Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecosystem services and land sparing potential of urban and peri-urban agriculture: A review

Abstract Agricultural expansion contributes to the degradation of biodiverse ecosystems and the services these systems provide. Expansion of urban and peri-urban agriculture (UPA), on the other hand, may hold promise to both expand the portfolio of ecosystem services (ES) available in built environments, where ES are typically low and to reduce pressure to convert sensitive non-urban, non-agricultural ecosystems to agriculture. However, few data are available to support these hypotheses. Here we review and summarize the research conducted on UPA from 320 peer-reviewed papers published between 2000 and 2014. Specifically, we explored the availability of data regarding UPA's impact on ES and disservices. We also assessed the literature for evidence that UPA can contribute to land sparing. We find that the growth in UPA research over this time period points to the emerging recognition of the potential role that UPA systems play in food production worldwide. However, few studies (n = 15) place UPA in the context of ES, and no studies in our review explicitly quantify the land sparing potential of UPA. Additionally, while few studies (n = 19) quantify production potential of UPA, data that are necessary to accurately quantify the role these systems can play in land sparing, our rough estimates suggest that agricultural extensification into the world's urban environments via UPA could spare an area approximately twice the size of the US state of Massachusetts. Expanding future UPA research to include quantification of ES and functions would shed light on the ecological tradeoffs associated with agricultural production in the built environment. As food demand increases and urban populations continue to grow, it will be critical to better understand the role urban environments can play in global agricultural production and ecosystem preservation.
Assessment of sleep‐disordered breathing using a non‐contact bio‐motion sensor

Obstructive sleep apnoea is a highly prevalent but under‐diagnosed disorder. The gold standard for diagnosis of obstructive sleep apnoea is inpatient polysomnography. This is resource intensive and inconvenient for the patient, and the development of ambulatory diagnostic modalities has been identified as a key research priority. SleepMinder (BiancaMed, NovaUCD, Ireland) is a novel, non‐contact, bedside sensor, which uses radio‐waves to measure respiration and movement. Previous studies have shown it to be effective in measuring sleep and respiration. We sought to assess its utility in the diagnosis of obstructive sleep apnoea. SleepMinder and polysomnographic assessment of sleep‐disordered breathing were performed simultaneously on consecutive subjects recruited prospectively from our sleep clinic. We assessed the diagnostic accuracy of SleepMinder in identifying obstructive sleep apnoea, and how SleepMinder assessment of the apnoea–hypopnoea index correlated with polysomnography. Seventy‐four subjects were recruited. The apnoea–hypopnoea index as measured by SleepMinder correlated strongly with polysomnographic measurement (r = 0.90; P ≤ 0.0001). When a diagnostic threshold of moderate–severe (apnoea–hypopnoea index ≥15 events h−1) obstructive sleep apnoea was used, SleepMinder displayed a sensitivity of 90%, a specificity of 92% and an accuracy of 91% in the diagnosis of sleep‐disordered breathing. The area under the curve for the receiver operator characteristic was 0.97. SleepMinder correctly classified obstructive sleep apnoea severity in the majority of cases, with only one case different from equivalent polysomnography by more than one diagnostic class. We conclude that in an unselected clinical population undergoing investigation for suspected obstructive sleep apnoea, SleepMinder measurement of sleep‐disordered breathing correlates significantly with polysomnography.
Different effects of exercise and edema on T2 relaxation in skeletal muscle

The hypothesis that increased muscle T2 after exercise is caused by increased extracellular fluid volume was tested by comparing the effects of exercise versus external leg negative pressure on muscle T2 relaxation in normal human subjects. T2 in lower leg muscles was measured by echo‐planar imaging at 63 echo times from 24 to 272 ms, and the relaxation spectrum was calculated by using a non‐negative least squares algorithm. T2 relaxation in anterior leg muscle before exercise was characterized by a single component with mean T2 = 29.3 ± 0.7 (SE, n = 5). After ankle dorsiflexion exercise, this single component broadened, and mean T2 increased to 38.3 ± 0.7 ms. In contrast, after leg negative pressure, which increased the total leg muscle cross‐sectional area by 21% (range 12–32% n = 6), there was a variable appearance of much slower‐relaxing components (60–500 ms). The results suggest that increased extracellular fluid can account for only a minor portion of the increase in muscle T2 observed during exercise.
Control of polygalacturonase synthesis in Fusarium oxysporum f.sp. radicis lycopersici.

