Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasma DNA, Microsatellite Alterations, and p53 Tumor Mutations Are Associated with Disease-Free Survival in Radically Resected Non-small Cell Lung Cancer Patients: A Study of the Perugia Multidisciplinary Team for Thoracic Oncology

Introduction: This prospective study examined association between circulating plasma DNA, microsatellite alterations (MA), p53 mutations with time to relapse and survival in surgically treated non-small cell lung cancer (NSCLC) patients (pts). Methods: Plasma samples, adjacent lung tissue, and lung tumor tissue specimens were collected from consecutive patients with stage I–III NSCLC. Blood samples of 66 matched healthy donors with positive smoking history were collected as controls. The plasma DNA amount was determined by real-time PCR. The analysis of MA at loci D3S1300, D3S1289, D3S1266, and D3S2338 on chromosome 3p was performed by radiolabeled PCR. p53 Mutations (exons 5, 6, 7, and 8) were detected by PCR-single-strand conformational polymorphism assay. Results: There were 76 patients, 65 men; median age was 68 years (range, 42–86), 20 had stage I, 40 stage II, and 16 stage III, the majority of pts (48.7%) had squamous-cell histology. Sixty-nine (91%) were smokers and most had good Eastern Cooperative Oncology Group performance status (0/1:72/4). Mean circulating DNA of all pts was 60 ng/ml versus 5 ng/ml in smoker-matched controls (p < 0.0001). In pts without recurrence, mean circulating DNA was 48.5 ng/ml at baseline, 32.8 ng/ml at 3rd month, and 20.6 ng/ml at 12th month after surgery. In pts with recurrence, mean circulating DNA at baseline was 97.1 ng/ml. At 3rd month after surgery, mean DNA concentration was significantly lower in disease-free pts than in patients with recurrent disease (32.8 versus 292.7 ng/ml; p = 0.0016). MA in at least one locus was found in 39.5% of NSCLC tumors. p53 Genomic mutations were observed in 54.0% of tumor samples. Statistically significant associations were observed between MA and squamous-cell histotype (p = 0.007) and between p53 mutations and lymph node involvement (p = 0.012). MA and p53 mutations were found to be significantly associated with recurrence of disease (p = 0.033 and 0.026, respectively). Conclusion: Our results suggest that MA and p53 mutations in tumor DNA have a potential prognostic role for disease recurrence in NSCLC patients, and elevated levels of plasma circulating DNA identify patients with possible systemic disease at diagnosis. This might be proposed as an early detection test of disease recurrence.
Neonatal and maternal platelets: Activation at time of birth

Determination of the plasma concentrations of beta‐thromboglobulin (BTG), thromboxane B2 (TxB2) and platelet factor 4 (PF4) were made at the time of birth in 18 newborns and their respective mothers. Both groups show significant elevation of all these molecular markers, suggesting marked platelet activation. The elevated TxB2 levels in the newborn group, 25 ± 8 pg/ml, are compatible with a normally functioning and activated platelet prostaglandin pathway. Mode of delivery, vaginal or caesarean section, does not significantly influence the degree of activation in either group. Ultrastructural platelet examination did not reveal any morphologic differences between maternal and newborn platelets. There appears to be marked activation of the newborn and maternal platelet systems at the time of birth, and we postulate that this may explain in part the transient platelet dysfunction observed in newborns.
Identification and molecular characterization of a transcriptional regulator from Pseudomonas aeruginosa PAO1 exhibiting structural and functional similarity to the FNR protein of Escherichia coli

A gene library of chromosomal DNA from Pseudomonas aeruginosa contained a DNA fragment which was able to restore anaerobic growth to an Escherichia coli fnr deletion mutant on glycerol/nitrate medium. The cloned gene (termed anr) was sequenced and shown to encode a protein of 244 amino acids with a calculated molecular weight of 27 129. The deduced amino acid sequence of the anr gene product showed considerable similarity to the FNR protein from E. coli. Expression of the anr gene in a T7 promoter/polymerase system identified ANR as a 31 kDa protein. Transcriptional analysis of the anr gene showed that it is monocistronic but apparently lacks the equivalent sites for negative autoregulation which have been shown to be present in the promoter region of the E. coli fnr gene. The ANR protein was shown to activate transcription of the pfl gene in E. coli in response to anaerobiosis, as well as being able to restore the activity of three anaerobicaliy inducible enzymes. A P. aeruginosa mutant incapable of growing anaerobically with nitrate or on arginine was fully complemented by the anr gene, indicating that it probably has a function in controlling anaerobic gene expression in Pseudomonas. Further corroboration for this assumption was provided by S1 nuclease analysis of transcription of the multiple promoters of the E. coli pfl operon in P. aeruginosa. Transcription was induced by oxygen limitation and was completely ANR‐dependent in both aerobic and anaerobic cells. Removal of the upstream regulatory sequence of the pfl operon, which includes the sequences required for FNR‐dependent regulation in E. coli, removed ANR‐dependent transcriptional control of the remaining pfl promoters, irrespective of the cellular oxygen status. These results imply that the mechanisms by which ANR and FNR regulate transcription are fundamentally similar.
Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extrachromosomal elements

Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565T together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).
Exploring genetic moderators and epigenetic mediators of contextual and family effects: From Gene × Environment to epigenetics

Abstract In the current manuscript, we provide an overview of a research program at the University of Georgia's Center for Family Research designed to expand upon rapid and ongoing developments in the fields of genetics and epigenetics. By placing those developments in the context of translational research on family and community determinants of health and well-being among rural African Americans, we hope to identify novel, modifiable environments and biological processes. In the first section of the article, we review our earlier work on genotypic variation effects on the association between family context and mental and physical health outcomes as well as differential responses to family-based intervention. We then transition to discuss our more recent research on the association of family and community environments with epigenetic processes. In this second section of the article, we begin by briefly reviewing terminology and basic considerations before describing evidence that early environments may influence epigenetic motifs that potentially serve as mediators of long-term effects of early family and community environments on longer term health outcomes. We also provide evidence that genotype may sometimes influence epigenetic outcomes. Finally, we describe our recent efforts to use genome-wide characterization of epigenetic patterns to better understand the biological impact of protective parenting on long-term shifts in inflammatory processes and its potential implications for young adult health. As will be clear, research on epigenetics as a mediator of the connections between family/community processes and a range of health outcomes is still in its infancy, but the potential to develop important insights regarding mechanisms linking modifiable environments to biological processes and long-term health outcomes already is coming into view.
Persistent Racial Disparity in Stroke Hospitalization and Economic Impact in Young Adults in the Buckle of Stroke Belt

Background and Purpose— Mounting evidence points to a decline in stroke incidence. However, little is known about recent patterns of stroke hospitalization within the buckle of the stroke belt. This study aims to investigate the age- and race-specific secular trends in stroke hospitalization rates, inpatient stroke mortality rates, and related hospitalization charges during the past decade in South Carolina. Methods— Patients from 2001 to 2010 were identified from the State Inpatient Hospital Discharge Database with a primary discharge diagnosis of stroke (International Classification of Diseases, Ninth Revision codes: 430–434, 436, 437.1). Age- and race-stroke–specific hospitalization rates, hospital charges, charges associated with racial disparity, and 30-day stroke mortality rates were compared between blacks and whites. Results— Of the 84 179 stroke hospitalizations, 31 137 (37.0%) were from patients aged <65 years and 29 846 (35.5%) were blacks. Stroke hospitalization rates decreased in the older population (aged ≥65 years) for both blacks and whites (P<0.001) but increased among the younger group (aged <65 years; P=0.004); however, this increase was mainly driven by a 17.3% rise among blacks (P=0.001), with no difference seen among whites (P=0.84). Of hospital charges totaling $2.77 billion, $453.2 million (16.4%) are associated with racial disparity (79.6% from patients aged <65 years). Thirty-day stroke mortality rates decreased in all age-race-stroke–specific groups (P<0.001). Conclusions— The stroke hospitalization rate increased in the young blacks only, which results in a severe and persistent racial disparity. It highlights the urgent need for a racial disparity reduction in the younger population to alleviate the healthcare burden.
A Human Aware Mobile Robot Motion Planner

Robot navigation in the presence of humans raises new issues for motion planning and control when the humans must be taken explicitly into account. We claim that a human aware motion planner (HAMP) must not only provide safe robot paths, but also synthesize good, socially acceptable and legible paths. This paper focuses on a motion planner that takes explicitly into account its human partners by reasoning about their accessibility, their vision field and their preferences in terms of relative human-robot placement and motions in realistic environments. This planner is part of a human-aware motion and manipulation planning and control system that we aim to develop in order to achieve motion and manipulation tasks in the presence or in synergy with humans.
The Host Galaxy of GRB 031203: Implications of Its Low Metallicity, Low Redshift, and Starburst Nature

