Miracle-dz/UniFAR-FTUs huggingface dataset:
Confidence Estimation in Stem Cell Classification

We study the problem of supervised classification of stem cell colonies and confidence estimation of the attained classification labels. The problem is investigated in the application context of heterogeneity labels of stem cell colonies observed by using fluorescent microscopy imaging. Given the features of colonies using numerous image statistics, we report the classification results using adaptive k-Nearest Neighbor (NN) algorithm. This algorithm minimizes typical k-NN classification bias by giving more weight to more informative features in predicting class posterior probabilities. We then estimate the confidence of each prediction for unlabeled data using transductive p-value and strangeness metrics. We show that such an introspection can gradually increase the accuracy of learned model, quantify false positives, and guide the resource-limited manual colony annotation process to provide training labels for the less confident unlabeled samples.
Risk factors for HIV‐1 infection in adults in a rural Ugandan community: a population study

ObjectiveTo determine sociodemographic risk factors associated with HIV-1 infection in a rural Ugandan population. DesignA population-based survey. MethodsAll adult residents (aged ≤13 years) in a cluster of 15 neighbouring villages of the Masaka District of south-west Uganda were invited to participate in a sociodemographic and serological survey. Questions relating to sexual behaviour were asked separately in an accompanying case-control study. Socioeconomic data and an unambiguous HIV-1 serostatus were obtained by house-to-house survey for 3809 (72%) of the adult population. The association between serostatus and the following variables were analysed: age, sex, marital status, tribe, religion, education, occupational group, place and frequency of travel and recent history of sexually transmitted disease. ResultsWomen aged 13–21 years were at a much higher risk than men of the same age lodds ratio (OR), 8.6; 95% confidence interval (Cl), 3.0–24.5]. Married people aged < 25 years were twice as likely to be infected as those who were not currently married (OR, 2.3; 95% Cl, 1.5–3.7). In contrast, in those aged ≤25 years, women were at a lower risk than men (OR, 0.72; 95% Cl, 0.52–0.98) as were those who were currently married compared with those who were not (OR, 0.47; 95% Cl, 0.34–0.64). In both age groups those with a history of a recent genital ulcer were approximately three times more likely to be infected. Muslims had lower risks than non-Muslims (OR, 0.58 for both age groups). ConclusionsThe people most at risk of HIV-1 infection in this rural Ugandan population are young married women who had, presumably, commenced sexual activity recently.
Using Visual Attention in a CBIR System - Experimental Results on Landmark and Object Recognition Tasks

Many novel applications in the field of object recognition and pose estimation have been built relying on local invariant features extracted from key points that rely on high-contrast regions of the images. The visual saliency of the those regions is not considered by state-of-the art detection algorithms that assume the user is interested in the whole image. In this paper we present the experimental results of the application of a biologically-inspired model of visual attention to the problem of local feature selection in landmark and object recognition tasks. The results show that the approach improves the accuracy of the classifier in the object recognition task and preserves a good accuracy in the landmark recognition task.
The histopathological evaluation of drug‐induced liver injury

Drug‐induced liver injury (DILI) presents unique challenges to the pathologist. It is not only an uncommon reason for liver biopsy, but the pathology of DILI is spread across the entire spectrum of hepatic injury patterns. It is important for the pathologist to suspect DILI when the histological changes are unusual or out of synchronicity with the patient's history. A systematic evaluation approach will yield the most information. It begins with the characterization of the general pattern of injury which, for most cases, will be found in a handful of necroinflammatory and cholestatic patterns. A careful assessment of the severity of injury across the various anatomic compartments will provide information on the probable natural history of the injury. Correlation of liver injury with the patient's medication history and clinical findings will help to narrow the differential diagnosis, particularly when it is recognized that most drugs have a limited range of histological findings and vary in their propensity to cause injury. This review provides an overview of the assessment of the liver biopsy and its use to confirm or exclude particular drugs as contributing to the patient's liver injury.
A Comparison of MCUSUM‐based and MEWMA‐based Spatiotemporal Surveillance Under Non‐homogeneous Populations

