Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM), has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26) with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs) were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.
CtBPs Promote Cell Survival through the Maintenance of Mitotic Fidelity

ABSTRACT CtBPs (CtBP1 and CtBP2) act in the nucleus as transcriptional corepressors and in the cytoplasm as regulators of Golgi apparatus fission. Studies in which the expression or function of CtBPs has been inhibited have independently identified roles for CtBPs in both suppressing apoptosis and promoting cell cycle progression. Here, we have analyzed the consequences of ablating CtBP expression in breast cancer-derived cell lines. We found that loss of CtBP expression suppresses cell proliferation through a combination of apoptosis, reduction in cell cycle progression, and aberrations in transit through mitosis. The third phenotype includes errors in mitotic chromosome segregation that are associated with decreased association of the chromosome passenger protein aurora B with mitotic chromatin and that are likely to be a primary cause of the proapoptotic and antiproliferative effects of CtBP loss. We also show that loss of CtBP expression results in the activation of the transcription factor p53 and that loss of p53 function renders cells more susceptible to CtBP small interfering RNA-induced apoptosis.
On the Simulation of Two‐dimensional Electronic Spectroscopy of Indole‐containing Peptides

A benchmark study of low‐cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near‐ultraviolet (UV) pump visible (VIS) probe (i.e. two‐color) two‐dimensional electronic spectra (2DES) of homo‐ and hetero‐aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited‐state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm−1. The 18–24 k cm−1 spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge‐transfer signatures in stacked aggregates. The small peptide Trp‐cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge‐transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near‐UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra‐short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited‐state absorption signals can be correlated to the polarity of the relevant states.
A Review on Evolution of 3GPP Systems Interworking with WLAN

Evolution of Radio Access Technologies (RATs) is succeeding on its fifth generation (5G). Over the past decade, interworking between heterogeneous RATs has undergone remarkable growth, as there is explosive growth in mobile devices such as smartphones supporting multiple RATs, especially Global System for Mobile communications (GSM), Code division multiple access (CDMA), Universal Mobile Telecommunications System (UMTS), High Speed Packet Access (HSPA), Long Term Evolution (LTE), Wireless Local Area Network (WLAN). WLAN is complementary options available to mobile operators when they consider expanding the user data traffic capacity further from the unlicensed spectrum. Since 2004 (Release-6), the Third Generation Partnership Project (3GPP) [1] has initiated to develop a 3GPPWLAN interworking architecture to allow 3GPP service providers to offload data traffic from wide area wireless spectrum to WLANs in indoor locations, hotspots, and other areas with high user density. The initial work in 3GPP specified loose integration (at the core network) and progressively introduced potential enhancements for tighter integration (at the radio access network) based on market trends and demands. This paper provides an insight on the evolution of 3GPP systems interworking with WLAN from 3GPP Release-6 to Release-13. Journal of ICT, Vol. 3, 133–156. doi: 10.13052/jicts2245-800X.322 c © 2016 River Publishers. All rights reserved. 134 R. Rajavelsamy et al.
Macroeconomic and Sectoral Effects of the EAC Regional Integration on Uganda: A Recursive Computable General Equilibrium Analysis

The paper empirically examines the implications of the implementation of the EAC regional integration on the Ugandan economy. Specifically, it analyses the likely effects of the asymmetric tariff reduction on the macro variables and quantifies the sectoral growth effects on the industrial, agricultural and services sectors. It adopts the General Equilibrium Model (CGE) for the analysis based on the Uganda 2007 Social Accounting Matrix. The primary policy simulation is the asymmetric reduction of internal tariffs across East African countries under assumptions of unemployment and free movement of factors of production. Other policy simulations that change these assumptions are analysed. Results indicate that the aggregate impact of internal tariff reduction under conditions of unemployment and free movement of factors of production is positive with average GDP growth improving by up to 0.3 percentage points over the period 2008 – 2021. However, the reduction in tariffs has negative implications for tax collections with import duties contracting by 0.3 percentage points, with no significant gains in direct taxes revenues. The rise in exports to the EAC region leads to a decline in the trade deficit by 0.8 percent during the simulation period. There are also significant growth gains for agriculture, industry and services sectors with the former registering growth improvements of 1.2 percentage points and the other two 0.7 percentage points. Therefore, Uganda should optimise gains within the EAC regional integration framework through tariff reduction and free movement of factors of production. Finally, the government should address infrastructural constraints (energy and transport) to foster growth in the manufacturing sector within the EAC region.
Neuronal Death in Cultured Murine Cortical Cells Is Induced by Inhibition of GAPDH and Triosephosphate Isomerase

