Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonreducing Terminal Modifications Determine the Chain Length of Polymannose O Antigens of Escherichia coli and Couple Chain Termination to Polymer Export via an ATP-binding Cassette Transporter*

The chain length of bacterial lipopolysaccharide O antigens is regulated to give a modal distribution that is critical for pathogenesis. This paper describes the process of chain length determination in the ATP-binding cassette (ABC) transporter-dependent pathway, a pathway that is widespread among Gram-negative bacteria. Escherichia coli O8 and O9/O9a polymannans are synthesized in the cytoplasm, and an ABC transporter exports the nascent polymer across the inner membrane prior to completion of the LPS molecule. The polymannan O antigens have nonreducing terminal methyl groups. The 3-O-methyl group in serotype O8 is transferred from S-adenosylmethionine by the WbdDO8 enzyme, and this modification terminates polymerization. Methyl groups are added to the O9a polymannan in a reaction dependent on preceding phosphorylation. The bifunctional WbdDO9a catalyzes both reactions, but only the kinase activity controls chain length. Chain termination occurs in a mutant lacking the ABC transporter, indicating that it precedes export. An E. coli wbdDO9a mutant accumulated O9a polymannan in the cytoplasm, indicating that WbdD activity coordinates polymannan chain termination with export across the inner membrane.
TV-based DOI De-blurring model for the dual-head flat-panel PET system

In the dual-head flat panel PET system (DHAPET), the unique detector arrangement leads to severe uncertainty of depth-of-interaction (DOI) and data truncation, which in turn result in poor image quality and data loss in the reconstructed images. To improve the distortions, we proposed a reconstruction strategy under the framework of the fast iterative shrinkage-thresholding algorithm (FISTA) for minimizing total variation and de-blurring the DOI effects. Through the FISTA, the time-consuming procedure of TV-constraint can be accelerated. Additionally, we incorporated the point spread function into the reconstruction procedure of the FISTA to account for the blurring effects of DOI. Our numerical results showed that the proposed method can not only achieve a fast convergence rate to facilitate its applications, but also compensate the DOI effect and artifacts to improve image quality.
Event Recognition Based on Deep Learning in Chinese Texts

Event recognition is the most fundamental and critical task in event-based natural language processing systems. Existing event recognition methods based on rules and shallow neural networks have certain limitations. For example, extracting features using methods based on rules is difficult; methods based on shallow neural networks converge too quickly to a local minimum, resulting in low recognition precision. To address these problems, we propose the Chinese emergency event recognition model based on deep learning (CEERM). Firstly, we use a word segmentation system to segment sentences. According to event elements labeled in the CEC 2.0 corpus, we classify words into five categories: trigger words, participants, objects, time and location. Each word is vectorized according to the following six feature layers: part of speech, dependency grammar, length, location, distance between trigger word and core word and trigger word frequency. We obtain deep semantic features of words by training a feature vector set using a deep belief network (DBN), then analyze those features in order to identify trigger words by means of a back propagation neural network. Extensive testing shows that the CEERM achieves excellent recognition performance, with a maximum F-measure value of 85.17%. Moreover, we propose the dynamic-supervised DBN, which adds supervised fine-tuning to a restricted Boltzmann machine layer by monitoring its training performance. Test analysis reveals that the new DBN improves recognition performance and effectively controls the training time. Although the F-measure increases to 88.11%, the training time increases by only 25.35%.
High sensitivity of BRCA1-deficient mammary tumors to the PARP inhibitor AZD2281 alone and in combination with platinum drugs

Whereas target-specific drugs are available for treating ERBB2-overexpressing and hormone receptor-positive breast cancers, no tailored therapy exists for hormone receptor- and ERBB2-negative (“triple-negative”) mammary carcinomas. Triple-negative tumors account for 15% of all breast cancers and frequently harbor defects in DNA double-strand break repair through homologous recombination (HR), such as BRCA1 dysfunction. The DNA-repair defects characteristic of BRCA1-deficient cells confer sensitivity to poly(ADP-ribose) polymerase 1 (PARP1) inhibition, which could be relevant to treatment of triple-negative tumors. To evaluate PARP1 inhibition in a realistic in vivo setting, we tested the PARP inhibitor AZD2281 in a genetically engineered mouse model (GEMM) for BRCA1-associated breast cancer. Treatment of tumor-bearing mice with AZD2281 inhibited tumor growth without signs of toxicity, resulting in strongly increased survival. Long-term treatment with AZD2281 in this model did result in the development of drug resistance, caused by up-regulation of Abcb1a/b genes encoding P-glycoprotein efflux pumps. This resistance to AZD2281 could be reversed by coadministration of the P-glycoprotein inhibitor tariquidar. Combination of AZD2281 with cisplatin or carboplatin increased the recurrence-free and overall survival, suggesting that AZD2281 potentiates the effect of these DNA-damaging agents. Our results demonstrate in vivo efficacy of AZD2281 against BRCA1-deficient breast cancer and illustrate how GEMMs of cancer can be used for preclinical evaluation of novel therapeutics and for testing ways to overcome or circumvent therapy resistance.
Transfusion‐transmitted cytomegalovirus (CMV) infections in a murine model: characterization of CMV‐infected donor mice

