Miracle-dz/UniFAR-FTUs huggingface dataset:
High Level 0-Acetylation of Sialic Acids on N-Linked Oligosaccharides of Rat Liver Membranes

0-Acetylation of sialic acids has previously been considered an uncommon modification found on certain salivary mucins and neural gangliosides. We show here that glycosidically bound sialic acids from total membranes of rat liver have surprisingly high levels (-20%) of 0-acetylation at the 7or 9-position. This 0-acetylation is further enriched in N-linked oligosaccharides but is barely detectable in ganglioside fractions from the same tissue. The position of O-acetylation on the sialic acid side chain varies between different subcellular fractions. In particular, 7-0acetylation was enriched in lysosomal membranes and 9-0-acetylation in plasma membranes, whereas Golgi membranes contained both types. This distribution fits with the ability of the rat liver sia1ate:O-acetyltransferase(s) to synthesize both 7and 9-0-acetyl esters (Diaz, S., Higa, H. H., Hayes, B. K., and Varki, A. (1989) J. Biol. Chem. 264,19416-19426) and the fact that 7-0-acetyl esters can migrate to the 9-position at physiological temperature but only under neutral or mildly alkaline conditions. Subcellular fractionation shows that sia1ate:O-acetyltransferase activity directed toward endogenous acceptors is enriched in Golgi fractions, whereas an intralumenal sialic acidspecific 0-acetylesterase activity is not. The O-acetyltransferase is labile and difficult to solubilize in the intact state and cannot be assayed with exogenous acceptors. However, a prelabeled [3H]acetyl intermediate can be solubilized from Golgi membranes with Triton X-100 and is stable for a prolonged time in the cold. In contrast to the transferase, the lumenal esterase is easily released in a stable and water-soluble form from membrane fractions by saponin permeabilization or repeated freeze-thaw. In keeping with this finding, differential subcellular fractionation and continuous sucrose gradients indicate that this enzyme is enriched in lysosomal fractions (see also the accompanying paper (Butor, C., Higa, H. H., and Varki, A. (1993) J. Biol. Chem. 268, 10207-10213). Based upon findings reported in this and previous studies, a model is proposed for the biosynthesis, maturation, and turnover of 7and 9-0-acetyl esters on the sialic acids of N-
Towards Linguistically-Grounded Spatial Logics

We propose a method to analyze the amount of coverage and adequacy of spatial calculi by relating a calculus to a linguistic ontology for space by using similarities and linguistic corpus data. This allows evaluating whether and where a spatial calculus can be used for natural language interpretation. It can also lead to 'more appropriate' spatial logics for spatial language.
One step versus two step approach for gestational diabetes screening: systematic review and meta-analysis of the randomized trials

Abstract Introduction: To compare both the prevalence of gestational diabetes mellitus (GDM) as well as maternal and neonatal outcomes by either the one-step or the two-step approaches. Material and methods: Electronic databases were searched from their inception until June 2017. We included all randomized controlled trials (RCTs) comparing the one-step with the two-step approaches for the screening and diagnosis of GDM. The primary outcome was the incidence of GDM. Results: Three RCTs (n = 2333 participants) were included in the meta-analysis. 910 were randomized to the one step approach (75 g, 2 hrs), and 1423 to the two step approach. No significant difference in the incidence of GDM was found comparing the one step versus the two step approaches (8.4 versus 4.3%; relative risk (RR) 1.64, 95%CI 0.77–3.48). Women screened with the one step approach had a significantly lower risk of preterm birth (PTB) (3.7 versus 7.6%; RR 0.49, 95%CI 0.27–0.88), cesarean delivery (16.3 versus 22.0%; RR 0.74, 95%CI 0.56–0.99), macrosomia (2.9 versus 6.9%; RR 0.43, 95%CI 0.22–0.82), neonatal hypoglycemia (1.7 versus 4.5%; RR 0.38, 95%CI 0.16–0.90), and admission to neonatal intensive care unit (NICU) (4.4 versus 9.0%; RR 0.49, 95%CI 0.29–0.84), compared to those randomized to screening with the two step approach. Conclusions: The one and the two step approaches were not associated with a significant difference in the incidence of GDM. However, the one step approach was associated with better maternal and perinatal outcomes.
Characterization of liver function in transdifferentiated hepatocytes

