Miracle-dz/UniFAR-FTUs huggingface dataset:
PAX3d mRNA over 2.76 copies/µL in the bloodstream predicts cutaneous malignant melanoma relapse

Objective The aim of this study was to evaluate if our molecular algorithm, based on tumor circulating transcripts, may predict relapse risk in cutaneous malignant melanoma (CMM). Results The multi-marker panel was able to differentiate patients with CMM from HC with high diagnostic sensitivity and specificity, especially for MITF-m and TGFB2 (91–100%) whose levels decreased during follow-up of recurrence-free patients, and remained stable in the case of relapse. PAX3d higher than 2.76 copies/µL emerged as a promising biomarker [specificity = 75–93% and negative predictive value = 75–98%] to stratify subjects at high risk of CMM recurrence independently of age, gender and AJCC staging [OD = 9.5(3.2–28.0), p < 0.001]. The survival analysis confirmed PAX3d performance in relapse prediction with significant differences in recurrence risk 12 months after the basal time-point (p = 0.008). Materials and Methods Peripheral blood was collected from 111 CMM patients and from 87 healthy controls (HC) randomly selected. Each specimen was examined by qRT-PCR analysis for the expression of 3 tumor-related transcripts (PAX3d, MITF-m and TGFB2) at diagnosis, and at the following 6 and 12 months during clinical monitoring. Conclusions We demonstrated the usefulness of our molecular algorithm to indirectly detect circulating melanoma cells in blood, along with PAX3d capability to assess patients’ progression and relapse prediction.
HIV prevalence among clients with possible clinical signs of HIV infection: using the provider initiated testing and counseling approach.

BACKGROUND Variations on HIV estimates have been reported using routine antenatal care (ANC) sentinel surveillance and voluntary counseling and testing (VCT). But there have been widespread concerns about the low participation rates of ANC and the slow uptake of the routine VCT in many parts of sub-Saharan Africa including Ethiopia. Thus estimates of HIV prevalence based on provider initiated HIV testing and counseling (PITC), can improve our understanding of the issues related to uptake, barriers and outcomes of HIV testing and counseling, and to develop and test different models for optimizing the use of voluntary testing and counseling in a way that ensures that people, are not put at risk. OBJECTIVES To estimate the prevalence of HIV among out patient department (OPD) clients with possible clinical signs of HIV infection using the provider initiated testing and counseling approach. METHODS Institution based cross-sectional study was conducted on 259 OPD clients with possible clinical signs of HIV infection in 12 government health centers in Addis Ababa. RESULT The HIV prevalence rate was 37.5% with 95% CI (31.6 - 43.4%). After adjusting for independent variables subjects in age group 35-44 years were about 4 times more likely to be positive for HIV than age group 15-24 years (AOR =3.58; 95% CI=1.31-9.82) and the odds of HIV infection in the 25-34 years was 2.41 (95% CI= 1.01-5.78) higher than age group 15-24. HIV prevalence significantly declines with educational status from 57.4% among illiterates to about 31-34% among those who read and write and with primary and above educational levels. About half of the participants perceived themselves as having risk for HIV, of whom 41.7% were HIV positive, higher than those who perceived no risk (31%), but significantly lower than among those who remained neutral (61%). Those with prior HIV testing were about 2 times less likely to be HIV positive compared to those who had never been tested CONCLUSION The relatively high HIV prevalence rate noted in this study indicates how useful the PITC approach is in detecting cases. We recommend that PITC needs to be implemented at all levels of health facilities in Ethiopia.
Memory traces of long‐range coordinated oscillations in the sleeping human brain

