Miracle-dz/UniFAR-FTUs huggingface dataset:
Parity Helix: Efficient protection for single-dimensional faults in multi-dimensional memory systems

Emerging die-stacked DRAMs provide several factors higher bandwidth and energy efficiency than 2D DRAMs, making them excellent candidates for future memory systems. To be deployed in server and high-performance computing systems, however, die-stacked DRAMs need to provide equivalent or better reliability than existing 2D DRAMs. This includes protecting against channel and die faults, which have been observed in existing 2D DRAM production systems. In this paper, we observe that memory subsystems can be viewed as a multi-dimensional collection of memory banks in which faults generally affect memory banks that lie along a single dimension. For instance, in die-stacked DRAMs, a die consists of a group of DRAM banks that lie in a horizontal plane while a channel consists of a vertical group of banks spanning across multiple dies. We exploit this fault behavior to propose Parity Helix to efficiently protect against single-dimensional faults in multi-dimensional memory systems. Parity Helix shares the same error correction resources across all dimensions to minimize error correction overheads. For die-stacked DRAMs, our evaluation shows that compared to a straightforward extension of previous schemes, Parity Helix increases memory capacity by 16.7%, reduces memory energy per program access by 21%, on average, and by up to 45%.
Pollen Tube Growth Oscillations and Intracellular Calcium Levels Are Reversibly Modulated by Actin Polymerization1[OA]

Prevention of actin polymerization with low concentrations of latrunculin B (Lat-B; 2 nm) exerts a profound inhibitory effect on pollen tube growth. Using flow-through chambers, we show that growth retardation starts after 10 min treatment with 2 nm Lat-B, and by 15 to 20 min reaches a basal rate of 0.1 to 0.2 μm/s, during which the pollen tube exhibits relatively few oscillations. If treated for 30 min, complete stoppage of growth can occur. Studies on the intracellular Ca2+ concentration indicate that the tip-focused gradient declines in parallel with the inhibition of growth. Tubes exhibiting nonoscillating growth display a similarly reduced and nonoscillating Ca2+ gradient. Studies on the pH gradient indicate that Lat-B eliminates the acidic domain at the extreme apex, and causes the alkaline band to move more closely to the tip. Removing Lat-B and returning the cells to control medium reverses these effects. Phalloidin staining of F-actin reveals that 2 nm Lat-B degrades the cortical fringe; it also disorganizes the microfilaments in the shank causing the longitudinally oriented elements to be disposed in swirls. Cytoplasmic streaming continues under these conditions, however the clear zone is obliterated with all organelles moving into and through the extreme apex of the tube. We suggest that actin polymerization promotes pollen tube growth through extension of the cortical actin fringe, which serves as a track to target cell wall vesicles to preferred exocytotic sites on the plasma membrane.
Topological correction of brain surface meshes using spherical harmonics

Surface reconstruction methods allow advanced analysis of structural and functional brain data beyond what can be achieved using volumetric images alone. Automated generation of cortical surface meshes from 3D brain MRI often leads to topological defects and geometrical artifacts that must be corrected to permit subsequent analysis. Here, we propose a novel method to repair topological defects using a surface reconstruction that relies on spherical harmonics. First, during reparameterization of the surface using a tiled platonic solid, the original MRI intensity values are used as a basis to select either a “fill” or “cut” operation for each topological defect. We modify the spherical map of the uncorrected brain surface mesh, such that certain triangles are favored while searching for the bounding triangle during reparameterization. Then, a low‐pass filtered alternative reconstruction based on spherical harmonics is patched into the reconstructed surface in areas that previously contained defects. Self‐intersections are repaired using a local smoothing algorithm that limits the number of affected points to less than 0.1% of the total, and as a last step, all modified points are adjusted based on the T1 intensity. We found that the corrected reconstructions have reduced distance error metrics compared with a “gold standard” surface created by averaging 12 scans of the same brain. Ninety‐three percent of the topological defects in a set of 10 scans of control subjects were accurately corrected. The entire process takes 6–8 min of computation time. Further improvements are discussed, especially regarding the use of the T1‐weighted image to make corrections. Hum Brain Mapp, 2011. © 2010 Wiley‐Liss, Inc.
Striatal Dopamine and the Interface between Motivation and Cognition

