Miracle-dz/UniFAR-FTUs huggingface dataset:
Mass mapping of a protein complex with the scanning transmission electron microscope.

A mass map of the hexagonally packed intermediate layer (HPI-layer), a regular protein monolayer from the cell envelope of Micrococcus radiodurans, has been obtained by scanning transmission electron microscopy. Samples were freeze-dried within the microscope, and low-dose images were recorded in the dark-field mode directly in digital form and processed by correlation averaging. The averaged projection of the unstained structure--i.e., the mass map--thus calculated shows a resolution to 3-nm period and reveals morphological features consistent with those obtained by negative staining. The mass of individual morphological domains was extracted by using variously the mass map itself or an average from a negatively stained HPI layer to define the domain boundaries. Protrusions as small as 1,300 daltons could be measured reproducibly within the unit cell of 655,000 daltons. The method developed opens an avenue to identify molecular species in situ and to correlate topographic information with biochemical data.
Automation of Polymerase Chain Reaction-Based Systems for Detection of Hepatitis C Virus RNA

Abstract Polymerase chain reaction-based molecular assays are gaining increasing importance in the diagnosis and monitoring of infectious diseases. Over the past several years, the development and application of these techniques has initiated a revolution in the diagnosis and monitoring of hepatitis C infection. Presently, molecular assays are exclusively done in especially dedicated laboratories. Advances in automation will bring these technologies into routine diagnostic laboratories and will make them widely used.
A Toxin-based Probe Reveals Cytoplasmic Exposure of Golgi Sphingomyelin*

Although sphingomyelin is an important cellular lipid, its subcellular distribution is not precisely known. Here we use a sea anemone cytolysin, equinatoxin II (EqtII), which specifically binds sphingomyelin, as a new marker to detect cellular sphingomyelin. A purified fusion protein composed of EqtII and green fluorescent protein (EqtII-GFP) binds to the SM rich apical membrane of Madin-Darby canine kidney (MDCK) II cells when added exogenously, but not to the SM-free basolateral membrane. When expressed intracellularly within MDCK II cells, EqtII-GFP colocalizes with markers for Golgi apparatus and not with those for nucleus, mitochondria, endoplasmic reticulum or plasma membrane. Colocalization with the Golgi apparatus was confirmed by also using NIH 3T3 fibroblasts. Moreover, EqtII-GFP was enriched in cis-Golgi compartments isolated by gradient ultracentrifugation. The data reveal that EqtII-GFP is a sensitive probe for membrane sphingomyelin, which provides new information on cytosolic exposure, essential to understand its diverse physiological roles.
Sagittal gait of a biped robot during the single support phase. Part 1: passive motion

It has been shown that compass-like bipeds can walk passively by gravity-induced motion. Similarly, it has been stated that the unipodal phase of human gait may be regarded as a passive motion. This paper is aimed at determining precisely to what extent the swing phase of human-like walking can be considered as a non-actuated motion. More specifically, a method is developed that makes it possible to adjust initial conditions, step length and walk speed, as well as mass and inertia distribution of a bipedal robot, in order to generate a passive swing motion. The approach is demonstrated by using a 7-link planar biped. Numerical simulations show that purely passive unipodal transferring cannot be fully satisfactory. This approach is further considered in Part 2 of the paper which consists in computing optimal actuating joint torques to create perfectly feasible motions.
Toll-like receptor 4 signaling leads to neutrophil migration impairment in polymicrobial sepsis*

