Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks

As pharmacodynamic drug-drug interactions (PD DDIs) could lead to severe adverse effects in patients, it is important to identify potential PD DDIs in drug development. The signaling starting from drug targets is propagated through protein-protein interaction (PPI) networks. PD DDIs could occur by close interference on the same targets or within the same pathways as well as distant interference through cross-talking pathways. However, most of the previous approaches have considered only close interference by measuring distances between drug targets or comparing target neighbors. We have applied a random walk with restart algorithm to simulate signaling propagation from drug targets in order to capture the possibility of their distant interference. Cross validation with DrugBank and Kyoto Encyclopedia of Genes and Genomes DRUG shows that the proposed method outperforms the previous methods significantly. We also provide a web service with which PD DDIs for drug pairs can be analyzed at http://biosoft.kaist. ac.kr/targetrw.
Two antiprothrombin antibodies against prothrombin and prothrombin–phosphatidyl serine show partial but not total identity

Recently, an enzyme-linked immunosorbent assay (ELISA) using prothrombin (PT) as the antigen has become a widely used test. Two ELISA methods for the detection of antiprothrombin antibody have been used extensively: one method employs PT as an antigen (aPT), and the other employs PT and phosphatidyl serine (aPT/PS) as antigens along with Ca2+. However, the results obtained by the two methods are not necessarily consistent with each other even using the same samples, suggesting the possibility that aPT and aPT/PS are different antibodies. We conducted an investigation to determine whether aPT and aPT/PS are identical or different antibodies. Five patients who were positive for both tests become negative to aPT after absorption with an aPT-ELISA plate or fluid-phase PT; however, they retained reactivity to aPT/PS after the same absorption procedure. These results suggest that aPT and aPT/PS are partially identical, yet still different antibodies. However, further examination employing more samples may be needed to verify our hypothesis including clarification of the clinicopathological significance of these antibodies in the future.
Mutation or Overexpression of a Terminal Oxidase Leads to a Cell Division Defect and Multiple Antibiotic Sensitivity in Pseudomonas aeruginosa *

Mutation of the cyanide-insensitive terminal oxidase of Pseudomonas aeruginosa leads to pleiotropic effects. A cio mutant and strains, including the wild-type, carrying the cioABgenes on a multicopy plasmid were temperature-sensitive and had a cell division defect, leading to the formation of non-septate, multinucleated filaments. Such strains of this intrinsically antibiotic-resistant bacterium were more sensitive to a range of antibiotics including chloramphenicol, β-lactams, quinolones, aminoglycosides, and macrolides. The effect of cio mutation on Δp-dependent accumulation of chloramphenicol suggested that antibiotic sensitivity resulted from loss of or damage to a multidrug efflux pump. The ability of reducing agents and catalase to suppress the temperature-sensitive phenotype and of catalase to partially suppress antibiotic sensitivity suggested that increased levels of reactive oxygen species might be the cause of the observed phenotypes. Consistent with this was the increased sensitivity of strains to H2O2 and their increased protein carbonyl content, an indicator of oxidative protein modification. The temperature-dependent synthesis of a specific catalase was absent in the cio mutant and in strains carrying multiple plasmid-borne copies of cioAB. We propose that reduced catalase levels result in oxidative modification and consequent loss of function of proteins involved in a range of cellular functions. How mutation or overexpression of the cyanide-insensitive terminal oxidase leads to a loss of catalase activity is unknown at present.
Polymorphic specialization for ML