Polyglutamine-containing proteins expressed in the CAG repeat diseases Huntington's disease and dentatorubralpallidoluyisian atrophy have recently been suggested to inhibit the key glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). To examine the consequences of GAPDH inhibition upon neuronal survival, we exposed murine neocortical cell cultures to the inhibitor of GAPDH and triosephosphate isomerase, alpha-monochlorohydrin. Cultures exposed to 6-15 mM alpha-monochlorohydrin for 48 h exhibited an increase in dihydroxyacetone phosphate and a decrease in neuronal ATP that was followed by progressive neuronal death; some glial death occurred at high drug concentrations. The neuronal death was characterized by cell body shrinkage and chromatin condensation and was sensitive to cycloheximide and to the caspase inhibitors Z-Val-Ala-Asp fluoromethylketone and tert-butoxycarbonyl-Asp fluoromethylketone. Neurons in striatal cell cultures were more vulnerable to death induced by exposure to alpha-monochlorohydrin, except that NADPH-diaphorase(+) neurons were selectively spared. Repeated addition of the glycolytic endpoint metabolite pyruvate to the bathing medium attenuated both the drop in neuronal ATP and the neuronal cell death.
The application of genetically engineered herpes simplex viruses to the treatment of experimental brain tumors.

Due to lack of effective therapy, primary brain tumors are the focus of intense investigation of novel experimental approaches that use vectors and recombinant viruses. Therapeutic approaches have been both indirect, whereby vectors are used, or direct to allow for direct cell killing by the introduced virus. Genetically engineered herpes simplex viruses are currently being evaluated as an experimental approach to eradicate malignant human gliomas. Initial studies with gamma (1)34.5 mutants, R3616 (from which both copies of the gamma (1)34.5 gene have been deleted) and R4009 (a construct with two stop codons inserted into the gamma (1)34.5 gene), have been assessed. In a syngeneic scid mouse intracranial tumor model, recombinant herpes simplex virus can be experimentally used for the treatment of brain tumors. These viruses and additional engineered viruses were subsequently tested in human glioma cells both in vitro and in vivo. Using a xenogeneic scid mouse intracranial glioma model, R4009 therapy of established tumors significantly prolonged survival. Most importantly, long-term survival was achieved, with histologic evidence that R4009 eradicated intracranial tumors in this model. Furthermore, the opportunity to evaluate gamma (1)34.5 mutants that have enhanced oncolytic activity, e.g., R8309 where the carboxyl terminus of the gamma (1)34.5 gene has been replaced by the murine homologue, MyD116, are considered.
An audit of fresh frozen plasma usage in an acute general hospital in Singapore.

BACKGROUND FFP is often inappropriately used despite existence of guidelines. An audit was conducted with the aim of making recommendations to reduce inappropriate use. MATERIALS AND METHODS A retrospective review of blood bank and electronic medical records of patients given FFP from October to December 2001 in an acute general hospital was undertaken. The criteria set by the College of American Pathologists in 1994 were used as the standards. RESULTS Nine hundred and thirty-two units of FFP were used during the study period for 359 transfusion episodes. Only 98 (27%) episodes were deemed appropriate. Percentage of inappropriate requests was similar across specialties. FFP used in the setting of inadequately prolonged coagulation profiles or absence of bleeding or surgical intervention was the commonest reasons for inappropriate use. CONCLUSIONS Our results showed significant proportion of FFP used outside of established international criteria. There may be many reasons for this and we suggest that a continual system of staff education and administrative intervention may help to reduce the inappropriate usage.
A Strategic Framework for Spare Parts Logistics

Strategically aligned and efficiently implemented spare parts logistics can differentiate a business from its competitors, lower costs, increase revenues, and thus help firms generate greater value for customers and ultimately increase profits. Based on multiple case studies with manufacturers in the machine and plant construction industry, this article examines the key components of a superior spare parts logistics strategy. The study suggests that an efficient spare parts logistics strategy can be developed with a three-step model that consists of nine components.
Pricing variance swaps by using two methods: replication strategy and a stochastic volatility model