Brain dopamine has long been known to be implicated in the domains of appetitive motivation and cognition. Recent work indicates that dopamine also plays a role in the interaction between appetitive motivation and cognition. Here we review this work. Animal work has revealed an arrangement of spiraling connections between the midbrain and the striatum that subserves a mechanism by which dopamine can direct information flow from ventromedial to more dorsal regions in the striatum. In line with current knowledge about dopamine's effects on cognition, we hypothesize that these striato-nigro-striatal connections provide the basis for functionally specific effects of appetitive motivation on cognition. One implication of this hypothesis is that appetitive motivation can induce cognitive improvement or impairment depending on task demands.
Structure generation and design of multiple loop feedback OTA-grounded capacitor filters

This paper addresses the structure generation, analysis and synthesis of multiple loop feedback OTA-C filters. A systematic approach is proposed for all-pole filters, and the generation and design of minimum component structures are extensively exemplified. Two general methods for transmission zero realization are also suggested and two architectures with simple design formulas are illustrated. Using the theory many new interesting configurations can be produced alongside some known structures. All the filter architectures contain only grounded capacitors and all internal nodes in canonical realizations have a grounded capacitor. A general method for sensitivity analysis of the structures is formulated. Numerical design examples and simulation results are also presented. The essence of the theory is the establishment of the relationship between the filter structure and the feedback matrix, which makes systematic structure generation and general design equation formulation possible.
Resolving and classifying haematopoietic bone‐marrow cell populations by multi‐dimensional analysis of flow‐cytometry data

The study of normal or malignant haematopoiesis requires the analysis of heterogeneous cell populations using multiple morphological and molecular criteria. Flow cytometry has the capacity to acquire multi‐parameter information of large haematopoietic cell populations, utilizing various combinations of >200 molecular markers (clusters of differentiation, CD). However, current flow cytometry analyses are based on serial gating of two‐parametric scatter plots – a process that is inherently incapable to discriminate all subgroups of cells in the data. Here we studied the cellular diversity of normal bone marrows (BM) using multi‐dimensional cluster analysis of six‐parametric flow cytometry data (four CD, forward scatter and side scatter), focusing mainly on the myeloid lineage. Twenty‐three subclasses of cells were resolved, many of them inseparable even when examined in all possible two‐parametric scatter plots. The multi‐dimensional analysis could distinguish the haematopoietic progenitors according to International Society of Haematotherapy and Graft Engineering criteria from other types of immature cells. Based on the defined clusters, we designed a classifier that assigns BM cells in samples to subclasses based on robust six‐dimensional position and extended shape. The analysis presented here can manage successfully both the increasing numbers of haematopoietic cellular markers and sample heterogeneity. This should enhance the ability to study normal haematopoiesis, and to identify and monitor haematopoietic disorders.
Sub-band Common Spatial Pattern (SBCSP) for Brain-Computer Interface

Brain-computer interface (BCI) is a system to translate humans thoughts into commands. For electroencephalography (EEG) based BCI, motor imagery is considered as one of the most effective ways. Different imagery activities can be classified based on the changes in mu and/or beta rhythms and their spatial distributions. However, the change in these rhythmic patterns varies from one subject to another. This causes an unavoidable time-consuming fine-tuning process in building a BCI for every subject. To address this issue, we propose a new method called sub-band common spatial pattern (SBCSP) to solve the problem. First, we decompose the EEG signals into sub-bands using a filter bank. Subsequently, we apply a discriminative analysis to extract SBCSP features. The SBCSP features are then fed into linear discriminant analyzers (LDA) to obtain scores which reflect the classification capability of each frequency band. Finally, the scores are fused to make decision. We evaluate two fusion methods: recursive band elimination (RBE) and meta-classifier (MC). We assess our approaches on a standard database from BCI Competition III. We also compare our method with two other approaches that address the same issue. The results show that our method outperforms the other two approaches and achieves similar result as compared to the best one in the literature which was obtained by a time-consuming fine-tuning process.
Escalated focal liver radiation and concurrent hepatic artery fluorodeoxyuridine for unresectable intrahepatic malignancies.

