Miracle-dz/UniFAR-FTUs huggingface dataset:
Substrate Specificity and Inhibitor Sensitivity of Plant UDP-Sugar Producing Pyrophosphorylases

UDP-sugars are essential precursors for glycosylation reactions producing cell wall polysaccharides, sucrose, glycoproteins, glycolipids, etc. Primary mechanisms of UDP sugar formation involve the action of at least three distinct pyrophosphorylases using UTP and sugar-1-P as substrates. Here, substrate specificities of barley and Arabidopsis (two isozymes) UDP-glucose pyrophosphorylases (UGPase), Arabidopsis UDP-sugar pyrophosphorylase (USPase) and Arabidopsis UDP-N-acetyl glucosamine pyrophosphorylase2 (UAGPase2) were investigated using a range of sugar-1-phosphates and nucleoside-triphosphates as substrates. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Fru-1-P and Fru-2-P (Km values over 10 mM). Contrary to an earlier report, their activity with Gal-1-P was extremely low. USPase reacted with a range of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P (Km of 1.3 mM), β-L-Ara-1-P and α-D-Fuc-1-P (Km of 3.4 mM), but not β-L-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P (Km of 1 mM) and, to some extent, D-Glc-1-P (Km of 3.2 mM). Generally, different conformations/substituents at C2, C4, and C5 of the pyranose ring of a sugar were crucial determinants of substrate specificity of a given pyrophosphorylase. Homology models of UDP-sugar binding to UGPase, USPase and UAGPase2 revealed more common amino acids for UDP binding than for sugar binding, reflecting differences in substrate specificity of these proteins. UAGPase2 was inhibited by a salicylate derivative that was earlier shown to affect UGPase and USPase activities, consistent with a common structural architecture of the three pyrophosphorylases. The results are discussed with respect to the role of the pyrophosphorylases in sugar activation for glycosylated end-products.
Exploiting task-document relations in support of information retrieval in the workplace

Increasingly, workplace information seeking takes place in digital information environments and is reliant upon search systems. Existing systems are designed to retrieve information that is relevant to the query, but are not capable of identifying information that is well-suited to the context and situation of a search. This is a problem for professionals who often are searching for a small amount of useful information that can be applied to a problem or task, and have limited time to browse through large sets of results. This inability of search systems to discriminate between topically relevant and useful documents is one of the core problems in information retrieval.
Statistical Investigation of Anomalous Fast Erase Dynamics in Charge Trapping NAND Flash

In nand Flash nonvolatile memories, the erase operation drives the memory cells threshold voltage toward negative values, barely representing a concern for multilevel architectures. However, during the analysis of the erase dynamics in charge trapping (CT) memory arrays using an incremental step pulse erase algorithm, it is found that a small population of memory cells ( ≈ 2%) may randomly exhibit anomalous fast erase dynamics, which causes threshold voltage fluctuations during cycling operations. The purpose of this letter is to provide a statistical characterization of this phenomenon in CT-nand Flash arrays, thus helping the comprehension of its underlying physical mechanisms.
Gene Expression Profiling of Gliomas Strongly Predicts Survival

In current clinical practice, histology-based grading of diffuse infiltrative gliomas is the best predictor of patient survival time. Yet histology provides little insight into the underlying biology of gliomas and is limited in its ability to identify and guide new molecularly targeted therapies. We have performed large-scale gene expression analysis using the Affymetrix HG U133 oligonucleotide arrays on 85 diffuse infiltrating gliomas of all histologic types to assess whether a gene expression-based, histology-independent classifier is predictive of survival and to determine whether gene expression signatures provide insight into the biology of gliomas. We found that gene expression-based grouping of tumors is a more powerful survival predictor than histologic grade or age. The poor prognosis samples could be grouped into three different poor prognosis groups, each with distinct molecular signatures. We further describe a list of 44 genes whose expression patterns reliably classify gliomas into previously unrecognized biological and prognostic groups: these genes are outstanding candidates for use in histology-independent classification of high-grade gliomas. The ability of the large scale and 44 gene set expression signatures to group tumors into strong survival groups was validated with an additional external and independent data set from another institution composed of 50 additional gliomas. This demonstrates that large-scale gene expression analysis and subset analysis of gliomas reveals unrecognized heterogeneity of tumors and is efficient at selecting prognosis-related gene expression differences which are able to be applied across institutions.
A synthetic heparin‐mimicking polyanionic compound binds to the LDL receptor‐related protein and inhibits vascular smooth muscle cell proliferation

