Miracle-dz/UniFAR-FTUs huggingface dataset:
Early transcriptomic events in microdissected Arabidopsis nematode-induced giant cells.

Root-knot nematodes differentiate highly specialized feeding cells in roots (giant cells, GCs), through poorly characterized mechanisms that include extensive transcriptional changes. While global transcriptome analyses have used galls, which are complex root structures that include GCs and surrounding tissues, no global gene expression changes specific to GCs have been described. We report on the differential transcriptome of GCs versus root vascular cells, induced in Arabidopsis by Meloidogyne javanica at a very early stage of their development, 3 days after infection (d.p.i.). Laser microdissection was used to capture GCs and root vascular cells for microarray analysis, which was validated through qPCR and by a promoter-GUS fusion study. Results show that by 3 d.p.i. , GCs exhibit major gene repression. Although some genes showed similar regulation in both galls and GCs, the majority had different expression patterns, confirming the molecular distinctiveness of the GCs within the gall. Most of the differentially regulated genes in GCs have no previously assigned function. Comparisons with other transcriptome analyses revealed similarities between GCs and cell suspensions differentiating into xylem cells. This suggests a molecular link between GCs and developing vascular cells, which represent putative GC stem cells. Gene expression in GCs at 3 d.p.i. was also found to be similar to crown galls induced by Agrobacterium tumefaciens, a specialized root biotroph.
Autonomous Growth of Isolated Single Listeria monocytogenes and Salmonella enterica Serovar Typhimurium Cells in the Absence of Growth Factors and Intercellular Contact

ABSTRACT The aim of this study was to observe growth of isolated single bacterial cells in the absence of growth factors and intercellular contact. In order to exclude stochastic uncertainties induced by dilution series, a new micromanipulation method was developed to ensure explicit results under visual control. This was performed with particular care for production of single prokaryotic cells and subsequent investigation of their autonomous growth. Over 450 single isolated Listeria monocytogenes and Salmonella enterica subsp. enterica serovar Typhimurium cells in lag, log, and stationary growth phases were investigated by this method, which included thoroughly washing the cells. The proportion of living cells within the initial cultures was compared to the proportion of positive samples after enrichment of the separated single cells. This resulted in P values of ≥0.05 using the chi-square test for statistical analysis, indicating no significant difference, and clearly demonstrates reproduction of isolated single bacterial cells without the need for growth factors or intercellular contact. Ease of handling of the apparatus and good performance of the cleaning procedures were achieved, as was validation of the method, demonstrating its suitability for routine laboratory use.
UNCERTAINTIES ANALYSIS FOR THE PLUTONIUM DOSIMETRY MODEL, DOSES-2005, USING MAYAK BIOASSAY DATA

The Doses-2005 model is a combination of the International Commission on Radiological Protection (ICRP) models modified using data from the Mayak Production Association cohort. Surrogate doses from inhaled plutonium can be assigned to approximately 29% of the Mayak workers using their urine bioassay measurements and other history records. The purpose of this study was to quantify and qualify the uncertainties in the estimates for radiation doses calculated with the Doses-2005 model by using Monte Carlo methods and perturbation theory. The average uncertainty in the yearly dose estimates for most organs was approximately 100% regardless of the transportability classification. The relative source of the uncertainties comes from three main sources: 45% from the urine bioassay measurements, 29% from the Doses-2005 model parameters, and 26% from the reference masses for the organs. The most significant reduction in the overall dose uncertainties would result from improved methods in bioassay measurement with additional improvements generated through further model refinement. Additional uncertainties were determined for dose estimates resulting from changes in the transportability classification and the smoking toggle. A comparison was performed to determine the effect of using the model with data from either urine bioassay or autopsy data; no direct correlation could be established. Analysis of the model using autopsy data and incorporation of results from other research efforts that have utilized plutonium ICRP models could improve the Doses-2005 model and reduce the overall uncertainty in the dose estimates.
Volume and density of microglomeruli in the honey bee mushroom bodies do not predict performance on a foraging task