We present a framework for offline partial evaluation for call-by-value functional programming languages with an ML-style typing discipline. This includes a binding-time analysis which is (1) polymorphic with respect to binding times; (2) allows the use of polymorphic recursion with respect to binding times; (3) is applicable to a polymorphically typed term; and (4) is proven correct with respect to a novel small-step specialization semantics.The main innovation is to build the analysis on top of the region calculus of Tofte and Talpin [1994], thus leveraging the tools and techniques developed for it. Our approach factorizes the binding-time analysis into region inference and a subsequent constraint analysis. The key insight underlying our framework is to consider binding times as properties of regions.Specialization is specified as a small-step semantics, building on previous work on syntactic-type soundness results for the region calculus. Using similar syntactic proof techniques, we prove soundness of the binding-time analysis with respect to the specializer. In addition, we prove that specialization preserves the call-by-value semantics of the region calculus by showing that the reductions of the specializer are contextual equivalences in the region calculus.
Utilization of glycerol as carbon source on the growth, pigment and lipid production in Spirulina platensis

The ability of the cyanobacterium Spirulina platensis to utilize glycerol as the carbon source was investigated. In this work, we report on some physiological parameters that characterize the adaptive response of Spirulina platensis for the utilization of glycerol as the carbon source. A marked decrease was observed in the pigments Chlorophyll a (Chl a) and phycocyanin content of Spirulina platensis grown on glycerol medium when compared to the control. The lipid content in the glycerol-grown groups was comparable with the control, but variations were observed in the fatty acid profile of the total lipid mainly in the level of monoenes and polyenes. There was an increase in the γ-linolenic acid (GLA) in the Neutral lipid (NL) fraction.
Leveraging hardware message passing for efficient thread synchronization

As the level of parallelism in manycore processors keeps increasing, providing efficient mechanisms for thread synchronization in concurrent programs is becoming a major concern. On cache-coherent shared-memory processors, synchronization efficiency is ultimately limited by the performance of the underlying cache coherence protocol. This paper studies how hardware support for message passing can improve synchronization performance. Considering the ubiquitous problem of mutual exclusion, we adapt two state-of-the-art solutions used on shared-memory processors, namely the server approach and the combining approach, to leverage the potential of hardware message passing. We propose HybComb, a novel combining algorithm that uses both message passing and shared memory features of emerging hybrid processors. We also introduce MP-Server, a straightforward adaptation of the server approach to hardware message passing. Evaluation on Tilera's TILE-Gx processor shows that MP-Server can execute contended critical sections with unprecedented throughput, as stalls related to cache coherence are removed from the critical path. HybComb can achieve comparable performance, while avoiding the need to dedicate server cores. Consequently, our queue and stack implementations, based on MP-Server and HybComb, largely outperform their most efficient pure-shared-memory counterparts.
Angular scattering properties of human epidermal layers

There is a defmite need to determine accurately optical parameters of tissues. It is required either when planning a laser treatment or trying to make diagnostic conclusions, based on differences in optical properties of healthy and pathological tissues. Scattering phase function is an important characteristic of medium optical properties1.Knowledge of scattering phase function of epidermal layers is necessary for direct calculations of light propagation through skin2. Changes in angular properties of scattered light may reflect pathology of tissue and can be used in investigation of skin diseases, like psoriasis3. Besides the self4mportance measurements of scattering phase function can be used in combination with integrating sphere measurements to determine absorption and scattering coefficients of tissue4. This combination can also be useful for testing of photoprotectors. Direct gomometric measurements of the angular distribution of radiation, scattered by human samples have been reported by several authors5'6. However, known literature data on angular scattering properties of human epidermis are still liniited7'8. In present paper we concentrate on outermost epidermal layers and report measurements, performed on samples, obtained by the novel technique3. We investigated also influence of various chemical's applications to skin surface on scattering phase function of epidermal layers.
National language-Specific Evaluation Sites for Retrieval Systems and Interfaces

An induction heating coil for a zone pulling of semiconductor rods assures the disturbance-free performance of the pulling process even at the high power densities required for large rod diameters (approximately 10 to 12 cm). According to the invention, the arc-over paths between surfaces in the region of the coil slot, which are at differing potentials, are covered by one or more movable planar structures of temperature-stable insulating material which are introduced into the coil slot.
Neural networks underlying contributions from semantics in reading aloud

