Miracle-dz/UniFAR-FTUs huggingface dataset:
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance

Summary Subterranean clover is an important annual forage legume, whose diploidy and inbreeding nature make it an ideal model for genomic analysis in Trifolium. We reported a draft genome assembly of the subterranean clover TSUd_r1. 1. Here we evaluate genome mapping on nanochannel arrays and generation of a transcriptome atlas across tissues to advance the assembly and gene annotation. Using a BioNano‐based assembly spanning 512 Mb (93% genome coverage), we validated the draft assembly, anchored unplaced contigs and resolved misassemblies. Multiple contigs (264) from the draft assembly coalesced into 97 super‐scaffolds (43% of genome). Sequences longer than >1 Mb increased from 40 to 189 Mb giving 1.4‐fold increase in N50 with total genome in pseudomolecules improved from 73 to 80%. The advanced assembly was re‐annotated using transcriptome atlas data to contain 31 272 protein‐coding genes capturing >96% of the gene content. Functional characterization and GO enrichment confirmed gene expression for response to water deprivation, flavonoid biosynthesis and embryo development ending in seed dormancy, reflecting adaptation to the harsh Mediterranean environment. Comparative analyses across Papilionoideae identified 24 893 Trifolium‐specific and 6325 subterranean‐clover‐specific genes that could be mined further for traits such as geocarpy and grazing tolerance. Eight key traits, including persistence, improved livestock health by isoflavonoid production in addition to important agro‐morphological traits, were fine‐mapped on the high‐density SNP linkage map anchored to the assembly. This new genomic information is crucial to identify loci governing traits allowing marker‐assisted breeding, comparative mapping and identification of tissue‐specific gene promoters for biotechnological improvement of forage legumes.
Designing Compensation for Distributed Solar Generation: Is Net Metering Ever Optimal?

Electricity customers who install solar panels often are paid the prevailing retail price for the electricity they generate. We demonstrate that this rate of compensation typically is not optimal. A payment for distributed generation (w) that is below the retail price of electricity (r) often will induce the welfare-maximizing level of distributed generation (DG) when the fixed costs of centralized electricity production and the network management costs of accommodating intermittent solar DG are large, and when centralized generation and DG produce similar (pollution) externalities. w can optimally exceed r under alternative conditions. The optimal DG compensation policy varies considerably as industry conditions change. Furthermore, a requirement to equate w and r can reduce aggregate welfare substantially and can generate pronounced distributional effects.
Implementing E-Government Strategy in Scotland: Current Situation and Emerging Issues

Using Information and Communications Technologies (ICTs) to transform public services is a central element of the current UK Governmentâ€™s strategy for modernising government. This paper explores the development of e-government by an in-depth study of the current position in the public sector in Scotland. The research involved an evaluation of the web sites of a wide range of public sector organisations, a survey of chief executives and interviews with five key stakeholders. The results of this research suggest that public sector organisations in Scotland recognise the importance of e-government but are currently at a very early stage in developing electronic services. There is a gap between the rhetoric about the potential of e-government and the reality on the ground. In particular, the public sector organisations involved in this research appear to be more sceptical about the ability of ICTs to break down barriers within and between organisations than those who advocate e-government as a solution to this problem. Issues on balancing conflicting objectives between implementing E-government strategy and other strategic initiatives will also be highlighted. The paper concludes by suggesting a number of key issues that will need to be addressed if e-government is to fulfil its potential and transform the way public sector organisations manage their activities and interact with customers and citizens.
Chemical exchange saturation transfer (CEST): What is in a name and what isn't?

Chemical exchange saturation transfer (CEST) imaging is a relatively new magnetic resonance imaging contrast approach in which exogenous or endogenous compounds containing either exchangeable protons or exchangeable molecules are selectively saturated and after transfer of this saturation, detected indirectly through the water signal with enhanced sensitivity. The focus of this review is on basic magnetic resonance principles underlying CEST and similarities to and differences with conventional magnetization transfer contrast. In CEST magnetic resonance imaging, transfer of magnetization is studied in mobile compounds instead of semisolids. Similar to magnetization transfer contrast, CEST has contributions of both chemical exchange and dipolar cross‐relaxation, but the latter can often be neglected if exchange is fast. Contrary to magnetization transfer contrast, CEST imaging requires sufficiently slow exchange on the magnetic resonance time scale to allow selective irradiation of the protons of interest. As a consequence, magnetic labeling is not limited to radio‐frequency saturation but can be expanded with slower frequency‐selective approaches such as inversion, gradient dephasing and frequency labeling. The basic theory, design criteria, and experimental issues for exchange transfer imaging are discussed. A new classification for CEST agents based on exchange type is proposed. The potential of this young field is discussed, especially with respect to in vivo application and translation to humans. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Volume Optimal Cycle: Tightest representative cycle of a generator on persistent homology

