Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Pre-Analytical Variables on Cancer Targeted Gene Sequencing Efficiency

Tumor specimens are often preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks, the most common clinical source for DNA sequencing. Herein, we evaluated the effect of pre-sequencing parameters to guide proper sample selection for targeted gene sequencing. Data from 113 FFPE lung tumor specimens were collected, and targeted gene sequencing was performed. Libraries were constructed using custom probes and were paired-end sequenced on a next generation sequencing platform. A PCR-based quality control (QC) assay was utilized to determine DNA quality, and a ratio was generated in comparison to control DNA. We observed that FFPE storage time, PCR/QC ratio, and DNA input in the library preparation were significantly correlated to most parameters of sequencing efficiency including depth of coverage, alignment rate, insert size, and read quality. A combined score using the three parameters was generated and proved highly accurate to predict sequencing metrics. We also showed wide read count variability within the genome, with worse coverage in regions of low GC content like in KRAS. Sample quality and GC content had independent effects on sequencing depth, and the worst results were observed in regions of low GC content in samples with poor quality. Our data confirm that FFPE samples are a reliable source for targeted gene sequencing in cancer, provided adequate sample quality controls are exercised. Tissue quality should be routinely assessed for pre-analytical factors, and sequencing depth may be limited in genomic regions of low GC content if suboptimal samples are utilized.
A systematic review and meta-analysis of dietary patterns and depression in community-dwelling adults.

BACKGROUND Studies of single nutrients on depression have produced inconsistent results, and they have failed to consider the complex interactions between nutrients. An increasing number of studies in recent years are investigating the association of overall dietary patterns and depression. OBJECTIVE This study aimed to systematically review current literature and conduct meta-analyses of studies addressing the association between dietary patterns and depression. DESIGN Six electronic databases were searched for articles published up to August 2013 that examined the association of total diet and depression among adults. Only studies considered methodologically rigorous were included. Two independent reviewers completed study selection, quality rating, and data extraction. Effect sizes of eligible studies were pooled by using random-effects models. A summary of the findings was presented for studies that could not be meta-analyzed. RESULTS A total of 21 studies were identified. Results from 13 observational studies were pooled. Two dietary patterns were identified. The healthy diet pattern was significantly associated with a reduced odds of depression (OR: 0.84; 95% CI: 0.76, 0.92; P < 0.001). No statistically significant association was observed between the Western diet and depression (OR: 1.17; 95% CI: 0.97, 1.68; P = 0.094); however, the studies were too few for a precise estimate of this effect. CONCLUSIONS The results suggest that high intakes of fruit, vegetables, fish, and whole grains may be associated with a reduced depression risk. However, more high-quality randomized controlled trials and cohort studies are needed to confirm this finding, specifically the temporal sequence of this association.
Multiple role juggling and daily mood states in working mothers: an experience sampling study.

The effects of multiple role juggling (i.e., simultaneously attending to demands of different roles) on daily mood states of employed mothers were examined. Ss completed activity and mood questionnaires 8 times a day for 8 days. Multiple role juggling had immediate negative effects on task enjoyment and mood. However, contrast effects and habituation to role juggling occurred when mood and satisfaction were examined over time. Furthermore, mood states tended to spill over from one episode to the next within a day, but contrast effects were found across days. These results reflect the complex nature of psychological adjustment to multiple role occupancy.
[Reasons for delay in treatment of breast cancer detected due to breast self-examination in women from the Lubelskie region].

