Miracle-dz/UniFAR-FTUs huggingface dataset:
Diffusion-Weighted Magnetic Resonance Imaging of Head and Neck

Our aim was to review the clinical applications of diffusion-weighted magnetic resonance imaging in the head and neck. Diffusion-weighted magnetic resonance imaging plays a role in the differentiation of benign from malignant head and neck tumors, squamous cell carcinoma from lymphoma, and metastatic from benign lymphadenopathy as well as in the selection of the biopsy site. It can be used for the differentiation of recurrent tumors from posttreatment changes and in monitoring the patient after radiotherapy. It helps in the differentiation of necrotic tumors from abscesses. Additionally, it can be used for the diagnosis and grading of diffuse autoimmune diseases, such as Sjogren and Graves diseases.
Kir 6 . 2 mutations causing neonatal diabetes prevent endocytosis of ATP-sensitive potassium channels

ATP-sensitive potassium (KATP) channels couple the metabolic status of a cell to its membrane potential—a property that endows pancreatic b-cells with the ability to regulate insulin secretion in accordance with changes in blood glucose. The channel comprises four subunits each of Kir6.2 and the sulphonylurea receptor (SUR1). Here, we report that KATP channels undergo rapid internalisation from the plasma membrane by clathrin-mediated endocytosis. We present several lines of evidence to demonstrate that endocytosis is mediated by a tyrosine based signal (YSKF) located in the carboxy-terminus of Kir6.2 and that SUR1 has no direct role. We show that genetic mutations, Y330C and F333I, which cause permanent neonatal diabetes mellitus, disrupt this motif and abrogate endocytosis of reconstituted mutant channels. The resultant increase in the surface density of KATP channels would predispose b-cells to hyperpolarise and may account for reduced insulin secretion in these patients. The data imply that endocytosis of KATP channels plays a crucial role in the (patho)-physiology of insulin secretion. The EMBO Journal (2006) 25, 4142–4151. doi:10.1038/ sj.emboj. 7601275; Published online 10 August 2006 Subject Categories: membranes & transport; molecular biology of disease
Protein folding in mode space: A collective coordinate approach to structure prediction

Does the dynamics of a protein encode its structure? Many studies have adressed the inverse of this question—how a three‐dimensional structure determines its dynamics—using molecular dynamics simulation, normal mode analysis, and similar methods. Recently we have developed a molecular dynamics (MD) simulation method to impose dynamic properties on ensembles of MD trajectories in the form of restraints on structural diversity in the directions of the principal components of motion of the molecule. In the current work, we investigate if these restraints in combination with a standard MD force field are sufficient to generate native structure in disordered structural ensembles. We present simulations from a series of increasingly disordered structural ensembles obtained by thermal unfolding or randomization of the coordinates of the native structure of two src‐homology 3 (SH3) domains. Native structure formation is observed under the sole action of the diversity restraint and the MD force field. We investigate the importance of accuracy of the description of native dynamics. Protein folding is a highly cooperative process. The dynamic restraints may enforce long‐range cooperativity and thus speed up the folding from unstructured states. Applications of the restraints to structure refinement and structure prediction are possible. Proteins 2002;49:365–377. © 2002 Wiley‐Liss, Inc.
Functional Redundancy of AtFtsH Metalloproteases in Thylakoid Membrane Complexes1

FtsH is an ATP-dependent metalloprotease found in bacteria, mitochondria, and plastids. Arabidopsis (Arabidopsis thaliana) contains 12 AtFtsH proteins, three in the mitochondrion and nine in the chloroplast. Four of the chloroplast FtsH proteins are encoded by paired members of closely related genes (AtFtsH1 and 5, and AtFtsH2 and 8). We have previously reported that AtFtsH2 and 8 are interchangeable components of AtFtsH complexes in the thylakoid membrane. In this article, we show that the var1 variegation mutant, which is defective in AtFtsH5, has a coordinate reduction in the AtFtsH2 and 8 pair, and that the levels of both pairs are restored to normal in var1 plants that overexpress AtFtsH1. Overexpression of AtFtsH1, but not AtFtsH2/VAR2, normalizes the pattern of var1 variegation, restoring a nonvariegated phenotype. We conclude that AtFtsH proteins within a pair, but not between pairs, are interchangeable and functionally redundant, at least in part. We further propose that the abundance of each pair is matched with that of the other pair, with excess subunits being turned over. The variegation phenotype of var1 (as well as var2, which is defective in AtFtsH2) suggests that a threshold concentration of subunits is required for normal chloroplast function. AtFtsH1, 2, 5, and 8 do not show evidence of tissue or developmental specific expression. Phylogenetic analyses revealed that rice (Oryza sativa) and Arabidopsis share a conserved core of seven FtsH subunit genes, including the AtFtsH1 and 5 and AtFtsH2 and 8 pairs, and that the structure of the present-day gene families can be explained by duplication events in each species following the monocot/dicot divergence.
LogLatt: A computational library for the calculus and flows on logarithmic lattices

