Miracle-dz/UniFAR-FTUs huggingface dataset:
Colorectal adenoma and cancer detection based on altered methylation pattern of SFRP1, SFRP2, SDC2, and PRIMA1 in plasma samples

ABSTRACT Aberrant methylation is one of the most frequent epigenetic alterations that can contribute to tumor formation. Cell-free DNA can originate from tumor tissue; therefore, the evaluation of methylation markers in cell-free DNA can be a promising method for cancer screening. Our aim was to develop a panel of biomarkers with altered methylation along the colorectal adenoma-carcinoma sequence in both colonic tissue and plasma. Methylation of selected CpG sites in healthy colonic (n = 15), adenoma (n = 15), and colorectal cancer (n = 15) tissues was analyzed by pyrosequencing. MethyLight PCR was applied to study the DNA methylation of SFRP1, SFRP2, SDC2, and PRIMA1 gene promoters in 121 plasma and 32 biopsy samples. The effect of altered promoter methylation on protein expression was examined by immunohistochemistry. Significantly higher (P < 0.05) DNA methylation levels were detected in the promoter regions of all 4 markers, both in CRC and adenoma tissues compared with healthy controls. Methylation of SFRP1, SFRP2, SDC2, and PRIMA1 promoter sequences was observed in 85.1%, 72.3%, 89.4%, and 80.9% of plasma samples from patients with CRC and 89.2%, 83.8%, 81.1% and 70.3% from adenoma patients, respectively. When applied as a panel, CRC patients could be distinguished from controls with 91.5% sensitivity and 97.3% specificity [area under the curve (AUC) = 0.978], while adenoma samples could be differentiated with 89.2% sensitivity and 86.5% specificity (AUC = 0.937). Immunohistochemical analysis indicated decreasing protein levels of all 4 markers along the colorectal adenoma-carcinoma sequence. Our findings suggest that this methylation biomarker panel allows non-invasive detection of colorectal adenoma and cancer from plasma samples.
Fast low-rank matrix approximation with locality sensitive hashing for quick anomaly detection

Detecting anomalous traffic is a critical task for advanced Internet management. The traditional approaches based on Principal Component Analysis (PCA) are effective only when the corruption is caused by small additive i.i. d. Gaussian noise. The recent Direct Robust Matrix Factorization (DRMF) is proven to be more robust and accurate in anomaly detection, but it incurs a high computation cost due to its need of singular value decomposition (SVD) for low-rank matrix approximation and the iterative use of SVD execution to find the final solution. To enable the anomaly detection for large traffic matrix with the use of DRMF, we formulate the low-rank matrix approximation problem as a problem of searching for the subspace to project the traffic matrix with the minimum error. We propose a novel approach, LSH-subspace, for fast low-rank matrix approximation. To facilitate the matrix partition for the quick search of the subspace, we propose several novel techniques: a multi-layer locality sensitive hashing (LSH) table to reorder the OD pairs based on LSH function, a partition principle to guide the partition to minimize the projection error, and a lightweight algorithm to exploit the sparsity of the outlier matrix to update the LSH table at low overhead. Our extensive simulations based on real trace data demonstrate that our LSH-subspace is 3 times faster than DRMF with high anomaly detection accuracy.
Sensory Effects of Transient Electrical Stimulation - Evaluation with a Neuroelectric Model

A model of myelinated nerve axon was used to study the initiation and propagation of action potentials for a variety of extracellular electrical stimuli. Frankenhaeuser-Huxley nonlinearities were incorporated at each of several nodes in a longitudinal array, and the extracellular current pulse was modeled as a spatial distribution of voltage disturbance along the membrane. Results from the model were compared to data from human sensory experiments and from animal electrophysiological experiments. Effects of polarity, electrode position, pulse duration, and biphasic oscillation frequency were examined. Biphasic pulses have higher excitation thresholds than monophasic pulses, provided the duration of a single phase is short relative to the time constant of the membrane depolarization process. The shapes of strength/duration curves from sensory experiments conform well to model predictions for monophasic stimuli. Strength/frequency curves derived from the model are similar to those from sensory stimulation with sinusoidal currents. The shapes of strength/frequency curves can be explained by membrane integration effects at high frequencies and membrane leakage effects at low frequencies. The model predicts lower thresholds for cathodal than for anodal stimulation: the predicted degree of polarity selectivity is confirmed by direct stimulation of axons in animal experiments, but is at variance with the selectivity found in human transcutaneous stimulation.
A comparison of several approaches to perform a vision-based long range navigation