OBJECTIVES A delay in diagnosis and treatment of breast cancer patients is observed despite access to modern diagnostic methods. The aim of the study was to evaluate time between the first symptoms of breast cancer and treatment commencement, as well as to analyze reasons for the delay MATERIALS AND METHODS The research was conducted on 260 breast cancer patients treated at the Oncology Center in Lublin between 2008 and 2011. 'Patient delay' was defined as the time gap of > 3 months between first symptoms of cancer and the doctor's appointment and 'system delay' as the time gap of > 1 month between the first medical consultation and commencement of treatment. RESULTS Mean patient delay was 32.2 +/- 63.8 weeks. The main reasons were: disregard of symptoms (51%) and fear of being diagnosed with cancer (48%). Factors which significantly influenced the length of patient delay included: age > 65 years, non-regular gynecologic care, lack of prior cancer screening and lack of family history of breast cancer Mean system delay was 3.1 +/- 2.9 weeks. Tumors < 5 cm in diameter and clinical presentation other than a tumor significantly influenced the system delay CONCLUSIONS A significant delay in diagnosis and treatment of breast cancer remains to be noted. Delay in seeking medical help was observed in 20% of the patients, whereas the referral was delayed due to system fault in 38% of the cases. Contrary to popular belief, patient delay (mean 32.2 +/- 63.8 weeks) is 10 times longer than system delay (3.1 +/- 2.9 weeks), suggesting an urgent need for further education of the general public and creating more accessible medical care.
Melanin production by a filamentous soil fungus in response to copper and localization of copper sulfide by sulfide-silver staining

Gaeumannomyces graminis var. graminis, a filamentous soil ascomycete, exhibited enhanced cell wall melanin accumulation when exposed to as little as 0.01 mM CuSO(inf4) in minimal broth culture. Because its synthesis was inhibited by tricyclazole, the melanin produced in response to copper was dihydroxynaphthalene melanin. An additional hyphal cell wall layer was visualized by electron microscopy when hyphae were grown in the presence of copper and fixed by cryotechniques. This electron-dense layer was between the outer cell wall and the inner chitin layer and doubled the total wall thickness. In copper-grown cells that were also treated with tricyclazole, this electron-dense layer was absent. Atomic absorption spectroscopy demonstrated that up to 3.5 mg of Cu per g of fungal mycelium was adsorbed or taken up by hyphae grown in 0.06 mM CuSO(inf4). A method for silver enhancement was developed to determine the cellular location of CuS. CuS was present in cell walls and septa of copper-grown hyphae. Electron microscopy of silver-stained cells suggested that CuS was associated with the melanin layer of cell walls.
Automated Extraction Information System from HUDs Images Using ANN

In this paper, the recognition information in aircraft images of Head-Up Display (HUD) was made using artificial neural network (ANN) and a correlation algorithm. During the flight tests, the images displayed on the HUD could be stored for later analysis. HUD images presents many aircraft data provided by its avionics system (e.g. Altitude, feet, time). Therefore, HUD images are a primary source of information for most aircraft and pilots, especially in military missions. At IPEV (Flight Test" & Research Institute), the extraction of information from HUD images is performed manually, frame by frame, for later analysis. The big issue is that in one hour of flight test about 36,000 frames are generated. Therefore, data extraction becomes complex, time consuming and prone to failures. To reduce these problems, the IPEV developed an algorithm that load HUD images and then partitions the images in regions that were classified, recognized and converted into text by using ANN and a correlation algorithm. The development of the algorithm is presented in this paper.
Zinc intake and status in Australian vegetarians

Vegetarians have a lower incidence of many chronic diseases than omnivores. However, vegetarian diets could potentially result in lower intakes of some minerals, particularly Zn. In a cross-sectional study, dietary Zn intake was measured using 12 d weighed records in ninety-nine vegetarians (ten vegans) aged 18–50 years and forty-nine age- and sex-matched omnivores. In men, the mean daily Zn intake and Zn density values were similar in omnivores, ovolactovegetarians and vegans, but in women they were significantly lower in vegetarians (mean intake 6·8 mg v. 8·4 mg in omnivores) and few achieved the recommended intake. Significantly more vegetarian than omnivorous women had a daily Zn intake < 6 mg (44 % v. 13 %). Mean serum Zn concentrations were similar in female omnivores and vegetarians, despite the differences in intake. However, omnivorous men had a lower mean serum Zn concentration (0·85 μg/ml v. 0·95 μg/ml) and more subjects had levels below the reference range of 0·72–1·44 μg/ml than ovolactovegetarians (P < 0·01). Overall more women than men had low Zn concentrations; and these women generally had intakes below 6 mg/d. There was a significant correlation between serum Zn concentration and dietary Zn density in vegetarians, especially females (P < 0·001), but not in omnivores. Ovolactovegetarians did not have a significantly greater risk of low Zn status than omnivores.
Maasai pastoralists : diversification and poverty

