Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistent sodium and calcium currents cause plateau potentials in motoneurons of chronic spinal rats.

After chronic spinal cord injury motoneurons exhibit large plateau potentials (sustained depolarizations triggered by brief inputs) that play a primary role in the development of muscle spasms and spasticity (Bennett et al. 2001a,b). The present study examined the voltage-gated persistent inward currents (PICs) underlying these plateaus. Adult rats were spinalized at the S2 sacral spinal level and after 2 mo, when spasticity developed, intracellular recordings were made from motoneurons below the injury. For recording, the whole sacrocaudal spinal cord was removed and maintained in vitro in normal artificial cerebral spinal fluid (nACSF), without application of neuromodulators. During a slow triangular voltage-clamp command (ramp) a PIC was activated with a threshold of -54.2 +/- 4.8 mV (similar to plateau threshold), with a peak current of 2.88 +/- 0.95 nA and produced a pronounced negative-slope region in the V-I relation. This PIC was in part mediated by Cav1.3 L-type calcium channels because it was low threshold and significantly reduced by 10 to 20 microM nimodipine or 400 microM Cd2+. The PIC that remained during a calcium channel blockade (in Cd2+) was completely and rapidly blocked by tetrodotoxin (TTX; 0.5 to 2 microM), and thus was a TTX-sensitive persistent sodium current. This persistent sodium current was activated rapidly about 7 mV below the spike threshold (spike threshold -46.1 +/- 4.5 mV), contributed approximately 1/2 of the initial peak of the total PIC, inactivated partly to contribute only approximately 1/3 of the sustained PIC (at 5 to 10 s), and deactivated rapidly with hyperpolarization (<50 ms). When TTX was added to the bath first, the nimodipine-sensitive persistent calcium current (L-type) was seen in isolation; it was slowly activated (>250 ms), had a low but variable threshold (either slightly above or below the spike threshold), contributed the other approximately 1/2 of the initial peak of the total PIC (before TTX), did not usually inactivate with time (contributed approximately two-thirds of the sustained PIC), and deactivated slowly with hyperpolarization to rest (in >300 ms). In summary, low-threshold persistent calcium (Cav1.3) and sodium currents spontaneously develop in motoneurons of chronic spinal rats and these enable large, rapidly activated plateaus that ultimately lead to spasticity.
Designing multimedia learning environments using animated pedagogical agents: factors and issues

Animated pedagogical agents (APAs) are known to possess great potential in supporting learning because of their ability to simulate a real classroom learning environment. But research in thisareahasproducedmixedresults.Thereasonforthisremainspuzzling. Thispaperiswritten with two purposes: (1) to examine some recent research and organize the findings in terms of classroom characteristics, and (2) to discuss and reveal any uncovered issues pertaining to the findings and provide input whenever possible.Aframework formed by usingAPAcharacteristics, APA presentation, and learners’ characteristics is used to analyse past research findings. ThefindingsfromtheanalysisrevealthatbecauseAPAsareregardedassocialmemberssimilar to humans, they are more effective in engaging learners in environments that require social communication and interactions. They therefore produce more definitive results in terms of affective gain and group learning. But such conditions also impose greater demand on designers to create more complex learning environments that can provide interactions with several agents and yet maintain a mode of communication that is pedagogically effective. The challengesforcreatingsuchenvironmentincludeusinganagent’sgesturestoduplicateitsspeechin instruction,whichisusuallyuncommoninhumanpractice,overcomingtheneedstouseinput‐ output interface for communication and taking into consideration the possible influence of the learners’characteristicssuchastheirsensorypreference.ThispapersuggeststhatAPAs’application in instruction should be seen in the light of affordances and be designed within its own practical limits. jca_299 203.218
Mid-Infrared Identification of 6 cm Radio-Source Counterparts in the Extended Groth Strip

A new 6 cm survey of almost 0.6 deg2 to a limit of 0.55 mJy beam-1 (10 σ) finds 37 isolated radio sources and seven radio-source pairs (not necessarily physical companions). Infrared Array Camera (IRAC) counterparts are identified for at least 92% of the radio sources within the area of deep IRAC coverage, which includes 31 isolated sources and six pairs. This contrasts with an identification rate of <74% to R < 23.95 in visible light. Eight of the IRAC galaxies have power-law spectral energy distributions, implying that the mid-infrared emission comes from a powerful active galactic nucleus (AGN). The remaining 26 IRAC galaxies show stellar emission in the mid-infrared, probably in most of these galaxies because the stellar emission is bright enough to outshine an underlying AGN. The infrared colors suggest that the majority of these galaxies are bulge-dominated and have redshifts 0.5 ≲ z ≲ 1. Visible spectra from the DEEP2 Redshift Survey, available for 11 galaxies, are consistent with this suggestion. The IRAC galaxies fall into two distinct groups in a color-magnitude diagram. One group (the "stripe") includes all the AGNs. The other group (the "blue clump") has blue 3.6-8 μm colors and a small range of 8 μm magnitudes. This separation should be useful in classifying galaxies found in other radio surveys.
Outsourcing CO2 within China

