Miracle-dz/UniFAR-FTUs huggingface dataset:
Chloride-cotransport blockade desynchronizes neuronal discharge in the "epileptic" hippocampal slice.

Antagonism of the chloride-cotransport system in hippocampal slices has been shown to block spontaneous epileptiform (i.e., hypersynchronized) discharges without diminishing excitatory synaptic transmission. Here we test the hypotheses that chloride-cotransport blockade, with furosemide or low-chloride (low-[Cl(-)](o)) medium, desynchronizes the firing activity of neuronal populations and that this desynchronization is mediated through nonsynaptic mechanisms. Spontaneous epileptiform discharges were recorded from the CA1 and CA3 cell body layers of hippocampal slices. Treatment with low-[Cl(-)](o) medium led to cessation of spontaneous synchronized bursting in CA1 >/=5-10 min before its disappearance from CA3. During the time that CA3 continued to burst spontaneously but CA1 was silent, electrical stimulation of the Schaffer collaterals showed that hyperexcited CA1 synaptic responses were maintained. Paired intracellular recordings from CA1 pyramidal cells showed that during low-[Cl(-)](o) treatment, the timing of action potential discharges became desynchronized; desynchronization was identified with phase lags in firing times of action potentials between pairs of neurons as well as a with a broadening and diminution of the CA1 field amplitude. Continued exposure to low-[Cl(-)](o) medium increased the degree of the firing-time phase shifts between pairs of CA1 pyramidal cells until the epileptiform CA1 field potential was abolished completely. Intracellular recordings during 4-aminopyridine (4-AP) treatment showed that prolonged low-[Cl(-)](o) exposure did not diminish the frequency or amplitude of spontaneous postsynaptic potentials. CA3 antidromic responses to Schaffer collateral stimulation were not significantly affected by prolonged low-[Cl(-)](o) exposure. In contrast to CA1, paired intracellular recordings from CA3 pyramidal cells showed that chloride-cotransport blockade did not cause a significant desynchronization of action potential firing times in the CA3 subregion at the time that CA1 synchronous discharge was blocked but did reduce the number of action potentials associated with CA3 burst discharges. These data support our hypothesis that the anti-epileptic effects of chloride-cotransport antagonism in CA1 are mediated through the desynchronization of population activity. We hypothesize that interference with Na(+),K(+),2Cl(-) cotransport results in an increase in extracellular potassium ([K(+)](o)) that reduces the number of action potentials that are able to invade axonal arborizations and varicosities in all hippocampal subregions. This reduced efficacy of presynaptic action potential propagation ultimately leads to a reduction of synaptic drive and a desynchronization of the firing of CA1 pyramidal cells.
Portable parallel performance from sequential, productive, embedded domain-specific languages

Domain-expert productivity programmers desire scalable application performance, but usually must rely on efficiency programmers who are experts in explicit parallel programming to achieve it. Since such programmers are rare, to maximize reuse of their work we propose encapsulating their strategies in mini-compilers for domain-specific embedded languages (DSELs) glued together by a common high-level host language familiar to productivity programmers. The nontrivial applications that use these DSELs perform up to 98% of peak attainable performance, and comparable to or better than existing hand-coded implementations. Our approach is unique in that each mini-compiler not only performs conventional compiler transformations and optimizations, but includes imperative procedural code that captures an efficiency expert's strategy for mapping a narrow domain onto a specific type of hardware. The result is source- and performance-portability for productivity programmers and parallel performance that rivals that of hand-coded efficiency-language implementations of the same applications. We describe a framework that supports our methodology and five implemented DSELs supporting common computation kernels. Our results demonstrate that for several interesting classes of problems, efficiency-level parallel performance can be achieved by packaging efficiency programmers' expertise in a reusable framework that is easy to use for both productivity programmers and efficiency programmers.
Attenuation Caused by a Distant Isothermal Turbulent Screen

We analyze in detail the attenuation caused by an isothermal turbulent distant foreground dust screen. The attenuation curve is well determined by two parameters, the absolute-to-relative attenuation ratio R = AV/E(B - V) and the absolute attenuation AV. We show quantitatively how these two observable quantities depend on the statistical properties of the local density and the mean attenuation ⟨AV⟩ and how they vary with the thickness of the screen measured in units of the largest turbulent scale. The attenuation through a turbulent medium is characterized by higher transparency and a flatter attenuation curve in comparison with a homogeneous dust screen. In general, the effect of a turbulent medium on the attenuation increases with slice thickness. In the limit of thick slices, typically larger than the maximum turbulent scale, R asymptotically approaches a maximum value.
Experiences from an Exploratory Case Study with a Software Risk Management Method

