Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucosamine 6‐phosphate deaminase in Plasmodium falciparum

Summary. The pathways of glucose utilization for energy production in the malaria parasite, Plasmodium falciparum, have been studied extensively. Little is known, however, about the reactions by which glucose is converted into complex carbohydrates in the parasite, and knowledge of the catabolism of these substances is likewise scanty. The present investigation was undertaken to determine whether the parasites possess a key enzyme of glucosamine catabolism, i.e. glucosamine 6‐phosphate deaminase (EC 5.3.1.40), which catalyses the conversion of the sugar phosphate to fructose 6‐phosphate and ammonia. Lysates of Plasmodium‐infected erythrocytes had substantially higher deaminase activity than control samples from normal erythrocytes, and an even higher specific activity was observed in extracts of isolated parasites, amounting to 20‐40 times that of uninfected cells. Anion exchange chromatography indicated that the parasite deaminase eluted in a retarded position when compared to the elution profile of the erythrocyte enzyme. The charge difference suggested by these findings was established more directly by chromatofocusing, which indicated pi values of 6‐85 and 8‐55 for the parasite and erythrocyte deaminases, respectively. Other differences were also observed, notably a greater thermolability on the part of the parasite enzyme. These results indicated that the parasites synthesize a specific deaminase that is distinct from the normal erythrocyte enzyme. Studies on synchronized parasite cultures further indicated that the parasite deaminase is developmentally regulated, because a dramatic increase in activity levels occurred during the later stages of parasite development.
Human colorectal tumors and metastases express Gb3 and can be targeted by an intestinal pathogen-based delivery tool

The targeting of solid tumors requires delivery tools that resist intracellular and extracellular inactivation, and that are taken up specifically by tumor cells. We have shown previously that the recombinant nontoxic B-subunit of Shiga toxin (STxB) can serve as a delivery tool to target digestive tumors in animal models. The aim of this study was to expand these experiments to human colorectal cancer. Tissue samples of normal colon, benign adenomas, colorectal carcinomas, and liver metastases from 111 patients were obtained for the quantification of the expression of the cellular STxB receptor, the glycosphingolipid globotriaosyl ceramide (Gb3 or CD77). We found that compared with normal tissue, the expression of Gb3 was strongly increased in colorectal adenocarcinomas and their metastases, but not in benign adenomas. Short-term primary cultures were prepared from samples of 43 patients, and STxB uptake was studied by immunofluorescence microscopy. Of a given tumor sample, on average, 80% of the cells could visibly bind STxB, and upon incubation at 37°C, STxB was transported to the Golgi apparatus, following the retrograde route. This STxB-specific intracellular targeting allows the molecule to avoid recycling and degradation, and STxB could consequently be detected on tumor cells even 5 days after initial uptake. In conclusion, the targeting properties of STxB could be diverted for the delivery of contrast agents to human colorectal tumors and their metastases, whose early detection and specific targeting remains one of the principal challenges in oncology. [Mol Cancer Ther 2008;7(8):2498–508]
Importance of pelvic muscle tenderness evaluation in women with chronic pelvic pain.

OBJECTIVE To determine the prevalence of pelvic muscle tenderness in women with chronic pelvic pain (CPP) and to assess the importance of evaluating muscle tenderness in such women. DESIGN Observational study of 48 healthy female volunteers and 108 women with CPP, who were clinically evaluated for pelvic muscle tenderness by two researchers blinded to all clinical data. RESULTS The frequency of clinically detected pelvic muscle tenderness was significantly higher in women with CPP than in healthy volunteers (58.3% vs 4.2%, P < 0.001). Among women with CPP, those with pelvic muscle tenderness had higher Beck Depression Index scores (22 [6-42] vs 13 [3-39], P = 0.02) and higher rates of dyspareunia (63.5% [40/63] vs 28.9% [13/45], P < 0.004) and constipation (46.0% [29/63] vs 26.7% [12/45], P = 0.05) than those without pelvic muscle tenderness. CONCLUSION Tenderness of pelvic muscles was highly prevalent among women with CPP and was associated with higher BDI scores and higher rates of dyspareunia and constipation. Determination of pelvic muscle tenderness may help in identifying women who require more intense treatment for CPP.
Recessive mutations in a common pathway block thymocyte apoptosis induced by multiple signals

