Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mediterranean ocean forecasting system: first phase of implementation (1998–2001)

Abstract. The Mediterranean Forecasting system Pilot Project has concluded its activities in 2001, achieving the following goals: 1. Realization of the first high-frequency (twice a month) Voluntary Observing Ship (VOS) system for the Mediterranean Sea with XBT profiles for the upper thermocline (0–700 m) and 12 n.m. along track nominal resolution; 2. Realization of the first Mediterranean Multidisciplinary Moored Array (M3A) system for the Near-Real-Time (NRT) acquisition of physical and biochemical observations. The actual observations consists of: air-sea interaction parameters, upper thermocline (0–500 m) temperature, salinity, oxygen and currents, euphotic zone (0–100 m) chlorophyll, nutrients, Photosinthetically Available Radiation (PAR) and turbidity; 3. Analysis and NRT dissemination of high quality along track Sea Level Anomaly (SLA), Sea Surface Temperature (SST) data from satellite sensors to be assimilated into the forecasting model; 4. Assembly and implementation of a multivariate Reduced Order Optimal Interpolation scheme (ROOI) for assimilation in NRT of all available data, in particular, SLA and VOS-XBT profiles; 5. Demonstration of the practical feasibility of NRT ten day forecasts at the Mediterranean basin scale with resolution of 0.125° in latitude and longitude. The analysis or nowcast is done once a week; 6. Development and implementation of nested regional (5 km) and shelf (2–3 km) models to simulate the seasonal variability. Four regional and nine shelf models were implemented successfully, nested within the forecasting model. The implementation exercise was carried out in different region/shelf dynamical regimes and it was demonstrated that one-way nesting is practical and accurate; 7. Validation and calibration of a complex ecosystem model in data reach shelf areas, to prepare for forecasting in a future phase. The same ecosystem model is capable of reproducing the major features of the primary producers’ carbon cycle in different regions and shelf areas. The model simulations were compared with the multidisciplinary M3A buoy observations and assimilation techniques were developed for the biochemical data. This paper overviews the methodological aspects of the research done, from the NRT observing system to the forecasting/modelling components and to the extensive validation/calibration experiments carried out with regional/shelf and ecosystem models. Key words. Oceanography: general (ocean prediction; instruments and techniques) Oceanography: physical (currents)
Ca(2+) entry activated by S-nitrosylation. Relationship to store-operated ca(2+) entry.

The coupling between Ca(2+) pools and store-operated Ca(2+) entry channels (SOCs) remains an unresolved question. Recently, we revealed that Ca(2+) entry could be activated in response to S-nitrosylation and that this process was stimulated by Ca(2+) pool emptying (Favre, C. J., Ufret-Vincenty, C. A., Stone, M. R., Ma, H-T. , and Gill, D. L. (1998) J. Biol. Chem. 273, 30855-30858). In DDT(1)MF-2 smooth muscle cells and DC-3F fibroblasts, Ca(2+) entry activated by the lipophilic NO donor, GEA3162 (5-amino-3-(3, 4-dichlorophenyl)1,2,3,4-oxatriazolium), or the alkylator, N-ethylmaleimide, was observed to be strongly activated by transient external Ca(2+) removal, closely resembling activation of SOC activity in the same cells. The nonadditivity of SOC and NO donor-activated Ca(2+) entry suggested a single entry mechanism. Calyculin A-induced reorganization of the actin cytoskeleton prevented SOC but had no effect on GEA3162-induced Ca(2+) entry. However, a single entry mechanism could account for both SOC and NO donor-activated entry if the latter reflected direct modification of the entry channel by S-nitrosylation, bypassing the normal coupling process between channels and pools. Small differences between SOC and GEA3162-activated Ba(2+) entry and sensitivity to blockade by La(3+) were observed, and in HEK293 cells SOC activity was observed without a response to thiol modification. It is concluded that in some cells, S-nitrosylation modifies an entry mechanism closely related to SOC and/or part of the regulatory machinery for SOC-mediated Ca(2+) entry.
Twists and Turns of the Cation-dependent Mannose 6-Phosphate Receptor

