Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethnically relevant consensus Korean reference genome towards personal reference genomes

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.
A Novel Functional Neuron Group for Respiratory Rhythm Generation in the Ventral Medulla

We visualized respiratory neuron activity covering the entire ventral medulla using optical recordings in a newborn rat brainstem–spinal cord preparation stained with voltage-sensitive dye. We measured optical signals from several seconds before to several seconds after the inspiratory phase using the inspiratory motor nerve discharge as the trigger signal; we averaged the optical signals of 50–150 respiratory cycles to obtain an optical image correlating particularly to inspiratory activity. The optical images we obtained from the ventral approach indicated that neuron activity first appeared during the respiratory cycle in the limited region of the rostral ventrolateral medulla (RVLM), preceding the onset of inspiratory activity by ∼500 msec. During the inspiratory phase, plateau activity appeared in the more caudal ventrolateral medulla at the level of the most rostral roots of the XIIth nerve. Comparison with electrophysiological recordings from respiratory neurons in the RVLM suggested that the optical signals preceding the inspiratory burst reflect preinspiratory neuron activity in this area. This RVLM area was determined to be ventrolateral to the facial nucleus and close to the ventral surface. We referred to this functional neuron group as the para-facial respiratory group (pFRG). Partial, bilateral electrical lesioning of the pFRG significantly reduced the respiratory frequency, together with changes in the spatiotemporal pattern of respiratory neuron activity. Our findings suggest that the pFRG comprises a neuronal population that is involved in the primary respiratory rhythm generation in the rostrocaudally extending respiratory neuron network of the medulla.
Reversal of Dopamine D2 Receptor Responses by an Anandamide Transport Inhibitor

We characterized the pharmacological properties of the anandamide transport inhibitorN-(4-hydroxyphenyl)-arachidonamide (AM404) in rats and investigated the effects of this drug on behavioral responses associated with activation of dopamine D2 family receptors. Rat brain slices accumulated [3H]anandamide via a high-affinity transport mechanism that was blocked by AM404. When administered alone in vivo, AM404 caused a mild and slow-developing hypokinesia that was significant 60 min after intracerebroventricular injection of the drug and was reversed by the CB1 cannabinoid receptor antagonist SR141716A. AM404 produced no significant catalepsy or analgesia, two typical effects of direct-acting cannabinoid agonists. However, AM404 prevented the stereotypic yawning produced by systemic administration of a low dose of apomorphine, an effect that was dose-dependent and blocked by SR141716A. Furthermore, AM404 reduced the stimulation of motor behaviors elicited by the selective D2family receptor agonist quinpirole. Finally, AM404 reduced hyperactivity in juvenile spontaneously hypertensive rats, a putative model of attention deficit hyperactivity disorder. The results support a primary role of the endocannabinoid system in the regulation of psychomotor activity and point to anandamide transport as a potential target for neuropsychiatric medicines.
Crystal Structures of the Free and Anisic Acid Bound Triple Mutant of Phospholipase a 2

Phospholipase A 2 catalyses the hydrolysis of the ester bond of 3-sn-phos-phoglycerides. Here, we report the crystal structures of the free and anisic acid-bound triple mutant (K53,56,120M) of bovine pancreatic phospho-lipase A 2. In the bound triple mutant structure, the small organic molecule p-anisic acid is found in the active site, and one of the carboxylate oxygen atoms is coordinated to the functionally important primary calcium ion. The other carboxylate oxygen atom is hydrogen bonded to the phenolic hydroxyl group of Tyr69. In addition, the bound anisic acid molecule replaces one of the functionally important water molecules in the active site. The residues 60 – 70, which are in a loop (surface loop), are disordered in most of the bovine pancreatic phospholipase A 2 structures. It is interesting to note that these residues are ordered in the bound triple mutant structure but are disordered in the free triple mutant structure. The organic crystallization ingredient 2-methyl-2,4-pentanediol is found near the active site of the free triple mutant structure. The overall tertiary folding and stereochemical parameters for the final models of the free and anisic acid-bound triple mutant are virtually identical.
Diversity of Cortical States at nonequilibrium Simulated by the Anti-Ferromagnetic Ising Model under Metropolis Dynamics