Cognition involves coordinated activity across distributed neuronal networks. Neuronal activity during learning triggers cortical plasticity that allows for reorganization of the neuronal network and integration of new information. Animal studies have shown post‐learning reactivation of learning‐elicited neuronal network activity during subsequent sleep, supporting consolidation of the reorganization. However, no previous studies, to our knowledge, have demonstrated reactivation of specific learning‐elicited long‐range functional connectivity during sleep in humans. We here show reactivation of learning‐induced long‐range synchronization of magnetoencephalography power fluctuations in human sleep. Visuomotor learning elicited a specific profile of long‐range cortico‐cortical synchronization of slow (0.1 Hz) fluctuations in beta band (12–30 Hz) power. The parieto‐occipital part of this synchronization profile reappeared in delta band (1–3.5 Hz) power fluctuations during subsequent sleep, but not during the intervening wakefulness period. Individual differences in the reactivated synchronization predicted postsleep performance improvement. The presleep resting‐state synchronization profile was not reactivated during sleep. The findings demonstrate reactivation of long‐range coordination of neuronal activity in humans, more specifically of reactivation of coupling of infra‐slow fluctuations in oscillatory power. The spatiotemporal profile of delta power fluctuations during sleep may subserve memory consolidation by echoing coordinated activation elicited by prior learning. Hum Brain Mapp, 36:67–84, 2015. © 2014 Wiley Periodicals, Inc.
Reduction of Raf Kinase Inhibitor Protein Expression is Associated with Lymph Node Metastasis in Resectable Non-small Cell Lung Cancer

Introduction: Raf kinase inhibitor protein (RKIP) had been identified as one of prognostic indictor in various malignant diseases. Association of RKIP expression and the clinical-pathological features were not investigated in patients with resectable non-small cell lung cancer (NSCLC). Materials and Methodology: 159 sectioned samples from surgical NSCLC patients were investigated by immunohistochemistry in order to reveal the associations between RKIP expression and clinical-pathologic features. Results: Statistically, Lower RKIP expression level was found in the group with higher N stage (P<0.01) and higher TNM stage (P<0.05). No significant correlation was observed between RKIP expressions and histologic type (P>0.05) and tumor size (P>0.05). Conclusions: Down expression level of RKIP was found relating to lymph node metastasis in resectable NSCLC patients in this study.
Improved one‐sided control charts for the mean of a positively skewed population using truncated saddlepoint approximations

This paper develops a truncated saddlepoint (TS) control chart for the mean of a population with a skewed density. This chart requires the estimation of only a few population cumulants from sample data and is relatively straightforward in construction. Performance is assessed at various levels of truncation in terms of type 1 and 2 error rates and compared with other heuristic control charts via the Monte Carlo simulation. The truncated saddlepoint (TS) chart is shown to generally outperform these charts, especially in cases with small sample sizes or high levels of population skewness. Copyright © 2011 John Wiley & Sons, Ltd.
Soft morphological filter optimization using a genetic algorithm for noise elimination

Digital image quality is of importance in almost all image processing applications. Many different approaches have been proposed for restoring the image quality depending on the nature of the degradation. One of the most common problems that cause such degradation is impulse noise. In general, well known median filters are preferred for eliminating different types of noise. Soft morphological filters are recently introduced and have been in use for many purposes. In this study, we present a Genetic Algorithm (GA) which combines different objectives as a weighted sum under a single evaluation function and generates a soft morphological filter to deal with impulse noise, after a training process with small images. The automatically generated filter performs better than the median filter and achieves comparable results to the best known filters from the literature over a set of benchmark instances that are larger than the training instances. Moreover, although the training process involves only impulse noise added images, the same evolved filter performs better than the median filter for eliminating Gaussian noise as well.
Debug Automation for Logic Circuits Under Timing Variations

This paper presents a novel approach to automate speedpath debugging taking into account variations. The proposed technique is based on Boolean Satisfiability. The approach is based on converting the timing behavior of a circuit into the functional domain, inserting a variation logic into the model, and using a Boolean Satisfiability solver to extract failing speedpaths.
When Formal Institutions Are Not Enough: Caste, Party Politics, and Distribution in Indian Village Councils

