Miracle-dz/UniFAR-FTUs huggingface dataset:
Medical Image Segmentation by Combining Graph Cuts and Oriented Active Appearance Models

In this paper, we propose a novel method based on a strategic combination of the active appearance model (AAM), live wire (LW), and graph cuts (GCs) for abdominal 3-D organ segmentation. The proposed method consists of three main parts: model building, object recognition, and delineation. In the model building part, we construct the AAM and train the LW cost function and GC parameters. In the recognition part, a novel algorithm is proposed for improving the conventional AAM matching method, which effectively combines the AAM and LW methods, resulting in the oriented AAM (OAAM). A multiobject strategy is utilized to help in object initialization. We employ a pseudo-3-D initialization strategy and segment the organs slice by slice via a multiobject OAAM method. For the object delineation part, a 3-D shape-constrained GC method is proposed. The object shape generated from the initialization step is integrated into the GC cost computation, and an iterative GC-OAAM method is used for object delineation. The proposed method was tested in segmenting the liver, kidneys, and spleen on a clinical CT data set and also on the MICCAI 2007 Grand Challenge liver data set. The results show the following: 1) The overall segmentation accuracy of true positive volume fraction TPVF >; 94.3% and false positive volume fraction FPVF <; 0.2% can be achieved; 2) the initializa- tion performance can be improved by combining the AAM and LW; 3) the multiobject strategy greatly facilitates initialization; 4) compared with the traditional 3-D AAM method, the pseudo-3-D OAAM method achieves comparable performance while running 12 times faster; and 5) the performance of the proposed method is comparable to state-of-the-art liver segmentation algorithm. The executable version of the 3-D shape-constrained GC method with a user interface can be downloaded from http://xinjianchen.word- press.com/research/.
The Limnohabitans Genus Harbors Generalistic and Opportunistic Subtypes: Evidence from Spatiotemporal Succession in a Canyon-Shaped Reservoir

ABSTRACT We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of “generalists” that were always present throughout the whole season as well as “specialists” that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed. IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.
Maximum-Likelihood Based Synthesis of Volumetric Textures From a 2D Sample

We propose a genuine 3D texture synthesis algorithm based on a probabilistic 2D Markov random field conceptualization, capable of capturing the visual characteristics of a texture into a unique statistical texture model. We intend to reproduce, in the volumetric texture, the interactions between pixels learned in an input 2D image. The learning is done by nonparametric Parzen-windowing. Optimization is handled voxel by a relaxation algorithm, aiming at maximizing the likelihood of each voxel in terms of its local conditional probability function. Variants are proposed regarding the relaxation algorithm and the heuristic strategies used for the simultaneous handling of the orthogonal slices containing the voxel. The procedures are materialized on various textures through a comparative study and a sensitivity analysis, highlighting the variants strengths and weaknesses. Finally, the probabilistic model is compared objectively with a nonparametric neighborhood-search-based algorithm.
An excitation function for LPC synthesis which retains the human Glottal phase characteristics

An excitation function for LPC synthesis is constructed from a best estimate of the glottal volume velocity waveform. By proper smoothing, inverse filtering, and truncation, the phase characteristics of the glottal wave are preserved, while the basic requirement of an essentially flat spectrum is also satisfied. The new function is suggested as an excitation for reducing the buzzy quality often perceived in the synthesis of low F 0 speech.
Dynamic heart rate response to deer hunting in men and women

The purpose of the present study was to examine the heart rate response and force tension associated with deer hunting activities in men and women. Fifteen men and women (body mass index: 25.6±5.2 kg/m2; age: 27±9 years) participated in this study. Subjects performed a maximal graded exercise test (GXT) to determine maximal heart rate (HRmax). Subjects completed a 0.8 km hike over typical hunting terrain. Following a short rest, subjects completed a 0.4 km drag using a fake deer weighing 56 kg (123 pounds, the weight of the average field dressed deer in Pennsylvania, USA) over similar terrain. HR was measured during the activities using a Polar Heart Rate Monitor. Force tension (TNmean) while dragging the deer was measured using a cable tensiometer. Women on average completed the 0.4 km drag course in 13±3 min, where men on average only needed 6±2 min to complete the drag. Women spent significantly more time ≥85% HRmax (9±4 min), than men (2±3 min) during the drag (P<0.05). Women, on average, completed 71.
THE PHLEBOMANOMETER: A NEW APPARATUS FOR DIRECT MEASUREMENT OF VANOUS PRESSURE IN LARGE AND SMALL VEINS