In this paper, we deal with the problem of realizing a vision-based long range navigation task in a cluttered environment. To perform such a task, we have already developed two main controllers: a visual servoing one in charge of the navigation in the free space, and an obstacle avoidance one able to guarantee non collision. We have added a topological map made of several characteristic landmarks to realize large displacements. To deal with the occlusions, we have designed an algorithm which can compute the necessary visual data when they are temporarily lost. However, this algorithm requires initial conditions not only on the visual features but also on their depth. If the first ones are given by the last image before the occlusion, the second one is not available on our robot. Thus, in this paper we first propose a supervision algorithm able to select the right controller at the right instant and to switch smoothly between the different control laws. Second, we address the problem of the depth reconstruction and we compare two interesting methods from a theoretical and practical point of view. Simulation results in a noisy context and a table summarizing the advantages and drawbacks of both methods are provided.
TREM2 governs Kupffer cell activation and explains belr1 genetic resistance to malaria liver stage infection

Significance Current efforts in malaria therapeutics and vaccine development include strategies aimed at deterring infection at the liver stage, preventing subsequent clinical complications and malaria transmission. To elucidate response mechanisms operating during liver stage infection, we searched for host genetic factors that control parasite expansion in a mouse model of malaria liver stage resistance. Here we report that the cell surface receptor TREM2 is expressed in innate immune cell types residing in the liver and takes part in a mechanism enabling such cells to control the yield of hepatocyte infection. This work highlights the relevance of innate immunity mechanisms in controlling expansion of the malaria parasite in the liver. Plasmodium liver stage infection is a target of interest for the treatment of and vaccination against malaria. Here we used forward genetics to search for mechanisms underlying natural host resistance to infection and identified triggering receptor expressed on myeloid cells 2 (TREM2) and MHC class II molecules as determinants of Plasmodium berghei liver stage infection in mice. Locus belr1 confers resistance to malaria liver stage infection. The use of newly derived subcongenic mouse lines allowed to map belr1 to a 4-Mb interval on mouse chromosome 17 that contains the Trem2 gene. We show that Trem2 expression in the nonparenchymal liver cells closely correlates with resistance to liver stage infection, implicating TREM2 as a mediator of the belr1 genetic effect. Trem2-deficient mice are more susceptible to liver stage infection than their WT counterparts. We found that Kupffer cells are the principle cells expressing TREM2 in the liver, and that Trem2−/− Kupffer cells display altered functional activation on exposure to P. berghei sporozoites. TREM2 expression in Kupffer cells contributes to the limitation of parasite expansion in isolated hepatocytes in vitro, potentially explaining the increased susceptibility of Trem2−/− mice to liver stage infection. The MHC locus was also found to control liver parasite burden, possibly owing to the expression of MHC class II molecules in hepatocytes. Our findings implicate unexpected Kupffer–hepatocyte cross-talk in the control Plasmodium liver stage infection and demonstrate that TREM2 is involved in host responses against the malaria parasite.
Ultrasonic evaluation of orbito-ocular trauma in Benin-City, Nigeria.