This article investigates the relationship between the interconnectivity and simulated dynamics of the thalamocortical system from the specific perspective of attempting to maximize the diversity of cortical states. This is achieved by designing the dynamics such that they favor opposing activity between adjacent regions, thus promoting dynamic diversity while avoiding widespread activation or de-activation. The anti-ferromagnetic Ising model with Metropolis dynamics is adopted and applied to four variations of the large-scale connectivity of the cat thalamocortical system: (a) considering only cortical regions and connections; (b) considering the entire thalamocortical system; (c) the same as in (b) but with the thalamic connections rewired so as to maintain the statistics of node degree and node degree correlations; and (d) as in (b) but with attenuated weights of the connections between cortical and thalamic nodes. A series of interesting findings are obtained, including the identification of specific substructures revealed by correlations between the activity of adjacent regions in case (a) and a pronounced effect of the thalamic connections in splitting the thalamocortical regions into two large groups of nearly homogenous opposite activation (i.e. cortical regions and thalamic nuclei, respectively) in cases (b) and (c). The latter effect is due to the existence of dense connections between cortical and thalamic regions and the lack of interconnectivity between the latter. Another interesting result regarding case (d) is the fact that the pattern of thalamic correlations tend to mirror that of the cortical regions. The possibility to control the level of correlation between the cortical regions by varying the strength of thalamocortical connections is also identified and discussed.
Effects of AlkyI-Lysophosphol ip ids on Human Leukemic Cell Lines Measured by Nuclear Magnetic Resonance 1

Part of the cytotoxic action of a lkyllysophosphol ip ids (ALP) on leukemic cells is known to result from the lack of an O-alkyl cleavage enzyme and its antimetabolic effect which results in a toxic lysophosphol ipid buildup. Further, ALP (5/.Lg/ml) suppresses c lonogenic i ty and trit iated thymidine uptake in HL60 cultures after 24 hr of exposure. The effect of ALP on two leukemic cell lines, HL60 and K562, measured by two nuclear magnetic resonance (NMR) techniques and examined by electron microscopy is reported. 31p-NMR spectroscopy indicates that the adenosine 5 ' t r iphosphate:adenosine 5 ' -d iphosphate ratios are unaffected after 24 hr, as is mitochondrial morphology, judging by electron micrographs. However, cell membrane integrity in HL60 is altered at that time. The earl iest ALP effects occur in NMR internal water relaxation at 1 hr after ALP exposure, fol lowed by a small reduct ion in tr it iated thymidine uptake at 4 hr. No effect is observed in K562 cell cultures in morphology or NMR measurements. No new 3~p-labeled metabolites were detected in either cell line as a result of drug treatment.
Key technologies of 3D surface inspection for complex workpiece using OMP60 probe

In this paper, some key technologies of surface inspection are presented. Based on a robot manipulator, a new radius compensation of spherically tipped touch probe is first discussed, and the calibration algorithm for robot hand to eye is proposed. Different from traditional CMM based approach, the point-set registration is derived as a constrained optimization problem, then some issues concerning with the inspection path planning for complex workpiece are described, which is formulated as points distribution, stylus obstacle avoidance and path optimization problems.
Improved Preservation of Residual Beta Cell Function by Atorvastatin in Patients with Recent Onset Type 1 Diabetes and High CRP Levels (DIATOR Trial)