The importance, clinically as well as experimentally, of quantitative venous pressure determinations is well known. With full realization of the value of venous pressure measurements, they are neglected because the apparatuses are difficult to use, are too bulky to carry as part of the physician's instruments of examination, are applicable only in fairly large veins and are difficult to clean and sterilize for subsequent use. About four years ago, Burch and Sodeman1described a simple direct method for measuring venous pressure. The method has proved of value clinically and has been used more and more by others. But it, like other direct methods which employ a column of a fluid as the manometer, has the disadvantage of being difficult to carry, prone to spillage of the fluid in the manometer either during use or when being transported from place to place, hard to use and bulky. In order to
Nonlinear Hyperspectral Unmixing With Robust Nonnegative Matrix Factorization

We introduce a robust mixing model to describe hyperspectral data resulting from the mixture of several pure spectral signatures. The new model extends the commonly used linear mixing model by introducing an additional term accounting for possible nonlinear effects, that are treated as sparsely distributed additive outliers. With the standard nonnegativity and sum-to-one constraints inherent to spectral unmixing, our model leads to a new form of robust nonnegative matrix factorization with a group-sparse outlier term. The factorization is posed as an optimization problem, which is addressed with a block-coordinate descent algorithm involving majorization-minimization updates. Simulation results obtained on synthetic and real data show that the proposed strategy competes with the state-of-the-art linear and nonlinear unmixing methods.
Whole-Genome Microarray and Gene Deletion Studies Reveal Regulation of the Polyhydroxyalkanoate Production Cycle by the Stringent Response in Ralstonia eutropha H16

ABSTRACT Poly(3-hydroxybutyrate) (PHB) production and mobilization in Ralstonia eutropha are well studied, but in only a few instances has PHB production been explored in relation to other cellular processes. We examined the global gene expression of wild-type R. eutropha throughout the PHB cycle: growth on fructose, PHB production using fructose following ammonium depletion, and PHB utilization in the absence of exogenous carbon after ammonium was resupplied. Our results confirm or lend support to previously reported results regarding the expression of PHB-related genes and enzymes. Additionally, genes for many different cellular processes, such as DNA replication, cell division, and translation, are selectively repressed during PHB production. In contrast, the expression levels of genes under the control of the alternative sigma factor σ54 increase sharply during PHB production and are repressed again during PHB utilization. Global gene regulation during PHB production is strongly reminiscent of the gene expression pattern observed during the stringent response in other species. Furthermore, a ppGpp synthase deletion mutant did not show an accumulation of PHB, and the chemical induction of the stringent response with dl-norvaline caused an increased accumulation of PHB in the presence of ammonium. These results indicate that the stringent response is required for PHB accumulation in R. eutropha, helping to elucidate a thus-far-unknown physiological basis for this process.
Maximum entropy (adaptive) filtering applied to radar clutter

An adaptive digital filtering scheme is presented which uses a lattice structure for adaptive prediction and elimination of radar clutter, using Burg's algorithm for the computation of the lattice coefficients. This method computes a minimum-phase prediction error filter directly from the radar data, while not having the end-bias problems common to many filtering schemes. This permits quick adaptation to changing clutter conditions. An integration decay constant allows the filter to adapt to longer duration signals (clutter) while passing shorter duration signals (targets). The filter design is described and experimental results are discussed.
Scalable Coding of Plenoptic Images by Using a Sparse Set and Disparities

One of the light field capturing techniques is the focused plenoptic capturing. By placing a microlens array in front of the photosensor, the focused plenoptic cameras capture both spatial and angular information of a scene in each microlens image and across microlens images. The capturing results in a significant amount of redundant information, and the captured image is usually of a large resolution. A coding scheme that removes the redundancy before coding can be of advantage for efficient compression, transmission, and rendering. In this paper, we propose a lossy coding scheme to efficiently represent plenoptic images. The format contains a sparse image set and its associated disparities. The reconstruction is performed by disparity-based interpolation and inpainting, and the reconstructed image is later employed as a prediction reference for the coding of the full plenoptic image. As an outcome of the representation, the proposed scheme inherits a scalable structure with three layers. The results show that plenoptic images are compressed efficiently with over 60 percent bit rate reduction compared with High Efficiency Video Coding intra coding, and with over 20 percent compared with an High Efficiency Video Coding block copying mode.
High resolution 2-D spectral analysis at low SNR