Recent studies have shown that the high standard of living enjoyed by people in the richest countries often comes at the expense of CO2 emissions produced with technologies of low efficiency in less affluent, developing countries. Less apparent is that this relationship between developed and developing can exist within a single country’s borders, with rich regions consuming and exporting high-value goods and services that depend upon production of low-cost and emission-intensive goods and services from poorer regions in the same country. As the world’s largest emitter of CO2, China is a prominent and important example, struggling to balance rapid economic growth and environmental sustainability across provinces that are in very different stages of development. In this study, we track CO2 emissions embodied in products traded among Chinese provinces and internationally. We find that 57% of China’s emissions are related to goods that are consumed outside of the province where they are produced. For instance, up to 80% of the emissions related to goods consumed in the highly developed coastal provinces are imported from less developed provinces in central and western China where many low–value-added but high–carbon-intensive goods are produced. Without policy attention to this sort of interprovincial carbon leakage, the less developed provinces will struggle to meet their emissions intensity targets, whereas the more developed provinces might achieve their own targets by further outsourcing. Consumption-based accounting of emissions can thus inform effective and equitable climate policy within China.
Lateral components in the cone terminals of the rabbit retina: Horizontal cell origin and glutamate receptor expression

We examined the identities of horizontal cell (HC) lateral components in cone terminals and the expression of glutamate receptors on the tips of HC dendrites. We injected A‐type horizontal cells (AHCs) with neurobiotin and demonstrated that neurobiotin labeled completely all AHCs within a patch of retina. We converted neurobiotin by using diaminobenzidine and considered labeled processes to be from AHCs and unlabeled processes to be from B‐type horizontal cells (BHCs). Three possible combinations of HC dendrites could exist in cone pedicles: both lateral components originating from AHCs, both from BHCs, or one from an AHC and the other from a BHC. EM observations revealed that a majority of cone terminals contained about equal numbers of lateral components originating from each of the two types of HCs and that each of the three possible combinations was present in equal numbers. Localization of different types of glutamate receptors on HC dendritic tips showed that 55% of AHC dendritic tips expressed AMPA receptors and 30% expressed kainate receptors, whereas, in the case of BHCs, 22% of dendritic tips expressed AMPA receptors and 33% expressed kainate receptors. This study suggests that cone photoreceptors feed the light signal equally into networks of AHCs and BHCs and that differential expression of AMPA/kainate receptors by different HCs could account for different functions. J. Comp. Neurol. 496:698–705, 2006. © 2006 Wiley‐Liss, Inc.
Inferring Invariants in Separation Logic for Imperative List-processing Programs

An algorithm is presented for automatically inferring loop invariants in separation logic for imperative list-processing programs. A prototype implementation for a C-like language is shown to be successful in generating loop invariants for a variety of sample programs. The programs, while relatively small, iteratively perform destructive heap operations and hence pose problems more than challenging enough to demonstrate the utility of the approach. The invariants express information not only about the shape of the heap but also conventional properties of the program data. This combination makes it possible, in principle, to solve a wider range of verification problems and makes it easier to incorporate separation logic reasoning into static analysis systems, such as software model checkers. It also can provide a component of a separation-logic-based code certification system a la proof-carrying code.
An efficient multi-level partitioning algorithm for VLSI circuits

In this paper, a new multi-level bipartitioning algorithm MLP, which integrates a clustering technique and an iterative improvement based partitioning process, is proposed to enhance the stability and the quality of partitioning results. The proposed clustering algorithm is used to reduce the partitioning complexity and improved the performance of partitioning. To generate a high-quality partitioning solution, a module migration based partitioning algorithm MMP is also proposed as the based partitioner for the MLP algorithm. The MMP algorithm implicitly promotes the move of clusters during the module migration processes by paying more attention to the neighbors of moved modules, relaxing the size constraints temporarily during the migration process, and controlling the module migration direction. Experimental results obtained show that the MLP algorithm generates high-quality partitioning results. The MLP algorithm outperforms MELO and CDIP/sub LA3/ by 23% and 10%, respectively and is competitive with hMetis and ML/sub c/ which have generated better results than many recent state-of-the-art partitioning algorithms.
New Phylogenetic Groups of Torque Teno Virus Identified in Eastern Taiwan Indigenes