Acknowledgements: We thank M.R. Hegde and his staff at the Karnataka State Election Commission, U.A. Vasanth Rao of the Chief Decentralization Analysis Cell of the Gram Swaraj Project, and especially Padmavathi B.S. of the international Academy for Creative Teaching (iACT) and her researchers at Bangalore University for their help with this project. Kanchan Chandra, Don Green, Drew Linzer, Ken Scheve, Steven Wilkinson, and seminar participants at Yale, Princeton, and the annual meetings of the Society for Political Methodology have provided very helpful comments on the broader project of which this paper forms part.
Unpacking Privacy Paradox: A Dual Process Theory Approach

Prior studies showed that some users tend to act against their stated privacy concerns (a phenomenon commonly known as privacy paradox). In this study, we adopt the dual process theory as our theoretical basis to account for conscious and unconscious modes of individual decision making processes to examine privacy paradox in order to gain an understanding of the reasons which cause inconsistency between privacy concern and information disclosure. We also posit that privacy paradox can occur due to the conscious mode (affected by bounded rationality) as well as unconscious biases.
Pharmacological screening of Coriandrum sativum Linn. for hepatoprotective activity

Objective: Coriandrum sativum (Linn.), a glabrous, aromatic, herbaceous annual plant, is well known for its use in jaundice. Essential oil, flavonoids, fatty acids, and sterols have been isolated from different parts of C. sativum. The plant has a very effective antioxidant profile showing 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, lipoxygenase inhibition, phospholipid peroxidation inhibition, iron chelating activity, hydroxyl radical scavenging activity, superoxide dismutation, glutathione reduction and antilipid peroxidation due to its high total phenolic content with the presence of constituents like pyrogallol, caffeic acid, glycitin, etc. Materials and Methods: This study was aimed at investigating the hepatoprotective activity of C. sativum against carbon tetrachloride (CCl4), with estimation of serum serum glutamyl oxaloacetic acid transaminase (SGOT), serum glutamyl pyruvate transaminase (SGPT), alkaine phosphatase (ALP) and bilirubin, and with liver histopathology. Results: Ethanolic extract was found to be rich in alkaloids, phenolic compounds and flavonoids, and high performance liquid chromatography (HPLC) fingerprinting showed the presence of iso-quercetin and quercetin. C. sativum signifies hepatoprotection by reducing the liver weight, activities of SGOT, SGPT, and ALP, and direct bilirubin of CCl4 intoxicated animals. Administration of C. sativum extract at 300 mg/kg dose resulted in disappearance of fatty deposit, ballooning degeneration and necrosis, indicating antihepatotoxic activity. Conclusion: The results of this study have led to the conclusion that ethanolic extract of C. sativum possesses hepatoprotective activity which may be due to the antioxidant potential of phenolic compounds.
Derivation of Corneal Keratocyte-Like Cells from Human Induced Pluripotent Stem Cells

Corneal diseases such as keratoconus represent a relatively common disorder in the human population. However, treatment is restricted to corneal transplantation, which only occurs in the most advanced cases. Cell based therapies may offer an alternative approach given that the eye is amenable to such treatments and corneal diseases like keratoconus have been associated specifically with the death of corneal keratocytes. The ability to generate corneal keratocytes in vitro may enable a cell-based therapy to treat patients with keratoconus. Human induced pluripotent stem cells (hiPSCs) offer an abundant supply of cells from which any cell in the body can be derived. In the present study, hiPSCs were successfully differentiated into neural crest cells (NCCs), the embryonic precursor to keratocytes, and then cultured on cadaveric corneal tissue to promote keratocyte differentiation. The hiPSC-derived NCCs were found to migrate into the corneal stroma where they acquired a keratocyte-like morphology and an expression profile similar to corneal keratocytes in vivo. These results indicate that hiPSCs can be used to generate corneal keratocytes in vitro and lay the foundation for using these cells in cornea cell-based therapies.
“So I Just Took Over”: African American Daughters Caregiving for Parents with Heart Failure

