Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and Functional Expression of Rat CLC-5, a Chloride Channel Related to Kidney Disease (*)

We have cloned a novel member of the CLC chloride channel family from rat brain, rCLC-5. The cDNA predicts a 83-kDa protein belonging to the branch including CLC-3 and CLC-4, with which it shares 80% identity. Expression of rCLC-5 in Xenopus oocytes elicits novel anion currents. They are strongly outwardly rectifying and have a conductivity sequence of NO3 > Cl > Br > I glutamate. Although CLC-5 has consensus sites for phosphorylation by protein kinase A, raising the intracellular cAMP concentration had no effect on these currents. Currents were also unchanged when rCLC-5 was coexpressed with rCLC-3 and rCLC-4, either singly or in combination. rCLC-5 is expressed predominantly in kidney and also in brain, lung, and liver. Along the nephron, rCLC-5 message is detectable in all tubule segments investigated, but expression in the glomerulus and the S2 segment of the proximal tubule is low.
Pilot-Scale Treatment of Selenium in Gravel Pit Seepage Water Using Biochemical Reactor Technology

Abstract. Water quality in the lower Colorado and Gunnison Rivers in western Colorado, and many of their tributaries, is impaired by selenium, which originates from the local Mancos shale. Because of the diffuse and widespread nature of this source, there are limited opportunities to reduce selenium inputs. One option is to treat selenium-contaminated surface water at strategic locations, such as point-source discharges. Gravel extraction is common along these rivers, and treatment of discharges from pit dewatering presents an opportunity for reducing selenium loading. The pilot test goals were: 1) demonstrate that a passive BCR can accomplish high-efficiency selenium removal at the pilot scale 2) determine the relationship between selenium removal efficiency and detention time 3) assesses the influence of seasonal temperature fluctuations on treatment performance 4) determine design parameters for a full-scale system (i.e., one with a footprint on the scale of up to a few acres). A single 4,380 cubic foot pilot BCR was constructed to treat flows ranging from 2 to 24 gallons per minute. The vertical-flow reactor media contains cow manure, hay, sawdust, wood chips, and limestone. Influent was drawn from a dewatering trench in a gravel pit next to the Colorado River near Grand Junction, Colorado. The pilot operated, with varying detention times, over a thirteen-month period from September 2008 until October 2009. The pilot achieved maximum selenium removal rates of 98% with a hydraulic retention time of 2.4 days and a minimum effluent concentration of 0.0005 mg/L (0.5 μg/L). The highest mass removal rate achieved by the BCR was 73 mg/day/m and the cumulative mass of total selenium removal was 600 grams. The BCR treatment process was effective throughout the cold winter months during which total selenium removal rates remained greater than 90%. The total capital cost for the pilot BCR was $39,200 or $0.50 per 1,000 gallons treated. The operations and maintenance costs for a passive BCR system are minimal. Based on the successful operation of the pilot, including high rates of selenium removal and consistent year-round operation, the BCR technology appears to be an effective, low-cost selenium treatment option. This project was funded by the US Bureau of Reclamation Science and Technology Program, Project #4414.
Independent Component Analysis on the Basis of Helmholtz Machine

This paper addresses an algorithm for independent component analysis on the basis of Helmholtz machine, which is an unsupervised learning machine. The algorithm is constructed by two terms. One is a term for obtaining a desired demixing process, which is the conventional rule on the base of the information theory. The other is a term for evaluating whether the inverse system and the set of obtained components are desirable or not. Due to this term, the algorithm effectively works in blind separation of overdetermined mixture with additive noise. We demonstrate the effectiveness by computer simulation.
Health Extension Workers Improve Tuberculosis Case Detection and Treatment Success in Southern Ethiopia: A Community Randomized Trial

