Miracle-dz/UniFAR-FTUs huggingface dataset:
Unsupervised Histopathology Image Synthesis

Hematoxylin and Eosin stained histopathology image analysis is essential for the diagnosis and study of complicated diseases such as cancer. Existing state-of-the-art approaches demand extensive amount of supervised training data from trained pathologists. In this work we synthesize in an unsupervised manner, large histopathology image datasets, suitable for supervised training tasks. We propose a unified pipeline that: a) generates a set of initial synthetic histopathology images with paired information about the nuclei such as segmentation masks; b) refines the initial synthetic images through a Generative Adversarial Network (GAN) to reference styles; c) trains a task-specific CNN and boosts the performance of the task-specific CNN with on-the-fly generated adversarial examples. Our main contribution is that the synthetic images are not only realistic, but also representative (in reference styles) and relatively challenging for training task-specific CNNs. We test our method for nucleus segmentation using images from four cancer types. When no supervised data exists for a cancer type, our method without supervision cost significantly outperforms supervised methods which perform across-cancer generalization. Even when supervised data exists for all cancer types, our approach without supervision cost performs better than supervised methods.
Adaptive uncertainty based iterative robust capon beamformer

This paper proposes an iterative robust capon beamformer (IRCB) with adaptive uncertainty level. The approach iteratively estimates the actual steering vector based on conventional RCB formulation. Instead of using a fixed uncertainty level, we adaptively update the uncertainty level at each iteration. The uncertainty is updated based on the projection of the presumed steering vector onto the noise subspace. The iteration converges when the noise subspace projection is zero. We additionally impose a constraint that restricts the estimated steering vector to be within a spatial sector in order to overcome inappropriate updating of the uncertainty due to subspace swap at low signal-to-noise ratio (SNR) case. Simulation results show that the adaptive uncertainty based IRCB converges faster than the fixed uncertainty based IRCB. Besides alleviating the need to assume any knowledge on the mismatch, the proposed beamformer requires lower computational cost as compared to the convex optimization based beamformer design.
Research interest

Data Mining/Machine Learning, Pattern Recognition and Information Retrieval techniques with applications to big data analytics (time series data, video, image and audio analytics). I implement PhotoDNA image hashing algorithm into Ocelot to detect child pornography uploaded in any Google product with hashes shared by the industry. I worked with different teams, including legal team, to design/implement a pipeline to evaluate coverage of different image hashing techniques. I work in Content & Community (CNC) Decision Sciences team, which responsible for building the social component of LinkedIn that enables our users to create, share, discuss and distribute highly relevant content across the LinkedIn network.
Enhanced Cytomegalovirus Infection of Developing Brain Independent of the Adaptive Immune System

ABSTRACT Cytomegalovirus (CMV) has been suggested as the most prevalent infectious agent causing neurological dysfunction in the developing brain; in contrast, CMV infections are rare in the adult brain. One explanation generally given for the developmental susceptibility to the virus is that the developing immune system is too immature to protect the central nervous system from viral infection, but as the immune system develops it can protect the brain. We suggest an alternate view: that developing brain cells are inherently more susceptible to CMV infection, independent of the immune system. We used a recombinant mouse CMV that leads to green fluorescent protein expression in infected cells. Control experiments demonstrated a high correlation between the number of cells detected with the viral GFP reporter gene and with immunocytochemical detection of the virus. After intracerebral inoculation, the number of CMV-infected cells in neonatal brains was many times greater than in mature control or mature immunodepressed SCID mice, and the mortality rate of neonates was substantially greater than SCID or control adults. Parallel experiments with live brain slices inoculated in vitro, done in the absence of the systemic immune system, generated similar data, with immature hippocampus, hypothalamus, cortex, striatum, and cerebellum showing substantially greater numbers of infected cells (100-fold) than found in adult slices in these same regions. Interestingly, in the cerebellar cortex, CMV-infected cells were more prevalent in the postmitotic Purkinje cell layer than in the mitotic granule cell layer, suggesting a selective infection of some cell types not dependent on cell division. Together, these data support the view that CMV has an intrinsic preference for infection of developing brain cells, independent, but not mutually exclusive, of the developmental status of the systemic immune system in controlling CMV infection.
MID-INFRARED SPECTROSCOPY OF SUBMILLIMETER GALAXIES: EXTENDED STAR FORMATION IN MASSIVE HIGH-REDSHIFT GALAXIES