Genetic control of polygalacturonase (PG) activity from Fusarium oxysporum f.sp. radicis lycopersici was analyzed on pectin and glucose cultures. One exopolygalacturonase from F. oxysporum f.sp. radicis lycopersici was strongly induced, in stationary culture, when the fungus was grown on apple pectin, while on glucose no extracellular PG activity could be detected. Although SDS-PAGE detected the presence of a putative PG band (66 kDa) in both conditions, specific antibodies obtained against the purified PG only detected it in PG-inducing conditions, that is to say, when apple pectin was used as the carbon source. Northern blot analysis of RNA of two isolates of F. oxysporum f.sp. radicis lycopersici (r6 and r2) confirmed that this regulation of PG synthesis was exerted at the transcriptional level. Only one single mRNA species of around 1400 nucleotides was detected on the cultures containing pectin and was absent in glucose-grown cultures. Southern blot analysis of genomic DNA indicated that pg gene seems to be present in a single copy in the genomes of F. oxysporum f.sp. radicis lycopersici r6 and r2 and Fusarium oxysporum f.sp. lycopersici, showing similar hybridization patterns in all species. The partial sequence of this pg gene from F. oxysporum f.sp. radicis lycopersici r6, which is also reported, showed high similarity to diverse PGs already reported. Exopolygalacturonase of F. oxysporum f.sp. radicis lycopersici r6 is heavily glycosylated; its deglycosylated form had a molecular mass of 50 kDa.
Ventricular dysfunction in a family with long QT syndrome type 3.

AIMS Long QT syndrome (LQTS) type 3 is characterized by prolonged ventricular repolarization due to persistent sodium inward current secondary to a mutation in SCN5a, the gene encoding for the α-subunit of the sodium channel. We speculated that by disrupting calcium homeostasis the persistent inward sodium current in patients with LQTS type 3 might cause derangement of diastolic function. We aimed to identify functional myocardial alterations in a family with a sodium channelopathy with a phenotype of both LQTS type 3 and Brugada syndrome. METHODS AND RESULTS The study group comprised 12 SCN5a mutation carriers (SCN5a-1795insD), 9 females and 3 males, mean age 35.7 ± 7.3 years, and 12 healthy controls. In addition to conventional echocardiographic measurements, two-dimensional speckle tracking was performed to assess tissue properties. Mean e' was lower in the patients compared with the controls (5.6 ± 0.75 vs. 6.7 ± 0.98 cm/s, P = 0.006). Onset QRS to maximum s' was longer in the patients than in the controls (0.20 ± 0.04 vs. 0.15 ± 0.05 s, P = 0.007), and the number of segments with post-systolic shortening was higher (6.58 ± 2.54 vs. 1.83 ± 1.64, P < 0.001). CONCLUSION Patients in this family with LQTS type 3 showed post-systolic shortening, as well as both left and right ventricular diastolic dysfunction. The underlying mechanism remains to be elucidated but the persistent sodium inward current leading to calcium overload might play a role, in particular regarding diastolic dysfunction.
Novel Mania: A semantic search engine for Urdu

With the increasing trend of reading Urdu e-novels, the retrieval of specific information regarding a particular novel is also important. This paper presents a new semantic search engine for Urdu novels named Novel Mania. The search engine is primarily composed of three layers namely ontology modeling, information retrieval and dynamic ontology updations. The ontology modeling is primarily responsible to represent the knowledge area via domain ontology. Then, a number of semantic queries retrieve the necessary information inside the ontology. Further, the engine has the flexibility to dynamically incorporate the modifications in domain ontology. By exploiting the engine user can extract the novel related parameters without going into the details and inefficient way. Also, the engine provides a single platform to the publisher community in order to represent their work in a coherent manner.
Learning from Limited Demonstrations in High Dimensional Feature Spaces