We present Keck/NIRSPEC near-IR images and Magellan/IMACS optical spectroscopy of the host galaxy of GRB 031203. The host is an actively star-forming galaxy at z = 0.1055 ± 0.0001. This is the lowest redshift GRB to date, aside from GRB 980425. From the hydrogen Balmer lines, we infer an extinction of AV = 3.62 ± 0.25 or a total reddening ET(B - V) = 1.17 ± 0.1 toward the sight line to the nebular regions. After correcting for reddening, we perform an emission-line analysis and derive an ISM temperature of T = 13400 ± 2000 K and electron density of ne = 300 cm-3. These imply a metallicity [O/H] = -0.72 ± 0.15 dex and a roughly solar abundance pattern for N, Ne, S, and Ar. Integrating Hα, we infer a dust-corrected star formation rate (SFR) of more than 11 M☉ yr-1. These observations have the following implications: (1) The galaxy has a low K'-band luminosity L ≈ L/5, typical of GRB host galaxies. (2) The low redshift indicates GRB 031203 had an isotropic-equivalent γ-ray energy release smaller than all previous confirmed GRB events. The burst discovery raises the likelihood of identifying many additional low-z, low-flux events with Swift. (3) The large SFR, low metallicity, and inferred hard radiation field are suggestive of massive star formation, supporting the collapsar model. (4) Several lines of evidence argue against the identification of GRB 031203 as an X-ray flash event.
Autographa californica Multiple Nucleopolyhedrovirus exon0 (orf141), Which Encodes a RING Finger Protein, Is Required for Efficient Production of Budded Virus

ABSTRACT exon0 (orf141) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a highly conserved baculovirus gene that codes for a predicted 261-amino-acid protein. Located in the C-terminal region of EXON0 are a predicted leucine-rich coiled-coil domain and a RING finger motif. The 5′ 114 nucleotides of exon0 form part of ie0, which is a spliced gene expressed at very early times postinfection, but transcriptional analysis revealed that exon0 is transcribed as a late gene. To determine the role of exon0 in the baculovirus life cycle, we used AcMNPV bacmids and generated exon0 knockout viruses (Ac-exon0-KO) by recombination in Escherichia coli. Ac-exon0-KO progressed through the very late phases in Sf9 cells, as evidenced by the development of occlusion bodies in the nuclei of the transfected or infected cells. However, production of budded virus (BV) in Ac-exon0-KO-infected cells was reduced at least 3 orders of magnitude in comparison to that in wild-type virus infection. Microscopy revealed that Ac-exon0-KO was restricted primarily to the cells initially infected, exhibiting a single-cell infection phenotype. Slot blot assays and Western blot analysis indicated that exon0 deletion did not affect the onset or levels of viral DNA replication or the expression of IE1, IE0, and GP64 prior to BV release. These results demonstrate that exon0 is required for efficient production of BV in the AcMNPV life cycle but does not affect late occlusion-derived virus.
Combinations of Cytochrome P450 Gene Polymorphisms Enhancing the Risk for Sporadic Colorectal Cancer Related to Red Meat Consumption

Susceptibility to sporadic colorectal cancers (CRC) is generally thought to be the sum of complex interactions between environmental and genetic factors, all of which contribute independently, producing only a modest effect on the whole phenomenon. However, to date, most research has concealed the notion of interaction and merely focused on dissociate analyses of risk factors to highlight associations with CRC. By contrast, we have chosen a combinative approach here to explore the joint effects of several factors at a time. Through an association study based on 1,023 cases and 1,121 controls, we examined the influence on CRC risk of environmental factors coanalyzed with combinations of six single nucleotide polymorphisms located in cytochrome P450 genes (c.−163A>C and c.1548T>C in CYP1A2, g.−1293G>C and g.−1053C>T in CYP2E1, c.1294C>G in CYP1B1, and c.430C>T in CYP2C9). Whereas separate analyses of the SNPs showed no effect on CRC risk, three allelic variant combinations were found to be associated with a significant increase in CRC risk in interaction with an excessive red meat consumption, thereby exacerbating the intrinsic procarcinogenic effect of this dietary factor. One of these three predisposing combinations was also shown to interact positively with obesity. Provided that they are validated, our results suggest the need to develop robust combinative methods to improve genetic investigations into the susceptibility to CRC. (Cancer Epidemiol Biomarkers Prev 2007;16(7):1460–7)
On complex fuzzy sets

The innovative concept of complex fuzzy sets is introduced. The novelty of the complex fuzzy set lies in the range of values its membership function may attain. In contrast to a traditional fuzzy membership function, this range is not limited to [0,1] but extended to the unit circle in the complex plane. Thus, the complex fuzzy set provides a mathematical framework for describing membership in a set in terms of a complex number. A study of this original concept is presented, including examples of possible applications, which demonstrate the new theory.
Gene duplication and neofunctionalization: POLR3G and POLR3GL

