Miracle-dz/UniFAR-FTUs huggingface dataset:
A Review of Content{Based Image Retrieval Systems in Medical Applications { Clinical Bene(cid:12)ts and Future Directions

Content{based visual information retrieval (CB-VIR) or Content{Based Image Retrieval (CBIR) has been one on the most vivid research areas in the (cid:12)eld of computer vision over the last 10 years. The availability of large and steadily growing amounts of visual and multimedia data, and the development of the Internet underline the need to create thematic access methods that o(cid:11)er more than simple text{ based queries or requests based on matching exact database (cid:12)elds. Many programs and tools have been developed to formulate and execute queries based on the visual or audio content and to help browsing large multimedia repositories. Still, no general breakthrough has been achieved with respect to large varied databases with documents of di(cid:11)ering sorts and with varying characteristics. Answers to many questions with respect to speed, semantic descriptors or objective image interpretations are still unanswered. In the
'Candidatus Phytoplasma malaysianum', a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus).

This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytoplasma distinguished the phytoplasma from all previously described 'Candidatus Phytoplasma' species. Pairwise sequence similarity scores, calculated through alignment of full-length 16S rRNA gene sequences, revealed that the MaPV phytoplasma 16S rRNA gene shared 96.5 % or less sequence similarity with that of previously described 'Ca. Phytoplasma' species, justifying the recognition of the MaPV phytoplasma as a reference strain of a novel taxon, 'Candidatus Phytoplasma malaysianum'. The 16S rRNA gene F2nR2 fragment from the MaPV phytoplasma exhibited a distinct restriction fragment length polymorphism (RFLP) profile and the pattern similarity coefficient values were lower than 0.85 with representative phytoplasmas classified in any of the 31 previously delineated 16Sr groups; therefore, the MaPV phytoplasma was designated a member of a new 16Sr group, 16SrXXXII. Phytoplasmas affiliated with this novel taxon and the new group included diverse strains infecting periwinkle, coconut palm and oil palm in Malaysia. Three phytoplasmas were characterized as representatives of three distinct subgroups, 16SrXXXII-A, 16SrXXXII-B and 16SrXXXII-C, respectively.
Improving ozone profile retrieval from spaceborne UV backscatter spectrometers using convergence behaviour diagnostics

Abstract. The Ozone Profile Algorithm (OPERA), developed at KNMI, retrieves the vertical ozone distribution from nadir spectral satellite measurements of back scattered sunlight in the ultraviolet and visible wavelength range. To produce consistent global datasets the algorithm needs to have good global performance, while short computation time facilitates the use of the algorithm in near real time applications. To test the global performance of the algorithm we look at the convergence behaviour as diagnostic tool of the ozone profile retrievals from the GOME instrument (on board ERS-2) for February and October 1998. In this way, we uncover different classes of retrieval problems, related to the South Atlantic Anomaly, low cloud fractions over deserts, desert dust outflow over the ocean, and the intertropical convergence zone. The influence of the first guess and the external input data including the ozone cross-sections and the ozone climatologies on the retrieval performance is also investigated. By using a priori ozone profiles which are selected on the expected total ozone column, retrieval problems due to anomalous ozone distributions (such as in the ozone hole) can be avoided. By applying the algorithm adaptations the convergence statistics improve considerably, not only increasing the number of successful retrievals, but also reducing the average computation time, due to less iteration steps per retrieval. For February 1998, non-convergence was brought down from 10.7% to 2.1%, while the mean number of iteration steps (which dominates the computational time) dropped 26% from 5.11 to 3.79.
Evolution of the “autophagamiR”

MicroRNAs (miRs) are increasingly important diagnostic and prognostic markers in cancer but have not been defined in medullary thyroid carcinoma (MTC). MiR microarray profiling was performed on 19 primary MTC tumors, validated with qPCR in 45 cases and correlated with clinical outcomes. MiRs-183 and 375 were overexpressed and miR-9* underexpressed in sporadic vs. hereditary MTC (SMTC; HMTC). MiR-183 and 375 overexpression predicted lateral nodal metastases, residual disease, distant metastases and mortality. MiR-183 knockdown in an MTC cell line (TT cells) reduced cellular proliferation in association with elevated LC3B expression. This is suggestive of increased autophagic flux and potential cell death via autophagy induction. MiRs may subsequently be shown to serve as efficacious therapeutic strategies in MTC with a mechanism based upon autophagy.
Perceived noise versus display noise in temporally filtered image sequences

