Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibodies That Detect O-Linked β-d-N-Acetylglucosamine on the Extracellular Domain of Cell Surface Glycoproteins*

Background: Seven antibodies that detect cytosolic and nuclear O-GlcNAc were examined for recognition of O-GlcNAc on cell surface glycoproteins. Results: Three antibodies recognized cell surface O-GlcNAc and also bound terminal β-GlcNAc on N-glycans. Conclusion: With careful controls, cell surface O-GlcNAc can be detected using antibodies CTD110.6, 18B10.C7, and 9D1.E4. Significance: Antibodies to monitor cell surface O-GlcNAcylated proteins were characterized. The transfer of N-acetylglucosamine (GlcNAc) to Ser or Thr in cytoplasmic and nuclear proteins is a well known post-translational modification that is catalyzed by the O-GlcNAc transferase OGT. A more recently identified O-GlcNAc transferase, EOGT, functions in the secretory pathway and transfers O-GlcNAc to proteins with epidermal growth factor-like (EGF) repeats. A number of antibodies that detect O-GlcNAc in cytosolic and nuclear extracts have been described previously. Here we compare seven of these antibodies (CTD110.6, 10D8, RL2, HGAC85, 18B10.C7(#3), 9D1.E4(#10), and 1F5.D6 (#14) for detection of the O-GlcNAc modification on extracellular domains of membrane or secreted glycoproteins that may also carry various N- and O-glycans. We found that CTD110.6 binds not only to O-GlcNAc on proteins but also to terminal β-GlcNAc on the complex N-glycans of Lec8 Chinese hamster ovary (CHO) cells that lack UDP-Gal transporter activity and express GlcNAc-terminating, complex N-glycans. We show that CTD110.6, #3, and #10 antibodies can be used to detect cell surface glycoproteins bearing O-GlcNAc. Cell surface glycoproteins recognized by CTD110.6 antibody included NOTCH1 that possesses many EGF repeats with a consensus site for EOGT. Knockdown of CHO Eogt reduced binding of CTD110.6 to Lec1 CHO cells, and expression of a human EOGT cDNA increased the O-GlcNAc signal on Lec1 cells and the extracellular domain of NOTCH1. Thus, with careful controls, antibodies CTD110.6 (IgM), #3 (IgG), and #10 (IgG) can be used to detect membrane and secreted proteins modified by O-GlcNAc on EGF repeats.
CYP2C19*2 and CYP2C9*3 alleles are associated with stent thrombosis: a case-control study.

AIMS despite treatment with clopidogrel on top of aspirin, stent thrombosis (ST) still occurs being the most serious complication after percutaneous coronary interventions (PCIs). In this study, we aimed to determine the effect of variations in genes involved in the absorption (ABCB1 C1236T, G2677T/A, C3435T), metabolism (CYP2C19*2 and *3, CYP2C9*2 and *3, CYP3A4*1B and CYP3A5*3), and pharmacodynamics (P2Y1 A1622G) of clopidogrel on the occurrence of ST. METHODS AND RESULTS the selected genetic variants were assessed in 176 subjects who developed ST while on dual antiplatelet therapy with aspirin and clopidogrel and in 420 control subjects who did not develop adverse cardiovascular events, including ST, within 1 year after stenting. The timing of the definite ST was acute in 66, subacute in 87, and late in 23 cases. The presence of the CYP2C19*2 and CYP2C9*3 variant alleles was significantly associated with ST (OR(adj): 1.7, 95% CI: 1.0-2.6, P = 0.018 and OR(adj): 2.4, 95% CI: 1.0-5.5, P = 0.043, respectively). The influence of CYP2C19*2 (OR(adj): 2.5, 95% CI: 1.1-5.5, P = 0.026) and CYP2C9*3 (OR(adj): 3.3, 95% CI: 1.1-9.9, P = 0.031) was most strongly associated with subacute ST. No significant associations of the other genetic variations and the occurrence of ST were found. CONCLUSION carriage of the loss-of-function alleles CYP2C19*2 and CYP2C9*3 increases the risk on ST after PCI.
HS1 deficiency impairs neutrophil recruitment in vivo and activation of the small GTPases Rac1 and Rap1