AIMS AND OBJECTIVES To find out the causes, time of presentation for ultrasound scan, pattern of eye injuries and orbital ultrasound findings in patients with orbito-ocular trauma. MATERIALS AND METHODS Retrospective study of request cards, case notes and ultrasound reports of 67 patients who had trauma to the eye and were assessed with ultrasonography over a 3-year period (between 20th January 2000 and 19th January 2003) was done. The collected data included age, sex, presenting complaint, past medical history, duration of the injury before presentation to ultrasonographic study and ultrasound findings. RESULT Sixty-seven patients were seen consisting of 54 males (83.58%) and 11 females (16.42%) with male to female ratio of 5:1. Age range was 4 to 91 years with mean age of 30.8 years. 44 patients (65. 67%) had blunt trauma while 23 patients (34.32%) had penetrating trauma. The causes of the ocular trauma include road traffic accidents 32 (47.76%), assaults 16 (23.88%), gunshot injuries 10 (14. 93%), sports injuries 5 (7.46%), and falls from heights 4 (5.92%) patients. 42 patients (53.73%), especially those with severe injuries presented late for ultrasonography. Those who made early presentation were cases of assault because of police involvement. Forty-five patients (67.16%) had structurally identifiable pathology in one or both eyes. Retinal detachment 18 (26.87%), vitreous haemorrhage 17 (25.37%), traumatic cataract 13 (19.40), ruptured globe 6 (8.96%) and posterior dislocation of the lens 6 (8.96) were the commonest abnormal sonographic findings. In 22 patients (32.84%) both eyes were normal. CONCLUSION Ultrasound scan is a useful imaging modality for examination of the globe in patients with ocular trauma. Road traffic accident is the commonest cause of traumatic ocular injury affecting the globe. Retinal detachment and vitreous haemorrhage are the most frequent injuries to the globe diagnosed by ultrasound scan. Measures to reduce road traffic accidents will have far reaching positive effect in preventing blindness resulting from orbito-ocular trauma in Nigeria.
Group I metabotropic glutamate receptors (mGluRs) modulate visual responses in the superficial superior colliculus of the rat

Group I metabotropic glutamate receptors (mGluRs) are expressed in cells in the superficial layers of the rat superior colliculus (SSC) and SSC afferents. The purpose of this study was to investigate the physiological effect of Group I mGluR activation on visual responses of SSC neurones using both in vivo and in vitro techniques. In the in vivo preparation, agonists and antagonists were applied by iontophoresis and single neurone activity was recorded extracellularly in anaesthetised rats. Application of the Group I agonist (S)‐3,5‐dihydroxyphenylglycine (DHPG) resulted in a reversible inhibition of the visual response. The effect of DHPG could be blocked by concurrent application of the Group I (mGluR1/mGluR5) antagonist (S)‐4‐carboxyphenylglycine (4CPG) or mGluR1 antagonist (+)‐2‐methyl‐4‐carboxyphenylglycine (LY367385). Application of 4CPG alone resulted in a facilitation of the visual response and this effect was not changed when the visual stimulus contrast was varied. Response habituation was observed when visual stimuli were presented at 0.5 s intervals, but this was not affected by DHPG or 4CPG. In slices of the superior colliculus, stimulation of the optic tract resulted in a field EPSP recorded from the SSC whose duration was increased in the presence of the GABA antagonists picrotoxin and CGP55845. Application of DHPG (5‐100 μM) reduced the field EPSP, and this effect could be reversed by the mGluR1 antagonist LY367385 (200 μM), but not by the mGluR5 antagonist MPEP (5 μM). These data show that activation of mGluR1, but probably not mGluR5, can modulate visual responses of SSC neurones in vivo, and that this could be via presynaptic inhibition of glutamate release from either retinal or, possibly, cortical afferents.
Host-Cell Lysosomal Response to Two Strains of Herpes Simplex Virus

A correlation has been made between the host lysosomal responses to and release of infectious virus from HEp-2 cells infected with two strains of herpes simplex virus (HSV). Supravital staining with acridine orange was used for morphological studies of macroplaque and microplaque HSV-infected cells. With the progression of infection, cells infected with either microplaque HSV or macroplaque HSV were observed to undergo different lysosomal and cytopathic changes, which could be correlated with increased accumulation of acid phosphatase and infectious virus in the extracellular fluid.
The Arabidopsis Abscisic Acid Catabolic Gene CYP707A2 Plays a Key Role in Nitrate Control of Seed Dormancy1[W]