Temporal noise-reduction filtering of image sequences is commonly applied in medical imaging and other applications, and a common assessment technique is to measure the reduction in display noise variance. Theoretically and experimentally, we demonstrate that this is inadequate because it does not account for the interaction with the human observer. Using a new forced-choice method, we compare detectability of low-contrast objects and find a noise level for an unfiltered sequence that gives the same detectability as the filtered sequence. We report the equivalent detectability noise variance ratio, or EDVR. For a digital low-pass filter that reduces the bandwidth by 1/2, display noise reduction predicts an EDVR of 0.5. The measured value averaged over three subjects, 0.93±0.19, compares favorably with the 0.85 predicted from a theoretical human observer model, and both are very close to the value of 1.0 expected for no filtering. Hence, the effective, perceived noise is relatively unchanged by temporal low-pass filtering. The computational observer model successfully evaluates a simple low-pass temporal filter, and we anticipate that it can be used to predict the observer response to other image enhancement filters.
Manufacture of a Polyaniline Nanofiber Ammonia Sensor Integrated with a Readout Circuit Using the CMOS-MEMS Technique

This study presents the fabrication of a polyaniline nanofiber ammonia sensor integrated with a readout circuit on a chip using the commercial 0.35 μm complementary metal oxide semiconductor (CMOS) process and a post-process. The micro ammonia sensor consists of a sensing resistor and an ammonia sensing film. Polyaniline prepared by a chemical polymerization method was adopted as the ammonia sensing film. The fabrication of the ammonia sensor needs a post-process to etch the sacrificial layers and to expose the sensing resistor, and then the ammonia sensing film is coated on the sensing resistor. The ammonia sensor, which is of resistive type, changes its resistance when the sensing film adsorbs or desorbs ammonia gas. A readout circuit is employed to convert the resistance of the ammonia sensor into the voltage output. Experimental results show that the sensitivity of the ammonia sensor is about 0.88 mV/ppm at room temperature.
Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Significance We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, providing details on total genes present in the genome. Genome analysis suggests that the peanut lineage was affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion since their formation by human hands. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants. This study also provides millions of structural variations that can be used as genetic markers for the development of improved peanut varieties through genomics-assisted breeding. Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45–56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.
Finnish patients with inflammatory bowel disease have fewer symptoms and are more satisfied with their treatment than patients in the previous European survey

Objective. Symptoms associated with inflammatory bowel diseases (IBD) have a negative impact on quality of life. The purpose of this study was to assess the quality of life in a large group of Finnish IBD patients and to compare it with that observed in a recent survey covering several other European countries. Material and methods. The European Federation of Crohn's and Ulcerative Colitis Associations (EFCCA) questionnaire, comprising questions about IBD symptoms, diagnosis, therapy, extraintestinal manifestations and their impact on patients’ quality of life, was sent to 3852 members of the Finnish Crohn and Colitis Association. The response rate was 63%. Results. IBD was diagnosed by a specialist in over 96% of cases and 94% of patients were continuously followed-up by a specialist. Fifty-eight percent of the patients had had IBD symptoms for over a year before consulting a specialist. The frequency of symptoms was lower in the Finnish patients and 93% of patients were satisfied with their current treatment compared with 76% in the European survey. For Crohn's disease, the rate of surgery was lower than that in the European survey (43% versus 52%). The patients reported improved quality of life after surgery, but 67% of patients with Crohn's disease and 34% with ulcerative colitis reported recurrence of symptoms. Comorbidity with ankylosing spondylitis was 22 times more common than in the general Finnish population and 49% of the patients suffered from joint pain. Conclusions. Finnish IBD patients are more satisfied with their treatment than those studied in the European survey. In Finland, gastroenterologists are usually responsible for the care, but the delay before the diagnosis remains long.
XII—Why Are Indexicals Essential?