Reading is an essential part of contemporary society, yet much is still unknown about the physiological underpinnings of its information processing components. Two influential cognitive models of reading, the connectionist and dual-route cascaded models, offer very different accounts, yet evidence for one or the other remains equivocal. These models differ in several ways, including the role of semantics (word meaning) in mapping spelling to sound. We used a new effective connectivity algorithm, IMaGES, to provide a network-level perspective on these network-level models. Left hemisphere regions of interest were defined based on main effects in functional magnetic resonance imaging and included two regions linked with semantic processing—angular gyrus (AG) and inferior temporal sulcus (ITS)—and two regions linked with phonological processing—posterior superior temporal gyrus (pSTG) and posterior middle temporal gyrus (pMTG). Participants read aloud words of high or low spelling-sound consistency, word frequency, and imageability. Only the connectionist model predicted increased contributions from semantic areas with those computing phonology for low-consistency words. Effective connectivity analyses revealed that areas supporting semantic processing (e.g., the ITS) interacted with phonological areas (e.g., the pSTG), with the pattern changing as a function of word properties. Connectivity from semantic to phonological areas emerged for high- compared to low-imageability words, and a similar pattern emerged for low-consistency words, though only under certain conditions. Analyses of individual differences also showed that variation in the strength of modulation of ITS by AG was associated with reading aloud performance. Overall, these results suggest that connections with semantic processing areas are not only associated with reading aloud, but that these connections are also associated with optimal reading performance.
Expression of the plasma prekallikrein gene: utilization of multiple transcription start sites and alternative promoter regions

Abstract The plasma prekallikrein gene is expressed in many different human tissues at distinctly different levels and therefore tissue-specific control of the gene transcription is likely. In this study we demonstrate that transcription of the plasma prekallikrein gene can be initiated at multiple sites, for which at least four different promoters are utilized. A comparison of the genomic and mRNA sequences of mouse plasma prekallikrein revealed that the sequence segment that was formerly regarded as the first exon of the mouse plasma prekallikrein gene consists of three exons, with the first exon localized 14.2 kbp upstream of the translation start. For the rat and human plasma prekallikrein genes, in silico analysis suggested an analogous exon-intron organization. Determination of the transcription start sites showed that in both mouse and human, the proximal and distal regions could be utilized for transcription initiation; however, the proximal region is preferred. A deletion mutation analysis of the proximal promoter region using a 1.7-kbp segment revealed a strong activating region immediately upstream of the known mRNA, followed by both a modest repressor and an enhancer region.
Maskless Microscopic Lithography through Shaping Ultraviolet Laser with Digital Micro-mirror Device

Laser shaping was introduced to maskless projection soft lithography by using digital micro-mirror device (DMD). The predesigned intensity pattern was imprinted onto the DMD and the input laser beam with a Gaussian or quasi-Gaussian distribution will carry the pattern on DMD to etch the resin. It provides a method of precise control of laser beam shapes and photon-induced curing behavior of resin. This technology provides an accurate micro-fabrication of microstructures used for micro-systems. As a virtual mask generator and a binary-amplitude spatial light modulator, DMD is equivalent to the masks in the conventional exposure system. As the virtual masks and shaped laser beam can be achieved flexibly, it is a good method of precision soft lithography for 2D/3D microstructures.
Credibilist SLAM performances with different laser set-ups

Navigation in the Intelligent Transportation Systems (ITS) domain is still divided between reliable solutions that require heavy and costly set-ups and affordable solutions that still lack performances. By proposing a new method for Simultaneous Localisation and Mapping (SLAM) based on Transferable Belief Model (TBM), the authors aimed at finding a reasonable compromise for urban environment [1]. This article supports this choice and proposes a comparison between different laser set-ups to expose advantages and drawbacks of this solution.
Fitness trade‐offs explain low levels of persister cells in the opportunistic pathogen Pseudomonas aeruginosa