A synthetic heparin‐mimicking polyaromatic anionic compound RG‐13577 (polymer of 4‐hydroxyphenoxy acetic acid and formaldehyde ammonium salt, Mr∼5800) exhibits specific binding to vascular smooth muscle cells (SMCs) and inhibits their proliferative response to growth promoting factors. Receptor binding of 14C‐RG‐13577 was efficiently competed by apolipoprotein E3 (apoE), lactoferrin, and the LRP (LDL receptor‐related protein) receptor associated 39 kDa protein (RAP). Unlike cell surface binding of apoE, binding of RG‐13577 to SMCs was not affected by heparin, heparan sulfate degrading enzymes, or low density lipoprotein (LDL). Moreover, wild‐type and heparan sulfate‐deficient Chinese hamster ovary (CHO) cells, as well as normal‐ and LDL receptor negative‐ human skin fibroblasts bind RG‐13577, but not apoE, to a similar extent. On the other hand, homozygous mouse embryonic fibroblasts deficient in the LDL receptor‐related protein (LRP) expressed a markedly reduced binding of RG‐13577 as compared to normal mouse embryonic fibroblasts. These results indicate that RG‐13577 and related compounds bind to the LRP receptor on the surface of vascular SMCs. Addition of lactoferrin to cultured SMCs protected the cells against the antiproliferative effect of compound RG‐13577, suggesting that this inhibition is mediated by RG‐13577 binding to LRP receptors on the SMC surface. Altogether, we have identified a series of synthetic polyaromatic anionic molecules that exhibit specific binding to LRP and therby exert an antiproliferative effect on vascular SMCs. These compounds are applied to suppress SMC proliferation associated with restenosis and accelerated atherosclerosis. J. Cell. Biochem. 81:114–127, 2001. © 2001 Wiley‐Liss, Inc.
Observation Results and Discussion on an Upward Leader Followed by a Long Continuing Current After a Return Stroke

An abnormal discharge process after a return stroke (RS) in a negative cloud‐to‐ground flash was studied in detail. Correlating high‐speed video images and electric field data, it was found that the abnormal discharge process was initiated at ground and transported positive charge from ground toward cloud. Moreover, there was a long continuing current (CC) initiated by the abnormal upward discharge process. Compared with the characteristics of RSs, CCs and M components, we conclude that the upward discharge process is a kind of upward positive leader. The 3‐D speeds of the positive leader range from 3.72 × 106 m/s to 14.48 × 106 m/s with average value of 6.5 × 106 m/s. As far as we know, it is the first report that a long CC follows the upward positive leader after RS, which is obviously different from traditional CCs. The discovery is helpful to gain a deeper understanding of the mechanism and physical process of negative cloud‐to‐ground flashes.
Deciding Correctness with Fairness for Simple Transducer Networks

Ensuring the correctness of a distributed system is an important challenge. Previously, two interpretations of correctness have been proposed: the rst interpretation is about determinism, saying that all innite fair computation traces produce the same output; and, the second interpretation is a conuence notion, saying that all nite computation traces can still be extended to produce the same output. A decidability result for the conuence notion was previously obtained for so-called simple transducer networks, a model from the eld of declarative networking. In the current paper, we also present a decidability result for simple transducer networks, but this time for the rst interpretation of correctness, with innite fair computation traces. We also compare the expressivity of simple transducer networks under both interpretations.
Neonatal Abstinence Syndrome and Corresponding Pharmacotherapy Approaches from 2 University-affiliated Neonatal Intensive Care Units in Puerto Rico (2018-2020).