Background One of the main strategies to control tuberculosis (TB) is to find and treat people with active disease. Unfortunately, the case detection rates remain low in many countries. Thus, we need interventions to find and treat sufficient number of patients to control TB. We investigated whether involving health extension workers (HEWs: trained community health workers) in TB control improved smear-positive case detection and treatment success rates in southern Ethiopia. Methodology/Principal Finding We carried out a community-randomized trial in southern Ethiopia from September 2006 to April 2008. Fifty-one kebeles (with a total population of 296, 811) were randomly allocated to intervention and control groups. We trained HEWs in the intervention kebeles on how to identify suspects, collect sputum, and provide directly observed treatment. The HEWs in the intervention kebeles advised people with productive cough of 2 weeks or more duration to attend the health posts. Two hundred and thirty smear-positive patients were identified from the intervention and 88 patients from the control kebeles. The mean case detection rate was higher in the intervention than in the control kebeles (122.2% vs 69.4%, p<0.001). In addition, more females patients were identified in the intervention kebeles (149.0 vs 91.6, p<0.001). The mean treatment success rate was higher in the intervention than in the control kebeles (89.3% vs 83.1%, p = 0.012) and more for females patients (89.8% vs 81.3%, p = 0.05). Conclusions/Significance The involvement of HEWs in sputum collection and treatment improved smear-positive case detection and treatment success rate, possibly because of an improved service access. This could be applied in settings with low health service coverage and a shortage of health workers. Trial Registration ClinicalTrials.gov NCT00803322
Visualizing Social Bookmarks

Social bookmarking tools are very popular nowadays. In most tools, users tag the bookmarks to describe them. Therefore, it is often hard for users to discover implicit structures between tags, users and bookmarks. We think that this is essential for both end users to discover new bookmarks that could be of interest to them, and for researchers who want to study how people use social information retrieval tools. In this work, a cluster map visualization application is customized to enable users to explore social bookmarks in the del.icio. us system [5]. The design of the application aims to automatically identify tag and community structures, and visualizes these structures in order to increase the users’ awareness of them.
Bio-inspired Robotic Fish with Multiple Fins

In order to improve the performance of AUVs in terms of efficiency and maneuverability, researchers have proposed biomimetic propulsion systems that swim using flapping fins rather than rotary propellers. This calls for the exploration of unique locomotion characteristics found in a variety of fish for use in underwater robots. (Sfakiotakis et. al., 1999) present a good review of fish swimming modes targeted at roboticists interested in aquatic locomotion. A classification scheme of fish locomotion mechanisms, originally presented in (Lindsey, 2006) and was modified in (Colgate & Lynch, 2004), is shown in Fig. 1. The three main swimming styles are characterized by undulatory body motion, undulatory fin motion, and oscillatory fin motion. A more traditional classification is one proposed by Breder (Breder, 1926) that broadly identifies two styles of swimming: one is Body and/or Caudal Fin (BCF) locomotion, and the other is Median and/or Paired Fin (BMP) locomotion. Fish classes that use varying degrees of body undulation and/or caudal fin oscillations for thrust generation are examples of BCF swimming, and fish that use paired fins like the left and right pectoral fins, dorsal, and ventral pelvic fins for thrust generation are classified under the MPF swimming style.
Unlocking bandwidth for GPUs in CC-NUMA systems

Historically, GPU-based HPC applications have had a substantial memory bandwidth advantage over CPU-based workloads due to using GDDR rather than DDR memory. However, past GPUs required a restricted programming model where application data was allocated up front and explicitly copied into GPU memory before launching a GPU kernel by the programmer. Recently, GPUs have eased this requirement and now can employ on-demand software page migration between CPU and GPU memory to obviate explicit copying. In the near future, CC-NUMA GPU-CPU systems will appear where software page migration is an optional choice and hardware cache-coherence can also support the GPU accessing CPU memory directly. In this work, we describe the trade-offs and considerations in relying on hardware cache-coherence mechanisms versus using software page migration to optimize the performance of memory-intensive GPU workloads. We show that page migration decisions based on page access frequency alone are a poor solution and that a broader solution using virtual address-based program locality to enable aggressive memory prefetching combined with bandwidth balancing is required to maximize performance. We present a software runtime system requiring minimal hardware support that, on average, outperforms CC-NUMA-based accesses by 1.95 ×, performs 6% better than the legacy CPU to GPU memcpy regime by intelligently using both CPU and GPU memory bandwidth, and comes within 28% of oracular page placement, all while maintaining the relaxed memory semantics of modern GPUs.
Response characteristics of single cells in the monkey superior colliculus following ablation or cooling of visual cortex.