Objective:We have documented an impaired neutrophil migration toward the infectious focus in severe sepsis. This phenomenon appears to be mediated by nitric oxide, the release of which is stimulated by circulating inflammatory cytokines released by immune cells after stimulation by bacteria and/or their products. Toll-like receptor 4 (TLR4) is the major recognition receptor for lipopolysaccharide, a component of Gram-negative bacterial cell walls. In the present study, we investigated whether TLR4 is involved in the failure of neutrophil migration in mice subjected to polymicrobial or Gram-negative sepsis. Design:Controlled animal study. Setting:University research laboratory. Subjects:Male C3H/HeJ (TLR4-deficient) and C3H/HePas (TLR4-normal) mice. Interventions:Mice were subjected to sublethal or lethal polymicrobial sepsis, both induced by cecal ligation and puncture or intraperitoneal polymicrobial inoculation, and subjected to sublethal Gram-negative sepsis induced by intraperitoneal Salmonella typhimurium inoculation (GNI). Survival was monitored for 5 days. In separate experiments, mice were killed 6 hrs after sepsis induction, and intraperitoneal neutrophil migration, bacteremia, lung neutrophil sequestration, and levels of cytokines, chemokines, and nitrate were evaluated. Measurements and Results:TLR4-deficient (C3H/HeJ) mice presented incapacity to promote neutrophil recruitment to the infectious site after sublethal GNI, resulting in high mortality. However, TLR4 signaling is not essential to display neutrophil migration in sublethal polymicrobial sepsis induced by both cecal ligation and puncture and polymicrobial inoculation models, but surprisingly, it is crucial to establish the impairment of neutrophil migration in lethal polymicrobial sepsis, since TLR4-deficient mice that underwent lethal cecal ligation and puncture or polymicrobial inoculation did not present failure of neutrophil migration to infectious focus. As a consequence, these animals presented low bacteremia and a high survival rate and did not display systemic inflammation, determined by high levels of circulating cytokines and lung neutrophil sequestration and chemokine production. Conclusion:These results highlight the harmful role of TLR4 signaling in polymicrobial severe sepsis.
Calcium and the heart: exchange at the tissue, cell, and organelle levels 1

Cellular calcium (Ca) exchange in arterially perfused whole heart is markedly perfusion‐limited. Therefore, a large fraction of exchangeable Ca recycles within the cell before exchanging with extracellular Ca. Ca enters the cell via sarcolemmal (SL) transient (T) and long‐lasting (L) channels activated at more negative and less negative membrane potential, respectively. The larger L currents are controlled via phosphorylation and G protein interaction to provide Ca to induce Ca release from sarcoplasmic reticulum (SR) and for direct myofilament activation. Troponin C (TNC) binds 3 mol of Ca/mol. Only the low affinity site is responsible for activation of force and regulation of myofilament ATPase rate. This occurs through a shift in troponin I (TNI) with respect to actin induced by the TNC Ca binding. Relaxation depends on reduction of cytosolic (Ca) and occurs via 1) Ca pumping into the longitudinal SR modulated by phospholamban; 2) the recently cloned high‐capacity electrogenic SL Na‐Ca exchanger; and 3) the SL Ca pump under complex regulation including calmodulin control. Mitochondria transport Ca, but this transport is directed primarily to the regulation of various Ca‐sensitive dehydrogenases so that oxidative metabolism can be adjusted to changes in energy demand. The regulation of Ca movements consumes about 25% of the cell's total energy output. Mitochondrial Ca exchanges with extracellular Ca most slowly (t ½ = 3.6 min), SR Ca quite rapidly (t½′s = 3 and 19 s), and an Na‐Ca exchange‐dependent compartment very rapidly (t½ = 500 ms). After further description of Ca handling by the individual organelles, Ca movement is followed through the cell during the course of contraction, and the contribution of each organelle or compartment to overall cellular Ca exchange is defined. —Langer, G. A. Calcium and the heart: exchange at the tissue, cell, and organelle levels. FASEB J. 6: 893‐902; 1992.
The pattern of recovery of ambulation after hip fracture differs with age in elderly patients.

BACKGROUND The main objective of this study was to analyze the independent effect of increasing age on the recovery of different areas of functioning 1 year after hip fracture. METHODS Consecutive 1-year survivors aged ≥ 65 years (n = 362) admitted to a single hospital for acute hip fracture surgery were followed prospectively for 1 year. Age was stratified as <75, 75-84, and ≥ 85 years. Basic activities of daily living and ambulation were measured by personal interview during hospitalization and phone contact at 3, 6, and 12 months. Longitudinal data of recovery in these areas were analyzed using generalized estimating equations. RESULTS Older age was strongly associated with poor recovery in all areas of function, except eating. The pattern of recovery of ambulation differed with age, peaking at 6 months in the younger group and continuing for at least 12 months in the eldest group. The pattern of recovery of overall and individual activities of daily living was similar in the three age groups. Recovery of areas associated with upper extremity function peaked at 3 months, whereas areas associated with lower extremity function peaked at 6 months. CONCLUSIONS The patterns of functional disability after hip fracture differ with areas of function and age with the oldest patients having a particular risk of decline and a prolonged time to recovery of ambulation.
Effects of two national environmental factors on e-commerce functionality adoption: a cross-country case study of a global bank