This paper presents a fully two-dimensional high-resolution spectral analysis technique. The method consists of extrapolating observed data beyond the observation window by means of 2-D least squares prediction filters. High-resolution spectral analysis is then obtained by a discrete Fourier transform of the extrapolated data. Previously, methods of obtaining a high-resolution spectrum analysis on 2-D data have applied 1-D high-resolution analyses sequentially to each dimension. The fully 2-D method presented here permits the use of nearly the square of the number of extrapolation coefficients that can be used by the sequential 1-D analyses. The advantage of the new procedure is that more coefficients permit extrapolating more 2-D sinusoids in the data and also provide reduced sensitivity to noise, thereby allowing operation at lower SNR's. A second technique for improving the performance of high-resolution spectral analysis in a chosen region of the transformed data is also presented. The technique consists of filtering the data with a 2-D FIR bandpass filter prior to the high-resolution transform. This method is also effective in reducing the sensitivity of the high-resolution analysis to noise and other sinusoids.
Angiogenesis and Histologic Scoring in Prostatic Carcinoma—A Valuable Cost Effective Prognostic Indicator

Objective: To find any correlation between microscopic angiogenesis grading system (MAGS) score and Gleason score and serum prostate specific antigen (S.PSA) in carcinoma of prostate. Study design: Examination of 30 patients with prostatic carcinoma compared with an age matched control group of 30 patients having histopathologically proven benign prostatic Hyperplasia. The Preoperative serum PSA level was determined in all patients. Histopathological examination for MAGS score was done in all patients and Gleason scoring was done for cases of prostatic carcinoma. Result: MAGS score had a definite correlation with Gleason score (Correlation coefficient, ). Studying the relationship between MAGS score and S.PSA, a statistically significant difference is found between S.PSA levels in study and control groups, and in the three MAGS score groups namely 21–30, 31–40 and 41–50. Conclusion: Gleason score and MAGS score are well related to each other. As tumor becomes more poorly differentiated with rising Gleason.
Multi-Viewpoint Panorama Construction With Wide-Baseline Images

We present a novel image stitching approach, which can produce visually plausible panoramic images with input taken from different viewpoints. Unlike previous methods, our approach allows wide baselines between images and non-planar scene structures. Instead of 3D reconstruction, we design a mesh-based framework to optimize alignment and regularity in 2D. By solving a global objective function consisting of alignment and a set of prior constraints, we construct panoramic images, which are locally as perspective as possible and yet nearly orthogonal in the global view. We improve composition and achieve good performance on misaligned areas. Experimental results on challenging data demonstrate the effectiveness of the proposed method.
Experiments in syllable-based recognition of continuous speech

An exploratory implementation of a syllable-based recognizer is described. Continuous speech is first divided into syllabic units, and the units are then matched against syllable templates using a dynamic programming algorithm. A hierarchical transition network is used to limit the syllable search to possible continuations of the current partial sentence hypotheses. Competing hypotheses are pruned by a 'beam search'. Experiments are reported on automatic recognition of English sentences with a 70-word vocabulary and restricted syntax produced by one male speaker. 85% of the sentences were correctly recognized. Comparable results were obtained for a similar task in French using a female speaker. The method is computationally efficient: real-time performance on dedicated hardware should be obtainable without difficulty. A method of scaling the distance measures used in the syllable matching is described. This scaling takes into account variability in syllable production, both as a function of position within the syllable and as a function of the various spectral parameters being used.
Limited wordlength and FDCT processing accuracy

For hardware realization of the fast discrete cosine transform (FDCT) processor, as the parameters can only be specified by a finite number of binary digits (bits), the computational accuracy is governed by the precision by which the parameters are represented. To measure the effect of limited word-length, mathematical analysis is used initially to develop theoretical effects of the sensitive parameters on the processing accuracy. By simulation, the theoretical results are verified, and the results are then extended for further detailed simulation studies. Finally, the simulation results are used to develop general guidelines for optimizing the hardware design of any size FDCT or fast inverse DCT (FIDCT) processor.
Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