We used the Spitzer Infrared Spectrograph (IRS) to study the mid-IR properties and investigate the energetics of 24 Submillimeter Galaxies (SMGs). This is the largest sample of SMGs observed with Spitzer IRS and covers the full extent of properties of the radio-identified population of SMGs in the redshift range of z ∼ 0.65–3.2. We observe broad emission features from polycyclic aromatic hydrocarbons in more than 80% of our sample. We find that the median mid-IR spectrum is well described by a starburst component with an additional power law, Fν ∼ ν−2, likely representing a <32% contribution from an active galactic nucleus to the bolometric luminosity. Our results thus confirm that starburst activity dominates the bolometric luminosity in SMGs. We find that SMGs show weaker silicate absorption at ∼9.7 μm than local ULIRGs. We also find stronger 6.2-μm PAH emission in SMGs (relative to the 7.7 μm PAH feature) than in local nuclear starbursts, which may be attributed to lower extinction by ice along the line of sight to SMGs. This suggests that the continuum and PAH emitting regions of SMGs are less obscured than in local starbursts and similarly luminous low-redshift ULIRGs. We interpret these results as evidence for a more extended distribution of cool and warm dust in SMGs compared to the more compact emitting regions in local ULIRGs and starbursts. Together these results suggest that SMGs are not simple high-redshift analogs of nuclear starbursts or local ULIRGs, but instead they appear to have star formation which resembles that seen in less-extreme star-forming environments at z ∼ 0–suggesting their intense activity is distributed across a far larger region than the ∼1 kpc nuclear bursts in local ULIRGs.
Oxidative Damage in Cardiac Tissue from Normotensive and Spontaneously Hypertensive Rats: Effect of Ageing

The spontaneously hypertensive rat (SHR) is a laboratory model of naturally developing hypertension and heart failure that appears to be similar in many aspects to essential hypertension in humans (Trippodo & Frohlich, 1981). Systolic blood pressure in SHR rapidly increases during 5 to 10 weeks of age and develops cardiac hypertrophy between 9 and 12 weeks of age (Shimamoto et al., 1982). Increasing evidence from different experimental models supports the concept that oxidative stress contributes to the pathogenesis of myocardial hypertrophy and in the process of myocardial remodeling leading to heart failure (Yucel et al., 1998; Lassegue & Griendling, 2004).
Simulating Network Delays: Applications, Algorithms, and Tools

Organizations are rushing to establish a presence on the World Wide Web (WWW). Researchers, designers, and users all recognize the importance of network delays, with longer delays frequently being associated with more negative user experiences. Although some delay is unavoidable, design decisions do contribute to the total delay users experience. In this article, a collection of tools that allow individuals to experience realistic network delays during informal evaluations, usability studies, and controlled experiments are described. These tools allow practitioners to more effectively assess usability in the context of realistic network delays, researchers to more effectively investigate the factors that affect the usability of information and applications delivered via the WWW, and educators to more effectively convey the importance of design decisions in the context of the WWW. This article describes how these tools may be used as well as the tools themselves, including the algorithms that make them effective. 2 approaches for validating simulations with results are presented. The first validation suggests that the simulation process utilized in the wide-area network delay simulator tools (Borella & Sears, 1997) effectively reproduces the network delays observed when retrieving material via the WWW. The second validation provides even stronger support, indicating that the simulation process can be used to reproduce a specific set of network conditions more accurately than the network itself. Directions for additional research are also discussed.
Efficient Fetal-Maternal ECG Signal Separation from Two Channel Maternal Abdominal ECG via Diffusion-Based Channel Selection