The mushroom bodies (MBs) are insect brain regions important for sensory integration, learning, and memory. In adult worker honey bees (Apis mellifera), the volume of neuropil associated with the MBs is larger in experienced foragers compared with hive bees and less experienced foragers. In addition, the characteristic synaptic structures of the calycal neuropils, the microglomeruli, are larger but present at lower density in 35‐day‐old foragers relative to 1‐day‐old workers. Age‐ and experience‐based changes in plasticity of the MBs are assumed to support performance of challenging tasks, but the behavioral consequences of brain plasticity in insects are rarely examined. In this study, foragers were recruited from a field hive to a patch comprising two colors of otherwise identical artificial flowers. Flowers of one color contained a sucrose reward mimicking nectar; flowers of the second were empty. Task difficulty was adjusted by changing flower colors according to the principle of honey bee color vision space. Microglomerular volume and density in the lip (olfactory inputs) and collar (visual inputs) compartments of the MB calyces were analyzed using anti‐synapsin I immunolabeling and laser scanning confocal microscopy. Foragers displayed significant variation in microglomerular volume and density, but no correlation was found between these synaptic attributes and foraging performance. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1057–1071, 2017
Yarrowia lipolytica SRP54 Homolog and Translocation of Kar2p

To investigate the role of Srp54p in protein translocation, the Yarrowia lipolytica SRP54 homolog was cloned. Sequencing revealed an open reading frame of 536 amino acids coding for a 57·2 kilodalton polypeptide with 55 to 57% sequence identity to Srp54ps of Saccharomyces cerevisiae, Schizosaccharomyces pombe, and mouse. Like these Srp54ps, Y. lipolytica Srp54p has an N‐terminal domain with a highly conserved GTP‐binding site and a methionine‐rich C‐terminal domain. Differing results regarding the essentiality of SRP subunits were obtained. SRP54 is important but not essential for growth, but it was reconfirmed that at least one SRP RNA gene is essential. Cells with SRP54 deleted grow about six times more slowly than wild type; faster‐growing colonies, still growing much slower than wild type, appeared quite frequently. In srp54Δ cells, no untranslocated alkaline extracellular protease precursor was detected. Therefore, to develop another reporter molecule the Y. lipolytica KAR2 homolog was cloned and Kar2p antibodies were produced. For Kar2p an untranslocated precursor was detected in srp54Δ but not in wild‐type cells, suggesting that its translocation was defective in the srp54Δ cells. These results confirm an in vivo role for SRP in protein translocation in Y. lipolytica, suggest that SRP RNA or an SRP core‐particle has functions not shared by Srp54p, and show that, as in S. cerevisiae and Sz. pombe, reporter molecules differ in their dependency on SRP for translocation. The SRP54 and KAR2 sequences have been deposited in GenBank under Accession Numbers U42418 and U63136.
Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes

The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of different evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta‐analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is ∼15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency‐dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre‐bottlenecked populations.
Alterations in the Expression of ELAM‐1, ICAM‐1 and VCAM‐1 after In Vitro Infection of Endothelial Cells with a Clinical Isolate of Human Cytomegalovirus

Human cytomegalovirus (HCMV) infection of endothelial cells resulted in increased adhesion of the cells to peripheral blood leukocytes. It was demonstrated by flow cytometry that increased adhesiveness parallels the increased expression of cell surface adhesion molecules (ELAM‐1, ICAM‐1, VCAM‐1). The increased adhesion of PMN and T‐lymphocytes was due to upregulation in the expression of ELAM‐1 and ICAM‐1. The upregulation of VCAM‐1 resulted in the increased adhesiveness of monocytes and T‐lymphocytes to HCMV‐infected HUVEC. The increased adhesiveness to leukocytes was caused by HCMV replication since endothelial cells exposed to HCMV‐free supernatants and UV‐inactivated HCMV did not show any increase in adhesiveness to any of the leukocytes tested.
Comparative Structural and Functional Analysis of Staphylococcus aureus Glucokinase with other Bacterial Glucokinases