ELECTROPHYSIOLOGICAL STUDIES have shown that the characteristics of single cells in the superior colliculus depend to a considerable extent on cortical input. In the cat, the majority of studies reveal a dramatic loss of binocularity and direction selectivity in superficial collicular units following ablation of the visual cortex (1, 18, 25). In the ground squirrel, removal of the visual cortex renders most cells in the intermediate and deep layers of the superior colliculus unresponsive to visual stimuli (14); this also appears to apply to the cat (22). Work on the rabbit, however, indicates that in this species, ablation of visual cortex produces no discernible effects on collicular function (10). The present study has been undertaken to investigate the contribution of visual cortex to collicular function in the rhesus monkey (Macaca mulatta), a species whose visual svstem is believed to be rather similar to that of man. Neuroanatomical work has indicated that in the monkey, as in the cat, retina and visual cortex project densely on the superior colliculus (8). In the monkey, a foveate animal, an interesting specialization has been reported: anterograde-degeneration and autoradiographic studies indicate that the anterior part of the colliculus, representing the central 5” of the visual field, receives extremely sparse or no terminations from the retina and, conversely, heavy projections from visual cortex (5, 9, 26) Single-unit studies of the superior colliculus of the intact monkey have disclosed that, as in the cat, most cells have binocular
Is P50 an epiphenomenon?

The mid-latency auditory evoked response (MLAER) consists of the P50, N100 and P200 components. P50 is widely used to examine sensory gating. There is growing evidence that phase-reorganization of the oscillatory components comprising EEG activity, and especially in the 4-8 Hz (theta) band, is responsible for MLAER generation. Consequently, all or part of the MLAER may be an epiphenomenon, indicating intervals of increased phase reorganization. In this study, we investigated the nature of P50. AEPs were obtained from 14 normal subjects using a double stimulus paradigm, and each artifact-free trial was decomposed into its constituent oscillatory components. Single trials were classified into 16 groups on the basis of the presence of N100/P200-like activity and the phase at stimulus onset in the 4-8 Hz band. It was found that P50 consists of low frequency (theta) and high frequency (gamma) activity. The appearance of P50-related theta activity was closely related to the presence of N100. The P50-related theta activity appeared only when the theta activity goes through a positive zero crossing at the moment of stimulus presentation. Thus it appears that the theta component of the P50 should be considered as an epiphenomenon
Quasirandom rumor spreading

We propose and analyse a quasirandom analogue to the classical push model for disseminating information in networks ("randomized rumor spreading"). In the classical model, in each round each informed node chooses a neighbor at random and informs it. Results of Frieze and Grimmett (Discrete Appl. Math. 1985) show that this simple protocol succeeds in spreading a rumor from one node of a complete graph to all others within <i>O</i><i>(log n)</i> rounds. For the network being a hypercube or a random graph <i>G(n, p)</i> with <i>p</i> ≥ (1 +ε)(log <i>n</i>)/<i>n</i>, also <i>O</i>(log <i>n</i>) rounds suffice (Feige, Peleg. Raghavan, and Upfal, Random Struct. Algorithms 1990). In the quasirandom model, we assume that each node has a (cyclic) list of its neighbors. Once informed, it starts at a random position of the list, but from then on informs its neighbors in the order of the list. Surprisingly, irrespective of the orders of the lists, the above mentioned bounds still hold. In addition, we also show a <i>O</i>(log <i>n</i>) bound for sparsely connected random graphs <i>G(n, p)</i> with <i>p</i> = (log <i>n</i> + <i>f(n))/n</i>, where <i>f(n)</i> → ∞ and <i>f(n)</i> = <i>O</i>(log log <i>n</i>). Here, the classical model needs Θ(log<sup>2</sup>(<i>n</i>)) rounds. Hence the quasirandom model achieves similar or better broadcasting times with a greatly reduced use of random bits.
Delivering Specialized Palliative Care in the Community: A New Role for Nurse Practitioners

