Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing.

Thousands of prolonged sequences of human ultra-conserved non-coding elements (UCNEs) share only one common feature: peculiarities in the unique composition of their dinucleotides. Here we investigate whether the numerous weak signals emanating from these dinucleotide arrangements can be used for computational identification of UCNEs within the human genome. For this purpose, we analyzed 4272 UCNE sequences, encompassing 1 393 448 nucleotides, alongside equally sized control samples of randomly selected human genomic sequences. Our research identified nine different features of dinucleotide arrangements that enable differentiation of UCNEs from the rest of the genome. We employed these nine features, implementing three Machine Learning techniques - Support Vector Machine, Random Forest, and Artificial Neural Networks - to classify UCNEs, achieving an accuracy rate of 82-84%, with specific conditions allowing for over 90% accuracy. Notably, the strongest feature for UCNE identification was the frequency ratio between GpC dinucleotides and the sum of GpG and CpC dinucleotides. Additionally, we investigated the entire pool of 31 046 SNPs located within UCNEs for their representation in the ClinVar database, which catalogs human SNPs with known phenotypic effects. The presence of UCNE-associated SNPs in ClinVar aligns with the expectation of a random distribution, emphasizing the enigmatic nature of UCNE phenotypic manifestation.

Non-thermal emission in gap-mode plasmon photoluminescence.

Photoluminescence from spatially inhomogeneous plasmonic nanostructures exhibits fascinating wavelength-dependent nonlinear behaviors due to the intraband recombination of hot electrons excited into the conduction band of the metal. The properties of the excited carrier distribution and the role of localized plasmonic modes are subjects of debate. In this work, we use plasmonic gap-mode resonators with precise nanometer-scale confinement to show that the nonlinear photoluminescence behavior can become dominated by non-thermal contributions produced by the excited carrier population that strongly deviates from the Fermi-Dirac distribution due to the confinement-induced large-momentum free carrier absorption beyond the dipole approximation. These findings open new pathways for controllable light conversion using nonequilibrium electron states at the nanoscale.

Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome.

Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.

Safety and efficacy of direct percutaneous endoscopic jejunostomy placement in patients with previous upper gastrointestinal resection: A retrospective cohort study.

BACKGROUND: Percutaneous jejunal enteral access can be obtained with percutaneous endoscopic gastric jejunostomy (PEGJ) and direct percutaneous endoscopic jejunostomy (DPEJ) tubes. PEGJ may not be feasible in patients with previous gastric resection (PGR) and DPEJ may be the only option. Our aim is to determine if DPEJ tubes can be placed successfully in patients with history of gastrointestinal (GI) surgery and if success rates are comparable to DPEJ or PEGJ in those without prior GI surgery. METHODS: We reviewed all tube placements performed from 2010 to present. Procedures were performed using a pediatric colonoscope. Previous upper GI surgery was defined as PGR or esophagectomy with gastric pull-up. Adverse events (AEs) were graded per American Society for Gastrointestinal Endoscopy criteria. Mild events included unplanned medical consultation or hospitalization <3 days, and moderate events included repeat endoscopy without surgical intervention. RESULTS: Successful placement rates were high regardless of GI surgical history. Patients receiving a DPEJ with a history of GI surgery were significantly less likely to experience an AE compared with those receiving DPEJ with no history and compared with PEGJ patients with or without a history. CONCLUSIONS: DPEJ placement in patients with previous upper GI surgery has very high success rate. It is associated with lower AE rates than patients receiving DPEJ without previous gastric surgery, or PEGJ regardless of previous gastric surgery. Patients with a history of upper GI surgery requiring enteral access may benefit from DPEJ over PEGJ placement considering its very high success rate and lower incidence of AEs.

Unique presentation of retroperitoneal malignant perivascular epithelioid cell tumor (PEComa) in a young male.

Perivascular Epithelioid Cell tumors (PEComas) are rare mesenchymal tumors composed of epithelioid and spindle cells that can be found almost anywhere in the body with predominance for abdominopelvic locations. They are usually diagnosed in middle-aged females and are associated with tuberous sclerosis complex. This report describes an unusual presentation of a malignant retroperitoneal PEComa in an otherwise healthy, young male. Treatment included radical nephrectomy and adrenalectomy followed by medical oncology evaluation.

Identification and classification of interstitial cells in the mouse renal pelvis.

