Miracle-dz/UniFAR-FTUs huggingface dataset:
DACH1: Its Role as a Classifier of Long Term Good Prognosis in Luminal Breast Cancer

Background Oestrogen receptor (ER) positive (luminal) tumours account for the largest proportion of females with breast cancer. Theirs is a heterogeneous disease presenting clinical challenges in managing their treatment. Three main biological luminal groups have been identified but clinically these can be distilled into two prognostic groups in which Luminal A are accorded good prognosis and Luminal B correlate with poor prognosis. Further biomarkers are needed to attain classification consensus. Machine learning approaches like Artificial Neural Networks (ANNs) have been used for classification and identification of biomarkers in breast cancer using high throughput data. In this study, we have used an artificial neural network (ANN) approach to identify DACH1 as a candidate luminal marker and its role in predicting clinical outcome in breast cancer is assessed. Materials and methods A reiterative ANN approach incorporating a network inferencing algorithm was used to identify ER-associated biomarkers in a publically available cDNA microarray dataset. DACH1 was identified in having a strong influence on ER associated markers and a positive association with ER. Its clinical relevance in predicting breast cancer specific survival was investigated by statistically assessing protein expression levels after immunohistochemistry in a series of unselected breast cancers, formatted as a tissue microarray. Results Strong nuclear DACH1 staining is more prevalent in tubular and lobular breast cancer. Its expression correlated with ER-alpha positive tumours expressing PgR, epithelial cytokeratins (CK)18/19 and ‘luminal-like’ markers of good prognosis including FOXA1 and RERG (p<0.05). DACH1 is increased in patients showing longer cancer specific survival and disease free interval and reduced metastasis formation (p<0.001). Nuclear DACH1 showed a negative association with markers of aggressive growth and poor prognosis. Conclusion Nuclear DACH1 expression appears to be a Luminal A biomarker predictive of good prognosis, but is not independent of clinical stage, tumour size, NPI status or systemic therapy.
Natural SIV Hosts: Showing AIDS the Door

Lessons from SIV HIV infection in humans is a chronic infection and, if left untreated, the majority of infected individuals will succumb to AIDS. Many species of African nonhuman primates are chronically infected with simian immunodeficiency virus (SIV); however, in the majority of these species, the animals remain healthy despite the presence of high viral loads. Chahroudi et al. (p. 1188) review the underlying immune mechanisms that help protect natural hosts from progressing to AIDS and how these responses differ from what is observed in HIV-infected humans and SIV-infected nonhuman primate species that develop AIDS. Many species of African nonhuman primates are naturally infected with simian immunodeficiency viruses (SIVs) in the wild and in captivity. In contrast to HIV-infected humans, these natural SIV hosts typically do not develop AIDS, despite chronic infection with a highly replicating virus. In this Review, we discuss the most recent advances on the mechanisms of protection from disease progression in natural SIV hosts, with emphasis on how they differ from pathogenic HIV/SIV infections of humans and rhesus macaques. These mechanisms include: (i) resolution of immune activation after acute infection, (ii) restricted pattern of target cell infection, and (iii) protection from mother-to-infant transmission. We highlight the areas that should be pursued in future studies, focusing on potential applications for the treatment and prevention of HIV infection.
Not As Smart As We Think: A Study of Collective Intelligence in Virtual Groups

Abstract Organizations increasingly use virtual groups for many types of work, yet little research has examined factors that make groups perform better across multiple different types of tasks. Previous research has proposed that groups, like individuals, have a general factor of collective intelligence, an ability to perform consistently across multiple types of tasks. We studied groups that used computer-mediated communication (CMC) to investigate whether collective intelligence is similar or different when groups work using CMC. A collective intelligence factor did not emerge among groups using CMC, suggesting that collective intelligence manifests itself differently depending on context. This is in contrast to previous findings. Our results surface a need for more research on boundary conditions of the construct of collective intelligence. Our findings also have practical implications: managers should take care when organizing virtual group work because groups that perform well on one type of task will not necessarily be the groups that do well on other tasks
Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana

Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers in Arabidopsis thaliana reproductive development. Plants lacking the CHD3 remodeler, PICKLE, exhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube, as well as delayed progression of ovule and embryo development. Genetic analyses demonstrate that these phenotypes result from loss of PICKLE in the maternal sporophyte. The paralogous gene PICKLE RELATED 2 is preferentially expressed in the endosperm and acts antagonistically with respect to PICKLE in the seed: loss of PICKLE RELATED 2 suppresses the large seed phenotype of pickle seeds. Surprisingly, the alteration of seed size in pickle plants is sufficient to determine the expression of embryonic traits in the seedling primary root. These findings establish an important role for CHD3 remodelers in plant reproduction and highlight how the epigenetic status of one tissue can impact the development of genetically distinct tissues.
M ODELLING THE B EHAVIOUR OF THE S POT P RICES OF V ARIOUS T YPES OF C OFFEE

This paper investigates long-run relationships among the spot prices of four coffee types. We find two cointegrating vectors: one between the prices of Other Milds and Colombian coffee, and the other one between Unwashed Arabicas and Robustas. Following Pesaran and Shin (1996), persistence profile analysis of the two cointegrating vectors shows a rapid adjustment towards their equilibrium value. This suggests that the four coffee markets are highly related, and that discrepancies in the equilibrium relationships are short-lived. Out of sample evaluation of the model is reasonably good, except for two occasions of sharp price increases following adverse weather conditions.
The Reorientation of T-Cell Polarity and Inhibition of Immunological Synapse Formation by CD46 Involves Its Recruitment to Lipid Rafts

Many infectious agents utilize CD46 for infection of human cells, and therapeutic applications of CD46-binding viruses are now being explored. Besides mediating internalization to enable infection, binding to CD46 can directly alter immune function. In particular, ligation of CD46 by antibodies or by measles virus can prevent activation of T cells by altering T-cell polarity and consequently preventing the formation of an immunological synapse. Here, we define a mechanism by which CD46 reorients T-cell polarity to prevent T-cell receptor signaling in response to antigen presentation. We show that CD46 associates with lipid rafts upon ligation, and that this reduces recruitment of both lipid rafts and the microtubule organizing centre to the site of receptor cross-linking. These data combined indicate that polarization of T cells towards the site of CD46 ligation prevents formation of an immunological synapse, and this is associated with the ability of CD46 to recruit lipid rafts away from the site of TCR ligation.
The influence of inorganic nitrogen fertilizer forms on micronutrient retranslocation and accumulation in grains of winter wheat

The fortification of cereal grains with metal micronutrients is a major target to combat human malnutrition of Fe and Zn. Based on recent studies showing that N fertilization can promote Fe and Zn accumulation in cereal grains, we investigated here the influence of nitrate- or ammonium-based N fertilization on the accumulation of Fe, Zn, and Cu as well as metal chelator pools in flag leaves and grains of winter wheat. Fertilization with either N form increased the concentrations of N and of the metal chelator nicotianamine (NA) in green leaves, while 2'-deoxymugineic acid (DMA) remained unaffected. Despite the differential response to N fertilization of NA and DMA levels in flag leaves, N fertilization remained without any significant effect on the net export of these metals during flag leaf senescence, which accounted for approximately one third of the total Fe, Zn, or Cu content in leaves. The significant increase in the accumulation of Fe, Zn, and Cu found in the grains of primarily ammonium-fertilized plants was unrelated to the extent of metal retranslocation from flag leaves. These results indicate that an increased N nutritional status of flag leaves promotes the accumulation of Fe, Zn, and Cu in flag leaves, which is accompanied by an increased pool of NA but not of DMA. With regard to the far higher concentrations of DMA relative to NA in leaves and leaf exudates, DMA may be more relevant for the mobilization and retranslocation of these metals in high-yielding wheat production.
Effect of a polysaccharide-rich hydrolysate from Saccharomyces cerevisiae (LipiGo®) in body weight loss: randomised, double-blind, placebo-controlled clinical trial in overweight and obese adults.