The rising population of older Americans with advanced illness challenges current care delivery models. We use the metaphor of advanced illness as a difficult journey and propose a specific role, that of the “OACIS NP [nurse practitioner],” who helps provide a place of refuge during this journey. “OACIS” is an acronym for Optimizing Advanced Complex Illness Support, a program to provide home-based palliative medical care. The 4 pillars of this collaborative model for advanced nursing care include care coordination, medical management, psychosocial support, and education. We make the case for this expanded role for nurse practitioners who specialize in palliative care.
Active Ranking in Practice: General Ranking Functions with Sample Complexity Bounds

This paper examines the problem of ranking a collection of objects using pairwise comparisons (rankings of two objects). In a companion paper in the regular NIPS 2011 program [1], we showed that if each object x ! R d is assigned a score f(x )= ||x " r|| for some unknown r ! R d , then our recently proposed active ranking algorithm can recover the ranking of the scores using about dlogn selectively chosen pairwise comparisons. Here we show that this same model contains all functions of the type g(x )= w T x for some unknown w ! R d , thus the same bound applies. We take advantage of this fact and use kernel methods to represent more general ranking functions. This extension includes popular ranking methods such as RankSVM, and we derive nontrivial query complexity bounds for active versions of such algorithms. The efficacy of the theory and method are demonstrated by applying our kernelized adaptive algorithm to two real datasets.
Re-assessing the WMT2013 Human Evaluation with Professional Translators Trainees

This paper presents experiments on the human ranking task performed during WMT2013. The goal of these experiments is to re-run the human evaluation task with translation studies students and to compare the results with the human rankings performed by the WMT development teams during WMT2013. More specifically, we test whether we can reproduce, and if yes to what extent, the WMT2013 ranking task and whether specialised knowledge from translation studies influences the results in terms of intraand inter-annotator agreement as well as in terms of system ranking. We present two experiments on the English-German WMT2013 machine translation output. Analysis of the data follows the methods described in the official WMT2013 report. The results indicate a higher interand intra-annotator agreement, less ties and slight differences in ranking for the translation studies students as compared to the WMT development teams.
Towards a Model for Object-Oriented Design Measurement

Object-oriented design plays a pivotal role in software development because it determines the structure of the software solution. Once the design has been implemented, it is difficult and expensive to change. Therefore the design should be good from the start. Metrics can help to evaluate and improve the quality of a design. Many metrics of object-oriented design have been proposed. Unfortunately, most of these metrics lack a precise and unambiguous definition. However, in order to automate design evaluation a precise definition of metrics is needed. Therefore the definitions should be based on a formal model of design. In this paper a formal model for object-oriented design called ODEM (Object-oriented DEsign Model) is presented. This model can serve as a foundation for the formal definition of object-oriented design metrics. ODEM is based on the UML meta-model, that provides a formal model of object-oriented designs expressed in UML, the most widespread design notation. Examples of the use of ODEM for defining object-oriented metrics are given. Two case studies on existing metrics suites for object-oriented design show the benefits of applying ODEM to established object-oriented design metrics.
Two-edge graphical linkage model for DSMGA-II

DSMGA-II, a model-based genetic algorithm, is capable of solving optimization problems via exploiting sub-structures of the problem. In terms of number of function evaluations (NFE), DSMGA-II has shown superior optimization ability to LT-GOMEA and hBOA on various benchmark problems as well as real-world problems. This paper proposes a two-edge graphical linkage model, which customizes recombination masks for each receiver according to its alleles, to further improve the performance of DSMGA-II. The new linkage model is more expressive than the original dependency structure matrix (DSM), providing far more possible linkage combinations than the number of solutions in the search space. To reduce unnecessary function evaluations, the two-edge model is used along with the supply bounds from the original DSM. Some new techniques are also proposed to enhance the model selection efficiency. Combining these proposed techniques, the empirical results show an average of 12.2% NFE reduction on eight benchmark problems compared with the original DSMGA-II.
On the Coupling Between Agent Internal and Agent/ Environmental Dynamics: Development of Spatial Representations in Evolving Autonomous Robots