Despite recent challenges, it is commonly held that certain indexical terms such as ‘I', ‘here’ and ‘now’ have a necessary or ‘essential’ role in certain kinds of action. I argue that this is correct, and I offer an explanation. A use of an indexical term of the kind in question connotes a specific relation between the thinking subject and the reference of the indexical. The mental representation of this relation has an epistemic feature that I call first-person redundancy . I show through a regress argument that a mental state of this kind is essential for common kinds of action, and perhaps for all actions.
Pilates exercise training vs. physical therapy for improving walking and balance in people with multiple sclerosis: a randomized controlled trial

Objective: Evaluate the effects of a Pilates exercise programme on walking and balance in people with multiple sclerosis and compare this exercise approach to conventional physical therapy sessions. Design: Randomized controlled trial. Setting: Multiple Sclerosis Center, Sheba Medical Center, Tel-Hashomer, Israel. Subjects: Forty-five people with multiple sclerosis, 29 females, mean age (SD) was 43.2 (11.6) years; mean Expanded Disability Status Scale (S.D) was 4.3 (1.3). Interventions: Participants received 12 weekly training sessions of either Pilates (n=22) or standardized physical therapy (n=23) in an outpatient basis. Main measures: Spatio-temporal parameters of walking and posturography parameters during static stance. Functional tests included the Time Up and Go Test, 2 and 6-minute walk test, Functional Reach Test, Berg Balance Scale and the Four Square Step Test. In addition, the following self-report forms included the Multiple Sclerosis Walking Scale and Modified Fatigue Impact Scale. Results: At the termination, both groups had significantly increased their walking speed (P=0.021) and mean step length (P=0.023). According to the 2-minute and 6-minute walking tests, both groups at the end of the intervention program had increased their walking speed. Mean (SD) increase in the Pilates and physical therapy groups were 39.1 (78.3) and 25.3 (67.2) meters, respectively. There was no effect of group X time in all instrumented and clinical balance and gait measures. Conclusions: Pilates is a possible treatment option for people with multiple sclerosis in order to improve their walking and balance capabilities. However, this approach does not have any significant advantage over standardized physical therapy.
Action to Language via the Mirror Neuron System: The role of vocal tract gestural action units in understanding the evolution of phonology

Language can be viewed as a structuring of cognitive units that can be transmitted among individuals for the purpose of communicating information. Cognitive units stand in specific and systematic relationships with one another, and linguists are interested in the characterization of these units and the nature of these relationships. Both can be examined at various levels of granularity. It has long been observed that languages exhibit distinct patterning of units in syntax and in phonology. This distinction, a universal characteristic of language, is termed duality of patterning (Hockett, 1960). Syntax refers to the structuring of words in sequence via hierarchical organization, where words are meaningful units belonging to an infinitely expandable set. But words also are composed of structured cognitive units. Phonology structures a small, closed set of recombinable, non-meaningful units that compose words (or signs, in the case of signed languages). It is precisely the use of a set of non-meaningful arbitrary discrete units that allows word creation to be productive. 1 In this chapter we outline a proposal that views the evolution of syntax and of phonology as arising from different sources and ultimately converging in a symbiotic relationship. Duality of patterning forms the intellectual basis for this proposal. Grasp and other manual gestures in early hominids are, as Arbib (Chapter 1, this volume) notes, well suited to provide a link from the iconic to the symbolic. Critically, the iconic aspects of manual gestures lend them a meaningful aspect that is critical to evolution of a system of symbolic units. However, we will argue that, given duality of patterning, phonological evolution crucially requires the emergence of effectively non-meaningful combinatorial units. We suggest that vocal tract action gestures are well suited to play a direct role in phonological evolution because, as argued by Studdert-Kennedy (2002a), they are
Eye movements when viewing advertisements

In this selective review, we examine key findings on eye movements when viewing advertisements. We begin with a brief, general introduction to the properties and neural underpinnings of saccadic eye movements. Next, we provide an overview of eye movement behavior during reading, scene perception, and visual search, since each of these activities is, at various times, involved in viewing ads. We then review the literature on eye movements when viewing print ads and warning labels (of the kind that appear on alcohol and tobacco ads), before turning to a consideration of advertisements in dynamic media (television and the Internet). Finally, we propose topics and methodological approaches that may prove to be useful in future research.
Street-Level Bureaucrats at Work: A Municipality-Level Institutional Analysis of Community-Based Natural Resource Management Implementation Practice in the Pasture Sector of Kyrgyzstan

The article looks into lowest-level policy implementers’ (street-level bureaucrats’) role in donor-initiated natural resource governance reforms. The article employs an institutional analysis framework with a specific policy implementation focus. A multiple case study reviews a resource user information campaign during the early phase of a community-based pasture management reform in Kyrgyzstan. It finds implementation rule simplification by policy implementers at the expense of full resource user involvement as a result of an insufficient contextual fit of the formal information rules. The results emphasize the need of well-designed implementation rules in order to ensure full and equitable resource user involvement in community-based natural resource management (CBNRM).
Subspace distribution clustering hidden Markov model