Reinforcement learning (RL) has recently gained a lot of popularity partially due to the success of deep Q-learning (DQN) on the Atari suite and AlphaGo. In these online domains DQN-RL performs favorably thanks to its ability to continuously learn at super human speeds. Unfortunately, in many real world applications, such as in robotics, the learning rate is limited due to the speed at which the agent can interact with its environment. It is therefore of paramount importance to limit the amount of real world training required to achieve exemplary performance on any given task. This paper proposes running RL in a virtual simulator which is aesthetically and kinematically similar to the real world agent and environment before continuing to train on the robot itself. Furthermore, often the reward function required for RL is not intuitive to design. In the application of robotics it is desirable for the reward function to be chosen such that the agent behaves similarly to how a human would for the same task. Learning the reward function from human demonstrations, known as Inverse Reinforcement Learning (IRL), is one way to achieve this. IRL usually requires a lot of training examples from an agent and environment that are aesthetically similar to those on which RL is to be performed. Often obtaining many training examples is costly in time and money and in some instances gaining demonstrations from aesthetically similar robots is unachievable. This paper investigates a Max-Entropy Inverse Reinforcement Learning approach that leverages the representational power of Google’s pretrained deep convolutional neural network (CNN), Inception, to learn a reward function from a limited number of demonstrations (in many cases one) and an agent with a different embodiment to the one being trained on (in this paper a human hand as opposed to robot arm).
Targeting slow‐proliferating ovarian cancer cells

Advanced ovarian cancer has a high rate of recurrence and mortality despite relative chemosensitivity at the time of initial treatment. Conventional chemotherapeutic agents typically target rapidly dividing cells. Disease relapse may therefore result from the survival and later emergence of latent slow‐proliferating and/or quiescent cancer cells. We sought to identify drugs that target this cell population and to investigate the influence of these cells on outcome of patients in remission from advanced ovarian cancer. Drugs with increased efficacy against slower proliferating cells were identified using correlation‐based screening of 44,657 compounds tested on the NCI‐60 panel of cancer cell lines. Validation of candidates was performed in comparison with Cisplatin or Paclitaxel and by manipulation of proliferation rates by serum deprivation. Cytostatic and cytocidal effects were evaluated using MTT assays and active caspase‐3 immunocytochemistry. Ki‐67 proliferation indices were determined for tumors from 104 patients in remission. UCN‐01 efficacy was correlated with longer doubling time among the NCI‐60 cell lines (R = 0.54, p < 0.0001) and in a panel of 24 ovarian cancer cell lines (R = 0.42, p = 0.04), whereas this was not the case for Cisplatin (R = −0.10, p = 0.65) and Paclitaxel efficacy correlated with shorter doubling time (R = −0.52, p = 0.009). Cytostatic and cytocidal effects of UCN‐01 were increased in serum‐deprived cells. A low proliferation index was associated with presence of persistent disease at second‐look surgery (p = 0.01) and poor survival (disease‐free survival, p = 0.002; overall survival, p = 0.04). These results suggest that targeting quiescent ovarian cancer cells may be a worthwhile therapeutic approach to improving survival of women with ovarian cancer.
Characterization of Wet-Heat Inactivation of Single Spores of Bacillus Species by Dual-Trap Raman Spectroscopy and Elastic Light Scattering

ABSTRACT Dual-trap laser tweezers Raman spectroscopy (LTRS) and elastic light scattering (ELS) were used to investigate dynamic processes during high-temperature treatment of individual spores of Bacillus cereus, Bacillus megaterium, and Bacillus subtilis in water. Major conclusions from these studies included the following. (i) After spores of all three species were added to water at 80 to 90°C, the level of the 1:1 complex of Ca2+ and dipicolinic acid (CaDPA; ∼25% of the dry weight of the spore core) in individual spores remained relatively constant during a highly variable lag time (Tlag), and then CaDPA was released within 1 to 2 min. (ii) The Tlag values prior to rapid CaDPA release and thus the times for wet-heat killing of individual spores of all three species were very heterogeneous. (iii) The heterogeneity in kinetics of wet-heat killing of individual spores was not due to differences in the microscopic physical environments during heat treatment. (iv) During the wet-heat treatment of spores of all three species, spore protein denaturation largely but not completely accompanied rapid CaDPA release, as some changes in protein structure preceded rapid CaDPA release. (v) Changes in the ELS from individual spores of all three species were strongly correlated with the release of CaDPA. The ELS intensities of B. cereus and B. megaterium spores decreased gradually and reached minima at T1 when ∼80% of spore CaDPA was released, then increased rapidly until T2 when full CaDPA release was complete, and then remained nearly constant. The ELS intensity of B. subtilis spores showed similar features, although the intensity changed minimally, if at all, prior to T1. (vi) Carotenoids in B. megaterium spores' inner membranes exhibited two changes during heat treatment. First, the carotenoid's two Raman bands at 1,155 and 1,516 cm−1 decreased rapidly to a low value and to zero, respectively, well before Tlag, and then the residual 1,155-cm−1 band disappeared, in parallel with the rapid CaDPA release beginning at Tlag.
Cell Proteins TIA-1 and TIAR Interact with the 3′ Stem-Loop of the West Nile Virus Complementary Minus-Strand RNA and Facilitate Virus Replication