Microbial populations often contain a fraction of slow‐growing persister cells that withstand antibiotics and other stress factors. Current theoretical models predict that persistence levels should reflect a stable state in which the survival advantage of persisters under adverse conditions is balanced with the direct growth cost impaired under favourable growth conditions, caused by the nonreplication of persister cells. Based on this direct growth cost alone, however, it remains challenging to explain the observed low levels of persistence (<<1%) seen in the populations of many species. Here, we present data from the opportunistic human pathogen Pseudomonas aeruginosa that can explain this discrepancy by revealing various previously unknown costs of persistence. In particular, we show that in the absence of antibiotic stress, increased persistence is traded off against a lengthened lag phase as well as a reduced survival ability during stationary phase. We argue that these pleiotropic costs contribute to the very low proportions of persister cells observed among natural P. aeruginosa isolates (3 × 10−8–3 × 10−4) and that they can explain why strains with higher proportions of persister cells lose out very quickly in competition assays under favourable growth conditions, despite a negligible difference in maximal growth rate. We discuss how incorporating these trade‐offs could lead to models that can better explain the evolution of persistence in nature and facilitate the rational design of alternative therapeutic strategies for treating infectious diseases.
Canadian Guidelines for the Evidence-Based Treatment of Tic Disorders: Behavioural Therapy, Deep Brain Stimulation, and Transcranial Magnetic Stimulation

This clinical guideline provides recommendations for nonpharmacological treatments for tic disorders. We conducted a systematic literature search for clinical trials on the treatment of tics. One evidence-based review (including 30 studies) and 3 studies on behavioural interventions, 3 studies on deep brain stimulation (DBS), and 3 studies on transcranial magnetic stimulation (TMS) met our inclusion criteria. Based on this evidence, we have made strong recommendations for the use of habit reversal therapy and exposure and response prevention, preferably embedded within a supportive, psychoeducational program, and with the option to combine either of these approaches with pharmacotherapy. Although evidence exists for the effcacy of DBS, the quality of this evidence is poor and the risks and burdens of the procedure are fnely balanced with the perceived benefts. Our recommendation is that this intervention continues to be considered an experimental treatment for severe, medically refractory tics that have imposed severe limitations on quality of life. We recommend that the procedure should only be performed within the context of research studies and by physicians expert in DBS programming and in the management of tics. There is no evidence to support the use of TMS in the treatment of tics. However, the procedure is associated with a low rate of known complications and could continue to be evaluated within research protocols. The recommendations we provide are based on current knowledge, and further studies may result in their revision in future.
Analyzing the Multicriteria of the Interaction Design of an Educational Map Application for Digital TV from User Preferences

The potential of digital TV demonstrates that it could be an excellent connection between map information suppliers and citizen, users of such information. The Brazilian digital television standard will be fully adopted in Brazil in 2016 and starts to be adopted in almost all Latin American Countries. It will reach many areas, being accessible to about 600000 people. Nevertheless, the Brazilian digital television standard and user population profile imposes restrictions on map access on TV or mobile screens, which leads to the challenge of this work. This article describes the analysis five criteria of three final prototypes of an educational application of maps for TV or mobile devices, based on ZAPROS III analysis. The results show the best interaction solutions suitable for DTV and mobile for maps.
Rate regions of secret key sharing in a new source model

