Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk Factors, DNA Damage, and Disease Progression in Barrett's Esophagus

Esophageal adenocarcinoma develops on a background of Barrett's esophagus. A number of risk factors have been linked to both conditions, including gastroesophageal reflux and smoking. However, the molecular mechanisms by which these factors influence disease progression remain unclear. One possibility is that risk factors generate promutagenic DNA damage in the esophagus. The comet assay was used to measure DNA damage in esophageal (Barrett's and squamous) and gastric mucosa of Barrett's patients with (n = 24) or without (n = 50) associated adenocarcinoma or high-grade dysplasia in comparison with control patients (squamous mucosa) without Barrett's esophagus (n = 64). Patients completed a questionnaire detailing exposure to some of the known risk factors for Barrett's esophagus and adenocarcinoma. In Barrett's esophagus patients, DNA damage was higher in Barrett's mucosa compared with normal esophageal and gastric mucosa (P < 0.001). In addition, the highest quartile of DNA damage in Barrett's mucosa was associated with an increased risk (odds ratio, 9.4; 95% confidence interval, 1.1-83.4; P = 0.044) of developing adenocarcinoma or high-grade dysplasia compared with DNA damage levels in the lowest quartile. Smoking was associated with higher DNA damage in squamous epithelium in all patient groups (P < 0.01) and in Barrett's mucosa (P < 0.05) in Barrett's esophagus patients only. In controls only, current reflux was associated with higher DNA damage, whereas anti-inflammatory drug use resulted in lower levels. Collectively, these data imply a genotoxic insult to the premalignant Barrett's mucosa that may explain the genetic instability in this tissue and the progression to adenocarcinoma. There is an indication for a role for smoking in inducing DNA damage in esophageal mucosa but an understanding of the role of reflux requires further investigation.
Passivity-based control of AC drives: theory for the user and application examples

Passivity-based control is a methodology to design (possibly nonlinear) controllers for nonlinear physical systems modifying its total energy function and damping characteristics. In this article, the basic principles of this technique, and some of the recent results of application for high performance AC drives, are briefly reviewed. Since the target audience of this article is the drives community, the material is presented emphasising its immediate practical applicability, with minimal mathematical details. However, it is underscored that in all applications, a rigorous stability analysis for the full nonlinear dynamics has been reported in the literature.
Internalization of the Ultra-Thin Ideal: Positive Implicit Associations with Underweight Fashion Models are Associated with Drive for Thinness in Young Women

This study examined whether young women who make implicit associations between underweight models and positive attributes report elevated eating disorder symptoms. Ninety nine female undergraduates completed a weight based implicit association test (IAT) and self report measures of body dissatisfaction, thin-ideal internalization and eating disorder symptoms. IAT scores were associated with drive for thinness (r = −0.26, p < 0.05). This relationship was moderated by attitude importance. The relationship between drive for thinness and IAT scores was stronger (r = 0.34; p < 0.02) in participants who report that the media is an important source of information about fashion and being attractive. The IAT used in the current study is sensitive enough to discriminate between participants on drive for thinness. Women who have developed cognitive schemas that associate being underweight with positive attributes report higher eating disorder symptoms. Attitude importance is highlighted as a key construct in thin ideal internalization.
Beam Search based MAP Estimates for the Indian Buffet Process

Nonparametric latent feature models offer a flexible way to discover the latent features underlying the data, without having to a priori specify their number. The Indian Buffet Process (IBP) is a popular example of such a model. Inference in IBP based models, however, remains a challenge. Sampling techniques such as MCMC can be computationally expensive and can take a long time to converge to the stationary distribution. Variational techniques, although faster than sampling, can be difficult to design, and can still remain slow on large data. In many problems, however, we only seek a maximum a posteriori (MAP) estimate of the latent feature assignment matrix. For such cases, we show that techniques such as beam search can give fast, approximate MAP estimates in the IBP based models. If samples from the posterior are desired, these MAP estimates can also serve as sensible initializers for MCMC based algorithms. Experimental results on a variety of datasets suggest that our algorithms can be a computationally viable alternative to Gibbs sampling, the particle filter, and variational inference based approaches for the IBP, and also perform better than other heuristics such as greedy search.
Multimodal Skipgram Using Convolutional Pseudowords

This work studies the representational mapping across multimodal data such that given a piece of the raw data in one modality the corresponding semantic description in terms of the raw data in another modality is immediately obtained. Such a representational mapping can be found in a wide spectrum of real-world applications including image/video retrieval, object recognition, action/behavior recognition, and event understanding and prediction. To that end, we introduce a simplified training objective for learning multimodal embeddings using the skip-gram architecture by introducing convolutional "pseudowords:" embeddings composed of the additive combination of distributed word representations and image features from convolutional neural networks projected into the multimodal space. We present extensive results of the representational properties of these embeddings on various word similarity benchmarks to show the promise of this approach.
Efficacy of intense screening and treatment for synchronous second primary cancers in patients with esophageal cancer.

