Miracle-dz/UniFAR-FTUs huggingface dataset:
Roles of HynAB and Ech, the Only Two Hydrogenases Found in the Model Sulfate Reducer Desulfovibrio gigas

ABSTRACT Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been proposed to contribute to the overall energy metabolism of the cell, but exactly in what role is not clear. Desulfovibrio spp. can produce or consume H2 when growing on organic or inorganic substrates in the presence or absence of sulfate. Because of the presence of only two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech hydrogenases, Desulfovibrio gigas is an excellent model organism for investigation of the specific function of each of these enzymes during growth. In this study, we analyzed the physiological response to the deletion of the genes that encode the two hydrogenases in D. gigas, through the generation of ΔechBC and ΔhynAB single mutant strains. These strains were analyzed for the ability to grow on different substrates, such as lactate, pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the expression of both hydrogenase genes in the three strains studied was assessed through quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is essential for growth on lactate-sulfate, indicating that hydrogen cycling is not indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is required for growth on H2 or by fermentation of pyruvate. Therefore, this enzyme seems to play a dominant role in D. gigas hydrogen metabolism.
A Classification Method for User-Independent Intent Recognition for Transfemoral Amputees Using Powered Lower Limb Prostheses

Powered lower limb prosthesis technologies hold the promise of providing greater ability and mobility to transfemoral amputees. Intent recognition systems for these devices may allow amputees to perform automatic, seamless transitions between locomotion modes. Prior studies in which pattern recognition algorithms have been trained to recognize subject-specific patterns within device-mounted sensor data have shown the feasibility of such systems. While effective, these strategies require substantial training regimens. To reduce this training burden, we developed and evaluated user-independent intent recognition systems. A novel mode-specific classification system was developed that allowed each locomotion transition to be statistically considered its own class. Various pattern recognition algorithms were trained with sensor data from a pool of eight lower limb amputees and performance was tested using data on a novel subject. For both user-dependent and user-independent classification, mode-specific classification reduced error ( ) on transitional steps by ~ 50% without affecting steady-state classification. Incorporating sensor time history and level-ground walking data from the novel subject into the training data resulted in decreasing errors ( ) on steady-state classification by over 60% without affecting transitional error. These strategies were combined to demonstrate significant overall system improvements from baseline conditions presented in prior research.
Seven Novel Variants of the Staphylococcal Chromosomal Cassette mec in Methicillin-Resistant Staphylococcus aureus Isolates from Ireland

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered in Irish hospitals between 1971 and 2002 were characterized using multilocus sequence typing (MLST) (n = 130) and SCCmec typing (n = 172). Where atypical SCCmec typing results were obtained, PCR amplification of entire SCCmec elements, analysis of amplimer mobility, and nucleotide sequencing were undertaken. MLST revealed that 129/130 isolates had the same genotypes as internationally spread MRSA clones, including ST239, ST247, ST250, ST5, ST22, ST36, and ST8. A novel genotype, ST496, was identified in one isolate. Half of the isolates (86/172) had SCCmec type I, IA, II, III, or IV. The remaining 86 isolates harbored novel SCCmec variants in three distinct genetic backgrounds: (i) 74/86 had genotype ST8 and either one of five novel SCCmec II (IIA, IIB, IIC, IID, and IIE) or one of two novel SCCmec IV (IVE and IVF) variants; (ii) 3/86 had genotype ST239 and a novel SCCmec III variant; (iii) 9/86 had a novel SCCmec I variant associated with ST250. SCCmec IVE and IVF were similar to SCCmec IVc and IVb, respectively, but differed in the region downstream of mecA. The five SCCmec II variants were similar to SCCmec IVb in the region upstream of the ccr complex but otherwise were similar to SCCmec II, except for the following regions: SCCmec IIA and IID had a novel mec complex, A.4 (ΔmecI-IS1182-ΔmecI-mecR1-mecA-IS431mec); SCCmec IIC and IIE had a novel mec complex, A.3 (IS1182-ΔmecI-mecR1-mecA-IS431mec); SCCmec IID and IIE lacked pUB110; SCCmec IIC and IIE lacked a region of DNA between Tn554 and the mec complex; and SCCmec IIB lacked Tn554. This study has demonstrated a hitherto-undescribed degree of diversity within SCCmec.
Lived Experiences of Women Facing Domestic Violence in India

