Miracle-dz/UniFAR-FTUs huggingface dataset:
The importance of stain normalization in colorectal tissue classification with convolutional networks

The development of reliable imaging biomarkers for the analysis of colorectal cancer (CRC) in hematoxylin and eosin (H&E) stained histopathology images requires an accurate and reproducible classification of the main tissue components in the image. In this paper, we propose a system for CRC tissue classification based on convolutional networks (ConvNets). We investigate the importance of stain normalization in tissue classification of CRC tissue samples in H&E-stained images. Furthermore, we report the performance of ConvNets on a cohort of rectal cancer samples and on an independent publicly available dataset of colorectal H&E images.
Movement, Habitat, and Home Range of Introduced Bullfrogs (Lithobates Catesbeianus) on Mad River Gravel Ponds (Humboldt Co., CA, USA), With Implications for Hydro-Modification as a Method of Management

ii ACKNOWLEDGMENTS . iv TABLE OF CONTENTS. v LIST OF TABLES . vii LIST OF FIGURES . viii LIST OF APPENDICES . x INTRODUCTION . 1 METHODS . 7 Study Site . 7 Telemetry . 10 Mark-Recapture . 11 Movement Extent, Home Range, and Habitat Use . 11 Visual Encounter Surveys . 12 Habitat Modification and Subsequent Monitoring . 13 RESULTS . 16 Movement Extent . 16 Home Range and Habitat Use . 19 Phenology and Visual Encounter Surveys . 23 Habitat Modification and Subsequent Monitoring . 26 DISCUSSION. 30 Overview . 30
Australia antigen associated hepatitis: radioimmunoassay in mother and infant.

To the Editor. — Neonatal hepatitis has been vigorously investigated, but to date the results have been confusing and contradictory. 1-6 The question of transplacental transmission is still unsettled. 2 Stokes et al transmitted hepatitis to human volunteers from the serum of a 9-month-old infant who seven months earlier had had hepatitis. 3 Blood from the infant's mother, although she had no history or hepatitis, was also shown to be capable of transmitting hepatitis to volunteers. The recent discovery of Australia antigen, which appears to be associated with serum hepatitis, provides a valuable tool for another investigation of this problem. Two studies are reported in which this had been attempted. 7,8 In the first report, although Australia antigen was still present in the mother's serum at time of delivery, 17 months after hepatitis, cord blood failed to show evidence of antigen by the Ouchterlony method. In the second study there were
Uncoupling of oxidative phosphorylation and ATP synthase reversal within the hyperthermic heart

Heart failure is a common cause of death with hyperthermia, and the exact cause of hyperthermic heart failure appears elusive. We hypothesize that the energy supply (ATP) of the heart may become impaired due to increased inner‐mitochondrial membrane permeability and inefficient oxidative phosphorylation (OXPHOS). Therefore, we assessed isolated working heart and mitochondrial function. Ex vivo working rat hearts were perfused between 37 and 43.5°C and showed break points in all functional parameters at ~40.5°C. Mitochondrial high‐resolution respirometry coupled to fluorometry was employed to determine the effects of hyperthermia on OXPHOS and mitochondrial membrane potential (ΔΨ) in vitro using a comprehensive metabolic substrate complement with isolated mitochondria. Relative to 37 and 40°C, 43°C elevated Leak O2 flux and depressed OXPHOS O2 flux and ∆Ψ. Measurement of steady‐state ATP production from mitochondria revealed decreased ATP synthesis capacity, and a negative steady‐state P:O ratio at 43°C. This approach offers a more powerful analysis of the effects of temperature on OXPHOS that cannot be measured using simple measures such as the traditional respiratory control ratio (RCR) or P:O ratio, which, respectively, can only approach 1 or 0 with inner‐membrane failure. At 40°C there was only a slight enhancement of the Leak O2 flux and this did not significantly affect ATP production rate. Therefore, during mild hyperthermia (40°C) there is no enhancement of ATP supply by mitochondria, to accompany increasing cardiac energy demands, while between this and critical hyperthermia (43°C), mitochondria become net consumers of ATP. This consumption may contribute to cardiac failure or permanent damage during severe hyperthermia.
The Effects of Smoking on Expression of IL-12 and IL-1β in Gingival Tissues of Patients with Chronic Periodontitis

