Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal distribution of Vibrio parahaemolyticus in freshwater environs and in association with freshwater fishes in Calcutta

The seasonal distribution of Vibrio parahaemolyticus in freshwater environs and in association with freshwater fishes was studied in 1982 and 1983. The occurrence of this organism in water and sediments at the three sites studied was very infrequent and was restricted to the summer months, although it was not always isolated during these months. The association of V. parahaemolyticus with plankton was chiefly confined to the summer months and progressively declined with the onset of monsoons, remaining below detectable levels during the postmonsoon and winter months. The incidence and counts of V. parahaemolyticus were consistently higher in association with plankton than with water and sediment samples. V. parahaemolyticus could be recovered throughout the period of investigation from freshly caught and market samples of freshwater fishes. The highest recovery rate of this halophile from fishes was invariably from fecal samples. Most of the strains isolated in this study were untypable, and those which could be typed were predominantly serotypes encountered in the environment. All the isolates were Kanagawa negative. From this study, it could be concluded that the survival of V. parahaemolyticus in freshwater ecosystems is transient and dependent on a biological host.
Mosaicing of Bladder Endoscopic Image Sequences: Distortion Calibration and Registration Algorithm

Cancers located on the internal wall of bladders can be detected in image sequences acquired with endoscopes. The clinical diagnosis and follow-up can be facilitated by building a unique panoramic image of the bladder with the images acquired from different viewpoints. This process, called image mosaicing, consists of two steps. In the first step, consecutive images are pairwise registered to find the local transformation matrices linking geometrically consecutive images. In the second step, all images are placed in a common and global coordinate system. In this contribution, a mutual information-based similarity measure and a stochastic gradient optimization method were implemented in the registration process. However, the images have to be preprocessed in order to register the data in a robust way. Thus, a simple correction method of the distortions affecting endoscopic images is presented. After the placement of all images in the global coordinate system, the parameters of the local transformation matrices are all adjusted to improve the visual aspect of the panoramic images. Phantoms are used to evaluate the global mosaicing accuracy and the limits of the registration algorithm. The mean distances between ground truth positions in the mosaiced image range typically in 1-3 pixels. Results given for in vivo patient data illustrate the ability of the algorithm to give coherent panoramic images in the case of bladders.
Satellite Associations in Down Syndrome

Abstract The association of acrocentric chromosomes by their satellites, referred as satellite associations (SAs), is implicated as a cause for non-disjunction and hence an etiological factor for Down syndrome. The present study compares the frequency of SAs observed in 30 children with Down syndrome and their parents to that seen in 16 healthy children and their parents. Silver (Ag-NOR) stained metaphases showed statistically significant increase in SAs in children with DS, compared to controls. Satellite associations were found to be also significantly increased in either parent with DS offspring. Two patients with Robertsonian translocation showed decreased SAs. This study supports the hypothesis that an increased tendency for satellite associations is an indicator for non-disjunction.
The clinical and pathological features of gastric impaction in twelve horses.

REASONS FOR PERFORMING STUDY Gastric impaction in the horse is poorly described in the veterinary literature. OBJECTIVES To review the clinical and pathological features of gastric impaction. METHODS The clinical details of horses presenting with colic over a 7-year period and cases in which gastric impaction was considered to determine the outcome were reviewed. Clinical and clinicopathological data were recorded. RESULTS Twelve cases of gastric impaction were recorded (1.4% of 857 horses hospitalised for colic). Diagnosis was achieved by ultrasonographic examination, gastroscopy, exploratory celiotomy and/or post mortem examination. Five out of 12 horses were successfully treated, 5/12 were subjected to euthanasia (3 at celiotomy and 2 due to recurrence of impaction) and 2/12 died. Three out of 12 horses had spontaneous gastric rupture despite attempted treatment (one was subjected to euthanasia at celiotomy and 2 died). Post mortem examination (7 horses) revealed gross muscular thickening of the stomach wall in 6/7 horses. Histological examination revealed focal fibrosis of the stomach wall in 4/6 and focal myositis in 1/6 horses. CONCLUSIONS AND PRACTICAL SIGNIFICANCE: Gastric impaction is a rare cause of colic and affected horses can present with acute, chronic or recurrent colic in the presence or absence of other gastrointestinal disease. Spontaneous gastric rupture may occur. A proportion of affected horses have gross thickening of the muscular layers of the stomach wall.
Eyelid Lymphatics I: Histochemical Comparisons Between the Monkey and Human

