Miracle-dz/UniFAR-FTUs huggingface dataset:
Early Cancer Detection at the Epithelial Surface

AbstractMalignant neoplastic lesions derived from epithelial tissue, carcinomas, account for 80% to 100% of all human cancers including some of the most deadly diseases such as cervical and non–small cell lung cancer. Many of these carcinomas present at readily accessible epithelial surfaces offering unique detection opportunities. Effective clinical management of carcinomas is enabled by early detection, at a time when full surgical resection is possible and before invasion of adjacent tissue or significant intravasation into blood vessels leading to metastasis. Good prognosis with long-term disease-free survival is more likely after early detection when progression is limited. At present, detection of carcinomas at epithelial surfaces largely relies on routine inspection with the naked eye (e.g., skin and oropharynx) or simple white light tools (e.g., cervix and colon). Emerging optical tools based on differential refraction, absorption, reflection, scattering, or fluorescence of carcinomas relative to normal tissues enable label-free visualization of neoplasia. However, the differences in intrinsic optical properties of normal and malignant tissues can be subtle, and relying on these may lead to high miss rates. Enhanced optical contrast offered by molecularly targeted agents can be used to improve early detection; and given that optical imaging and sensing tools can be readily combined, integrated systems that image over a range of scales, or detect multiple parameters, can be developed to aid in early detection. Diagnosis is, at present, made by histologic examination of tissue biopsies after identification of suspicious lesions. Miniature and handheld microscopic imaging tools have recently been developed, and integration of these tools with wide-field optical surveillance devices offers both rapid detection and confirmatory histologic examination at the point-of-care, that can provide guidance for biopsy and/or resection. A wide variety of targeted probe strategies have been described with demonstrated benefit in preclinical models and in a limited number of human studies. Here, we present examples of integrated multimodality optical imaging and sensing tools that use combinations of intrinsic and extrinsic optical contrast for early detection or margin delineation for carcinomas at epithelial surfaces. We will discuss several new technologies that have use in detecting the most common carcinomas that derive from the epithelium of the skin, gastrointestinal and urogenital tracts, and bronchoalveoli.
Evaluation of Antioxidant Compounds and Total Sugar Content in a Nectarine [Prunus persica (L.) Batsch] Progeny

Epidemiological studies suggest that consumption of fruit rich in phenolic compounds is associated with health-protective effects due to their antioxidant properties. For these reasons quality evaluation has become an important issue in fruit industry and in breeding programs. Phytochemical traits such as total phenolics, flavonoids, anthocyanins, L-ascorbic acid, sugar content and relative antioxidant capacity (RAC) were analyzed over four years in flesh fruit of an F1 population “Venus” × “Big Top” nectarines. Other traits such as harvesting date, yield, fruit weight, firmness, soluble solids concentration (SSC), pH, titratable acidity (TA) and ripening index (RI) were also determined in the progeny. Results showed high variability among genotypes for all analyzed traits. Total phenolics and flavonoids showed significant positive correlations with RAC implying that both are important antioxidant bioactive compounds in peaches. We found genotypes with enhanced antioxidant capacity and a better performance than progenitors, and in consequence the best marketability.
Testing the Influence of Two ICT management Practices on Business/ICT Alignment

Business/ICT (Information and Communication Technology) alignment is an ongoing concern for both academics and practitioners. However, little academic research focuses on the process or practice of alignment. In this paper we build a theoretical model and test it empirically. We investigate the influence of ICT managemen t intensity and investment justification on alignment. Four indicators are used for the ICT management intensity construct: ICT portfolio management, ICT performance management, ICT risk management and ICT change management. Investment justification reflec ts on how organizations justify ICT investments in the business case. We used the following indicators: e conomic impact, impact on building a competitive advantage, impact on keeping up with the competitors and impact on enhancing management information. Furthermore, we also examine d the influence of alignment on the use of ICT for competitive advantage. The study relies on a rich data set of 641 European organizations. Our results indicate that ICT management intensity and investment justification are both positively associated with alignment.
A Firewall for Routers: Protecting against Routing Misbehavior

