Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of superoxide dismutases and NAD(P)H quinone oxidoreductases with prognosis of patients with breast carcinomas

Associations of transcript levels of oxidative stress‐modifying genes SOD2, SOD3, NQO1 and NQO2 and their functional single nucleotide polymorphisms (SNPs) rs4880, rs1799895, rs2536512, rs699473, rs1800566 and rs1143684 with prognosis of breast cancer patients were studied. SNPs were assessed by allelic discrimination in a cohort of 321 breast cancer patients from the Czech Republic. Transcript levels were determined by real‐time polymerase chain reaction (PCR) with absolute quantification in tumor and adjacent non‐neoplastic control tissues. Both genotypes and transcript levels were then compared with available clinical data on patients. Patients carrying low activity allele Leu in NQO2 rs1143684 had a greater incidence of stage 0 or I disease (i.e., better prognosis) than patients with the Phe/Phe genotype. This association was more evident in patients without expression of progesterone receptors (p = 0.031). Patients carrying the Thr allele in SOD3 rs2536512 SNP had a significantly greater incidence of tumors expressing estrogen receptors than patients carrying the Ala/Ala genotype (p = 0.007). SOD3 transcript level was significantly higher in grade 1 or 2 tumors than in grade 3 tumors (p = 0.006). Patients carrying T allele in SOD3 rs699473 SNP had significantly poorer progression‐free survival (PFS) than patients carrying the CC genotype (p = 0.038). The same applied to the subgroup of patients treated by hormonal regimens (p = 0.021). Patients carrying the high activity Ala/Ala genotype in SOD2 (rs4880) had significantly poorer PFS than Val allele carriers in the group treated by cyclophosphamide but not hormonal regimens (p = 0.004). Our results suggest that NQO2, SOD2 and SOD3 may significantly modify prognosis of breast cancer patients and that their significance should be further characterized.
3D Shape Analysis of Powder for Laser Beam Melting by Synchrotron X-ray CT

The quality of components made by laser beam melting (LBM) additive manufacturing is naturally influenced by the quality of the powder bed. A packing density <1 and porosity inside the powder particles lead to intrinsic voids in the powder bed. Since the packing density is determined by the particle size and shape distribution, the determination of these properties is of significant interest to assess the printing process. In this work, the size and shape distribution, the amount of the particle’s intrinsic porosity, as well as the packing density of micrometric powder used for LBM, have been investigated by means of synchrotron X-ray computed tomography (CT). Two different powder batches were investigated: Ti–6Al–4V produced by plasma atomization and stainless steel 316L produced by gas atomization. Plasma atomization particles were observed to be more spherical in terms of the mean anisotropy compared to particles produced by gas atomization. The two kinds of particles were comparable in size according to the equivalent diameter. The packing density was lower (i.e., the powder bed contained more voids in between particles) for the Ti–6Al–4V particles. The comparison of the tomographic results with laser diffraction, as another particle size measurement technique, proved to be in agreement.
ExsD Inhibits Expression of the Pseudomonas aeruginosa Type III Secretion System by Disrupting ExsA Self-Association and DNA Binding Activity

ABSTRACT Pseudomonas aeruginosa utilizes a type III secretion system (T3SS) to damage eukaryotic host cells and evade phagocytosis. Transcription of the T3SS regulon is controlled by ExsA, a member of the AraC/XylS family of transcriptional regulators. ExsA-dependent transcription is coupled to type III secretory activity through a cascade of three interacting proteins (ExsC, ExsD, and ExsE). Genetic data suggest that ExsD functions as an antiactivator by preventing ExsA-dependent transcription, ExsC functions as an anti-antiactivator by binding to and inhibiting ExsD, and ExsE binds to and inhibits ExsC. T3SS gene expression is activated in response to low-calcium growth conditions or contact with host cells, both of which trigger secretion of ExsE. In the present study we reconstitute the T3SS regulatory cascade in vitro using purified components and find that the ExsD·ExsA complex lacks DNA binding activity. As predicted by the genetic data, ExsC addition dissociates the ExsD·ExsA complex through formation of an ExsD·ExsC complex, thereby releasing ExsA to bind T3SS promoters and activate transcription. Addition of ExsE to the purified system results in formation of the ExsE·ExsC complex and prevents ExsC from dissociating the ExsD·ExsA complex. Although purified ExsA is monomeric in solution, bacterial two-hybrid analyses demonstrate that ExsA can self-associate and that ExsD inhibits self-association of ExsA. Based on these data we propose a model in which ExsD regulates ExsA-dependent transcription by inhibiting the DNA-binding and self-association properties of ExsA.
Aspect-oriented programming

