Miracle-dz/UniFAR-FTUs huggingface dataset:
YspM, a Newly Identified Ysa Type III Secreted Protein of Yersinia enterocolitica

ABSTRACT Yersinia enterocolitica has three type three secretion systems, the flagellar, the plasmid Ysc type III secretion system (T3SS), and the chromosomal Ysa T3SS. The Ysc T3SS, through the proteins it secretes (Yops), prevents phagocytosis of Y. enterocolitica and is required for disease processes in the mouse host. Recent data demonstrate a role for the Ysa T3SS during initial colonization of the mouse via secretion of Ysps (Yersinia secreted proteins). This work characterizes the discovery of a newly identified Ysa type III secreted protein, YspM. Expression of yspM is regulated by temperature, NaCl concentration, and other known regulators of the ysa system. In addition, YspM is translocated into host cells via the Ysa T3SS. YspM is homologous to proteins classified as GDSL bacterial lipases, which possess a catalytic triad of amino acids (Ser, Asp, and His) located in three of five blocks of amino acid identity. Sequence analysis of the JB580v strain of Y. enterocolitica shows that, due to a premature stop codon, it no longer encodes the fifth block of amino acid identity containing the predicted catalytic histidine. However, seven other biotype 1B strains sequenced did possess the domain. A functional difference between the forms was revealed when YspM was expressed in Saccharomyces cerevisiae. Yeast growth was uninhibited when YspM from JB580v was expressed but greatly inhibited when YspM from Y295 (YspMY295) was expressed. Site-directed mutagenesis of the histidine of YspMY295 ablated the toxic effects. These results indicate that YspM is secreted by the Ysa T3SS and that, possibly due to lipase activity, it targets eukaryotic cellular component(s).
Investigation of optimal extraction, antioxidant, and antimicrobial activities of Achillea biebersteinii and A. wilhelmsii

Objective: Achillea species are endowed with multiple biological activities including antioxidant properties. However, no study has yet investigated the impact of extraction method and pH on the biological activities of these plants. The present study aimed to investigate the antioxidant and antimicrobial effects of methanol extracts from the aerial parts of the species Achillea biebersteinii Afan and Achillea wilhelmsii C. Koch (Asteraceae). In addition, the impact of extraction method and pH on these biological activities was evaluated. Materials and methods: Methanol extracts of A. biebersteinii and A. wilhelmsii were prepared using classical maceration and high-intensity ultrasound methods. Ultrasound-assisted extraction was performed at three different pH values: 5.7, 6.3 and 6.9. Results: Total phenolic compounds (range: 20.16–108.54 vs. 17.18–59.61 mg gallic acid equivalent/g sample in A. biebersteinii and A. wilhelmsii, respectively), total flavonoids (range: 8.33–12.97 vs. 7.79–9.41 mg catechin equivalent/g sample), 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (IC50: 40.63–346.34 vs. 84.02–462.41) and reducing power (IC50: 504.44–4406.67 vs. 1710.00–5501.67) were significantly higher in A. biebersteinii vs. A. wilhelmsii and ultrasound-assisted vs. classical maceration extracts of both species. The aforementioned items were higher at pH = 6.3, followed by pHs of 6.9 and 5.7, respectively. Overall, A. biebersteinii extracts were more active against all of the tested microorganisms than A. wilhelmsii. Sensitivities of Gram-positive bacteria were higher for both Achillea extracts than the Gram-negative bacteria. No observable inhibitory activity was found from different extracts against Aspergillus niger. Conclusion: The findings of the present study suggest that methanol extracts of A. biebersteinii and A. wilhelmsii possess antioxidant and antimicrobial activity, being higher in the former. Ultrasound-assisted extraction and pH of 6.3 have significant augmenting impact on the total phenolic and flavonoid content as well as antioxidant activities of both species.
Conception et simulation des générateurs, crypto-systèmes et fonctions de hachage basés chaos performants