Motivated by the application in health‐care surveillance under non‐homogeneous populations, this paper compares the performance of multivariate exponentially weighted moving average (MEWMA)‐based methods with that of multivariate cumulative sum (MCUSUM)‐based methods for spatiotemporal chronic disease surveillance. We perform the comprehensive simulation studies of the MEWMA‐based methods for the selection of weight parameters. Under temporally or spatially non‐homogeneous population trends, we compare the MEWMA methods with the MCUSUM methods, which are specific forms of the spatiotemporal scan statistics if the baseline rate is known. The performance of the MCUSUM methods has extreme variations depending on whether the change occurs on a small population or a large population. When the change occurs in the time period or within the spatial region with a small population, the weighted likelihood ratio‐based MCUSUM has better detection speed, but worse identification of detection clusters than the likelihood ratio‐based MCUSUM. On the other hand, when the change occurs in the time period or within the region with a large population, the weighted likelihood ratio‐based MCUSUM has worse detection speed, but better identification than the likelihood ratio‐based MCUSUM. Unlike the MCUSUM methods, the MEWMA‐based methods show relatively stable and robust performance in terms of detection speed, and they show better identification than the MCUSUM‐based methods under most cases. Copyright © 2014 John Wiley & Sons, Ltd.
p63, a p53 Homologue, Is a Selective Nuclear Marker of Myoepithelial Cells of the Human Breast

Myoepithelial cells (MCs) constitute the basal cell layer of normal mammary epithelia, and their identification is of particular diagnostic value because they are retained in most benign lesions while being lost in malignancy. Several MC immunocytochemical markers are currently available for diagnostic purposes, with special reference to smooth muscle-related antigens. p63 is a member of the p53 gene family, and its germline mutations are associated with severe mammary developmental defects in both rodents and humans. Different p63 isoforms have been identified, some of which (&Dgr;Np63) are preferentially expressed in the epithelial basal cells of different organs and have been considered as possible markers of stem cells/reserve cells. We investigated immunohistochemically 384 samples of normal and diseased human breast, including 300 invasive carcinomas, using four antibodies recognizing all p63 isoforms, or the &Dgr;Np63 isoforms. Twenty cytologic specimens were also investigated. Furthermore, snap-frozen tissue samples from three fibroadenomas and 10 invasive ductal carcinomas with their paired non-neoplastic tissues and three corresponding lymph node metastases were evaluated for the expression of p63 mRNA by RT-PCR. In normal breast tissue p63 immunoreactivity was confined to the nuclei of MCs. In all benign lesions p63-immunoreactive cells formed a continuous basal rim along the epithelial structures. Stromal cells, and in particular myofibroblasts, were consistently unreactive. Adenomyoepitheliomas showed nuclear staining in most neoplastic cells. A peripheral rim of p63-immunoreactive cells was retained surrounding lobular and ductal carcinoma in situ, although it was discontinuous as opposed to the normal structures. Invasive breast carcinomas were consistently devoid of nuclear p63 staining, with the exception of the two adenoid–cystic carcinomas, of the two ductal carcinomas with squamous metaplasia, and of 11 (4.6%) ductal carcinomas not otherwise specified, showing p63 immunoreactivity in a minor fraction (5–15%) of the neoplastic cells. In comparison with other MC markers, p63 was the most specific, being restricted exclusively to MCs, whereas antibodies to smooth muscle actin and, to a lesser extent, calponin also decorated stromal myofibroblasts. In the cytologic preparations p63 immunoreactivity was a consistent feature of “naked nuclei” and of a subset of cells surrounding benign epithelial clusters. RT-PCR experiments with primers specific for different p63 isoforms documented that normal tissues and fibroadenomas preferentially expressed the &Dgr;Np63 isoforms. Our study demonstrates that in normal and pathologic breast tissues MCs consistently express the &Dgr;Np63 isoforms. We suggest p63 as a reliable, highly specific, and sensitive MC marker in both histologic and cytologic preparations. Furthermore, because p63 immunoreactivity in adult epithelia is normally restricted to progenitor cells, it can be speculated that it might be a clue for the identification of the still elusive breast progenitor cells.
New disease severity classification of patients with stable chronic obstructive pulmonary disease in Shanghai