BACKGROUND The optimum management of esophageal cancers with synchronous second primary cancer (SPC) has not been determined. The aim of this study was to evaluate the efficacy of intense screening and treatment for esophageal cancers with synchronous SPC. METHODS Between 1981 and 1997, 1479 patients with esophageal cancers were screened for synchronous SPC during the process of initial staging. Radical treatment was recommended for esophageal cancer and synchronous SPC in cases for whom both cancers were curable. Treatment results for esophageal cancer patients with or without synchronous SPC were compared. RESULTS Among 1479 patients, 155 (10.5%) were found to have 166 synchronous SPC. Primary sites included the stomach in 65, the head and neck in 44, the colon/rectum in 27, the lung in 14 and other sites in 16 patients. Clinical stages of synchronous SPC were stage I in 41%, stage II in 20%, stage III in 25% and stage IV in 14%. The 5-year overall survival rates by clinical stages of esophageal cancers (stage 0, I, II, III, IV) in patients with synchronous SPC were 51% (95% CI, 23-78%), 43% (95% CI, 18-68%), 11% (95% CI, 0-22%), 14% (95% CI, 0-28%) and 12% (95% CI, 1-22%), respectively. The 5-year overall survival rate for patients with or without synchronous SPC were 20% (95% CI, 13-28%) and 32% (95% CI, 29-35%), respectively. No significant difference was observed between both groups (p = 0.2562). CONCLUSIONS Intense screening and treatment may be justifiable in the light of the high detection rate of curable SPC and the reasonable survival of patients with synchronous SPC. However, a prospective study including cost-benefit analysis is needed to provide the evidence to justify the intense screening and treatment.
A dedicated animal model for mechanical thrombectomy in acute stroke.

BACKGROUND Recent studies have focused on mechanical thrombectomy as a means to reduce the time required for revascularization and increase the revascularization rate in acute stroke. To date no systematic evaluation has been made of the different mechanical devices in this novel and fast-developing field of endovascular interventions. To facilitate such evaluations, we developed a specific in vivo model for mechanical thrombectomy that allows visualization of dislocation or fragmentation of the thrombus during angiographic manipulation. METHODS Angiography and embolization with a preformed thrombus was performed in 8 swine. The thrombus was generated by mixing 25 IU bovine thrombin and 10 mL autologous blood. For visualization during angiography, 1 g barium sulfate was added. RESULTS The preformed thrombus exhibited mechanical stability, reproducibility, and high radiographic absorption, providing excellent visibility during angiography. The setting allowed selective embolization of targeted vessels without thrombus fragmentation. Despite the application of barium sulfate no local or systemic reaction occurred. Histologic evaluation revealed no intimal damage caused by the thrombus or contrast agent washout. CONCLUSION The model presented here allows selective and reliable thromboembolization of vessels that reproduce the anatomic and hemodynamic situation in acute cerebrovascular stroke. It permits visualization of the thrombus during angiography and intervention, providing unique insight into the behavior of both thrombus and device, which is potentially useful in the development and evaluation of mechanical clot retrieval in acute cerebrovascular stroke.
Vertex-Based Compatible Discrete Operator Schemes on Polyhedral Meshes for Advection-Diffusion Equations

Abstract We devise and analyze vertex-based, Péclet-robust, lowest-order schemes for advection-diffusion equations that support polyhedral meshes. The schemes are formulated using Compatible Discrete Operators (CDO), namely, primal and dual discrete differential operators, a discrete contraction operator for advection, and a discrete Hodge operator for diffusion. Moreover, discrete boundary operators are devised to weakly enforce Dirichlet boundary conditions. The analysis sheds new light on the theory of Friedrichs' operators at the purely algebraic level. Moreover, an extension of the stability analysis hinging on inf-sup conditions is presented to incorporate divergence-free velocity fields under some assumptions. Error bounds and convergence rates for smooth solutions are derived and numerical results are presented on three-dimensional polyhedral meshes.
Decision Making and Reward in Frontal Cortex

Patients with damage to the prefrontal cortex (PFC)—especially the ventral and medial parts of PFC—often show a marked inability to make choices that meet their needs and goals. These decision-making impairments often reflect both a deficit in learning concerning the consequences of a choice, as well as deficits in the ability to adapt future choices based on experienced value of the current choice. Thus, areas of PFC must support some value computations that are necessary for optimal choice. However, recent frameworks of decision making have highlighted that optimal and adaptive decision making does not simply rest on a single computation, but a number of different value computations may be necessary. Using this framework as a guide, we summarize evidence from both lesion studies and single-neuron physiology for the representation of different value computations across PFC areas.
A Candidate HIV/AIDS Vaccine (MVA-B) Lacking Vaccinia Virus Gene C6L Enhances Memory HIV-1-Specific T-Cell Responses