In this work, we present the novel idea of route normalization by correcting on the fly routing traffic on behalf of a local router to protect the local network from malicious and misconfigured routing updates. Analogous to traffic normalization for network intrusion detection systems, the proposed RouteNormalizer patches ambiguities and eliminates semantically incorrect routing updates to protect against routing protocol attacks. Furthermore, it serves the purpose of a router firewall by identifying resource-based attacks against routers. Upon detecting anomalous routing changes, it suggests local routing policy modifications to improve route selection decisions. Deploying a RouteNormalizer requires no modification to routers if desired using a transparent TCP proxy setup. In this paper, we present the detailed design of the RouteNormalizer and evaluate it using a prototype implementation based on empirical BGP routing updates. We validate its effectiveness by showing that many well-known routing problems from operator mailing lists are correctly identified.
On Deformation of A-M Interface in Single Crystal Shape Memory Alloys and Some Related Issues

Recent experimental results on the deformation field of single crystal CuNiAl shape memory alloys (SMA) by using Moire interference technique are reported and two kinds of austenite-martensite (A-M) interfaces with different deformation features are identified. The experimental discovery questioned the invariant plane hypothesis used in crystallographic theory of martensitic transformation. Some fundamental issues on the property of A-M interface and the related micro- and macro-deformation features are discussed.
Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chemical, biochemical, biological, and medical information. These developments depend on a range of factors: the principles of chemical identifiers and their role in relationships between chemical and biological entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration. © 2013 John Wiley & Sons, Ltd.
Can appearance patterns improve pedestrian detection?

This paper studies the usefulness of appearance patterns for the challenging task of pedestrian detection. Despite appearance specific models being common in rigid object detection, the technique is still little understood for pedestrians. Three main approaches for reasoning over orientation, occlusion, and visual cues in obtaining the appearance patterns are compared. This work demonstrates that large gains in detection performance (up to 17 AP points on the challenging KITTI dataset) can be made using a state-of-the-art pedestrian detector.
Prevalence and associations of hand pain in the community: results from a population-based study

Objectives: To assess the prevalence and associations of hand symptoms in a community setting. Methods: The North West Adelaide Health Study (NWAHS) is a longitudinal cohort study of people aged ≥ 18 years. Analysis was performed in participants who completed a telephone interview, a quality of life questionnaire [the 36‐item short-form health survey, (SF-36)], and the Australian/Canadian (AUSCAN) Osteoarthritis (OA) Hand Index, and underwent grip strength measurement. Results: Overall, 477 (13.7%) reported hand pain, aching, or stiffness. Of these, 169 (35.8%) had been diagnosed with hand arthritis. Women were more likely to have hand symptoms than men, as were those aged ≥ 50 years (p < 0.001). Hand symptoms were associated with lower quality of life scores (p < 0.05). Participants with hand arthritis had more severe pain, stiffness, and poorer physical functioning as reflected by higher AUSCAN scores. Grip strength was reduced in those with hand symptoms and hand arthritis (p < 0.05) and inversely associated with mean AUSCAN subscores and SF-36 physical functioning scores (p < 0.001). Conclusions: Hand symptoms were present in 14% of the population and were more common in women and those aged ≥ 50 years. Hand symptoms were associated with reduced grip strength and reduced quality of life. Hand arthritis was associated with higher AUSCAN scores. Hand symptoms and hand arthritis have a significant impact on physical functioning and quality of life.
Consecutive Nucleation Events During Divetrification of Zr52.5Cu17.9Ni14.6Al10Ti5 Bulk Metallic Glass

Differential scanning calorimetry, x-ray, and in-situ synchrotron diffraction were used to study the divitrification of Zr52.5Cu17. 9Ni14.6Al10Ti5 bulk metallic glass. Two consecutive exothermal peaks were identified by differential scanning calorimetry during both isochronal and isothermal scans. Examination of the X-ray and in-situ synchrotron diffraction patterns at various stages of annealing confirms that the exothermal peaks correspond to two nucleation events, with different local atomic structures. Modeling of the calorimetry data indicates that the devitrification in this alloy is adequately described by Johnson CMehl CAvrami theory with a two-step consecutive reaction model.
Chronic blockade of brain "ouabain" prevents sympathetic hyper-reactivity and impairment of acute baroreflex resetting in rats with congestive heart failure.

