% in ICUs and hospital-wide at 5%; ranges of costs and infection rates were based on published data. Four S&I strategies were compared to a do-nothing scenario: S&I of previously documented carriers (“flagged” patients); S&I of flagged patients and ICU admissions; S&I of flagged and group of “frequent” patients; S&I of all hospital admissions (universal screening). Evaluated levels of efficacy of S&I were 10%, 25%, 50% and 100%. Our model predicts that S&I of flagged and S&I of flagged and ICU patients are the most cost-saving strategies with fastest return of investment. For low isolation efficacy universal screening and S&I of flagged and “frequent” patients may never become cost-saving. Universal screening is predicted to prevent hardly more infections than S&I of flagged and “frequent” patients, albeit at higher costs. Whether an intervention becomes cost-saving within 10 years critically depends on costs per infection in ICU, costs of screening and isolation efficacy.