We previously demonstrated that dexamethasone (Dex) induces the transdifferentiation (or conversion) of the pancreatic progenitor cell line AR42J‐B13 (B13) to hepatocytes based on the expression of liver proteins. We have extended our original observations to determine: (1) the effects of Dex on pancreatic gene expression; (2) the time course of expression of liver enriched transcription factors during conversion from pancreatic to hepatic phenotype; (3) the functional potential of transdifferentiated hepatocytes; (4) the proliferative capacity of transdifferentiated hepatocytes; and (5) whether ectopic expression of transcription factors can induce the hepatic phenotype in pancreatic B13 cells. The results were as follows. The B13 cell markers amylase, synaptophysin, and neurofilament were lost in transdifferentiated hepatocytes compared to control cells and the liver enriched transcription factors C/EBPβ and C/EBPα were induced first, followed by HNF4α and then RXRα. Using RT‐PCR analysis and immunolocalisation studies, we detected hepatic markers (e.g., apolipoprotein B) in Dex‐treated cells. In transdifferentiated hepatocytes albumin was secreted, insulin stimulated lipid deposition and ciprofibrate enhanced the expression of catalase. Proliferation of transdifferentiated hepatocytes is promoted in the presence of HGF and NEAA as indicated by the co‐expression of the cell cycle markers cyclin D and phosphohistone H3 with liver proteins. Lastly, ectopic expression of C/EBPα or C/EBPβ in AR42J‐B13 cells was sufficient to induce transdifferentiation, based on nuclear localization of HNF4α and induction of UDP‐glucuronosyltransferase expression. These results indicate that the B13 progenitor cell model is suitable for studying liver function and for understanding the molecular and cellular events that occur during transdifferentiation. © 2005 Wiley‐Liss, Inc.
Physically-based simulation of cracks on drying 3D solid

This paper describes a new physically based method for synthesizing 3D cracking patterns in clay solids by incorporating a moisture model. We measure temporal transitions of the physical parameters used in the model. Then we describe a new approach to synthesize cracking patterns in a 3D freeform object by its approximate quantized shape and the mesh relation of its original shape. With this new method, an animated synthesis of not only external cracks but also internal cracks of 3D freeform solids is possible.
The unexpected discovery of blind snakes (Serpentes: Typhlopidae) in Micronesia: two new species of Ramphotyphlops from the Caroline Islands

Two new blind snakes in the genus Ramphotyphlops are described from Ulithi (R. hatmaliyeb sp. nov.) and Ant Atoll (R. adocetus sp. nov.) in the Caroline Islands, the first blind snake species known from Micronesia east of Palau (excluding Ramphotyphlops braminus). Both species are unusual in being known only from small, low-lying atolls. They can be dis-tinguished from other Ramphotyphlops by the combination of 22 scale rows over the length of the body; a wedge-shaped snout, without a keratinized keel; and a broad, pyriform (R. adocetus) or ovate (R. hatmaliyeb) rostral scale.
Reactivation of occult hepatitis B virus infection following cytotoxic lymphoma therapy in an anti‐HBc negative patient

Screening hepatitis B virus (HBV) surface antigen (HBsAg) and HBV core antibody (anti‐HBc) is recommended prior to cytotoxic or immunosuppressive therapy. This case describes an anti‐HBc negative, DNA positive occult HBV infection in a 71‐year‐old Caucasian male following rituximab‐based treatment for follicular lymphoma. Pre‐screening serology indicated negative HBsAg and anti‐HBc. However, following sequential treatment cycles the patient developed weak HBsAg with a low HBV DNA load (<1,000 IU/ml), but remained anti‐HBc negative. The DNA load peaked 5 months later (>1 × 106 IU/ml) and he was subsequently treated with Tenofovir. Currently the patient remains anti‐HBc negative, and is anti‐HBe negative, anti‐HBs negative, HBeAg positive. No clinical or biochemical evidence of hepatitis has occurred. Sequencing and phylogenetic analysis identified the HBV genosubtype as D4, most probably acquired some years ago during a stay in Papua New Guinea, in spite of prior hepatitis B vaccination. Four amino acid substitutions were detected within the HBsAg loop yet none in the core protein. This case questions the dependability of anti‐HBc testing and highlights the role of HBV DNA testing prior to and throughout cytotoxic or immunosuppressive regimes. As this case exemplifies, vaccination protects against clinical infection but may not exclude seronegative occult infection with the possibility of reactivation. J. Med. Virol. 85:597–601, 2013. © 2013 Wiley Periodicals, Inc.
Nonhuman primate hybridization and the taxonomic status of Neanderthals.

