Miracle-dz/UniFAR-FTUs huggingface dataset:
CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells

DNA damaging agents can promote aging, disease and cancer and they are ubiquitous in the environment and produced within human cells as normal cellular metabolites. Ironically, at high doses DNA damaging agents are also used to treat cancer. The ability to quantify DNA damage responses is thus critical in the public health, pharmaceutical and clinical domains. Here, we describe a novel platform that exploits microfabrication techniques to pattern cells in a fixed microarray. The ‘CometChip’ is based upon the well-established single cell gel electrophoresis assay (a.k.a. the comet assay), which estimates the level of DNA damage by evaluating the extent of DNA migration through a matrix in an electrical field. The type of damage measured by this assay includes abasic sites, crosslinks, and strand breaks. Instead of being randomly dispersed in agarose in the traditional assay, cells are captured into an agarose microwell array by gravity. The platform also expands from the size of a standard microscope slide to a 96-well format, enabling parallel processing. Here we describe the protocols of using the chip to evaluate DNA damage caused by known genotoxic agents and the cellular repair response followed after exposure. Through the integration of biological and engineering principles, this method potentiates robust and sensitive measurements of DNA damage in human cells and provides the necessary throughput for genotoxicity testing, drug development, epidemiological studies and clinical assays.
Identification of Lipoteichoic Acid as a Ligand for Draper in the Phagocytosis of Staphylococcus aureus by Drosophila Hemocytes1

Phagocytosis is central to cellular immunity against bacterial infections. As in mammals, both opsonin-dependent and -independent mechanisms of phagocytosis seemingly exist in Drosophila. Although candidate Drosophila receptors for phagocytosis have been reported, how they recognize bacteria, either directly or indirectly, remains to be elucidated. We searched for the Staphylococcus aureus genes required for phagocytosis by Drosophila hemocytes in a screening of mutant strains with defects in the structure of the cell wall. The genes identified included ltaS, which encodes an enzyme responsible for the synthesis of lipoteichoic acid. ltaS-dependent phagocytosis of S. aureus required the receptor Draper but not Eater or Nimrod C1, and Draper-lacking flies showed reduced resistance to a septic infection of S. aureus without a change in a humoral immune response. Finally, lipoteichoic acid bound to the extracellular region of Draper. We propose that lipoteichoic acid serves as a ligand for Draper in the phagocytosis of S. aureus by Drosophila hemocytes and that the phagocytic elimination of invading bacteria is required for flies to survive the infection.
From self-assembly of microstructures to mechanics : multiscale modeling of polymer networks : Multiscale modeling of polymer networks

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Is Histologic Subtype Significant in the Management of NSCLC

Histologic subtype has emerged as a potential prognostic and/or predictive factor in advanced non-small cell lung cancer (NSCLC). Several studies support the importance of differentiating between squamous and non-squamous NSCLC in terms of efficacy of chemotherapeutics (e.g. pemetrexed) or treatment-related toxicities (e.g. bevacizumab). In addition, molecular markers and gene profiles have been correlated with histologic subtype. This review examines the emerging clinical significance of histologic type in the management of NSCLC, discusses caveats in accurate histologic diagnosis, and reviews biomarkers with potential predictive value for NSCLC chemotherapeutics.
Computerized expert system for evaluation of automated visual fields from the Ischemic Optic Neuropathy Decompression Trial: methods, baseline fields, and six-month longitudinal follow-up.

PURPOSE To validate a computerized expert system evaluating visual fields in a prospective clinical trial, the Ischemic Optic Neuropathy Decompression Trial (IONDT). To identify the pattern and within-pattern severity of field defects for study eyes at baseline and 6-month follow-up. DESIGN Humphrey visual field (HVF) change was used as the outcome measure for a prospective, randomized, multicenter trial to test the null hypothesis that optic nerve sheath decompression was ineffective in treating nonarteritic anterior ischemic optic neuropathy and to ascertain the natural history of the disease. METHODS An expert panel established criteria for the type and severity of visual field defects. Using these criteria, a rule-based computerized expert system interpreted HVF from baseline and 6-month visits for patients randomized to surgery or careful follow-up and for patients who were not randomized. RESULTS A computerized expert system was devised and validated. The system was then used to analyze HVFs. The pattern of defects found at baseline for patients randomized to surgery did not differ from that of patients randomized to careful follow-up. The most common pattern of defect was a superior and inferior arcuate with central scotoma for randomized eyes (19.2%) and a superior and inferior arcuate for nonrandomized eyes (30.6%). Field patterns at 6 months and baseline were not different. For randomized study eyes, the superior altitudinal defects improved (P = .03), as did the inferior altitudinal defects (P = .01). For nonrandomized study eyes, only the inferior altitudinal defects improved (P = .02). No treatment effect was noted. CONCLUSIONS A novel rule-based expert system successfully interpreted visual field defects at baseline of eyes enrolled in the IONDT.
Genome-Wide Profiling of Histone H3 Lysine 4 and Lysine 27 Trimethylation Reveals an Epigenetic Signature in Prostate Carcinogenesis