This paper presents the results of an exploratory case study in which a risk management method was used and compared with a method currently used by the organization. The goal of the case study was to obtain feedback on an early version of a risk management method, called Riskit, that has been developed at the University of Maryland. This paper also presents an overview of Riskit method version 0.10 and describes the comparison method currently used by the case study organization, as well as the case study design.
Using machines to learn method-specific compilation strategies

Support Vector Machines (SVMs) are used to discover method-specific compilation strategies in Testarossa, a commercial Just-in-Time (JiT) compiler employed in the IBM® J9 Java™ Virtual Machine. The learning process explores a large number of different compilation strategies to generate the data needed for training models. The trained machine-learned model is integrated with the compiler to predict a compilation plan that balances code quality and compilation effort on a per-method basis. The machine-learned plans outperform the original Testarossa for start-up performance, but not for throughput performance, for which Testarossa has been highly hand-tuned for many years.
Modeling of Elastic Robot Joints with Nonlinear Damping and Hysteresis

Elastic robot joints gain in importance since the nowadays robotics tends to the lightweight structures. The lightweight metals and composite materials deployed not only in the links but also in the joint assemblies affect the overall stiffness of robotic system. The elastic joints provide the loaded robot motion with additional compliance and can lead to significant control errors and vibrations in the joint as well as operational space. A better understanding of the compliant joint behavior can help not only to analyze and simulate robotic systems but also to improve their control performance. Elastic robot joints are often denoted as flexible joints or compliant joints as well. The former modeling approaches aimed to describe the dynamic behavior of elastic robot joints lead back to Spong (1987). Spong extended the general motion equation of a rigid roboticmanipulator to the case of joint elasticity captured by a linear connecting spring. Remember that the general motion equation derived either from Lagrange or Newton-Euler formalism for a class of rigid robotic manipulators (Sciavicco & Siciliano (2000)) can be expressed as
Bioaerosol health effects and exposure assessment: progress and prospects.

Exposures to bioaerosols in the occupational environment are associated with a wide range of health effects with major public health impact, including infectious diseases, acute toxic effects, allergies and cancer. Respiratory symptoms and lung function impairment are the most widely studied and probably among the most important bioaerosol-associated health effects. In addition to these adverse health effects some protective effects of microbial exposure on atopy and atopic conditions has also been suggested. New industrial activities have emerged in recent years in which exposures to bioaerosols can be abundant, e.g. the waste recycling and composting industry, biotechnology industries producing highly purified enzymes and the detergent and food industries that make use of these enzymes. Dose-response relationships have not been established for most biological agents and knowledge about threshold values is sparse. Exposure limits are available for some contaminants, e.g. wood dust, subtilisins (bacterial enzymes) and flour dust. Exposure limits for bacterial endotoxin have been proposed. Risk assessment is seriously hampered by the lack of valid quantitative exposure assessment methods. Traditional culture methods to quantify microbial exposures have proven to be of limited use. Non-culture methods and assessment methods for microbial constituents [e.g. allergens, endotoxin, beta(1-->3)-glucans, fungal extracellular polysaccharides] appear more successful; however, experience with these methods is generally limited. Therefore, more research is needed to establish better exposure assessment tools and validate newly developed methods. Other important areas that require further research include: potential protective effects of microbial exposures on atopy and atopic diseases, inter-individual susceptibility for biological exposures, interactions of bioaerosols with non-biological agents and other potential health effects such as skin and neurological conditions and birth effects.
BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs:

In this paper, we construct a biomedical semantic role labeling (SRL) system that can be used to facilitate relation extraction. First, we construct a proposition bank on top of the popular biomedical GENIA treebank following the PropBank annotation scheme. We only annotate the predicate-argument structures (PAS's) of thirty frequently used biomedical predicates and their corresponding arguments. Second, we use our proposition bank to train a biomedical SRL system, which uses a maximum entropy (ME) model. Thirdly, we automatically generate argument-type templates which can be used to improve classification of biomedical argument types. Our experimental results show that a newswire SRL system that achieves an F-score of 86.29% in the newswire domain can maintain an F-score of 64.64% when ported to the biomedical domain. By using our annotated biomedical corpus, we can increase that F-score by 22.9%. Adding automatically generated template features further increases overall F-score by 0.47% and adjunct arguments (AM) F-score by 1.57%, respectively.
Circular DNA resulting from recombination between V-(D)-J joining signals and switch repetitive sequences in mouse thymocytes

During the course of analyzing circular DNA in mouse thymocytes, novel recombinants were identified with immunoglobulin heavy chain joining gene and switch region probes. These circles represent excision products of recombination between the heptamer-nonamer motif for V-(D)- J joining and a repetitive sequence for class switching. The molecular mechanisms that generate "hybrid circles" are discussed.
On Solution Correspondences in Answer-Set Programming

We introduce a general framework for specifying program correspondence under the answer-set semantics. The framework allows to define different kinds of equivalence notions, including previously defined notions like strong and uniform equivalence, in which programs are extended with rules from a given context, and correspondence is determined by means of a binary relation. In particular, refined equivalence notions based on projected answer sets can be defined within this framework, where not all parts of an answer set are of relevance. We study general characterizations of inclusion and equivalence problems, introducing novel semantical structures. Furthermore, we deal with the issue of determining counterexamples for a given correspondence problem, and we analyze the computational complexity of correspondence checking.
Co-Localization of Alpha1-Adrenoceptors and GPR55: A Novel Prostate Cancer Paradigm?