Mannose 6-phosphate receptors (MPRs) participate in the biogenesis of lysosomes in higher eukaryotes by transporting soluble acid hydrolases from the trans-Golgi network to late endosomal compartments. The receptors release their ligands into the acidic environment of the late endosome and then return to the trans-Golgi network to repeat the process. However, the mechanism that facilitates ligand binding and dissociation upon changes in pH is not known. We report the crystal structure of the extracytoplasmic domain of the homodimeric cation-dependent MPR in a ligand-free form at pH 6.5. A comparison of the ligand-bound and ligand-free structures reveals a significant change in quaternary structure as well as a reorganization of the binding pocket, with the most prominent change being the relocation of a loop (residues Glu134–Cys141). The movements involved in the bound-to-free transition of the cation-dependent MPR are reminiscent of those of the oxy-to-deoxy hemoglobin transition. These results allow us to propose a mechanism by which the receptor regulates its ligand binding upon changes in pH; the pK a of Glu133appears to be responsible for ligand release in the acidic environment of the late endosomal compartment, and the pK a values of the sugar phosphate and His105 are accountable for its inability to bind ligand at the cell surface where the pH is about 7.4.
Women, careers, and work-life preferences

ABSTRACT There are no sex differences in cognitive ability but enduring sex differences in competitiveness, life goals, the relative emphasis on agency versus connection. Policy-makers’ and feminist emphasis on equal opportunities and family-friendly policies assumes that sex discrimination is the primary source of sex differentials in labour market outcomes—notably the pay gap between men and women. However, some careers and occupations cannot be domesticated—examples are given—and this also poses limits to social engineering. Recent research shows that high levels of female employment and family-friendly policies reduce gender equality in the workforce and produce the glass ceiling. Preference theory is the only theory that can explain these new trends, the continuing pay gap and occupational segregation. Preference theory implies that there are at least three types of career rather than one. However, the differences between men and women's career goals are smaller than sometimes thought.
Promoter Region-Specific Histone Incorporation by the Novel Histone Chaperone ANP32B and DNA-Binding Factor KLF5

ABSTRACT Regulation of chromatin in eukaryotic transcription requires histone-modifying enzymes, nucleosome remodeling complexes, and histone chaperones. Specific regulation of histone incorporation/eviction by histone chaperones on the promoter (e.g., region specific) is still poorly understood. In the present study, we show that direct and functional interaction of histone chaperone and DNA-binding transcription factor leads to promoter region-specific histone incorporation and inhibition of histone acetylation. We report here that the DNA-binding transcription factor Krüppel-like factor 5 (KLF5) interacts with the novel histone chaperone acidic nuclear phosphoprotein 32B (ANP32B), leading to transcriptional repression of a KLF5-downstream gene. We further show that recruitment of ANP32B onto the promoter region requires KLF5 and results in promoter region-specific histone incorporation and inhibition of histone acetylation by ANP32B. Extracellular stimulus (e.g., phorbol ester) regulates this mechanism in the cell. Collectively, we have identified a novel histone chaperone, ANP32B, and through analysis of the actions of this factor show a new mechanism of promoter region-specific transcriptional regulation at the chromatin level as mediated by the functional interaction between histone chaperone and DNA-binding transcription factor.
Proposal and Evaluation of a Telerehabilitation Platform Designed for Patients With Partial Rotator Cuff Tears: A Preliminary Study

Objective To propose and evaluate the effectiveness of a telerehabilitation platform designed for patients with rotator cuff (RC) tears. Methods During the first study phase, a virtual service platform that included information on RC tear pathology, joint care, and a series of instructions regarding therapeutic exercise was designed and created. Subsequently, in the clinical phase, a quasi-experimental study was performed. The platform was tested on patients and evaluated at baseline and at 1, 2, 3, and 6 months with respect to their pain levels and functionality on the Constant-Murley (CM) scale. Results Eleven patients were included, 5 women and 6 men, with a median age of 55 years (range, 42–68 years). Pain diminished from a baseline value of 64 mm (range, 40–80 mm) to 16 mm (range, 0–30 mm) at 6 months (p<0.001). Points on the CM scale rose from a baseline value of 54 points (range, 51–66 points) to 85 points (range, 70–100 points) at 6 months (p=0.001). Functionality in daily living and work activities, movement, and strength exhibited significant changes at 6 months (p<0.05). Conclusion Significant changes were observed in pain and functionality in this group of participants who used a telerehabilitation platform. To the best of our knowledge, this is the first study that included a specific program for RC tears.
Effects of timing information for a magnetic recording channel in the presence of non-linearities