Aspect-Oriented Programming (AOP) aims at modularising cross-cutting concerns that show up in software. The success of AOP has been almost viral and nearly all areas in Software Engineering and Programming Languages have become “infected” by the AOP bug in one way or another. Interestingly the functional programming community (and, in particular, the pure functional programming community) seems to be resistant to the pandemic. The goal of this paper is to debate the possible causes of the functional programming community’s resistance and to raise awareness and interest by showcasing the beneﬁts that could be gained from having a functional AOP language. At the same time, we identify the main challenges and explore the possible design-space.
Subdivision schemes for fluid flow

The motion of fluids has been a topic of study for hundreds of years. In its most general setting, fluid flow is governed by a system of non-linear partial differential equations known as the Navier-Stokes equations. However, in several important settings, these equations degenerate into simpler systems of linear partial differential equations. This paper will show that flows corresponding to these linear equations can be modeled using subdivision schemes for vector fields. Given an initial, coarse vector field, these schemes generate an increasingly dense sequence of vector fields. The limit of this sequence is a continuous vector field defining a flow that follows the initial vector field. The beauty of this approach is that realistic flows can now be modeled and manipulated in real time using their associated subdivision schemes. CR Categories: I.3. 5 [Computer Graphics]: Computational Geometry and Object Modeling— Physically based modeling; I.6. 5 [Simulation and Modeling]: Model Development—Modeling Methodologies
Journal of Economic Behavior & Organization Conflict, Settlement, and the Shadow of the Future

JEL classification: C72 C91 D74 H1 H56 Keywords: War Settlement Property rights Shadow of the future a b s t r a c t We examine a conflictual setting in which adversaries cannot contract on an enforcement variable (arms) and where the future strategic positions of adversaries are very different when there is open conflict than when there is settlement. We show that, as the future becomes more important in this setting, open conflict becomes more likely than settlement. We demonstrate the theoretical robustness of this finding and test it in a laboratory experiment. As predicted, we find that subjects are more likely to engage in destructive conflict as the future becomes more important. " Efforts to maintain collective security are at the heart of human history. Yet, insecurity not only remains, it has become a primary development challenge of our time.
Antioxidant, anti-inflammatory, and antiproliferative activities of organic fractions from the Mediterranean brown seaweed Cystoseira sedoides.