Aim: The purpose of this study was to compare IL-1β and IL-12 gene expression in the gingival tissue of smokers and non-smokers either with healthy periodontium or with chronic periodontitis. Materials and Methods: 41 individuals consisting of 21 healthy controls (11 non-smokers and 10 smokers) and 20 chronic periodontitis patients (10 non-smokers and 10 smokers) participated in this study. Samples were collected from papillary regions of targeted areas and cytokines were analyzed using Real Time PCR. Shapiro-Wilk, Mann-Witney and Independent T tests were employed for statistical analysis. Results: IL-1β gene expression in gingival tissue of non-smoker group with chronic periodontitis was significantly higher than non-smoker-healthy group (p=0.011). Smoker-chronic periodontitis group showed lower IL-1β gene expression than non-smoker-chronic periodontitis group (p=0.003). IL-12 gene expression was not significantly different between analyzed groups. Conclusion: IL-1β gene expression increases in gingival tissue of non-smoker-chronic periodontitis patients due to inflammatory processes but smoking reduces the expression of this cytokine in diseased periodontal tissues. On the other hand periodontal condition and smoking habits do not seem to affect IL-12 gene expressions in gingival tissues. Authors concluded that reduced levels of IL1 and in some extent IL12 in smoking patients are responsible for higher tissue and bone degenerations and less treatment responses in smokers.
Evaluating the Effectiveness of REDCAP to Recover the Locality Missed by Today's Linux Systems

In order to know how different conditions influence the behavior of the RAM Enhanced Disk Cache Project (RED-CAP), we have analyzed the impact of the file system and the REDCAP cache size. The results show that, for work-loads which exhibit some spatial locality the application time can be reduced by more than 80% for file systems that split the disk into block groups, while for those that do not use this division the reduction can be more than 55%. REDCAP has the same performance as a traditional system for those workloads with a random or sequential access pattern. The experiments also show that the cache size can determine the results, depending on the file system and the number of processes.
Profiling Internet BackboneTraffic : Behavior Models and Applications

Recent spates of cyber-attacks and frequent emergence of applications affecting Internet traffic dynamics have made it imperative to develop effective techniques that can extract, and make sense of, significant communication patterns from Internet traffic data for use in network operations and security management. In this paper, we present a general methodology for building comprehensive behavior profiles of Internet backbone traffic in terms of communication patterns of end-hosts and services. Relying on data mining and information-theoretic techniques, the methodology consists of significant cluster extraction, automatic behavior classification and structural modeling for in-depth interpretive analyses. We validate the methodology using data sets from the core of the Internet. The results demonstrate that it indeed can identify common traffic profiles as well as anomalous behavior patterns that are of interest to network operators and security analysts.
No Critical Peripheral Fatigue Threshold during Intermittent Isometric Time to Task Failure Test with the Knee Extensors

It has been proposed that group III and IV muscle afferents provide inhibitory feedback from locomotor muscles to the central nervous system, setting an absolute threshold for the development of peripheral fatigue during exercise. The aim of this study was to test the validity of this theory. Thus, we asked whether the level of developed peripheral fatigue would differ when two consecutive exercise trials were completed to task failure. Ten trained sport students performed two exercise trials to task failure on an isometric dynamometer, allowing peripheral fatigue to be assessed 2 s after maximal voluntary contraction (MVC) post task failure. The trials, separated by 8 min, consisted of repeated sets of 10 × 5-s isometric knee extension followed by 5-s rest between contractions. In each set, the first nine contractions were performed at a target force at 60% of the pre-exercise MVC, while the 10th contraction was a MVC. MVC and evoked force responses to supramaximal electrical femoral nerve stimulation on relaxed muscles were assessed during the trials and at task failure. Stimulations at task failure consisted of single stimulus (SS), paired stimuli at 10 Hz (PS10), paired stimuli at 100 Hz (PS100), and 50 stimuli at 100 Hz (tetanus). Time to task failure for the first trial (12.84 ± 5.60 min) was longer (P < 0.001) than for the second (5.74 ± 1.77 min). MVC force was significantly lower at task failure for both trials compared with the pre-exercise values (both P < 0.001), but there were no differences in MVC at task failure in the first and second trials (P = 1.00). However, evoked peak force for SS, PS100, and tetanus were all reduced more at task failure in the second compared to the first trial (P = 0.014 for SS, P < 0.001 for PS100 and tetanus). These results demonstrate that subjects do not terminate exercise at task failure because they have reached a critical threshold in peripheral fatigue. The present data therefore question the existence of a critical peripheral fatigue threshold during intermittent isometric exercise to task failure with the knee extensors.
Sharp estimates for metastable lifetimes in parabolic SPDEs: Kramers' law and beyond