The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls genes necessary to initiate glucocorticoid-induced thymocyte apoptosis. We have performed a genetic analysis of thymocyte cell death by isolating and characterizing a panel of GR+ dexamethasone- resistant mutants of the murine WEHI7.2 thymocyte cell line. These apoptosis-defective (Apt-) mutants were used to identify previously unknown early steps in the apoptotic pathway. The Apt- mutants contain nonglucocorticoid receptor, recessive mutations in genes that represent multiple complementation groups. These mutations block apoptosis induced by dexamethasone, gamma irradiation, and c-AMP treatment before the point where Bcl-2 exerts its protective effect. We propose that different signals share a common apoptotic pathway, and that the induction of apoptosis involves multiple precommitment steps that can be blocked by recessive mutations.
JNK MAPK Pathway Regulates Constitutive Transcription of CCL5 by Human NK Cells through SP11

The MAPKs ERK, JNK, and p38 control diverse aspects of the immune response, including regulation of cytotoxin biology in NK cells and CTL. The chemokine CCL5 is coreleased with the cytotoxins, perforin, the granzymes, and granulysin, during the lethal hit administered by cytotoxic CD8+ T cells (CTL). CCL5 expression is up-regulated relatively late in CTL coincident with their functional maturation 3–7 days after activation. Unlike T cells, NK cells have the ability to kill virally infected or transformed cells when directly isolated from the peripheral circulation. In this study, we show that in contrast to T cells, peripheral blood NK cells express CCL5 constitutively. The use of specific inhibitors of the JNK, ERK, and p38 MAPK pathways showed that the JNK pathway controls expression of CCL5 by NK cells. Promoter-reporter assays identified a compact region of the CCL5 promoter responsible for the constitutive transcription of CCL5 by NK cells. EMSA, chromatin immune precipitation, the use of heterologous promoters, and site-directed mutagenesis demonstrated that transcription in NK cells is largely controlled through binding of the transcription factor specificity protein 1 to a region −75 to −56 upstream of the site of transcriptional initiation. Specificity protein 1 expression, and in turn the constitutive expression of CCL5, was found to be controlled through constitutive activation of the JNK/MAPK pathway in peripheral blood NK cells.
Relationship between Female University Students' Knowledge on Menstruation and Their Menstrual Hygiene Practices: A Study in Tamale, Ghana

Positive perception about menstruation and good menstrual hygiene practice safeguards the health of postpubescent females by reducing their vulnerability to reproductive and urinary tract infections. Using a questionnaire, a cross-sectional study involving 293 randomly selected female undergraduate students in northern Ghana assessed the relationship between knowledge on menstruation and the practice of safe menstrual hygiene. Data collected was analyzed using GraphPad 5.01. This study found that although majority of respondents (73.4%) were aware of menstruation before menarche, most of them experienced fear and panic when it occurred. Mothers were the first to be informed when menstruation occurred, although teachers first provided them knowledge on menstruation. Respondents' knowledge on menstruation was average (57.3%) but their menstrual hygiene practice was good (80.2%). Age (p = 0.005) and course of study (p = 0.0008) significantly influenced respondents' knowledge on menstruation with older students as well as the medical and midwifery students being most knowledgeable. Muslim rather than Christian female students practiced better menstrual hygiene (p = 0.0001). Average knowledge score on menstruation indicated a deficit of knowledge on the anatomy and physiology of the female reproductive system. Increasing knowledge on menstruation had a positive and significant effect on practice of good menstrual hygiene.
Model predictive control application to spacecraft rendezvous in mars sample return scenario