In order to offer new services and gain competitive advantages, e-commerce has been widely adopted, particularly in the banking industry. Unfortunately, despite the growing adoption of e-commerce in the banking industry, the issue that web-based B2C e-commerce functionality adoption varies between banks or a bank's branches across nations has not received sufficient attention. Many factors affect e-commerce functionality adoption. However, two national environmental factors (information infrastructure and demographics) are particularly important because they relate to the availability of technologies in use and the characteristics of customers, respectively. This research conducts a cross-country case study of a global bank's Beijing (China), Chicago (USA), and Dubai (UAE) branches to investigate how the two national environmental factors affect e-commerce functionality adoption. The specific objectives are to discover how information infrastructure (measured by number of PCs per 1000 people and Internet access cost) and demographics (measured by population composition and income) affect e-commerce functionality adoption of the global bank's three branches. Secondary data were collected for information infrastructure and demographics; additionally, focused interviews with these three branches' IT and business managers provided sources for answering ‘how’. The key finding demonstrates that the differences in e-mail ordering and online shopping adoptions between these branches are mainly attributed to proposed factors of population composition and Internet access cost, and the new factor of individual credit reference system. This research contributes to theory development in this emerging important research subject.
Informal organizational culture: the foundation of knowledge workers' performance

Purpose – The paper aims to serve as a reminder of the fact that creating a strong atmosphere of trust and longevity in employee relations is ultimately the most robust route to maintaining a sustainable competitive edge.Design/methodology/approach – In addition to a literature review, empirical evidence is drawn from qualitative interview data. The research setting covers five distinct business organizations representing technology industries and knowledge‐intensive business services.Findings – The paper indicates that even in knowledge‐intensive firms a good team spirit and skilful management remain more important than the use of the latest technology. Furthermore, it is maintained that the role of information technology in supporting the decision‐making process in knowledge work is often very much overemphasized. However, modern information technology continues the long trend of the automation and mechanization of work and, if used properly, it can indirectly contribute to creating more space for inter.
Deliverable D 1 . 1 Web-platform security guide : Security assessment of the Web ecosystem

This deliverable reports on the broad web security assessment of STREWS. As part of this report, we provide a clear and understandable overview of the Web ecosystem, and discuss the vulnerability landscape, as well as of the underlying attacker models. In addition, we provide a catalog of best practices with existing countermeasures and mitigation techniques, to guide European industrial players to improve step-by-step the trustworthiness of their IT infrastructures. The report concludes with interesting challenges for securing the Web platform, opportunities for future research and trends in improving web security.
Anti-lipid peroxidation and induction of apoptosis in the erythroleukaemic cell line K562 by extracts from (Tunisian) Rhamnus alaternus L. (Rhamnaceae)

Total oligomer flavonoids (TOF) enriched and ethyl acetate (EA) extracts from Rhamnus alaternus induce apoptotic death in human chronic myelogenous leukaemia K562 cell line, as demonstrated by gel electrophoresis, which demonstrates the characteristic ladder patterns of DNA fragmentation and the proteolytic cleavage of poly(ADP ribose) polymerase (PARP). The effect of R. alaternus extract in reducing oxidative stress was evaluated by anti-lipid peroxidation which was monitored by measuring malondialdehyde level in K562 cultured cells. The TOF and EA extracts were found to be effective to protect against lipid peroxidation. Their IC50 values were 196 and 273 µg mL−1, respectively. These findings suggest that R. alaternus extracts exhibit potential antioxidant and proapoptotic properties.
Cellular automata and two-level systems dynamics - Spreading of disorder

We focus on description of disorder in a system which is composed of a large number of two level subsystems using the cellular automata formalism. We introduce parameters which can be used as a measure of disorder spreading in such a complex system. These parameters are defined via the entropy and we show their usefulness for description of disorder in the system discussed.
Loss of mouse epidermal protein kinase C isozyme activities following treatment with phorbol ester and non-phorbol ester tumor promoters.