α1-adrenoceptors (α1-ARs) and “cannabinoid-like” G Protein Coupled Receptor 55 (GPR55) belong to the G-protein coupled receptor (GPCR) family and play a crucial role in regulating prostate function. Although physical and functional interactions between the cannabinoid and adrenergic systems have been reported, analysis of functional interactions between α1-AR and GPR55 in normal and neoplastic prostate has not been reported. Since GPR55 levels are high in rodent adrenal gland, we propose a function link between the adrenergic system and GPR55 receptor. Confocal Laser Scanning Microscopy (CLSM) was employed to examine the endogenous α1-AR and GPR55 expression and their co-localization, expressed as fluorescence, in vitro in human andro-gen-insensitive PC-3 and androgen-sensitive LNCaP prostatic carcinoma cell lines, using the fluo-rescent ligands—Syto 62 (nuclear stain), BODIPY FL-Prazosin (QAPB; fluorescent quinazoline α1-AR ligand) and Tocriflour (T1117; a novel fluorescent diarylpyrazole cannabinoid/GPR55 ligand). Fluorescent ligand binding in untreated PC-3 cells and LNCaP cells and spheroids showed hetero-geneous expression of both α1-ARs and GPR55. A small proportion of cells had both α1-ARs and GPR55 in relatively equal numbers indicating a degree of co-localization. Co-localization of fluo-rescent ligand binding exhibited a stronger correlation in LNCaP (0.87) as compared to PC-3 (0.63) cells. Upregulation of α1-AR was observed in PC-3 cells following chronic doxazosin incubation. Robust T1117 binding, suggestive of GPR55 upregulation, was also observed in these cells. The presence of subtype-rich cells with a degree of co-localization between α1-ARs and GPR55 indicates a possibility for dimerisation or functional interaction and a new paradigm for functional synergism in which interactions may be either between cells or involve converging intracellular signaling processes.
Photoelectric Heating and [C II] Cooling in Translucent Clouds: Results for Cloud Models Based on Simulations of Compressible Magnetohydrodynamic Turbulence

Far-ultraviolet (FUV) photons expel electrons from interstellar dust grains and the excess kinetic energy of the electrons is converted into gas thermal energy through collisions. This photoelectric heating is believed to be the main heating mechanism in cool H I clouds. The heating rate cannot be directly measured, but it can be estimated through observations of the [C II] line emission, since this is believed to be the main coolant in regions where the photoelectric effect dominates the heating. Furthermore, the comparison of the [C II] emission with the far-infrared (FIR) emission allows us to constrain the efficiency of the photoelectric heating using model calculations that take into account the strength of the radiation field. Recent [C II] observations carried out with the Infrared Space Observatory satellite have made this study possible. In this work, we study the correlation between FUV absorption and FIR emission using three-dimensional models of the density distribution in H I clouds. The density distributions are obtained as the result of numerical simulations of compressible magnetohydrodynamic turbulence, with rms sonic Mach numbers of the flow ranging from subsonic to highly supersonic, 0.6 ≤ MS ≤ 10. The FIR intensities are solved with detailed radiative transfer calculations. The [C II] line radiation is estimated assuming local thermodynamic equilibrium where the [C II] line cooling equals the FUV absorption multiplied by the unknown efficiency of the photoelectric heating, ϵ. The average ratio between the predicted [C II] and FIR emissions is found to be remarkably constant between different models, implying that the derived values of ϵ should not depend on the rms Mach number of the turbulence. The comparison of the models with the empirical data from translucent, high-latitude clouds yields an estimate of the photoelectric heating efficiency of ϵ ~ 2.9 × 10-2 on the basis of the dust model of Li & Draine. This value confirms previous theoretical predictions. The observed correlation between [C II] and FIR emission contains a large scatter, even within individual clouds. Our models show that most of the scatter can be understood as resulting from the highly fragmented density field in turbulent H I clouds. The scatter can be reproduced with density distributions from supersonic turbulence, while subsonic turbulence fails to generate the observed scatter.
Lateral Mobility of Presynaptic α7-Containing Nicotinic Receptors and Its Relevance for Glutamate Release

