bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated classifiers for early detection and diagnosis of retinopathy in diabetic eyes
Authors: Somfai Gábor Márk , Tátrai Erika , Laurik Lenke , Varga Boglárka , Ölvedy Veronika , Jiang Hong , Wang Jianhua , Smiddy William E , Somogyi Anikó , DeBuc Delia Cabrera 
Published: April 2014

Abstract

Background
Artificial neural networks (ANNs) have been used to classify eye diseases, such as diabetic retinopathy (DR) and glaucoma. DR is the leading cause of blindness in working-age adults in the developed world. The implementation of DR diagnostic routines could be feasibly improved by the integration of structural and optical property test measurements of the retinal structure that provide important and complementary information for reaching a diagnosis. In this study, we evaluate the capability of several structural and optical features (thickness, total reflectance and fractal dimension) of various intraretinal layers extracted from optical coherence tomography images to train a Bayesian ANN to discriminate between healthy and diabetic eyes with and with no mild retinopathy.

Results
When exploring the probability as to whether the subject’s eye was healthy (diagnostic condition, Test 1), we found that the structural and optical property features of the outer plexiform layer (OPL) and the complex formed by the ganglion cell and inner plexiform layers (GCL + IPL) provided the highest probability (positive predictive value (PPV) of 91% and 89%, respectively) for the proportion of patients with positive test results (healthy condition) who were correctly diagnosed (Test 1). The true negative, TP and PPV values remained stable despite the different sizes of training data sets (Test 2). The sensitivity, specificity and PPV were greater or close to 0.70 for the retinal nerve fiber layer’s features, photoreceptor outer segments and retinal pigment epithelium when 23 diabetic eyes with mild retinopathy were mixed with 38 diabetic eyes with no retinopathy (Test 3).

Conclusions
A Bayesian ANN trained on structural and optical features from optical coherence tomography data can successfully discriminate between healthy and diabetic eyes with and with no retinopathy. The fractal dimension of the OPL and the GCL + IPL complex predicted by the Bayesian radial basis function network provides better diagnostic utility to classify diabetic eyes with mild retinopathy. Moreover, the thickness and fractal dimension parameters of the retinal nerve fiber layer, photoreceptor outer segments and retinal pigment epithelium show promise for the diagnostic classification between diabetic eyes with and with no mild retinopathy.
Time-dependent pH sensing phenomena using CdSe/ZnS quantum dots in EIS structure
Authors: Kumar Pankaj , Maikap Siddheswar , Prakash Amit , Tien Ta-Chang 
Published: April 2014

Abstract
Time-dependent pH sensing phenomena of the core-shell CdSe/ZnS quantum dot (QD) sensors in EIS (electrolyte insulator semiconductor) structure have been investigated for the first time. The quantum dots are immobilized by chaperonin GroEL protein, which are observed by both atomic force microscope and scanning electron microscope. The diameter of one QD is approximately 6.5 nm. The QDs are not oxidized over a long time and core-shell CdSe/ZnS are confirmed by X-ray photon spectroscopy. The sensors are studied for sensing of hydrogen ions concentration in different buffer solutions at broad pH range of 2 to 12. The QD sensors show improved sensitivity (38 to 55 mV/pH) as compared to bare SiO2 sensor (36 to 23 mV/pH) with time period of 0 to 24 months, owing to the reduction of defects in the QDs. Therefore, the differential sensitivity of the QD sensors with respect to the bare SiO2 sensors is improved from 2 to 32 mV/pH for the time period of 0 to 24 months. After 24 months, the sensitivity of the QD sensors is close to ideal Nernstian response with good linearity of 99.96%. Stability and repeatability of the QD sensors show low drift (10 mV for 10 cycles) as well as small hysteresis characteristics (<10 mV). This QD sensor is very useful for future human disease diagnostics.
Contrasting Alterations to Synaptic and Intrinsic Properties in Upper-Cervical Superficial Dorsal Horn Neurons following Acute Neck Muscle Inflammation
Authors: Harris Belinda M , Hughes David I , Bolton Philip S , Tadros Melissa A , Callister Robert J , Graham Brett A 
Published: April 2014