The present study was conducted to evaluate the antioxidant, anti-inflammatory, and antiproliferative activities of organic fractions from Cystoseira sedoides (Desfontaines) C. Agardh . Various fractions of C. sedoides (chloroform (F-CHCl3), ethyl acetate (F-AcOEt), and methanol (F-MeOH)) were screened for total phenol content, as well as antioxidant activity, using the stable radical 1,1-diphenyl-2-picrylhydrazyl (DPPH), and assays for determining the reducing power of these fractions. The anti-inflammatory properties of these fractions were assessed using the carrageenan-induced rat paw oedema model. The antiproliferative activity of C. sedoides fractions was evaluated on normal Madin-Darby canine kiney (MDCK), and fibroblast cells and on cancer cell lines (A549, MCF7, and HCT15), using the ability of the cells to metabolically reduce 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) formazan dyes. The F-CHCl3 and F-AcOEt fractions showed significant total phenolic content at 55.09 and 61.30 mg gallic-acid equivalent/g dried sample, respectively. Using the DPPH method, the F-CHCl3 and the F-AcOEt fractions exhibited the strongest radical scavenging activity, with IC50 120 µg/mL for F-CHCl3 and 121 µg/mL for F-AcOEt, which approaches the activity of the powerful antioxidant standard, Trolox (IC50 = 90 µg/mL). The reducing power of the samples was in the following order: F-AcOEt > F-CHCl3 > F-MeOH fraction. The F-CHCl3 and F-AcOEt fractions of C. sedoides tested at different doses (25 and 50 mg/kg, intraperitoneally (i.p)), exhibited a dose-dependent reduction of rat paw oedema. The percentage of inhibition of oedema, 3 h after carrageenan injection, ranged from 67.71% to 73.49% and from 67.74% to 74.58%, for F-CHCl3 and F-AcOEt, respectively. Their effects are comparable with that of lysine acetylsalicylate (300 mg/kg body mass; i.p.), which is used as a reference drug with the ability to inhibit oedema by 66.14%. Our results revealed that the F-CHCl3 and F-AcOEt fractions from C. sedoides showed important antiproliferative properties towards all of the cancer cell lines studied here, as judged by their IC50 values, which ranged from 52.6 to 66.5 µg/mL for A549; 22.4 to 70.2 µg/mL for MCF7, and 250.6 to 255.3 µg/mL for HCT15. Moreover, no visible destruction or alteration of normal cells was observed, even at 500 µg/mL F-CHCl3 or F-AcOEt. These results suggest that C. sedoides fractions might be used as a potential source of natural antioxidant, anti-inflammatory, and antitumor agents. The purification and determination of the chemical structures of the compounds in these active fractions are under investigation. The results could provide a compound(s) with a promising role in future medicines and nutrition, when used either as a drug or a dietary supplement.
Head and neck adaptive radiotherapy: Predicting the time to replan

Head and neck (H&N) cancer patients can undergo anatomical change throughout radiotherapy treatment. Adaptive radiotherapy (ART) is effective in addressing the impact of this change on the planned dose distribution. The aim of this study was to identify pretreatment factors that influence the need for and timing of replanning for patients receiving chemoradiotherapy for node‐positive nasopharyngeal (NPC) and oropharyngeal carcinoma (OPC).
Attending to Characters in Neural Sequence Labeling Models

Sequence labeling architectures use word embeddings for capturing similarity, but suffer when handling previously unseen or rare words. We investigate character-level extensions to such models and propose a novel architecture for combining alternative word representations. By using an attention mechanism, the model is able to dynamically decide how much information to use from a word- or character-level component. We evaluated different architectures on a range of sequence labeling datasets, and character-level extensions were found to improve performance on every benchmark. In addition, the proposed attention-based architecture delivered the best results even with a smaller number of trainable parameters.
Structural subtyping and the notion of power type

data types; if it is a kind, the instances of abstract types are second-class values, as it happens in most module systems. Eliminating the distinctions between types and kinds through Type:Type, also indirectly confuses the distinctions between values and types. For example consider the program f = fun(A:Type) fun(x:A) x, and try and answer the question "is x a value? ", or "is the result of f a value? ". This cannot be determined, because the following applications are both legal: f(Integer)(3) and f(Type)(Integer). This mixing of value and type levels becomes a considerable obstacle when considering compiled languages, or languages extended with imperative features, which must make a clear distinction between compile-time and run-time phases. In such cases, one should at least make a proper distinction between types and kinds, or otherwise stratify the system in order to eliminate Type:Type. Unfortunately, the confusion between compile-time and run-time phases can be caused by dependent types alone, even without Type:Type. This is because of the All Elimination rule, where B{x←a} requires an arbitrary term (possibly a run-time value) to be substituted inside a (compile-time) type.
A novel noninvasive genotyping method of Helicobacter pylori using stool specimens.