Surface diffusion of postsynaptic receptors shapes synaptic transmission. Presynaptic receptors also influence transmission, but the relevance of their mobility for synaptic function is unknown. Using single-particle tracking with quantum dots, we show that calcium-permeable α7-containing nicotinic acetylcholine receptors (α7–nAChRs), capable of promoting transmitter release, are mobile on presynaptic terminals but constrained in synaptic space on rat hippocampal neurons in culture. Additional immobilization of presynaptic α7-nAChRs by antibody crosslinking increases glutamate release capacity as seen in the frequency of spontaneous miniature postsynaptic currents and the size of the readily releasable pool of transmitter. Conversely, blocking glutamate release by targeting tetanus toxin to individual synapses increases α7–nAChR dwell time at presynaptic sites. The effects on release require functional α7–nAChRs and may to depend on CAST/ELKS (calpastatin/glutamine, leucine, lysine, and serine-rich protein), which an unbiased proteomic screen yielded. The results support a new homeostatic regulatory mechanism in which α7–nAChR restrain may be adjusted as needed at presynaptic sites via active zone proteins to maintain transmitter release capability.
Fast Shape Retrieval Based on Invariant Feature Alignment

This paper proposes an invariant feature alignment for shape-based image indexing and retrieval. We have found that some recently published systems have employed complex shape matchers to achieve high accuracy, at the cost of relatively high pairwise matching times. Using invariant feature alignment, our method can effectively increase the speed of shape retrieval without sacrificing accuracy. The key to its success is the use of a normalization procedure to generate a linear number of canonical reference frames as a function of the number of key points, the use of Haar transform to fast decompose the normalized curse into approximate polygons, and the use of fixed correspondences on those Haar expansion coefficients. The experimental results and comparisons show the good performance of the proposed technique
Learning Attention from Multi-Modal Imaging and Text: Application for Lesion Localisation in DWI

Strokes are one of the leading causes of death and disability in the UK. There are two main types of stroke: ischemic and hemorrhagic, with the majority of stroke patients suffering from the former. During an ischemic stroke, parts of the brain lose blood supply, and if not treated immediately, can lead to irreversible tissue damage and even death. Ischemic lesions can be detected by diffusion weighted magnetic resonance imaging (DWI), but localising and quantifying these lesions can be a time consuming task for clinicians. Work has already been done in training neural networks to segment these lesions, but these frameworks require a large amount of manually segmented 3D images, which are very time consuming to create. We instead propose to use past examinations of stroke patients which consist of DWIs, corresponding radiological reports and diagnoses in order to develop a learning framework capable of localising lesions. This is motivated by the fact that the reports summarise the presence, type and location of the ischemic lesion for each patient, and thereby provide more context than a single diagnostic label. Acute lesions prediction is aided by an attention mechanism which implicitly learns which regions within the DWI are most relevant to the classification.
New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction

Background Intercalated disks are unique structures in cardiac tissue, in which adherens junctions, desmosomes, and GAP junctions co-localize, thereby facilitating cardiac muscle contraction and function. Protocadherins are involved in these junctions; however, their role in heart physiology is poorly understood. We aimed to analyze the transcriptomic profile of adhesion molecules in patients with ischemic cardiomyopathy (ICM) and relate the changes uncovered with the hemodynamic alterations and functional depression observed in these patients. Methods and Results Twenty-three left ventricular tissue samples from patients diagnosed with ICM (n = 13) undergoing heart transplantation and control donors (CNT, n = 10) were analyzed using RNA sequencing. Forty-two cell adhesion genes involved in cellular junctions were differentially expressed in ICM myocardium. Notably, the levels of protocadherin PCDHGA3 were related with the stroke volume (r = –0.826, P = 0.003), ejection fraction (r = –0.793, P = 0.004) and left ventricular end systolic and diastolic diameters (r = 0.867, P = 0.001; r = 0.781, P = 0.005, respectively). Conclusions Our results support the importance of intercalated disks molecular alterations, closely involved in the contractile function, highlighting its crucial significance and showing gene expression changes not previously described. Specifically, altered PCDHGA3 gene expression was strongly associated with reduced stroke volume and ventricular dysfunction in ICM, suggesting a relevant role in hemodynamic perturbations and cardiac performance for this unexplored protocadherin.
Automatic Reference Models Development: A Framework

Software reuse allows the software industry to simultaneously reduce development cost and improve product quality. Reuse of early-stage artifacts has been acknowledged to be more beneficial than reuse of later-stage artifacts. In this regard, early-stage reference models have been considered as good tools to allow reuse across applications within the same domain. However, our literature survey reported in this paper reveals that the problem of automatically developing reference models from given instances has not caught enough researchers' attention yet. Accordingly, in this paper we propose a framework for building a reference model that captures the common and variable analysis/design practices, across the different applications in a domain. The framework considers multi-view models in assessing the commonalities and variabilities among given instances. The proposed framework incorporates learning capabilities to allow improving the quality and reusability of the reference model as it is being used.