OBJECTIVE Neonatal abstinence syndrome (NAS) is a set of drug withdrawal symptoms suffered by neonates exposed to drugs in utero. Several studies have widely described NAS incidence and treatment approach; however, little is known regarding the incidence and manifestations of this disease in Puerto Rico (PR). The principal aim of this study was to describe NAS incidence in the neonatal units of hospitals affiliated with the University of PR in terms of occurrence, clinical manifestations, and treatment approaches. METHODS Our study evaluated the medical records of NAS babies diagnosed from 2018 through 2020 at 2 hospitals affiliated with the University of PR Medical Sciences Campus. Descriptive and inferential statistics were employed to analyze trends. RESULTS We identified 12 neonates diagnosed with NAS, 5 with low birthweights (<2500 g); for a NAS incidence of 2 cases per 1000 admitted for the 3 years of recollected data. The urine toxicology results revealed that 9 had experienced intrauterine polydrug exposure. Phenobarbital loading dose were determined on the day of diagnosis (indicated by Finnegan score). The first manifestation of NAS symptoms varied: 8 neonates showed symptoms within 48 hours after birth, whereas 4 had withdrawal symptoms within 72-120 hours of their births. Differences between dosing practices and guidelines were observed, ranging from a 0.69% to a 25% difference during treatment initiation. CONCLUSION Further research on the incidence of NAS in PR (national level) is needed for a deeper understanding that we hope will lead to the development of enhanced treatment protocols in PR.
BCR‐ABL‐positive lymphoblastoid cells display limited proliferative capacity under in vitro culture conditions

We studied the kinetics of EBV‐transformed B‐cell lines from patients with chronic myeloid leukaemia (CML) using RT‐PCR for BCR‐ABL transcripts and immunoglobulin heavy chain (IgH) gene rearrangements. Peripheral blood mononuclear cells, obtained from four patients with CML in chronic phase and from one in accelerated phase, were incubated with supernatant from the B95‐8 EBV producing cell line. In 11/25 (44%) B‐cell cultures established we demonstrated the presence of BCR‐ABL transcripts at intervals ranging from 32 to 125 d post EBV transformation. In all but two cases, evidence of BCR‐ABL transcripts disappeared with time. Cultures were initially polyclonal with respect to IgH rearrangements but became progressively oligoclonal, suggesting the longer‐term survival of fewer clones, all of which were BCR‐ABL negative. We conclude that BCR‐ABL‐positive lymphoid cultures can be established in the short term from the majority of patients with CML but they have limited capacity to survive in the longer term. Therefore, in lymphoid cells the presence of the BCR‐ABL chimaeric gene appears to confer no survival advantage.
Biochemical and molecular evidences on the protection by magnesium oxide nanoparticles of chlorpyrifos-induced apoptosis in human lymphocytes

Background: Chlorpyrifos (CP) is one of the most widely used organophosphate (OP) insecticides in agricultural and residential pest control with its attendant adverse health effect. In the present study, it is proposed to investigate the possible modulatory role of magnesium oxide nanoparticles (MgO NPs) against CP-induced toxicity in human lymphocytes and determine the mechanisms lying behind this protection by viability and biochemical assays. Materials and Methods: Isolated lymphocytes were exposed to 12 μg/mL CP either alone or in combination with different concentrations of MgO NPs (0.1 μg/mL, 1 μg/mL, 10 μg/mL, and 100 μg/mL). After a 3-day incubation, the viability and oxidative stress markers including cellular mitochondrial activity, caspase-3 and -9 activities, total antioxidant power, lipid peroxidation, and myeloperoxidase (MPO) activity were measured. Also, the levels of tumor necrosis factor-α (TNF-α) as inflammatory index, along with acetylcholinesterase (AChE) activity were measured. Statistical differences were determined using one-way analysis of variance (ANOVA) and Dunnett's multiple comparison tests. Results: It is indicated that CP-exposed lymphocytes treated with MgO NPs resulted in a substantial reduction in the pace of mortality as well as the stages of oxidative stress in a dose-dependent manner. Also, MgO NPs (100 μg/mL) meaningfully restored CP-induced increase of TNF-α (P < 0.001) and decrease of AChE activity (P < 0.001) and were capable of preventing CP-treated human lymphocytes from apoptosis (P < 0.001). Conclusion: Our results demonstrate that MgO NPs in approximate 100 nm diameter not only make cells resistant to the toxic properties of CP but also attenuate toxic effects of CP, which is demonstrating the potential of MgO NPs to be applied in future immune deficiency therapeutic strategies.
Bactericidal Activity of Rifampin-Amikacin against Mycobacterium ulcerans in Mice