There is a need for affordable, widely deployable maternal-fetal ECG monitors to improve maternal and fetal health during pregnancy and delivery. Based on the diffusion-based channel selection, here we present the mathematical formalism and clinical validation of an algorithm capable of accurate separation of maternal and fetal ECG from a two channel signal acquired over maternal abdomen. The proposed algorithm is the first algorithm, to the best of the authors' knowledge, focusing on the fetal ECG analysis based on two channel maternal abdominal ECG signal, and we apply it to two publicly available databases, the PhysioNet non-invasive fECG database (adfecgdb) and the 2013 PhysioNet/Computing in Cardiology Challenge (CinC2013), to validate the algorithm. The state-of-the-art results are achieved when compared with other available algorithms. Particularly, the F1 score for the R peak detection achieves 99.3% for the adfecgdb and 87.93% for the CinC2013, and the mean absolute error for the estimated R peak locations is 4.53 ms for the adfecgdb and 6.21 ms for the CinC2013. The method has the potential to be applied to other fetal cardiogenic signals, including cardiac doppler signals.
Transcriptional Regulation of Latent Feline Immunodeficiency Virus in Peripheral CD4+ T-lymphocytes

Feline immunodeficiency virus (FIV), the lentivirus of domestic cats responsible for feline AIDS, establishes a latent infection in peripheral blood CD4+ T-cells approximately eight months after experimental inoculation. In this study, cats experimentally infected with the FIV-C strain in the asymptomatic phase demonstrated an estimated viral load of 1 infected cell per approximately 103 CD4+ T-cells, with about 1 copy of viral DNA per cell. Approximately 1 in 10 proviral copies was capable of transcription in the asymptomatic phase. The latent FIV proviral promoter was associated with deacetylated, methylated histones, which is consistent with a condensed chromatin structure. In contrast, the transcriptionally active FIV promoter was associated with histone acetylation and demethylation. In addition, RNA polymerase II appeared to be paused on the latent viral promoter, and short promoter-proximal transcripts were detected. Our findings for the FIV promoter in infected cats are similar to results obtained in studies of human immunodeficiency virus (HIV)-1 latent proviruses in cell culture in vitro studies. Thus, the FIV/cat model may offer insights into in vivo mechanisms of HIV latency and provides a unique opportunity to test novel therapeutic interventions aimed at eradicating latent virus.
Linear Algebra

The subject of linear algebra includes the solution of linear equations, a topic properly belonging to college algebra. Earlier in this text, the theory of linear algebraic equations was presented, without the aid of vector-matrix notation. The project before us is to introduce specialized vector-matrix notation and to extend the methods used to solve linear algebraic equations. Enrichment includes a full study of rank, nullity and basis from the vector-matrix viewpoint. Engineers can view linear algebra as the essential language interface between an application and a computer algebra system or a computer numerical laboratory. Without the language interface, computer assist would be impossibly tedious.
PARENTAL ATTITUDES TOWARD THE PRESCRIPTION OF PSYCHOTROPIC MEDICATIONS FOR THEIR CHILDREN

Objective: To explore parental attitudes towards the prescription of psychotropic medication for their children. Method: A questionnaire built to collect socio-demographic data of parents and their attitudes was distributed among parents. Results: One thousand and ten questionnaires were filled by parents. Fathers who completed the questionnaire were double the number of mothers. Eight hundred and eighteen parents (84.3%) agreed to the dispensing psychotropic medication to their children if necessary. About 83.5% preferred to start with psychotherapy before trying medication. Fathers are more than twice likely than mothers to agree to the use of psychotropic drugs. Older parents more easily agreed to give their children psychotropic drugs. Parents who used psychotropic drug themselves were more likely to agree to the use of psychotropic drug by their children. Having a child with a psychiatric illness is the most significant factor in making parents accede to giving children psychotropic medication. Other factors such as pressure from schools and the side effects of drugs could also modify decision of parents. Conclusion: Although most parents agreed to give their children psychotropic drugs if necessary, they preferred to start with psychotherapy sessions before giving them the drugs. Fear and worries about such issues as side effects of drugs or addiction should be considered. Pressure from school should also be considered when deciding on drug therapy.
Increased Plasma Natriuretic Peptide Levels Reflect Symptom Onset in Aortic Stenosis