We introduce LogLatt, an efficient MATLAB library for the calculus and operations between functions on multi-dimensional lattices of logarithmically distributed nodes in Fourier space. The computational applicabilities are available in one, two and three dimensions and include common differential operators, norms and functional products, which are local convolutions in Fourier space. All operations are encoded as MATLAB function handles, so their implementations result in elegant and intuitive scripts. Particularly, when applied to dynamics, governing equations may be coded exactly as they are mathematically written. Codes and results for some problems of fluid flow are given as examples of implementation. We expect that this library will serve as an efficient and accessible computational tool in the study of logarithmic models for nonlinear differential equations.
Transmitting Antenna's Reflected Power and its Influence on Reverberation Chamber Calibration

For the reverberation chamber operating at low frequencies, the reflected power at the transmitting antenna's terminal is very large. In this paper, we analyzed the statistical property of this large reflected power. Furthermore, two different normalization methods used for chamber calibration are compared. Through measurement results, it is shown that using net power to do the normalization will give better chi-square and uniformity results than using transmission power to do the normalization. However, from the view of the practical testing, the later one greatly reduces the testing complexity and is accurate enough for the engineering application
Robust Cell Extraction Method for Form Documents Based on Intersection Searching and Global Optimization

This paper presents a method to extract cells from form documents of an unknown format based on intersection tracking and global optimization. Because of the increasing varieties of forms and complications in the forms, cell extraction has become a key factor in automatic form recognition. The proposed method produces cell candidates by using intersection features and tracing intersection points to form closed regions. Then, global optimization is carried out to determine a set of cells having the highest likelihood. Maintaining precision for 82 kinds of forms, the proposed method achieved a recall rate of 80.4% whereas the conventional method achieved a recall rate of 77.1%.
Zishi: A Smart Garment for Posture Monitoring

Zishi is a garment designed to support posture monitoring for the purposes of rehabilitation training. It has been designed with attention to presenting accurate and informative feedback to patients regarding their thoracic and shoulder posture as well as comfort, ease of use, wearability and aesthetics. Zishi can be useful during rehabilitation training for a variety of patient groups. So far, we have been concerned with two broad training scenarios a) for arm-hand (neurological) rehabilitation training after stroke or for MS and spinal cord injury patients. B) for shoulder patients. Zishi consists of a garment integrated with smart textiles and wearable electronics. It presents real-time feedback as a vibration delivered through the garment, visual and audio instructions through android-hand held device (smartphone or tablet).
Multicellular Secretory Trichome Development on Soybean and Related Glycine Gynoecia

Multicellular glandular trichomes form on gynoecia of wild annual Glycine species, annual soybean cultivars, and wild perennial Glycine species. These trichomes occur from the ovary base to the style base and, in perennial species, along the style as well. Trichomes form at least 2 d before anthesis, and new trichomes develop throughout flowering and also on young seed pods. Trichome structure is similar in all taxa examined, usually five to seven linearly arranged cells. Stalk cells with callose walls become highly vacuolate, and their cytoplasms have reduced numbers of Golgi bodies and endoplasmic reticulum. During secretion, two to four distal cells develop dense cytoplasms containing both prominent Golgi bodies with large vesicles and endoplasmic reticulum with enlarged lumens. Both organelles are involved in forming carbohydrate/protein secretory products. Internal secretion begins with products exuding between the plasmalemma and the primary wall of each distal cell. Secretion progresses between the primary wall and the outermost cuticle that entirely covers the trichome, which is thicker and more highly modified than a normal cuticle. This cuticle separates from cell walls in secretion regions. Products are exuded outside, occur on the inner surface of trichome and gynoecium, and are more obvious in perennial than in annual taxa. The composition and function of products are unknown.
1 GENETIC ABLATION OF CALCIUM-INDEPENDENT PHOSPHOLIPASE A 2 γ ( iPLA 2 γ ) ATTENUATES CALCIUM-INDUCED OPENING OF THE MITOCHONDRIAL PERMEABILITY TRANSITION PORE AND RESULTANT CYTOCHROME C RELEASE