A source model for secret key generation between terminals is considered. Two users, namely users 1 and 2, at one side communicate with another user, namely user 3, while at the other side via a public channel where three users can observe i.i. d. outputs of correlated sources. Each of users 1 and 2 intends to share a secret key with user 3 where user 1 acts as a wiretapper for user 2 and vice versa. In this model, two situations are considered: communication from users 1 and 2 to user 3 (the forward key strategy) and from user 3 to users 1 and 2 (the backward key strategy). In both situations, the goal is sharing a secret key between user 1 and user 3 while leaking no effective information about that key to user 2, and simultaneously, sharing another secret key between user 2 and user 3 while leaking no effective information about the latter key to user 1. This model is motivated by wireless communications when considering user 3 as a base station and users 1 and 2 as network users. For both the forward and backward key strategies, inner and outer bounds of secret key capacity regions are derived. In special situations where one of users 1 and 2 is only interested in wiretapping and not key sharing, the results agree with that of Ahlswede and Csiszar. Also, the authors investigate some special cases in which the inner bound coincides with the outer bound and secret key capacity region is deduced.
The Contribution of NMDA Receptor Signaling in the Corticobasal Ganglia Reward Network to Appetitive Pavlovian Learning

NMDA receptors (NMDARs) contribute to phasic transmission and synaptic plasticity and are thought to be important for learning. To better understand where NMDAR signaling is necessary for learning, we combined viral genetic strategies with genetic mouse models to investigate the contribution of NMDARs in the dopamine system to appetitive Pavlovian conditioning. NMDAR signaling in dopamine neurons was not required for Pavlovian conditioning; however, NMDARs in D1 dopamine receptor (D1R)-expressing medium spiny neurons (MSNs), which receive input from dopamine neurons, were critical for this type of learning. NMDAR signaling was also required in brain regions that project to dopamine neurons, because removing NMDARs from afferent neurons to the ventral tegmental area (VTA) also prevented learning. This effect was likely attributable to loss of NMDAR signaling in the neurons of the prefrontal cortex (PFC), because learning could be restored in these animals by rescuing NMDAR expression in the PFC. Moreover, removing NMDARs exclusively from the PFC also prevented learning. Our findings suggest that NMDARs in neurons that project to and receive projections from the VTA are necessary for Pavlovian conditioning and specifically implicate the PFC and D1R-expressing MSNs in associative learning.
Continuous Arteriovenous Hemofiltration in the Critically Ill Patient: Clinical Use and Operational Characteristics

: Continuous arteriovenous hemofiltration is an extracorporeal technique for the treatment of fluid overload and electrolyte disturbances and for the removal of urea nitrogen. This technique is especially applicable in critically ill patients with hemodynamic instability. A special filter and modified hemodialysis blood lines can easily and rapidly be attached to a patient. No special blood access is needed. Fluids and solutes are removed from the patient by ultrafiltration. A net filtration pressure inside the filter causes an ultrafiltrate to form. The extracorporeal circuit can be kept in place for hours or days.
On Computing Min-Degree Elimination Orderings

We study faster algorithms for producing the minimum degree ordering used to speed up Gaussian elimination. This ordering is based on viewing the non-zero elements of a symmetric positive definite matrix as edges of an undirected graph, and aims at reducing the additional non-zeros (fill) in the matrix by repeatedly removing the vertex of minimum degree. It is one of the most widely used primitives for pre-processing sparse matrices in scientific computing. Our result is in part motivated by the observation that sub-quadratic time algorithms for finding min-degree orderings are unlikely, assuming the strong exponential time hypothesis (SETH). This provides justification for the lack of provably efficient algorithms for generating such orderings, and leads us to study speedups via degree-restricted algorithms as well as approximations. Our two main results are: (1) an algorithm that produces a min-degree ordering whose maximum degree is bounded by $\Delta$ in $O(m \Delta \log^3{n})$ time, and (2) an algorithm that finds an $(1 + \epsilon)$-approximate marginal min-degree ordering in $O(m \log^{5}n \epsilon^{-2})$ time. Both of our algorithms rely on a host of randomization tools related to the $\ell_0$-estimator by [Cohen `97]. A key technical issue for the final nearly-linear time algorithm are the dependencies of the vertex removed on the randomness in the data structures. To address this, we provide a method for generating a pseudo-deterministic access sequence, which then allows the incorporation of data structures that only work under the oblivious adversary model.