KEY POINTS: Platelet-derived growth factor receptor-α (PDGFRα) is a novel biomarker along with smooth myosin heavy chain for the pacemaker cells (previously termed 'atypical' smooth muscle cells) in the murine and cynomolgus monkey pelvis-kidney junction. PDGFRα+ cells present in adventitial and urothelial layers of murine renal pelvis do not express smooth muscle myosin heavy chain (smMHC) but are in close apposition to nerve fibres. Most c-Kit+ cells in the renal pelvis are mast cells. Mast cells (CD117+ /CD45+ ) are more abundant in the proximal renal pelvis and pelvis-kidney junction regions whereas c-Kit+ interstitial cells (CD117+ /CD45- ) are found predominantly in the distal renal pelvis and ureteropelvic junction. PDGFRα+ cells are distinct from c-Kit+ interstitial cells. A subset of PDGFRα+ cells express the Ca2+ -activated Cl- channel, anoctamin-1, across the entire renal pelvis. Spontaneous Ca2+ transients were observed in c-Kit+ interstitial cells, smMHC+ PDGFRα cells and smMHC- PDGFRα cells using mice expressing genetically encoded Ca2+ sensors. ABSTRACT: Rhythmic contractions of the renal pelvis transport urine from the kidneys into the ureter. Specialized pacemaker cells, termed atypical smooth muscle cells (ASMCs), are thought to drive the peristaltic contractions of typical smooth muscle cells (TSMCs) in the renal pelvis. Interstitial cells (ICs) in close proximity to ASMCs and TSMCs have been described, but the role of these cells is poorly understood. The presence and distributions of platelet-derived growth factor receptor-α+ (PDGFRα+ ) ICs in the pelvis-kidney junction (PKJ) and distal renal pelvis were evaluated. We found PDGFRα+ ICs in the adventitial layers of the pelvis, the muscle layer of the PKJ and the adventitia of the distal pelvis. PDGFRα+ ICs were distinct from c-Kit+ ICs in the renal pelvis. c-Kit+ ICs are a minor population of ICs in murine renal pelvis. The majority of c-Kit+ cells were mast cells. PDGFRα+ cells in the PKJ co-expressed smooth muscle myosin heavy chain (smMHC) and several other smooth muscle gene transcripts, indicating these cells are ASMCs, and PDGFRα is a novel biomarker for ASMCs. PDGFRα+ cells also express Ano1, which encodes a Ca2+ -activated Cl- conductance that serves as a primary pacemaker conductance in ICs of the GI tract. Spontaneous Ca2+ transients were observed in c-Kit+ ICs, smMHC+ PDGFRα cells and smMHC- PDGFRα cells using genetically encoded Ca2+ sensors. A reporter strain of mice with enhanced green fluorescent protein driven by the endogenous promotor for Pdgfra was shown to be a powerful new tool for isolating and characterizing the phenotype and functions of these cells in the renal pelvis.

Excitation and Amplification of Spin Waves by Spin-Orbit Torque.

The emerging field of nanomagnonics utilizes high-frequency waves of magnetization-spin waves-for the transmission and processing of information on the nanoscale. The advent of spin-transfer torque has spurred significant advances in nanomagnonics, by enabling highly efficient local spin wave generation in magnonic nanodevices. Furthermore, the recent emergence of spin-orbitronics, which utilizes spin-orbit interaction as the source of spin torque, has provided a unique ability to exert spin torque over spatially extended areas of magnonic structures, enabling enhanced spin wave transmission. Here, it is experimentally demonstrated that these advances can be efficiently combined. The same spin-orbit torque mechanism is utilized for the generation of propagating spin waves, and for the long-range enhancement of their propagation, in a single integrated nanomagnonic device. The demonstrated system exhibits a controllable directional asymmetry of spin wave emission, which is highly beneficial for applications in nonreciprocal magnonic logic and neuromorphic computing.

Evidence for Dyakonov-Perel-like Spin Relaxation in Pt.

We utilize nanoscale spin valves with Pt spacer layers to characterize spin relaxation in Pt. Analysis of the spin lifetime indicates that Elliott-Yafet spin scattering is dominant at room temperature, but an unexpected intrinsic Dyakonov-Perel-like spin relaxation becomes dominant at cryogenic temperatures. We also observe suppression of spin relaxation in a Pt layer interfaced with a ferromagnet, likely caused by the competition between the effective exchange and spin-orbit fields.

Anti-reflection coating design for metallic terahertz meta-materials.

We demonstrate a silicon-based, single-layer anti-reflection coating that suppresses the reflectivity of metals at near-infrared frequencies, enabling optical probing of nano-scale structures embedded in highly reflective surroundings. Our design does not affect the interaction of terahertz radiation with metallic structures that can be used to achieve terahertz near-field enhancement. We have verified the functionality of the design by calculating and measuring the reflectivity of both infrared and terahertz radiation from a silicon/gold double layer as a function of the silicon thickness. We have also fabricated the unit cell of a terahertz meta-material, a dipole antenna comprising two 20-nm thick extended gold plates separated by a 2 µm gap, where the terahertz field is locally enhanced. We used the time-domain finite element method to demonstrate that such near-field enhancement is preserved in the presence of the anti-reflection coating. Finally, we performed magneto-optical Kerr effect measurements on a single 3-nm thick, 1-µm wide magnetic wire placed in the gap of such a dipole antenna. The wire only occupies 2% of the area probed by the laser beam, but its magneto-optical response can be clearly detected. Our design paves the way for ultrafast time-resolved studies, using table-top femtosecond near-infrared lasers, of dynamics in nano-structures driven by strong terahertz radiation.