Neutrophil extravasation is a critical step of the innate immune system's response to inflammation. This multistep process is tightly regulated by adhesion and signaling molecules in the endothelium and neutrophils. Activation of the β2 integrin LFA‐1 is critical for adhesion of leukocytes to postcapillary venules. This step requires coordinated activation of signaling pathways in chemokine‐stimulated neutrophils, including GTPase activation and cytoskeletal remodeling, leading to conformational changes in LFA‐1. Hematopoietic cell‐specific lyn substrate 1 (HS1) is a cortactin‐related and leukocyte‐specific actin‐binding protein (ABP) that regulates several processes in various immune cells. It has been shown in vitro that HS1 is important for neutrophil chemotaxis and transendothelial migration of NK cells, but its role in neutrophil extravasation in vivo has not been investigated yet. Intravital microscopy of CXCL1‐stimulated cremaster venules revealed an increased rolling velocity and reduced neutrophil adhesion and transmigration in HS1 knockout (KO) mice. CXCL1‐induced rapid neutrophil arrest in vivo and adhesion under flow conditions in vitro were also reduced significantly. Whereas random motility of neutrophils was unaffected, chemotaxis toward a CXCL1 gradient was reduced in the absence of HS1. Further analysis of the underlying mechanisms demonstrated that HS1 controls CXCL1‐induced activation of the small GTPases Ras‐related C3 botulinum toxin substrate 1 (Rac1) and Ras‐related protein 1 (Rap1), thus supporting LFA‐1‐mediated neutrophil adhesion. Importantly, with the use of Rac1 KO neutrophils, we could show that Rac1 acts upstream of Rap1. Our results establish HS1 as an important regulator of proper Rac1 and Rap1 activation and neutrophil extravasation.
The Use of Global Profiling in Biomarker Development for Gliomas

The diffuse gliomas are a heterogeneous group of malignancies with highly variable outcomes and diagnosis is largely based on the histological appearance of the tumors. Tumor classification according to cello type and grade provides some prognostic information. However, the diversity of gliomas, within tumor type and grade categories, has made prognostic determinations based purely on clinicopathologic variables difficult. There is an increasing body of data suggesting a significant amount of molecular diversity accounts for the heterogeneity of clinical observations, such as response to treatment and time to progression. The last decade has witnessed an explosive advance in our knowledge of the molecular genetics of brain tumors, due in large part to the availability of high‐throughput profiling techniques, including new sequencing methodologies as well as multidimensional profiling by the Cancer Genome Atlas project. The large amount of data generated by these efforts has enabled the identification of prognostic and predictive factors and helping to identify pathways that are driving tumor growth. Identification of biomarkers, especially when coupled to clinical trials of newer targeted therapies, will enable better patient stratification and individualization of treatment.
The Role of Lower Airway Dysbiosis in Asthma: Dysbiosis and Asthma

With the development of culture-independent techniques, numerous studies have demonstrated that the lower airway is not sterile in health and harbors diverse microbial communities. Furthermore, new evidence suggests that there is a distinct lower airway microbiome in those with chronic respiratory disease. To understand the role of lower airway dysbiosis in the pathogenesis of asthma, in this article, we review the published reports about the lung microbiome of healthy controls, provide an outlook on the contribution of lower airway dysbiosis to asthma, especially steroid-resistant asthma, and discuss the potential therapies targeted for lower airway dysbiosis.
Compiler verification in the context of pervasive system verification