Sung Ho Moon, Christopher M. Jenkins, Michael A. Kiebish, Harold F. Sims, David J. Mancuso, and Richard W. Gross From the Departments of Medicine and Developmental Biology, Division of Bioorganic Chemistry and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri 63110 and the Department of Chemistry, Washington University, St. Louis, Missouri 63130 Running Title: iPLA2γ-mediated mPTP Opening
An Algorithm to Compute the X-ray Transform

The X-ray transform models a forward projection operator of image formation, which has been widely used for tomographic image reconstruction. We propose a new algorithm to compute that transform of an image represented by unit (pixel/voxel) basis functions, for various two-dimensional (2D)/three-dimensional (3D) scanning geometries, such as 2D/3D parallel beam, 2D fan beam, 3D circular/helical cone beam, etc. Since the transform is acting as a line integral, the fundamental task is to calculate this integral of the unit basis functions, which is equivalently the intersection length of the ray with the associated unit. For a given ray, using the support of unit basis function, we derive the sufficient and necessary condition of non-vanishing intersectability, and obtain the analytic formula for the intersection length, which can be used to distinguish the units that produce valid intersections with the given ray, and then perform simple calculations only for those units. The algorithm is easy to be implemented, and the computational cost is optimal. Moreover, we discuss the intrinsic ambiguities of the problem itself that perhaps happen, and present a solution. The algorithm not only possesses the adaptability with regard to the center position, scale and size of the image, and the scanning geometry as well, but also is quite suited to parallelize with optimality. The resulting projection matrix can be sparsely stored and output if needed, and the adjoint of X-ray transform can be also computed by the algorithm. Finally, we validate the correctness of the algorithm by the aforementioned scanning geometries.
SPANBRE: An Efficient Hierarchical Clustering Algorithm for Spatial Data with Neighborhood Relations

Due to the attributes of the neighbors are always similar or associated to each other, we address the problem of discovering spatial relationships in spatial data through the identification of clusters based on spatial neighborhood relations. We present an efficient clustering algorithm called SPANBRE that generates high quality clusters in O(nlogn) time and in O(n2) message complexity. SPANBRE is kind of agglomerative hierarchical method. By using a sequence data structure, SPANBRE avoids the complex spatial join operation. SPANBRE also execute an optimization strategy for clustering splitting and merging to achieve high clustering quality. The experimental results on traffic flow data sets show that the clustering quality and the algorithm efficiency of SPANBRE are superior to other alternative techniques.
Prevention of tissue damage by water jet during cavitation

Cavitation bubbles accompany explosive vaporization of water following pulsed energy deposition in liquid media. Bubbles collapsing at the tip of a surgical endoprobe produce a powerful and damaging water jet propagating forward in the axial direction of the probe. We studied interaction of such jet with tissue using fast flash photography and modeled the flow dynamics using a two-dimensional Rayleigh-type hydrodynamic simulation. Maximal velocity of the jet generated at pulse energies of up to 1 mJ was about 80 m/s. The jet can produce tissue damage at a distance exceeding the radius of the cavitation bubble by a factor of 4. We demonstrate that formation of this flow and associated tissue damage can be prevented by application of the concave endoprobes that slow down the propagation of the back boundary of the bubble. Similar effect can be achieved by positioning an obstacle to the flow, such as a ring behind the tip.
Why Do Platforms Charge Proportional Fees? Commitment and Seller Participation

Abstract This paper deals with trade platforms whose operators not only allow third party sellers to offer their products to consumers, but also offer products themselves. In this context, the platform operator faces a hold-up problem if he uses classical two-part tariffs only as potential competition between the platform operator and sellers reduces platform attractiveness. Since some sellers refuse to join the platform, some products that are not known to the platform operator will not be offered at all. We find that revenue-based fees lower the platform operator’s incentives to compete with sellers, increasing platform attractiveness. Therefore, charging such proportional fees can be profitable, which may explain why several trade platforms indeed charge proportional fees.
Curvature detectors in human vision?