Background Increasing evidence implicates the critical roles of epigenetic regulation in cancer. Very recent reports indicate that global gene silencing in cancer is associated with specific epigenetic modifications. However, the relationship between epigenetic switches and more dynamic patterns of gene activation and repression has remained largely unknown. Methodology/Principal Findings Genome-wide profiling of the trimethylation of histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) was performed using chromatin immunoprecipitation coupled with whole genome promoter microarray (ChIP-chip) techniques. Comparison of the ChIP-chip data and microarray gene expression data revealed that loss and/or gain of H3K4me3 and/or H3K27me3 were strongly associated with differential gene expression, including microRNA expression, between prostate cancer and primary cells. The most common switches were gain or loss of H3K27me3 coupled with low effect on gene expression. The least prevalent switches were between H3K4me3 and H3K27me3 coupled with much higher fractions of activated and silenced genes. Promoter patterns of H3K4me3 and H3K27me3 corresponded strongly with coordinated expression changes of regulatory gene modules, such as HOX and microRNA genes, and structural gene modules, such as desmosome and gap junction genes. A number of epigenetically switched oncogenes and tumor suppressor genes were found overexpressed and underexpressed accordingly in prostate cancer cells. Conclusions/Significance This work offers a dynamic picture of epigenetic switches in carcinogenesis and contributes to an overall understanding of coordinated regulation of gene expression in cancer. Our data indicate an H3K4me3/H3K27me3 epigenetic signature of prostate carcinogenesis.
Epstein-Barr virus LMP2A bypasses p53 inactivation in a MYC model of lymphomagenesis

Although Epstein-Barr virus (EBV) is linked to Burkitt's lymphoma (BL), the role of the virus in lymphomagenesis is unclear. LMP2A, encoded by EBV, can be detected in BL biopsies and has prosurvival functions. We generated mice expressing MYC and LMP2A in B cells. LMP2A/λ-MYC mice show greatly accelerated tumor onset. Similar to previous work, we found p53 mutations in λ-MYC tumors; however, we detected no mutations in the rapidly arising LMP2A/λ-MYC tumors. We further demonstrate that the p53 pathway is functionally intact in LMP2A/λ-MYC tumors, which have increased levels of PUMA and sensitivity to p53 activation by Nutlin. This work shows that LMP2A can permit tumorigenesis in the presence of an intact p53 pathway, identifying an important contribution of EBV to BL.
Patterns of maternal weight gain in pregnancy

Summary. A retrospective study of 1145 pregnant women showed that trends in mean maternal weight gain from the time of booking until delivery were not linear. Statistically significant lower rates of maternal weight gain were seen before 16 weeks, after 36 weeks and between 28 and 32 weeks gestation (P < 0.05). The mean maternal weight gain was 10.71 kg (SD 4.3) and the mean weekly weight gain was 0.38 kg (SD 0.16). A wide variation of maternal weight gain was seen in women with a normal outcome. The mean weight gain in heavy (>68 kg) and light (<55.4 kg) women was less than that in women whose weight was in the third quartile (60–68 kg, P<0.05). The mean maternal weight gain was less in young (<20 years) women than in older women (>25 years; P <0.05), less in parous than in primigravid women from week 37 onwards (P<0.05), less in smokers than in non‐smokers from 20 weeks onwards (P<0.05), and greater in hypertensive women (BP> 140/90) than in normotensive women (P<0.05) from week 24 onwards. The mean weight gain in women who had small for gestational age (SGA) infants was not significantly different from that in women who had infants that were of appropriate size for gestational age. After taking into account infant and placental weight using multiple regression analysis, the factors that were associated with statistically significant differences in average weekly weight gain were parity, body mass index, smoking habit and raised blood pressure. Only 9.6% of the variation in average weekly weight gain could be predicted using these variables. It is unlikely that the measurement of maternal weight gain would be useful in detecting women who will have SGA infants or will develop hypertension.
Association between severity of type A hepatitis and nucleotide variations in the 5` non-translated region of hepatitis A virus RNA: strains from fulminant hepatitis have fewer nucleotide substitutions