This thesis presents the formal verification of the compiling specification for a simple, non-optimizing compiler from the C-like programming language C0 to VAMP assembly code. The main result is a step-by-step simulation theorem between C0 programs and the compiled code (which is specified by the compiling specification). Additionally, a C0 small-step semantics and a verification methodology for VAMP assembly have been developed. This work is part of the Verisoft project which aims at the pervasive formal verification of an entire computer system. The key concept in Verisoft’s methodology is to prove properties of computer systems at the relatively abstract C0 layer and to transfer them via several intermediate layers down to the concrete hardware layer. After successful transfer of a property to the hardware layer, we can be sure that no oversimplifications have been done in the formalizations of the more abstract layers. This context of pervasive system verification imposes several special requirements to our compiler correctness theorem. In particular, the simulation theorem had to be formulated based on small-step semantics to allow for reasoning about non-terminating and interleaving programs. Another important feature is that our result incorporates resource restrictions at the hardware layer and allows to discharge them at the C0 layer. All results presented in this thesis have been formalized in the theorem prover Isabelle / HOL.
Method and apparatus for measuring the moisture content of the biological material

How to measure automatically operating the water content of the biological material is disclosed. Said method: comprising the step of providing a reference database of known plurality of different materials types in accordance with the moisture content. Additionally, wood chips, pulp, grain, crop or the biological material sample, such as sugarcane, is scanned with electromagnetic radiation of at least two different energy levels, and the transmitted through the sample of the biological material 2 One of determining the amount of radiation with different energy levels. Then, the most similar material types in the biological material of the sample, the material type specified, and the water content of the biological material samples were identified from among the reference database, and the sample determined on the basis of the amount calculated for the transmitted radiation.
Ieee Transactions on Visualization and Computer Graphics 1 Fracturing Rigid Materials

— We propose a novel approach to fracturing (and denting) brittle materials. To avoid the computational burden imposed by the stringent time step restrictions of explicit methods or with solving nonlinear systems of equations for implicit methods, we treat the material as a fully rigid body in the limit of infinite stiffness. In addition to a triangulated surface mesh and level set volume for collisions, each rigid body is outfitted with a tetrahedral mesh upon which finite element analysis can be carried out to provide a stress map for fracture criteria. We demonstrate that the commonly used stress criteria can lead to arbitrary fracture (especially for stiff materials) and instead propose the notion of a time averaged stress directly into the FEM analysis. When objects fracture, the virtual node algorithm provides new triangle and tetrahedral meshes in a straightforward and robust fashion. Although each new rigid body can be rasterized to obtain a new level set, small shards can be difficult to accurately resolve. Thus we propose a novel collision handling technique for treating both rigid bodies and rigid body thin shells represented by only a triangle mesh.
Fourier transform for the spatial quincunx lattice

We derive a new, two-dimensional nonseparable signal transform for computing the spectrum of spatial signals residing on a finite quincunx lattice. The derivation uses the connection between transforms and polynomial algebras, which has long been known for the discrete Fourier transform (DFT), and was extended to other transforms in recent research. We also show that the new transform can be computed with O(n/sup 2/ log(n)) operations, which puts it in the same complexity class as its separable counterparts.
Dynamic rate adaptation and integrated rate and error control in cellular WCDMA networks

Optimal dynamic rate allocation among mobile stations for variable rate packet data transmission in a cellular wireless network is an NP-complete problem; therefore, suboptimal solutions to this problem are sought for. In this paper, three novel suboptimal dynamic rate adaptation schemes, namely, peak-interference-based rate allocation, sum-interference-based rate allocation, and mean-sense approximation-based rate allocation, are proposed for uplink packet data transmission in cellular variable spreading factor wide-band code division multiple access (WCDMA) networks. The performances of these schemes are compared to the performance of the optimal dynamic link adaptation for which the rate allocation is found by an exhaustive search. The optimality criterion is the maximization of the average number of radio link level frames transmitted per frame time under constrained signal-to-interference-plus-noise ratio (SINR) at the base station receiver. Two different error control alternatives for variable rate packet transmission environment are presented. We demonstrate that the dynamic rate adaptation problem under constrained SINR can be mapped into the radio link level throughput maximization problem with integrated rate and error control. Performance evaluation is carried out under random and directional micromobility models with uncorrelated and correlated long-term fading, respectively, in a cellular WCDMA environment for both the homogeneous (or uniform) and the nonhomogeneous (or nonuniform) traffic load scenarios.
Coordinate lentiviral expression of Cre recombinase and RFP/EGFP mediated by FMDV 2A and analysis of Cre activity