Background A recent randomized placebo-controlled trial of the effect of atorvastatin treatment on the progression of newly diagnosed type 1 diabetes suggested a slower decline of residual beta cell function with statin treatment. Aim of this secondary analysis was to identify patient subgroups which differ in the decline of beta cell function during treatment with atorvastatin. Methodology/Principal Findings The randomized placebo-controlled Diabetes and Atorvastatin (DIATOR) Trial included 89 patients with newly diagnosed type 1 diabetes and detectable islet autoantibodies (mean age 30 years, 40% females), in 12 centers in Germany. Patients received placebo or 80 mg/d atorvastatin for 18 months. As primary outcome stimulated serum C-peptide levels were determined 90 min after a standardized liquid mixed meal. For this secondary analysis patients were stratified by single baseline characteristics which were considered to possibly be modified by atorvastatin treatment. Subgroups defined by age, sex or by baseline metabolic parameters like body mass index (BMI), total serum cholesterol or fasting C-peptide did not differ in C-peptide outcome after atorvastatin treatment. However, the subgroup defined by high (above median) baseline C-reactive protein (CRP) concentrations exhibited higher stimulated C-peptide secretion after statin treatment (p = 0.044). Individual baseline CRP levels correlated with C-peptide outcome in the statin group (r2 = 0.3079, p<0.004). The subgroup with baseline CRP concentrations above median differed from the corresponding subgroup with lower CRP levels by higher median values of BMI, IL-6, IL-1RA, sICAM-1 and E-selectin. Conclusions/Significance Atorvastatin treatment may be effective in slowing the decline of beta cell function in a patient subgroup defined by above median levels of CRP and other inflammation associated immune mediators. Trial Registration ClinicalTrials.gov NCT00974740
Terminology Extraction and Term Ranking for Standardizing Term Banks

This paper presents how word alignment techniques could be used for building standardized term banks. It is shown that time and effort could be saved by a relatively simple evaluation metric based on frequency data from term pairs, and source and target distributions inside the alignment results. The proposed Q-value metric is shown to outperform other tested metrics such as Dice’s coefficient, and simple pair frequency.
Triphenylmethyl Derivatives Enhances the Anticancer Effect of Immunotoxins

The combined use of several drugs targeting different cellular functions is one approach to achieve tumor control in cancer. We studied the effects of Pseudomonas exotoxin A (PE)-based immunotoxins (ITs), the 9.2. 27PE and the 425.3PE, together with 2 different triphenylmethyl derivatives, triphenylmethyl phosphonates and phosphonochloridates (TPMP)-I-2 and 4BI. Combining the triphenylmethyl derivatives with ITs enhanced the cytotoxic effect of the ITs, with TPMP-I-2 in combination with the 425.3PE (targeting the epidermal growth factor receptor) being the most promising combination. The cytotoxicity involving signs of apoptosis was observed in cancer cells from different origins in vitro. It is interesting to note that treatment with IT, TPMP-I-2, or 4BI alone or in combination resulted in strongly decreased protein levels of stearoyl-CoA desaturase. Stearoyl-CoA desaturase is the rate-limiting enzyme for converting saturated fatty acids into monounsaturated fatty acids needed for membrane genesis. Furthermore, the combination of 425.3PE and TPMP-I-2 prolonged the survival time of nude rats in a simulated micrometastatic cervical cancer model. In addition, we demonstrate that a combination of the 425.3PE and 4BI was more effective in reducing tumor growth in a breast cancer model in nude mice compared with either agent alone.
Efficient MRF Deformation Model for Image Matching ( Version 1 . 50 )

We propose a novel MRF-based model for image matching. Given two images, the task is to estimate a mapping from one image to another, in order to maximize the matching quality. We consider mappings defined by discrete deformation field constrained to preserve 2-dimensional continuity. We approach the corresponding optimization problem by the TRW-S (sequential Tree-reweighted message passing) algorithm [11, 5]. Our model design allows for a considerably wider class of natural transformation and yields a compact representation of the optimization task. For this model TRW-S algorithm demonstrated nice practical performance in experiments. We also propose a concise derivation of the TRW-S algorithm as a sequential maximization of the lower bound on the energy function.
Plasma Membrane Transporters in Modern Liver Pharmacology