Glucokinase is classified in bacteria based upon having ATP binding site and ‘repressor/open reading frames of unknown function/sugar kinases’ motif, the sequence of glucokinase gene (JN645812) of Staphylococcus aureus ATCC12600 showed presence of ATP binding site and ‘repressor/open reading frames of unknown function/sugar kinases’ motif. We have earlier observed glucokinase of S. aureus has higher affinity towards the substrate compared to other bacterial glucokinase and under anaerobic condition with increased glucose concentration S. aureus exhibited higher rate of biofilm formation. To establish this, 3D structure of glucokinase was built using homology modeling method, the PROCHECK and ProSA-Web analysis indicated this built glucokinase structure was close to the crystal structure. This structure was superimposed with different bacterial glucokinase structures and from the root-mean-square deviation values, it is concluded that S. aureus glucokinase exhibited very close homology with Enterococcus faecalis and Clostridium difficle while with other bacteria it showed high degree of variations both in domain and nondomain regions. Glucose docking results indicated -12.3697 kcal/mol for S. aureus glucokinase compared with other bacterial glucokinase suggesting higher affinity of glucose which correlates with enzyme kinetics and higher rate of biofilm formation.
Activation of Rac2 and Cdc42 on Fc and complement receptor ligation in human neutrophils

Phagocytosis is a complex process engaging a concerted action of signal‐transduction cascades that leads to ingestion, subsequent phagolysosome fusion, and oxidative activation. We have previously shown that in human neutrophils, C3bi‐mediated phagocytosis elicits a significant oxidative response, suggesting that activation of the small GTPase Rac is involved in this process. This is contradictory to macrophages, where only Fc receptor for immunoglobulin G (FcγR)‐mediated activation is Rac‐dependent. The present study shows that engagement of the complement receptor 3 (CR3) and FcγR and CR3‐ and FcγR‐mediated phagocytosis activates Rac, as well as Cdc42. Furthermore, following receptor‐engagement of the CR3 or FcγRs, a downstream target of these small GTPases, p21‐activated kinase, becomes phosphorylated, and Rac2 is translocated to the membrane fraction. Using the methyltransferase inhibitors N‐acetyl‐S‐farnesyl‐L‐cysteine and N‐acetyl‐S‐geranylgeranyl‐L‐cysteine, we found that the phagocytic uptake of bacteria was not Rac2‐ or Cdc42‐dependent, whereas the oxidative activation was decreased. In conclusion, our results indicate that in neutrophils, Rac2 and Cdc42 are involved in FcR‐ and CR3‐induced activation and for properly functioning signal transduction involved in the generation of oxygen radicals.
Electrical characterization method to study barrier integrity in 3D through-silicon vias

In this paper, the controlled I-V (IVctrl) method is adopted for the barrier integrity characterization of TSVs at wafer level. Planar capacitor structures are used for the initial validation of the IVctrl method with respect to the traditional time dependent dielectric breakdown (TDDB) methodology. The TDDB field acceleration factor of the TSV liner is extracted by IVctrl in a reasonable time, and the results demonstrate that defective barriers can degrade TDDB field acceleration factor and thus TSV liner reliability.
Characterization of Herpes Simplex Virus type 1 thymidine kinase mutants engineered for improved ganciclovir or acyclovir activity

