Miracle-dz/UniFAR-FTUs huggingface dataset:
High-resolution three-dimensional images from confocal scanning laser microscopy. Quantitative study and mathematical correction of the effects from bleaching and fluorescence attenuation in depth.

Three-dimensional images can be assembled by piling up consecutive confocal fluorescent images obtained by confocal scanning laser microscopy. The present work was based on three-dimensional (50-microns-deep) images at high (x, y) resolution obtained with an MRC-500 after en bloc staining of thick slices of rat liver by chromomycin A3 for nuclear DNA. The results of studies on bleaching, fluorescence excitation and emission intensities at various depths of histologic preparations are described. These effects could be evaluated separately by acquiring piled-up ("brick-stepping") and non-piled-up ("side-stepping") (x, y) images at consecutive depths and also (x, z) images. Empirical equations allowed the fitting of experimental plots of bleaching versus time, at different laser intensities and at different depths, and of fluorescence emission intensity versus depth. The main conclusions were that under our experimental conditions: (1) there was no attenuation by depth of the fluorochrome penetration, (2) there was no attenuation of the exciting beam intensity up to at least 50 microns deep, (3) there was an attenuation of the fluorescence emission intensity by depth, (4) bleaching happened equally on all planes above and below any confocal plane being studied, and (5) the fluorescence bleaching half-life was independent of depth. A mathematical correction scheme designed to compensate for bleaching and for attenuation of fluorescence emission in depth is presented. This correction is required for obtaining three-dimensional images of better quality, for optimal three-dimensional image segmentation and for any quantitative analysis based upon voxel-discretized emission intensities (gray levels)--e.g., estimating, by confocal image cytometry, textural chromatin parameters and nuclear DNA amounts.
Oral contraceptives and breast cancer. In vitro effect of contraceptive steroids on human mammary cell growth

The proliferative response of human mammary epithelial cells cultured in medium containing oral contraceptive steroids, singly and in combination, was measured. Cells came from 59 normal, nonmalignant atypical, and malignant breast tissue specimens. Growth of most cultures was stimulated by the estrogens 17β‐estradiol and ethinyl estradiol, and any combination containing ethinyl estradiol. Most (75%) malignant specimens were stimulated by one or more of the progestins, whereas none of the nonmalignant cells were. For two of the estrogen/progestin combinations found in many birth control pills, malignant cells were stimulated to grow faster than nonmalignant cells. It was concluded that oral contraceptive steroids can stimulate the growth of mammary epithelia in cell culture and might do the same in vivo. These data corroborate epidemiologic data which suggest oral contraceptives might act as tumor promoters, especially in the older user, who is more likely to have malignant cells already present in the breast. Cancer 59:281–287, 1987.
The Flux Variability of Markarian 501 in Very High Energy Gamma Rays

The BL Lacertae object Markarian 501 was identified as a source of γ-ray emission at the Whipple Observatory in 1995 March. Here we present a flux variability analysis on several timescales of the 233 hr data set accumulated over 213 nights (from March 1995 to July 1998) with the Whipple Observatory 10 m atmospheric Cerenkov imaging telescope. In 1995, with the exception of a single night, the flux from Markarian 501 was constant on daily and monthly timescales and had an average flux of only 10% that of the Crab Nebula, making it the weakest very high energy source detected to date. In 1996, the average flux was approximately twice the 1995 flux and showed significant month-to-month variability. No significant day-scale variations were detected. The average γ-ray flux above ~350 GeV in the 1997 observing season rose to 1.4 times that of the Crab Nebula—14 times the 1995 discovery level—allowing a search for variability on timescales shorter than 1 day. Significant hour-scale variability was present in the 1997 data, with the shortest, observed on MJD 50,607, having a doubling time of ~2 hr. In 1998 the average emission level decreased considerably from that of 1997 (to ~20% of the Crab Nebula flux), but two significant flaring events were observed. Thus the emission from Markarian 501 shows large amplitude and rapid flux variability at very high energies, as does Markarian 421. It also shows large mean flux level variations on year-to-year timescales, behavior that has not been seen from Markarian 421 so far.
DNA Sequence Alignment during Homologous Recombination*

Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination.
Mechanisms and variation in plant development: sorting the wood from the trees in Vermont

The biannual FASEB summer research conference `Mechanisms in Plant Development' was recently held in Saxtons River, Vermont and was organised by Neelima Sinha and Cris Kuhlemeier. Although most of the work discussed at the meeting concentrated on developmental mechanisms and on studies in Arabidopsis and maize, the meeting also emphasised the importance of variation between species and the elaboration of a broader range of model systems.
Prolonged episodes of acute diarrhea reduce growth and increase risk of persistent diarrhea in children.

BACKGROUND & AIMS Prolonged episodes of acute diarrhea (ProD; duration 7-13 days) or persistent diarrhea (PD; duration ≥14 days) are important causes of undernutrition, yet the epidemiology and nutritional impact of ProD are poorly understood. METHODS We conducted a 10-year cohort study of 414 children from a Brazilian shantytown who were followed from birth; data were collected on diarrhea, enteric pathogens, and anthropometry. RESULTS During 1276 child-years of observation, we recorded 3257 diarrheal episodes. ProD was twice as common as PD (12% and 5% of episodes, respectively); ProD and PD together accounted for 50% of all days with diarrhea. ProD was more common in infants whose mothers had not completed primary school (relative risk [RR], 2.1; 95% confidence interval: 1.02-2.78). Early weaning was associated with earlier onset of ProD (Spearman ρ = 0.309; P = .005). Infants with ProD were twice as likely to develop PD in later childhood (log rank, P = .002) compared with infants with only acute diarrhea (AD; duration <7 days), even after controlling for confounders. Children's growth was more severely stunted before their first episode of ProD, compared with AD (mean height-for-age Z score (HAZ) -0.81 vs -0.51, respectively, P < . 05, unpaired t test). Following ProD, HAZ (ΔHAZ = -0.232) and weight-for-age (ΔWAZ = -0.26) significantly decreased (P < .005 in paired t tests). ProD was associated with Cryptosporidium and Shigella infections. CONCLUSIONS ProD accounts for significant morbidity and identifies children at risk of a vicious cycle of diarrhea and malnutrition. Further studies are needed to address the recognition and control of ProD and its consequences in resource-limited settings and assess its role in PD pathogenesis.
A Comparative Description of Syllable Reduction in the Cariban Language Family

L'A. examine la reduction de la syllabe finale du radical verbal dans cinq langues carib. Il montre que pour quatre de ces langues, appartenant a la branche du nord, les conditions d'environnement de la reduction syllabique ont les memes bases prosodiques, morphologiques et segmentales. Pour la cinquieme langue, appartenant a la branche du sud, un phenomene de reduction syllabique similaire est observe, mais l'environnement n'est pas aussi caracterise que pour la branche du nord. D'autre part, si les cinq langues partagent la meme motivation prosodique pour la reduction syllabique, la forme de la syllabe reduite differe dans les cinq langues. L'A. rend compte de cette variation en fonction du developpement historique de chacune des langues
Do Contributors to Intellect Explain the Moral Judgment Abilities of Gifted Youth?