In rats with congestive heart failure (CHF) post myocardial infarction (MI) acute blockade of brain "ouabain" reverses sympathetic hyperactivity and chronic blockade prevents the desensitization of baroreflex function. This study was conducted to determine: i) if chronic blockade of brain "ouabain" maintains normal sympathetic reactivity; and ii) if acute baroreflex resetting (another parameter of baroreflex function) also becomes impaired, and if so, does brain "ouabain" contribute to impairment in acute baroreflex resetting. CHF post MI was induced by acute coronary artery ligation in Wistar rats. Animals were treated with 200 microg x day(-1) i.c. v. or i.v. Fab fragments (which bind brain "ouabain" with high affinity), or treated with 200 microg x day(-1) i.c. v. gamma-globulins (control group). The length of treatment was 0.5-8 weeks or 4-8 weeks post MI. At 8 weeks mean arterial pressure (MAP), central venous pressure (CVP), heart rate (HR), and renal sympathetic nerve activity (RSNA) were recorded in concious rats at rest and in response to: i) air-jet stress, ii) i.c. v. guanabenz (an alpha2-adrenoceptor agonist), and iii) a 30 min i.v. infusion of nitroprusside (NP). Excitatory responses to air stress and inhibitory responses to guanabenz of MAP, HR, and RSNA were significantly enhanced in rats with CHF versus the sham-operated treated group. This enhancement was prevented in the CHF group treated with i.c. v. , but not i.v. , Fab. Nitroprusside induced a sustained decrease in MAP (approximately 25 mmHg) and a transient decrease in CVP. Heart rate and RSNA increased significantly within 1 min of beginning the infusion. The peak increases as well as the product of changes in MAP-HR and RSNA-HR were significantly smaller in rats with CHF treated with gamma-globulins versus sham rats and versus CHF rats treated with i.c. v. Fab. In sham-operated rats and CHF rats treated with i.c. v. Fab, RSNA and HR began to decrease within 3-4 min of beginning the NP infusion and had returned to baseline by 20 min. In contrast, RSNA and HR remained increased throughout the infusion in the CHF rats treated with gamma-globulins. These data indicate that in rats with CHF acute resetting of the arterial baroreflex in response to a lower BP becomes impaired, and chronic blockade of brain "ouabain" prevents both this change in baroreflex resetting as well as sympathetic hyperactivity.
Protein Content of Polyhedral Organelles Involved in Coenzyme B12-Dependent Degradation of 1,2-Propanediol in Salmonella enterica Serovar Typhimurium LT2