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Trichotillomania with gastric trichobezoar

Bezoars are collections or concretions of indigestible foreign material in the gastrointestinal tract. Trichotillomania is an impetuous disorder of pulling out one's own hair, whereas trichobezoar is the formation of a hairball after trichophagia [1], which contains a large quantity of hair, varying in length, matted together. A 13-year-old patient presented with abdominal pain beginning 1 month ago. During this period the patient had reported pain intensity to be from mild to moderate and localized to epigastrium. The patient experienced non-projectile vomiting, containing undigested food particles. General physical examination exposed patchy alopecia as shown in Fig. 1. Abdominal examination revealed an irregular and non-tender lump overlying a part of the epigastrium. An ultrasound of the abdomen showed an echogenic area with dense acoustic shadow in the stomach region. An upper gastrointestinal endoscopy was performed, revealing a large ball of hair in the body as well as pylorus of the stomach, as shown in Fig. 2A displaying the trichobezoar. Considering the size, the trichobezoar was removed laproscopically (Fig. 2B) and the patient was referred to a psychiatrist for treatment of trichotillomania. Figure 1 Patchy alopecia due to trichotillomania Figure 2 (A) Endoscopy showing ball of hair in the stomach (B) Laparoscopically removed trichobezoar from stomach Trichobezoar is the most common form of bezoars reported, with hairballs extending to the small intestine causing Rapunzel syndrome in a few cases. Trichophagia is equated to pica syndrome. Abdominal pain, anemia, and weight loss are the most common complaints. Evaluation involves ultrasonography, computed tomography and endoscopy. Endoscopic removal has been tried in few cases, however surgical elimination remains the preferred choice [2]. Treatment of trichotillomania is behavioral therapy. The importance and severity of trichotillomania should not be underrated and alertness of these disorders should be encouraged at primary health care level [3].
Automatic detection of age-related macular degeneration pathologies in retinal fundus images

Advanced techniques in image processing and analysis are being extensively studied to assist clinical diagnoses. Digital colour retinal fundus images are widely utilised to investigate various eye diseases. In this paper, we describe the detection of optic disc (OD), macula and age-related macular degeneration (ARMD) pathologies of the macular regions in colour fundus images. ARMD causes the loss of central vision in older adults. If the disease is detected early and treated promptly, much of the vision loss can be prevented. Eighty colour retinal fundus images were tested using our proposed algorithm. The Hough transform was employed for OD determination. A fundus coordinate system was established based on the macula location. An ARMD pathology detection methodology using a subtraction process after contrast-limited adaptive histogram equalisation operations was proposed. The accuracies of the automated segmentations of the OD, macula and ARMD pathologies obtained were 100%, 100% and 95.49%, respectively. These results show that our algorithm is a useful tool for detecting ARMD in retinal fundus images. The application of our method may reduce the time needed by ophthalmologists to diagnose ARMD pathology while providing dependable detection precision. Integration of our technique into traditional software could be used in clinical implementations as an aid in disease diagnosis and as a tool for quantitative evaluation of treatment effectiveness.
HMGB1 IS MARKEDLY ELEVATED WITHIN 6 HOURS OF MECHANICAL TRAUMA IN HUMANS

High-mobility group box 1 (HMGB1) is a late mediator of the systemic inflammation associated with sepsis. Recently, HMGB1 has been shown in animals to be a mediator of hemorrhage-induced organ dysfunction. However, the time course of plasma HMGB1 elevations after trauma in humans remains to be elucidated. Consequently, we hypothesized that mechanical trauma in humans would result in early significant elevations of plasma HMGB1. Trauma patients at risk for multiple organ failure (ISS ≥15) were identified for inclusion (n = 23), and postinjury plasma samples were assayed for HMGB1 by enzyme-linked immunosorbent assay. Comparison of postinjury HMGB1 levels with markers for patient outcome (age, injury severity score, units of red blood cell (RBC) transfused per first 24 h, and base deficit) was performed. To investigate whether postinjury transfusion contributes to elevations of circulating HMGB1, levels were determined in both leuko-reduced and non-leuko-reduced packed RBCs. Plasma HMGB1 was elevated more than 30-fold above healthy controls within 1 h of injury (median, 57.76 vs. 1.77 ng/mL; P < 0.003), peaked from 2 to 6 h postinjury (median, 526.18 ng/mL; P < 0.01 vs. control), and remained elevated above control through 136 h. No clear relationship was evident between postinjury HMGB1 levels and markers for patient outcome. High-mobility group box 1 levels increase with duration of RBC storage, although concentrations did not account for postinjury plasma levels. Leuko-reduced attenuated HMGB1 levels in packed RBCs by approximately 55% (P < 0.01). Plasma HMGB1 is significantly increased within 1 h of trauma in humans with marked elevations occurring from 2 to 6 h postinjury. These results suggest that, in contrast to sepsis, HMGB1 release is an early event after traumatic injury in humans. Thus, HMGB1 may be integral to the early inflammatory response to trauma and is a potential target for future therapeutics.