The present study has examined changes in activities and levels of four protein kinase C (PKC) isozymes (PKC alpha, PKC beta, PKC gamma and PKC delta) detectable in mouse epidermal preparations following both single and multiple treatments with 12-O-tetradecanoylphorbol-13-acetate (TPA). In addition, PKC epsilon and PKC eta protein levels were monitored by immunoblotting following TPA application. Finally, PKC isozyme activity profiles were also examined in epidermal preparations from mice treated with single applications of two non-phorbol ester tumor promoters: chrysarobin (CHRY) and okadaic acid (OA). Fifteen minutes following topical treatment with a tumor promoting dose of TPA (3.4 nmol), the activities of PKC beta and PKC gamma decreased in the epidermal cytosol to 30% and 50% of control values, respectively, while these activities were increased in the epidermal particulate fraction by approximately 50%. PKC delta activity, found predominantly in the particulate fraction of control epidermis, was greatly diminished in both subcellular fractions at 15 min while PKC alpha activity was translocated approximately 20% from cytosol to particulate fraction. Significant reductions in all four detectable PKC isozyme activities in both particulate and cytosol fractions were observed 48 h after a single treatment with TPA, although particulate PKC alpha activity appeared to be less affected at this point in time compared to the other PKC isozymes. Immunoblotting analyses of PKC isozyme protein levels after TPA treatment followed the changes in activity for cytosolic PKC alpha, PKC beta and PKC gamma. However, particulate PKC delta and PKC epsilon protein levels remained relatively unchanged while particulate PKC eta protein levels were significantly down-regulated after a single TPA treatment. Multiple topical treatments (twice-weekly for 2 weeks) with TPA produced a pattern of loss followed by only partial recovery of total PKC activity. Furthermore, all four PKC isozyme activities examined by hydroxylapatite (HA) chromatography were significantly reduced, including PKC alpha, after four applications of TPA. Cytosolic PKC alpha, PKC beta and PKC gamma protein levels as determined by immunoblotting again followed the activity profiles; particulate PKC eta protein levels were significantly reduced, whereas particulate PKC delta and PKC epsilon levels again appeared relatively unchanged. Fifteen minutes after topical application of 220 nmol CHRY, an approximately 25% decrease in particulate associated with PKC alpha activity was observed while particulate activities associated with PKC beta, PKC gamma and PKC delta were unaffected by CHRY at this time point. (ABSTRACT TRUNCATED AT 400 WORDS)
Membrane lipids, EGF receptors, and intracellular signals colocalize and are polarized in epithelial cells moving directionally in a physiological electric field

Directed cell migration is essential for tissue formation, inflammation, and wound healing. Chemotaxis plays a major role in these situations and is underpinned by asymmetric intracellular signaling. Endogenous electric fields (EFs) are common where cell movement occurs, such as in wound healing, and cells respond to electric field gradients by reorienting and migrating directionally (galvanotaxis/electrotaxis). We show that a physiological EF redistributed both EGF (epidermal growth factor) receptors and detergent‐insoluble membrane lipids asymmetrically, leading to cathodal polarization and enhanced activation of the MAP kinase, ERK1/2. This induced leading‐edge actin polymerization in directionally migrating mammalian epithelial cells. Inhibiting the EGF receptor‐MAP kinase signaling pathway significantly decreased leading edge actin asymmetry and directional migration. We propose a model in which EF‐polarized membrane lipid domains and EGF receptors cause asymmetric signaling through MAP kinase, which drives directional cell migration. A comparison is made with the mechanisms underpinning chemotaxis.
A web based multi-linguists symbol-to-text AAC application

There are several commercial or freely available symbol sets for Augmentative and Alternative Communication (AAC) use; all these symbol sets have the same issue when trying to use them in a multiple lingual setting. Symbol Dragoman is a Web based application that aims to allow the user who has no spoken language and uses pictograms or images to communicate in Arabic or English. It combines chosen 'symbols' in any way they want to produce a sentence that can be read or heard in both languages with the potential of offering any combination of languages in the future.
Increased MET gene copy number negatively affects survival of surgically resected non-small-cell lung cancer patients.