The liver plays a crucial role in the detoxification of drugs used in the treatment of many diseases. The liver itself is the target for drugs aimed to modify its function or to treat infections and tumours affecting this organ. Both detoxification and pharmacological processes occurring in the liver require the uptake of the drug by hepatic cells and, in some cases, the elimination into bile. These steps have been classified as detoxification phase 0 and phase III, respectively. Since most drugs cannot cross the plasma membrane by simple diffusion, the involvement of transporters is mandatory. Several members of the superfamilies of solute carriers (SLC) and ATP-binding cassette (ABC) proteins, with a minor participation of other families of transporters, account for the uptake and efflux, respectively, of endobiotic and xenobiotic compounds across the basolateral and apical membranes of hepatocytes and cholangiocytes. These transporters are also involved in the sensitivity and refractoriness to the pharmacological treatment of liver tumours. An additional interesting aspect of the role of plasma membrane transporters in liver pharmacology regards the promiscuity of many of these carriers, which accounts for a variety of drug-drug, endogenous substances-drug and food components-drug interactions with clinical relevance.
A Content Searching Scheme Using Popularity and Link Degree of Nodes in Unstructured P2P Networks with Cache Routers

This paper improves the conventional scheme of contents sharing in unstructured P2P networks, where each of the peers and content cache routers keeps contents cache as well as query transmission records, which are used to guide content searching queries and reduce the number of the queries without losing contents discovery rates. In this paper, the decision whether a content item is cached or not on the router is executed as a part of the algorithm running in the contents sharing system according to the content item's popularity and the degree of the router as a network node, in order to reduce the frequency of contents loss caused by the displacement or overwriting of caches in the routers. The efficiency of the improvement is discussed using the results of computer simulations.
Monoids, Embedding Functors and Quantum Groups*

We show th a t th e left regular representation n l of a discrete q uantum group (A , A) has the absorbing property and forms a monoid (ni,m ,fj) in th e representation category Rep(A , A). N ext we show th a t an absorbing monoid in an ab stra ct tensor ^-category C gives rise to an em bedding functor (or fiber functor) E : C ^ Vectc, and we identify conditions on th e monoid, satisfied by (nl,r h,fj), im plying th a t E is ^-preserving. As is well-known, from an em bedding functor E : C ^ Hilb the generalized T annaka theorem produces a discrete quantum group (A, A) such th a t C ~ R epƒ (A, A ). Thus, for a C*-tensor category C w ith conjugates and irreducible u n it th e following are equivalent: (1) C is equivalent to the representation category of a discrete quantum group (A, A ), (2) C adm its an absorbing monoid, (3) there exists a ^-preserving em bedding functor E : C ^ Hilb.
Comparison of the Conjugate Gradient of NAS benchmark and of the multisplitting algorithm with the Jace environment

The aim of this paper is to study the behaviors of the well known conjugate gradient (CG) algorithm and the multisplitting algorithm in a grid context. We focus on the CG implementation used in the NAS benchmark and on the multisplitting approach which produces similar results (from a numerical point of view). By grid context we mean an architecture composed of several heterogeneous clusters geographically distributed and the use of a software environment able to tackle the heterogeneity of the nodes. Under these hypothesis, we performed a set of experiments on the Grid'5000 platform using the pure Java Jace V2 environment. We show that, by drastically reducing global synchronizations, the asynchronous multi-splitting method outperforms the NAS CG implementation, with distant sites, whatever the communication protocol used.
Emotional Creativity as Predictor of Intrinsic Motivation and Academic Engagement in University Students: The Mediating Role of Positive Emotions