Nonlinear effects arise in the high-density magnetic recording, which causes a performance degradation of the corresponding detector. Design of the timing recovery is crucial for the detector, and it becomes complicated in the presence of the nonlinear effects. In this article, we examine the effects of the Muller & Mueller's phase detector for a nonlinear magnetic recording channel. For simplicity, computer simulations are used to demonstrate the nonlinear effects for a partial response class IV equalized channel. The nonlinear effects, transition shift and partial erasure, are simulated. The results show that a transition shift causes a non-uniform shift of the S-curve with a different timing error, and the partial erasure effect decreases the slope of the S-curve.
Kinetics of Steady-state Currents and Charge Movements Associated with the Rat Na+/Glucose Cotransporter (*)

The rat Na+/glucose cotransporter (SGLT1) was expressed in Xenopus oocytes and steady-state and transient currents were measured using a two-electrode voltage clamp. The maximal glucose induced Na+-dependent inward current was ∼300-500 nA. The apparent affinity constants for sugar (α-methyl-D-glucopyranoside; αMDG) (KαMDG0.5) and sodium (KNa0.5) at a membrane potential of −150 mV were 0.2 mM and 4 mM. The KαMDG0. 5 increased continuously with depolarizing potentials reaching 40 mM at −30 mV. KαMDG0. 5 was steeply voltage dependent, 0.46 mM at −30 mV and 1 mM at −10 mV. From all tested monovalent cations only Li+ could substitute for Na+, but with lower affinity. The relative substrate specificity was D-glucose > αMDG ≈ D-galactose > 3-O-Me-Glc β-naphthyl-D-glucoside uridine. Phlorizin (Pz), the specific blocker of sugar transport, showed an extremely high affinity for the rat cotransporter with an inhibitor constant (KPzi) of 12 nM. SGLT1 charge movements in the absence of sugar were fitted by the Boltzmann equation with an apparent valence of the movable charge of ∼1, a potential for 50% maximal charge transfer (VαMDG) of −43 mV, and a maximal charge (Qmax) of 9 nanocoulombs. The apparent turnover number for the rat SGLT1 was 30 s−1. Model simulations showed that the kinetics of the rat SGLT1 are described by a six-state ordered nonrapid equilibrium model, and comparison of the kinetics of the rat, rabbit and human cotransporters indicate that they differ mainly in their presteady-state kinetic parameters.
Better Understanding of Factors Influencing Likelihood of Using Shared Bicycle Systems and Frequency of Use

Planning and transportation professionals are promoting a variety of sustainable travel alternatives, such as public transit usage, walking, and cycling, as affordable transportation options to counter the negative effects of widespread car use. In their traditional form, these alternative transport modes do not always offer the flexibility or convenience of the car; therefore, innovative solutions have been developed to allow active and public transport to compete better with the car. Shared bicycle systems have been adopted by a growing number of cities and regions throughout the world, yet little is known about the users of the systems and their motivations. A survey was conducted in Montreal, Quebec, Canada, in the summer of 2010 to determine the factors that encouraged individuals to use the system and the elements that influenced frequency of use. The factor found to have the greatest effect on the likelihood for use of a shared bicycle system was the proximity of home to docking stations. Ownership of a yearly shared bicycle membership was associated with cyclists riding shared bicycles 15 additional times per year. Respondents indicated that they valued the shared bicycle's trendy status and the role that it could play in bicycle theft prevention. The potential of shared bicycle systems can be maximized by increasing the number of docking stations in residential neighborhoods and by emphasizing the popularity of shared bicycles and theft prevention in advertising campaigns.
The clinicopathological spectrum and management of intraductal papillary mucinous neoplasm of the bile duct (IPMN-B)