This article examines the experiences of African American women who are caring for a parent with heart failure. Seven adult daughter caregivers completed in-depth, qualitative interviews, and a phenomenological approach was used for data analysis. Results suggest the presence of caregiving stressors, including heart failure symptoms and comorbidity, caregiving duties, social–emotional stressors, and distrust of the health system. Relevant coping strategies included valuing the caregiving role, coordinating care with siblings, taking charge, and spirituality. Social workers can play a critical role in supporting and advocating for caregivers of persons with heart failure, helping them to cope with stressors associated with advanced illness, connecting families with culturally acceptable services, and facilitating communication between families and health care providers.
History, Commemoration, and Belief: Abraham Lincoln in American Memory, 1945-2001

Ever since Maurice Halbwachs's pioneering work, most scholars have been content to explore collective memory through texts and commemorative symbolism. Assuming that a study of collective memory has fuller meaning when it takes into account what ordinary people think about the past, we compare historians' and commemorative agents' representations of Abraham Lincoln to what four national samples of Americans believe about him. Five primary images-Savior of the Union, Great Emancipator, Man of the People, First (Frontier) American, and Self-Made Man-are prominent in the cumulative body of Lincoln representations, but recent surveys show that only one of these images, the Great Emancipator, is dominant within the public. Lincoln's one-dimensional Emancipator image, which differs from the multi—dimensional one evident in a 1945 sample, reflects new perceptions of the Civil War shaped by late twentieth-century minority rights movements. Thus, “bringing men [and women] back in” involves survey evidence being added to historiographic and commemoration analysis to clarify one of sociology's most ambiguous concepts, collective memory, and to explore its social and generational roots.
Leishmania parasites and their ploys to disrupt macrophage activation

Leishmania are intracellular protozoan parasites of macrophages. At the cellular level, the disease leishmaniasis involves the invasion of tissue macrophages by the parasite, the avoidance of cellular killing mechanisms, and the subsequent intracellular replication of parasites, with the eventual spread of the organisms to adjacent macrophages. This paper describes the process by which Leishmania organisms invade macrophages, with an overview of some of the molecules involved in this process; the mechanisms available to macrophages that have the potential to restrict the growth of Leishmania within them; and the ways that Leishmania and Leishmania-derived molecules can modulate macrophage functions and circumvent leukocyte antimicrobial responses.
On persistence properties in fractional weighted spaces

In this work we derive a point-wise formula that will allows us to study the well-posedness of initial value problem associated to nonlinear dispersive equations in fractional weighted Sobolev spaces $H^s(\R)\cap L^2(|x|^{2r}dx)$, $s, r \in \R$. As an application of this formula we will study local and global well posedness of the $k$-generalized Korteweg-de Vries equation in these weighted Sobolev spaces.
Detecting program modules with low testability

We model the relationship between static software product measures and a dynamic quality measure, testability. To our knowledge, this is the first time a dynamic quality measure has been modeled using static software product measures. We first give an overview of testability analysis and discriminant modeling. Using static software product measures collected from a real time avionics software system, we develop two discriminant models and classify the component program modules as having low or high testability. The independent variables are principal components derived from the observed software product measures. One model is used to evaluate the quality of fit and one is used to assess classification performance. We show that for this study, the quality of fit and classification performance of the discriminant modeling methodology are excellent and yield a potentially useful insight into the relationship between static software measures and testability.
Brain Injury and Altered Brain Growth in Preterm Infants: Predictors and Prognosis