Introduction Sub-Saharan African pastoralism involves highly fluid production systems responding flexibly to variable and unpredictable arid and semi arid rangeland environments. Consequently, a critical feature of the pastoral production system is access to extensive public land offering potential grazing and water resources that affords pastoralists the necessary flexibility to relocate their livestock when local rangelands fail. As such, increasingly restricted access to key resources of pasture, water and through-passage in East Africa has increased pastoralist vulnerability to drought herd loss and threatens the sustainability of the pastoral production system.
Digital Secure-Communication Using Robust Hyper-Chaotic Systems

In this paper, we propose a robust hyper-chaotic system that is suitable for digital secure-communication. The system consists of many coupled robust logistic maps that form a hyper-chaotic system. It has a higher degree of complexity than traditional discrete-time secure-communication systems that use only a single map. Moreover, the system has a very large parameter space which grows along with system precision. Hence, attacking the system by the method of map reconstruction in current computation technology is not feasible. Statistical analysis shows that the system achieves very high security level. Finally, two hardware architectures (multiple-cycle and pipelined) are proposed for area and performance optimization, respectively.
Plasmon Enhanced Photoconduction in Porphyrin-Gold Nanoparticle Assemblies

This thesis describes a series of experiments to both determine the origins of charge transport and enhanced photoconduction in metal nanoparticle arrays linked with zinc-porphyrin complexes, but to also determine the nucleation and growth mechanisms related to Ferroelectric Nanolithography (FNL) as a platform for hybrid devices. The development of test structures on glass substrates was undertaken to not only allow the study of the mechanisms controlling charge transport but the photoconduction of zinc-porphyrin linked gold nanoparticle (AuNP) arrays. In this study, the dominate charge transport mechanism was determined to be thermally assisted tunneling and the origins of enhanced photoconduction in these systems was attributed to three mechanisms: direct exciton formation in the molecules, hot electrons and a field effect (optical antenna) due to the excitation of surface plasmons. In the hope of developing a platform for hybrid devices, FNL was utilized to systematically vary the parameters that effect the deposition of metal nanoparticles through domain directed deposition on ferroelectric surfaces. The nucleation and growth mechanisms were determined through this work, where thevintegrated photon flux controlled the particle density and the interface between the particle and the ferroelectric surface determined the particles size. Finally, with the ability to control the deposition of AuNPs on a ferroelectric surface, hybrid devices of zinc-porphyrin linked AuNPs were realized with FNL. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Materials Science & Engineering First Advisor Dawn A. Bonnell
Underground Localization in 3-D Using Magneto-Inductive Tracking

Localization of mobile devices underground is extremely challenging, with radio propagation (such as used in GPS and VHF) severely attenuated by soil and moisture. However, low frequency magnetic fields are able to penetrate the ground with minimal loss. Mobile underground tracking devices record magnetic field strengths generated by an array of transmitting coils placed above the area of interest. This information is stored in flash memory, for opportunistic upload over a conventional radio link when the device is above ground. As a particular application of this technology, the underground movements of wild European badgers (Meles meles) were tracked in 3-D within their burrow systems, by equipping them with lightweight tracking collars. Typical localization accuracy is 0.45 m RMS over a 15 m × 15 m area and collar lifetime is of the order of 9 months from a 1.4 Ah lithium cell.
Haematological and biochemical toxicity induced by methanol in rats: Ameliorative effects of Opuntia vulgaris fruit extract