Abstract Background. Intraductal papillary mucinous neoplasm of the bile duct (IPMN-B) is a rare but increasingly diagnosed clinical entity. Typical cholangioscopic findings usually include intraductal protruding papillary tumors that secrete mucus. Methods. Clinical, radiological and histopathological data of seven consecutive patients who were found to have IPMN-B were analyzed. Results. Six of the seven patients presented with obstructive jaundice/cholangitis as the presenting complaint. ERCP and other imaging were equivocal in five of these patients and peroral cholangioscopy (POCS, single-operator cholangioscopy system) was performed. This revealed mucin-producing intraductal tumors with numerous frond-like papillary projections; a macroscopic appearance consistent with IPMN-B. Preoperative biopsy revealed adenoma, with low-grade dysplasia in two patients and high-grade dysplasia in three. Three patients underwent Whipple resection; one underwent total pancreatectomy with left hepatectomy, one patient a pancreas preserving duodenectomy with common bile duct reimplantation and one patient an extended right hepatectomy. These patients were found to have IPMN-B with adenomatous changes with varying grades of dysplasia and even cholangiocarcinoma on final histopathology. One patient first underwent endoscopic papillectomy and on follow-up was found to have cholangiocarcinoma with metastases to the liver. Conclusion. POCS can be a key diagnostic investigation in the evaluation of patients with papillary tumors of the bile duct. IPMN-B has a heterogenous pathology and varying grades of dysplasia and even carcinoma may exist in the same patient. Surgical management should be radical and based on tumor extent.
In vivo results of real-time freehand elasticity imaging

We are developing a system for real-time estimation and display of tissue elastic properties using a clinical ultrasonic imaging system. Our hypothesis is that real-time feedback of elasticity images is essential in obtaining high-quality data. Extensive experience with laboratory fixtures and off-line processing of elasticity data showed that problems occurring in data acquisition often resulted in poor elasticity image quality. Our experience with real-time freehand elasticity imaging shows that images with high contrast-to-noise can be obtained. Results in volunteer patients have shown that high quality elasticity images are easily obtained in vivo in breast and thyroid pathologies. The key element to successful scanning is real-time visual feedback which guides the patient positioning and compression direction. Results show that individual images of axial strain in tissues can be quite misleading and that a 'movie loop' of strain images provides significantly more information adding to intuition.
Aging Cognitive Influence Factors Analysis Based on Propensity Score

In this paper, the 2011-2012 cross section data (CLHLS2011-2012) of the Chinese elderly health impact factor tracking survey (CLHLS) project group is used to analyze the influencing factors of elderly people with dementia based on propensity score method. Furthermore, we analyze the influence of the occupation of the elderly before retirement on the cognitive aging. We find out the different occupation has significant difference on the cognitive impairment. Manual workers are more likely to develop cognitive disorder disease compared to mental workers. And the probability of manual workers¡¯ morbidity trend after retirement is 38.5% higher than that of mental workers. As a result, the elderly who engaged in manual work should concern about their own cognitive deterioration more in daily life.
Experimental therapy of systemic lupus erythematosus: the treatment of NZB/W mice with mouse soluble interferon‐γ receptor inhibits the onset of glomerulonephritis

Female NZB/W F1 mice develop an autoimmune disease similar to human systemic lupus erythematosus (SLE), and ultimately die of glomerulonephritis. Starting at the age of 16 weeks NZB/W F1 mice were treated for a period of 19 weeks with soluble interferon‐γ receptor (sIFN‐γR), anti‐IFN‐γ monoclonal antibody (mAb) or IFN‐γ. All mice treated with sIFN‐γR or anti‐IFN‐γ mAb were alive 4 weeks after the treatment was discontinued, whereas 50% of mice died in the placebo groups and 78% of the mice died in the IFN‐γ‐treated group. Histologically, there was severe membrano‐proliferative glomerulonephritis in IFN‐γ‐ and placebo‐treated mice, and minimal or no mesangioproliferative disease in mice receiving sIFN‐γR or anti‐IFN‐γ mAb. The renal mononuclear infiltrate (T lymphocytes and monocytes), expression of major histocompatibility complex class II antigen and glomerular immunoglobulin and complement deposition were reduced in those mice. These data suggest that an IFN‐γ inhibitor, such as the soluble IFN‐γR, can be used for SLE therapy in the early stages of the disease.
Smokeless tobacco (shammah) in Saudi Arabia: a review of its pattern of use, prevalence, and potential role in oral cancer.

