Miracle-dz/UniFAR-FTUs huggingface dataset:
Dosimetric Evaluation of a Simple Planning Technique for Improving Intensity-Modulated Radiotherapy for Nasopharyngeal Cancer

Purpose To evaluate the dosimetric outcomes of a simple planning technique for improving intensity-modulated radiotherapy (IMRT) for nasopharyngeal cancer (NPC). Methods For 39 NPC cases, generally acceptable original plans were generated and were improved by the two planning techniques, respectively: (1) a basal-dose-compensation (BDC) technique, in which the treatment plans were re-optimized based on the original plans; (2) a local-dose-control (LDC) technique, in which the original plans were re-optimized with constraints for hot and cold spots. The BDC, original, and LDC plans were then compared regarding homogeneity index (HI) and conformity index (CI) of planning target volumes (PTVs), organ-at-risk (OAR) sparing and monitor units (MUs) per fraction. The whole planning times were also compared between the BDC and LDC plans. Results The BDC plans had superior HIs / CIs, by 13-24% / 3-243%, respectively, over the original plans. Compared to the LDC plans, the BDC plans provided better HIs only for PTVnx (the PTV of nasopharyngeal primary tumor) by 11% and better CIs for all PTVs by 2-134%. The BDC technique spared most OARs, by 1-9%. The average MUs of the BDC, original, and LDC plans were 2149, 2068 and 2179, respectively. The average whole planning times were 48 and 69 minutes for the BDC and LDC plans, respectively. Conclusions For the IMRT of nasopharyngeal cancer, the BDC planning technique can improve target dose homogeneity, conformity and OAR sparing, with better planning efficiency.
Nonlinear Dimensionality Reduction as Information Retrieval

Nonlinear dimensionality reduction has so far been treated either as a data representation problem or as a search for a lowerdimensional manifold embedded in the data space. A main application for both is in information visualization, to make visible the neighborhood or proximity relationships in the data, but neither approach has been designed to optimize this task. We give such visualization a new conceptualization as an information retrieval problem; a projection is good if neighbors of data points can be retrieved well based on the visualized projected points. This makes it possible to rigorously quantify goodness in terms of precision and recall. A method is introduced to optimize retrieval quality; it turns out to be an extension of Stochastic Neighbor Embedding, one of the earlier nonlinear projection methods, for which we give a new interpretation: it optimizes recall. The new method is shown empirically to outperform existing dimensionality reduction methods.
Germanium-on-Silicon for Integrated Silicon Photonics

To meet the unprecedented demands for data transmission speed and bandwidth silicon integrated photonics that can generate, modulate, process and detect light signals is being developed. Integrated silicon photonics that can be built using existing CMOS fabrication facilities offers the tantalizing prospect of a scalable and cost-efficient solution to replace electrical interconnects. Silicon, together with commonly used dielectric materials in CMOS processes such as silicon dioxide, is a great material system for optical confinement and wave transmission in near infrared range. However, silicon is not a good choice for active photonic devices due to its transparency in such wavelength range. Germanium and GeSi alloy, the materials that have long been adopted to improve the performance of silicon transistors in many ways, have been showing their potential as the building blocks of such active integrated optical devices. This chapter discusses the research of using germanium and GeSi for silicon-integrated photodetection and light source in the contexts of material physics and growth, device design and fabrication. This introduction section briefly introduces the background of integrated silicon photonics and some germanium properties which are important for photonic applications. Next section focuses on waveguide-integrated germanium photodetectors which can readily be integrated with silicon waveguide on mature silicon or silicon-on-insulator (SOI) platform. The physics and design considerations of these devices are presented with details. The fabrication processes of these devices are also discussed with some extent. Next section includes a newly developed field that using germanium for light sources in silicon photonics applications such as light-emitting-diodes (LEDs) and lasers. There has been a few breakthroughs in this topic including the author’s work of epitaxial germanium LEDs and optically pumped lasers operating at room temperature. The physics of this unusual concept of using indirect band gap material for light emission is discussed in details and some important results are presented.
Twenty years of bacterial RNases and RNA processing: how we've matured