Background—The onset of symptoms is a critical point in the natural history of aortic stenosis and the cardinal indication for valve replacement. This study assessed the associations between natriuretic peptide levels, disease severity, and cardiac symptoms in aortic stenosis. Methods and Results—Seventy-four patients with isolated aortic stenosis underwent independent assessment of symptoms, transthoracic echocardiography, and measurement of plasma levels of atrial natriuretic peptide, brain natriuretic peptide (BNP), and N-BNP. Natriuretic peptide levels were also measured in 100 clinically normal control subjects. The aortic valve area was smaller in symptomatic patients (n=45) than in asymptomatic patients (n=29; mean, 0.71±0.23 cm2 and 0.99±0.31 cm2, respectively;P <0.0001). Plasma natriuretic peptide levels were higher in symptomatic patients than in asymptomatic patients (for N-BNP: median, 112 versus 33 pmol/L; interquartile range, 70 to 193 versus 16 to 58 pmol/L, respectively;P =0.0002). After adjustment for age, sex, serum creatinine, aortic valve area, and left ventricular ejection fraction, N-BNP levels were 1.74 times higher (95% confidence interval, 1.12 to 2.69) for symptomatic than asymptomatic patients with aortic stenosis (P =0.014). Natriuretic peptide levels increased with the New York Heart Association class (for N-BNP median values were 13, 34, 105, and 202 pmol/L for normal control subjects, class I, class II, and class III/IV patients, respectively; interquartile ranges for the same patients were 8 to 21, 16 to 58, 57 to 159, and 87 to 394 pmol/L;P <0.0001). Similar associations were observed for BNP and atrial natriuretic peptide. Conclusions—Plasma natriuretic peptide levels are elevated in symptomatic patients with aortic stenosis. Measurement of natriuretic peptides may complement clinical and echocardiographic evaluation of patients with aortic stenosis.
Recent Developments to Improve Crack Opening Areas for R6 Leak-Before-Break Procedures

This paper provides an overview of developments that have been undertaken in recent years in order to extend the Crack Opening Area (COA) solutions for Leak-Before-Break (LBB) within the R6 Flaw Evaluation Procedures. For high temperature operations, the effect of creep strains on COA has been studied using finite element (FE) models of a centre-cracked plate with combined primary and secondary stresses. Primary creep, as well as secondary creep, has been included in the studies. The ultimate aim of this work is to further develop and validate by FE analysis, simplified expressions for the prediction of COA under realistic loading conditions for high temperature operations. For COA evaluations in general, work has been undertaken by FE modelling of the following aspects: • Straight-fronted cracks under combined loading. • Converging/diverging cracks whereby the length on one surface is different to that on the other surface (i.e. cases where there is a through-wall variation in crack length). • Weld strength mis-match effects. • Component features effects.Copyright © 2008 by ASME
Long-term potentiation in the anterior cingulate cortex and chronic pain

Glutamate is the primary excitatory transmitter of sensory transmission and perception in the central nervous system. Painful or noxious stimuli from the periphery ‘teach’ humans and animals to avoid potentially dangerous objects or environments, whereas tissue injury itself causes unnecessary chronic pain that can even last for long periods of time. Conventional pain medicines often fail to control chronic pain. Recent neurobiological studies suggest that synaptic plasticity taking place in sensory pathways, from spinal dorsal horn to cortical areas, contributes to chronic pain. Injuries trigger long-term potentiation of synaptic transmission in the spinal cord dorsal horn and anterior cingulate cortex, and such persistent potentiation does not require continuous neuronal activity from the periphery. At the synaptic level, potentiation of excitatory transmission caused by injuries may be mediated by the enhancement of glutamate release from presynaptic terminals and potentiated postsynaptic responses of AMPA receptors. Preventing, ‘erasing’ or reducing such potentiation may serve as a new mechanism to inhibit chronic pain in patients in the future.
Delayed hemolytic transfusion reaction in children with sickle cell disease