BACKGROUND Shammah is a traditional form of chewing tobacco [smokeless tobacco, (ST)] that is commonly used in the Middle East especially in Saudi Arabia (KSA), Yemen and Sudan. The Substance Abuse Research Centre (SARC) at Jazan University noted that no adequate research and information on the prevalence of shammah use in the province of Jazan, and KSA as well, has been provided in the scientific literature. MATERIALS AND METHODS An intensive systematic review of online databases was performed, including AMED (The Allied and Complementary Medicine Database), Biological Abstracts, Cochrane Collection Plus, Dentistry and Oral Sciences Source, E-Journals Database, EBSCO Discovery Service, MEDLINE, PEMSoft, PEP Archive, PsycARTICLES, scopus, Sciencedirect and Google Scholar. RESULTS Shammah is a mixture of powdered tobacco, lime, ash, black pepper, oils and flavorings. ST in KSA is placed in the buccal or lower labial vestibule of the mouth. The user (or dipper) spits out insoluble debris. The importation of ST products is prohibited in KSA. Accessible information on legislative action to control the use of ST in KSA appeared in 1990. The actual percentage use may be higher, than reported since shammah is illegal in KSA and there may be some reluctance to admit to its use. CONCLUSIONS This review paper is an initial step in a funded research project by SARC to understand the pattern of use of shammah and provide adequate epidemiological data. One goal of this review is to generate further data for public health education.
Ribonucleotide Reductases of Salmonella Typhimurium: Transcriptional Regulation and Differential Role in Pathogenesis

Ribonucleotide reductases (RNRs) are essential enzymes that carry out the de novo synthesis of deoxyribonucleotides by reducing ribonucleotides. There are three different classes of RNRs (I, II and III), all having different oxygen dependency and biochemical characteristics. Salmonella enterica serovar Typhimurium (S. Typhimurium) harbors class Ia, class Ib and class III RNRs in its genome. We have studied the transcriptional regulation of these three RNR classes in S. Typhimurium as well as their differential function during infection of macrophage and epithelial cells. Deletion of both NrdR and Fur, two main transcriptional regulators, indicates that Fur specifically represses the class Ib enzyme and that NrdR acts as a global repressor of all three classes. A Fur recognition sequence within the nrdHIEF promoter has also been described and confirmed by electrophoretic mobility shift assays (EMSA). In order to elucidate the role of each RNR class during infection, S. Typhimurium single and double RNR mutants (as well as Fur and NrdR mutants) were used in infection assays with macrophage and epithelial cell lines. Our results indicate class Ia to be mainly responsible for deoxyribonucleotide production during invasion and proliferation inside macrophages and epithelial cells. Neither class Ib nor class III seem to be essential for growth under these conditions. However, class Ib is able to maintain certain growth in an nrdAB mutant during the first hours of macrophage infection. Our results suggest that, during the early stages of macrophage infection, class Ib may contribute to deoxyribonucleotide synthesis by means of both an NrdR and a Fur-dependent derepression of nrdHIEF due to hydrogen peroxide production and DNA damage associated with the oxidative burst, thus helping to overcome the host defenses.
Estimation of short temporal intervals in Alzheimer's disease.

This study investigated the estimation of short temporal intervals in Alzheimer's disease (AD). Eight patients with dementia of the Alzheimer type, and eight age-matched controls were evaluated in a time-estimation task. The task consisted in the production of three short empty intervals (5, 10, and 25 s). Results indicated that AD patients show deficits both in the accuracy and precision of time judgments: in the three intervals evaluated, the magnitude of absolute error and the variability in time judgments were significantly greater in AD patients than healthy respondents (p < .01). These findings are discussed taking into account the contribution of attentional processes during the performance of temporal tasks. It is concluded that the estimation of short temporal intervals could be useful as an objective indicator of cognitive decline in AD.
NRC Publications Archive Archives des publications du CNRC

Abstact-Modern data generated in many ields are in a strong need of integrative machine learning models in order to better make use of heterogeneous information in decision making and knowledge discovery. How data from multiple sources are incorporated in a learning system is key step for a successful analysis. In this paper, we provide a comprehensive review on data integration techniques from a machine learning perspective.