Highly curved image sensors: a practical approach for improved optical performance.

The significant optical and size benefits of using a curved focal surface for imaging systems have been well studied yet never brought to market for lack of a high-quality, mass-producible, curved image sensor. In this work we demonstrate that commercial silicon CMOS image sensors can be thinned and formed into accurate, highly curved optical surfaces with undiminished functionality. Our key development is a pneumatic forming process that avoids rigid mechanical constraints and suppresses wrinkling instabilities. A combination of forming-mold design, pressure membrane elastic properties, and controlled friction forces enables us to gradually contact the die at the corners and smoothly press the sensor into a spherical shape. Allowing the die to slide into the concave target shape enables a threefold increase in the spherical curvature over prior approaches having mechanical constraints that resist deformation, and create a high-stress, stretch-dominated state. Our process creates a bridge between the high precision and low-cost but planar CMOS process, and ideal non-planar component shapes such as spherical imagers for improved optical systems. We demonstrate these curved sensors in prototype cameras with custom lenses, measuring exceptional resolution of 3220 line-widths per picture height at an aperture of f/1.2 and nearly 100% relative illumination across the field. Though we use a 1/2.3" format image sensor in this report, we also show this process is generally compatible with many state of the art imaging sensor formats. By example, we report photogrammetry test data for an APS-C sized silicon die formed to a 30° subtended spherical angle. These gains in sharpness and relative illumination enable a new generation of ultra-high performance, manufacturable, digital imaging systems for scientific, industrial, and artistic use.

Spin Transfer due to Quantum Magnetization Fluctuations.

We utilize a nanoscale magnetic spin-valve structure to demonstrate that current-induced magnetization fluctuations at cryogenic temperatures result predominantly from the quantum fluctuations enhanced by the spin transfer effect. The demonstrated spin transfer due to quantum magnetization fluctuations is distinguished from the previously established current-induced effects by a nonsmooth piecewise-linear dependence of the fluctuation intensity on current. It can be driven not only by the directional flows of spin-polarized electrons, but also by their thermal motion and by scattering of unpolarized electrons. This effect is expected to remain non-negligible even at room temperature, and entails a ubiquitous inelastic contribution to spin-polarizing properties of magnetic interfaces.

Radiographic Comparison of Anterior Acetabular Rim Morphology Between Pincer Femoroacetabular Impingement and Control.

PURPOSE: To define and compare 3 new parameters (anterior rim angle [ARA], anterior wall angle [AWA], and anterior margin ratio [AMR]), in addition to the lateral center-edge angle of Wiberg and the Tönnis angle, for measuring pincer-type femoroacetabular impingement (FAI) in an asymptomatic versus symptomatic FAI population. METHODS: We reviewed anteroposterior pelvis radiographs of patients verified to have no hip complaints between December 2009 and December 2011. We also reviewed anteroposterior pelvis radiographs of patients who underwent a rim-trimming procedure for pincer FAI between December 2010 and December 2011. Patients aged older than 65 years or younger than 18 years were excluded. Radiographs with a Tönnis grade of 2 or greater were also excluded. For the group of patients with symptomatic hip impingement, radiographs that did not have a crossover sign were excluded. The 2 cohorts were matched for age, sex, and body mass index. Measurements included the Tönnis angle, lateral center-edge angle of Wiberg, ARA, AWA, and AMR. These measurements were compared between the groups. RESULTS: Seventy-two asymptomatic hips were measured. There were 44 female patients (61%) and 28 male patients (39%), aged 25 to 51 years, in the asymptomatic group. The mean ARA was 88.91° ± 8.06°, the mean AWA was 34.89° ± 8.09°, and the mean AMR was 0.49 ± 0.15. Seventy-two symptomatic hips were measured. There were 40 female patients (56%) and 32 male patients (44%), aged 27 to 58 years, in the symptomatic group. The mean ARA was 82.98° ± 10.82°, the mean AWA was 39.11° ± 9.00°, and the mean AMR was 0.56 ± 0.14. The mean difference in the ARA between asymptomatic patients and symptomatic patients was 5.92° (P = .0001). The mean difference in the AWA was 4.22° (P = .0019). The mean difference in the AMR was 0.07 (P = .0039). CONCLUSIONS: Our study provides information on several measurements within an asymptomatic cohort and a symptomatic cohort. Although we found statistically significant differences between the 2 populations, the clinical significance remains unknown. We recommend using this asymptomatic population as a guideline for limits on resection of the anterior acetabular rim. LEVEL OF EVIDENCE: Level III, retrospective comparative study.