BACKGROUND: Donor and recipient mechanisms that modulate the incidence and severity of transfusion‐transmitted cytomegalovirus (TT‐CMV) are unclear. The kinetics of murine CMV (MCMV) infection in the peripheral blood of donor mice were investigated to determine the utility of this model for studying TT‐CMV.
The mouse as a suitable host for an isolate of Schistosoma haematobium from Niger

ABSTRACT The host-parasite relationships of a Schistosoma haematobium isolate, originating from Niger, and the white mouse are described. Swiss OF1 albino mice were exposed individually to 200 cercariae and worms were recovered 9, 12, 16 and 20 weeks post infection. The mean worm returns ranged between 10·54 and 13·5% and did not alter significantly between 9 and 20 weeks post infection. The sex ratio of worms was always in favour of males; from 7·9:1 at 9 weeks after infection it decreased regularly to 3·28:1 at 20 weeks. Male worms reached a mean length of 8·72 mm at 20 weeks. From the 12th week post infection, a high number of eggs was found in the liver and gut. At 20 weeks, eggs were also found in the bladder. Viable eggs and infective miracidia were obtained. The infection of Bulinus truncatus from Niger succeeded with a mean rate of 61% after the first passage through mice. The isolate of S. haematobium was maintained in the laboratory during 3 successive passages through mice. These entirely new results are very probably linked to genetic characteristics peculiar to the S. haematobium populations from Niger.
Reserve Size and Fragmentation Alter Community Assembly, Diversity, and Dynamics

Researchers have disputed whether a single large habitat reserve will support more species than many small reserves. However, relatively little is known from a theoretical perspective about how reserve size affects competitive communities structured by spatial abiotic gradients. We investigate how reserve size affects theoretical communities whose assembly is governed by dispersal limitation, abiotic niche differentiation, and source-sink dynamics. Simulations were conducted with varying scales of dispersal across landscapes with variable environmental spatial autocorrelation. Landscapes were inhabited by simulated trees with seedling and adult stages. For a fixed total area in reserves, we found that small reserve systems increased the distance between environments dominated by different species, diminishing the effects of source-sink dynamics. As reserve size decreased, environmental limitations to community assembly became stronger, α species richness decreased, and γ richness increased. When dispersal occurred across short distances, a large reserve strategy caused greater stochastic community variation, greater α richness, and lower γ richness than in small reserve systems. We found that reserve size variation trades off between preserving different aspects of natural communities, including α diversity versus γ diversity. Optimal reserve size will depend on the importance of source-sink dynamics and the value placed on different characteristics of natural communities. Anthropogenic changes to the size and separation of remnant habitats can have far-reaching effects on community structure and assembly.
Superheating Antigen Retrieval

Heat-induced antigen retrieval in a variety of solutions has been shown to enhance the immunoreactivity of a wide range of antigens in routine formalin-fixed, paraffin-embedded tissues. Accurate time and temperature control is important for standardization and optimization of the procedure but is difficult to achieve. This study used a device to attain precise time and temperature control for antigen retrieval at 120°C under 1.9 bar pressure. It compares the efficacy of this method with antigen retrieval in a conventional pressure cooker, by microwave heating at 98°C, and ultrasound retrieval at 40 and 70 W for 40 and 100 seconds. Multitissue and multitumor blocks containing a spectrum of normal tissues and a variety of tumors, respectively, were used, and 42 routine diagnostic antibodies were applied with a standard peroxidase conjugated streptavidin technique. Sections in which antigen retrieval was not performed served as controls. The three heat-induced methods showed distinctly better immunostaining for all antigens compared with those obtained with ultrasound retrieval. The latter method did not produce consistent staining and intensity, and the extent of staining was only marginally better than sections not subjected to antigen retrieval. Superheating at 120°C produced the best overall results with the exception of antibodies to cytokeratin clones Cam 5.2, AE1/3, and 34BE12 in which superheating resulted in slightly inferior immunostaining compared with heating in a pressure cooker and at 98°C.
Molecular characterization of an Enterobacter cloacae outer membrane protein (OmpX)