RNA polymerase III (Pol III) occurs in two versions, one containing the POLR3G subunit and the other the closely related POLR3GL subunit. It is not clear whether these two Pol III forms have the same function, in particular whether they recognize the same target genes. We show that the POLR3G and POLR3GL genes arose from a DNA-based gene duplication, probably in a common ancestor of vertebrates. POLR3G- as well as POLR3GL-containing Pol III are present in cultured cell lines and in normal mouse liver, although the relative amounts of the two forms vary, with the POLR3G-containing Pol III relatively more abundant in dividing cells. Genome-wide chromatin immunoprecipitations followed by high-throughput sequencing (ChIP-seq) reveal that both forms of Pol III occupy the same target genes, in very constant proportions within one cell line, suggesting that the two forms of Pol III have a similar function with regard to specificity for target genes. In contrast, the POLR3G promoter—not the POLR3GL promoter—binds the transcription factor MYC, as do all other promoters of genes encoding Pol III subunits. Thus, the POLR3G/POLR3GL duplication did not lead to neo-functionalization of the gene product (at least with regard to target gene specificity) but rather to neo-functionalization of the transcription units, which acquired different mechanisms of regulation, thus likely affording greater regulation potential to the cell.
Logic-Base Interconnect Design for Near Memory Computing in the Smart Memory Cube

Hybrid memory cube (HMC) has promised to improve bandwidth, power consumption, and density for the next-generation main memory systems. In addition, 3-D integration gives a second shot for revisiting near memory computation to fill the gap between processors and memories. In this paper, we study the required infrastructure inside the HMC to support near memory computation in a modular and flexible fashion. We propose a fully backward compatible extension to the standard HMC called the smart memory cube, and design a high bandwidth, low latency, and Advanced eXtensible Interface-4.0 compatible logic base (LoB) interconnect to serve the huge bandwidth demand by the HMCs serial links, and to provide extra bandwidth to a generic processor-in-memory (PIM) device embedded in the LoB. This interconnect features a novel address scrambling mechanism for the reduction in the vault/bank conflicts and robust operation even in the presence of pathological traffic patterns. Our cycle accurate simulation results demonstrate that this interconnect can easily meet the demands of the latest HMC specifications (up to 205 GB/s read bandwidth with 4 serial links and 32 memory vaults for injected random traffic). It further shown that the default addressing scheme of the HMC (low interleaving) is not reliable enough and operates poorly in the presence of specific traffic patterns from real applications. This is while the proposed scrambling mechanism operates robustly even in those cases. The interference between the PIM traffic and the main links is shown to be negligible when the number of PIM ports is limited to 2, requesting up to 64 GB/s without pushing the system into saturation. Finally, logic synthesis with Synopsys Design Compiler confirms that our interconnect is implementable and effective in terms of power, area, and timing (power consumption less than 5 mW up to 1 GHz and area less than 0.4 mm2).
Conversational recommenders with adaptive suggestions

We consider a conversational recommender system based on example-critiquing where some recommendations are suggestions aimed at stimulating preference expression to acquire an accurate preference model. User studies show that suggestions are particularly effective when they present additional opportunities to the user according to the look-ahead principle [32]. This paper proposes a strategy for producing suggestions that exploits prior knowledge of preference distributions and can adapt relative to users' reactions to the displayed examples. We evaluate the approach with simulations using data acquired by previous interactions with real users. In two different settings, we measured the effects of prior knowledge and adaptation strategies with satisfactory results.
Exploration of unconventional fodder for arid land rehabilitation

ABSTRACT Exploring new wild plant species of economic importance with tolerance to harsh environmental conditions in arid countries may be a viable option to improve forage yield. The present study was conducted during two consecutive years and aimed to investigate the nutritional values of eleven selected wild fodder species, six annuals, and five perennials. Detailed analyses of the nutritional values during two different seasons for perennials and two different growth stages for annuals are presented. The results showed that most studied plants have high nutritional values compared to earlier studies on taxonomically related species growing in different arid areas. The mean content of dry matter, ash, crude protein and lipids was 27, 13, 14, and 3.5%, respectively. Neutral detergent fiber, acid detergent fiber, lignin, cellulose and hemicellulose were 44, 26.5, 6.2, 20.2, and 13.7%, respectively. The studied species showed means of 43 and 49% for in vitro dry matter disappearance (IVDMD) for perennials and annuals, respectively. In general, there were slight differences between the 2 years for both perennials and annual species and significant differences among different seasons for perennials and between growth stages for annuals. The study strongly recommends further detailed experimental studies on A. graecizans, Boerhavia diffusa and Cymbopogon schoenanthus, which showed more crude protein, a low fiber content and high IVDMD, as unconventional forage crops in arid lands.