BACKGROUND In the present study we evaluated the weight loss effect of a polysaccharide-rich food supplement, LipiGo®, comprising a specific β-glucan-chitin-chitosan fraction (BGCC) obtained from the chemical hydrolysis of Saccharomyces cerevisiae, resulting as a by-product of the brewing process. RESULTS A randomised, double-blind, placebo-controlled clinical trial was performed enrolling 56 overweight and obese subjects (body mass index, BMI, 25-35 kg m-2 ) who were not following any specific diet, and were given placebo or BGCC (3 g d-1 ) for 12 weeks. Results were analysed by intention-to-treat (ITT) and per-protocol (PP) methods. Body weight increased in the placebo group compared to baseline (ITT: 1.0 kg, P < 0.001; PP: 1.5 kg, P = 0.003), while it was slightly lowered in the BGCC group (ITT: -0.8 kg, P = 0.210; PP: -1.1 kg, P = 0.182). BGCC, but not the consumption of placebo, also resulted in a reduction of waist circumference and body fat compared to baseline. CONCLUSIONS Results suggest that daily supplementation of BGCC may be useful for improving body weight and waist circumference in overweight and obese subjects, without relevant adverse effects. © 2017 Society of Chemical Industry.
Accuracy of staging in primary biliary cirrhosis.

AIMS: To evaluate sampling variability of liver biopsy in patients with primary biliary cirrhosis (PBC). METHODS: Sections from 50 PBC liver specimens obtained at transplantation were examined. The degree of fibrosis was assessed on a scale of 0-4 using two methods: (1) simulated needle biopsy in fields approximately the size of conventional needle biopsy; and (2) whole section scanning in areas with little and extensive fibrosis. RESULTS: Considerable variation in the range of stages of fibrosis was found when the whole section scanning method was used. Only 10 (20%) samples had a consistent degree of fibrosis in all sections scanned. By contrast, the same fibrosis stage was assigned in 30 (60%) specimens examined using the simulated needle biopsy method. When the results obtained by the two methods were compared, there was a discrepancy of one or two stages in 32 samples. This discrepancy was the result of discovering areas with a lesser degree of fibrosis in whole sections compared with the simulated needle biopsy specimens. CONCLUSION: There is considerable variation in the degree of fibrosis in the livers of patients with PBC, even when end stage specimens obtained at transplantation are examined. Consistent results were obtained when simulated needle biopsy specimens were examined. This, however, may be a reflection of the procedure applied when staging liver needle biopsy specimens, where the greatest degree of abnormality is used in determining the stage. The practice of staging of PBC in small needle biopsy specimens is valuable as long as the appearances are interpreted with caution, bearing in mind that there is considerable variability in the degree of fibrosis.
Quorum sensing, virulence and secondary metabolite production in plant soft-rotting bacteria

Quorum sensing describes the ability of bacteria to sense their population density and respond by modulating gene expression. In the plant soft-rotting bacteria, such as Erwinia, an arsenal of plant cell wall-degrading enzymes is produced in a cell density-dependent manner, which causes maceration of plant tissue. However, quorum sensing is central not only to controlling the production of such destructive enzymes, but also to the control of a number of other virulence determinants and secondary metabolites. Erwinia synthesizes both N-acylhomoserine lactone (AHL) and autoinducer-2 types of quorum sensing signal, which both play a role in regulating gene expression in the phytopathogen. We review the models for AHL-based regulation of carbapenem antibiotic production in Erwinia. We also discuss the importance of quorum sensing in the production and secretion of virulence determinants by Erwinia, and its interplay with other regulatory systems.
Release of Markers of Myocardial Damage Evaluated in the Coronary Sinus During Cardiac Surgery