By 1995, the year that publication of RNA began, the field of RNA processing was already well established. A dedicated cadre of scientists was actively engaged in studying how RNA precursors are converted to their mature, functional forms, and conferences dealing with the topic were held at regular intervals. In fact, members of the RNA processing community were instrumental in founding the RNA Society and starting RNA. What follows are the personal reflections and biases of one who has worked in the RNA processing field from very early on. Emphasis will be on advances in bacterial systems, with which I am most familiar, but readers should be aware that the last 20 years has seen an explosion of information about RNA metabolism in eukaryotic systems, leading to the realization that organisms from bacteria to mammals share much in common in their RNA metabolic processes. As a consequence, information gleaned in one organism has had important ramifications for studies in all systems.
Validity of the multi-directional reach test: a practical measure for limits of stability in older adults.

BACKGROUND Falls occur not only in the forward direction, but also to the side and backward. The purpose of this study was to develop a portable and valid tool to measure limits of stability in the anterior-posterior and medial-lateral directions. METHODS Two hundred fifty-four community-dwelling older persons were administered the Berg Balance Test (BBT), the Timed Up & Go Test (TUG), and the Multi-Directional Reach Test (MDRT). For the MDRT, subjects performed maximal reaches with the outstretched arm forward (FR), to the right (RR), to the left (LR), and leaning backward (BR), with feet flat on the floor. Reach was measured by the subject's total hand excursion along a yardstick affixed to a telescoping tripod. RESULTS Mean scores on the MDRT were FR = 8.89 +/- 3.4 in. , BR = 4.64 +/- 3.07 in. , RR = 6.15 +/- 2.99 in. , and LR = 6.61 +/- 2.88 in. Interclass Correlation (ICC2,1) for the reaches were greater than.92. Reliability analysis (Cronbach's Alpha,.842) demonstrated that directional reaches measure similar but unique aspects of the MDRT. The MDRT demonstrated significant correlation with the BBT sum and significant inverse relationship with the scores on the TUG. Regression analysis revealed that activity level contributed to scores in the forward, right, and left direction and that fear of falling contributed to scores in the backward direction. CONCLUSION The Multi-Directional Reach Test is an inexpensive, reliable, and valid tool for measuring the limits of stability as derived by reach in four directions. Values obtained on relatively healthy community-dwelling older adults serve as norms for screening patient populations.
Simple and Eﬃcient Two-Server ORAM ∗

We show a protocol for two-server oblivious RAM (ORAM) that is simpler and more eﬃcient than the best prior work. Our construction combines any tree-based ORAM with an extension of a two-server private information retrieval scheme by Boyle et al., and is able to avoid recursion and thus use only one round of interaction. In addition, our scheme has a very cheap initialization phase, making it well suited for applications to RAM-based secure computation. A practical instantiation of our protocol has excellent concrete parameters: for storing an N -element array of arbitrary size data blocks with statistical security parameter λ , the servers each store 4 N encrypted blocks, the client stores λ +2 log N blocks, and the total communication per logical access is roughly 10 log N encrypted blocks.
Statistical optimization of octree searches

This work emerged from the following observation: usual search procedures for octrees start from the root to retrieve the data stored at the leaves. But as the leaves are the farthest nodes to the root, why start from the root? With usual octree representations, there is no other way to access a leaf. However, hashed octrees allow direct access to any node, given its position in space and its depth in the octree. Search procedures take the position as an input, but the depth remains unknown. This work proposes to estimate the depth of an arbitrary node through a statistical optimization of the average cost of search procedures. As the highest costs of these algorithms are obtained when starting from the root, this method improves on both the memory footprint by the use of hashed octrees, and execution time through the proposed optimization.
Residual approach on a hierarchical segmentation

Residual operators analyze the evolution of an image subject to the application of a series of transformations, for example a series of openings of increasing size. When a significant object is filtered out by a transformation corresponding to its size, an important residue is observed. Maximal residues are kept for each pixel, indicating the most significant objects present in the image. Different families of operators have been used in the literature: morphological openings or closings, attribute openings or openings by reconstruction. In this paper we propose to compute residues on a hierarchy of partitions, computing the differences between regions at different hierarchical levels based on the classical earth mover's distance. The advantage of our approach is that it is autodual and generic as it can be applied with any hierarchical approach.
rab3D protein is a specific marker for zymogen granules in gastric chief cells of rats and rabbits.