PURPOSE To evaluate the response, time to progression, survival, and impact of radiation (RT) dose on survival in patients with intrahepatic malignancies treated on a phase I trial of escalated focal liver RT. PATIENTS AND METHODS From April 1996 to January 1998, 43 patients with unresectable intrahepatic hepatobiliary cancer (HB; 27 patients) and colorectal liver metastases (LM; 16 patients) were treated with high-dose conformal RT. The median tumor size was 10 x 10 x 8 cm. The median RT dose was 58.5 Gy (range, 28.5 to 90 Gy), 1.5 Gy twice daily, with concurrent continuous-infusion hepatic arterial fluorodeoxyuridine (0.2 mg/kg/d) during the first 4 weeks of RT. RESULTS The response rate in 25 assessable patients was 68% (16 partial and one complete response). With a median potential follow-up period of 26.5 months, the median times to progression for all tumors, LM, and HB were 6, 8, and 3 months, respectively. The median survival times of all patients, patients with LM, and patients with HB were 16, 18, and 11 months, respectively. On multivariate analyses, escalated RT dose was independently associated with improved progression-free and overall survival. The median survival of patients treated with 70 Gy or more has not yet been reached (16.4+ months), compared with 11.6 months in patients treated with lower RT doses (P =.0003). CONCLUSION The excellent response rate, prolonged intrahepatic control, and improved survival in patients treated with RT doses of 70 Gy or more motivate continuation of dose-escalation studies for patients with intrahepatic malignancies.
Up-Regulation of Intestinal Vascular Endothelial Growth Factor by Afa/Dr Diffusely Adhering Escherichia coli

Background Angiogenesis has been recently described as a novel component of inflammatory bowel disease pathogenesis. The level of vascular endothelial growth factor (VEGF) has been found increased in Crohn's disease and ulcerative colitis mucosa. To question whether a pro-inflammatory Escherichia coli could regulate the expression of VEGF in human intestinal epithelial cells, we examine the response of cultured human colonic T84 cells to infection by E. coli strain C1845 that belongs to the typical Afa/Dr diffusely adhering E. coli family (Afa/Dr DAEC). Methodology VEGF mRNA expression was examined by Northern blotting and q-PCR. VEGF protein levels were assayed by ELISA and its bioactivity was analysed in endothelial cells. The bacterial factor involved in VEGF induction was identified using recombinant E. coli expressing Dr adhesin, purified Dr adhesin and lipopolysaccharide. The signaling pathway activated for the up-regulation of VEGF was identified using a blocking monoclonal anti-DAF antibody, Western blot analysis and specific pharmacological inhibitors. Principal Findings C1845 bacteria induce the production of VEGF protein which is bioactive. VEGF is induced by adhering C1845 in both a time- and bacteria concentration-dependent manner. This phenomenon is not cell line dependent since we reproduced this observation in intestinal LS174, Caco2/TC7 and INT407 cells. Up-regulation of VEGF production requires: (1) the interaction of the bacterial F1845 adhesin with the brush border-associated decay accelerating factor (DAF, CD55) acting as a bacterial receptor, and (2) the activation of a Src protein kinase upstream of the activation of the Erk and Akt signaling pathways. Conclusions Results demonstrate that a Afa/Dr DAEC strain induces an adhesin-dependent activation of DAF signaling that leads to the up-regulation of bioactive VEGF in cultured human intestinal cells. Thus, these results suggest a link between an entero-adherent, pro-inflammatory E. coli strain and angiogenesis which appeared recently as a novel component of IBD pathogenesis.
Analysis of an Asymptotic Preserving Scheme for Linear Kinetic Equations in the Diffusion Limit