Dans cette these, nous etudions la problematique de la securite de l’information basee sur les sequences chaotiques, et ses services a savoir : la confidentialite, l’integrite des donnees et l’authentification de la source. D’abord, le probleme de la generation des sequences chaotiques performantes est traite. A ce sujet, nous proposons trois generateurs performants, incluant chacun une technique de perturbation afin de palier aux inconvenients de la precision finie. Le premier generateur utilise un couplage de fonctions booleennes non lineaires. Le deuxieme s’appuie sur une couche de diffusion globale, flexible et efficace. Le troisieme generateur utilise le couplage en parallele de deux filtres recursifs. Ensuite la question, de la conception et de la realisation des crypto-systemes bases chaos robustes et rapides, est etudiee et analysee. A ce propos, nous proposons deux crypto-systemes bases chaos dynamiques, de structure SPN, tres performants compares a l’algorithme AES. Le deuxieme crypto-systeme, contient par rapport au premier, une couche de diffusion efficace, mais ne necessite pas d’operations de conversion decimal vers binaire et binaire vers decimal. La quantification des performances est realisee, aux niveaux de chaque couche et globalement, grâce au developpement et a l’application d’une panoplie d’outils adequats. Les deux crypto-systemes sont realisables en logiciel et en materiel. Enfin, une nouvelle fonction de hachage basee chaos performante, avec ou sans cle est proposee. Elle permet d’achever efficacement le service d’authentification de la source et l’integrite des donnees.
The great efficacy of personal and equipment assistance in reducing disability.

OBJECTIVES Personal and equipment assistance are common strategies to reduce disability. This study sought to determine how often assistance reduces or even completely resolves health-related difficulties in everyday tasks. METHODS Data are from the NHANES I Epidemiologic Followup Study. Adults aged 35 to 90 reported difficulty doing 12 everyday tasks on their own without assistance. Those stating that they had much difficulty or were unable were asked if they had personal assistance and/or equipment assistance, and their degree of difficulty with assistance. Use and efficacy of assistance are studied by gender, age, intrinsic (unassisted) degree of difficulty, and type of assistance. RESULTS Most people use assistance for the 12 tasks; "personal assistance only" is the principal type used for upper-extremity and body transfer tasks; "equipment only" ranks first for lower-extremity tasks. Assistance reduces difficulty for the great majority of persons (75% to 85%) and completely resolves difficulty for about 25%. Equipment only proves to be the most efficacious strategy for reducing and resolving limitations. CONCLUSIONS Equipment's success may be due to greater perceived gains when people accomplish the assistance by themselves.
ZD1839 induces p15INK4b and causes G1 arrest by inhibiting the mitogen-activated protein kinase/extracellular signal–regulated kinase pathway

Inactivation of the retinoblastoma protein pathway is the most common abnormality in malignant tumors. We therefore tried to detect agents that induce the cyclin-dependent kinase inhibitor p15INK4b and found that ZD1839 (gefitinib, Iressa) could up-regulate p15INK4b expression. ZD1839 has been shown to inhibit cell cycle progression through inhibition of signaling pathways such as phosphatidylinositol 3′-kinase-Akt and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) cascades. However, the mechanism responsible for the differential sensitivity of the signaling pathways to ZD1839 remains unclear. We here showed that ZD1839 up-regulated p15INK4b, resulting in retinoblastoma hypophosphorylation and G1 arrest in human immortalized keratinocyte HaCaT cells. p15INK4b induction was caused by MAPK/ERK kinase inhibitor (PD98059), but not by Akt inhibitor (SH-6, Akt-III). Moreover, mouse embryo fibroblasts lacking p15INK4b were resistant to the growth inhibitory effects of ZD1839 compared with wild-type mouse embryo fibroblasts. Additionally, the status of ERK phosphorylation was related to the antiproliferative activity of ZD1839 in human colon cancer HT-29 and Colo320DM cell lines. Our results suggest that induction of p15INK4b by inhibition of the MAPK/ERK pathway is associated with the antiproliferative effects of ZD1839. [Mol Cancer Ther 2007;6(5):1579–1587]
High-Resolution Structural Analysis of Chromatin at Specific Loci: Saccharomyces cerevisiae Silent Mating-Type Locus HMRa