ABSTRACT It was reported previously that four baby hamster kidney (BHK) proteins with molecular masses of 108, 60, 50, and 42 kDa bind specifically to the 3′-terminal stem-loop of the West Nile virus minus-stand RNA [WNV 3′(−) SL RNA] (P. Y. Shi, W. Li, and M. A. Brinton, J. Virol. 70:6278-6287, 1996). In this study, p42 was purified using an RNA affinity column and identified as TIAR by peptide sequencing. A 42-kDa UV-cross-linked viral RNA-cell protein complex formed in BHK cytoplasmic extracts incubated with the WNV 3′(−) SL RNA was immunoprecipitated by anti-TIAR antibody. Both TIAR and the closely related protein TIA-1 are members of the RNA recognition motif (RRM) family of RNA binding proteins. TIA-1 also binds to the WNV 3′(−) SL RNA. The specificity of these viral RNA-cell protein interactions was demonstrated using recombinant proteins in competition gel mobility shift assays. The binding site for the WNV 3′(−) SL RNA was mapped to RRM2 on both TIAR and TIA-1. However, the dissociation constant (Kd) for the interaction between TIAR RRM2 and the WNV 3′(−) SL RNA was 1.5 × 10−8, while that for TIA-1 RRM2 was 1.12 × 10−7. WNV growth was less efficient in murine TIAR knockout cell lines than in control cells. This effect was not observed for two other types of RNA viruses or two types of DNA viruses. Reconstitution of the TIAR knockout cells with TIAR increased the efficiency of WNV growth, but neither the level of TIAR nor WNV replication was as high as in control cells. These data suggest a functional role for TIAR and possibly also for TIA-1 during WNV replication.
Interaction of tubulin with drugs and alkylating agents. 2. Effects of colchicine, podophyllotoxin, and vinblastine on the alkylation of tubulin.

The antimitotic drugs colchicine, podophyllotoxin, and vinblastine are known to be potent inhibitors of microtubule polymerization, but little is known about how they affect the chemical properties of the tubulin molecule. In the preceding paper [Ludueña, R. F. , & Roach, M. C. (1981) Bio-chemistry (preceding paper in this issue)], we have shown that the alkylating agent iodo[14C]acetamide reacts specifically with the sulfhydryl groups of tubulin and that its bifunctional analogue, N,N'-ethylenebis(iodoacetamide) (EBI), reacts with native tubulin to convert beta-tubulin into a form, designated beta*, which appears to represent an intrachain cross-linked form of beta. In this paper, we have incubated tubulin with the drugs prior to alkylation and measured their effects on the alkylation reactions. We have found that at 100 microM concentrations, podophyllotoxin, colchicine, and vinblastine inhibited the reaction of tubulin with iodo[14C]acetamide by 19-32%, 33-47%, and 62-72%, respectively; each drug was half-maximally effective at 3-5 microM, indicating that the suppressive effects of the drugs were mediated by their high-affinity binding sites. Similarly, beta* formation induced by EBI was suppressed by 92-94% in the presence of either colchicine or podophyllotoxin In contrast, vinblastine enhanced beta* formation by 40%. Alkylation with longer chain analogues of EBI revealed no evidence that the reactive sulfhydryls were being pushed apart by the drugs. These results indicate that each of the drugs has potent effects on the accessibility of the sulfhydryl groups of tubulin and that the effects of vinblastine are very different from those of either colchicine or podophyllotoxin.
Shadow Identification in Food Images using Extreme Learning Machine