The present study examines the taxonomic status of Middle Paleolithic Neanderthals by comparing their observed minimum genetic divergence from Upper Paleolithic modern humans in Europe with that observed between macaque species from Sulawesi that are known to hybridize and fully intergrade in the wild. The genetic divergence, and differentiation between Neanderthals and Upper Paleolithic modern humans, as indicated by pairwise minimum genetic distances and F(ST) values calculated from the estimated minimum genetic relationship (R) matrix derived from craniometric data, are significantly greater than those observed both between hybridizing and noninterbreeding Sulawesi macaque species, suggesting that mate recognition and the possibility of gene flow between Neanderthals and Upper Paleolithic modern humans might have been greatly reduced. These results support a species-level taxonomic distinction for the Neanderthals as suggested by proponents of the replacement model. Furthermore, assumptions regarding the monophyletic origin of modern humans from outside Europe are likely valid.
The plasmid status of satellite bacteriophage P4.

P4 is a natural phasmid (phage-plasmid) that exploits different modes of propagation in its host Escherichia coli. Extracellularly, P4 is a virion, with a tailed icosahedral head, which encapsidates the 11.6-kb-long double-stranded DNA genome. After infection of the E. coli host, P4 DNA can integrate into the bacterial chromosome and be maintained in a repressed state (lysogeny). Alternatively, P4 can replicate as a free DNA molecule; this leads to either the lytic cycle or the plasmid state, depending on the presence or absence of the genome of a helper phage P2 in the E. coli host. As a phage, P4 is thus a satellite of P2 phage, depending on the helper genes for all the morphogenetic functions, whereas for all its episomal functions (integration and immunity, multicopy plasmid replication) P4 is completely autonomous from the helper. Replication of P4 DNA depends on its alpha protein, a multifunctional polypeptide that exhibits primase and helicase activity and binds specifically the P4 origin. Replication starts from a unique point, ori1, and proceeds bidirectionally in a straight theta-type mode. P4 negatively regulates the plasmid copy number at several levels. An unusual mechanism of copy number control is based on protein-protein interaction: the P4-encoded Cnr protein interacts with the alpha gene product, inhibiting its replication potential. Furthermore, expression of the replication genes cnr and alpha is regulated in a complex way that involves modulation of promoter activity by positive and negative factors and multiple mechanisms of transcription elongation-termination control. Thus, the relatively small P4 genome encodes mostly regulatory functions, required for its propagation both as an episomal element and as a temperate satellite phage. Plasmids that, like P4, propagate horizontally via a specific transduction mechanism have also been found in the Archaea. The presence of P4-like prophages or cryptic prophages often associated with accessory bacterial functions attests to the contribution of satellite phages to bacterial evolution.
Incremental Machine Learning Approach for Component-based Recognition

This study proposes an on-line machine learning approach for object recognition, where new images are continuously added and the recognition decision is made without delay. Random forest (RF) classifier has been extensively used as a generative model for classification and regression applications. We extend this technique for the task of building incremental component-based detector. First we employ object descriptor model based on bag of covariance matrices, to represent an object region then run our on-line RF learner to select object descriptors and to learn an object classifier. Experiments of the object recognition are provided to verify the effectiveness of the proposed approach. Results demonstrate that the propose model yields in object recognition performance comparable to the benchmark standard RF, AdaBoost, and SVM classifiers.
Activation of a Ribosomal S6 Protein Kinase in Rapidly Emerging Diethylnitrosamine-Induced Gamma - Glut Amyltranspeptidase-Positive Hyperplastic Liver Lesions of the Rat