Torque teno virus (TTV) is a single-stranded DNA virus highly prevalent in the world. It has been detected in eastern Taiwan indigenes with a low prevalence of 11% by using N22 region of which known to underestimate TTV prevalence excessively. In order to clarify their realistic epidemiology, we re-analyzed TTV prevalence with UTR region. One hundred and forty serum samples from eastern Taiwanese indigenous population were collected and TTV DNA was detected in 133 (95%) samples. Direct sequencing revealed an extensive mix-infection of different TTV strains within the infected individual. Entire TTV open reading frame 1 was amplified and cloned from a TTV positive individual to distinguish mix-infected strains. Phylogenetic analysis showed eleven isolates were clustered into a monophyletic group that is distinct from all known groups. In addition, another our isolate was clustered with recently described Hebei-1 strain and formed an independent clade. Based on the distribution pattern of pairwise distances, both new clusters were placed at phylogenetic group level, designed as the 6th and 7th phylogenetic group. In present study, we showed a very high prevalence of TTV infection in eastern Taiwan indigenes and indentified new phylogenetic groups from the infected individual. Both intra- and inter-phylogenetic group mix-infections can be found from one healthy person. Our study has further broadened the field of human TTVs and proposed a robust criterion for classification of the major TTV phylogenetic groups.
Cloning of the Cryptochrome-Encoding PeCRY1 Gene from Populus euphratica and Functional Analysis in Arabidopsis

Cryptochromes are photolyase-like blue/UV-A light receptors that evolved from photolyases. In plants, cryptochromes regulate various aspects of plant growth and development. Despite of their involvement in the control of important plant traits, however, most studies on cryptochromes have focused on lower plants and herbaceous crops, and no data on cryptochrome function are available for forest trees. In this study, we isolated a cryptochrome gene, PeCRY1, from Euphrates poplar (Populus euphratica), and analyzed its structure and function in detail. The deduced PeCRY1 amino acid sequence contained a conserved N-terminal photolyase-homologous region (PHR) domain as well as a C-terminal DQXVP-acidic-STAES (DAS) domain. Secondary and tertiary structure analysis showed that PeCRY1 shares high similarity with AtCRY1 from Arabidopsis thaliana. PeCRY1 expression was upregulated at the mRNA level by light. Using heterologous expression in Arabidopsis, we showed that PeCRY1 overexpression rescued the cry1 mutant phenotype. In addition, PeCRY1 overexpression inhibited hypocotyl elongation, promoted root growth, and enhanced anthocyanin accumulation in wild-type background seedlings grown under blue light. Furthermore, we examined the interaction between PeCRY1 and AtCOP1 using a bimolecular fluorescence complementation (BiFc) assay. Our data provide evidence for the involvement of PeCRY1 in the control of photomorphogenesis in poplar.
ScratchTalk and social computation: towards a natural language scripting model

Natural Language interfaces have been proposed as a solution to make application functionality more accessible to end users. Practical implementation of such systems has been hampered by both semantic and knowledge-engineering challenges. This paper introduces Social Computation, a theoretical model targeting both challenges. The model employs natural language in a planning framework to enable communities of end-users to collaborate, explicitly and implicitly, in the development of new functionality. The model intrinsically supports the acquisition of user goals and natural language semantics in the context of the application domain. ScratchTalk is a prototype of the natural language planning component of the model applied to the Scratch programming environment. This serves to ground the framework and provide insights into the space of applications likely to be addressable by the Social Computation model.
Antemortem versus postmortem methods for detection of betanodavirus in Senegalese sole (Solea senegalensis)

The suitability of nested reverse transcription polymerase chain reaction (nRT-PCR) to detect betanodavirus in blood samples from naturally infected Senegalese sole (Solea senegalensis) was evaluated in comparison with other diagnostic methods. Results indicated that histologic examination of brain lesions could be regarded as the most consistent indicator of nodavirus infection in this species. The nRT-PCR showed low to moderate levels of detection; the best values were obtained in brain samples followed by blood samples. Inoculation of SSN-1 and SAF-1 cells with fish samples did not cause cytopathic effect, although virus was detected by reverse transcription polymerase chain reaction in approximately 25% of the SSN-1 inoculated wells. The efficiency of detection of the viral genome was dramatically increased by the use of nRT-PCR, reaching 90.6% of positives in brain samples and 84.4% in blood samples. The sensitivity and the negative predictive value of nRT-PCR in blood samples were slightly lower than those obtained using brain samples. Nevertheless, it is suggested that the advantage of being able to perform diagnosis on live fish adequately counterbalances the slightly lower sensitivity of nRT-PCR on blood samples. This technique is proposed as a useful tool, not only for the selection of nodavirus-free breeders but also to check the fish status during ongrowing.
Learning Speaker-Specific Characteristics With a Deep Neural Architecture