BACKGROUND & AIMS The source(s) of the infection and the route(s) of transmission of Helicobacter pylori have not yet been clarified. This is to introduce a noninvasive protocol allowing molecular typing of H pylori using stool specimens. METHODS The genotyping method is based on 2 H pylori-specific biprobe real-time polymerase chain reaction assays using fragments of the glmM and the recA genes as target sequences. Discrimination between strains results from differences in the melting temperature during melting curve analysis. In case of identical melting temperatures in both assays, sequence analysis of the glmM amplicon was performed to confirm strain identity. The method was validated using gastric biopsy specimens and stool specimens of 97 unrelated individuals suffering from abdominal pain and stool specimens of members of 10 families in Austria (infected index child and family members) and 8 African households. RESULTS Of the 97 patients, 27 were infected as shown by culture, histology, and rapid urease test. The sensitivity of each of the assays was 100% in gastric biopsy specimens and 92.2% in stool specimens; the specificity was 100%. The discriminatory capacity of the method was 100%. Clonal identities were found in 9 of 10 (90%) European and 7 of 8 (87.5%) African households. In 2 African households, 2 different clonal lineages each were found. CONCLUSIONS The genotyping protocol introduced allows for both accurate detection and discrimination of H pylori strains in stool samples. Large-scale studies using this protocol may contribute to the clarification of the transmission pathways of infection with H pylori.
Photocatalytic degradation of alizarin red dye in aqueous solution using titania-nickel and titania-cobalt nanocomposites

Titanium dioxide (TiO 2 ) was prepared by Sol-gel method which involved hydrolysis of Titanium trichloride (TiCl 3 ) with concentrated hydrochloric acid and oxidation by hydrogen peroxide. Doping of the TiO 2 was effected at 10% Ni-TiO 2 and 10% Co-TiO 2 using aqueous solutions of nickel nitrate and cobalt nitrate respectively. Characterization by X-ray Diffraction Crystallography (XRD) and Scanning Electron Microscopy (SEM) showed that the surface area and crystallinity of TiO 2 increased through doping. The XRD and SEM data confirmed the observed increase in the photocatalytic activities of the doped versus the undoped TiO 2 photocatalysts. Photocatalytic activities of both the doped and undoped TiO 2 was investigated on the photodegradation of Alizarin red dye. With a constant dye concentration of 25 ppm and temperature of 40 o C, it was observed that for all varying concentrations except 0.25 g/l of catalyst at 240 mins, the percentage degradation was of the order TiO 2 < Co-TiO 2 < Ni-TiO 2 . At the 0.25 g/l concentration of catalyst at 240 mins, the photocatalytic activities of the Ni-TiO 2 and Co-TiO 2 were observed respectively to be about 9 times and 12 times that of the TiO 2 . Keywords: Titanium dioxide, titania-nickel, titania-cobalt,alizarin red and photocatalysts
Epidemiological Survey of Listeria monocytogenes in a gravlax salmon processing line

Listeria monocytogenes is a cause of concern to food industries, mainly for those producing ready-to-eat (RTE) products. This microorganism can survive processing steps such as curing and cold smoking and is capable of growing under refrigeration temperatures. Its presence in RTE fish products with extended shelf life may be a risk to the susceptible population. One example of such a product is gravlax salmon; a refrigerated fish product not exposed to listericidal processes and was the subject of this study. In order to evaluate the incidence and dissemination of L. monocytogenes 415 samples were collected at different steps of a gravlax salmon processing line in São Paulo state, Brazil. L. monocytogenes was confirmed in salmon samples (41%), food contact surfaces (32%), non-food contact surfaces (43%) and of food handlers’ samples (34%), but could not be detected in any ingredient. 179 L. monocytogenes isolates randomly selected were serogrouped and typed by PFGE. Most of L. monocytogenes strains belonged to serogroup 1 (73%). 61 combined pulsotypes were found and a dendrogram identified six clusters: most of the strains (120) belonged to cluster A. It was suggested that strains arriving into the plant via raw material could establish themselves in the processing environment contaminating the final product. The wide dissemination of L. monocytogenes in this plant indicates that a great effort has to be taken to eliminate the microorganism from these premises, even though it was not observed multiplication of the microorganism in the final product stored at 4°C up to 90 days.
Foot kinematics during a bilateral heel rise test in participants with stage II posterior tibial tendon dysfunction.