The gamma-glutamyl transpeptidase (GGT)-positive hyperplastic liver lesions which developed in the Fisher 344 rat 7 and 60 days following a single carcinogenic dose of diethylnitrosamine (DENA, 200 mg/kg body weight), short-term dietary exposure to 0.02 % 2-acetylaminofluorene (AAF) to suppress the growth of normal hepatocytes, and partial hepatectomy to actuate rapid growth of DENA altered hepatocytes not suppressed by AAF, showed an increased activity of a kinase which specifically phosphorylates the ribosomal S6 protein in vitro. Sham-operated animals showed, on the contrary, no GGT-positive cells and low S6 kinase activity, under the same conditions. After partial hepatectomy, activation of S6 kinase and elevated levels of phosphorylated S6 protein in vitro were detected in the early phases of « normal » hepatocyte proliferation, during liver regeneration, in DENA-treated, GGT-negative preparations, when the « selection » agent AAF was omitted from the diet. The observed activation of S6 kinase in GGT-positive hepatocytes and/or liver nodules could represent an early manifestation of the enhanced proliferation of altered hepatocytes during tumor induction and/or promotion under these conditions.
Orthogonal PLS (OPLS) Modeling for Improved Analysis and Interpretation in Drug Design

Partial least squares (PLS) regression is a flexible data analytical approach, which can be made even more versatile and useful by various modifications. In this article we describe the extension into orthogonal PLS modeling, in terms of two new methods, called OPLS and O2PLS, with similar prediction capacity but improved model interpretation.
Performance of chick pea under the influence of gibberellic acid and oxygenated peptone during germination

The experiments were carried out at the Post Graduate Research Center, to study the influence of Gibberellic Acid (50 ppm) and Oxygenated Peptone (1% aqueous solution) on chick pea (Cicer arietinum L. cv. Vijay) during germination by giving pre-sowing soaking treatment for 6 hours using petriplate method. Both the treatments enhanced the germination process. GA treatment was useful to increase shoot length, mobilization efficiency, emergence index, speed of germination and co-efficient of germination while oxygenated peptone showed an upper hand in root length, shoot/root ratio, biomass and vigour index. GA led to comparatively more synthesis of nucleic acids while oxygenated peptone showed more increase in total carbohydrates and soluble protein content. However, the activity of enzymes like amylase, catalase and protease showed upper hand with oxygenated peptone as compared to GA. In fact GA is costlier and can not be used in organic farming as it enters metabolic pathways of plant and alters them. Hence the use of oxygenated peptone is recommended being less expensive and usable under organic farming condition as it does not enter the plant metabolic pathways and yet brings about significant positive effect.
Uncovering New Metabolic Capabilities of Bacillus subtilis Using Phenotype Profiling of Rifampin-Resistant rpoB Mutants

ABSTRACT RNA polymerase is a central macromolecular machine controlling the flow of information from genotype to phenotype, and insights into global transcriptional regulation can be gained by studying mutational perturbations in the enzyme. Mutations in the RNA polymerase β subunit gene rpoB causing resistance to rifampin (Rifr) in Bacillus subtilis were previously shown to lead to alterations in the expression of a number of global phenotypes known to be under transcriptional control, such as growth, competence for transformation, sporulation, and germination (H. Maughan, B. Galeano, and W. L. Nicholson, J. Bacteriol. 186:2481-2486, 2004). To better understand the global effects of rpoB mutations on metabolism, wild-type and 11 distinct congenic Rifr mutant strains of B. subtilis were tested for utilization of 95 substrates by use of Biolog GP2 MicroPlates. A number of alterations of substrate utilization patterns were observed in the Rifr mutants, including the utilization of novel substrates previously unknown in B. subtilis, such as gentiobiose, β-methyl-d-glucoside, and d-psicose. The results indicate that combining global metabolic profiling with mutations in RNA polymerase provides a system-wide approach for uncovering previously unknown metabolic capabilities and further understanding global transcriptional control circuitry in B. subtilis.
RETE and chart parsing from bottom-up call-graph caching