The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, involved in regulation of host immune responses, but its role is unknown. Here, we have characterized the C6 protein and its effects in virus replication, innate immune sensing and immunogenicity in vivo. C6 is a 18.2 kDa protein, which is expressed early during virus infection and localizes to the cytoplasm of infected cells. Deletion of the C6L gene from the poxvirus vector MVA-B expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (MVA-B ΔC6L) had no effect on virus growth kinetics; therefore C6 protein is not essential for virus replication. The innate immune signals elicited by MVA-B ΔC6L in human macrophages and monocyte-derived dendritic cells (moDCs) are characterized by the up-regulation of the expression of IFN-β and IFN-α/β-inducible genes. In a DNA prime/MVA boost immunization protocol in mice, flow cytometry analysis revealed that MVA-B ΔC6L enhanced the magnitude and polyfunctionality of the HIV-1-specific CD4+ and CD8+ T-cell memory immune responses, with most of the HIV-1 responses mediated by the CD8+ T-cell compartment with an effector phenotype. Significantly, while MVA-B induced preferentially Env- and Gag-specific CD8+ T-cell responses, MVA-B ΔC6L induced more Gag-Pol-Nef-specific CD8+ T-cell responses. Furthermore, MVA-B ΔC6L enhanced the levels of antibodies against Env in comparison with MVA-B. These findings revealed that C6 can be considered as an immunomodulator and that deleting C6L gene in MVA-B confers an immunological benefit by enhancing IFN-β-dependent responses and increasing the magnitude and quality of the T-cell memory immune responses to HIV-1 antigens. Our observations are relevant for the improvement of MVA vectors as HIV-1 vaccines.
NeTS-NOSS : Creating an Architecture for Wireless Sensor Networks

Wireless Sensor Networks (WSNs) are an important new class of networked system. Simultaneously presenting intellectually deep CISE research challenges and promising tremendous societal impact through scientific progress, better engineering, improved productivity, and enhanced security, research in this area has progressed substantially in the past decade. Early efforts to build the requisite hardware began in earnest around 1999. Before these efforts, researchers used simulation and small laptop/PC104 testbeds to study relatively narrow algorithmic questions, such as redundancy management and topology formation. One notable exception is Directed Diffusion [25], which provided a more general framework for querying sensor network nodes. In 2000, a hardware/software platform [22] became widely available that more accurately captured the salient attributes of this domain limited resources, significant scale, and deep integration with a noisy physical world. The TinyOS mote enabled pilot deployments and helped researchers focus on some of the most limiting factors for deployments, such as robust, stable multihop routing in the presence of time varying lossy links, holistic power management, time synchronization and in-network query processing. Today, many individual network system components have been researched, designed, developed and evaluated in stand-alone form; in addition, limited collections have been integrated into complete applications. Much more work remains in developing these components. However, this steady accretion of components, while necessary, is not sufficient for continued progress. The protocols and subsystems that have been developed make a wide range of differing assumptions about the other parts of the system and how the parts should interact. The extent to which these components can be combined to build usable systems is quite limited. This is a very unfortunate state of affairs. In order to produce running systems, various research groups have produced “vertically integrated” designs in which their own set of components are specifically designed to work together, but are unable to interoperate with components from other groups. This greatly reduces the synergy between research efforts, and has impeded progress in the field. It is the central tenet of this proposal that the primary factor currently limiting progress in the field is not any specific technical challenge (though many remain, and deserve much further study) but is instead the lack of an overall sensor network architecture. Such an architecture would help identify the essential components and, most importantly, provide a framework in which to compose them. This proposal is intended to help the community move towards an architecture for wireless sensor networks. It is important to remember that an architecture is not an end in itself: it is merely a tool that helps us accomplish the task at hand. For wireless sensor networks, we define the task at hand to be:
SNR efficient transmission for compressive sensing based wireless sensor networks

Compressive sensing(CS) is an emerging technology that can recover a signal from under sampled measurements based on sparsity of the signal in some basis domain. Even though CS associated with wireless sensor networks (WSNs) has contributed in developing efficient compression and detection algorithms, most research has focused on detection problem with a simple model without considering properties of physical channels. This paper considers a compressive sensing based WSN, that exploits channel gain to transmit and detect signals efficiently. Assuming that measured signals at each sensor are correlated and sparse at some basis domain, we propose a novel sensor selection scheme and associated signaling channel design to improve detection performance. The simulation results show that the proposed method support reduction in the number of measurmenets by 60~80% for a wide range of sparsity level at high and low SNRs.
Synaptic localization of P2X7 receptors in the rat retina