Model Predictive Control (MPC) is an optimization-based control strategy that is considered extremely attractive in the autonomous space rendezvous scenarios. The Online Recon¦guration Control System and Avionics Architecture (ORCSAT) study addresses its applicability in Mars Sample Return (MSR) mission, including the implementation of the developed solution in a space representative avionic architecture system. With respect to a classical control solution High-integrity Autonomous RendezVous and Docking control system (HARVD), MPC allows a signi¦cant performance improvement both in trajectory and in propellant save. Furthermore, thanks to the online optimization, it allows to identify improvements in other areas (i. e., at mission de¦nition level) that could not be known a priori.
Learning with Heterogeneous Side Information Fusion for Recommender Systems

Collaborative filtering (CF) based methods have become the most popular technique for recommender systems (RSs). In recent years, various types of side information such as social connections among users and metadata of items have been introduced into CF and shown to be effective for improving recommendation performance. Moreover, side information can alleviate data sparsity and cold start problems facing conventional CF based methods. However, previous works process different types of information separately, thus losing information that might exist across different types of side information. In this work, we study the application of Heterogeneous Information Network (HIN), which offers flexible representation of different types of side information, to enhance CF based recommendation methods. Since HIN could be a complex graph representing multiple types of relations between entity types, we need to tackle two challenging issues facing HIN-based RSs: How to capture the complex semantics that determines the similarities between users and items in a HIN, and how to fuse the heterogeneous side information to support recommendation. To address these issues, we apply metagraph to HIN-based RSs and solve the information fusion problem with a "matrix factorization (MF) + factorization machine (FM)" framework. For the MF part, we obtain the user-item similarity matrix from each metagraph and then apply low-rank matrix approximation to obtain latent features for both users and items. For the FM part, we apply FM with Group lasso (FMG) on the features obtained from the MF part to train the recommending model and at the same time identify the usefulness of the metagraphs. Experimental results on two large real-world datasets, i.e., Amazon and Yelp, show that our proposed approach is better than FM and other state-of-the-art HIN-based recommendation methods.
Coastal Subsidence Induced Several Tsunamis During the 2018 Sulawesi Earthquake

The height of the tsunami caused by the Sulawesi earthquake in 2018 was higher than that estimated from the magnitude of the earthquake, and its cause is not well understood. Although it is conceivable that tsunamis originated from landslides in several cases, it is not known whether landslides were occurring in the coastal area at the time. This report describes the results of a field survey conducted to investigate the traces of subsidence and the characteristics of the tsunami incidents in the bay far from the epicenter. Subsidence was observed at a minimum of seven points along the coast; in accord with the reports of eyewitnesses, this suggests that subsidence might have generated tsunamis.
Tumorigenesis in tuberous sclerosis complex is autophagy and p62/sequestosome 1 (SQSTM1)-dependent

Tuberous sclerosis complex (TSC) is a tumor suppressor syndrome characterized by benign tumors in multiple organs, including the brain and kidney. TSC-associated tumors exhibit hyperactivation of mammalian target of rapamycin complex 1 (mTORC1), a direct inhibitor of autophagy. Autophagy can either promote or inhibit tumorigenesis, depending on the cellular context. The role of autophagy in the pathogenesis and treatment of the multisystem manifestations of TSC is unknown. We found that the combination of mTORC1 and autophagy inhibition was more effective than either treatment alone in inhibiting the survival of tuberin (TSC2)-null cells, growth of TSC2-null xenograft tumors, and development of spontaneous renal tumors in Tsc2+/− mice. Down-regulation of Atg5 induced extensive central necrosis in TSC2-null xenograft tumors, and loss of one allele of Beclin1 almost completely blocked macroscopic renal tumor formation in Tsc2+/− mice. Surprisingly, given the finding that lowering autophagy blocks TSC tumorigenesis, genetic down-regulation of p62/sequestosome 1 (SQSTM1), the autophagy substrate that accumulates in TSC tumors as a consequence of low autophagy levels, strongly inhibited the growth of TSC2-null xenograft tumors. These data demonstrate that autophagy is a critical component of TSC tumorigenesis, suggest that mTORC1 inhibitors may have autophagy-dependent prosurvival effects in TSC, and reveal two distinct therapeutic targets for TSC: autophagy and the autophagy target p62/SQSTM1.
Assessing Superspheroids in Modeling the Scattering Matrices of Dust Aerosols