In this article we describe how a population of evolving robots can autonomously develop forms of spatial representation which allow them to self-localize and to discriminate different locations of their environment by integrating sensory-motor information over time. The evolving robots also display a remarkable ability to generalize their skill in new environmental conditions that they have never experienced before. The analysis of the obtained results indicates that the evolved robots come up with simple and robust solutions that exploit quasi-periodic limit cycle dynamics emerging from the coupling between the robot/environmental dynamics and a robot's internal dynamics. More specifically, the variations of a robot's internal states are governed by transient dynamical processes originating from the fact that these internal states tend to slowly approximate fixed attractor points, corresponding to different types of sensory states that last for a limited time duration and alternate while the robot moves in the environment.
Adaptive Successive Erosion-based Cell Image Segmentation for p53 Immunohistochemistry in Bladder Inverted Papilloma

Cell nuclei segmentation is a critical issue in automatic cell analysis for cancer diagnosis and prognosis. Marker-controlled watershed segmentation algorithm is used the most commonly. In this paper, adaptive successive erosion-based (ASE) marker extraction method for watershed algorithm is presented, with the goal of extracting markers labelling each individual nucleus, including overlapping cell nuclei. Based on the new marker detection method, an integrated cell image segmentation algorithm is developed for p53 immunohistochemistry in bladder inverted papilloma. Experiments were performed on a number of images, and results demonstrate that the algorithm produces more accurate segmentation than other methods
Chronic obstructive pulmonary disease.

1 Chronic Obstructive Pulmonary Disease Chronic obstructive pulmonary disease (COPD) is a major public health problem, a cause of poor health and death worldwide and a significant contributor to healthcare costs and comorbidity2-4. COPD causes approximately 1.3 million deaths annually, and in 2006, the disease resulted in 12 million disability-adjusted-life-years5. In New Zealand, COPD ranks third among the most common causes of death in males and fourth in women6. COPD has been estimated to cost the New Zealand community an estimated $102–$192 million annually7.
Decrease in Tonic Inhibition Contributes to Increase in Dentate Semilunar Granule Cell Excitability after Brain Injury

Brain injury is an etiological factor for temporal lobe epilepsy and can lead to memory and cognitive impairments. A recently characterized excitatory neuronal class in the dentate molecular layer, semilunar granule cell (SGC), has been proposed to regulate dentate network activity patterns and working memory formation. Although SGCs, like granule cells, project to CA3, their typical sustained firing and associational axon collaterals suggest that they are functionally distinct from granule cells. We find that brain injury results in an enhancement of SGC excitability associated with an increase in input resistance 1 week after trauma. In addition to prolonging miniature and spontaneous IPSC interevent intervals, brain injury significantly reduces the amplitude of tonic GABA currents in SGCs. The postinjury decrease in SGC tonic GABA currents is in direct contrast to the increase observed in granule cells after trauma. Although our observation that SGCs express Prox1 indicates a shared lineage with granule cells, data from control rats show that SGC tonic GABA currents are larger and sIPSC interevent intervals shorter than in granule cells, demonstrating inherent differences in inhibition between these cell types. GABAA receptor antagonists selectively augmented SGC input resistance in controls but not in head-injured rats. Moreover, post-traumatic differences in SGC firing were abolished in GABAA receptor blockers. Our data show that cell-type-specific post-traumatic decreases in tonic GABA currents boost SGC excitability after brain injury. Hyperexcitable SGCs could augment dentate throughput to CA3 and contribute substantively to the enhanced risk for epilepsy and memory dysfunction after traumatic brain injury.