A new mechanism is presented for graph instantiation. It is used to investigate various bottom-up data-driven AI algorithms. The author views instances as fairly autonomous objects that inherit graph information (e.g. links or relations) from their classes. Instances themselves can be instantiated. For example, a parse tree symbol is an instance of a grammar class-graph symbol, which itself is a symbol of instance. The model focuses on underlying computational processes, and makes little use of program text. Instead of transforming programs, CGC (call graph caching) is used to instantiate processes. Experimental results show that RETE matching, efficient context-free parsing, and truth maintenance are different manifestations of the same underlying computational process. <<ETX>>
Effects of Subthreshold Shocks on Wavelet Propagation during Atrial Fibrillation in Humans

Summary Objectives: Our objectives are: first to investigate the effects of internal cardioversion energies on the wave fronts propagation in the right atrium immediately after the energy delivery; second, to track the time course of these effects. Methods: The study is based on a measure of organization of the endoatrial electrograms obtained by a multipolar basket catheter inserted in the right atrium. We estimated the level of organization by computing the percentage of points laying on the signal baseline (i.e., number of occurrences, NO). NO values were computed on two-second long windows. Six non-overlapped windows were selected, one just before and five just after the last unsuccessful shock. Results: Immediately after the shock most of the patients exhibited an increase in the organization patterns. This increase was more evident in those patients with rather disorganized patterns and higher energy threshold. This effect fades within a few seconds after the shock delivery. Conclusions: Our data confirm the idea that the electrical shock causes a widespread extinction of electrical wavefronts, which regenerates after the shock. Since an increase of organization may lead to a reduction of energy threshold, a potential application of these findings might consist in the delivery of multiple subthreshold shocks instead of a single one.
Characterization of the Interaction of the Stress Kinase SPAK with the Na+-K+-2Cl– Cotransporter in the Nervous System

Activity of heterologously expressed NKCC1 was analyzed under basal and activated conditions in the presence and absence of binding of Ste20-related proline-alanine-rich kinase (SPAK). Mutant NKCC1 that lacks the ability to bind to this kinase showed K+ transport function identical to wild-type NKCC1. Thus, preventing the binding of the kinase to the cotransporter does not affect cotransporter function. In contrast, several experiments suggest a possible role for SPAK as a scaffolding protein. First, Western blot analysis revealed the presence, and in some tissues abundance, of truncated forms of SPAK and OSR1 in which the kinase domains are affected and thus lack kinase activity. Second, a yeast two-hybrid screen of proteins that interact with the regulatory (binding) domain of SPAK identified several proteins all involved in cellular stress pathways. Third, p38, one of the three major MAPKs, can be coimmunoprecipitated with SPAK and with NKCC1 in an activity-dependent manner. The amount of p38 coimmunoprecipitated with the kinase and the cotransporter significantly decreases upon cellular stress, whereas the interaction of the kinase with NKCC1 remains unchanged. These findings suggest that cation-chloride cotransporters might act as “sensors” for cellular stress, and SPAK, by interacting with the cotransporter, serves as an intermediate in the response to cellular stress.
Common-path heterodyne interferometric and magnetic sensitivity-enhanced surface plasmon resonance carbon monoxide gas sensor

Combining magnetic catalysis effect, surface plasmon resonance phenomena, and common-path heterodyne interferometry, a highly sensitive and highly stable carbon monoxide sensing technique was proposed in this paper. Magnetic catalysis material SnO2-Fe3O4 was prepared and was spin coated on the gold film of SPR prism. The SPR apparatus can provide a highly sensitive ability to carbon monoxide. Carbon monoxide gas at different concentrations was measured under different strengths of applied magnetic fields. The experimental results reveal that the system has a best resolution of 0.0507 ppm applied 24 Gauss magnetic field in normal direction. Due to the introduction of common-path heterodyne interferometer, the system is stable against environment vibrations.
A Survey on Routing Techniques in Wireless Sensor Network

: Wireless Sensor Networks (WSNs) comprised of small nodes embedded with sensing, computation and wireless communications capabilities. Power management, routing and data aggregation techniques have been specifically designed for WSNs where energy consumption is a critical design issue. The emphasis, however, has been laid on the routing protocols which can be different from each other depending on the application, operation and network architecture. In this paper first the design issues for routing protocols in WSNs are discussed after that a comprehensive survey of different routing techniques are given.