To assess reaction time and attributional complexity as factors contributing to the relatively high moral judgment of gifted youth, a sample of 30 gifted youth and 30 college students responded to a computerized measure of moral judgment development, which also indexed reaction time. Additionally, participants completed a measurement of attributional complexity and reported American College Test (ACT) scores. Statistically significant differences favored the gifted in moral judgment development, reaction time, and attributional complexity. Regression analysis revealed that attributional complexity explained a significant amount of variance, whereas ACT scores and reaction times accounted for minimal variance. Although reaction time did not predict moral judgment developmental difference, discussion is offered to suggest how gifted youth, such as those in this study, might benefit from using their reaction time when considering moral situations. Putting the Research to Use: The results of this study support the view that complex information processing and reaction time abilities of gifted youth are transferred to their moral judgment development. In sum, in comparison with a control group of college students, the gifted youth considered in this study appeared to process reasons for moral decisions in a more in-depth manner and were able to do so in a more efficient manner. Currently, it is unknown why and how this occurs, whether obstacles exist that could block this process, and whether practices exist that could help to facilitate these areas. Applications of these findings should therefore expound on these issues so that the utility of research on gifted moral judgment ability is increased. Applied research should also focus on transferring this understanding to general populations in the hopes of affecting the understanding of moral judgment development overall.
ReDHiP: Recalibrating Deep Hierarchy Prediction for Energy Efficiency

Recent hardware trends point to increasingly deeper cache hierarchies. In such hierarchies, accesses that lookup and miss in every cache involve significant energy consumption and degraded performance. To mitigate these problems, in this paper we propose Recalibrating Deep Hierarchy Prediction (ReDHiP), an architectural mechanism that predicts last-level cache (LLC) misses in advance. An LLC miss means that all cache levels need not be accessed at all. Our design for ReDHiP focuses on a simple, compact prediction table that can be efficiently recalibrated over time. We find that a simpler scheme, while sacrificing accuracy, can be more accurate per bit than more complex schemes through recalibration. Our evaluation shows that ReDHiP achieves an average of 22% cache energy savings and 8% performance improvement for a wide range of benchmarks. ReDHiP achieves these benefits at a hardware cost of less than 1% of the LLC. We also demonstrate how ReDHiP can be used to reduce the energy overhead of hardware data prefetching while being able to further improve the performance.
Epigenetic regulation of drug transporter expression in human tissues

ABSTRACT Introduction: Drug transporters are expressed in a number of tissues such as the intestine, liver, and kidney, and play key roles in drug absorption, distribution, and excretion. Variations in drug transporter gene expression significantly contribute to interindividual differences in drug responses. Epigenetic regulation of drug transporter genes has recently emerged as an important mechanism. Epigenetic regulation alters the expression of genes without changing DNA sequences. Epigenetic control mechanisms are associated with DNA methylation, histone modifications, and microRNAs. Herein we discuss recent advances in the study of the transcriptional and post-transcriptional mechanisms of drug transporters with a focus on epigenetic regulation. Areas covered: This review summarizes recent research on the epigenetic regulation of drug transporter genes, and highlights the importance of identifying novel biomarkers based on epigenetics for use in individualized drug therapy. Expert opinion: Researchers are actively attempting to elucidate the epigenetic mechanisms that control the expression of drug transporters, which affect the pharmacokinetics of drugs. Current evidence suggests that epigenetic changes play an important role in drug transporter function. A clearer understanding of epigenetic regulation in drug transporter genes will provide an insight into novel approaches to individualized drug therapy.
Likely Health Outcomes for Untreated Acute Febrile Illness in the Tropics in Decision and Economic Models; A Delphi Survey