The ameliorative effects of Opuntia vulgaris fruit extract (OE) were evaluated against methanol-induced haematological and biochemical toxicity in rats. The methanol-induced haematological and biochemical perturbation significantly decreased the levels of red blood cell (RBC), haemoglobin (Hb), haematocrit (Ht), serum total protein and increased glucose, cholesterol, and triglyceride levels in serum. Treatment of rats with methanol significantly increased lipid peroxidation (LPO) level and decreased the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) in erythrocytes. OE treatment could increase significantly the levels of RBC, Hb, Ht and total protein, and decrease glucose, cholesterol and triglyceride levels in serum, and increase the activities of SOD, CAT and GPx in erythrocytes, when compared with methanol-treated group. Spleen histopathology showed that OE could significantly reduce the incidence of spleen lesion induced by methanol. These results suggested that OE could exhibit a potential source of natural antioxidants against methanol-induced haematological and biochemical disruption in rats. The protective effects of OE may be due to the modulation of antioxidant enzymes activities and inhibition of LPO.
Scene shape priors for superpixel segmentation

Unsupervised over-segmentation of an image into super-pixels is a common preprocessing step for image parsing algorithms. Superpixels are used as both regions of support for feature vectors and as a starting point for the final segmentation. In this paper we investigate incorporating a priori information into superpixel segmentations. We learn a probabilistic model that describes the spatial density of the object boundaries in the image. We then describe an over-segmentation algorithm that partitions this density roughly equally between superpixels whilst still attempting to capture local object boundaries. We demonstrate this approach using road scenes where objects in the center of the image tend to be more distant and smaller than those at the edge. We show that our algorithm successfully learns this foveated spatial distribution and can exploit this knowledge to improve the segmentation. Lastly, we introduce a new metric for evaluating vision labeling problems. We measure performance on a challenging real-world dataset and illustrate the limitations of conventional evaluation metrics.
Pax3
 GFP
 , a new reporter for the melanocyte lineage, highlights novel aspects of PAX3 expression in the skin

The paired box gene 3 (Pax3) is expressed during pigment cell development. We tested whether the targeted allele Pax3GFP can be used as a reporter gene for pigment cells in the mouse. We found that enhanced green fluorescent protein (GFP) can be seen readily in every melanoblast and melanocyte in the epidermis and hair follicles of Pax3GFP/+ heterozygotes. The GFP was detected at all differentiation stages, including melanocyte stem cells. In the dermis, Schwann cells and nestin‐positive cells of the piloneural collars resembling the nestin‐positive hair follicle multipotent stem cells exhibited a weaker GFP signal. Pigment cells could be purified by fluorescent activated cell sorting and grown in vitro without feeder cells, giving pure cultures of melanocytes. The Schwann cells and nestin‐positive cells of the piloneural collars were FACS‐isolated based on their weak expression of GFP. Thus Pax3GFP can discriminate distinct populations of cells in the skin.
Plasma levels of soluble thrombomodulin, C-reactive protein, and serum amyloid A protein in the atherosclerotic coronary circulation.

Plasma levels of C-reactive protein (CRP) and serum amyloid A protein (SAA), inflammatory markers, and soluble thrombomodulin (s-TM), a marker of endothelial damage. are thought to be related to coronary artery disease. However, the relationship between these inflammatory markers and endothelial injury in atherosclerotic coronary arteries is still unclear. Fifty-five patients who underwent coronary angiography were classified into 3 groups according to the severity of left coronary arterial atherosclerosis evaluated by the Gensini score (GS; normal: score = 0, n = 15; mild: 0 < score < 15, n = 29; severe: score > or = 15, n = 11). Blood samples were obtained from the aortic root (Ao) and coronary sinus (CS) and plasma CRP and SAA levels were measured by latex turbidimetric immunoassays, and s-TM levels were determined by an enzyme-linked immunosorbent assay. The difference between marker concentrations in the Ao and CS of the coronary circulation was expressed as the coronary sino-arterial (CS-Ao) difference. The CS-Ao differences of s-TM and SAA were significantly higher in patients with severe atherosclerosis than in normal patients (P < 0.01), and showed weak but significant positive correlations with the GS (r = 0.34, P < 0.01 and r = 0.33, P < 0.05, respectively). The CS-Ao differences in CRP did not differ among the three groups, and did not correlate with the GS. The results of our study reveal a possible relationship between endothelial cell injury and inflammation in atherosclerotic coronary arteries.
Periodontal Status amongst Substance Abusers in Indian Population