Background: Acute and chronic pain in axial structures, like the back and neck, are difficult to treat, and have incidence as high as 15%. Surprisingly, most preclinical work on pain mechanisms focuses on cutaneous structures in the limbs and animal models of axial pain are not widely available. Accordingly, we developed a mouse model of acute cervical muscle inflammation and assessed the functional properties of superficial dorsal horn (SDH) neurons. Results: Male C57/Bl6 mice (P24-P40) were deeply anaesthetised (urethane 2.2 g/kg i.p) and the rectus capitis major muscle (RCM) injected with 40 μl of 2% carrageenan. Sham animals received vehicle injection and controls remained anaesthetised for 2 hrs. Mice in each group were sacrificed at 2 hrs for analysis. c-Fos staining was used to determine the location of activated neurons. c-Fos labelling in carrageenan-injected mice was concentrated within ipsilateral (87% and 63% of labelled neurons in C1 and C2 segments, respectively) and contralateral laminae I – II with some expression in lateral lamina V. c-Fos expression remained below detectable levels in control and sham animals. In additional experiments, whole cell recordings were obtained from visualised SDH neurons in transverse slices in the ipsilateral C1 and C2 spinal segments. Resting membrane potential and input resistance were not altered. Mean spontaneous EPSC amplitude was reduced by ∼20% in neurons from carrageenan-injected mice versus control and sham animals (20.63 ± 1.05 vs. 24.64 ± 0.91 and 25.87 ± 1.32 pA, respectively). The amplitude (238 ± 33 vs. 494 ± 96 and 593 ± 167 pA) and inactivation time constant (12.9 ± 1.5 vs. 22.1 ± 3.6 and 15.3 ± 1.4 ms) of the rapid A type potassium current (IAr), the dominant subthreshold current in SDH neurons, were reduced in carrageenan-injected mice. Conclusions: Excitatory synaptic drive onto, and important intrinsic properties (i.e., IAr) within SDH neurons are reduced two hours after acute muscle inflammation. We propose this time point represents an important transition period between peripheral and central sensitisation with reduced excitatory drive providing an initial neuroprotective mechanism during the early stages of the progression towards central sensitisation.
Addressing population heterogeneity and distribution in epidemics models using a cellular automata approach
Authors: López Leonardo , Burguerner Germán , Giovanini Leonardo 
Published: April 2014

AbstractBackgroundThe spread of an infectious disease is determined by biological and social factors. Models based on cellular automata are adequate to describe such natural systems consisting of a massive collection of simple interacting objects. They characterize the time evolution of the global system as the emergent behaviour resulting from the interaction of the objects, whose behaviour is defined through a set of simple rules that encode the individual behaviour and the transmission dynamic.MethodsAn epidemic is characterized trough an individual–based–model built upon cellular automata. In the proposed model, each individual of the population is represented by a cell of the automata. This way of modeling an epidemic situation allows to individually define the characteristic of each individual, establish different scenarios and implement control strategies.ResultsA cellular automata model to study the time evolution of a heterogeneous populations through the various stages of disease was proposed, allowing the inclusion of individual heterogeneity, geographical characteristics and social factors that determine the dynamic of the desease. Different assumptions made to built the classical model were evaluated, leading to following results:i) for low contact rate (like in quarantine process or low density population areas) the number of infective individuals is lower than other areas where the contact rate is higher, andii) for different initial spacial distributions of infected individuals different epidemic dynamics are obtained due to its influence on the transition rate and the reproductive ratio of disease.ConclusionsThe contact rate and spatial distributions have a central role in the spread of a disease. For low density populations the spread is very low and the number of infected individuals is lower than in highly populated areas. The spacial distribution of the population and the disease focus as well as the geographical characteristic of the area play a central role in the dynamics of the desease.
Clinical validation of the EndoPredict test in node-positive, chemotherapy-treated ER+/HER2− breast cancer patients: results from the GEICAM 9906 trial
Authors: Martin Miguel , Brase Jan C , Calvo Lourdes , Krappmann Kristin , Ruiz-Borrego Manuel , Fisch Karin , Ruiz Amparo , Weber Karsten E , Munarriz Blanca , Petry Christoph , Rodriguez Cesar A , Kronenwett Ralf , Crespo Carmen , Alba Emilio , Carrasco Eva , Casas Maribel , Caballero Rosalia , Rodriguez-Lescure Alvaro 
Published: April 2014

Abstract
Introduction
EndoPredict (EP) is an RNA-based multigene test that predicts the likelihood of distant recurrence in patients with estrogen receptor-positive (ER+), human epidermal growth factor receptor 2–negative (HER2−) breast cancer (BC) who are being treated with adjuvant endocrine therapy. Herein we report the prospective-retrospective clinical validation of EP in the node-positive, chemotherapy-treated, ER+/HER2− BC patients in the GEICAM 9906 trial.