Background Transfusion is a cornerstone of the management of sickle cell disease but carries a high risk of hemolytic transfusion reaction, probably because of differences in erythrocyte antigens between blood donors of European descent and patients of African descent. Patients may experience hemolytic transfusion reactions that are delayed by from a few days to two weeks and manifest as acute hemolysis (hemoglobinuria, jaundice, and pallor), symptoms suggesting severe vaso-occlusive crisis (pain, fever, and acute chest syndrome), and profound anemia, often with reticulocytopenia. This case-series study aims to describe the main characteristics of this syndrome, to discuss its pathophysiology, and to propose a management strategy. Design and Methods We identified 8 pediatric cases of delayed hemolytic transfusion reactions between 2006 and 2009 in the database of the Necker Hospital, France. All patients had received cross-matched red cell units compatible in the ABO, RH, and KEL systems. We reviewed the medical charts in the computerized blood transfusion databases. All patients were admitted to the intensive care unit. We progressively adopted the following strategy: intravenous immunoglobulins, and darbopoietin alpha when the reticulocyte count was below 150×109/L, without further blood transfusion during the acute episode unless absolutely necessary. Results The median time between the transfusion and the diagnosis of delayed hemolytic transfusion reaction was six days. All patients had severe bone pain; all but one had a high-grade fever. Five patients had hemoglobin levels less than than 4g/dL and 3 had reticulocytopenia. In 5 patients, no new antibody was found; one patient had weakly reactive antibodies. Only 2 patients had new allo-antibodies possibly responsible for the delayed hemolytic reaction. Conclusions The initial symptoms of delayed hemolytic transfusion reaction were complex and mimicked other complications of sickle cell disease. In most of our cases, no new antibody was identified, which underlines the complexity of the pathophysiology of this syndrome.
Retrospective analysis of age-adjusted body mass index among pre-pregnant women in the Lithuanian urban area during three decades

Background The prevalence of maternal obesity at the beginning of pregnancy is increasing. However, there are some studies reporting the stabilisation of obesity epidemic or even the downward trend in the general population. Objective To determine the prevalence of overweight and obesity in Lithuanian pre-pregnant women during 3 decades. Methods This observational retrospective study included a sample of 2827, women aged 18–44 years who gave birth in 1987–1989, 1996–1997 and 2007–2010: 861 (30.5%), 995 (35.2%) and 971 (34.3%), respectively. All women were divided into groups by body mass index (BMI) calculated from self-reported weight and height, and age reported during the first antenatal visit. Quantitative parametric variables were expressed as mean and SD; qualitative variables, as absolute numbers (n) and percentage (%). For parametric data, analysis of variance (ANOVA) was used. Differences were considered statistically significant at p<0.05. Results The prevalence of overweight and obesity among women aged 18–24 years decreased from 20.9% in 1987–1989 to 9.5% in 1996–1997 but increased to 15.7% in 2007–2010; among women aged 25–34 years, decreased from 35.5% in 1987–1989 to 23% in 1996–1997 and to 22.4% in 2007–2010; and among women aged 35–44 years decreased from 64.9% in 1987–1989 to 34% in 1996–1997 but increased to 45.3% in 2007–2010. BMI increased with an increasing age (r=0.254, p<0.05). Analysis by separate periods (1987–1989, 1996–1997 and 2007–2010) revealed a positive correlation between BMI and age at the first antenatal visit in all periods (r=0.325, p<0.01; r=0.266, p<0.01; and r=0.210, p<0.01, respectively). Conclusions The prevalence of overweight and obesity among pre-pregnant women tended to decrease in the Lithuanian urban area during 3 decades. A slight increase in overweight and obesity documented in 2007–2010 compared with 1996–1997 most likely was caused by older maternal age.
On computing with types

We express in terms of binary trees seen as Gödel System T types (with the empty type as the only primitive type) arithmetic computations within time and space bounds comparable to binary arithmetic and derive an efficiently testable total ordering on types, isomorphic to the ordering of natural numbers. A few novel algorithms are derived in the process, that enable arithmetic computations with type trees. The use of a Haskell type class describing the "axiomati-zation" of the shared structure present in System T's type language and natural numbers, together with Haskell instances representing "twin" interpretations connected by an iso-functor that transports operations between the two instances, provides instant empirical testability. The self-contained source code of the paper is available at http://logic.cse. unt.edu/tarau/research/2012/stypes.hs.