Nitrate releases seed dormancy in Arabidopsis (Arabidopsis thaliana) Columbia accession seeds in part by reducing abscisic acid (ABA) levels. Nitrate led to lower levels of ABA in imbibed seeds when included in the germination medium (exogenous nitrate). Nitrate also reduced ABA levels in dry seeds when provided to the mother plant during seed development (endogenous nitrate). Transcript profiling of imbibed seeds treated with or without nitrate revealed that exogenous nitrate led to a higher expression of nitrate-responsive genes, whereas endogenous nitrate led to a profile similar to that of stratified or after-ripened seeds. Profiling experiments indicated that the expression of the ABA catabolic gene CYP707A2 was regulated by exogenous nitrate. The cyp707a2-1 mutant failed to reduce seed ABA levels in response to both endogenous and exogenous nitrate. In contrast, both endogenous and exogenous nitrate reduced ABA levels of the wild-type and cyp707a1-1 mutant seeds. The CYP707A2 mRNA levels in developing siliques were positively correlated with different nitrate doses applied to the mother plants. This was consistent with a role of the CYP707A2 gene in controlling seed ABA levels in response to endogenous nitrate. The cyp707a2-1 mutant was less sensitive to exogenous nitrate for breaking seed dormancy. Altogether, our data underline the central role of the CYP707A2 gene in the nitrate-mediated control of ABA levels during seed development and germination.
Increased Akt and phosphorylated Akt expression are associated with malignant biological features of prostate cancer in Japanese men

To investigate the relationship between the expression of Akt (a serine/threonine kinase that plays a central role in tumorigenesis), phosphorylated Akt (p‐Akt), prostate cancer tumour grade, androgen receptor (AR)‐staining score, and Ki67 labelling index (LI) in Japanese men.
Application of subjective global assessment as a screening tool for malnutrition in pediatric surgical patients.

OBJECTIVES To determine the incidence of malnutrition in the pediatric surgical ward and to evaluate the value of SGA as a nutrition assessment tool in this patient group. PATIENTS AND METHOD Consecutive pediatric patients aged 2 months-16 years who were admitted for an operation in the pediatric surgical ward, Songklanagarind Hospital from February to September 2001 were included. Nutritional assessment was performed for each case, using a translated version of the SGA questionnaire. Anthropometric measurements and laboratory tests were performed as a routine pre-operative evaluation. The result of the SGA ratings were tested against the other parameters and Gomez's weight for age (W/A) criteria for protein energy malnutrition. SGA and the other parameters were tested for association with post-operative infectious complications. Each SGA question was analyzed by multivariate logistic regression analysis, to determine an independent correlation between the question item and final SGA rating. RESULTS The study included 78 patients. At least one item of SGA history was positive in 28 cases (35.9%). The SGA rating was class A in 50 cases (64.1%), class B in 17 cases and class C in 11 cases. According to the Gomez classification, 42 cases (53.8%) were considered normal or overweight, whereas 23 cases (29.5%) were in the first degree underweight, 9 cases were in the second degree and 4 cases were in the third degree. Malnutrition by SGA rating correlated significantly with Gomez's second and third degree malnutrition, lower z-score, lower BMI and hypoalbuminemia. Malnutrition by SGA rating and hypoalbuminemia were associated with increased risk of an infectious complication, whereas a significant relation between a complication and anthropometric malnutrition could not be demonstrated. Moreover, SGA malnutrition was significantly associated with a longer post-operative stay. Among 5 items of SGA questions, history of weight change in the recent 2 weeks and increased energy need considered by an underlying disease were found to be independently associated with a final SGA rating of malnutrition. History of weight loss and gastrointestinal symptoms were the 2 most sensitive questions. CONCLUSIONS SGA is a sensitive and specific nutrition assessment tool useful in a pre-operative pediatric setting. Application of the protocol as a complement of standard anthropometric tool should be considered.
Stat6 Signaling Suppresses VLA-4 Expression by CD8+ T Cells and Limits Their Ability to Infiltrate Tumor Lesions In Vivo1

VLA-4 plays a critical role in T cell trafficking into inflammatory sites. Our recent studies have suggested that VLA-4 expression on CD8+ T cells is negatively controlled by IL-4 and serves as a functionally distinguishing variable for why Type-1, but not Type-2, CD8+ T cells are able to traffic into tumors. In this study, using in vitro culture of murine CD8+ T cells under Type-1 and Type-2 cytokine conditions, we show that IL-4-mediated down-regulation of VLA-4 expression is completely abrogated in Stat6-deficient CD8+ T cells. Conversely, CD8+ T cells expressing a constitutively active mutant form Stat6 (Stat6VT) failed to express VLA-4 even in the absence of IL-4-stimulation. Notably, Type-2 CD8+ T cells developed from Stat6−/− but not wild-type mice were competent to migrate into tumor lesions in vivo. These results suggest that Stat6-signaling is necessary and sufficient to restrict CD8+ T cell expression of VLA-4 (by IL-4), thereby serving as a regulator for CD8+ T cell infiltration into tumors.
Bad Habits and the Endogenous Timing of Urges