ABSTRACT Genetic and biochemical evidence implicates chromatin structure in the silencing of the two quiescent mating-type loci near the telomeres of chromosome III in yeast. With high-resolution micrococcal nuclease mapping, we show that the HMRa locus has 12 precisely positioned nucleosomes spanning the distance between the E and I silencer elements. The nucleosomes are arranged in pairs with very short linkers; the pairs are separated from one another by longer linkers of ∼20 bp. Both the basic amino-terminal region of histone H4 and the silent information regulator protein Sir3p are necessary for the organized repressive chromatin structure of the silent locus. Compared to HMRa, only small differences in the availability of the TATA box are present for the promoter in the cassette at the active MATa locus. Features of the chromatin structure of this silent locus compared to the previously studied HMLα locus suggest differences in the mechanisms of silencing and may relate to donor selection during mating-type interconversion.
Previsão de recalques em fundações profundas utilizando redes neurais artificiais do tipo Perceptron

A previsao de recalque em fundacoes profundas do tipo estacas helice continua, escavada e cravada metalica e o objeto principal desse estudo. O recalque e o deslocamento vertical para baixo que uma fundacao apresenta quando submetida a um determinado carregamento. A estimativa dos recalques em fundacoes profundas pode ser feita utilizando-se diversas metodologias, dentre as quais os metodos numericos e os teoricos. Diferentes variaveis influenciam os recalques ocorridos nas fundacoes profundas do tipo estaca destacando-se as caracteristicas de resistencia e deformabilidade dos materiais envolvidos, a estratigrafia do solo de fundacao e a geometria do elemento estrutural de fundacao, dentre outras, configurando-se, portanto, como um problema multi-variado e de grande complexidade. Uma alternativa para a estimativa mais realista dos recalques em fundacoes profundas consiste no emprego das redes neurais artificiais, que sao modelos que trabalham analogamente ao cerebro humano que tem, recentemente, contribuido na resolucao de problemas complexos em diversas areas da Engenharia Civil. Nessa pesquisa foram utilizadas redes neurais multicamadas alimentadas adiante (perceptron multi-camadas) para o desenvolvimento de um modelo de previsao de recalques em estacas, a partir de um treinamento supervisionado, que utiliza o algoritmo de retropropagacao do erro (error back propagation). Para o desenvolvimento do modelo foram coletados resultados de ensaios SPT e provas de carga estatica, e com auxilio do programa QNET2000 foram treinados e validados varios modelos de redes neurais. Apos as analises e comparacoes entre os resultados de diferentes configuracoes, constatou-se que as redes neurais artificiais foram capazes de entender o comportamento das fundacoes profundas do tipo helice continua, cravada metalica e escavada no que tange a influencia das variaveis de entrada consideradas para a estimativa dos recalques. Alem disto, constatou-se que os resultados obtidos pelo modelo desenvolvido permitem, dentre outras coisas, a definicao das cargas de trabalho e cargas limites na estaca. A arquitetura desse modelo e formada por 6 nos na camada de entrada, 20 neuronios distribuidos em 3 camadas ocultas, e 1 neuronio na camada de saida, correspondente ao recalque medido para a estaca. O processo de alteracao dos pesos sinapticos, na fase de validacao do modelo, com 4 milhoes de iteracoes resultou no maior coeficiente de correlacao entre os recalques estimados e os recalques medidos, que foi de 0,89, o qual pode ser considerado satisfatorio, em se tratando da previsao de um fenomeno complexo.
Multibeam scanning electron microscope: Experimental results

The authors present the first results obtained with their multibeam scanning electron microscope. For the first time, they were able to image 196 (array of 14×14) focused beams of a multielectron beam source on a specimen using single beam scanning electron microscope (SEM) optics. The system consists of an FEI Novanano 200 SEM optics column equipped with a multielectron beam source module. The source module consists of the multibeam source and an accelerator lens. In the multibeam source, the wide angle beam of a high brightness Schottky source is divided into 196 beamlets and focused by an aperture lens array. The accelerator lens is positioned on the image plane of the multibeam source to direct the beams toward the SEM column. The array of source images is further imaged by the SEM magnetic lenses, and the beam opening angle is defined at the variable aperture of the SEM. The system is designed to deliver 14×14 arrays of beamlets with a minimum probe size of 1 nm. In this article, the performance of the system is examined for a fixed magnification case.
Stage-dependent loss of cortical gyrification as Parkinson disease “unfolds”