Methods
The patients (N = 1,246) were treated either with six cycles of fluorouracil, epirubicin and cyclophosphamide (FEC) or with four cycles of FEC followed by eight weekly courses of paclitaxel (FEC-P), as well as with endocrine therapy if they had hormone receptor–positive disease. The patients were assigned to EP risk categories (low or high) according to prespecified cutoff levels. The primary endpoint in the clinical validation of EP was distant metastasis-free survival (MFS). Metastasis rates were estimated using the Kaplan-Meier method, and multivariate analysis was performed using Cox regression.

Results
The molecular EP score and the combined molecular and clinical EPclin score were successfully determined in 555 ER+/HER2− tumors from the 800 available samples in the GEICAM 9906 trial. On the basis of the EP, 25% of patients (n = 141) were classified as low risk. MFS was 93% in the low-risk group and 70% in the high-risk group (absolute risk reduction = 23%, hazard ratio (HR) = 4.8, 95% confidence interval (CI) = 2.5 to 9.5; P < 0.0001). Multivariate analysis showed that, in this ER+/HER2− cohort, EP results are an independent prognostic parameter after adjustment for age, grade, lymph node status, tumor size, treatment arm, ER and progesterone receptor (PR) status and proliferation index (Ki67). Using the predefined EPclin score, 13% of patients (n = 74) were assigned to the low-risk group, who had excellent outcomes and no distant recurrence events (absolute risk reduction vs high-risk group = 28%; P < 0.0001). Furthermore, EP was prognostic in premenopausal patients (HR = 6.7, 95% CI = 2.4 to 18.3; P = 0.0002) and postmenopausal patients (HR = 3.3, 95% CI = 1.3 to 8.5; P = 0.0109). There were no statistically significant differences in MFS between treatment arms (FEC vs FEC-P) in either the high- or low-risk groups. The interaction test results between the chemotherapy arm and the EP score were not significant.

Conclusions
EP is an independent prognostic parameter in node-positive, ER+/HER2− BC patients treated with adjuvant chemotherapy followed by hormone therapy. EP did not predict a greater efficacy of FEC-P compared to FEC alone.
Colchicine-induced degeneration of the micronucleus during conjugation in Tetrahymena
Authors: Chen Pin-Fang , Singhal Sita , Bushyhead Daniel , Broder-Fingert Sarabeth , Wolfe Jason 
Published: April 2014

ABSTRACT
One of the most dramatic examples of nuclear morphogenesis occurs during conjugation in Tetrahymena when the micronucleus elongates to a size longer than the cell itself. After contraction to a spherical shape, the nucleus moves directly to chromosome separation in the first meiotic division. Here we investigate the consequences of interrupting the elongation process. Colchicine, a microtubule inhibitor, caused retraction of elongated structures. With time, cells began to lose their micronuclei, and by five hours more than half of the paired cells had at least one cell missing a micronucleus. After reversing the colchicine block, existing micronuclei did not undergo elongation again, nor did meiosis occur. These observations indicate that micronuclear elongation is critical to subsequent meiotic division. Further, nuclear elimination occurs, which could be due to meiotic failure or possibly a problem downstream from meiosis. An analysis of the process of colchicine-induced micronuclear degeneration indicated that it was regulated by a caspase-dependent mechanism, characteristic of apoptosis, and then resorbed by a lysosome-dependent autophagic mechanism. Amicronucleate cells failed to grow when returned to nutrient medium, likely because of a lesion in the post-conjugation reconstruction of a functioning oral apparatus. The ease by which a large number of nuclei are induced to “self-destruct” may make this system useful in investigating the link between colchicine treatment and nuclear death in Tetrahymena, and in investigating how nuclear death could be regulated in living cells more generally. Finally, we note that this phenomenon might relate to the evolution of amicronucleate species of Tetrahymena.
B7h Triggering Inhibits the Migration of Tumor Cell Lines
Authors: Dianzani Chiara , Minelli Rosalba , Gigliotti Casimiro Luca , Occhipinti Sergio , Giovarelli Mirella , Conti Laura , Boggio Elena , Shivakumar Yogesh , Baldanzi Gianluca , Malacarne Valeria , Orilieri Elisabetta , Cappellano Giuseppe , Fantozzi Roberto , Sblattero Daniele , Yagi Junji , Rojo Josè Maria , Chiocchetti Annalisa , Dianzani Umberto 
Published: April 2014