Herpes Simplex Virus type 1 (HSV‐1) thymidine kinase (TK) is currently the most widely used suicide agent for gene therapy of cancer. Tumor cells that express HSV‐1 thymidine kinase are rendered sensitive to prodrugs due to preferential phosphorylation by this enzyme. Although ganciclovir (GCV) is the prodrug of choice for use with TK, this approach is limited in part by the toxicity of this prodrug. From a random mutagenesis library, seven thymidine kinase variants containing multiple amino acid substitutions were identified on the basis of activity towards ganciclovir and acyclovir based on negative selection in Escherichia coli. Using a novel affinity chromatography column, three mutant enzymes and the wild‐type TK were purified to homogeneity and their kinetic parameters for thymidine, ganciclovir, and acyclovir determined. With ganciclovir as the substrate, one mutant (mutant SR39) demonstrated a 14‐fold decrease in Km compared to the wild‐type enzyme. The most dramatic change is displayed by mutant SR26, with a 124‐fold decrease in Km with acyclovir as the substrate. Such new “prodrug kinases” could provide benefit to ablative gene therapy by now making it feasible to use the relatively nontoxic acyclovir at nanomolar concentrations or ganciclovir at lower, less immunosuppressive doses.
Comparability and Quality Control in Cancer Registration; Karachi (data monitoring 1995-2001).

INTRODUCTION Comparability and Quality Control in Cancer Registration remains an essential component of standardisation of cancer incidence data. The information provided by registries is used as a base-line data for cancer control and cancer research. As such misleading information will encourage fictious cancer patterns with over or under registration of some cancer sites. METHODOLOGY The registration in Karachi started in 1995 and was confined to a single district of Karachi, the South District. Since 1998 the registration has extended to Karachi Division. For both the data sets, recommendations of the International Agency for Research on Cancer (IARC) and the International Association of Cancer Registries (IACR) have been followed to assure comparability and Quality Control of the results. RESULTS The 2 data sets from Karachi show well-recorded demographic details of cases. Age was not a true indicator of validity in our case, as we have approximate ages of patients aggregated around quintiles and decades. All the cancer cases were reported from a minimum of 3 sources. Microscopic verifications (MV) were high. Cancers with the highest histological verification (HV) were those located in easily accessible sites e.g. breast, oral cavity and cervix. The age specific incidence rates (ASR) for Karachi South, all sites (1995-1999) was 148.1 males and 175.5 females. The same for Karachi Division (1998-99) was 132.4 males and 133.0 females. CONCLUSION The cancer data in 1995 during the initial phase of registration was incomplete and suffered from inaccuracies associated with a lack of awareness in early years of registration. By the year 2001, the data (1995-1999) showed improved completion and accuracy. The incidence rates have shown no dramatic changes during the past 2 years. The malignancies also show a stable pattern, despite the possibility of under-registration of clinically diagnosed cases. The microscopic verification is high compared with the world region and similar to those observed in developed countries. This may be due to the widely available diagnostic facilities in Karachi and should therefore be considered an indicator of validity of registered data.
Information lifecycle management: the EMC perspective

Information is a strategic component of modern business, and its effective management has become a critical business challenge. Electronic information has not only been growing in volume at unprecedented rates, its value to business has never been greater. Around-the-clock operations, electronic commerce, corporate governance rules and legally-mandated retention laws have all added to the pressure for better information management. Information lifecycle management (ILM) is a business-centric strategy for proactive management of information throughout its life, from its creation and use to its ultimate disposal. EMC's ILM initiative is enhancing our customers' information management capabilities through data classification, centralized management, automation, product integration, and policy-based management. Research issues related to ILM include information classification and optimization of policy-based information management.
The Transmission of Financial Shocks on a Global Scale: Some New Empirical Evidence

ABSTRACT We examine shocks to capital flows from the United States, the Eurozone, and China. A US interest rate rise is contractionary for the United States but produces positive growth elsewhere. Cross-border claims and US interest rate shocks have been more subdued since the global financial crisis, consistent with the portfolio rebalancing hypothesis. Negative claims shocks from the Eurozone have opposite macroeconomic effects than when the same shock hits the United States due to the predominance of bank-intermediated financing in the Eurozone. Real and financial link exists between China and the Eurozone. The United States is relatively immune to shocks from China of the kind investigated here.
GLOBALLY UNIFORM HARMONIZED SYSTEM NOMENCLATURE? WAIVERS FOR DEVELOPING COUNTRIES AND MEMBERSHIP DEVELOPMENT: SITUATION 2017