Purpose: To study the lymphatic drainage of the cynomolgus monkey and human eyelid and periocular tissue by means of histochemistry. Methods: Eyelid and periocular tissue from three cynomolgus monkeys undergoing sacrifice for glaucoma and retina research purposes and discarded tissue from a wedge resection of one human eyelid were used for histochemical analysis. Lymphatic capillaries were distinguished histochemically in monkey and human eyelids by light microscopy with a 5′-nucleotidase (5′-Nase) staining method. Identification of lymphatic vessels was based on strict morphologic criteria combined with specific 5′-Nase staining. Results: Histochemical analysis with 5′-nucleotidase revealed a subcutaneous and pretarsal lymphatic plexus in both the human and monkey. Conclusions: Histochemical results demonstrate similar lymphatic plexi in the monkey and human. Future studies will help to clarify the lymphatic drainage pathways of monkey and human eyelids.
Agnostic Selective Classification

For a learning problem whose associated excess loss class is (β, B)-Bernstein, we show that it is theoretically possible to track the same classification performance of the best (unknown) hypothesis in our class, provided that we are free to abstain from prediction in some region of our choice. The (probabilistic) volume of this rejected region of the domain is shown to be diminishing at rate $O(B\theta (\sqrt{1/m}))^\beta)$, where θ is Hanneke's disagreement coefficient. The strategy achieving this performance has computational barriers because it requires empirical error minimization in an agnostic setting. Nevertheless, we heuristically approximate this strategy and develop a novel selective classification algorithm using constrained SVMs. We show empirically that the resulting algorithm consistently outperforms the traditional rejection mechanism based on distance from decision boundary.
Vision-based navigation and environmental representations with an omnidirectional camera

Proposes a method for the visual-based navigation of a mobile robot in indoor environments, using a single omnidirectional (catadioptric) camera. The geometry of the catadioptric sensor and the method used to obtain a bird's eye (orthographic) view of the ground plane are presented. This representation significantly simplifies the solution to navigation problems, by eliminating any perspective effects. The nature of each navigation task is taken into account when designing the required navigation skills and environmental representations. We propose two main navigation modalities: topological navigation and visual path following. Topological navigation is used for traveling long distances and does not require knowledge of the exact position of the robot but rather, a qualitative position on the topological map. The navigation process combines appearance based methods and visual servoing upon some environmental features. Visual path following is required for local, very precise navigation, e.g., door traversal, docking. The robot is controlled to follow a prespecified path accurately, by tracking visual landmarks in bird's eye views of the ground plane. By clearly separating the nature of these navigation tasks, a simple and yet powerful navigation system is obtained.
Animation of natural scene by virtual eye-movements evokes high precision and low noise in V1 neurons

Synaptic noise is thought to be a limiting factor for computational efficiency in the brain. In visual cortex (V1), ongoing activity is present in vivo, and spiking responses to simple stimuli are highly unreliable across trials. Stimulus statistics used to plot receptive fields, however, are quite different from those experienced during natural visuomotor exploration. We recorded V1 neurons intracellularly in the anaesthetized and paralyzed cat and compared their spiking and synaptic responses to full field natural images animated by simulated eye-movements to those evoked by simpler (grating) or higher dimensionality statistics (dense noise). In most cells, natural scene animation was the only condition where high temporal precision (in the 10–20 ms range) was maintained during sparse and reliable activity. At the subthreshold level, irregular but highly reproducible membrane potential dynamics were observed, even during long (several 100 ms) “spike-less” periods. We showed that both the spatial structure of natural scenes and the temporal dynamics of eye-movements increase the signal-to-noise ratio by a non-linear amplification of the signal combined with a reduction of the subthreshold contextual noise. These data support the view that the sparsening and the time precision of the neural code in V1 may depend primarily on three factors: (1) broadband input spectrum: the bandwidth must be rich enough for recruiting optimally the diversity of spatial and time constants during recurrent processing; (2) tight temporal interplay of excitation and inhibition: conductance measurements demonstrate that natural scene statistics narrow selectively the duration of the spiking opportunity window during which the balance between excitation and inhibition changes transiently and reversibly; (3) signal energy in the lower frequency band: a minimal level of power is needed below 10 Hz to reach consistently the spiking threshold, a situation rarely reached with visual dense noise.
Quadratic Electrooptic Modulation Of Dye-Doped Polymers: Measurement Of Third Order Electronic Nonlinear Optical Susceptibilities

Quadratic electrooptic modulation of thin dye-doped polymer films is used to evaluate the electronic third-order susceptibility, χ(3) . To determine this susceptibility, the other contributing mechanisms, including orientational effects, electrostriction, electrode attraction, trapped charge movement, and heating, must be considered. The two dominant non-electronic effects are the orientational effect and the electric field-induced electrooptic effect. The degree of molecular motion of the dye molecules in the polymer matrix is measured with electric field-induced second-harmonic generation below the glass transition temperature of the composite. The microscopic orientational elastic constants, as determined from these second-harmonic measurements, are used to predict the orientational contributions. The molecular electronic third-order susceptibility of a poly(methyl methacrylate)/azo dye system, determined with the electrooptic measurement, is consistent with values derived from third-harmonic generation measurements.
Synthesizing Robust Adversarial Examples