Objective: Nigrostriatal terminal losses are known to progress most rapidly in early-stage Parkinson disease (PD) and then plateau, whereas cortical pathology continues and may provide a better marker of PD progression in later stages. We investigated cortical gyrification indices in patients with different durations of PD, since cortical folding may capture complex processes involving transverse forces of neuronal sheets or underlying axonal connectivity. Methods: Longitudinal cohort structural MRI were obtained at baseline, 18 months, and 36 months from 70 patients with PD without dementia and 70 control participants. Cortical local gyrification index (LGI) was compared between controls and PD subgroups based upon duration of illness (DOI, <1 year [PDE, n = 17], 1–5 years [PDM, n = 19], >5 years [PDL, n = 24]) and adjusted using false discovery rate. Associations between LGI and clinical measurements were assessed using multiple linear regression. Areas having significantly reduced LGI also were analyzed using baseline data from a newly established cohort (PD n = 87, control n = 66) to validate our findings. Results: In the longitudinal cohort, PDL had significantly reduced overall gyrification, and bilaterally in the inferior parietal, postcentral, precentral, superior frontal, and supramarginal areas, compared to controls (p < 0.05). Longitudinally, loss of gyrification was accelerated in PDM participants, compared to controls. LGI showed robust correlations with DOI and also was correlated with PD-related clinical measurements. Similar results were obtained in the validation sample. Conclusions: Loss of cortical gyrification may be accelerated within the first few years after PD diagnosis, and become particularly prominent in later stages. Thus, it may provide a metric for monitoring progression in vivo.
Line-Enhanced Deformable Registration of Pulmonary Computed Tomography Images Before and After Radiation Therapy With Radiation-Induced Fibrosis

Purpose: The deformable registration of pulmonary computed tomography images before and after radiation therapy is challenging due to anatomic changes from radiation fibrosis. We hypothesize that a line-enhanced registration algorithm can reduce landmark error over the entire lung, including the irradiated regions, when compared to an intensity-based deformable registration algorithm. Materials: Two intensity-based B-spline deformable registration algorithms of pre-radiation therapy and post-radiation therapy images were compared. The first was a control intensity–based algorithm that utilized computed tomography images without modification. The second was a line enhancement algorithm that incorporated a Hessian-based line enhancement filter prior to deformable image registration. Registrations were evaluated based on the landmark error between user-identified landmark pairs and the overlap ratio. Results: Twenty-one patients with pre-radiation therapy and post-radiation therapy scans were included. The median time interval between scans was 1.2 years (range: 0.3-3.3 years). Median landmark errors for the line enhancement algorithm were significantly lower than those for the control algorithm over the entire lung (1.67 vs 1.83 mm; P < .01), as well as within the 0 to 5 Gy (1.40 vs 1.57; P < .01) and >5 Gy (2.25 vs 3.31; P < .01) dose intervals. The median lung mask overlap ratio for the line enhancement algorithm (96.2%) was greater than that for the control algorithm (95.8%; P < .01). Landmark error within the >5 Gy dose interval demonstrated a significant inverse relationship with post-radiation therapy fibrosis enhancement after line enhancement filtration (Pearson correlation coefficient = −0.48; P = .03). Conclusion: The line enhancement registration algorithm is a promising method for registering images before and after radiation therapy.
Iliofemoral Deep Vein Thrombosis: Conventional Therapy Versus Lysis and Percutaneous Transluminal Angioplasty and Stenting

ObjectiveTo compare conventional treatment (heparin and warfarin) of iliofemoral venous thrombosis with multimodality treatment (lysis and stenting). Summary Background DataSeveral studies have reported on conventional therapy for iliofemoral venous thrombosis with disappointing results. However, more recent studies have reported better results with multimodality treatment. MethodsFifty-one consecutive patients with extensive iliofemoral venous thrombosis were treated during a 10-year period. If there were no contraindications, patients were given the option to choose between conventional therapy (group 1) and multimodality therapy (group 2). The multimodality treatment strategy included catheter-directed lysis followed by percutaneous transluminal balloon angioplasty (PTA) and stenting for residual iliac stenoses. All patients underwent routine venous duplex imaging at 30 days, 3 months, 6 months, and every 6 months thereafter. ResultsThere were 33 patients in group 1 and 18 patients in group 2. Demographic and clinical characteristics were comparable for both groups. Initial lysis was achieved in 16 of 18 patients (89%) in group 2. Ten of 18 patients in group 2 had residual stenosis after lysis (8 primary and 2 secondary to malignancy), and they were treated with PTA/stenting with an initial success rate of 90%. Two patients in group 1 (6%) had a symptomatic pulmonary embolism (none in group 2). At 30 days, venous patency and symptom resolution were achieved in 1 of 33 patients (3%) in group 1 versus 15 of 18 (83%) in group 2. Kaplan-Meier analysis showed primary iliofemoral venous patency rates at 1, 3, and 5 years of 24%, 18%, and 18% and 83%, 69%, and 69% for groups 1 and 2, respectively. Long-term symptom resolution was achieved in 10 of 33 patients (30%) in group 1 versus 14 of 18 (78%) in group 2. Kaplan-Meier life table analysis showed similar survival rates at 1, 3, and 5 years of 100%, 93%, and 85% for group 1 and 100%, 93%, and 81% for group 2. ConclusionsLysis/stenting treatment was more effective than conventional treatment in patients with iliofemoral vein thrombosis.
Vehicle representation and classification of surveillance video based on sparse learning