Abstract
Vascular endothelial cells (ECs) and several cancer cells express B7h, which is the ligand of the ICOS T cell costimulatory molecule. We have previously shown that B7h triggering via a soluble form of ICOS (ICOS-Fc) inhibits the adhesion of polymorphonuclear and tumor cell lines to HUVECs; thus, we suggested that ICOS-Fc may act as an anti-inflammatory and antitumor agent. Because cancer cell migration and angiogenesis are crucial for metastasis dissemination, the aim of this work was to evaluate the effect of ICOS-Fc on the migration of cancer cells and ECs. ICOS-Fc specifically inhibited the migration of HUVECs, human dermal lymphatic ECs, and the HT29, HCT116, PC-3, HepG2, JR8, and M14 tumor cell lines expressing high levels of B7h, whereas it was ineffective in the RPMI7932, PCF-2, LM, and BHT-101 cell lines expressing low levels of B7h. Furthermore, ICOS-Fc downmodulated hepatocyte growth factor facilitated the epithelial-to-mesenchymal transition in HepG2 cells. Moreover, ICOS-Fc downmodulated the phosphorylation of focal adhesion kinase and the expression of β-Pix in both HUVECs and tumor cell lines. Finally, treatment with ICOS-Fc inhibited the development of lung metastases upon injection of NOD-SCID-IL2Rγnull mice with CF-PAC1 cells, as well as C57BL/6 mice with B16-F10 cells. Therefore, the B7h−ICOS interaction may modulate the spread of cancer metastases, which suggests the novel use of ICOS-Fc as an immunomodulatory drug. However, in the B16-F10–metastasized lungs, ICOS-Fc also increased IL-17A/RORc and decreased IL-10/Foxp3 expression, which indicates that it also exerts positive effects on the antitumor immune response.
Leukotriene B4 Modulates P2X7 Receptor–MediatedLeishmania amazonensisElimination in Murine Macrophages
Authors: Chaves Mariana M. , Marques-da-Silva Camila , Monteiro Ana Paula T. , Canetti Cláudio , Coutinho-Silva Robson 
Published: April 2014

AbstractATP is an important signaling molecule in the immune system, and it is able to bind the P2X7 purinergic receptor. Recently, our group showed that ATP-treated macrophages eliminate Leishmania amazonensis. It has been reported that leukotriene B4 (LTB4) reduces the parasitic load of infected macrophages. Additionally, it has been demonstrated that the P2X7 receptor can induce PLA2 activation and arachidonic acid mobilization. Based on these findings, we investigated whether LTB4 is produced upon P2X7 receptor activation and examined whether LTB4 modulates parasite elimination. Using macrophages lacking the P2X7 receptor, we observed that ATP was not able to reduce L. amazonensis load. This result suggests a role of the P2X7 purinergic receptor in parasite elimination. In addition, ATP was sufficient to induce LTB4 release from infected control macrophages but not from macrophages lacking the P2X7 receptor. Moreover, we found that ATP failed to decrease the parasitic load in 5-lipoxygenase (LO)–deficient macrophages. Treatment with the 5-LO inhibitor AA861 also impairs the ATP effect on parasitic loads. Furthermore, macrophages from 5-LO knockout mice eliminated L. amazonensis in the presence of exogenous LTB4, and macrophages obtained from P2X7 receptor knockout mice eliminated L. amazonensis when incubated with ionomycin. Finally, we demonstrated that in the presence of CP105696, an antagonist for LTB4 high-affinity receptor, ATP was not able to reduce parasitic load. These results indicate that P2X7 receptor activation leads to LTB4 formation, which is required for L. amazonensis elimination.
A Silencer-Proximal Intronic Region Is Required for Sustained CD4 Expression in Postselection Thymocytes
Authors: Henson David M. , Chou Chun , Sakurai Nagisa , Egawa Takeshi 
Published: April 2014