This article describes the lived experiences of domestic violence victims among a convenience sample of 21 low-income Indian women. The experiences of abuse are drawn from in-depth, face-to-face interviews conducted in Mumbai, India. The qualitative analysis describes four major categories of their lived experiences: (a) types of abuse, (b) family involvement in abuse, (c) treatment of children, and (d) abandonment. Domestic violence in Indian culture includes violence from the husband as well as the in-laws. Women are expected to endure violence for fear of bringing shame to their families. Social and financial support for abused woman is lacking.
Dilemmas in introducing World Wide Web-based information technology in primary care: a focus group study.

BACKGROUND When implementing a computer-based decision support system for any disease group in a primary health care centre, success will depend on the introductory efforts put into the project. The users must have plenty of information, above all regarding what can and what cannot be done by the computer-based decision support system. A personal introduction including a personal instruction session in front of the computer is imperative. Different aspects of technical maturity of the system must be met. Communication within and outside of the local net must be stable. METHODS Using a designated focus group methodology, we studied the introduction of advanced information technology in primary care by applying an inter/intranet decision support system for ambulatory ear, nose and throat diagnostics using a World Wide Web tool at the Skänninge health centre in Ostergötland, Sweden. CONCLUSIONS A computer-based decision support system of the kind studied here may after a refinement period have all the qualities asked for by the users, and this study can be used as part of a user-developer dialogue for a future system.
Association of Class II Histone Deacetylases with Heterochromatin Protein 1: Potential Role for Histone Methylation in Control of Muscle Differentiation

ABSTRACT Class II histone deacetylases (HDACs) 4, 5, 7, and 9 repress muscle differentiation through associations with the myocyte enhancer factor 2 (MEF2) transcription factor. MEF2-interacting transcription repressor (MITR) is an amino-terminal splice variant of HDAC9 that also potently inhibits MEF2 transcriptional activity despite lacking a catalytic domain. Here we report that MITR, HDAC4, and HDAC5 associate with heterochromatin protein 1 (HP1), an adaptor protein that recognizes methylated lysines within histone tails and mediates transcriptional repression by recruiting histone methyltransferase. Promyogenic signals provided by calcium/calmodulin-dependent kinase (CaMK) disrupt the interaction of MITR and HDACs with HP1. Since the histone methyl-lysine residues recognized by HP1 also serve as substrates for deacetylation by HDACs, the interaction of MITR and HDACs with HP1 provides an efficient mechanism for silencing MEF2 target genes by coupling histone deacetylation and methylation. Indeed, nucleosomal histones surrounding a MEF2-binding site in the myogenin gene promoter are highly methylated in undifferentiated myoblasts, when the gene is silent, and become acetylated during muscle differentiation, when the myogenin gene is expressed at high levels. The ability of MEF2 to recruit a histone methyltransferase to target gene promoters via HP1-MITR and HP1-HDAC interactions and of CaMK signaling to disrupt these interactions provides an efficient mechanism for signal-dependent regulation of the epigenetic events controlling muscle differentiation.
Pulmonary homograft morphology after the Ross procedure: a computed tomography study.