ABSTRACT To identify the most active curative treatment of Buruli ulcer, two regimens incorporating the use of rifampin (RIF) were compared with the use of RIF alone in a mouse footpad model of Mycobacterium ulcerans infection. Treatments began after footpad swelling from infection and continued for 12 weeks with five doses weekly of one of the following regimens: (i) 10 mg of RIF/kg alone; (ii) 10 mg of RIF/kg and 100 mg of amikacin (AMK)/kg; and (iii) 10 mg of RIF/kg, 100 mg of clarithromycin (CLR)/kg, and 50 mg of sparfloxacin (SPX)/kg. The activity of each regimen was assessed in terms of the reduction of the average lesion index and acid-fast bacillus (AFB) and CFU counts. All three regimens displayed various degrees of bactericidal activity against M. ulcerans. The ranking of bactericidal activity was found to be as follows: RIF-AMK > RIF-CLR-SPX > RIF. RIF-AMK was able to cure M. ulcerans-infected mice and prevent relapse 26 weeks after completion of treatment. To determine the impact of different rhythms of administration of RIF-AMK on the suppression of M.ulcerans growth, mice were given the RIF-AMK combination for 4 weeks but doses were administered either 5 days a week or twice or once weekly. After completion of treatment, the mice were kept under supervision for 30 additional weeks. M. ulcerans was considered to have grown in the footpad if swelling was visually observed and harvests contained more than 5 × 105 AFB per footpad. The proportion of mice in which growth of M. ulcerans occurred, irrespective of drug dosage, was compared with the control mice to determine the proportion of M. ulcerans killed. Each dosage of RIF-AMK was bactericidal for M. ulcerans (P < 0.001), but the effect was significantly stronger in mice treated 5 days per week. The promising results of RIF-AMK treatment in M. ulcerans-infected mice support the clinical trial that is currently in progress under World Health Organization auspices in Ghana.
Joint Relay-and-Antenna Selection in Multi-Antenna Relay Networks

For the decode-and-forward protocol in relay networks, opportunistic relaying (OR) and selection cooperation (SC) are two major relay selection schemes, which have been studied only for single antenna terminals. We study OR and SC in a multi-antenna relay network where each terminal has multiple antennas. To fully exploit multiple antennas without incurring high feedback overhead, we adopt transmit antenna selection (TAS). Specifically, we first propose two joint relay-and-antenna selection schemes which combine OR and SC, respectively, with TAS: joint OR-TAS and joint SC-TAS. For each joint selection scheme, a single best transmit antenna at the source, a single best relay, and a single best transmit antenna at this selected relay are jointly determined in an optimum sense. In this network, at the first time slot, the selected antenna at the source transmits a symbol to the selected relay; at the second time slot, the selected antenna at the selected relay retransmits the detected symbol to the destination. We derive the outage probability of joint OR-TAS. Also, we obtain the outage probability of joint SC-TAS by proving that the outage probability of joint SC-TAS is identical to that of joint OR-TAS.
Evidence for genes associated with the ability of Mycobacterium avium subsp. hominissuis to escape apoptotic macrophages