In this paper we investigate pricing of variance swaps contracts. The literature is mostly dedicated to the pricing using replication with portfolio of vanilla options. In some papers the valuation with stochastic volatility models is discussed as well. Stochastic volatility is becoming more and more interesting to the investors. Therefore we decided to perform valuation with the Heston stochastic volatility model, as well as by using replication strategy. The thesis was done at SunGard Front Arena, so for testing the replica- tion strategy Front Arena software was used. For calibration and testing of the Heston model we used MatLab.
We Need to Compare, But How? Measurement Equivalence in Comparative Public Administration

There is an increasing interest to study public administrations, public managers or citizens interactions with, and views towards government from a comparative perspective in order to put theories to test using cross-national surveys. However, this will only succeed if we adequately deal with the diverse ways respondents in different countries, and regions perceive, and respond to survey measures. In this article, we provide an examination of the concept of cross-national measurement equivalence in public management, and how to proceed in establishing equivalence. We examine two different methodologies that test, and correct for measurement non-equivalence, namely 1) multiple group confirmatory factor analysis, and 2) item response theory. These techniques are then used to test, and subsequently establish the cross-national measurement equivalence of two popular measurement constructs, citizen satisfaction with public services, and trust in public institutions. Results show how appropriately dealing with non-equivalence accounts for different forms of biases, which would otherwise stay undetected. In doing so, this article contributes to the methodological advancement in studying public administration beyond domestic borders.
Polo-like Kinase 1-mediated Phosphorylation of Forkhead Box Protein M1b Antagonizes Its SUMOylation and Facilitates Its Mitotic Function*

Background: PLK1-mediated phosphorylation of FoxM1b leads to full activation of FoxM1b. Results: FoxM1b SUMOylation leads to suppression of FoxM1b activity, which is abrogated by PLK1-mediated phosphorylation. Conclusion: PLK1-mediated phosphorylation of FoxM1b antagonizes its SUMOylation and, thereby, facilitates its mitotic function. Significance: Elucidating the PLK1-mediated regulation of FoxM1b would greatly facilitate targeted therapeutic interventions. Transcription factor Forkhead box protein M1b (FoxM1b) plays an important role during mitotic entry and progression. Our previous studies identified polo-like kinase 1 (PLK1) as a major regulator of FoxM1b. During G2/M transition, PLK1 directly interacts with and phosphorylates FoxM1b, resulting in full activation of the transactivation capacity of FoxM1b. Such a vital regulatory mechanism is essential for timely mitotic entry and progression. However, the molecular mechanism by which PLK1-mediated phosphorylation enhances the transcriptional activity of FoxM1b remains to be determined. We demonstrate that FoxM1b can be SUMOylated in vitro and in vivo, preferentially by SUMO-1. SUMOylation of FoxM1b was found to occur at multiple sites, leading to suppression of FoxM1b transcriptional activity. Such a posttranslational modification of FoxM1b was antagonized by PLK1-mediated phosphorylation. By immunofluorescence staining and subcellular fractionation, we demonstrate that SUMO conjugation promotes cytosolic translocation of FoxM1b. Moreover, SUMO modification of FoxM1b facilitates the ubiquitin-mediated proteasomal degradation of FoxM1b. PLK1-mediated phosphorylation of FoxM1b abrogates the inhibitory effect on FoxM1b by SUMO modification, thereby promoting its nuclear translocation and preventing its proteolytic degradation in the cytoplasm. Such an antagonistic regulatory mechanism is essential for the mitotic function of FoxM1b, ensuring timely mitotic entry and progression. Taken together, our studies have revealed a working mechanism by which PLK1 positively regulates the activity and level of FoxM1b, which would greatly facilitate therapeutic interventions that focus on targeting the PLK1-mediated and/or FoxM1-mediated signaling network.
An Asset Allocation Puzzle: Comment