BACKGROUND AND AIM OF THE STUDY In patients undergoing the Ross procedure the autograft morphological characteristics have been well studied, but those of the homograft are less clear. The study aim was to describe the radiomorphological homograft characteristics in Ross patients, and to compare them with such characteristics in normal (control) subjects. METHODS A total of 79 Ross patients (68 males, 11 females; mean age 43 +/- 12.3 years) underwent a computed tomography (CT) scan at a mean of 31 +/- 26 months after surgery. A group of 123 patients without cardiovascular disease served as controls. Cryopreserved homografts were implanted in all Ross patients, with the majority being obtained from a single source. RESULTS The mean donor age was 47 +/- 11 years, and the mean homograft diameter 25.4 +/- 1.3 mm (as provided at source). Electrocardiographic-gated CT reconstructions were used for the measurements. The smallest diameters were at the proximal anastomosis, and maximum diameters at the distal anastomosis (p <0.001). In controls, the minimum diameter was just proximal to the pulmonary valve annulus. In Ross patients, the homograft diameters were significantly smaller at all levels compared to controls. This effect persisted after taking into consideration patient age, height, gender, body surface area, and time since surgery. Notably, the measured homograft diameters were significantly smaller than those provided at source. CONCLUSION The study results provided evidence of homograft shrinkage at all levels after the Ross procedure but, most prominently, at the level of the proximal suture line. This may have implications for novel preservation methods, as well as homograft size selection and implantation techniques.
More taxa, more characters: the hoatzin problem is still unresolved.

The apparently rapid and ancient diversification of many avian orders complicates the resolution of their relationships using molecular data. Recent studies based on complete mitochondrial DNA (mtDNA) sequences or shorter lengths of nuclear sequence have helped corroborate the basic structure of the avian tree (e.g., a basal split between Paleognathae and Neognathae) but have made relatively little progress in resolving relationships among the many orders within Neoaves. We explored the potential of a moderately sized mtDNA data set ( approximately 5000 bp for each of 41 taxa), supplemented with data from a nuclear intron ( approximately 700 bp per taxon), to resolve relationships among avian orders. Our sampling of taxa addresses two issues: (1). the sister relationship and monophyly, respectively, of Anseriformes and Galliformes and (2). relationships of the enigmatic hoatzin Opisthocomus hoazin. Our analyses support a basal split between Galloanserae and Neoaves within Neognathae and monophyly of both Galliformes and Anseriformes. Within Galliformes, megapodes and then cracids branch basally. Within Anseriformes, mitochondrial data support a screamer (Anhimidae) plus magpie goose (Anseranatidae) clade. This result, however, may be an artifact of divergent base composition in one of the two anatids we sampled. With deletion of the latter taxon, Anseranas is sister to anatids as in traditional arrangements and recent morphological studies. Although our data provide limited resolution of relationships within Neoaves, we find no support for a sister relationship between either cuckoos (Cuculiformes) or turacos (Musophagiformes) and hoatzin. Both mitochondrial and nuclear data are consistent with a relationship between hoatzin and doves (Columbiformes), although this result is weakly supported. We also show that mtDNA sequences reported in another recent study included pervasive errors that biased the analysis towards finding a sister relationship between hoatzin and turacos.
An Adaptive Approximator-Based Backstepping Control Approach for Piezoactuator-Driven Stages

This paper investigates precise trajectory tracking of a piezoactuator-driven stage with hysteresis behavior by using an approximator-based adaptive tracking control approach. Differential equations consisting of the dynamics of a linear motion system and a hysteresis function are first studied for describing the dynamics of motion of the piezoactuator-driven stage with hysteresis behavior. Then, a numerical optimization method is taken to identify the values of the parameters adopted in the differential equations. From the differential equations, an equivalent state-space model with an augmented integral input and with a defined hysteresis variable is established. Moreover, to approximate the unavailable hysteresis variable, an adaptive approximator that comprises a Gaussian radial-basis function network is adopted. Furthermore, from the state-space model, an adaptive approximator-based backstepping trajectory-tracking control is developed. Using the proposed control approach to trajectory tracking of the piezoactuator-driven stage, an improvement in transient performance and tracking errors, and robustness to the disturbance load, can be provided. Last, to show the validity of the proposed control approach, an implementation of the control algorithm on the computer-controlled single-axis piezoactuator-driven stage was developed. From the experimental results, the feasibility of the proposed control for practical applications can be confirmed.
Peter Praet: Calibrating unconventional monetary policy