Most contemporary laboratory recognizers require too much memory to run, and are too slow for mass applications. One major cause of the problem is the large parameter space of their acoustic models. In this paper, we propose a new acoustic modeling methodology which we call subspace distribution clustering hidden Markov modeling (SDCHMM) with the aim of achieving much more compact acoustic models. The theory of SDCHMM is based on tying the parameters of a new unit, namely the subspace distribution, of continuous density hidden Markov models (CDHMMs). SDCHMMs can be converted from CDHMMs by projecting the distributions of the CDHMMs onto orthogonal subspaces, and then tying similar subspace distributions over all states and all acoustic models in each subspace, by exploiting the combinatorial effect of subspace distribution encoding, all original full-space distributions can be represented by combinations of a small number of subspace distribution prototypes. Consequently, there is a great reduction in the number of model parameters, and thus substantial savings in memory and computation. This renders SDCHMM very attractive in the practical implementation of acoustic models. Evaluation on the Airline Travel Information System (ATIS) task shows that in comparison to its parent CDHMM system, a converted SDCHMM system achieves seven- to 18-fold reduction in memory requirement for acoustic models, and runs 30%-60% faster without any loss of recognition accuracy.
Operating characteristics of PROMIS four-item depression and anxiety scales in primary care patients with chronic pain.

OBJECTIVE Depression and anxiety are prevalent in patients with chronic pain and adversely affect pain, quality of life, and treatment response. The purpose of this psychometric study was to determine the reliability and validity of the four-item Patient Reported Outcomes Measurement Information System (PROMIS) depression and anxiety scales in patients with chronic pain. DESIGN Secondary analysis of data from the Stepped Care to Optimize Pain care Effectiveness study, a randomized clinical trial of optimized analgesic therapy. SETTING Five primary care clinics at the Roudebush VA Medical Center (RVAMC) in Indianapolis, Indiana. SUBJECTS Two hundred forty-four primary care patients with chronic musculoskeletal pain. METHODS All patients completed the four-item depression and anxiety scales from the PROMIS 29-item profile, as well as several other validated psychological measures. The minimally important difference (MID) using the standard error of measurement (SEM) was calculated for each scale, and convergent validity was assessed by interscale correlations at baseline and 3 months. Operating characteristics of the PROMIS measures for detecting patients who had probable major depression or were anxiety-disorder screen-positive were calculated. RESULTS The PROMIS scales had good internal reliability, and the MID (as represented by two SEMs) was 2 points for the depression scale and 2.5 points for the anxiety scale. Convergent validity was supported by strong interscale correlations. The optimal screening cutpoint on the 4- to 20-point PROMIS scales appeared to be 8 for both the depression and anxiety scales. CONCLUSIONS The PROMIS four-item depression and anxiety scales are reasonable options as ultra-brief measures for screening in patients with chronic pain.
Polypyrimidine Tract-Binding Protein Is Critical for the Turnover and Subcellular Distribution of CD40 Ligand mRNA in CD4+ T Cells

CD40L (CD154) is regulated at the posttranscriptional level by an activation-induced process that results in a highly stable transcript at extended times of T cell activation. Transcript stability is mediated by polypyrimidine tract-binding protein (PTB)-containing complexes (complex I and II) that bind to three adjacent CU-rich sequences within the 3′ untranslated region. To assess the role of PTB in the expression and distribution of CD40L mRNA, PTB was targeted using short hairpin RNA in both primary T cells and a T cell line that recapitulates the stability phase of regulated CD40L mRNA decay. PTB knockdown resulted in a marked decrease in the mRNA stability that resulted in lowered CD40L surface expression. PTB was also critical for appropriate distribution of CD40L mRNA between the nucleus and cytoplasm and in the cytoplasm between the cytosol and the translating polysomes. The activation-induced formation of PTB-specific ribonucleoprotein complexes was observed only with cytoplasmic and not nuclear PTB indicating functional differences in the protein defined by cellular localization. Finally, we observed that cytoplasmic and nuclear PTB isoforms were differentially modified relative to each other and that the changes in cytoplasmic PTB were consistent with activation-induced phosphorylation. Together this work suggests that differentially modified PTB regulates CD40L expression at multiple steps by 1) retaining CD40L mRNA in the nucleus, 2) directly regulating mRNA stability at late times of activation, and 3) forming a ribonuclear complex that preferentially associates with translating ribosomes thus leading to an enhanced level of CD40L protein.