The purpose of this note is to look at the rationale behind popular advice on portfolio allocation among cash, bonds, and stocks. We argue that the typical investment advice is not inconsistent with the behavior of risk-averse expected-utility maximizers. We propose an additional solution to the asset allocation puzzle posed by Niko Canner et al. (1997), who argue that popular advice contradicts financial theory because it is inconsistent with the capital asset pricing model (CAPM) mutual-fund separation theorem. The CAPM asserts that investors should hold the same selection of risky assets, while popular advice is that investors should hold a proportion of bonds to stocks that increases with risk aversion. Using mean-variance (MV) analysis and the CAPM, Canner et al. show that recommended portfolios are far from optimal and that losses from the apparent failure of optimization are not substantial. However, they failed to explain the popular advice within an economic model. We offer a rational model based on stochastic dominance to demonstrate that all popular financial advice portfolios belong to the efficient set for all risk-averse investors. Using the historical annual real returns on bonds and stocks in Canner et al., we cannot ascertain that investment advisors indeed offer bad advice. Rather, we maintain that acting as agents for numerous clients, advisors recommend portfolios that are not inefficient for all risk-averse investors. I. Overview
Class-C PA-VCO Cell for FSK and GFSK Transmitters

In this paper, a Class-C PA-VCO cell tailored to FSK/GFSK transmitters is presented. In the proposed solution, a Class-C VCO and a common-gate stage PA are stacked in a current-reuse architecture operating with 1.2 V power supply. The PA and the VCO efficiencies are maximized by adjusting their voltage headroom without the use of any DC-DC converters. The PA-VCO is inserted in a transmitter based on an open-loop architecture. The presented prototype, fabricated in 0.13 μm CMOS technology, occupies an active area of 0.2 mm2. A maximum TX efficiency of 17.5% is achieved while the TX is delivering an output power of -1 dBm at 2.45 GHz. A phase noise of -129 dBc/Hz at 2.5 MHz frequency offset results in a carrier-frequency drift below 7 Hz/s and an FSK error below 0.7%, which allows the transmitter to operate in open-loop while delivering long data-packets. The transmitter is also compliant to BLE specifications when FSK and GFSK modulations with index of 0.5 are applied.
Essays on Price Rigidity in the UK: Evidence from Micro Data and Implications for Macro Models

This study consists of three individual essays which all shed light on assessing the price rigidity by using price micro data in the UK. The relevant implications for macro models are also discussed in each essay respectively. The first essay gives a unified framework a la Dixon (2012) to gauge the price rigidity from three perspectives: frequency, hazard function and distribution across firms. On average, the monthly frequency of consumer price change is 19% between 1996 and 2007. Sales and substitutions will significantly affect the frequency of consumer price change. The frequency of consumer price change varies considerable across sectors. The fraction of price changes which are decreasing is about 40%. The hazard function is downward sloping with 12-month spike. The censoring and sampling issues in the estimation of hazard function are discussed thoroughly. The distribution across firms is derived from estimated hazard function, which is consistent with the frequency of price changes. Two benchmark sticky price models are calibrated and simulated. Furthermore, a multiple Calvo and multiple menu costs model are also simulated, based on the empirical finding in micro data. The simulation results suggest that introducing heterogeneity into sticky price models can improve models' fitness in respect to matching micro evidence. The second essay mainly focus on "the monthly frequency of price changes", which is a prominent feature of many studies of the CPI micro-data. In this essay, we see how much the frequency ties down the behavior of price-setters ("firms") in steady-state in terms of the average length of price-spells across firms. We are able to divide an upper and lower bound for the mean duration of price-spells averaged across firms. We use the UK CPI data at the aggregate and sectoral level and find that the actual mean is about twice the theoretical minimum consistent with the observed frequency. We estimate the distribution using the hazard function and find that although the estimated hazard differs significantly from the Calvo distribution, the means and medians are similar. However, despite the micro differences, we find that the artificial Calvo distributions generated using the sectoral frequencies result in very similar impulse responses to the estimated hazards when used in the Smets-Wouters (2003) model. The third essay examines the behavior of individual producer prices in the UK. A number of stylized facts about price setting behavior are uncovered. A time-varying Ss model is set up in a way that is consistent with the stylized facts obtained from the UK PPI data. A duration model (semiparametric survival analysis model) is built in line with the time-varying Ss model. This duration model is estimated by controlling for observed and unobserved heterogeneity across firms. The estimation results suggest that the increase in the inflation rate will significantly increase the hazard rate of price change. The other factors considered in the model will also affect the hazard rate of price change, while in different magnitude.