We prove a Kramers-type law for metastable transition times for a class of one-dimensional parabolic stochastic partial differential equations (SPDEs) with bistable potential. The expected transition time between local minima of the potential energy depends exponentially on the energy barrier to overcome, with an explicit prefactor related to functional determinants. Our results cover situations where the functional determinants vanish owing to a bifurcation, thereby rigorously proving the results of formal computations announced in a previous work. The proofs rely on a spectral Galerkin approximation of the SPDE by a finite-dimensional system, and on a potential-theoretic approach to the computation of transition times in finite dimension.
Analysis of uplink transmissions in cellular networks: A stochastic geometry approach

In this paper, we exploit tools from stochastic geometry to develop a tractable model for uplink transmissions in single-tier cellular wireless networks with truncated channel inversion power control. Our model gives simple expressions for the outage probability and spectral efficiency which characterize the network performance in terms of the design parameters. In particular, the model reveals a transfer point in the uplink system behavior that depends on the tuple: BS intensity (λ), maximum transmit power of UEs (P<sub>u</sub>), and power control cutoff threshold ρ<sub>o</sub>. More specifically, when P<sub>u</sub> is a tight operational constraint with respect to [w.r. t. ] λ and ρ<sub>o</sub>, the uplink performance highly depends on the values of λ and ρ<sub>o</sub>. In contrast, when P<sub>u</sub> is a non-binding operational constraint w.r. t. λ and ρ<sub>o</sub>, the uplink performance becomes independent of λ and ρ<sub>o</sub>.
Statistical Applications in Genetics and Molecular Biology

Changes in cytosine methylation at CpG nucleotides are observed in many cancers and offer great potential for translational research. Diseases such as ovarian cancer that are especially challenging to diagnose and treat are of particular interest, and abnormal methylation in the tandem repeats Sat2 and NBL2 has been observed in a collection of ovarian carcinomas. In earlier analyses of double-stranded methylation patterns in 0.2 kb regions of Sat2 and NBL2, we detected clusters of identically methylated sites in close proximity. These clusters could not be explained by random variation, and our findings suggested a high degree of site-to-site dependence. However, previously developed stochastic models for methylation change have either treated CpG sites independently or employed a context dependent approach to adjust model parameters according to regional methylation levels. In this paper, we introduce a novel neighboring sites model as an alternative methodology for considering dependence in methylation patterns, and we compare the three models in their ability to generate simulated sequences statistically similar to our Sat2 and NBL2 carcinoma samples.
Safety of Cyclosporin A in HCV‐Infected Patients

Abstract: Because of the relatively high prevalence of both hepatitis C virus (HCV) infection and autoimmune disorders (ADs), it is not rare to encounter in daily clinical practice patients with ADs also carrying HCV. Corticosteroids and/or immunosuppressant drugs are needed to treat ADs, but they place HCV‐infected patients at risk of worsening the infection. So, rheumatologists have often refrained from using corticosteroids or immunosuppressants in AD when HCV–RNA is also present. Cyclosporin A (CsA) is an immunosuppressive agent used to treat a wide range of ADs, but there is a large evidences in the literature, both in vitro and in vivo, suggesting that CsA also exerts an inhibitory effect on HCV replication at standard therapeutic dose. Therefore, this evidence has opened new ways to improve the therapy and the prognosis in patients with HCV‐related liver diseases, including those with transplants. Recent reports, although limited in number, also suggest the safety of CsA in the treatment of patients with AD and concomitant HCV infection. In this review we also report our personal experience on the combination treatment with CsA and anti‐TNF‐α agents in rheumatoid arthritis.
E-Cadherin and Cell Adhesion: a Role in Architecture and Function in the Pancreatic Islet