Speech by Mr Peter Praet, Member of the Executive Board of the European Central Bank, at The ECB and Its Watchers XVIII Conference, organised by the Center for Financial Studies and the Institute for Monetary and Financial Stability at Goethe University Frankfurt, panel on the "Assessment of the expanded asset purchase programme" (with John Taylor and Jan Hatzius), Frankfurt am Main, 6 April 2017.
Enhancing the Availability of Docker Swarm Using Checkpoint-and-Restore

More and more software developers and information-technology professionals embrace the container technology, because it packs the required libraries and settings of software into a single image so that the deployment can be easily done anywhere without the issues of compatibility. On top of single containers, orchestration tools are essential to automate the deployment and operation of complex systems that involve multiple containers on a cluster of machines. In this paper, we present the idea of using checkpoint-and-restore technique to enhance the availability of Docker Swarm, a state-of-art orchestration tool for Docker containers. We used multi-version checkpoints to strengthen the availability of containers and investigated the optimal storage and performance for checkpoint-and-restore. Experiments show that the proposed method can save about 50% of storage space with few overhead on the original process.
Immunofluorescence in Cells Derived from Burkitt's Lymphoma

Henle, Gertrude (Children's Hospital of Philadelphia, Philadelphia, Pa.), and Werner Henle. Immunofluorescence in cells derived from Burkitt's lymphoma. J. Bacteriol. 91:1248–1256. 1966. —Indirect immunofluorescence tests led to the brilliant staining of a small proportion of the cells in five different cultures derived from Burkitt's (African) lymphomas. The reaction was not restricted to the 17 sera from cases of this disease but extended to many sera from American individuals, whether healthy donors or patients suffering from a variety of illnesses. The incidence of positive sera increased with age from about 30% in childhood to > 90% in adults. Fluorescein-isothiocyanate-conjugated human γ-globulins were suitable for direct staining of the same proportion of cells. The stained cells appeared to be in varying stages of degeneration, but cultural conditions leading to an increase in the cellular death rates failed to result in a rise in fluorescent cells. Several observations suggest that the stainable cells might be those which are seen to harbor virus particles under the electron microscope. Two cell lines derived from leukemic patients in this country also contained a small fraction of stainable cells but two others, and numerous primary human leukocyte cultures, gave consistently negative results. Attempts to relate the staining to known viral antigens have failed to implicate herpes simplex, varicella, cytomegalo, and reo viruses types 1, 2, and 3. The nature of the virus carried by the lymphoma cells as well as of the staining reactions remains to be determined.
Ankle muscle strength influence on muscle activation during dynamic and static ankle training modalities

Abstract Muscle weakness is considered a risk factor for ankle injury. Balance training and barefoot running have been used in an attempt to strengthen the muscles crossing the ankle. It is expected that training tasks that successfully strengthen the ankle would elicit increased muscular activity. However, it is unknown how an individual's ankle strength will influence the muscle activity used during a given task. Twenty-six participants performed dynamic (shod, barefoot running) and static tasks (squat on ground, squat on ®Bosu Ball) believed to strengthen the muscles surrounding the ankle. Electromyographic signals of the tibialis anterior, peroneus longus, gastrocnemius lateralis (GL) and gastrocnemius medialis (GM) were recorded and analysed using a non-linearly scaled wavelet analysis. Participants were divided into a strong group and a weak group according to their isometric plantar-flexion torque. The weak group required more relative GL and GM muscle activity during each training task compared to the strong group. No difference was observed between shod and barefoot running. There was a significant effect of training task on muscle activation level for the weak group. Differences in ankle strength had a significant impact on muscle activation.
Structural Changes Are Associated with Soluble N-Ethylmaleimide-sensitive Fusion Protein Attachment Protein Receptor Complex Formation*