Objective: Emotional creativity (EC) implies experiencing a complex emotional life, which is becoming increasingly necessary in societies that demand innovation and constant changes. This research studies the relation of EC as a dispositional trait with intrinsic motivation (IM) and academic engagement (AE). Methods: A sample of 428 university Chilean students, 36.5% men and 63.5% women, with ages from 18 to 45 years-old (M = 20.37; DT = 2.71). Additionally, the mediating function of class-related positive emotions in this relation is explored. Results: The obtained data indicate that developing high levels of dispositional EC enhances the activation of positive emotions, such as gratitude, love and hope, in the classroom. Furthermore, EC predicts IM and AE of university students by the experience of positive emotions. Conclusion: These results compel us to be aware of the importance that university students can understand the complexity of the emotional processes they undergo. A greater control of these emotions would allow students to maintain higher levels of interest in their studies at the different educational stages and to avoid the risk of school failure.
The Three Waves of Party System Institutionalisation Studies: A Multi- or Uni-Dimensional Concept?:

Since Mainwaring and Scully’s resurrection of the concept in 1995, party system institutionalisation has become something of a buzzword to which many refer without a proper definition. Indeed, most scholars simply assume that its meaning is clear and unproblematic, focusing all subsequent efforts on developing operational indicators, but without really concerning themselves with its conceptual refinement. However, an in-depth literature review of all major works dealing with the concept reveals that in reality there is very little agreement on what party system institutionalisation actually is or how it should be measured. In fact, since Huntington introduced the notion of institutionalisation some 50 years ago, party system institutionalisation has been characterised as a multi-dimensional (mostly four, but also three and two) as well as a uni-dimensional (around stability) concept. Now that half a century has passed, the time has come to look back and, with the benefit of hindsight, take stock of the wa.
Practical and prospective slow light Surface Nanoscale Axial Photonics (SNAP) devices

Miniature slow light Surface Nanoscale Axial Photonics (SNAP) devices are reviewed. The fabrication precision of these devices is two orders of magnitude higher and the transmission losses are two orders of magnitude smaller than for any of the previously reported technologies for fabrication of miniature photonic circuits. In the first part of the report, a SNAP bottle resonator with a few nm high radius variation is demonstrated as the record small, slow light, and low loss 2.6 ns dispersionless delay line of 100 ps pulses. Next, a record small SNAP bottle resonator exhibiting the 20 ns/nm dispersion compensation of 100 ps pulses is demonstrated. In the second part of the report, the prospects of the SNAP technology in applications to telecommunications, optical signal processing, quantum computing, and microfluidics are discussed.
FSA-based link assignment and routing in low-earth orbit satellite networks

We propose a new framework for the link assignment (i.e., topological design) problem that arises from the use of intersatellite links (ISL's) in low-earth orbit (LEO) satellite networks. In the proposed framework, we model an LEO satellite network as a finite state automaton (FSA), where each state corresponds to an equal-length interval in the system period of the LEO satellite network. This FSA-based framework allows the link assignment problem in LEO satellite networks to be treated as a set of link assignment problems in fixed topology networks. Within this framework, we study various link assignment and routing schemes. In particular, both regular link assignment and link assignment optimized by simulated annealing are considered. For each link assignment, both static and dynamic routing schemes are considered. Our simulation results show that the optimized link assignment combined with static routing achieves the best performance in terms of both newly initiated call blocking probability and ongoing call blocking probability. The results also show that when the link assignment is the same, static routing gives better performance than dynamic routing since the latter requires a substantial amount of time to stabilize its routing table after a state transition.
Complexity aspects of multi-machine aggregations in a rough-granular computation framework

We investigate computational complexity of a task of optimizing multi-machine execution of analytical data processing operations. We concentrate on an example of aggregation queries in Infobright's database engine, which is designed using the paradigms of rough sets and granular computing. The task is to optimize decomposition of data blocks and aggregation groups among machines having access to a shared data storage. The paper includes some examples of optimization functions and constraints, as well as the proof of NP-hardness of the considered task for some of them. It can be treated as a guideline for developing scalable data processing and mining methods based on massive parallelism and approximate computing.