Background/Aims: The efficient secretion of insulin from β-cells requires extensive intra-islet communication. The cell surface adhesion protein epithelial (E)-cadherin (ECAD) establishes and maintains epithelial tissues such as the islets of Langerhans. In this study, the role of ECAD in regulating insulin secretion from pseudoislets was investigated. Methods: The effect of an immuno-neutralising ECAD on gross morphology, cytosolic calcium signalling, direct cell-to-cell communication and insulin secretion was assessed by fura-2 microfluorimetry, Lucifer Yellow dye injection and insulin ELISA in an insulin-secreting model system. Results: Antibody blockade of ECAD reduces glucose-evoked changes in [Ca2+]i and insulin secretion. Neutralisation of ECAD causes a breakdown in the glucose-stimulated synchronicity of calcium oscillations between discrete regions within the pseudoislet, and the transfer of dye from an individual cell within a cell cluster is attenuated in the absence of ECAD ligation, demonstrating that gap junction communication is disrupted. The functional consequence of neutralising ECAD is a significant reduction in insulin secretion. Conclusion: Cell adhesion via ECAD has distinct roles in the regulation of intercellular communication between β-cells within islets, with potential repercussions for insulin secretion.
Technology and the delivery of the curriculum of the future: Opportunities and challenges

There is increasing availability of a wide range of technology that has the potential to support and enhance the curriculum of the future. Learners expect to use technology for their learning, but this requires the development of information and digital literacy skills to maximise the potential learning opportunities. Learning resources will be increasingly delivered by a variety of mobile devices and also through different immersive and virtual learning environments. Mobile devices and Web 2.0 technology provide opportunities for learners to create their own deep and personalised learning experiences that are relevant for future professional practice. Tutors have a crucial guidance and support role for the effective use of technology for learning. There is a little evidence base to support the impact on learning for many of the potential scenarios and further research is urgently required.
Fine‐scale climate change: modelling spatial variation in biologically meaningful rates of warming

The existence of fine‐grain climate heterogeneity has prompted suggestions that species may be able to survive future climate change in pockets of suitable microclimate, termed ‘microrefugia’. However, evidence for microrefugia is hindered by lack of understanding of how rates of warming vary across a landscape. Here, we present a model that is applied to provide fine‐grained, multidecadal estimates of temperature change based on the underlying physical processes that influence microclimate. Weather station and remotely derived environmental data were used to construct physical variables that capture the effects of terrain, sea surface temperatures, altitude and surface albedo on local temperatures, which were then calibrated statistically to derive gridded estimates of temperature. We apply the model to the Lizard Peninsula, United Kingdom, to provide accurate (mean error = 1.21 °C; RMS error = 1.63 °C) hourly estimates of temperature at a resolution of 100 m for the period 1977–2014. We show that rates of warming vary across a landscape primarily due to long‐term trends in weather conditions. Total warming varied from 0.87 to 1.16 °C, with the slowest rates of warming evident on north‐east‐facing slopes. This variation contributed to substantial spatial heterogeneity in trends in bioclimatic variables: for example, the change in the length of the frost‐free season varied from +11 to −54 days and the increase in annual growing degree‐days from 51 to 267 °C days. Spatial variation in warming was caused primarily by a decrease in daytime cloud cover with a resulting increase in received solar radiation, and secondarily by a decrease in the strength of westerly winds, which has amplified the effects on temperature of solar radiation on west‐facing slopes. We emphasize the importance of multidecadal trends in weather conditions in determining spatial variation in rates of warming, suggesting that locations experiencing least warming may not remain consistent under future climate change.
LAMP: A Framework for Large-Scale Addressing of Muddy Points