Atmospheric dust particles are known to have diverse and irregular morphologies. In order to account for nonsphericity, the spheroidal model with an aspect ratio distribution has been extensively used for modeling the optical properties of dust. The spheroidal model is superior to the spherical shape assumption, but it requires further improvement. In this study, superspheroids' modeling capabilities were systematically examined by comprehensively comparing the spheroid's and superspheroid's scattering matrices. Superspheroids have one more degree of freedom than spheroids and can be nonspherical at an aspect ratio of unity. The invariant imbedding T‐matrix and the improved geometrical optics methods were employed to compute superspheroids' single‐scattering properties with a wide distribution of aspect ratios and a number of roundness parameters. We then assessed the spheroidal and superspheroidal models' applicability for simulating the scattering matrices of 25 dust samples from the Amsterdam‐Granada Light Scattering Database. It was found that extreme aspect ratios for spheroids in reproducing the measurements were unnecessary if superspheroids were used. Even with equi‐probable aspect ratio distribution, superspheroids with constrained roundness parameters (from 2.4 to 3.0) could achieve better performances in concurrently matching six nonzero scattering matrix elements from the laboratory measurements. Moreover, superspheroids demonstrated better performances than spheroids in achieving spectral consistency for modeling dust scattering matrices. Therefore, superspheroids appear to be highly promising for atmospheric radiative transfer and remote sensing applications.
Circulating carotenoid levels are negatively associated with previous reproductive success in Florida Scrub-Jays (Aphelocoma coerulescens)

The relationship between individual fitness and antioxidants and oxidative stress has come under increasing scrutiny of late. In particular, associations between oxidative balance indicators and reproductive success in the wild have been inconsistent in the limited prior work on this topic. Studies spanning multiple seasons and antioxidant types are particularly lacking. Here, we examined associations between reproductive success over two breeding seasons and several metrics of circulating antioxidants (antioxidant capacity, uric acid, carotenoids, and vitamin E, measured in the intervening nonbreeding season) in Florida Scrub-Jays (Aphelocoma coerulescens (Bosc, 1795)). We found that carotenoid levels in the nonbreeding season were negatively associated with reproductive success in the preceding breeding season but unassociated with that in the subsequent breeding season. This correlation may be driven by the cost of reproduction (i.e., carotenoid depletion while breeding) or some other unmeasured and in.
Making programming languages to dance to: live coding with tidal

Live coding of music has grown into a vibrant international community of research and practice over the past decade, providing a new research domain where computer science blends with the performing arts. In this paper the domain of live coding is described, with focus on the programming language design challenges involved, and the ways in which a functional approach can meet those challenges. This leads to the introduction of Tidal 0.4, a Domain Specific Language embedded in Haskell. This is a substantial restructuring of Tidal, which now represents musical pattern as functions from time to events, inspired by Functional Reactive Programming.
Following the Turnover of Soil Bioavailable Phosphate in Mediterranean Savanna by Oxygen Stable Isotopes

Soil phosphate oxygen isotope analysis (δ18OP) emerges as an effective method to trace the cycling of phosphorus (P) in soils. This study uses δ18OP measurements to learn how the nutrient status (P and N) affects the biological turnover rates of P in the soil of a Mediterranean holm oak Savanna. Such ecosystems cover >3 × 106 ha at the Iberian Peninsula. The analysis was part of a large‐scale nutrient manipulation experiment, where N and P were added. We followed the changes in δ18O values of soil bioavailable P during incubation of soils with a pulse of P and in addition measured the δ18OP in soil sampled at the site. In the incubations, the δ18OP values changed from the original value of the added P and approached a steady state of 16.3‰, which is 3.8‰ higher than the isotopic equilibrium with water. The steady state was higher with 18O‐enriched incubation media water. The change in δ18OP values was more pronounced under trees, indicating a faster microbial P turnover rate. Incubation of soils fertilized with either P or N showed faster P turnover rate than control, implying N and P colimitation. Soil samples from P‐fertilized plots displayed higher δ18OP than the fertilizer, rather than the expected decrease toward steady‐state values, found at the control and N plots. The microbial P turnover rates during incubations were slower than the rates reported for lowland tropical forest with lower bioavailable P concentrations but resemble ecosystems with similar concentrations.
Pseudo-inverse based iterative learning control for plants with unmodelled dynamics