Mycobacterium avium subsp. hominissuis (MAH) is an environmental bacteria that infects immunocompromised humans. MAH cases are increasing in incidence, making it crucial to gain knowledge of the pathogenic mechanisms associated with the bacterium. MAH infects macrophages and after several days the infection triggers the phagocyte apoptosis. Many of the intracellular MAH escape the cell undergoing apoptosis leading to infection of neighboring macrophages. We screened a transposon bank of MAH mutants in U937 mononuclear phagocytes for the inability to escape macrophages undergoing apoptosis. Mutations in genes; MAV_2235, MAV_2120, MAV_2410, and MAV_4563 resulted in the inability of the bacteria to exit macrophages upon apoptosis. Complementation of the mutations corrected the phenotype either completely or partially. Testing for the ability of the mutants to survive in macrophages compared to the wild-type bacterium revealed that the mutant clones were not attenuated up to 4 days of infection. Testing in vivo, however, demonstrated that all the MAH clones were attenuated compared with the wild-type MAC 104 in tissues of mice. Although the mechanism associated with the bacterial inability to leave apoptotic macrophages is unknown, the identification of macrophage cytoplasm targets for the MAH proteins suggest that they interfere either with protein degradation machinery or post-translation mechanisms. The identification of tatC as a MAH protein involved in the ability of MAH to leave macrophages, suggests that secreted effector(s) are involved in the process. The study reveals a pathway of escape from macrophages, not shared with Mycobacterium tuberculosis.
Development of a Chemical Genetic Approach for Human Aurora B Kinase Identifies Novel Substrates of the Chromosomal Passenger Complex*

To understand how the chromosomal passenger complex ensures chromosomal stability, it is crucial to identify its substrates and to find ways to specifically inhibit the enzymatic core of the complex, Aurora B. We therefore developed a chemical genetic approach to selectively inhibit human Aurora B. By mutating the gatekeeper residue Leu-154 in the kinase active site, the ATP-binding pocket was enlarged, but kinase function was severely disrupted. A unique second site suppressor mutation was identified that rescued kinase activity in the Leu-154 mutant and allowed the accommodation of bulky N6-substituted adenine analogs. Using this analog-sensitive Aurora B kinase, we found that retention of the chromosomal passenger complex at the centromere depends on Aurora B kinase activity. Furthermore, analog-sensitive Aurora B was able to use bulky ATPγS analogs and could thiophosphorylate multiple proteins in cell extracts. Utilizing an unbiased approach for kinase substrate mapping, we identified several novel substrates of Aurora B, including the nucleosomal-binding protein HMGN2. We confirmed that HMGN2 is a bona fide Aurora B substrate in vivo and show that its dynamic association to chromatin is controlled by Aurora B.
Improving UAV imaging quality by optical sensor fusion: an initial study

ABSTRACT The most frequent application of unmanned aerial vehicle (UAVs) is to collect optical colour images from an area of interest. Thus, high spatial resolution colour images with high amount of signal to noise ratio (SNR) are of great importance in UAV applications. Currently, most UAVs use single sensor colour filter array (CFA) cameras for image collection, within which the Bayer-pattern sensors are the most frequently used ones. Due to the limitations of the CFAs, the quality (in terms of spatial resolution, SNR, and sharpness) of UAV colour images is not optimal. In this article, a sensor fusion solution is proposed to improve the quality of UAV imaging. In the proposed solution, a high-resolution colour (HRC) Bayer-pattern sensor is replaced by a dual camera set containing a panchromatic (Pan) sensor, with the same pixel size and a Bayer-pattern colour (or a four-band multi-spectral) sensor with larger pixel size; the resulting images of the dual camera set are then fused. The enlarged pixel size of the colour sensor provides a higher SNR for the cost of lower spatial resolution. However, the accompanied Pan sensor provides single band images with high SNR and high spatial resolution. Fusing the images of the dual camera set generates colour (or MS) images with high spatial resolution, SNR, and sharpness compensating for the major problems of the Bayer-pattern filters. This replacement solution is initially tested in a laboratory experiment. The results of quality assessments show that the SNR is increased by 2–3 times, the sharpness is improved by around 2 times, and the spatial resolution is increased up to the level of the pan images, while the colour errors remained almost as low as the original colour images. In addition, image classification capability of the images is examined using two methods: Support Vector Machine (SVM) and Maximum Likelihood (ML). The results of image classification also confirmed around 20–40% increase in accuracy. Therefore, the proposed sensor fusion can be a good alternative for UAV colour sensors.