SNAP-25, syntaxin, and synaptobrevin play a key role in the regulated exocytosis of synaptic vesicles, but their mechanism of action is not understood. In vitro, the proteins spontaneously assemble into a ternary complex that can be dissociated by the ATPase N-ethylmaleimide-sensitive fusion protein and the cofactors α-, β-, and γ-SNAP. Since the structural changes associated with these reactions probably form the basis of membrane fusion, we have embarked on biophysical studies aimed at elucidating such changes in vitro using recombinant proteins. All proteins were purified in a monomeric form. Syntaxin showed significant α-helicity, whereas SNAP-25 and synaptobrevin exhibited characteristics of largely unstructured proteins. Formation of the ternary complex induced dramatic increases in α-helicity and in thermal stability. This suggests that structure is induced in SNAP-25 and synaptobrevin upon complex formation. In addition, the stoichiometry changed from 2:1 in the syntaxin-SNAP-25 complex to 1:1:1 in the ternary complex. We propose that the transition from largely unstructured monomers to a tightly packed, energetically favored ternary complex connecting two membranes is a key step in overcoming energy barriers for membrane fusion.
Impact of short‐term high‐fat feeding on glucose and insulin metabolism in young healthy men

A high‐fat, high‐calorie diet is associated with obesity and type 2 diabetes. However, the relative contribution of metabolic defects to the development of hyperglycaemia and type 2 diabetes is controversial. Accumulation of excess fat in muscle and adipose tissue in insulin resistance and type 2 diabetes may be linked with defective mitochondrial oxidative phosphorylation. The aim of the current study was to investigate acute effects of short‐term fat overfeeding on glucose and insulin metabolism in young men. We studied the effects of 5 days’ high‐fat (60% energy) overfeeding (+50%) versus a control diet on hepatic and peripheral insulin action by a hyperinsulinaemic euglycaemic clamp, muscle mitochondrial function by 31P magnetic resonance spectroscopy, and gene expression by qrt‐PCR and microarray in 26 young men. Hepatic glucose production and fasting glucose levels increased significantly in response to overfeeding. However, peripheral insulin action, muscle mitochondrial function, and general and specific oxidative phosphorylation gene expression were unaffected by high‐fat feeding. Insulin secretion increased appropriately to compensate for hepatic, and not for peripheral, insulin resistance. High‐fat feeding increased fasting levels of plasma adiponectin, leptin and gastric inhibitory peptide (GIP). High‐fat overfeeding increases fasting glucose levels due to increased hepatic glucose production. The increased insulin secretion may compensate for hepatic insulin resistance possibly mediated by elevated GIP secretion. Increased insulin secretion precedes the development of peripheral insulin resistance, mitochondrial dysfunction and obesity in response to overfeeding, suggesting a role for insulin per se as well GIP, in the development of peripheral insulin resistance and obesity.
Adhesion of calcium oxalate monohydrate crystals to renal epithelial cells is inhibited by specific anions.

Adhesion of urinary crystals to the apical surface of renal tubular cells could be a critical step in the formation of kidney stones. The interaction between renal epithelial cells (BSC-1 line) and the most common crystal in kidney stones, calcium oxalate monohydrate (COM), was studied in a tissue culture model system. COM crystals bound to the cell surface within seconds in a concentration-dependent manner to a far greater extent than did brushite, another calcium-containing crystal found in urine. Adhesion of COM crystals to cells was blocked by the polyanion, heparin. Other glycosaminoglycans including chondroitin sulfate A or B, heparan sulfate, and hyaluronic acid, but not chondroitin sulfate C, prevented binding of COM crystals. Two nonsulfated polyanions, polyglutamic acid and polyaspartic acid, also blocked adherence of COM crystals. Three molecules found in urine, nephrocalcin, uropontin, and citrate, each inhibited binding of COM crystals, whereas Tamm-Horsfall glycoprotein (THP) did not. Prior exposure of crystals but not cells to inhibitory molecules blocked adhesion, suggesting that these agents exert their effect at the crystal surface. Inhibition of crystal binding followed a linear Langmuir adsorption isotherm for each inhibitor identified, suggesting that these molecules bind to a single class of sites on the crystal that are important for adhesion to the cell surface. Inhibition of crystal adhesion by heparin was rapidly overcome by the polycation protamine, suggesting that the glycosaminoglycan regulates cell-crystal interactions in a potentially reversible manner. (ABSTRACT TRUNCATED AT 250 WORDS)