Learning control is a very effective approach for tracking repetitive processes. In this paper, the authors' stable-inversion based learning controller (1999) is modified to accommodate linear nonminimum phase plants with uncertainties. The design of the learning controller is based on the computation of an approximate inverse of the nominal model of the linear plant, rather than its exact inverse. The advantages of this approach are that the output of the plant need not be differentiated and also the plant model need not be exact. A low-pass zero-phase filter is used in the iteration loop to achieve robustness to plant uncertainty. The structure of the controller is such that the low frequency components of the trajectory converge faster than the high frequency components.
Sea-level rise vulnerability mapping for adaptation decisions using LiDAR DEMs

Global sea-level rise (SLR) is projected to accelerate over the next century, with research indicating that global mean sea level may rise 18–48 cm by 2050, and 50–140 cm by 2100. Decision-makers, faced with the problem of adapting to SLR, utilize elevation data to identify assets that are vulnerable to inundation. This paper reviews techniques and challenges stemming from the use of Light Detection and Ranging (LiDAR) digital elevation models (DEMs) in support of SLR decision-making. A significant shortcoming in the methodology is the lack of comprehensive standards for estimating LiDAR error, which causes inconsistent and sometimes misleading calculations of uncertainty. Workers typically aim to reduce uncertainty by analyzing the difference between LiDAR error and the target SLR chosen for decision-making. The practice of mapping vulnerability to SLR is based on the assumption that LiDAR errors follow a normal distribution with zero bias, which is intermittently violated. Approaches to correcting discrepancies between vertical reference systems for land and tidal datums may incorporate tidal benchmarks and a vertical datum transformation tool provided by the National Ocean Service (VDatum). Mapping a minimum statistically significant SLR increment of 32 cm is difficult to achieve based on current LiDAR and VDatum errors. LiDAR DEMs derived from ‘ground’ returns are essential, yet LiDAR providers may not remove returns over vegetated areas successfully. LiDAR DEMs integrated into a GIS can be used to identify areas that are vulnerable to direct marine inundation and groundwater inundation (reduced drainage coupled with higher water tables). Spatial analysis can identify potentially vulnerable ecosystems as well as developed assets. A standardized mapping uncertainty needs to be developed given that SLR vulnerability mapping requires absolute precision for use as a decision-making tool.
Fast Gaussian Process Regression using KD-Trees

The computation required for Gaussian process regression with n training examples is about O(n3) during training and O(n) for each prediction. This makes Gaussian process regression too slow for large datasets. In this paper, we present a fast approximation method, based on kd-trees, that significantly reduces both the prediction and the training times of Gaussian process regression.
Rearing Honey Bees, Apis mellifera, in vitro 1: Effects of Sugar Concentrations on Survival and Development

Abstract A new method for rearing honey bees, Apis mellifera L. (Hymenoptera: Apidae), in vitro was developed and the effects of sugar concentrations on survival and development were studied. Seven different glucose (G) and fructose (F) compositions (0%G+0%F, 3%G+3%F, 6%G+6%F, 12%G+12%F, 0%G+12%F, 12%G+0%F, and 4%G+8%F) were tested. Larvae were able to grow to the post defecation stage without addition of sugars (Diet 1), but they were not able to metamorphose and pupate. Adults were reared from diets 2–7. The average larval survival, prepupal larval weights, adult weights, and ovariole numbers were affected significantly due to the sugar compositions in the diets. High sugar concentrations (12%G+12%F) increased the number of queens and intercastes.