All the colours of the rainbow.

Our perception of colour has always been a source of fascination, so it's little wonder that studies of the phenomenon date back hundreds of years. What, though, can modern scientists learn from medieval literature — and how do we go about it

All the colours of the rainbow

Our perception of colour has always been a source of fascination, so it's little wonder that studies of the phenomenon date back hundreds of years. What, though, can modern scientists learn from medieval literature — and how do we go about it

Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma

\ua9 2023 by the authors.Background: Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural variants, which has not previously been tested in neuroblastoma. We used OGM to identify copy number and structural variants (SVs) in neuroblastoma which may have been missed by standard cytogenetic techniques. Methods: Five neuroblastoma cell lines (SH-SY5Y, NBLW, GI-ME-N, NB1691 and SK-N-BE2(C)) and two neuroblastoma tumours were analysed using OGM with the Bionano Saphyr\uae instrument. The results were analysed using Bionano Access software and compared to previous genetic analyses including G-band karyotyping, FISH (fluorescent in situ hybridisation), single-nucleotide polymorphism (SNP) array and RNA fusion panels for cell lines, and SNP arrays and whole genome sequencing (WGS) for tumours. Results: OGM detected copy number abnormalities found using previous methods and provided estimates for absolute copy numbers of amplified genes. OGM identified novel SVs, including fusion genes in two cell lines of potential clinical significance. Conclusions: OGM can reliably detect clinically significant structural and copy number variations in a single test. OGM may prove to be more time- and cost-effective than current standard cytogenetic techniques for neuroblastoma

The roles of apex dipoles and field penetration in the physics of charged, field emitting, single-walled carbon nanotubes

A 1 μm long, field emitting, (5, 5) single-walled carbon nanotube (SWCNT) closed with a fullerene cap, and a similar open nanotube with hydrogen-atom termination, have been simulated using the modified neglect of diatomic overlap quantum-mechanical method. Both contain about 80 000 atoms. It is found that field penetration and band bending, and various forms of chemically and electrically induced apex dipole play roles. Field penetration may help explain electroluminescence associated with field emitting CNTs. Charge-density oscillations, induced by the hydrogen adsorption, are also found. Many of the effects can be related to known effects that occur with metallic or semiconductor field emitters; this helps both to explain the effects and to unify our knowledge about FE emitters. However, it is currently unclear how best to treat correlation-and-exchange effects when defining the CNT emission barrier. A new form of definition for the field enhancement factor (FEF) is used. Predicted FEF values for these SWCNTs are significantly less than values predicted by simple classical formulae. The FEF for the closed SWCNT decreases with applied field; the FEF for the H-terminated open SWCNT is less than the FEF for the closed SWCNT but increases with applied field. Physical explanations for this behavior are proposed but the concept of FEF is clearly problematical for CNTs. Curved Fowler-Nordheim plots are predicted. Overall, the predicted field emission performance of the H-terminated open SWCNT is slightly better than that of the closed SWCNT, essentially because a C-H dipole is formed that reduces the height of the tunneling barrier. In general, the physics of a charged SWCNT seems much more complex than hitherto realized. © 2008 American Institute of Physics.published_or_final_versio

Three geographically separate domestications of Asian rice

Domesticated rice (Oryza sativa L.) accompanied the dawn of Asian civilization(1) and has become one of world's staple crops. From archaeological and genetic evidence various contradictory scenarios for the origin of different varieties of cultivated rice have been proposed, the most recent based on a single domestication(2,3). By examining the footprints of selection in the genomes of different cultivated rice types, we show that there were three independent domestications in different parts of Asia. We identify wild populations in southern China and the Yangtze valley as the source of the japonica gene pool, and populations in Indochina and the Brahmaputra valley as the source of the indica gene pool. We reveal a hitherto unrecognized origin for the aus variety in central India or Bangladesh. We also conclude that aromatic rice is a result of a hybridization between japonica and aus, and that the tropical and temperate versions of japonica are later adaptations of one crop. Our conclusions are in accord with archaeological evidence that suggests widespread origins of rice cultivation(1,4). We therefore anticipate that our results will stimulate a more productive collaboration between genetic and archaeological studies of rice domestication, and guide utilization of genetic resources in breeding programmes aimed at crop improvement.European Research Council [339941]info:eu-repo/semantics/publishedVersio

Bone mineral content after renal transplantation

Forearm bone mineral content (BMC), as evaluated by photonabsorption densitometry, was measured in 28 cadaver kidney donor recipients who entered the study 8 weeks postoperatively and were followed up for 18 months. BMC decreased signifiantly (p<0.05) but marginally in placebo-treated patients (n=14) (initial BMC 1.09±0.25 g/cm; final BMC 1.05±0.24). Fourteen patients were prophylactically given 1,25(OH)2vitamin D3 in a dose which avoided hypercalcemia and hypercalciuria (sim0.25 µg/day); under 1,25(OH)2 vitamin D3 prophylaxis a significant decrease of forearm BMC was observed no longer (initial BMC 0.94±0.21 g/cm; final BMC 0.95±0.21), but the difference between placebo and 1,25(OH)2 vitamin D3 narrowly missed statistical significance (p=0.066). It is concluded that the decrease of forearm BMC is negligible in transplant recipients with low steroid regimens. The data suggest a trend for prophylaxis with 1,25(OH)2 vitamin D3 to slightly ameliorate forearm (cortical) BMC loss