PURPOSE To investigate the prognostic role of genomic gain for MET and epidermal growth factor receptor (EGFR) genes in surgically resected non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS This retrospective study included 447 NSCLC patients with available tumor tissue from primary lung tumor and survival data. EGFR and MET status was evaluated by fluorescent in situ hybridization (FISH) in tissue microarray sections. RESULTS EGFR FISH results were obtained in 376 cases. EGFR gene amplification and high polysomy (EGFR FISH+) were observed in 10.4% and 32.4% of cases, respectively. EGFR FISH-positive patients had a nonsignificant shorter survival than EGFR FISH-negative patients (P = .4). Activating EGFR mutations were detected in 9.7% of 144 stage I-II disease with no impact on survival. MET FISH analysis was performed in 435 cases. High MET gene copy number (mean > or = 5 copies/cell) was observed in 48 cases (MET+, 11.1%), including 18 cases with true gene amplification (4.1%). MET+ status was associated with advanced stage (P = .01), with grade 3 (P = .016) and with EGFR FISH+ result (P < .0001). No patient with activating EGFR mutation resulted MET+. In the whole population, MET-positive patients had shorter survival than MET-negative patients (P = .005). Multivariable model confirmed that MET-negative patients had a significant reduction in the risk of death than MET-positive patients (hazard ratio, 0.66; P = .04). CONCLUSION MET increased gene copy number is an independent negative prognostic factor in surgically resected NSCLC. EGFR gene gain does not impact survival after resection.
A Novel High-Temperature Planar Package for SiC Multichip Phase-Leg Power Module

This paper presents the design, development, and testing of a phase-leg power module packaged by a novel planar packaging technique for high-temperature (250°C) operation. The nanosilver paste is chosen as the die-attach material as well as playing the key functions of electrically connecting the devices' pads. The electrical characteristics of the SiC-based power semiconductors, SiC JFETs, and SiC Schottky diodes have been measured and compared before and after packaging. No significant changes (<;5%) are found in the characteristics of all the devices. Prototype module is fabricated and operated up to 400 V, 1.4 kW at junction temperature of 250°C in the continuous power test. Thermomechanical robustness has also been investigated by passive thermal cycling of the module from -55°C to 250°C. Electrical and mechanical performances of the packaged module are characterized and considered to be reliable for at least 200 cycles.
Hypocalcemic cardiomyopathy-different mechanisms in adult and pediatric cases.

BACKGROUND Hypocalcemic cardiomyopathy (CMP) is a rare but potentially reversible cause of heart failure. However, the mechanism of hypocalcemia seems to differ between infants and adults. Although severe vitamin D deficiency alone is the usual cause of hypocalcemic CMP in infants, in adult patients significant cardiac dysfunction usually occurs as a result of hypoparathyroidism, either isolated or in combination with vitamin D deficiency. We present two cases of hypocalcemic CMP-one adult and one pediatric-to highlight these differences. CASE PRESENTATION The first patient was a 47-year-old female who presented with progressive dyspnea and fatigue and was found to have severe left ventricular (LV) systolic dysfunction (LV ejection fraction, 25%). Her serum calcium level was 3.5 mg/dL, serum phosphorus level was 5.7 mg/dL, and serum 25-hydroxyvitamin D level was 14.1 ng/mL, along with a serum PTH level of 11.8 pg/mL. Her LV ejection fraction normalized completely over 6 months with calcium and calcitriol treatment. In contrast, the second patient was an infant who had presented in cardiogenic shock. Investigations revealed serum calcium of 4.5 mg/dL, serum phosphorus of 11.9 mg/dL, 25-hydroxyvitamin D of 8.9 ng/mL, and serum PTH level of 670 pg/mL. Calcium and calcitriol supplementation resulted in rapid and complete clinical and hemodynamic recovery. CONCLUSION Hypocalcemia is a rare but treatable cause of dilated CMP. In infants, hypocalcemia is usually due to maternal vitamin D deficiency and is accompanied by compensatory hyperparathyroidism. In contrast, in adult patients, hypocalcemic CMP is usually a result of hypoparathyroidism, with or without concomitant vitamin D deficiency.