Background Modelling is widely used to inform decisions about management of malaria and acute febrile illnesses. Most models depend on estimates of the probability that untreated patients with malaria or bacterial illnesses will progress to severe disease or death. However, data on these key parameters are lacking and assumptions are frequently made based on expert opinion. Widely diverse opinions can lead to conflicting outcomes in models they inform. Methods and Findings A Delphi survey was conducted with malaria experts aiming to reach consensus on key parameters for public health and economic models, relating to the outcome of untreated febrile illnesses. Survey questions were stratified by malaria transmission intensity, patient age, and HIV prevalence. The impact of the variability in opinion on decision models is illustrated with a model previously used to assess the cost-effectiveness of malaria rapid diagnostic tests. Some consensus was reached around the probability that patients from higher transmission settings with untreated malaria would progress to severe disease (median 3%, inter-quartile range (IQR) 1–5%), and the probability that a non-malaria illness required antibiotics in areas of low HIV prevalence (median 20%). Children living in low transmission areas were considered to be at higher risk of progressing to severe malaria (median 30%, IQR 10–58%) than those from higher transmission areas (median 13%, IQR 7–30%). Estimates of the probability of dying from severe malaria were high in all settings (medians 60–73%). However, opinions varied widely for most parameters, and did not converge on resurveying. Conclusions This study highlights the uncertainty around potential consequences of untreated malaria and bacterial illnesses. The lack of consensus on most parameters, the wide range of estimates, and the impact of variability in estimates on model outputs, demonstrate the importance of sensitivity analysis for decision models employing expert opinion. Results of such models should be interpreted cautiously. The diversity of expert opinion should be recognised when policy options are debated.
ATP-Driven Exchange of Histone H2AZ Variant Catalyzed by SWR1 Chromatin Remodeling Complex

The conserved histone variant H2AZ has an important role in the regulation of gene expression and the establishment of a buffer to the spread of silent heterochromatin. How histone variants such as H2AZ are incorporated into nucleosomes has been obscure. We have found that Swr1, a Swi2/Snf2-related adenosine triphosphatase, is the catalytic core of a multisubunit, histone-variant exchanger that efficiently replaces conventional histone H2A with histone H2AZ in nucleosome arrays. Swr1 is required for the deposition of histone H2AZ at specific chromosome locations in vivo, and Swr1 and H2AZ commonly regulate a subset of yeast genes. These findings define a previously unknown role for the adenosine triphosphate–dependent chromatin remodeling machinery.
On the benefits of subspace dimension reduction for Grassmannian multiuser beamformers

Block diagonalization (BD) is a linear precoding technique to eliminate inter-user interference (IUI) in multiple-input multipleoutput (MIMO) multiuser wireless communication systems. In this paper, a limited feedback-based BD algorithm with Grassmannian codebook is studied. When the number of bits available for feeding back channel state information (CSI) from multiple terminals to the basestation (BS) is limited, we demonstrate feeding back singular vector corresponding to the largest singular value provides a better capacity performance as compared to feeding back the whole signal subspace.
Prevention of crescentic glomerulonephritis by immunoneutralization of the fractalkine receptor CX3CR1 rapid communication.

BACKGROUND Fractalkine is a newly identified T-cell and monocyte/macrophage (Mphi) chemokine with a transmembrane domain and is a cell-surface protein on activated endothelium. It can mediate adhesion of cells expressing the fractalkine receptor CX3CR1. These unique features make fractalkine well suited for leukocyte recruitment in tissues with high blood flow as in the renal glomerulus. METHODS Fractalkine expression in glomeruli and response of isolated glomerular inflammatory cells to fractalkine were studied in the Wistar-Kyoto (WKY) crescentic glomerulonephritis model. Antibody was used to confirm the proinflammatory role of fractalkine. RESULTS Fractalkine was markedly induced in the endothelium of nephritic rat glomeruli, and inflammatory leukocytes infiltrating the glomeruli expressed increased levels of CX3CR1. Anti-CX3CR1 antibody treatment dramatically blocked leukocyte infiltration in the glomeruli, prevented crescent formation, and improved renal function. CONCLUSIONS Fractalkine plays a central role in leukocyte trafficking at the endothelium in the high-flow glomerular circuit and, in turn, implicates CX3CR1 as a prime drug target for therapeutic intervention of endothelium-related inflammatory diseases.
A Scan Matrix Design for Low Power Scan-Based Test