Standard methods for generating adversarial examples for neural networks do not consistently fool neural network classifiers in the physical world due to a combination of viewpoint shifts, camera noise, and other natural transformations, limiting their relevance to real-world systems. We demonstrate the existence of robust 3D adversarial objects, and we present the first algorithm for synthesizing examples that are adversarial over a chosen distribution of transformations. We synthesize two-dimensional adversarial images that are robust to noise, distortion, and affine transformation. We apply our algorithm to complex three-dimensional objects, using 3D-printing to manufacture the first physical adversarial objects. Our results demonstrate the existence of 3D adversarial objects in the physical world.
Field Evaluation of PIMA Point-of-Care CD4 Testing in Rakai, Uganda

Objective To assess the accuracy of PIMA Point-of-Care (POC) CD4 testing in rural Rakai, Uganda. Methods 903 HIV positive persons attending field clinics provided a venous blood sample assessed on site using PIMA analyzers per manufacturer's specifications. The venous samples were then run on FACSCalibur flow cytometry at a central facility. The Bland–Altman method was used to estimate mean bias and 95% limits of agreement (LOA). Sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) were calculated for a CD4 threshold of <350 and <500 cells/uL for antiretroviral eligibility. Results There was a high correlation between PIMA and FACSCalibur CD4 counts (r = 0.943, p<0.001). Relative to FACSCalibur, the PIMA POC CD4 had negative mean bias of −34.6 cells/uL (95% LOA: −219.8 to 150.6) overall. The dispersion at CD4<350 cells/uL was 5.1 cells/uL (95% LOA: −126.6 to 136.8). For a threshold of CD4<350 cells/uL, PIMA venous blood had a sensitivity of 88.6% (95%CI 84.8–92.4%), specificity of 87.5% (95%CI 84.9–90.1%), NPV of 94.9% (95%CI 93.1–96.7%), and PPV of 74.4% (95%CI 69.6–79.2%). PIMA sensitivity and PPV significantly increased to 96.1% and 88.3% respectively with increased threshold of 500 cells/uL. Conclusions Overall, PIMA POC CD4 counts demonstrated negative bias compared to FACSCalibur. PIMA POC sensitivity improved significantly at a higher CD4 threshold of 500 than a 350 cells/uL threshold.
Changes in Prefrontal-Limbic Function in Major Depression after 15 Months of Long-Term Psychotherapy

Neuroimaging studies of depression have demonstrated treatment-specific changes involving the limbic system and regulatory regions in the prefrontal cortex. While these studies have examined the effect of short-term, interpersonal or cognitive-behavioural psychotherapy, the effect of long-term, psychodynamic intervention has never been assessed. Here, we investigated recurrently depressed (DSM-IV) unmedicated outpatients (N = 16) and control participants matched for sex, age, and education (N = 17) before and after 15 months of psychodynamic psychotherapy. Participants were scanned at two time points, during which presentations of attachment-related scenes with neutral descriptions alternated with descriptions containing personal core sentences previously extracted from an attachment interview. Outcome measure was the interaction of the signal difference between personal and neutral presentations with group and time, and its association with symptom improvement during therapy. Signal associated with processing personalized attachment material varied in patients from baseline to endpoint, but not in healthy controls. Patients showed a higher activation in the left anterior hippocampus/amygdala, subgenual cingulate, and medial prefrontal cortex before treatment and a reduction in these areas after 15 months. This reduction was associated with improvement in depressiveness specifically, and in the medial prefrontal cortex with symptom improvement more generally. This is the first study documenting neurobiological changes in circuits implicated in emotional reactivity and control after long-term psychodynamic psychotherapy.
A context-dependent combination of Wnt receptors controls axis elongation and leg development in a short germ insect