Myocardial damage is a frequent complication of cardiac surgery by direct mechanical trauma during the surgical procedure and by myocardial ischemia, which occurs during the cardiopulmonary bypass (CBP). Because the concentrations of biomarkers in the blood collected from the coronary sinus are the best witness of the myocardial damages, we measured the levels of specific cardiac troponin I (c-TnI) and nonspecific (adenosine, myoglobin) markers of left ventricular damages in the coronary sinus of patients during cardiac surgery. Thirty patients who underwent aortic valve replacement for aortic stenosis were included. Blood samples were collected in the coronary sinus and in the radial artery at the beginning (T0), at the end of the CBP (T1), and then 24 hours later (T2). At T0 and T1, adenosine, c-TnI, and myoglobin levels were significantly higher in the coronary sinus than in the radial artery (T0: adenosine: mean +27%; c-TnI: +41%; myoglobin: +28%; T1: adenosine: mean +58%; c-TnI: +58%; myoglobin: +25%; p < .001). These parameters were significantly higher in the coronary sinus at T1 compared with T0 (adenosine: +50%; c-TnI: +229%; myoglobin: +94%; p < .01) and in the radial artery (adenosine: +21%; c-TnI: +194%; myoglobin: +98%; p < .01). At T2, c-TnI further increased. Damages to the myocardium during cardiac surgery are minimal in our surgical conditions but are probably underestimated when using markers measured at the peripheral level. However, most of the damages appear several hours after the surgery.
Herbal medicines supplied by community pharmacies in Lagos, Nigeria: pharmacists’ knowledge

Background The use of herbal medicines is on the increase globally and they are usually supplied in pharmacies as non-prescription medicines. Pharmacists are, therefore, responsible for educating and informing the consumers about rational use of herbal medicines. Objective To evaluate the knowledge of pharmacists in Lagos, Nigeria with regards to the herbal medicines they supplied by their pharmacies. Methods Pharmacists in charge of randomly selected 140 community pharmacies from 20 Local Government Areas in Lagos were required to fill out a self-administered questionnaire. We gathered information on their knowledge of the indications, adverse effects, potential drug-herb interactions and contraindications of the herbal medicines they supply in their pharmacies. Results Of the 140 questionnaires distributed, 103 (72.9%) participants completed the questionnaire appropriately. The majority (74; 71.8%) of the participants were males and 36-50 years (56; 54.4%). The pharmacies supplied mostly Yoyo cleanser bitters® (101; 98.5%), ginseng (97; 98.5%), Jobelyn® (91; 88.3%), Ciklavit® (68; 66.6%), gingko (66; 64.1%), herbal tea (66; 64.1%), and Aloe vera (57; 55.3%). The pharmacists self-rated their knowledge of herbal medicines mostly as fair (39%) and good (42%), but they exhibited poor knowledge with regards to the indications, contraindications and safety profiles. Seventy participants consulted reference materials such as leaflet insert in the herbal medicines (56%) and internet (20%) before supplying herbal medicines. The information most frequently sought was herb-drug interactions (85%), contraindications (75%) and adverse effects (70%). Conclusions Community pharmacists need to be informed about the indications and safety profiles of herbal medicines.
Toward More Powerful Recombinations

This paper suggests a exible framework for n-dimensional crossover, consisting of cutting, classi cation, and copying of genes. We prove that under this framework, any cutting strategy generates two equivalence classes of genes, making the framework appropriate as a crossover scheme. Three notable features of this framework are: (i) it enables more e ective use of genes' geographical linkage, (ii) it enables more diverse ways of cutting than traditional multi-point crossover on linear strings or existing 2-dimensional crossover schemes, and (iii) it can be readily used within most existing genetic algorithm implementations, i.e., the underlying problem need not be inherently multidimensional. We provide guidelines for designing a crossover strategy under this framework, along with two example crossovers. Experimental results show that one can design new crossovers under this framework which outperform traditional crossover on linear strings, uniform crossover, and existing two-dimensional crossovers.
Verification-based decoding for packet-based low-density parity-check codes

