Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct Mechanisms for Ctr1-mediated Copper and Cisplatin Transport*

The Ctr1 family of integral membrane proteins is necessary for high affinity copper uptake in eukaryotes. Ctr1 is also involved in cellular accumulation of cisplatin, a platinum-based anticancer drug. Although the physiological role of Ctr1 has been revealed, the mechanism of action of Ctr1 remains to be elucidated. To gain a better understanding of Ctr1-mediated copper and cisplatin transport, we have monitored molecular dynamics and transport activities of yeast Saccharomyces cerevisiae Ctr1 and its mutant alleles. Co-expression of functional Ctr1 monomers fused with either cyan or yellow fluorescent protein resulted in fluorescence resonance energy transfer (FRET), which is consistent with multimer assembly of Ctr1. Copper near the Km value of Ctr1 enhanced FRET in a manner that correlated with cellular copper transport. In vitro cross-linking of Ctr1 confirmed that copper-induced FRET reflects conformational changes within pre-existing Ctr1 complexes. FRET assays in membrane-disrupted cells and protein extracts showed that intact cell structure is necessary for Ctr1 activity. Despite Ctr1-dependent cellular accumulation, cisplatin did not change Ctr1 FRET nor did it attenuate copper-induced FRET. A Ctr1 allele defective in copper transport enhanced cellular cisplatin accumulation. N-terminal methionine-rich motifs that are dispensable for copper transport play a critical role for cisplatin uptake. Taken together, our data reveal functional roles for structural remodeling of the Ctr1 multimeric complex in copper transport and suggest distinct mechanisms employed by Ctr1 for copper and cisplatin transport.
On the fidelity of DNA replication.

The effect of metal activators on the fidelity of DNA synthesis has been examined. Using the DNA polymerase from avian myeloblastosis virus, the accuracy of CO”~-, Mn”‘-, and Ni’+-activated DNA synthesis was determined with different polynucleotide templates. With poly[d(A-T)l as the template, the error frequency for dCMP incorporation was 1:1400, 1:1100, and 1:600 for Mg”+, Co”+, and Mn”+, respectively, at maximally activating concentrations. The error frequency was invariant with respect to [Mg”+l but increased with greater than activating concentrations of Coz+ and Mn”+. This increase resulted from differential rates of complementary and noncomplementary nucleotide incorporation. The enhanced error frequency was nonspecific as it occurred with all polynucleotide templates and with all noncomplementary deoxyand ribonucleotides which were tested. Nearest neighbor analyses of the reaction products indicated that the noncomplementary deoxynucleotides were incorporated as single ba>e substitutions. The fidelity of Ni’--activated DNA synthesis was invariant with respect to [Ni”‘] and was similar to that obtained using Mg”’ . During DNA synthesis with Mg’ I, the addition of Co”+, M&l, or NiYi resulted in a decrease in the fidelity of DN4 synthesis. The relationship between decreases in the fidelity of DNA synthesis and metal mutagenesis, or carcmopenesls, or both, is considered.
Cell shape changes and the mechanism of inversion in Volvox

Inversion is a dominant aspect of morphogenesis in Volvox. In this process, the hollow, spheroidal Volvox embryo turns inside-out through a small opening called the phialopore to bring flagella from its inner to its outer surface. Analyses of intact, sectioned, and fragmented embryos by light, scanning electron, and transmission electron microscopy, suggest that shape changes preprogrammed into the cells cause inversion. First, cells throughout the embryo change from pear to spindle shape, which causes the embryo to contract and the phialopore to open. Then cells adjacent to the phialopore become flask-shaped, with long, thin stalks at their outer ends. Simultaneously, the cytoplasmic bridges joining all adjacent cells migrate from the midpoint of the cells to the stalk tips. Together, these changes cause the lips of cells at the phialopore margin to curl outward. Now cells progressively more distal to the phialopore become flask-shaped while the more proximal cells become columnar, causing the lips to curl progressively further over the surface of the embryo until the latter has turned completely inside-out. Fine structural analysis reveals a peripheral cytoskeleton of microtubules that is apparently involved in cellular elongation. Cell clusters isolated before inversion undergo a similar program of shape changes; this suggests that the changes in cellular shape are the cause rather than an effect of the inversion process.
The Distinct Temporal Origins of Olfactory Bulb Interneuron Subtypes