STUDY DESIGN Experimental laboratory study using a cross-sectional design. OBJECTIVES To compare foot kinematics, using 3-dimensional tracking methods, during a bilateral heel rise between participants with posterior tibial tendon dysfunction (PTTD) and participants with a normal medial longitudinal arch (MLA). BACKGROUND The bilateral heel rise test is commonly used to assess patients with PTTD; however, information about foot kinematics during the test is lacking. METHODS Forty-five individuals volunteered to participate, including 30 patients diagnosed with unilateral stage II PTTD (mean +/- SD age, 59.8 +/- 11.1 years; body mass index, 29.9 +/- 4.8 kg/m2) and 15 controls (mean +/- SD age, 56.5 +/- 7.7 years; body mass index, 30.6 +/- 3.6 kg/m2). Foot kinematic data were collected during a bilateral heel rise task from the calcaneus (hindfoot), first metatarsal, and hallux, using an Optotrak motion analysis system and Motion Monitor software. A 2-way mixed-effects analysis of variance model, with normalized heel height as a covariate, was used to test for significant differences between the normal MLA and PTTD groups. RESULTS The patients in the PTTD group exhibited significantly greater ankle plantar flexion (mean difference between groups, 7.3 degrees ; 95% confidence interval [CI]: 5.1 degrees to 9.5 degrees ), greater first metatarsal dorsiflexion (mean difference between groups, 9.0 degrees ; 95% CI: 3.7 degrees to 14.4 degrees ), and less hallux dorsiflexion (mean difference, 6.7 degrees ; 95% CI: 1.7 degrees to 11.8 degrees ) compared to controls. At peak heel rise, hindfoot inversion was similar (P = .130) between the PTTD and control groups. CONCLUSION Except for hindfoot eversion/inversion, the differences in foot kinematics in participants with stage II PTTD, when compared to the control group, mainly occur as an offset, not an alteration in shape, of the kinematic patterns.
Annals of the New York Academy of Sciences Orbitofrontal Contributions to Value-based Decision Making: Evidence from Humans with Frontal Lobe Damage Is Economic Value Represented in the Brain?

The work described here aims to isolate the component processes of decision making that rely critically on particular subregions of the human prefrontal cortex, with a particular focus on the orbitofrontal cortex. Here, experiments isolating specific aspects of decision making, using very simple preference judgment and reinforcement learning paradigms, were carried out in patients with focal frontal damage. The orbitofrontal cortex and the adjacent ventro-medial prefrontal cortex play a critical role in decisions based on subjective value, across many categories of stimuli, and in learning to choose between stimuli based on value feedback. However, these regions are not required for learning to choose between actions based on feedback, which instead seems to rely critically on the dorsomedial prefrontal cortex. These results point to a potentially common role for the orbitofrontal cortex in representing the context-sensitive, subjective value of stimuli to allow consistent choices between them. They also argue for multiple, parallel, value-based processes that influence behavior through dissociable mechanisms. Decision making: a novel window on the human brain Life is full of choices, large and small. Making the best of our environment involves determining the value of the possibilities that the environment presents, and acting to obtain those with more value. Effective decision making will confer an adaptive advantage, and it is thus likely that the brain is organized to ensure optimal decisions. This may be particularly true for decisions about primary goods like food, water, or mating opportunities but probably applies quite generally to the more abstract choices that are also part of everyday human experience. Viewing human behavior through the lens of decision making provides an interesting perspective for cognitive neuroscience that has led to novel insights about the functional organization of the brain. This vantage point leads to a series of basic questions: how is value abstracted from environmental information, how is it represented in the brain, and how do these representations influence behavior? Over the last several years, progress in answering these questions has come from two directions: the first has been to build on an extensive literature on reinforcement learning in animals, and the second to combine analytic models and behavioral paradigms drawn from economics and decision psychology with cognitive neuroscience methods. This volume as a whole showcases these different approaches. Here, I will review work based on both of these frameworks applied in human subjects with focal brain injury. Figure 1 provides a general …