ABSTRACT Salmonella enterica forms polyhedral organelles during coenzyme B12-dependent growth on 1,2-propanediol (1,2-PD). Previously, these organelles were shown to consist of a protein shell partly composed of the PduA protein, the majority of the cell's B12-dependent diol dehydratase, and additional unidentified proteins. In this report, the polyhedral organelles involved in B12-dependent 1,2-PD degradation by S. enterica were purified by a combination of detergent extraction and differential and density gradient centrifugation. The course of the purification was monitored by electron microscopy and gel electrophoresis, as well as enzymatic assay of B12-dependent diol dehydratase. Following one- and two-dimensional gel electrophoresis of purified organelles, the identities and relative abundance of their constituent proteins were determined by N-terminal sequencing, protein mass fingerprinting, Western blotting, and densitometry. These analyses indicated that the organelles consisted of at least 15 proteins, including PduABB′CDEGHJKOPTU and one unidentified protein. Seven of the proteins identified (PduABB′JKTU) have some sequence similarity to the shell proteins of carboxysomes (a polyhedral organelle involved in autotrophic CO2 fixation), suggesting that the S. enterica organelles and carboxysomes have a related multiprotein shell. In addition, S. enterica organelles contained four enzymes: B12-dependent diol dehydratase, its putative reactivating factor, aldehyde dehydrogenase, and ATP cob(I)alamin adenosyltransferase. This complement of enzymes indicates that the primary catalytic function of the S. enterica organelles is the conversion of 1,2-PD to propionyl coenzyme A (which is consistent with our prior proposal that the S. enterica organelles function to minimize aldehyde toxicity during growth on 1,2-PD). The possibility that similar protein-bound organelles may be more widespread in nature than currently recognized is discussed.
Correspondence Bias in Performance Evaluation: Why Grade Inflation Works

Performance (such as a course grade) is a joint function of an individual’s ability (such as intelligence) and the situation (such as the instructor’s grading leniency). Prior research has documented a human bias toward dispositional inference, which ascribes performance to individual ability, even when it is better explained through situational influences on performance. It is hypothesized here that this tendency leads admissions decisions to favor students coming from institutions with lenient grading because those students have their high grades mistaken for evidence of high ability. Three experiments show that those who obtain high scores simply because of lenient grading are favored in selection. These results have implications for research on attribution because they provide a more stringent test of the correspondence bias and allow for a more precise measure of its size. Implications for university admissions and personnel selection decisions are also discussed.
Maximum Likelihood Estimation of Dynamic Stochastic Theories with an Application to New Keynesian Pricing

This paper proposes a novel Maximum Likelihood (ML) strategy to estimate Euler equations implied by dynamic stochastic theories. The strategy exploits rational expectations cross-equation restrictions, but circumvents the problem of multiple solutions that arises in Sargent's (1979) original work by imposing the restrictions on the forcing variable rather than the endogenous variable of the Euler equation. The paper then contrasts the proposed strategy to an alternative, widely employed method that avoids the multiplicity problem by constraining the ML estimates to yield a unique stable solution. I argue that imposing such a uniqueness condition makes little economic sense and can lead to severe misspecification. To illustrate this point, I estimate Gali and Gertler's (1999) hybrid New Keynesian Phillips Curve using labor income share as the measure of real marginal cost. My ML estimates indicate that forward-looking behavior is predominant and that the model provides a good approximation of U.S. inflation dynamics. By contrast, if the same estimates are constrained to yield a unique stable solution, forward-looking behavior becomes much less important and the model as a whole is rejected.
Cyclic Deformation Behaviour and Potential Automobile Application of Magnesium Die Casting Alloys AZ91 and AM50

Low-cycle fatigue life, cyclic strain hysteresis loops, cyclic strain hardening, cyclic mean stress relaxation of magnesium die casting alloys AZ91 and AM5 are investigated in this paper. Depending on the material characters and components working load, the potential automobile application has been discussed. It is considered that the magnesium alloy die castings with a big cyclic strain hysteresis loop and cyclic strain hardening tendency is beneficial for increasing NVH of a car, but the mean stress relaxation phenomenon remind that the tightness of bolt connection is easy to loos under a cyclic stress for a moving car. Compared with AZ91HP-F, AZ91HP-T6 and AM50HP -F, AZ91HP-T4 is more favourable to make automobile components.
Limits on the accuracy of 3-D thickness measurement in magnetic resonance images-effects of voxel anisotropy