Olfactory bulb (OB) interneurons are a heterogeneous population produced beginning in embryogenesis and continuing through adulthood. Understanding how this diversity arises will provide insight into how OB microcircuitry is established as well as adult neurogenesis. Particular spatial domains have been shown to contribute specific interneuron subtypes. However, the temporal profile by which OB interneuron subtypes are produced is unknown. Using inducible genetic fate mapping of Dlx1/2 precursors, we analyzed the production of seven OB interneuron subtypes and found that the generation of each subpopulation has a unique temporal signature. Within the glomerular layer, the production of tyrosine hydroxylase-positive interneurons is maximal during early embryogenesis and decreases thereafter. In contrast, the generation of calbindin interneurons is maximal during late embryogenesis and declines postnatally, whereas calretinin (CR) cell production is low during embryogenesis and increases postnatally. Parvalbumin interneurons within the external plexiform layer are produced only perinatally, whereas the generation of 5T4-positive granule cells in the mitral cell layer does not change significantly over time. CR-positive granule cells are not produced at early embryonic time points, but constitute a large percentage of the granule cells born after birth. Blanes cells in contrast are produced in greatest number during embryogenesis. Together we provide the first comprehensive analysis of the temporal generation of OB interneuron subtypes and demonstrate that the timing by which these populations are produced is tightly orchestrated.
Thrombolytic therapy in acute myocardial infarction: Experience at a university hospital in Kuwait.

BACKGROUND There is conclusive evidence from large clinical trials that thrombolytic therapy reduces mortality and morbidity in acute myocardial infarction (AMI). However, only a small proportion of patients receive thrombolytic treatment. Estimates have varied from 20%-50% in North America and Europe. Data from the Arab Middle East is sparse. The purpose of our study was to determine the use of thrombolytic therapy in our hospital. METHODS We conducted a retrospective analysis of 343 patients (358 incidents of AMI), who were either discharged from or died at the coronary care unit of the Mubarak Al-Kabeer Hospital during the one-year period between June 1994 and May 1995. RESULTS Our patients were relatively younger (63% were 7lt;55 years) and had a much higher prevalence (44%) of diabetes compared to European patients. We observed a high rate (62%) of thrombolysis and a lesser shortfall (8%) when compared to that reported for European patients. The main reason for withholding thrombolytic therapy was non-diagnostic electrocardiogram (ECG) on initial presentation. Women were less likely to be thrombolyzed than men (38% vs. 66%, P=0.0001). Older patients (aged >65 years) were also less likely to be thrombolyzed than younger patients (42% vs. 66%; P=0.0006). CONCLUSION We conclude that the use of thrombolytic therapy in this university hospital in Kuwait is appropriate. However, as observed in other reports as well, the underutilization of thrombolytic therapy in women and the elderly needs to be addressed in future studies.
High-strength materials: in-situ investigations of dislocation behaviour in Cu-Nb multifilamentary nanostructured composites

Abstract The fundamental mechanisms of the deformation of heavily deformed multiphase materials are not clearly understood despite the vast literature and the amount of data on this subject. This paper presents a new plastic flow mechanism observed by in-situ transmission electron microscopy deformation on Cu-Nb continuous multifilamentary nanostructured composites. The observed mechanism is interpreted in terms of dislocation loops nucleating in closely spaced parallel planes in the Cu channels. This behaviour explains many previous observations made on such composites such as the semicoherency of the interface and the 4° disorientation between the two phases. The modelling of the loop mechanism predicts the strength of the Cu-Nb nanocomposites. The very good agreement between the model and the experimental data suggests that the assumptions based on the in-situ observations are valid. The basic aspects of co-deformation of fcc-bcc nanostructured systems are reviewed in this new context.
Automatic quantification of microtubule dynamics enables RNAi‐screening of new mitotic spindle regulators

The genetic integrity of every organism depends on the faithful partitioning of its genome between two daughter cells in mitosis. In all eukaryotes, chromosome segregation requires the assembly of the mitotic spindle, a bipolar array of dynamic microtubules. Perturbations in microtubule dynamics affect spindle assembly and maintenance and ultimately result in aberrant cell divisions. To identify new regulators of microtubule dynamics within the hundreds of mitotic hits, reported in RNAi screens performed in C. elegans, Drosophila and mammalian tissue culture cells [Sonnichsen et al., 2005; Goshima et al., 2007; Neumann et al., 2010], we established a fast and quantitative assay to measure microtubule dynamics in living cells. Here we present a fully automated workflow from RNAi transfection, via image acquisition and data processing, to the quantitative characterization of microtubule behaviour. Candidate genes are knocked down by solid‐phase reverse transfection with siRNA oligos in HeLa cells stably expressing EB3‐EGFP, a microtubule plus end marker. Mitotic cells are selected using an automatic classifier [Conrad et al., 2011] and imaged on a spinning disk confocal microscope at high temporal and spatial resolution. The time‐lapse movies are analysed using a multiple particle tracking software, developed in‐house, that automatically detects microtubule plus ends, tracks microtubule growth events over consecutive frames and calculates growth speeds, lengths and lifetimes of the tracked microtubules. The entire assay provides a powerful tool to analyse the effect of essential mitotic genes on microtubule dynamics in living cells and to dissect their contribution in spindle assembly and maintenance.
Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice

This study was designed to investigate at the molecular level how a transgenic version of rice “Nipponbare” obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT) and a transgenic version (erf71) that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF) family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.
Personalizing energy expenditure estimation using physiological signals normalization during activities of daily living

In this paper we propose a generic approach to reduce inter-individual variability of different physiological signals (HR, GSR and respiration) by automatically estimating normalization parameters (e.g. baseline and range). The proposed normalization procedure does not require a dedicated personal calibration during system setup. On the other hand, normalization parameters are estimated at system runtime from sedentary and low intensity activities of daily living (ADLs), such as lying and walking. When combined with activity-specific energy expenditure (EE) models, our normalization procedure improved EE estimation by 15 to 33% in a study group of 18 participants, compared to state of the art activity-specific EE models combining accelerometer and non-normalized physiological signals.
Motif Discoveries in Unaligned Molecular Sequences using Self-Organizing Neural Networks

In this paper, we study the problem of motif discoveries in unaligned DNA and protein sequences. The problem of motif identification in DNA and protein sequences has been studied for many years in the literature. Major hurdles at this point include computational complexity and reliability of the search algorithms. We propose a self-organizing neural network structure for solving the problem of motif identification in DNA and protein sequences. Our network contains several layers, with each layer performing classifications at different levels. The top layer divides the input space into a small number of regions and the bottom layer classifies all input patterns into motifs and nonmotif patterns. Depending on the number of input patterns to be classified, several layers between the top layer and the bottom layer are needed to perform intermediate classifications. We maintain a low computational complexity through the use of the layered structure so that each pattern's classification is performed with respect to a small subspace of the whole input space. Our self-organizing neural network will grow as needed (e.g., when more motif patterns are classified). It will give the same amount of attention to each input pattern and will not omit any potential motif patterns. Finally, simulation results show that our algorithm outperforms existing algorithms in certain aspects. In particular, simulation results show that our algorithm can identify motifs with more mutations than existing algorithms. Our algorithm works well for long DNA sequences as well.
Three-dimensional forces exerted by leukocytes and vascular endothelial cells dynamically facilitate diapedesis

Significance Diapedesis is a key step in the innate immune response. Emerging evidence suggests that mechanical forces exerted by leukocytes and/or vascular endothelial cells (VECs) could play an important role during diapedesis. However, it is unclear how these forces physically pull the VEC junctions apart and drive the transmigration of the leukocyte. In this study, we quantify the sequence of mechanical events involved in paracellular diapedesis and experimentally demonstrate that the forces exerted by leukocytes can modulate the VEC tensions to open junctional gaps, and subsequently push into the underlying matrix to thrust an invasive protrusion. We also show that diapedesis can be mechanically facilitated by proinflammatory signals that increase VEC contractility, leading to spatial heterogeneities in VEC monolayer tensions. Leukocyte transmigration across vessel walls is a critical step in the innate immune response. Upon their activation and firm adhesion to vascular endothelial cells (VECs), leukocytes preferentially extravasate across junctional gaps in the endothelial monolayer (paracellular diapedesis). It has been hypothesized that VECs facilitate paracellular diapedesis by opening their cell–cell junctions in response to the presence of an adhering leukocyte. However, it is unclear how leukocytes interact mechanically with VECs to open the VEC junctions and migrate across the endothelium. In this study, we measured the spatial and temporal evolution of the 3D traction stresses generated by the leukocytes and VECs to elucidate the sequence of mechanical events involved in paracellular diapedesis. Our measurements suggest that the contractile stresses exerted by the leukocytes and the VECs can separately perturb the junctional tensions of VECs to result in the opening of gaps before the initiation of leukocyte transmigration. Decoupling the stresses exerted by the transmigrating leukocytes and the VECs reveals that the leukocytes actively contract the VECs to open a junctional gap and then push themselves across the gap by generating strong stresses that push into the matrix. In addition, we found that diapedesis is facilitated when the tension fluctuations in the VEC monolayer were increased by proinflammatory thrombin treatment. Our findings demonstrate that diapedesis can be mechanically regulated by the transmigrating leukocytes and by proinflammatory signals that increase VEC contractility.
Heparins Increase Endothelial Nitric Oxide Bioavailability by Liberating Vessel-Immobilized Myeloperoxidase