BACKGROUND & AIMS Pepsinogen secretion from gastric chief cells requires a series of intracellular vesicle interactions. The final step of exocytosis involves fusion of secretory granules with the plasmalemma, culminating in the release of the digestive enzyme pepsinogen into the lumina of gastric glands. A group of specialized proteins tht confer membrane recognition, targeting, and fusion events are involved in regulated exocytosis. The aim of this study was to examine the distribution of rab3D, a low-molecular-weight guanosine 5'-triphosphate-binding protein, in gastric chief cells. METHODS rab3D immunoreactivity was evaluated by Western blot analysis and by immunocytochemical studies at both confocal and electron-microscopic levels. RESULTS rab3D immunoreactivity was specifically localized to the secretory granules in chief cells. Double labeling of gastric glands with rab3D and pepsinogen antibodies confirmed rab3D immunoreactivity localization to chief cells but not acid-secreting parietal cells. Immunoelectron microscopy revealed a near exclusive localization of the rab3D-like protein to the cytoplasmic face of the zymogen granules. After short-term stimulation consequent to feeding, rab3D immunoreactivity appeared to relocate from an apical region of duct cells to an unidentified cytoplasmic compartment. CONCLUSIONS The localization and redistribution of the rab3D-like protein in the chief cell suggests that it may play an important role in regulated exocytosis.
Invariance Principles for Homogeneous Sums: Universality of Gaussian Wiener Chaos

We compute explicit bounds in the normal and chi-square approximations of multilinear homogenous sums (of arbitrary order) of general centered independent random variables with unit variance. Our techniques combine an invariance principle by Mossel, O'Donnell and Oleszkiewicz with a refinement of some recent results by Nourdin and Peccati, about the approximation of laws of random variables belonging to a fixed (Gaussian) Wiener chaos. In particular, we show that chaotic random variables enjoy the following form of \textsl{universality}: (a) the normal and chi-square approximations of any homogenous sum can be completely characterized and assessed by first switching to its Wiener chaos counterpart, and (b) the simple upper bounds and convergence criteria available on the Wiener chaos extend almost verbatim to the class of homogeneous sums. These results partially rely on the notion of ``low influences'' for functions defined on product spaces, and provide a generalization of central and non-central limit theorems proved by Nourdin, Nualart and Peccati. They also imply a further drastic simplification of the method of moments and cumulants -- as applied to the proof of probabilistic limit theorems -- and yield substantial generalizations, new proofs and new insights into some classic findings by de Jong and Rotar'. Our tools involve the use of Malliavin calculus, and of both the Stein's method and the Lindeberg invariance principle for probabilistic approximations.
Summer training factors and risk of musculoskeletal injury among high school cross-country runners.