This paper shows a mathematical formalization, algorithms and computation software of volume optimal cycles, which are useful to understand geometric features shown in a persistence diagram. Volume optimal cycles give us concrete and optimal homologous structures, such as rings or cavities, on a given data. The key idea is the optimality on $(q + 1)$-chain complex for a $q$th homology generator. This optimality formalization is suitable for persistent homology. We can solve the optimization problem using linear programming. For an alpha filtration on $\mathbb{R}^n$, volume optimal cycles on an $(n-1)$-th persistence diagram is more efficiently computable using merge-tree algorithm. The merge-tree algorithm also gives us a tree structure on the diagram and the structure has richer information. The key mathematical idea is Alexander duality.
Combined colorimetric and gravimetric CMUT sensor for detection of phenylacetone

The detection of phenylacetone is of interest as it is a common precursor for the synthesis of (meth)amphetamine. Resonant gravimetric sensors can be used to detect the mass and hereby the concentration of a gas while colorimetric arrays typically have an exceptional selectivity to the target analyte if the right colorimetric dyes are chosen. We present a sensor system consisting of a Capacitive Micromachined Ultrasonic Transducer (CMUT) and a colorimetric array for detection of phenylacetone. The CMUT is used as a resonant gravimetric gas sensor where the resonance frequency shift due to mass loading of the plate. A single Local Oxidation of Silicon (LOCOS) step was used to define the cavities which were sealed with a Si3N4 plate with a thickness of 100nm, resulting in a resonance frequency of 38:8MHz and a theoretical mass sensitivity of 28:3 zg/Hz·μ2. The CMUTs were functionalized with the same dyes used to fabricate colorimetric arrays. While both the CMUTs and the colorimetric arrays showed selectivity to phenylacetone, the best selectivity was achieved by the colorimetric array. Furthermore, the mass of the phenylacetone was found as a function of time. Thus, the combination of the colorimetric array and the CMUT results in a good selectivity and a quantitative value for the mass.
Biomechanical Response of Stented Carotid Arteries to Swallowing and Neck Motion

Purpose: To examine the effects of swallowing and side-to-side head turning on stents in the internal carotid artery. Methods: Seven patients (4 men; mean age 76.9 years) who underwent carotid artery stenting for the treatment of atherosclerotic cervical carotid artery disease were examined with cine fluoroscopy. Geometric processing techniques were used to quantify carotid stent deformations due to head turning and swallowing forces. The variables measured included radial, axial, and crush deformations, as well as radii of stent curvatures during tested maneuvers. Results: Radial deformations of the stented vessels were significantly less than axial and crush deformations, ranging from −10.2% to 15.5%. Axial deformations in response to both swallowing and head turning were positive (average 4.5%, range −14.5% to 14.1%), indicating a general lengthening of the stented vessel due to biomechanical motions. Crush strains exhibited the largest range of all of the deformation modes during both swallowing and head turning. Strain values ranged from −18.7% to 25.9% in the anteroposterior direction and from −25.6% to 21.9% in the lateral direction. Head turning produced fairly symmetrical crushing of the stent. Conversely, swallowing resulted in a preferential medial crush of the stented artery due to contraction of the pharyngeal constrictor muscles. Curvature measurements revealed a tightest radius of curvature of ∼1.5 cm during ipsilateral head turning, with average values during both swallowing and head turning of ∼10 cm. Conclusion: In general, head turning toward the stented artery produced greater deformation in the vessels than swallowing. Since patients are expected to undergo far more swallowing cycles than head turns, however, the accumulated deformations from swallowing may be more significant and should be considered in the design of fatigue resistant stents for carotid arteries.
Multimode Impedance Representation of Scattering, Absorption and Extinction Cross-Sectional Areas for Plasmonic Nanoparticles

In plasmonic nanoparticles, scattering and absorption phenomena are exploited to functionalize them for various applications. Recent research in plasmonic nanoparticles has extended the classic circuit concepts to the optical domain, but under the assumption of only accounting for the fundamental mode (dipole mode) with restrictions placed on the wavelength and size of the nanoparticle. In this paper, we propose an extended approach to the impedance representation of metallic nanoparticles and develop a solution consisting of circuit elements representing their behaviour without any constraints on wavelength, size and material properties. This model offers an intuitive understanding of the qualitative behaviour of a metallic nanoparticle, and rigorously develops an all-mode (i.e., TEm,n and TMm,n mode with m = 1 and n varying from 1 → ∞) exact impedance model. The proposed model originates from the rigorous Mie solution. Quantities such as scattering, extinction and absorption cross-sectional areas are derived using voltages, currents and circuit elements and their equivalence is compared with well-known field solutions and full-wave simulations.
Microwaving Biological Cells: Intracellular Analysis with Microwave Dielectric Spectroscopy