Measuring the thickness of sheet-like thin anatomical structures, such as articular cartilage and brain cortex, in three-dimensional (3-D) magnetic resonance (MR) images is an important diagnostic procedure. This paper investigates the fundamental limits on the accuracy of thickness determination in MR images. We defined thickness here as the distance between the two sides of boundaries measured at the subvoxel resolution, which are the zero-crossings of the second directional derivatives combined with Gaussian blurring along the normal directions of the sheet surface. Based on MR imaging and computer postprocessing parameters, characteristics for the accuracy of thickness determination were derived by a theoretical simulation. We especially focused on the effects of voxel anisotropy in MR imaging with variable orientation of sheet-like structure. Improved and stable accuracy features were observed when the standard deviation of Gaussian blurring combined with thickness determination processes was around /spl radic/2/2 times as large as the pixel size. The relation between voxel anisotropy in MR imaging and the range of sheet normal orientation within which acceptable accuracy is attainable was also clarified, based on the dependences of voxel anisotropy and the sheet normal orientation obtained by numerical simulations. Finally, in vitro experiments were conducted using an acrylic plate phantom and a resected femoral head to validate the results of theoretical simulation. The simulated thickness was demonstrated to be well-correlated with the actual in vitro thickness.
How to Center Deep Boltzmann Machines

This work analyzes centered Restricted Boltzmann Machines (RBMs) and centered Deep Boltzmann Machines (DBMs), where centering is done by subtracting offset values from visible and hidden variables. We show analytically that (i) centered and normal Boltzmann Machines (BMs) and thus RBMs and DBMs are different parameterizations of the same model class, such that any normal BM/RBM/DBM can be transformed to an equivalent centered BM/RBM/DBM and vice versa, and that this equivalence generalizes to artificial neural networks in general, (ii) the expected performance of centered binary BMs/RBMs/DBMs is invariant under simultaneous flip of data and offsets, for any off-set value in the range of zero to one, (iii) centering can be reformulated as a different update rule for normal BMs/RBMs/DBMs, and (iv) using the enhanced gradient is equivalent to setting the offset values to the average over model and data mean. Furthermore, we present numerical simulations suggesting that (i) optimal generative performance is achieved by subtracting mean values from visible as well as hidden variables, (ii) centered binary RBMs/DBMs reach significantly higher log-likelihood values than normal binary RBMs/DBMs, (iii) centering variants whose offsets depend on the model mean, like the enhanced gradient, suffer from severe divergence problems, (iv) learning is stabilized if an exponentially moving average over the batch means is used for the offset values instead of the current batch mean, which also prevents the enhanced gradient from severe divergence, (v) on a similar level of log-likelihood values centered binary RBMs/DBMs have smaller weights and bigger bias parameters than normal binary RBMs/DBMs, (vi) centering leads to an update direction that is closer to the natural gradient, which is extremely efficient for training as we show for small binary RBMs, (vii) centering eliminates the need for greedy layer-wise pre-training of DBMs, which often even deteriorates the results independently of whether centering is used or not, and (ix) centering is also beneficial for auto encoders.
Global Small RNA Chaperone Hfq and Regulatory Small RNAs Are Important Virulence Regulators in Erwinia amylovora

ABSTRACT Hfq is a global small RNA (sRNA) chaperone that interacts with Hfq-regulated sRNAs and functions in the posttranscriptional regulation of gene expression. In this work, we identified Hfq to be a virulence regulator in the Gram-negative fire blight pathogen Erwinia amylovora. Deletion of hfq in E. amylovora Ea1189 significantly reduced bacterial virulence in both immature pear fruits and apple shoots. Analysis of virulence determinants in strain Ea1189Δhfq showed that Hfq exerts pleiotropic regulation of amylovoran exopolysaccharide production, biofilm formation, motility, and the type III secretion system (T3SS). Further characterization of biofilm regulation by Hfq demonstrated that Hfq limits bacterial attachment to solid surfaces while promoting biofilm maturation. Characterization of T3SS regulation by Hfq revealed that Hfq positively regulates the translocation and secretion of the major type III effector DspE and negatively controls the secretion of the putative translocator HrpK and the type III effector Eop1. Lastly, 10 Hfq-regulated sRNAs were identified using a computational method, and two of these sRNAs, RprA and RyhA, were found to be required for the full virulence of E. amylovora.