Wavelength-scale stationary-wave integrated Fourier-transform spectrometry

Spectrometry is a general physical-analysis approach for investigating light-matter interactions. However, the complex designs of existing spectrometers render them resistant to simplification and miniaturization, both of which are vital for applications in micro- and nanotechnology and which are now undergoing intensive research. Stationary-wave integrated Fourier-transform spectrometry (SWIFTS)-an approach based on direct intensity detection of a standing wave resulting from either reflection (as in the principle of colour photography by Gabriel Lippmann) or counterpropagative interference phenomenon-is expected to be able to overcome this drawback. Here, we present a SWIFTS-based spectrometer relying on an original optical near-field detection method in which optical nanoprobes are used to sample directly the evanescent standing wave in the waveguide. Combined with integrated optics, we report a way of reducing the volume of the spectrometer to a few hundreds of cubic wavelengths. This is the first attempt, using SWIFTS, to produce a very small integrated one-dimensional spectrometer suitable for applications where microspectrometers are essential

Clinical relevance of biomarkers of oxidative stress

SIGNIFICANCE Oxidative stress is considered to be an important component of various diseases. A vast number of methods have been developed and used in virtually all diseases to measure the extent and nature of oxidative stress, ranging from oxidation of DNA to proteins, lipids, and free amino acids. Recent Advances: An increased understanding of the biology behind diseases and redox biology has led to more specific and sensitive tools to measure oxidative stress markers, which are very diverse and sometimes very low in abundance. CRITICAL ISSUES The literature is very heterogeneous. It is often difficult to draw general conclusions on the significance of oxidative stress biomarkers, as only in a limited proportion of diseases have a range of different biomarkers been used, and different biomarkers have been used to study different diseases. In addition, biomarkers are often measured using nonspecific methods, while specific methodologies are often too sophisticated or laborious for routine clinical use. FUTURE DIRECTIONS Several markers of oxidative stress still represent a viable biomarker opportunity for clinical use. However, positive findings with currently used biomarkers still need to be validated in larger sample sizes and compared with current clinical standards to establish them as clinical diagnostics. It is important to realize that oxidative stress is a nuanced phenomenon that is difficult to characterize, and one biomarker is not necessarily better than others. The vast diversity in oxidative stress between diseases and conditions has to be taken into account when selecting the most appropriate biomarker. Antioxid. Redox Signal. 00, 000-000

Anisotropic interactions of a single spin and dark-spin spectroscopy in diamond

The nitrogen-vacancy (N-V) center in diamond is a promising atomic-scale system for solid-state quantum information processing. Its spin-dependent photoluminescence has enabled sensitive measurements on single N-V centers, such as: electron spin resonance, Rabi oscillations, single-shot spin readout and two-qubit operations with a nearby 13C nuclear spin. Furthermore, room temperature spin coherence times as long as 58 microseconds have been reported for N-V center ensembles. Here, we have developed an angle-resolved magneto-photoluminescence microscopy apparatus to investigate the anisotropic electron spin interactions of single N-V centers at room temperature. We observe negative peaks in the photoluminescence as a function of both magnetic field magnitude and angle that are explained by coherent spin precession and anisotropic relaxation at spin level anti-crossings. In addition, precise field alignment unmasks the resonant coupling to neighboring dark nitrogen spins that are not otherwise detected by photoluminescence. The latter results demonstrate a means of investigating small numbers of dark spins via a single bright spin under ambient conditions.Comment: 13 pages, 4 figure

Filter-based stochastic algorithm for global optimization

We propose the general Filter-based Stochastic Algorithm (FbSA) for the global optimization of nonconvex and nonsmooth constrained problems. Under certain conditions on the probability distributions that generate the sample points, almost sure convergence is proved. In order to optimize problems with computationally expensive black-box objective functions, we develop the FbSA-RBF algorithm based on the general FbSA and assisted by Radial Basis Function (RBF) surrogate models to approximate the objective function. At each iteration, the resulting algorithm constructs/updates a surrogate model of the objective function and generates trial points using a dynamic coordinate search strategy similar to the one used in the Dynamically Dimensioned Search method. To identify a promising best trial point, a non-dominance concept based on the values of the surrogate model and the constraint violation at the trial points is used. Theoretical results concerning the sufficient conditions for the almost surely convergence of the algorithm are presented. Preliminary numerical experiments show that the FbSA-RBF is competitive when compared with other known methods in the literature.The authors are grateful to the anonymous referees for their fruitful comments and suggestions.The first and second authors were partially supported by Brazilian Funds through CAPES andCNPq by Grants PDSE 99999.009400/2014-01 and 309303/2017-6. The research of the thirdand fourth authors were partially financed by Portuguese Funds through FCT (Fundação para Ciência e Tecnologia) within the Projects UIDB/00013/2020 and UIDP/00013/2020 of CMAT-UM and UIDB/00319/2020