Background The Global Initiative for Chronic Obstructive Lung Disease (GOLD) presented a new ABCD group classification of chronic obstructive pulmonary disease (COPD). We aimed to examine the association of spirometric classification and the new GOLD classification with exacerbations, and to compare symptoms in different ways. Methods We investigated 848 patients with stable COPD from 24 hospitals. The annual frequencies of acute exacerbation and hospitalization were compared between the old and new classification. The symptom level was assessed using COPD assessment test (CAT) and modified British Medical Research Council (mMRC) questionnaire. Results A total of 848 patients were included in this study. According to spirometric classification, there were 32 patients of grade I (3.8%), 315 of grade II (37.1%), 366 of grade III (43.2%), and 135 of grade IV (15.9%). According to GOLD 2011 classification, there were 59 patients of group A (7.0%), 172 of group B (20.3%), 55 of group C (6.5%), and 562 of group D (66.3%). In spirometric classification, the annual frequencies of acute exacerbation and associated hospitalization were respectively 1 (0–3) and 0 (0–2) for grade I; 1 (0–5) and 0 (0–2) for grade II; 2 (0–6) and 1 (0–3) for grade III, and 3 (0–6) and 2 (0–3) for grade IV. In GOLD 2011, respectively 0 (0–3) and 0 (0–1) (group A), 1 (0–4) and 0 (0–3) (group B), 1 (0–5) and 0 (0–3) (group C), and 3 (0–6) and 1 (0–3) (group D). There were no significant difference between group B and C (Z= ‐1.347, P=0.178; Z= ‐0.772, P=0.440, respectively). The coincidence rate using mMRC=1 and CAT=10 as cutoff points was 86.6% (734/848, &kgr;=0.706), compared with 77.9% (661/848, &kgr;=0.60) using mMRC=2 and CAT=10. Conclusions Lung function test may be a better predictor of acute exacerbation and associated hospitalization of COPD. It is more appropriate to use mMRC=1 as cutoff point for assessing COPD symptoms.
Multiple-Valued Logic: An Introduction and Overview

MULTIPLE-VALUED logic has been a subject of research work for many years [1], [2]. Until the late 1960's most of the reported work was of a theoretical nature, leaving little impact on the firmly established binary approaches in the design of digital systems. Then, as LSI technology proceeded to develop rapidly, it became apparent that multiple-valued logic offers not only a rich logic structure, but also a considerable potential for application in physical systems [2], [3].
OBSIDIAN BLADE PRODUCTION FOR CRAFT CONSUMPTION AT KAMINALJUYU

Abstract The interpretation of craft activity in Mesoamerica has been hindered by difficulties in recognizing and defining the archaeological signatures associated with obsidian blade production and consumption. Theoretical advances and experimental approaches have improved our understanding, but few studies have investigated the role of obsidian blade production in craft activity using empirical data from archaeological assemblages. The present study addresses this problem by presenting an analysis of obsidian flakes and blades recovered from a workshop refuse context at Kaminaljuyu, Guatemala. Technological and use wear analyses suggest that core-shaping by-products in the form of irregular percussion and pressure blades were used in craft activity. Fine blades were underrepresented in the assemblage, suggesting that cores or blades left the workshop as finished goods. These analyses demonstrate that the actual behavior of artisans likely did not conform exactly to the dichotomous theoretical categories of production and consumption that archaeologists routinely use.
A quadrature bandpass /spl Sigma//spl Delta/ modulator for digital radio