Probing biological materials with electromagnetic waves, which has been investigated for decades [1]-[6], involves characterizing the sample with its dielectric properties that are frequency dependent. Dielectric spectroscopy is performed by placing a high-frequency circuit close to the biological species under study. Passing through the biological medium, the electric properties of the biological elements modify the electromagnetic field. The complex permittivity of the medium under test may, therefore, be extracted and provides a dielectric signature of the sample.
MicroRNAs in pancreas development

The development of the pancreas is a tightly regulated process involving extensive morphogenesis, proliferation and differentiation of the epithelium. The finely orchestrated control of gene expression plays a key role in this equilibrium by coordinating the expression of selected gene products at specific moments and in precise locations. MicroRNAs (miRNAs) are small non‐coding RNAs that function in general as negative regulators of gene transcripts by interacting with the three prime untranslated regions (3′UTR) of target mRNAs. MiRNAs modulate the expression of numerous target genes that are involved in a variety of cellular systems. Hence the homeostatic control of miRNA biosynthesis and activity is important for the fine‐tuning of many physiological processes such as cell differentiation, cell proliferation and organ development. In the present review, we will focus on the implication of these miRNAs on the development of the pancreas and more specifically on β‐cells.
Trading Ancillary Services for Frequency Regulation in Competitive Electricity Markets

With the introduction of the electricity market the system operators as well as the market operators are facing more and more unpredictable challenges. As a completive for the Day Ahead Market, the Balancing Market is meant to perform a more market oriented frequency regulation by using a merit order for real-time dispatch of the generators, particularly for the secondary regulation as well as for the tertiary regulation. Due to the social implications of the electricity market, the market mechanism should be designed so that to avoid market speculations of some participants and to obtain the smallest price possible of energy and ancillary services while maintaining a necessary active power reserve to ensure a certain level of the network security. Based on the actual expected changes in the generation sector of the Romanian power systems as well as the implementation of a possible regional market, the authors will propose some suggestions for the balancing market mechanism to maximize the reserves available for frequency regulation and to minimize the cost of the regulation energy. A comparison between actual implemented mechanism and the proposed mechanism will be performed.
Subchondral cystlike lesions develop longitudinally in areas of bone marrow edema-like lesions in patients with or at risk for knee osteoarthritis: detection with MR imaging--the MOST study.

PURPOSE To assess the association of prevalent bone marrow edema-like lesions (BMLs) and full-thickness cartilage loss with incident subchondral cyst-like lesions (SCs) in the knee to evaluate the bone contusion versus synovial fluid intrusion theories of SC formation. MATERIALS AND METHODS The Multicenter Osteoarthritis study is a longitudinal study of individuals who have or are at risk for knee osteoarthritis. The HIPAA-compliant protocol was approved by the institutional review boards of all participating centers, and written informed consent was obtained from all participants. Magnetic resonance images were acquired at baseline and 30-month follow-up and read semiquantitatively by using the Whole-Organ Magnetic Resonance Imaging Score system. The tibiofemoral and patellofemoral joints were subdivided into 14 subregions. BMLs and SCs were scored from 0 to 3. Cartilage morphology was scored from 0 to 6. The association of prevalent BMLs and full-thickness cartilage loss with incident SCs in the same subregion was assessed by using logistic regression with mutual adjustment for both predictors. RESULTS A total of 1283 knees were included. After adjustment for full-thickness cartilage loss, prevalent BMLs showed a strong and significant association with incident SCs in the same subregion, with an odds ratio of 12.9 (95% confidence interval [CI]: 8.9, 18.6). After adjustment for BMLs, prevalent full-thickness cartilage loss showed a significant but much less important association with incident SCs in the same subregion (odds ratio, 1.4; 95% CI: 1.0, 2.0). There was no apparent relationship between severity of full-thickness cartilage loss at baseline and incident SCs. CONCLUSION Prevalent BMLs strongly predict incident SCs in the same subregion, even after adjustment for full-thickness cartilage loss, which supports the bone contusion theory of SC formation.
Parent-reported competence and emotional and behavioral problems in Finnish adolescents

This study was part of an 8-year follow-up study of the Epidemiological Multicenter Child Psychiatric Study in Finland. The Child Behavior Checklists (CBCLs) were analyzed for 598 15- to 16-year-old adolescents living in the southwestern area of Finland in 1997. The internal consistency of the CBCL syndrome scales was adequate (the alpha coefficient ranged from 0.66 to 0.89). The CBCL scores differentiated between non-referred adolescents and adolescents who had been referred to the mental health service or had severe problems according to the parents. Boys had more externalizing problems than girls in the maladjustment group. Girls had more somatic symptoms in the maladjustment group than boys.
Subsequent reproduction and calf performance of nonpregnant cows compared with pregnant cows and replacement females.