I present a theory of harmful addiction in which “giving in” to an unwanted urge (⁠i.e. consumption) delays the recurrence of urges in the short-run, but increases their long-run frequency. The theory offers new predictions as to how the frequency, levels, cue-dependence, and temporal consistency of consumption evolve during habituation, while uniquely capturing near-term substitution in demand across time. New welfare implications for restrictions on consumption and on marketing are also addressed.
The Effects of Switching Behavior on the Evolutionary Diversification of Generalist Consumers

Mathematical models of consumer‐resource systems explore the evolution of a morphological trait that determines two resource acquisition rates in a generalist consumer. The consumer also has the ability to adjust its relative consumption of the two resources via behavioral (or developmental) plasticity subject to a trade‐off. The analysis examines both stable systems and those with sustained fluctuations in abundance. In both cases, it seeks to determine how the behavioral choice affects the evolution of the morphological characters. The presence of adaptive switching behavior transforms the shape of the relationship between the morphological character and fitness in a manner that usually leads to evolution of two or more morphological types. As in models without switching, the presence of sustained cycles in resource densities often allows the evolution of a generalist as well as two specialists. However, switching expands and shifts the parameter regions yielding this outcome and in some cases allows the evolution and coexistence of at least two generalists as well as the two specialists. This level of diversity supported by only two resources is not seen in the absence of behavioral choice and resource cycles. The results suggest major roles for both behavior and environmental variation in adaptive radiation.
Microwave versus saline-linked radiofrequency (Aquamantys) assisted liver resection in a porcine liver resection model. A safety and feasibility pilot study.

PURPOSE The aim of this study was to compare the feasibility, efficacy and safety of microwave ablation and saline-linked radiofrequency (Aquamantys) in liver resection. METHODS Sixteen domestic pigs (8 per group) underwent thermoablations. Group A consisted of 8 pigs in which microwave left lateral liver resection was performed. Group B consisted of 8 pigs which underwent left lateral liver resection by the Aquamantys system. After 28 days of close follow-up, the animals were sacrificed in order to study the macroscopic and microscopic findings of each intervention on the liver edge. RESULTS An average of 47.13 min was enough for the entire operation to take place using Aquamantys, whereas an average of 59.13 min was needed in the microwave liver resection group. Mean blood loss was 40 ml (range 5-85) with Aquamantys whereas mean blood loss was 72.37 ml (range 42-100) using microwave. Postoperative complications rates were extremely low in both groups. There was no intra- or postoperative mortality. CONCLUSIONS Our study demonstrated that left lateral liver resection using Aquamantys system is technically feasible in the porcine model and proved to be highly effective and a safer hemostatic method compared to microwave ablation.
In vitro synergistic activity of colistin with tigecycline or β-lactam antibiotic/β-lactamase inhibitor combinations against carbapenem-resistant Acinetobacter baumannii

Objective Nosocomial infection caused by carbapenem-resistant Acinetobacter baumannii is a worldwide problem and treatment options remain controversial. This study investigated the in vitro effect of various antibiotic combinations against carbapenem-resistant A. baumannii strains. Methods Antibiotic susceptibility of A. baumannii strains was analysed. In vitro synergistic efficacy of colistin combined with tigecycline, cefoperazone/sulbactam or piperacillin/tazobactam was tested against carbapenem-resistant A. baumannii strains. Synergy studies were performed using an eplisometer test-strip method. Results Of the 50 carbapenem-resistant A. baumannii strains tested, 96% were susceptible to colistin and 64% were susceptible to tigecycline. Colistin–tigecycline, colistin–cefoperazone/sulbactam and colistin–piperacillin/tazobactam combinations were found to have synergistic effects against six (12%), two (4%), and one (2%), respectively, of the strains tested. Conclusions Colistin combined with tigecycline, cefoperazone/sulbactam or piperacillin/tazobactam revealed synergistic effects in some carbapenem-resistant A. baumannii strains. These results, together with the shortage of treatment options and the risk of developing resistance to colistin, suggest that clinicians should use colistin combined with other antibiotics or β-lactamase inhibitors when treating carbapenem-resistant A. baumannii infection.