STUDY DESIGN Prospective cohort. OBJECTIVES To examine the relationship between summer training practices and risk of injury during the first month of a high school interscholastic cross-country season. BACKGROUND Several prospective studies have reported a high incidence of injury in adolescent cross-country runners. However, limited reports exist on the role of summer training practices and risk of injury among these runners. METHODS Four hundred twenty-one athletes (186 girls, 235 boys) who competed in interscholastic cross-country were followed during a cross-country season. At the start of the season, all participants completed a questionnaire regarding summer training routines. Time-loss, running-related injuries were tracked during the subsequent season. Logistic regression analysis was used to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) for the risk of initial injury during the first month of the season associated with summer training variables. RESULTS Sixty-seven runners (15.9%) had a confirmed injury during the first month of the season, with a higher percent among girls (19.4%) than boys (13.2%) (P = .06). Overall, 60.1% of the participants ran during the summer prior to the season, with a significantly higher percent among girls (71.5%) than boys (51.1%) (P<.0001). Overall, no significant association (OR = 0.9; 95% CI: 0.5, 1.5; P = .90) was found between not running sometime during the preceding summer and increased risk of initial injury during the first month of the season. Among only the runners who ran during the summer, after adjusting for sex and prior injury, first-month injuries were more common among those who did not frequently alternate short and long mileage on different days (OR = 3.0; 95% CI: 1.4, 6.4; P = .005), and/or who ran 8 weeks or fewer (OR = 2.7; 95% CI: 1.2, 5.8; P = .01) during their summer training. Running 8 weeks or fewer (P = .03), not frequently alternating mileage on different days (P = .01), and running a higher percentage of time on predominantly hill (P = .001) and irregular terrains (P = .004) were associated with increased risk of injury for girls. CONCLUSION These findings suggest that injuries during the first month of the high school cross-country season may be reduced if runners who participate in summer training activities run a greater number of weeks and frequently vary their daily running mileage during the summer. For girls, training programs that reduce mileage on hills and irregular terrains may help to minimize the occurrence of running-related injury. LEVEL OF EVIDENCE Prognosis, level 1b-.
XMM-Newton Observations of the Supernova Remnant IC 443. I. Soft X-Ray Emission from Shocked Interstellar Medium

The shocked interstellar medium around IC 443 produces strong X-ray emission in the soft energy band (E ≲ 1.5 keV). We present an analysis of such emission as observed with the EPIC MOS cameras on board the XMM-Newton observatory, with the purpose to find clear signatures of the interactions with the interstellar medium (ISM) in the X-ray band, which may complement results obtained in other wavelengths. We found that the giant molecular cloud mapped in CO emission is located in the foreground and gives an evident signature in the absorption of X-rays. This cloud may have a torus shape, and the part of torus interacting with the IC 443 shock gives rise to 2MASS Ks emission in the southeast. The measured density of emitting X-ray-shocked plasma increases toward the northeastern limb, where the remnant is interacting with an atomic cloud. We found an excellent correlation between emission in the 0.3-0.5 keV band and bright optical/radio filament on large spatial scales. The partial shell structure seen in this band therefore traces the encounter with the atomic cloud.
LogCut - Efficient Graph Cut Optimization for Markov Random Fields

Markov Random Fields (MRFs) are ubiquitous in low- level computer vision. In this paper, we propose a new approach to the optimization of multi-labeled MRFs. Similarly to a-expansion it is based on iterative application of binary graph cut. However, the number of binary graph cuts required to compute a labelling grows only logarithmically with the size of label space, instead of linearly. We demonstrate that for applications such as optical flow, image restoration, and high resolution stereo, this gives an order of magnitude speed-up, for comparable energies. Iterations are performed by "fusion" of solutions, done with QPBO which is related to graph cut but can deal with non- submodularity. At convergence, the method achieves optima on a par with the best competitors, and sometimes even exceeds them.
Prospect of Molecular Ecology in Microbial Communities of Biofilms

Use the latest molecular ecology to parse the dynamic changes of microbial community in biofilm under a variety of influences, which further reveals microbiological processes in the nitrogen and phosphorus removal reactor, and has great significance to study in-depth simple, efficient, low consumption of nutrient removal technology and its theory. This article described the extraction of total DNA, PCR, DGGE and other common molecular ecology techniques, summarized researches at domestic and foreign, discussed the application prospects of molecular ecology techniques for study of microbial communities in biofilm.
The mobiware toolkit: programmable support for adaptive mobile networking