We introduce and analyze verification-based decoding for low-density parity-check (LDPC) codes, an approach specifically designed to manipulate data in packet-sized units. Verification-based decoding requires only linear time for both encoding and decoding and succeeds with high probability under random errors. We describe how to utilize code scrambling to extend our results to channels with errors controlled by an oblivious adversary.
CXCL4 and CXCL10 Predict Risk of Fatal Cerebral Malaria

Plasmodium falciparum in a subset of patients can lead to a diffuse encephalopathy known as cerebral malaria (CM). Despite treatment, mortality caused by CM can be as high as 30% while 10% of survivors of the disease may experience short- and long-term neurological complications. The pathogenesis of CM involves alterations in cytokine and chemokine expression, local inflammation, vascular injury and repair processes. These diverse factors have limited the rate of discovery of prognostic predictors of fatal CM. Identification of reliable early predictors of CM severity will enable clinicians to adjust this risk with appropriate management of CM. Recent studies revealed that elevated levels of CXCL10 expression in cerebrospinal fluid and peripheral blood plasma independently predicted severe and fatal CM. CXCR3, a promiscuous receptor of CXCL10, plays an important role in pathogenesis of mouse model of CM. In this study the role of corresponding CXCR3 ligands (CXCL11, CXCL10, CXCL9 & CXCL4) in fatal or severe CM was evaluated by comparing their levels in 16 healthy control (HC), 26 mild malaria (MM), 26 cerebral malaria survivors (CMS) and 12 non-survivors (CMNS) using enzyme linked immunosorbent assay (ELISA). Levels of CXCL4 and CXCL10 were significantly elevated in CMNS patients (p < 0.05) when compared with HC, MM and CMS. Elevated plasma levels of CXCL10 and CXCL4 were tightly associated with CM mortality. Receiver Operating Characteristic (ROC) curve analysis revealed that CXCL4 and CXCL10 can discriminate CMNS from MM (p < 0.0001) and CMS (p < 0.0001) with an area under the curve (AUC) = 1. These results suggest that CXCL4 and CXCL10 play a prominent role in pathogenesis of CM associated death and may be used as functional or surrogate biomarkers for predicting CM severity.
Stable Throughput of Cognitive Radios With and Without Relaying Capability

A scenario with two single-user links, one licensed to use the spectral resource (primary) and one unlicensed (secondary or cognitive), is considered. According to the cognitive radio principle, the activity of the secondary link is required not to interfere with the performance of the primary. Therefore, in this paper, it is assumed that the cognitive link accesses the channel only when sensed idle. Moreover, the analysis includes: (1) random packet arrivals; (2) sensing errors due to fading at the secondary link; (3) power allocation at the secondary transmitter based on long-term measurements. In this framework, the maximum stable throughput of the cognitive link (in packets/slot) is derived for a fixed throughput selected by the primary link. The model is modified so as to allow the secondary transmitter to act as a ldquotransparentrdquo relay for the primary link. In particular, packets that are not received correctly by the intended destination might be decoded successfully by the secondary transmitter. The latter can, then, queue and forward these packets to the intended receiver. A stable throughput of the secondary link with relaying is derived under the same conditions as before. Results show that benefits of relaying strongly depend on the topology (i.e., average channel powers) of the network.
Use of 2-aminoacetophenone production in identification of Pseudomonas aeruginosa

A grapelike odor is often of diagnostic importance in detecting the growth of Pseudomonas aeruginosa in culture and in burn wounds. The compound responsible for the odor has been identified as 2-aminoacetophenone by mass spectroscopy. Although the grape odor is sometimes difficult to detect in culture media, gas chromatographic, fluorometric, and colorimetric methods can be utilized to assay 2-aminoacetophenone production in a variety of media. Its synthesis occurs relatively early in the growth cycle. It has proved easy and convenient to detect 2-aminoacetophenone excretion by P. aeruginosa after 24 h of incubation on blood agar plates employing a fluorometric assay of ether extracts of the agar medium.