Short germ embryos elongate their primary body axis by consecutively adding segments from a posteriorly located growth zone. Wnt signalling is required for axis elongation in short germ arthropods, including Tribolium castaneum, but the precise functions of the different Wnt receptors involved in this process are unclear. We analysed the individual and combinatorial functions of the three Wnt receptors, Frizzled-1 (Tc-Fz1), Frizzled-2 (Tc-Fz2) and Frizzled-4 (Tc-Fz4), and their co-receptor Arrow (Tc-Arr) in the beetle Tribolium. Knockdown of gene function and expression analyses revealed that Frizzled-dependent Wnt signalling occurs anteriorly in the growth zone in the presegmental region (PSR). We show that simultaneous functional knockdown of the Wnt receptors Tc-fz1 and Tc-fz2 via RNAi resulted in collapse of the growth zone and impairment of embryonic axis elongation. Although posterior cells of the growth zone were not completely abolished, Wnt signalling within the PSR controls axial elongation at the level of pair-rule patterning, Wnt5 signalling and FGF signalling. These results identify the PSR in Tribolium as an integral tissue required for the axial elongation process, reminiscent of the presomitic mesoderm in vertebrates. Knockdown of Tc-fz1 alone interfered with the formation of the proximo-distal and the dorso-ventral axes during leg development, whereas no effect was observed with single Tc-fz2 or Tc-fz4 RNAi knockdowns. We identify Tc-Arr as an obligatory Wnt co-receptor for axis elongation, leg distalisation and segmentation. We discuss how Wnt signalling is regulated at the receptor and co-receptor levels in a dose-dependent fashion.
The Amphichronic Program vs. Evolutionary Phonology

Abstract 1. Synchronic and historical explanation Evolutionary Phonology. Evolutionary Phonology seeks to derive typological generalizations from recurrent patterns of language change, themselves assumed to be rooted in perception, production, and acquisition. The goal is to eliminate UG by providing diachronic explanations for the cross-linguistic evidence that has been used to motivate it.
ACLAME: A CLAssification of Mobile genetic Elements, update 2010

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac.be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added.
Prediction of sepsis in trauma patients

Trauma is one of the leading causes of death worldwide. Approximately 39.5% of deaths occur in the hospital, and the mortality rate of delayed death caused by septic complications is still high. Early prediction of the development of sepsis can help promote early intervention and treatment for patients and contribute to improving patient outcomes. Thus so far, biomarkers, patient demographics and injury characteristics are the main methods used for predicting sepsis in trauma patients. However, studies that verify their predictive value are limited, and the results are still controversial. More work should be conducted to explore more efficient and accurate ways to predict post-traumatic sepsis.
Intracardiac mobile thrombus and D-dimer fragment of fibrin in patients with mitral stenosis.

OBJECTIVE--To investigate the relation between intracardiac thrombus and blood coagulability in patients with mitral stenosis. DESIGN--Prospective study. Cross sectional echocardiography and plasma concentrations of the D-dimer fragment of fibrin were used concurrently to detect intracardiac thrombus in patients with mitral stenosis. SETTING--Department of Medicine, National Cardiovascular Centre, Osaka, Japan. PATIENTS--63 patients with mitral stenosis. None of them had been receiving any anticoagulants or antiplatelet agents. MAIN OUTCOME MEASURES--Plasma concentrations of D-dimer in patients with a mobile intracardiac thrombus, those in patients with a non-mobile intracardiac thrombus, and those in patients without an intracardiac thrombus. RESULTS--A mobile intracardiac thrombus was found in 10 patients and a non-mobile thrombus in eight. The remaining 45 patients had no intracardiac thrombi. Plasma concentrations of D-dimer in the 10 patients with a mobile thrombus were all greater than 300 ng/ml (mean 983.3, 95% confidence interval 498.9 to 1467.7 ng/ml) and they were significantly higher than those in the patients with a non-mobile thrombus (226.2, 33.6 to 418.8 ng/ml) and the patients without an intracardiac thrombus (147.2, 110.4 to 184 ng/ml). CONCLUSIONS--A high plasma concentration of D-dimer seemed to reflect a hypercoagulable intracardiac state and may be a helpful indicator of the possible presence of mobile intracardiac thrombus in patients with mitral stenosis.
Multi-step-ahead Prediction with Neural Networks : a Review

We review existing approaches in using neural networks for solving multi -step-ahead prediction problems. A few experiments allow us to further explore the relationship between the abilit y to learn longer-range dependencies and performance in multi -stepahead prediction. We eventually focus on characteristics of various multi -step-ahead prediction problems that encourage us to prefer one method over another.
Resorbed co‐twin as an explanation for discrepant chorionic villus results: Non‐mosaic 47,XX, +16 in villi (direct and culture) with normal (46,XX) amniotic fluid and neonatal blood

Non‐mosaic trisomy 16 was observed in chorionic villus cytotrophoblasts (direct) as well as cultured mesenchymal core cells derived from the pregnancy of a 38‐year‐old woman. Chromosome preparations from amniotic fluid and neonatal cultures (cord blood) were 46,XX. Normal fetal growth as determined by serial ultrasound examinations occurred throughout the pregnancy, which resulted in a healthy 2724 g female. Multiple biopsies taken from the umbilical cord, placental cotyledons, and fetal membranes were 46,XX. However, a placental nodule and three of six cultures initiated from membranes (amnion and chorion) showed 46,XX/47,XX, + 16 mosaicism.