In a bandpass /spl Sigma//spl Delta/ modulator, bandpass filtering and feedback around a low-resolution quantizer shape the noise spectrum, facilitating accurate A/D conversion on narrow-band input signals. This is extended to the quadrature, or complex, case if a complex filter - having complex-valued coefficients and thus not restricted to a symmetrical frequency response - is placed in a /spl Sigma//spl Delta/ loop. The modulator performs a "complex" A/D conversion on the pair of analog inputs, that are in phase-quadrature, and it has two high-speed bit stream outputs: one represents the real output; the other the imaginary output. When combined, these outputs form a complex signal that accurately represents the complex input within a narrow frequency band. This quadrature modulator is useful in architectures for a single-chip digital-radio receiver. The receiver ideally has no image response, and thus the bulky narrow-band image-rejection filter in the RF stage of a single-path receiver can be replaced with a broadband one. The architecture alleviates many problems of the direct-conversion receiver, often considered for single-chip implementations, since the input signal is mixed to a non-zero IF where 1/f noise and DC offsets cause no problem and self-interference is not an issue because oscillator frequency is offset from the carrier frequency. The quadrature modulator IC uses standard fully-differential switched-capacitor circuit techniques and is implemented in 0.8 /spl mu/m CMOS technology.
Peripheral B‐cell maturation: the intersection of selection and homeostasis

Summary: B cells complete maturation after migrating to the periphery, where they transit several intermediate developmental stages prior to recruitment into the long‐lived primary pool. Because B‐lineage commitment is not regulated by peripheral pool size and most peripheral B cells are quiescent, the primary factors governing steady‐state numbers are the proportion of immature B cells surviving transit through later developmental stages and the longevity of mature B cells themselves. Substantial evidence indicates that the B‐cell receptor (BCR) plays an essential role in all these processes, but recent findings suggest a central role for the recently described tumor necrosis factor (TNF) family member, B‐lymphocyte stimulator (BLyS). Signaling through one of the BLyS receptors, BLyS receptor 3 (BR3), controls B‐cell numbers in two ways: by varying the proportion of cells that complete transitional B‐cell development and by serving as the primary determinant of mature B‐cell longevity. The recent discovery that BCR signaling is selectively coupled to BR3 expression in a developmentally regulated fashion links BCR‐ and BLyS‐mediated events, suggesting that specificity‐based selection and survival may be mechanistically similar processes.
New food sources of essential trace elements produced by biotechnology facilities

Population satiety with trace elements (TE) is a problem that is widely discussed in nutrition science. For optimal nutrition, the form of TE eaten in food is very important. Organic forms of TE in nutrition are appropriate as human metabolism has adapted to these kinds of nutrients during species evolution. This is now considered a reason for the beneficial use of biotechnologically produced TE sources in human food. Advanced matrixes for TE incorporation are unicellular organisms such as yeast, lactobacilli and Spirulina. Addition of inorganic salts at certain concentrations into cultivation media enables the mineral ions to incorporate into the microbial biomass. As a consequence, the biomass becomes enriched with organic forms of incorporated TE, which are presented by their complexes with amino acids, proteins and probably lipids and polysaccharides. In addition, a new direction of research has made good advances, in which technology has been developed for production of organic forms of TE through complex formation between transition metals (zinc, copper, manganese, chromium, iron) with amino acids and peptides formed during enzymatic hydrolysis of food protein. This brief review discusses the results demonstrating the advances in the biotechnological production of new TE sources, to obtain food components destined for wide prophylaxis of TE deficiency or for dietary treatment of the adverse consequences of these deficiencies.
Intrusion Detection Systems in Wireless Sensor Networks: A Review

Wireless Sensor Networks (WSNs) consist of sensor nodes deployed in a manner to collect information about surrounding environment. Their distributed nature, multihop data forwarding, and open wireless medium are the factors that make WSNs highly vulnerable to security attacks at various levels. Intrusion Detection Systems (IDSs) can play an important role in detecting and preventing security attacks. This paper presents current Intrusion Detection Systems and some open research problems related to WSN security.
A persistent method for parameter identification of a seven-axes manipulator

SUMMARY This paper presents a persistent method for the identification problem of open-chained robotic systems. Based on the Projection Equation, a new, direct method to collect the dynamic and friction parameters in linear form is worked out. However, in this form, linear dependencies in the parameters occur and they are canceled out with the help of the QR algorithm. The obtained linear independent parameters are the base parameters of the system. To ensure a good excitation, the identification is improved by using optimized trajectories defined by Fourier-series, taking also physical constraints into account. The evaluation of the dynamic robot parameters is realized with a least squares error optimization. Furthermore, the result strongly depends on a special choice of weighting matrices for the error. Experimental results for a seven-axes robotic system (standard six-axes industrial manipulator mounted on a linear axis) are presented in detail. Additionally, the influence of temperature effects to base parameter changes is discussed.
Mechanism of alpha-lipoic acid in attenuating kanamycin-induced ototoxicity