BACKGROUND: To define the nature and frequency of brain injury and brain growth impairment in very preterm (VPT) infants by using MRI at term-equivalent age and to relate these findings to perinatal risk factors and 2-year neurodevelopmental outcomes. METHODS: MRI scans at term-equivalent age from 3 VPT cohorts (n = 325) were reviewed. The severity of brain injury, including periventricular leukomalacia and intraventricular and cerebellar hemorrhage, was graded. Brain growth was assessed by using measures of biparietal width (BPW) and interhemispheric distance. Neurodevelopmental outcome at age 2 years was assessed across all cohorts (n = 297) by using the Bayley Scales of Infant Development, Second Edition (BSID-II) or Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III), and evaluation for cerebral palsy. RESULTS: Of 325 infants, 107 (33%) had some grade of brain injury and 33 (10%) had severe injury. Severe brain injury was more common in infants with lower Apgar scores, necrotizing enterocolitis, inotropic support, and patent ductus arteriosus. Severe brain injury was associated with delayed cognitive and motor development and cerebral palsy. Decreased BPW was related to lower gestational age, inotropic support, patent ductus arteriosus, necrotizing enterocolitis, prolonged parenteral nutrition, and oxygen at 36 weeks and was associated with delayed cognitive development. In contrast, increased interhemispheric distance was related to male gender, dexamethasone use, and severe brain injury. It was also associated with reduced cognitive development, independent of BPW. CONCLUSIONS: At term-equivalent age, VPT infants showed both brain injury and impaired brain growth on MRI. Severe brain injury and impaired brain growth patterns were independently associated with perinatal risk factors and delayed cognitive development.
Cromer‐Related Antigens – Blood Group Determinants on Decay‐Accelerating Factor

Abstract. Cromer‐related antigens, a series of blood group antigens phenotypically related to each other through various serological characteristics, have recently been shown to be carried on the complement regulatory glycoprotein decay‐accelerating factor (DAF). Cromer‐related antigens, therefore, represent a number of inherited variants and polymorphisms of DAF. The Inab phenotype, a ‘Cromer‐null’ phenotype in which the red cells lack all Cromer‐related antigens, appears to be an inherited DAF deficiency.
Modulation of ADAR1 editing activity by Z-RNA in vitro

RNA editing by A-to-I modification has been recognized as an important molecular mechanism for generating RNA and protein diversity. In mammals, it is mediated by a family of adenosine deaminases that act on RNAs (ADARs). The large version of the editing enzyme ADAR1 (ADAR1-L), expressed from an interferon-responsible promoter, has a Z-DNA/Z-RNA binding domain at its N-terminus. We have tested the in vitro ability of the enzyme to act on a 50 bp segment of dsRNA with or without a Z-RNA forming nucleotide sequence. A-to-I editing efficiency is markedly enhanced in presence of the sequence favoring Z-RNA. In addition, an alteration in the pattern of modification along the RNA duplex becomes evident as reaction times decrease. These results suggest that the local conformation of dsRNA molecules might be an important feature for target selectivity by ADAR1 and other proteins with Z-RNA binding domains.
The Lsm2-8 complex determines nuclear localization of the spliceosomal U6 snRNA

Lsm proteins are ubiquitous, multifunctional proteins that are involved in the processing and/or turnover of many, if not all, RNAs in eukaryotes. They generally interact only transiently with their substrate RNAs, in keeping with their likely roles as RNA chaperones. The spliceosomal U6 snRNA is an exception, being stably associated with the Lsm2-8 complex. The U6 snRNA is generally considered to be intrinsically nuclear but the mechanism of its nuclear retention has not been demonstrated, although La protein has been implicated. We show here that the complete Lsm2-8 complex is required for nuclear accumulation of U6 snRNA in yeast. Therefore, just as Sm proteins effect nuclear localization of the other spliceosomal snRNPs, the Lsm proteins mediate U6 snRNP localization except that nuclear retention is the likely mechanism for the U6 snRNP. La protein, which binds only transiently to the nascent U6 transcript, has a smaller, apparently indirect, effect on U6 localization that is compatible with its proposed role as a chaperone in facilitating U6 snRNP assembly.