This study was conducted with Angus, Polled Hereford and Santa Gertrudis straightbred and crossbred cows. The subsequent cow breeding and calf performance of cows that were nonpregnant (NP) were compared with cows that were pregnant (PG) at the time calves were weaned. All NP cows had a calf the year previous to their being nonpregnant. They were diagnosed as physically sound with no detection (by rectal palpation) of an abnormal reproductive tract. The NP and PG cows were aged 4 to 9 yr. Also, the NP cows were compared with replacement females exposed to calve first as 2- and 3-yr-olds (H2 and H3, respectively), and with cows exposed for second calving as 3-yr-olds (C2). Cows were assigned within breed composition and age to sire breeding groups on pasture. Subsequent calving and weaning rates were similar for NP, PG and H2 cows, similar for H3 and H2 cows and lowest (P less than .05) for C2 cows. Calves from NP and H3 cows were born earlier (P less than .05) in the calving period than calves from PG and H2 cows, whereas calves from C2 cows were born later (P less than .05) than those from NP, PG and H3 cows. Calving difficulty was similar for NP, PG and C2 and greatest (P less than .05) for H2 cows. Calf 205-d weights were highest (P less than .05) for NP, similar for PG and H3 and lowest (P less than .05) for C2 and H2 cows. Calf weaning weight per cow exposed for breeding from NP cows was 13.8, 32.3, 55.2 and 1.0 kg higher than from PG, H2, C2 and H3 cows, respectively. Causes for cows being nonpregnant were reported. Also, calving patterns during 6 consecutive calving periods (6 yr) were evaluated.
Efficacy of Acute Caffeine Ingestion for Short-term High-Intensity Exercise Performance: A Systematic Review

Astorino, TA and Roberson, DW. Efficacy of acute caffeine ingestion for short-term high-intensity exercise performance: A systematic review. J Strength Cond Res 24(1): 257-265, 2010-Caffeine is the most widely used drug in the world, commonly ingested in coffee, tea, soda, and energy drinks. Its ability to enhance muscular work has been apparent since the early 1900s. Caffeine typically increases endurance performance; however, efficacy of caffeine ingestion for short-term high-intensity exercise is equivocal, which may be explained by discrepancies in exercise protocols, dosing, and subjects' training status and habitual caffeine intake found across studies. The primary aim of this review is to critically examine studies that have tested caffeine's ability to augment performance during exercise dependent on nonoxidative metabolism such as sprinting, team sports, and resistance training. A review of the literature revealed 29 studies that measured alterations in short-term performance after caffeine ingestion. Each study was critically analyzed using the Physiotherapy Evidence Database (PEDro) scale. The mean PEDro score was 7.76 ± 0.87. Eleven of 17 studies revealed significant improvements in team sports exercise and power-based sports with caffeine ingestion, yet these effects were more common in elite athletes who do not regularly ingest caffeine. Six of 11 studies revealed significant benefits of caffeine for resistance training. Some studies show decreased performance with caffeine ingestion when repeated bouts are completed. The exact mechanism explaining the ergogenic effect of caffeine for short-term exercise is unknown.
Dose-related effects of venlafaxine on pCREB and brain-derived neurotrophic factor (BDNF) in the hippocampus of the rat by chronic unpredictable stress

Background: The molecular pathogenesis of depression and psychopharmacology of antidepressants remain elusive. Recent hypotheses suggest that changes in neurogenesis and plasticity may underlie the aetiology of depression. The hippocampus is affected by depression and shows neuronal remodelling during adulthood. Objective: The present study on the adult rat hippocampus, was to evaluate the dose-related effects of chronic venlafaxine on the expression of brain-derived neurotrophic factor (BDNF) and phosphorylated cyclic-AMP response element binding protein (pCREB). Methods: Sprague-Dawley rats were exposed to a variety of chronic unpredictable stressors (CUSs) to establish a depression model. Rats were treated for either 14 or 28 days with venlafaxine (5 and 10 mg/kg, respectively). The hippocampal expression of pCREB and BDNF mRNA and protein was assessed by using immunohistochemistry, western blotting and reverse transcription polymerase chain reaction (RT-PCR). Results: Rats subjected to CUS procedure consumed less sucrose solution compared with non-stressed rats. The CUS influenced exploratory activity resulting in a reduction of the motility counts. Chronic low dose (5 mg/kg, 14 and 28 days), but not high dose (10 mg/kg, 14 and 28 days) of venlafaxine treatment increased the expression of pCREB and BDNF mRNA and protein in the CUS rat hippocampus. Conclusion: Neuronal plasticity-associated proteins such as pCREB and BDNF play an important role both in stress-related depression and in antidepressant effect.