Abstract
It has been proposed that differential kinetics of CD4/CD8 coreceptors regulate fate choice of selected thymocytes. Sustained signals by interaction between MHC class II and TCR/CD4 is required for commitment to the CD4 helper lineage. Although prematurely terminated MHC–TCR/CD4 interaction in transgenic mouse models results in lineage redirection, it is unclear whether CD4 expression is actively maintained by endogenous cis-elements to facilitate prolonged signaling under physiological conditions. In this article, we show that sustained CD4 expression in postselection thymocytes requires an intronic sequence containing an uncharacterized DNase I hypersensitivity (DHS) site located 3′ to the silencer. Despite normal CD4 expression before selection, thymocytes lacking a 1.5-kb sequence in intron 1 including the 0.4-kb silencer and the DHS, but not the 0.4-kb silencer alone, failed to maintain CD4 expression upon positive selection and are redirected to the CD8 lineage after MHC class II–restricted selection. Furthermore, CpG dinucleotides adjacent to the DHS are hypermethylated in CD8+ T cells. These results indicate that the 1.5-kb cis-element is required in postselection thymocytes for helper lineage commitment, presumably mediating the maintenance of CD4 expression, and suggest that inactivation of the cis-element by DNA methylation may contribute to epigenetic Cd4 silencing.
Smurf2 Negatively Modulates RIG-I–Dependent Antiviral Response by Targeting VISA/MAVS for Ubiquitination and Degradation
Authors: Pan Yu , Li Rui , Meng Jun-Ling , Mao He-Ting , Zhang Yu , Zhang Jun 
Published: April 2014

Abstract
VISA (also known as MAVS, Cardif, IPS-1) is the essential adaptor protein for virus-induced activation of IFN regulatory factors 3 and 7 and production of type I IFNs. Understanding the regulatory mechanisms for VISA will provide detailed insights into the positive or negative regulation of innate immune responses. In this study, we identified Smad ubiquitin regulatory factor (Smurf) 2, one of the Smad ubiquitin regulator factor proteins, as an important negative regulator of virus-triggered type I IFN signaling, which targets at the VISA level. Overexpression of Smurf2 inhibits virus-induced IFN-β and IFN-stimulated response element activation. The E3 ligase defective mutant Smurf2/C716A loses the ability to suppress virus-induced type I IFN signaling, suggesting that the negative regulation is dependent on the ubiquitin E3 ligase activity of Smurf2. Further studies demonstrated that Smurf2 interacted with VISA and targeted VISA for K48-linked ubiquitination, which promoted the degradation of VISA. Consistently, knockout or knockdown of Smurf2 expression therefore promoted antiviral signaling, which was correlated with the increase in protein stability of VISA. Our findings suggest that Smurf2 is an important nonredundant negative regulator of virus-triggered type I IFN signaling by targeting VISA for K48-linked ubiquitination and degradation.
Phagocytosis of Staphylococcus aureus by Human Neutrophils Prevents Macrophage Efferocytosis and Induces Programmed Necrosis
Authors: Greenlee-Wacker Mallary C. , Rigby Kevin M. , Kobayashi Scott D. , Porter Adeline R. , DeLeo Frank R. , Nauseef William M. 
Published: April 2014

Abstract
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) pose a significant threat to human health. Polymorphonuclear leukocytes (PMN) are the first responders during staphylococcal infection, but 15–50% of the initial ingested inoculum survives within the PMN phagosome and likely contributes directly or indirectly to disease pathogenesis. We hypothesize that surviving intracellular CA-MRSA undermine effective phagocyte-mediated defense by causing a decrease in macrophage uptake of PMN containing viable S. aureus and by promoting PMN lysis. In support of this hypothesis, PMN harboring viable CA-MRSA strain USA300 (PMN-SA) upregulated the “don't eat me” signal CD47, remained bound to the surface, and were inefficiently ingested by macrophages. In addition, coculture with PMN-SA altered the macrophage phenotype. Compared to macrophages fed USA300 alone, macrophages challenged with PMN-SA produced more IL-8 and less IL-1 receptor antagonist, TNF-α, activated caspase-1, and IL-1β. Although they exhibited some features of apoptosis within 3 h following ingestion of S. aureus, including phosphatidylserine exposure and mitochondrial membrane depolarization, PMN-SA had sustained levels of proliferating cell nuclear Ag expression, absence of caspase activation, and underwent lysis within 6 h following phagocytosis. PMN lysis was dependent on receptor-interacting protein 1, suggesting that PMN-SA underwent programmed necrosis or necroptosis. These data are the first demonstration, to our knowledge, that bacteria can promote sustained expression of proliferating cell nuclear Ag and that human PMN undergo necroptosis. Together, these findings demonstrate that S. aureus surviving within PMN undermine the innate immune response and may provide insight into the pathogenesis of S. aureus disease.