Shadow identification is important for food images. Different applications require an accurate shadow identification or removal. A shadow varies from one image to another based on different factors such as lighting, colors, shape of objects, and their arrangement. This makes shadow identification complex problem and lacking systematic approach. Machine learning has high potential to be used for shadow recognition if it is used to train algorithms on wide number of scenarios. In this article, Extreme Learning Machine (ELM) has been used to identify shadow in shadow mask area. This shadow mask area was determined in the image based on edge detection, and morphological operations. ELM has been compared with Support Vector Machine (SVM) for shadow identification and shown better performance.
Coinfection with Streptococcus pneumoniae Modulates the B Cell Response to Influenza Virus

ABSTRACT Pathogen-specific antibodies (Abs) protect against respiratory infection with influenza A virus (IAV) and Streptococcus pneumoniae and are the basis of effective vaccines. Sequential or overlapping coinfections with both pathogens are common, yet the impact of coinfection on the generation and maintenance of Ab responses is largely unknown. We report here that the B cell response to IAV is altered in mice coinfected with IAV and S. pneumoniae and that this response differs, depending on the order of pathogen exposure. In mice exposed to S. pneumoniae prior to IAV, the initial virus-specific germinal center (GC) B cell response is significantly enhanced in the lung-draining mediastinal lymph node and spleen, and there is an increase in CD4+ T follicular helper (TFH) cell numbers. In contrast, secondary S. pneumoniae infection exaggerates early antiviral antibody-secreting cell formation, and at later times, levels of GCs, TFH cells, and antiviral serum IgG are elevated. Mice exposed to S. pneumoniae prior to IAV do not maintain the initially robust GC response in secondary lymphoid organs and exhibit reduced antiviral serum IgG with diminished virus neutralization activity a month after infection. Our data suggest that the history of pathogen exposures can critically affect the generation of protective antiviral Abs and may partially explain the differential susceptibility to and disease outcomes from IAV infection in humans. IMPORTANCE Respiratory tract coinfections, specifically those involving influenza A viruses and Streptococcus pneumoniae, remain a top global health burden. We sought to determine how S. pneumoniae coinfection modulates the B cell immune response to influenza virus since antibodies are key mediators of protection.
Differing Relationship of Nocturnal Fluid Shifts to Sleep Apnea in Men and Women With Heart Failure

Background—In men with heart failure, nocturnal rostral fluid shift is associated with an overnight increase in the neck circumference (NC) and with severity of obstructive sleep apnea. Because the prevalence of obstructive sleep apnea is lower in women than in men with heart failure, we hypothesized that less fluid would shift into the neck in association with less severe obstructive sleep apnea in women than in men with heart failure. Methods and Results—In 35 men and 30 women with heart failure, we assessed overnight changes in NC (&Dgr;NC) and leg fluid volume before and after polysomnography. The severity of obstructive sleep apnea was assessed by the apnea–hypopnea index. Although the changes in leg fluid volume did not differ significantly between men and women (−131 ± 90 versus −180 ± 132 mL, P=0.081), in women, &Dgr;NC was smaller (P<0.001) than in men. Furthermore, although in men, changes in leg fluid volume correlated inversely with &Dgr;NC (r=−0.755, P<0.001) and apnea–hypopnea index (r=−0.765, P<0.001), it did not in women. Conclusions—Despite no difference in overnight displacement of fluid from the legs compared with in men, in women, less of this fluid reached the neck, and unlike men, there was no relationship between changes in leg fluid volume and either &Dgr;NC or apnea–hypopnea index. These findings suggest a differing relationship between overnight fluid shift from the legs and severity of obstructive sleep apnea in women than in men with heart failure.
Hormones as epigenetic signals in developmental programming

In mammals, including man, epidemiological and experimental studies have shown that a range of environmental factors acting during critical periods of early development can alter adult phenotype. Hormones have an important role in these epigenetic modifications and can signal the type, severity and duration of the environmental cue to the developing feto‐placental tissues. They affect development of these tissues both directly and indirectly by changes in placental phenotype. They act to alter gene expression, hence the protein abundance in a wide range of different tissues, which has functional consequences for many physiological systems both before and after birth. By producing an epigenome specific to the prevailing condition in utero, hormones act as epigenetic signals in developmental programming, with important implications for adult health and disease. This review examines the role of hormones as epigenetic signals by considering their responses to environmental cues, their effects on phenotypical development and the molecular mechanisms by which they programme feto‐placental development, with particular emphasis on the glucocorticoids.