We present a mathematical analysis of the asymptotic preserving scheme proposed in [M. Lemou and L. Mieussens, SIAM J. Sci. Comput. , 31 (2008), pp. 334-368] for linear transport equations in kinetic and diffusive regimes. We prove that the scheme is uniformly stable and accurate with respect to the mean free path of the particles. This property is satisfied under an explicitly given CFL condition. This condition tends to a parabolic CFL condition for small mean free paths and is close to a convection CFL condition for large mean free paths. Our analysis is based on very simple energy estimates.
New Insights into the Developmental History of the Bacterial Cell Division Site

Cell division in Escherichia coli involves several sequential stages: identification of the correct site for septum formation, differentiation of this site in preparation for the septation event, and fabrication of the division septum by the coordinated ingrowth of all of the cell envelope layers. Over the past decade, differentiation of the bacterial cell division site has been studied extensively by examining the assembly of the proteins that comprise the division machinery, using fluorescence-based techniques to localize the proteins within intact cells. These studies have shown that the proteins assemble into a narrow FtsZ-based cytokinetic ring at an early stage of differentiation of the future division site (reviewed in reference 10). However, little is known about other changes that occur at the division site as part of its developmental history.
Heterogeneous Cellular Networks With LoS and NLoS Transmissions—The Role of Massive MIMO and Small Cells

We develop a framework for downlink heterogeneous cellular networks with line-of-sight (LoS) and non-LoS transmissions. Using stochastic geometry, we derive tight approximation of average downlink rate that enables us to compare the performance between densifying small cells and expanding base station (BS) antenna arrays. Interestingly, we find that adding small cells into the network improves the downlink rate much faster than expanding antenna arrays at the macro BS. However, when the small cell density exceeds a critical threshold, the spatial densification will lose its benefits and further impair the network capacity. To this end, we provide the optimal small cell density that maximizes the rate via numerical results for practical deployment guidance. In contrast, expanding macro BS antenna array can always benefit the capacity until an upper bound caused by pilot contamination, and this bound also surpasses the peak rate obtained from the deployment of small cells. Furthermore, we find that allocating part of antennas to distributed small cell BSs works better than centralizing all antennas at the macro BS, and the optimal allocation proportion is also given numerically for practical configuration reference. In summary, this paper provides a further understanding on how to leverage small cells and massive MIMO in future heterogeneous cellular networks deployment.
Template-Based Dielectric Resonator Antenna Arrays for Millimeter-Wave Applications

An approach suitable for millimeter-wave dielectric resonator antenna (DRA) arrays is presented. The methodology involves fabricating precise cavities in acrylic templates and filling them with composite dielectric materials to create a monolithic polymer-based DRA (PRA) array layer. The excitation feed lines are fabricated on a separate substrate layer and the two layers are aligned and bonded together to form the PRA antenna array module. The impact of the acrylic frame on the PRA performance is analyzed through simulations. A four-element array operating at 60 GHz is realized to demonstrate the approach. The performance is characterized through simulation and also experimentally verified. The array offers a wide 12% impedance bandwidth at 60 GHz and broadside radiation with 10.5-dBi realized gain and stable radiation patterns. The use of polymer-based materials provides opportunities for cost-effective volume fabrication using molding techniques.
The Relationship between Capital Structure and Profitability

This study seeks to extend Abor’s (2005), and Gill, et al., (2011) findings regarding the effect of capital structure on profitability by examining the effect of capital structure on profitability of the industrial companies listed on Amman Stock Exchange during a six-year period (2004-2009). The problem statement to be analyzed in this study is: Does capital structure affect the Industrial Jordanian companies? The study sample consists of 39 companies. Applying correlations and multiple regression analysis, the results reveal significantly negative relation between debt and profitability. This suggests that profitable firms depend more on equity as their main financing option. Yet recommendations based on findings are offered to improve certain factors like the firm must consider using an optimal capital structure and future research should investigate generalizations of the findings beyond the manufacturing sectors.
On Large-Batch Training for Deep Learning: Generalization Gap and Sharp Minima