Background: Type A hepatitis is still a considerable problem in both underdeveloped and developed countries. Why some patients progress to fulminant type A hepatitis and others do not is unclear. Aims: To determine if nucleotide differences in the genome of hepatitis A virus (HAV) are responsible for the range of clinical severities, we analysed the 5` non-translated region (5`NTR) of the HAV genome, which has an internal ribosomal entry site and is important for cap independent translation of the viral message. Methods: Serum samples from 84 Japanese patients with sporadic type A hepatitis from five distant regions of Japan, comprising 12 patients with fulminant hepatitis (FH), 13 with severe acute hepatitis (AHs), and 59 with acute hepatitis (AH), were examined for HAV RNA. The fragment between nucleotides 75 and 638 of the 5`NTR was amplified by reverse transcription-polymerase chain reaction, and the nucleotide sequence was determined by direct sequencing. Results: Comparison of sequences of the 5`NTR revealed relatively fewer nucleotide substitutions in FH and AHs patients compared with the considerable sequence variations found in strains of AH. This tendency was most prominent between nucleotides 200 and 500. Strains from FH and AHs cases had fewer nucleotide substitutions (p<0.001) in this region. Conclusions: Nucleotide variations in the central portion of the 5`NTR of HAV may influence the severity of type A hepatitis.
Grafting of Poly(n-butylacrylate)-b-poly(2-hydroxyethyl methacrylate) on Carbon Fiber and its Effect on Composite Properties

A treatment method based on the grafting of block copolymer on carbon fiber (CF) surface was proposed for obtaining a controlled interface between carbon fibers and epoxy resin. The block copolymer poly(n-butylacrylate)-b-poly(2-hydroxyethyl methacrylate) (PnBA-b-PHEMA) was grafted on the CF by controlled polymerization. Research shows that the grafting block copolymer can improve interfacial adhesion, and the chain structure, lengths and grafting density of block copolymer can affect the fiber/matrix interfacial adhesion. The study of mechanical properties indicated the introduction of PnBA-b-PHEMA in the interface could both improve the flexural strength, modulus and impact toughness of composites.
Slope One Predictors for Online Rating-Based Collaborative Filtering

Rating-based collaborative filtering is the process of predicting how a user would rate a given item from other user ratings. We propose three related slope one schemes with predictors of the form f(x) = x + b, which precompute the average difference between the ratings of one item and another for users who rated both. Slope one algorithms are easy to implement, efficient to query, reasonably accurate, and they support both online queries and dynamic updates, which makes them good candidates for real-world systems. The basic slope one scheme is suggested as a new reference scheme for collaborative filtering. By factoring in items that a user liked separately from items that a user disliked, we achieve results competitive with slower memory-based schemes over the standard benchmark EachMovie and Movielens data sets while better fulfilling the desiderata of CF applications.
Coordination Capacity

We develop elements of a theory of cooperation and coordination in networks. Rather than considering a communication network as a means of distributing information, or of reconstructing random processes at remote nodes, we ask what dependence can be established among the nodes given the communication constraints. Specifically, in a network with communication rates {Ri,j} between the nodes, we ask what is the set of all achievable joint distributions p(x1, ., xm) of actions at the nodes of the network. Several networks are solved, including arbitrarily large cascade networks. Distributed cooperation can be the solution to many problems such as distributed games, distributed control, and establishing mutual information bounds on the influence of one part of a physical system on another.
Metabolic effects of telmisartan and irbesartan in type 2 diabetic patients with metabolic syndrome treated with rosiglitazone

Background and objective: Angiotensin II receptor blockers represent a class of effective and well‐tolerated orally active antihypertensive drugs in the general hypertensive population and in diabetic patients. The aim of our study was to investigate the metabolic effects of telmisartan and irbesartan in diabetic subjects treated with rosiglitazone.
High‐Temperature Tribological Behavior of CrN‐Ag Self‐lubricating Coatings

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Surnames in the Azores: Analysis of the Isonymy Structure