Muddy Points (MP) is a strategy to elicit and address individual students' doubts. While this can be effectively implemented in small classes, it is a challenge to do so in a large class. In this paper we propose LAMP, a framework for Large-scale Addressing of Muddy Points, as a mechanism for instructors to ensure that every individual student's doubts are addressed even in large classes. LAMP has three phases: Collection, Addressal, and Closure. In the collection phase, MPs are systematically collected through four different modes. In the addressal phase, MPs are categorized into six categories and addressed accordingly. In the closure phase, the discussions on MPs are summarized. We investigated the effectiveness of LAMP in an introductory computer science course having 450 students. We found that 68% of students confirmed they were able to pose their questions and 57% of students confirmed that there was closure to their questions.
A general approach for a trusted deployment of a business process in clouds

It is recognized that the most important obstacle to the development of the cloud is the variety of new security threats which requests new methods and mechanisms. This is even truer for those who want to deploy business processes, because of the critical knowledge they encapsulate in terms of know-how and data. This paper proposes an approach combining modeling techniques and cloud selection for a trusted deployment of a security risk-aware business process in security constrained clouds.
Patterns of hypothalamic regionalization in amphibians and reptiles: common traits revealed by a genoarchitectonic approach

Most studies in mammals and birds have demonstrated common patterns of hypothalamic development highlighted by the combination of developmental regulatory genes (genoarchitecture), supporting the notion of the hypothalamus as a component of the secondary prosencephalon, topologically rostral to the diencephalon. In our comparative analysis we have summarized the data on the expression patterns of different transcription factors and neuroactive substances, used as anatomical markers, in the developing hypothalamus of the amphibian Xenopus laevis and the juvenile turtle Pseudemys scripta. This analysis served to highlight the organization of the hypothalamus in the anamniote/amniotic transition. We have identified supraoptoparaventricular and the suprachiasmatic regions (SCs) in the alar part of the hypothalamus, and tuberal and mammillary regions in the basal hypothalamus. Shared features in the two species are: (1) The supraoptoparaventricular region (SPV) is defined by the expression of Otp and the lack of Nkx2.1/Isl1. It is subdivided into rostral, rich in Otp and Nkx2.2, and caudal, only Otp-positive, portions. (2) The suprachiasmatic area contains catecholaminergic cell groups and lacks Otp, and can be further divided into rostral (rich in Nkx2.1 and Nkx2.2) and a caudal (rich in Isl1 and devoid of Nkx2.1) portions. (3) Expression of Nkx2.1 and Isl1 define the tuberal hypothalamus and only the rostral portion expresses Otp. (4) Its caudal boundary is evident by the lack of Isl1 in the adjacent mammillary region, which expresses Nkx2.1 and Otp. Differences in the anamnio-amniote transition were noted since in the turtle, like in other amniotes, the boundary between the alar hypothalamus and the telencephalic preoptic area shows distinct Nkx2.2 and Otp expressions but not in the amphibian (anamniote), and the alar SPV is defined by the expression of Otp/Pax6, whereas in Xenopus only Otp is expressed.
Reply to 'Mitochondrial changes in skeletal muscle in amyotrophic lateral sclerosis and other neurogenic atrophies--a comment'.

Based on new biochemical data, Vielhaber et al . (2005) made some comments on our recent findings on mitochondrial changes in skeletal muscle of patients with sporadic amyotrophic lateral sclerosis (ALS) (Krasnianski et al ., 2005). However, the interpretation of the new data by Vielhaber et al . needs some critical discussion. There are three separate issues that have clearly to be differentiated: (i) mitochondrial dysfunction in the CNS in ALS, (ii) mitochondrial dysfunction in skeletal muscle in ALS and (iii) mitochondrial dysfunction in atrophic skeletal muscle due to other neurogenic diseases. There is accumulating evidence for mitochondrial dysfunction in the CNS in ALS (Bowling et al ., 1993; Fujita et al ., 1996; Borthwick et al ., 1999; Wiedemann et al ., 2002). This issue, however, was neither the objective of our study nor of the studies by Vielhaber et al . (2000, 2003, 2005). In contrast to mitochondrial involvement in the CNS, the data on dysfunction of skeletal muscle mitochondria in ALS are controversial. For a long time it has been clearly established that chronic denervation can be associated with histological abnormalities such as core and target formations suggesting non-specific mitochondrial changes in denervated muscle (Dubowitz and Brooke, 1973). This implies that any investigation of mitochondrial …