The stochastic gradient descent (SGD) method and its variants are algorithms of choice for many Deep Learning tasks. These methods operate in a small-batch regime wherein a fraction of the training data, say $32$-$512$ data points, is sampled to compute an approximation to the gradient. It has been observed in practice that when using a larger batch there is a degradation in the quality of the model, as measured by its ability to generalize. We investigate the cause for this generalization drop in the large-batch regime and present numerical evidence that supports the view that large-batch methods tend to converge to sharp minimizers of the training and testing functions - and as is well known, sharp minima lead to poorer generalization. In contrast, small-batch methods consistently converge to flat minimizers, and our experiments support a commonly held view that this is due to the inherent noise in the gradient estimation. We discuss several strategies to attempt to help large-batch methods eliminate this generalization gap.
Analysis of the SWI4/SWI6 protein complex, which directs G1/S-specific transcription in Saccharomyces cerevisiae

SWI4 and SWI6 play a crucial role in START-specific transcription in Saccharomyces cerevisiae. SWI4 and SWI6 form a specific complex on the SCB (SWI4/6-dependent cell cycle box) sequences which have been found in the promoters of HO and G1 cyclin genes. Overproduction of SWI4 eliminates the SWI6 dependency of HO transcription in vivo and results in a new SWI6-independent, SCB-specific complex in vitro, which is heterogeneous and reacts with SWI4 antibodies. The C terminus of SWI4 is not required for SWI6-independent binding of SWI4 to SCB sequences, but it is necessary and sufficient for association with SWI6. Both SWI4 and SWI6 contain two copies of a 33-amino-acid TPLH repeat, which has been implicated in protein-protein interactions in other proteins. These repeats are not required for the SWI4-SWI6 association. Alanine substitutions in both TPLH repeats of SWI6 reduce its activity but do not affect the stability of the protein or its association with SWI4. However, these mutations reduce the ability of the SWI4/6 complex to bind DNA. Deletion of the lucine zipper motif in SWI6 also allows SWI4/6 complex formation, but it eliminates the DNA-binding ability of the SWI4/6 complex. This indicates that the integrity of two different regions of SWI6 is required for DNA binding by the SWI4/6 complex. From these data, we propose that the sequence-specific DNA-binding domain resides in SWI4 but that SWI6 controls the accessibility of this domain in the SWI4/6 complex.
CrowdAtlas: self-updating maps for cloud and personal use

The inaccuracy of manually created digital road maps is a persistent problem, despite their high economic value. We present CrowdAtlas, which automates map update based on people's travels, either individually or crowdsourced. Its mobile navigation app detects significant portions of GPS traces that do not conform to the existing map, as determined by state-of-the-art Viterbi map matching. When there is sufficient evidence collected, map inference algorithms can automatically update the map. The CrowdAtlas server aggregates exceptional traces from users with the navigation app as well as from other, large-scale data sources. From these it automatically generates high quality map updates, which can be propagated to its navigation app and other interested applications. Using CrowdAtlas app, we mapped out a 4.5 km^2 street block in Shanghai in less than half an hour and built a walking/cycling map of the SJTU campus. Using taxi traces collected from Beijing, we contributed completely computer-generated roads for this large, 61 km of missing roads to OpenStreetMap, the first set of open-source map community.
Comparative movements of four large fish species in a lowland river.

A multi-year radio-telemetry data set was used to comparatively examine the concurrent movements of the adults of three large-bodied Australian native freshwater fishes (Murray cod Maccullochella peelii, trout cod Maccullochella macquariensis and golden perch Macquaria ambigua) and the introduced carp Cyprinus carpio. The study was conducted over a reach scale in the regulated Murray River in south-eastern Australia. Differences were identified in the movements among these species. The predominant behaviour was the use of small movements (<1 km) for all species, and although larger-scale movements (>1 km) did occur, the frequency varied considerably among species. Large-scale movements were least evident for M. macquariensis and more common for M. ambigua and C. carpio with these two species also having a greater propensity to change locations. Macquaria ambigua displayed the largest movements and more M. ambigua moved on a 'continual' basis. Although a degree of site fidelity was evident for all species, the highest levels were exhibited by M. macquariensis and M. peelii. Homing was also evident to some degree in all species, but was greatest for M. peelii.