Background— Neutrophils and monocytes are centrally linked to vascular inflammatory disease, and leukocyte-derived myeloperoxidase (MPO) has emerged as an important mechanistic participant in impaired vasomotor function. MPO binds to and transcytoses endothelial cells in a glycosaminoglycan-dependent manner, and MPO binding to the vessel wall is a prerequisite for MPO-dependent oxidation of endothelium-derived nitric oxide (NO) and impairment of endothelial function in animal models. In the present study, we investigated whether heparin mobilizes MPO from vascular compartments in humans and defined whether this translates into increased vascular NO bioavailability and function. Methods and Results— Plasma MPO levels before and after heparin administration were assessed by ELISA in 109 patients undergoing coronary angiography. Whereas baseline plasma MPO levels did not differ between patients with or without angiographically detectable coronary artery disease (CAD), the increase in MPO plasma content on bolus heparin administration was higher in patients with CAD (P=0.01). Heparin treatment also improved endothelial NO bioavailability, as evidenced by flow-mediated dilation (P<0.01) and by acetylcholine-induced changes in forearm blood flow (P<0.01). The extent of heparin-induced MPO release was correlated with improvement in endothelial function (r=0.69, P<0.01). Moreover, and consistent with this tenet, ex vivo heparin treatment of extracellular matrix proteins, cultured endothelial cells, and saphenous vein graft specimens from CAD patients decreased MPO burden. Conclusions— Mobilization of vessel-associated MPO may represent an important mechanism by which heparins exert antiinflammatory effects and increase vascular NO bioavailability. These data add to the growing body of evidence for a causal role of MPO in compromised vascular NO signaling in humans.
Predictors of Maternal Depression Management among Primary Care Physicians

Purpose. The present surveillance study examined predictors of the management of maternal depression in primary care settings. Methods. A total of 217 physicians completed a 60-item survey assessing demographics, physicians' attitudes, beliefs, efficacy, current practices, and perceived barriers regarding the management of maternal depression. Structural equation modeling was used to estimate a model that examined the relationships among physicians' knowledge, beliefs, self-efficacy, perceived barriers, past training toward and current management practices for maternal depression. Results. In a model predicting physician depression management practices, a good overall fit was observed (χ 2 = 136.63, CFI = .97, TLI = .95, RMSEA = .05), with physician comfort with, confidence in, and perceived responsibility for managing maternal depression all having prominent positive associations. Conclusions. These findings will guide the development of future multifaceted intervention strategies to enhance physician skills in managing maternal depression in primary care settings.
Re-entry by early afterdepolarisations in a computational model

Afterdepolarisations are one mechanism suggested for the spontaneous initiation of re-entrant arrhythmias in the ventricles but are difficult to study experimentally. We have conducted a systematic investigation of the initiation of reentry by afterdepolarisations using a computational model of cardiac ventricular tissue. We implemented a mono- domain model of a ID fibre, where the excitability of the cell membrane was described by the 4 variable Fenton-Karma (FK4V) model. We embedded additional behaviour into the FK4V model, so a prescribed region produced afterdepolarisations. By changing the size of this region, and duration, amplitude and frequency of the afterdepolarisation potentials, we were able to look in detail at how after- depolarizations can initiate propagating action potentials. This study has shown that afterdepolarisations are capable of producing re-entry, but the duration and amplitude of the afterdepolarisation potential are important in determining whether re-entry is produced.
Efficient Feature Extraction, Encoding, and Classification for Action Recognition

Local video features provide state-of-the-art performance for action recognition. While the accuracy of action recognition has been continuously improved over the recent years, the low speed of feature extraction and subsequent recognition prevents current methods from scaling up to real-size problems. We address this issue and first develop highly efficient video features using motion information in video compression. We next explore feature encoding by Fisher vectors and demonstrate accurate action recognition using fast linear classifiers. Our method improves the speed of video feature extraction, feature encoding and action classification by two orders of magnitude at the cost of minor reduction in recognition accuracy. We validate our approach and compare it to the state of the art on four recent action recognition datasets.
Activity-based costing di usion across organizations : an exploratory empirical analysis of Finnish ® rms

This study aims to explain what drives innovation diusion in management accounting during its various phases. Based on Abrahamson [Abrahamson, E. (1991). Managerial fads and fashions: the diusion and rejection of innovations. Academy of Management Review, 16, 586±612], four perspectives with potential to explain the diusion of accounting innovations are identi®ed: the ecient-choice, forced selection, fad and fashion perspectives. The diusion of activity-based costing (ABC) in Finland provides an empirical context to study how these four perspectives apply to management accounting innovation. Data comes from a set of four surveys (total n=490, response rate 39.5%, 114 ABC cases), from interviews of consultants, academics and software industry employees, and from archival sources. The study proposes that the driving forces behind innovation diusion in management accounting change over the course of diusion. Ecient choice may explain the earliest adoptions, whereas fashion-setting organizations exert considerable in ̄uence in the take-o stage. Later on, the in ̄uence of fashion setting organizations diminishes. Further diusion is explained both by mimetic behaviour and ecient-choice. # 1999 Elsevier Science Ltd. All rights reserved.