Background. In India there have been limited number of studies on periodontal status among drug addicts, and thus this study aims to assess the Oral hygiene and periodontal status in substance abusers and compare it with non-substance abusers. Methods. A comparative study was conducted to assess the periodontal status in substance abusers. Non-substance abusers were procured from the general population of Bangalore. From the control group 250 non-substance abusers were age and sex matched with the study population of substance abusers. The oral hygiene and periodontal condition of all subjects was assessed using Oral hygiene index- simplified (OHI-S), Russell's periodontal indices and Gingival bleeding index. Results. The mean of OHI-S and Periodontal Index (Russell's Index) scores were higher (2.70 and 3.68, resp.) in substance abusers than the control group (2.45 and 2.59, resp.). The mean Gingival bleeding score was lower (9.69) in substance abusers than the control group (22.7) and found to be statistically significant. A positive correlation found between OHI-S and Russell's periodontal index whereas negative correlation was found between OHI-S and Gingival bleeding in substance abusers. Conclusions. Though the oral hygiene was fair, more periodontal destruction and less of gingival bleeding were observed in substance abusers as compared to control group.
Stochastic inference with deterministic spiking neurons

The seemingly stochastic transient dynamics of neocortical circuits observed in vivo have been hypothesized to represent a signature of ongoing stochastic inference. In vitro neurons, on the other hand, exhibit a highly deterministic response to various types of stimulation. We show that an ensemble of deterministic leaky integrate-and-fire neurons embedded in a spiking noisy environment can attain the correct firing statistics in order to sample from a well-defined target distribution. We provide an analytical derivation of the activation function on the single cell level; for recurrent networks, we examine convergence towards stationarity in computer simulations and demonstrate sample-based Bayesian inference in a mixed graphical model. This establishes a rigorous link between deterministic neuron models and functional stochastic dynamics on the network level.
Identification of the epiplasmins, a new set of cortical proteins of the membrane cytoskeleton in Paramecium

In most ciliates, the epiplasm, a superficial cytoskeletal layer of variable thickness, both surrounds basal bodies and interacts tightly with adjacent membrane networks; it constitutes the predominant structure in Paramecium cell ghosts. Previous indirect data suggested several cortical proteins as potential constituents of the epiplasm. New sharp monoclonal antibodies presented in this paper, positive both on immunotransfers and in immunocytochemical tests carried out on permeabilized cells and ultrathin sections, definitively identify the epiplasmins: a set of about twenty protein bands ranging from 45 to 33 kDa and making up the bulk of the epiplasmic layer. The complete epiplasmin pattern characterized from gradient-purified cortex is also present in unfractionated whole cells, confirming that the pattern is not generated artifactually. Comparative one-step extractions, performed either in 1 M KI or in 4 M urea, solubilize the epiplasmins as a whole, indicating that all of them share very similar biochemical properties. Two-dimensional electrophoresis shows the great complexity of this epiplasmin group. Epiplasmin solubilization properties are discussed with respect to other models of membrane-cytoskeleton interaction developed among protists and metazoans and also to intermediate filaments, specially lamins. Immunofluorescent labelling combined with confocal microscopy permits a more detailed study of epiplasm formation at the level of the fission furrow, with new insights into two successive steps of epiplasm growth. A first series of interspecific reactions has been carried out with one of the anti- epiplasmin antibodies, yielding results which are discussed in an evolutionary framework.