Geographic isolation is a significant factor to consider when characterizing human populations. The knowledge of the genetic structure of isolated populations has been of great importance to disease-locus positioning and gene identification. To investigate the genetic structure of the Azorean population, we conducted a survey based on the frequencies of surnames listed in the 2001 telephone book. We calculated the following parameters: isonymy (I), the random component of inbreeding (FST), genetic diversity according to Fisher (α), Karlin-McGregor's migration rate (ν), and Nei's distance. For the 1,271 subscribers and 163 different surnames, Graciosa island presented the lowest value of abundance of surnames (α = 15.75), suggesting great genetic isolation compared to the other eight islands. Migration, calculated on the basis of the diversity of surnames within islands, ranged from 0.2747 (Corvo island) to 0.0026 (São Miguel island), indicating that people migrated preferentially toward the economically more developed islands. The value of the random component of inbreeding obtained for the whole population (FST = 0.0039) indicates little genetic differentiation (Wright's FST<0.05). Moreover, isonymy similarity revealed using the UPGMA method shows three subclusters corresponding to the geographic distribution of the islands.
Livestock-Associated Staphylococcus aureus: The United States Experience

Staphylococcus aureus is a gram-positive bacterium that colonizes a variety of animal species [1]. S. aureus infections in animals are most commonly reported as a cause of mastitis in dairyproducing animals (including cattle and goats) and “bumblefoot” in chickens [2], as well as being identified as a pathogen of farmed rabbits [3]. Most reports characterizing animalassociated S. aureus have demonstrated that strains affecting animals are distinct from those infecting humans, suggesting that there are host-specific lineages which only rarely cross species boundaries [4]. Livestock-associated strains may evolve on farms because of the use of antibiotics in animal husbandry. These may be used as feed additives for growth promotion in industrial livestock and poultry [5], for prevention of disease within a herd, or for treatment of an existing disease outbreak. Agricultural-use antibiotics include many classes that are relevant for human health, including tetracyclines, macrolides, penicillins, and sulfonamides, among others. Antimicrobial resistance generated during animal husbandry may then be spread to the general human population in a number of different manners: contact with contaminated meat products (via handling or ingestion); occupational contact (farmers, meat packers, butchers, etc.) and potential secondary spread into the larger community from those who are occupationally exposed; entry into and transmission via hospitals or other health care facilities; or spread via environmental routes including air, water, or manure in areas in proximity to live animal farms or crop farms where manure has been used as a fertilizer (Fig. 1). While methicillin resistance has been the most commonly investigated phenomenon and will be the main topic of this review, resistance to any of these antibiotics can occur and can potentially be a threat to successful treatment of S. aureus infections and therefore to human health outcomes. As such, my research group and others have begun to look more broadly at any S. aureus present on farms, including those that may be susceptible to methicillin but resistant to other antibiotics.
Replace: An incremental placement algorithm for field programmable gate arrays

Recompiling a large circuit after making a few logic changes is a time-consuming process. We present an incremental placement algorithm for FPGAs that is focused on extremely fast runtime for changes which can be localized. It is capable of handling multiple changes across large regions of an FPGA. This is especially useful when used with a floorplan where a modified subcircuit is instantiated several times in the design hierarchy or where several subcircuits are modified. The algorithm is simpler and faster than past approaches because its insertion and legalization steps are based on CPU-efficient shifting steps which do not continuously evaluate the impact of each move on costs. Instead, any lost quality is recovered by a fast, low-temperature anneal at the end. When 35,000 out of 50,000 LUTs are modified, the incremental placement (including fast anneal) is 7 times faster than VPR's “fast placement“ from scratch with only 2% quality degradation. The key concepts utilized in the incremental placement algorithm include uses of floor-planning constraints, CPU-efficient CLB shifting, super placement grid and a tuned annealing refinement process.
Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

Crystallization of lysozyme with (R)-2-methyl-2,4-pentanediol produces more ordered crystals and a higher resolution protein structure than crystallization with (S)-2-methyl-2,4-pentanediol. The results suggest that chiral interactions with chiral additives are important in protein crystal formation.
An Approach for Network Security Analysis Using Logic Exploitation Graph

Recent work in network security has focused on the fact that combinations of exploits are the typical means by which an attacker breaks into a network. Researchers have proposed a variety of graph-based analysis approach, and there is often a lack of logical formalism. This paper describes a new approach to represent and analyze network vulnerability. We propose logical exploitation graph, which directly illustrate logical dependencies among exploitation goals and network configure. Our logical exploitation graph generation tool builds upon LEG-NSA, a network security analyzer based on Prolog logical programming. We demonstrate how to reason all exploitation paths using bottom-up and top-down evaluation algorithms in the Prolog logic- programming engine. We show experimental evidence that our logical exploitation graph generation algorithm is very efficient.