ABSTRACT The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases.
Metabolic Engineering of Acinetobacter baylyi ADP1 for Improved Growth on Gluconate and Glucose

ABSTRACT A high growth rate in bacterial cultures is usually achieved by optimizing growth conditions, but metabolism of the bacterium limits the maximal growth rate attainable on the carbon source used. This limitation can be circumvented by engineering the metabolism of the bacterium. Acinetobacter baylyi has become a model organism for studies of bacterial metabolism and metabolic engineering due to its wide substrate spectrum and easy-to-engineer genome. It produces naturally storage lipids, such as wax esters, and has a unique gluconate catabolism as it lacks a gene for pyruvate kinase. We engineered the central metabolism of A. baylyi ADP1 more favorable for gluconate catabolism by expressing the pyruvate kinase gene (pykF) of Escherichia coli. This modification increased growth rate when cultivated on gluconate or glucose as a sole carbon source in a batch cultivation. The engineered cells reached stationary phase on these carbon sources approximately twice as fast as control cells carrying an empty plasmid and produced similar amount of biomass. Furthermore, when grown on either gluconate or glucose, pykF expression did not lead to significant accumulation of overflow metabolites and consumption of the substrate remained unaltered. Increased growth rate on glucose was not accompanied with decreased wax ester production, and the pykF-expressing cells accumulated significantly more of these storage lipids with respect to cultivation time.
A Wilderness Therapy Program as an Alternative to Adolescent Psychiatric Hospitalization

In two pilot backpacking trips, 14 adolescent inpatients were taken from acute psychiatric hospitals into the wilder ness. Patients selected were either withdrawn or acting out, except for four adolescents diagnosed as ADD or conduct disordered. The former group showed greater change than the latter on a variety of measures including treatment plan objectives, behavioral symptomatology and locus of control. In general, change during the Wilderness Therapy Program (WTP) was more rapid than during other phases of hospitalization. Future research should employ more controls and a larger sample of patients. WTP appears to be a promising alternative to traditional programs.
Extension of the Substrate Utilization Range of Ralstonia eutropha Strain H16 by Metabolic Engineering To Include Mannose and Glucose

ABSTRACT The Gram-negative facultative chemolithoautotrophic bacterium Ralstonia eutropha strain H16 is known for its narrow carbohydrate utilization range, which limits its use for biotechnological production of polyhydroxyalkanoates and possibly other products from renewable resources. To broaden its substrate utilization range, which is for carbohydrates and related compounds limited to fructose, N-acetylglucosamine, and gluconate, strain H16 was engineered to use mannose and glucose as sole carbon sources for growth. The genes for a facilitated diffusion protein (glf) from Zymomonas mobilis and for a glucokinase (glk), mannofructokinase (mak), and phosphomannose isomerase (pmi) from Escherichia coli were alone or in combination constitutively expressed in R. eutropha strain H16 under the control of the neokanamycin or lac promoter, respectively, using an episomal broad-host-range vector. Recombinant strains harboring pBBR1MCS-3::glf::mak::pmi or pBBR1MCS-3::glf::pmi grew on mannose, whereas pBBR1MCS-3::glf::mak and pBBR1MCS-3::glf did not confer the ability to utilize mannose as a carbon source to R. eutropha. The recombinant strain harboring pBBR1MCS-3::glf::pmi exhibited slower growth on mannose than the recombinant strain harboring pBBR1MCS-3::glf::mak::pmi. These data indicated that phosphomannose isomerase is required to convert mannose-6-phosphate into fructose-6-phosphate for subsequent catabolism via the Entner-Doudoroff pathway. In addition, all plasmids also conferred to R. eutropha the ability to grow in the presence of glucose. The best growth was observed with a recombinant R. eutropha strain harboring plasmid pBBR1MCS-2::P nk ::glk::glf. In addition, expression of the respective enzymes was demonstrated at the transcriptional and protein levels and by measuring the activities of mannofructokinase (0.622 ± 0.063 U mg−1), phosphomannose isomerase (0.251 ± 0.017 U mg−1), and glucokinase (0.518 ± 0.040 U mg−1). Cells of recombinant strains of R. eutropha synthesized poly(3-hydroxybutyrate) to ca. 65 to 67% (wt/wt) of the cell dry mass in the presence of 1% (wt/vol) glucose or mannose as the sole carbon sources.