The Harmonized Commodity Description and Coding System (HS) is the mostsuccessful legally binding instrument of the World Customs Organization (WCO) with 156contracting parties. More and more countries and economic regions are applying the HSnomenclature worldwide. But not all member states are applying the same version of the HSnomenclature. Developing countries are allowed to use another (earlier) version of thenomenclature according to article 4 HS, however the WCO does not define the term“developing countries”. In the main section this paper discusses the term “developing countries” andexamines the nomenclature application by HS member states and non-member states. Itdisplays data from 2008 and 2017 on the positon of HS parties regarding the version of thenomenclature they apply and explains that not only developing nations are not applying themost actual HS 2017 nomenclature but also two advanced economies (Iceland andSingapore): 83 out of 156 contracting parties have successfully implemented the HS 2017and 56 HS member states are still using older HS versions. Four contracting parties areplanning to implement the HS 2017 in 2018 and one in 2019. 46 HS applicants are so callednon-members and not HS member states in 2017. Three non-members are advancedeconomies (all three are WTO members): Hong Kong, Macao and Liechtenstein.The membership development of the HS is examined and future accessions areforecasted. This paper is researched by help of the WCO publications on the HS, the legal textsof the HS and the position of parties for the HS, the WCO publications for the signature andratification of the Harmonised System Convention and by help of WTO publications on theirmembership and observers. The methods used during the study are analysis, synthesis, comparison,generalization, systematic and functional analysis.
Cognitive Enhancement Therapy Improves Resting-State Functional Connectivity in Early Course Schizophrenia

Objective: Cognitive remediation is emerging as an effective psychosocial intervention for addressing untreated cognitive and functional impairments in persons with schizophrenia, and might achieve its benefits through neuroplastic changes in brain connectivity. This study seeks to examine the effects of cognitive enhancement therapy (CET) on fronto-temporal brain connectivity in a randomized controlled trial with individuals in the early course of schizophrenia. Method: Stabilized, early course outpatients with schizophrenia or schizoaffective disorder (N = 41) were randomly assigned to CET (n = 25) or an active enriched supportive therapy (EST) control (n = 16) and treated for 2 years. Functional MRI data were collected annually, and pseudo resting-state functional connectivity analysis was used to examine differential changes in fronto-temporal connectivity between those treated with CET compared with EST. Results: Individuals receiving CET evidenced significantly less functional connectivity loss between the resting-state network and the left dorsolateral prefrontal cortex as well as significantly increased connectivity with the right insular cortex compared to EST (all corrected p< .01). These neural networks are involved in emotion processing and problem-solving. Increased connectivity with the right insula significantly mediated CET effects on improved emotion perception (z′ = −1.96, p = .021), and increased connectivity with the left dorsolateral prefrontal cortex mediated CET-related improvements in emotion regulation (z′ = −1.71, p = .052). Conclusions: These findings provide preliminary evidence that CET, a psychosocial cognitive remediation intervention, may enhance connectivity between frontal and temporal brain regions implicated in problem-solving and emotion processing in service of cognitive enhancement in schizophrenia.
Ultra-Low Field NMR of  ${\rm UF}_{6}$ for  $^{235}{\rm U}$ Detection and Characterization

We have demonstrated the first ultra-low field (ULF) nuclear magnetic resonance measurements of uranium hexafluoride (UF6), which is used in the uranium enrichment process. A sensitive non-invasive detection system would have an important role in non-proliferation surveillance. A two-frequency technique was employed to remove the transients induced by rapidly switching off the 50 mT pre-polarization field. A mean transverse relaxation time T2 of 24 ms was estimated for the un-enriched UF6 sample measured at a mean temperature of 80degC.