In view of the theory that alpha-lipoic acid effectively prevents cochlear cells from injury caused by various factors such as cisplatin and noise, this study examined whether alpha-lipoic acid can prevent kanamycin-induced ototoxicity. To this end, healthy BALB/c mice were injected subcutaneously with alpha-lipoic acid and kanamycin for 14 days. Auditory brainstem response test showed that increased auditory brainstem response threshold shifts caused by kanamycin were significantly inhibited. Immunohistochemical staining and western blot analysis showed that the expression of phosphorylated p38 mitogen-activated protein kinase and phosphorylated c-Jun N-terminal kinase in mouse cochlea was significantly decreased. The experimental findings suggest that phosphorylated p38 and phosphorylated c-Jun N-terminal kinase mediated kanamycin-induced ototoxic injury in BALB/c mice. Alpha-lipoic acid effectively attenuated kanamycin ototoxicity by inhibiting the kanamycin-induced high expression of phosphorylated p38 and phosphorylated c-Jun N-terminal kinase.
Chromoplast Biogenesis in Cucumis sativus Corollas (Rapid Effect of Gibberellin A3 on the Accumulation of a Chromoplast-Specific Carotenoid-Associated Protein)

The development of cucumber (Cucumis sativus L.) corollas is accompanied by the accumulation of chromoplasts. In mature corollas, chromoplasts, but no chloroplasts, were detected by electron microscopy. Chlorophyll was also undetectable in corollas at anthesis. The contents of carotenoids and a carotenoid-associated, chromoplast-specific, 35-kD protein in corollas increased in parallel with flower development, peaking concomitantly at anthesis. The involvement of phytohormones and light in the regulation of their expression was studied. When gibberellin A3 (GA3) was added to an in vitro bud culture system, accumulation of both carotenoids and the 35-kD protein was markedly enhanced. The specific up-regulation of the 35-kD protein was very rapid: after only 2 h of culture, increased levels were detected in GA3-treated versus untreated corollas. During this period, corolla fresh weight and total protein and carotenoid contents remained unchanged. Inclusion of abscisic acid in the culture medium counteracted the effect of GA3. Accumulation of the 35-kD protein was also enhanced when flower buds on plants were sprayed with GA3 or etiolated.
Primary hyperoxaluria type 1 in the Canary Islands: A conformational disease due to I244T mutation in the P11L-containing alanine:glyoxylate aminotransferase

Primary hyperoxaluria type 1 (PH1) is an inborn error of metabolism resulting from a deficiency of alanine:glyoxylate aminotransferase (AGXT; EC 2.6.1.44). Most of the PH1 alleles detected in the Canary Islands carry the Ile-244 → Thr (I244T) mutation in the AGXT gene, with 14 of 16 patients homozygous for this mutation. Four polymorphisms within AGXT and regional microsatellites also were shared in their haplotypes (AGXT*LTM), consistent with a founder effect. The consequences of these amino acid changes were investigated. Although I244T alone did not affect AGXT activity or subcellular localization, when present in the same protein molecule as Leu-11 → Pro (L11P), it resulted in loss of enzymatic activity in soluble cell extracts. Like its normal counterpart, the AGXT*LTM protein was present in the peroxisomes but it was insoluble in detergent-free buffers. The polymorphism L11P behaved as an intragenic modifier of the I244T mutation, with the resulting protein undergoing stable interaction with molecular chaperones and aggregation. This aggregation was temperature-sensitive. AGXT*LTM expressed in Escherichia coli, as a GST-fusion protein, and in insect cells could be purified and retained enzymatic activity. Among various chemical chaperones tested in cell culture, betaine substantially improved the solubility of the mutant protein and the enzymatic activity in cell lysates. In summary, I244T, the second most common mutation responsible for PH1, is a protein conformational disease that may benefit from new therapies with pharmacological chaperones or small molecules to minimize protein aggregation.