The distribution of P2X7 receptor (P2X7R) subunits was studied in the rat retina using a subunit‐specific antiserum. Punctate immunofluorescence was observed in the inner and outer plexiform layers. Double labeling of P2X7 and the horizontal cell marker, calbindin, revealed extensive colocalization in the outer plexiform layer (OPL). Significant colocalization of P2X7R and kinesin, a marker of photoreceptor ribbons, was also observed, indicating that this receptor may be expressed at photoreceptor terminals. Furthermore, another band of P2X7R puncta was identified below the level of the photoreceptor terminals, adjacent to the inner nuclear layer (INL). This band of P2X7R puncta colocalized with the active‐zone protein, bassoon, suggesting that “synapse‐like” structures exist outside photoreceptor terminals. Preembedding immunoelectron microscopy demonstrated P2X7R labeling of photoreceptor terminals adjacent to ribbons. In addition, some horizontal cell dendrites and putative “desmosome‐like” junctions below cone pedicles were labeled. In the inner plexiform layer (IPL), P2X7R puncta were observed surrounding terminals immunoreactive for protein kinase C‐α, a marker of rod bipolar cells. Double labeling with bassoon in the IPL revealed extensive colocalization, indicating that P2X7R is likely to be found at conventional cell synapses. This finding was confirmed at the ultrastructural level: only processes presynaptic to rod bipolar cells were found to be labeled for the P2X7R, as well as other conventional synapses. These findings suggest that purines play a significant role in neurotransmission within the retina, and may modulate both photoreceptor and rod bipolar cell responses. J. Comp. Neurol. 472:13–23, 2004. © 2004 Wiley‐Liss, Inc.
PERFORMANCE DRIVEN DESIGN OF FIBER REINFORCED CEMENTITIOUS COMPOSITES

This paper describes the performance driven approach in the design of fiber reinforced cementitious composites. This approach is illustrated with structural durability as an example. The identified material property, crack width, is then related quantitatively to material structures - fiber, matrix and interface properties, by means of micromechanics. It is suggested that tailoring of material structure can lead to controlled crack widths, and hence directly influences the durability of built structures. Success in the performance driven design of fiber reinforced cementitious composites will depend on future research in quantifying links between specific structural performance, material properties, and material structures. (A) For the covering abstract of the conference see IRRD 862056.
Voxel-Based Correlation Between Whole-Brain CT Perfusion With 320-Row Area Detector CT and Iodine 123 Iodoamphetamine Brain Perfusion SPECT in Patients With Cerebrovascular Disease

Objective We compared cerebral blood flow (CBF) measured using computed tomographic (CT) perfusion (CTP) and N-isopropyl-p-[(123) I]-iodoamphetamine cerebral perfusion single-photon emission computed tomography (SPECT). Methods We used a 320-row area detector CT and N-isopropyl-p-[(123) I]-iodoamphetamine cerebral perfusion SPECT under similar conditions in patients with chronic cerebrovascular disease. Images were automatically aligned 3-dimensionally for voxel-by-voxel comparisons. Results Linear positive correlations were observed between CTP-CBF including high-blood-flow areas and SPECT-CBF over the whole brain (r = 0.001–0.6, P < 0.01), superior cerebral level (r = 0.45–0.93, P < 0.01), basal ganglia level (r = 0.44–0.77, P < 0.01), and skull base (r = 0.02–0.66, P < 0.01). Correlations between CTP-CBF excluding high-blood-flow areas were significantly higher (P < 0.0001). Conclusions Computed tomographic perfusion overestimated CBF compared with SPECT and showed poor correlation at the skull base. Computed tomographic perfusion CTP excluding high-blood-flow areas improved the correlation over the whole brain in patients with chronic cerebrovascular disease.
Pulsed Plasma Deposition from Vinyltrimethylsilane/Oxygen Mixtures

In this work, SiO 2 -like films have been deposited in a capacitive coupled parallel plate reactor using low pressure, pulsed O 2 /VTMS plasmas. The influence of the duty cycle and of the period on the structure of films at fixed gas feed composition are shown. It has been demonstrated that the chemical process developed depends very much on the modulation parameters, and that the OFF time significantly contributes to the overall process kinetics. Furthermore, some indication have been obtained on the possibility of getting multistack gas barrier coatings by alternating organic and inorganic layers, in which the inorganic layer is deposited by means of modulated plasma processes based on vinyltrimethylsilane feeds.