Existing mobile systems (e.g., mobile IP, mobile ATM, and third-generation cellular systems) lack the intrinsic architectural flexibility to deal with the complexity of supporting adaptive mobile applications in wireless and mobile environments. We believe that there is a need to develop alternative network architectures from the existing ones to deal with the tremendous demands placed on underlying mobile signaling, adaptation management, and wireless transport systems in support of new mobile services (e.g., interactive multimedia and Web access). We present the design, implementation, and evaluation of mobiware, a mobile middleware toolkit that enables adaptive mobile services to dynamically exploit the intrinsic scalable properties of mobile multimedia applications in response to time-varying mobile network conditions. The mobiware toolkit is software-intensive and is built on CORBA and Java distributed object technology. Based on an open programmable paradigm developed by the COMET Group, mobiware runs on mobile devices, wireless access points, and mobile-capable switch/routers providing a set of open programmable interfaces and algorithms for adaptive mobile networking.
Optical links for cryogenic focal plane array readout

An optical link can provide an interface channel for the focal-plane array that is immune to electromagnetic interference (EMI) and can lower the heat load on the dewar. Our approach involves the use of fiber-optics and an on-focal-plane optical modulator to provide an interface to the focal-plane array (FPA). The FPA drives the modulator with an electrical signal. We evaluated specially fabricated AlGaAs/GaAs multiple quantum well (MQW) optical modulators, operating near 840 nm, for analog modulation, and we have used the results to calculate the performance of an optical interface link using experimentally determined device parameters. Link noise and dynamic range for an analog link were estimated from a separate experiment using pigtailed fiber components. The performance of the MQW modulator system is compared to alternative strategies. Significant improvement in performance in comparison to conventional electronic interfaces appears to be possible.
Information-theoretic thresholds for community detection in sparse networks

We give upper and lower bounds on the information-theoretic threshold for community detection in the stochastic block model. Specifically, consider the symmetric stochastic block model with $q$ groups, average degree $d$, and connection probabilities $c_\text{in}/n$ and $c_\text{out}/n$ for within-group and between-group edges respectively; let $\lambda = (c_\text{in}-c_\text{out})/(qd)$. We show that, when $q$ is large, and $\lambda = O(1/q)$, the critical value of $d$ at which community detection becomes possible---in physical terms, the condensation threshold---is \[ d_\text{c} = \Theta\! \left( \frac{\log q}{q \lambda^2} \right) \, , \] with tighter results in certain regimes. Above this threshold, we show that any partition of the nodes into $q$ groups which is as `good' as the planted one, in terms of the number of within- and between-group edges, is correlated with it. This gives an exponential-time algorithm that performs better than chance; specifically, community detection becomes possible below the Kesten-Stigum bound for $q \ge 5$ in the disassortative case $\lambda 0$ (similar upper bounds were obtained independently by Abbe and Sandon). Conversely, below this threshold, we show that no algorithm can label the vertices better than chance, or even distinguish the block model from an \ER\ random graph with high probability. Our lower bound on $d_\text{c}$ uses Robinson and Wormald's small subgraph conditioning method, and we also give (less explicit) results for non-symmetric stochastic block models. In the symmetric case, we obtain explicit results by using bounds on certain functions of doubly stochastic matrices due to Achlioptas and Naor; indeed, our lower bound on $d_\text{c}$ is their second moment lower bound on the $q$-colorability threshold for random graphs with a certain effective degree.
Silvicultural Implications Arising from a Simple Simulation Model for Endospermum medullosum in Vanuatu

SUMMARY Whitewood (Endospermum medullosum) is a tree species that shows promise for plantation timber production in Vanuatu, but few growth data are available to inform yield forecasts. Three simple relationships summarizing stand dynamics, namely height-age, diameter-height-stocking, and mortality-basal area relationships, were calibrated with data from 15 plots to form the basis of a model for silvicultural and management decisions. Despite the simplicity of the model, it offers predictions consistent with independent data. The model suggests that the optimal silviculture involves planting 635 stems/ha, thinning at 20 and 26 years, and clearfelling at age 36 when trees have a diameter of 55 cm dbh. However, many options offer a net present value within 5% of this nominal optimum. The flexibility to vary the timing and intensity of harvests over a wide range while maintaining good financial returns, coupled with good growth and timber properties, suggests that whitewood warrants further domestication and promotion in Vanuatu.