For the scan design, the circuit under test (CUT) in the test mode usually has larger switching activity than in the function mode, causing excessive power dissipation. In this paper, we propose a new Scan Matrix (SM) architecture for the scan-based design to achieve low power testing. The scan flip-flops are connected in a matrix style for test and its addressing is controlled by two ring generators during pattern scanning in. Unlike the traditional scan, for which scan-in data need to pass through a long path and many scan flip-flops switch simultaneously, the proposed approach dynamically forms a low-power scan path to reduce test energy and peak power during shift significantly. The architecture is scalable for large designs and has minimal circuit performance penalty. Experimental results show that, for some larger designs, nearly 99% power savings have been achieved.
Babel's tower revisited: a universal resource for cross-referencing across annotation databases

MOTIVATION Annotation databases are widely used as public repositories of biological knowledge. However, most of these resources have been developed by independent groups which used different designs and different identifiers for the same biological entities. As we show in this article, incoherent name spaces between various databases represent a serious impediment to using the existing annotations at their full potential. Navigating between various such name spaces by mapping IDs from one database to another is a very important issue which is not properly addressed at the moment. RESULTS We have developed a web-based resource, Onto-Translate (OT), which effectively addresses this problem. OT is able to map onto each other different types of biological entities from the following annotation databases: Swiss-Prot, TrEMBL, NREF, PIR, Gene Ontology, KEGG, Entrez Gene, GenBank, GenPept, IMAGE, RefSeq, UniGene, OMIM, PDB, Eukaryotic Promoter Database, HUGO Gene Nomenclature Committee and NetAffx. Currently, OT is able to perform 462 types of mappings between 29 different types of IDs from 17 databases concerning 53 organisms. Among these, over 300 types of translations and 15 types of IDs are not currently supported by any other tool or resource. On average, OT is able to correctly map between 96 and 99% of the biological entities provided as input. In terms of speed, sets of approximately 20 000 IDs can be translated in <30 s, in most cases. AVAILABILITY OT is a part of Onto-Tools, which is freely available at http://vortex.cs. wayne.edu/Projects.html
EXAMINING TWO ASPECTS OF CONTACT ON THE STIGMA OF MENTAL ILLNESS

Abstract This study expands on earlier research by our group that has shown that contact with people with mental illness has significant effects on changing stigmatizing attitudes. Two factors that affect contact are examined in this study: the medium through which contact is experienced, and the level of stereotype disconfirmation engendered in contact. One hundred sixty-four individuals were randomly assigned to one of five conditions. Three of the conditions allowed us to examine the effects of medium: no stigma-control, in vivo contact with moderate disconfirmation, and videotaped contact with moderate disconfirmation. Along with the moderate disconfirmation videotape, two additional videotaped conditions —little or no disconfirmation and high disconfirmations—defined the three groups for our second set of hypotheses on disconfirmation. Research participants completed the Social Distance Scale prior to being assigned to condition and immediately upon completion. In terms of the medium of contact, resu.
Mastery learning

Mastery learning breaks subject matter and learning content into units with clearly specified objectives which are pursued until they are achieved. Learners work through each block of content in a series of sequential steps and must demonstrate a high level of success on tests, typically about 80%, before progressing to the next unit. Those who do not reach the required level are provided with additional tuition, peer support, small group discussions, or homework, so that they can reach the expected level.
Wedding rituals and the struggle over national identities

This article argues that rituals are the creative link between state hegemony and the everyday practices of ordinary people. Based on the idea of ritual as experimental technology developed by the Comaroffs (1993), we analyse the Tajik wedding as a means to deal creatively with the tension between the nation-state's claims to exert control over its citizens, on the one hand, and the use of traditions as historical continuity to create a common identity, on the other. Whereas weddings conform to state law and have thus adapted to the changing legal frames during the Soviet period and continue to do so in independent Tajikistan, they have also been used as rituals of cultural resistance in which ethnic, local and national identities are asserted against homogenizing efforts. Taking an historical perspective on weddings, this article contributes to the debate on the role of rituals in the creation and contestation of national identity and state ideologies.