The site‐specific recombination mediated by Cre recombinase has been utilized extensively in genetic engineering and gene function studies. Efficient delivery of a Cre enzyme with enzymatic activity and the ability to monitor the enzyme expression are required in applications, and lentiviral constructs with a fluorescent protein (FP) to report the Cre expression are suitable for most studies. However, the current lentiviral vector systems have some deficiencies in precise reporting the Cre expression through fluorescence. To solve the problem, we generated a lentiviral system with Cre and RFP or EGFP bridged by an FMDV 2A sequence in an open reading frame expressed by a CMV promoter. We then examined the capabilities of the constructs to package with VSVG into infectious virus and to mediate expression of the Cre enzyme and fluorescent reporter. Furthermore, we monitored the bioactivities of the expressed products. We demonstrated the coordinate expression of the enzyme and the reporter. The expressed Cre was efficient at removing LoxP‐flanked fragments in cells and did not show obvious cellular toxicity, and the expressed FPs allowed direct observation under fluorescent microscope. Therefore, the conjugation of CMV‐Cre‐2A‐FP represents a significant improvement to the current lentiviral Cre delivery systems for obtaining a required Cre activity while accurately monitoring its presence. Our study also provides information concerning application of the established vector system. J. Cell. Biochem. 113: 2909–2919, 2012. © 2012 Wiley Periodicals, Inc.
Genetic analysis of second-site revertants of bacteriophage lambda integrase mutants

Bacteriophage lambda site-specific recombination is catalyzed by the phage-encoded integrase (Int) protein. Using a collection of 21 recombination-defective Int mutants, we performed a second-site reversion analysis. One of the primary mutants contained a valine-to-glutamic acid change at position 175 (V175E), and a pseudorevertant with a lysine change at this site (V175K) was also isolated. Relative to the wild-type protein, the V175E protein was defective in its ability to form the attL complex and to catalyze excision in vivo and in vitro. A mutant containing an alanine substitution (V175A) was made by site-directed mutagenesis, and it was more efficient than the V175K protein in forming the attL complex and promoting excision. These results indicate that a nonpolar side chain at residue 175 is required for function. The second primary mutant contained a proline-to-leucine change at position 243 (P243L). A true second-site revertant was isolated that contained a glutamic acid-to-lysine change (E218K). The P243L-E218K protein promoted recombination and bound arm-type sites more efficiently than the original P243L protein but not as efficiently as the protein containing the E218K substitution alone. The E218K substitution also restored activity to a mutant with a threonine-to-isoleucine substitution at position 270 (T270I). This result showed that suppression by the E218K change is not allele specific and suggests that the substitution improves an inherent activity of Int rather than directly compensating for the defect caused by the primary substitutions. Results with challenge phages carrying attL sites with altered core sites indicate that the E218K change may improve binding to the core site.
Identification of fault location in power distribution system with distributed generation using support vector machines

This paper presents a multi-class support vector machine (SVMs) approach for locating and diagnosing faults in electric power distribution feeders with the penetration of Distributed Generations (DGs). The proposed approach is based on the three phase voltage and current measurements which are available at all the sources i.e. substation and at the connection points of DG. To illustrate the proposed methodology, a practical distribution feeder emanating from 132/11kV-grid substation in India with loads and suitable number of DGs at different locations is considered. To show the effectiveness of the proposed methodology, practical situations in distribution systems (DS) such as all types of faults with a wide range of varying fault locations, source short circuit (SSC) levels and fault impedances are considered for studies. The proposed fault location scheme is capable of accurately identify the fault type, location of faulted feeder section and the fault impedance. The results demonstrate the feasibility of applying the proposed method in practical in smart grid distribution automation (DA) for fault diagnosis.
Effect of Dietary Intake of Isoflavones on the Estrogen and Progesterone Receptor Status of Breast Cancer