Speech signals convey various yet mixed information ranging from linguistic to speaker-specific information. However, most of acoustic representations characterize all different kinds of information as whole, which could hinder either a speech or a speaker recognition (SR) system from producing a better performance. In this paper, we propose a novel deep neural architecture (DNA) especially for learning speaker-specific characteristics from mel-frequency cepstral coefficients, an acoustic representation commonly used in both speech recognition and SR, which results in a speaker-specific overcomplete representation. In order to learn intrinsic speaker-specific characteristics, we come up with an objective function consisting of contrastive losses in terms of speaker similarity/dissimilarity and data reconstruction losses used as regularization to normalize the interference of non-speaker-related information. Moreover, we employ a hybrid learning strategy for learning parameters of the deep neural networks: i.e., local yet greedy layerwise unsupervised pretraining for initialization and global supervised learning for the ultimate discriminative goal. With four Linguistic Data Consortium (LDC) benchmarks and two non-English corpora, we demonstrate that our overcomplete representation is robust in characterizing various speakers, no matter whether their utterances have been used in training our DNA, and highly insensitive to text and languages spoken. Extensive comparative studies suggest that our approach yields favorite results in speaker verification and segmentation. Finally, we discuss several issues concerning our proposed approach.
Extracting Various Classes of Data From Biological Text Using the Concept of Existence Dependency

One of the key goals of biological natural language processing (NLP) is the automatic information extraction from biomedical publications. Most current constituency and dependency parsers overlook the semantic relationships between the constituents comprising a sentence and may not be well suited for capturing complex long-distance dependences. We propose in this paper a hybrid constituency-dependency parser for biological NLP information extraction called EDCC. EDCC aims at enhancing the state of the art of biological text mining by applying novel linguistic computational techniques that overcome the limitations of current constituency and dependency parsers outlined earlier, as follows: 1) it determines the semantic relationship between each pair of constituents in a sentence using novel semantic rules; and 2) it applies a semantic relationship extraction model that extracts information from different structural forms of constituents in sentences. EDCC can be used to extract different types of data from biological texts for purposes such as protein function prediction, genetic network construction, and protein-protein interaction detection. We evaluated the quality of EDCC by comparing it experimentally with six systems. Results showed marked improvement.
Parsing interindividual drug variability: an emerging role for systems pharmacology

There is notable interindividual heterogeneity in drug response, affecting both drug efficacy and toxicity, resulting in patient harm and the inefficient utilization of limited healthcare resources. Pharmacogenomics is at the forefront of research to understand interindividual drug response variability, but although many genotype‐drug response associations have been identified, translation of pharmacogenomic associations into clinical practice has been hampered by inconsistent findings and inadequate predictive values. These limitations are in part due to the complex interplay between drug‐specific, human body and environmental factors influencing drug response and therefore pharmacogenomics, whilst intrinsically necessary, is by itself unlikely to adequately parse drug variability. The emergent, interdisciplinary and rapidly developing field of systems pharmacology, which incorporates but goes beyond pharmacogenomics, holds significant potential to further parse interindividual drug variability. Systems pharmacology broadly encompasses two distinct research efforts, pharmacologically‐orientated systems biology and pharmacometrics. Pharmacologically‐orientated systems biology utilizes high throughput omics technologies, including next‐generation sequencing, transcriptomics and proteomics, to identify factors associated with differential drug response within the different levels of biological organization in the hierarchical human body. Increasingly complex pharmacometric models are being developed that quantitatively integrate factors associated with drug response. Although distinct, these research areas complement one another and continual development can be facilitated by iterating between dynamic experimental and computational findings. Ultimately, quantitative data‐derived models of sufficient detail will be required to help realize the goal of precision medicine. WIREs Syst Biol Med 2015, 7:221–241. doi: 10.1002/wsbm.1302
Weak Semi-Markov CRFs for Noun Phrase Chunking in Informal Text

This paper introduces a new annotated corpus based on an existing informal text corpus: the NUS SMS Corpus (Chen and Kan, 2013). The new corpus includes 76,490 noun phrases from 26,500 SMS messages, annotated by university students. We then explored several graphical models, including a novel variant of the semi-Markov conditional random fields (semi-CRF) for the task of noun phrase chunking. We demonstrated through empirical evaluations on the new dataset that the new variant yielded similar accuracy but ran in significantly lower running time compared to the conventional semi-CRF.