We cast vehicle recognition as problem of feature representation and classification, and introduce a sparse learning based framework for vehicle recognition and classification in this paper. After objects captured with a GMM background subtraction program, images are labeled with vehicle type for dictionary learning and decompose the images with sparse coding (SC), a linear SVM trained with the SC feature for vehicle classification. A simple but efficient active learning strategy is adopted by adding the false positive samples into previous training set for dictionary and SVM model retraining. Compared with traditional feature representation and classification realized with SVM, SC method achieves dramatically improvement on classification accuracy and exhibits strong robustness. The work is also validated on real-world surveillance video.
Feature++: Cross dimension feature fusion for road detection

Road detection is a key component of Advanced Driving Assistance Systems, which provides valid space and candidate regions of objects for vehicles. Mainstream road detection methods have focused on extracting discriminative features. In this paper, we propose a robust feature fusion framework, called “Feature++”, which is combined with superpixel feature and 3D feature extracted from stereo images. Then a neural network classifier is been trained to decide whether a superpixel is road region or not. Finally, the classified results are further refined by conditional random field. Experiments conducted on the KITTI ROAD benchmark show that the proposed “Feature++” method outperforms most manually designed features, and are comparable with state-of-the-art methods that based on deep learning architecture.
Pediatric Mood and Anxiety Syndromes in Primary Care: Who Gets Identified?

Objective: To seek clues to the enhancement of primary care management by (i) Determining how often and in whom primary care clinicians in the United States, Puerto Rico, and Canada identify pediatric mood or anxiety syndromes; (ii) Determining which clinical and demographic features predict higher rates of identification; (iii) Describing assessment methods used. Methods: This report uses the database of the multi-site Child Behavior Study. This cross-sectional study involved 206 primary care practices in the United States, Puerto Rico, and Canada; 395 clinicians and 20,861 primary care attenders aged 4–15 years. Clinicians completed a visit questionnaire addressing presence and type of psychosocial problems and how assessed. Parents completed a questionnaire addressing family demographics, child symptoms (Pediatric Symptom Checklist) and functioning, and child service use. Results: Clinicians identified psychosocial problems on 17.9% of visits, but mood or anxiety syndromes on only 3.3%, most commonly in children judged to have co-morbid behavioral syndromes, of whom the majority (66.7%) already had contact with specialized mental health. Neither parental concerns about mood and anxiety symptoms nor clinician familiarity with the patient were major predictors of identification. When making a diagnosis of a pure internalizing syndrome (i.e., without a co-morbid behavioral syndrome) clinicians rarely used standardized tools or school reports. Conclusions: Neither screening for nor diagnosis of mood and anxiety syndromes is a routine part of primary care of children and adolescents. Efforts to improve care must include practical, validated screening procedures to enhance assessment for mood and anxiety syndromes, particularly among children in whom primary care clinicians identify psychosocial problems.
Models, Fictions, and Realism: Two Packages

Some philosophers of science—myself included—appeal to fiction as an interpretation of the practice of modeling. This raises the specter of an incompatibility with realism, since fiction making is essentially nontruth regulated. I argue that the prima facie conflict can be resolved in two ways, each involving a distinct notion of fiction and a corresponding formulation of realism. The main goal of the essay is to describe these two packages. I comment also on how to choose between them.