To examine if higher intake of isoflavones prior to diagnosis was associated with a positive status of estrogen receptors (ER) and progesterone receptors (PR) in breast tumor tissue, a retrospective study was conducted in 2004 to 2005 in 756 Chinese women with histologically confirmed breast cancer. We administered a food frequency questionnaire by face-to-face interview to assess the intake of the isoflavones daidzein and genistein. Unconditional logistic regression analysis was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) adjusted for potential confounders. Comparing the highest to lowest intake quartiles, the adjusted ORs for daidzein were 1.94 (95% CI = 1.20–3.32) and 2.18 (95% CI = 1.28–3.73) for ER positive and PR positive tumors, respectively, in premenopausal patients. The ORs for both ER and PR positive status combined were 2.48 (95% CI = 1.37–4.49) for daidzein and 1.94 (95% CI = 1.21–3.14) for genistein in premenopausal patients with statistically significant tests for trend. There was little or no evidence of associations in postmenopausal patients. We conclude that higher intake of daidzein and genistein before diagnosis was associated with ER and PR positive status in premenopausal Chinese women with breast cancer. The association might confer a more favorable prognosis.
Theory of Mind as a potential trait marker of schizophrenia: A family study

Introduction. Although there is some evidence that Theory of Mind (ToM) deficits may be trait markers of schizophrenia it is not clear yet if ToM deficits are primary deficits, that is, to be independent of deficits in general intellectual abilities and executive function. The aim was to examine if ToM deficits may be trait markers of the illness and the effect of cognitive inhibition, general intellectual abilities and depression on ToM abilities of patients with schizophrenia and their unaffected parents. Methods. We assessed ToM abilities (first-order and second-order ToM stories, The Revised Eyes Test), cognitive inhibition (Stroop Task), general intellectual ability (Standard Progressive Matrices Test Plus) in patients with schizophrenia (N=21) and their unaffected fathers (N=21) and mothers (N=21) in comparison with healthy control families (healthy control males, N=21, healthy control fathers, N=21, healthy control mothers, N=21) Results. Patients showed deficits in first-order ToM tasks but some of these deficits were mediated by general intellectual abilities. Impairments in cognitive inhibition mediated only patients’ performance in The Revised Eyes Test. Patients showed deficits in second-order ToM stories independently of deficits in general intellectual abilities and cognitive inhibition. Unaffected parents did not show deficits in first-order ToM tasks, whereas they showed deficits in second-order ToM stories. However, the deficits that unaffected parents showed in second-order ToM stories were mediated by their deficits in general intellectual abilities, and there was an effect of remitted depression on the unaffected mothers’ performance. Conclusions. The results suggest that intact neurocognitive and general intellectual abilities are necessary in order patients and their unaffected parents to pass successfully ToM tasks. Patients and their unaffected parents show ToM deficits but these deficits are not similar. Patients show ToM deficits but these deficits seem to be a component of the pathophysiology of the illness (e.g., deficits in executive function, general intellectual abilities).
Causal Inference in the Social Sciences: Variance Theory, Process Theory, and System Dynamics

The social sciences are in need of an alternative to the variance approach to causal inference, which—because it requires a counterfactual—restricts the claim of valid inference to conclusions drawn from experimental and quasi-experimental methods. Process theory proposes an alternative by way of demonstrating the presence of observable characteristics of the causal mechanism, a method that, while accepted in principle, has proven elusive in practice. It is suggested that system dynamics can improve the process approach, and in so doing open a path for itself to wider application in the social sciences. Educational research is suggested as a place to start, and results from two models drawn on topics from that field are offered as examples.