A chromosomal gene of Enterobacter cloacae encoding an outer membrane protein (OmpX) has been cloned. Overproduction of the OmpX protein decreased the quantity of porins in the outer membrane of the parental strain and of Escherichia coli HB101. The ompX gene was located by insertions of the gamma delta sequence into the recombinant plasmid. The polarity of the gene was determined by in vitro transcription and translation of the gamma delta-containing plasmids. The nucleotide sequence of the ompX gene was elucidated by using both inverted terminal repeats of the gamma delta sequence as starting points for M13 dideoxy sequencing. The gene was found to encode a precursor of the OmpX protein consisting of 172 amino acid residues with a molecular mass of 18.6 kDa. The protein contains an N-terminal signal sequence of 23 amino acid residues. The exact cleavage point was established by sequencing the N-terminal part of the mature protein. The OmpX protein has several characteristics in common with outer membrane proteins of gram-negative bacteria. The protein is rather hydrophilic and is devoid of long hydrophobic stretches. On the basis of these results, we present a model for the OmpX protein folding in an outer membrane.
Investment and the WACC: New Micro Evidence for France

We exploit a new dataset of consolidated balance sheets for some 1,850, mostly nonlisted, French corporate groups, in order to investigate the relationship between corporate investment and the cost of capital. Our empirical model is motivated by a standard Q-theory of investment and relates the rate of investment to a proxy for profits, the cost of capital and firm- and sector-level controls. We notably construct firm-level measures of the weighted average cost of capital (WACC) that account for industry-specific values of the cost of equity and reflect the actual capital structure of firms. We find a confirmation that a high WACC drags down investment: a one SD increase in the real WACC (+2 pp) is associated on average with a reduction by 0.65 pp in the investment rate. The effect is somewhat larger for manufacturing firms and when firms are highly leveraged or more dependent on external finance. We also investigate the impact of lower competition or higher uncertainty on business investment and do not find evidence in support of any role of these two factors in France in recent years.
Identification of emerging FLT3 ITD‐positive clones during clinical remission and kinetics of disease relapse in acute myeloid leukaemia with mutated nucleophosmin

FLT3 internal tandem duplication (ITD) mutations are frequently detected at diagnosis in cytogenetically normal acute myeloid leukaemia (CN‐AML) and predict unfavourable outcome. FLT3 ITD is an unstable aberration and may be lost or acquired at relapse. Recent whole genome sequencing studies have suggested that FLT3 ITD+ve AML relapse may evolve from small subclones undetectable at diagnosis by routine polymerase chain reaction (PCR). We developed a patient‐specific real‐time quantitative‐PCR (RQ‐PCR) to implement FLT3 ITD detection in six AML patients whose blasts carried wild‐type FLT3 at diagnosis and who relapsed with FLT3 ITD by routine PCR. Patient‐specific forward primers were designed after cloning and sequencing the FLT3 ITD in each case. The assay allowed retrospective detection of FLT3 ITD in diagnostic samples of 4/6 cases and to establish the kinetics of clonal evolution preceding relapse. After conventional chemotherapy, all patients had early relapse despite having been classified as NPM1+ve/FLT3 ITD−ve at presentation, with shorter remissions being observed in four patients re‐classified as FLT3 ITD+ve by the new assay. Notably, FLT3 ITD clone became detectable by conventional PCR in three patients tested during remission after initial treatment. Our data underscore the need of identifying low FLT3 ITD levels, which are probably associated with relapse in otherwise good prognosis CN‐AML.
Trade-Off in Multifactor Smart Beta Investing: Factor Premium and Implementation Cost

The authors study the impact of the inclusion of the momentum and size factors, and the selectiveness in stock screening, on the performance and implementation cost of a multifactor strategy. Whereas the cost of implementing a stand-alone momentum strategy is quite high because of its extraordinarily high turnover, adding momentum to a mix of the value, low beta, profitability, investment, and size factors helps lower tracking error and improves the information ratio without a significant increase in implementation cost because offsetting trades cancel each other out. Contrary to conventional wisdom, the inclusion of the size factor does not negatively affect the multifactor strategy’s trading costs in light of its relatively low turnover. Additionally, including the size factor improves the performance and coverage of the multifactor strategy, which otherwise would be constructed with only large and mid-size companies. As expected, by using factor portfolios with more concentrated holdings, investors can improve the performance of a multifactor strategy, but these benefits come at the expense of high turnover and high trading costs. The authors specify portfolio design as a conscious choice made on the trade-off between the effective harvesting of the factor premium and low-cost implementation. They highlight the importance of the thoughtful portfolio construction work required to deliver a smart beta multifactor strategy that serves investors’ needs.
A Privacy-Preserving Vehicular Crowdsensing-Based Road Surface Condition Monitoring System Using Fog Computing

In the recent past, great attention has been directed toward road surface condition monitoring. As a matter of fact, this activity is of critical importance in transportation infrastructure management. In response, multiple solutions have been proposed which make use of mobile sensing, more specifically contemporary applications and architectures that are used in both crowdsensing and vehicle-based sensing. This has allowed for automated control as well as analysis of road surface quality. These innovations have thus encouraged and showed the importance of cloud to provide reliable transport services to clients. Nonetheless, these initiatives have not been without challenges that range from mobility support, locational awareness, low latency, as well as geo-distribution. As a result, a new term has been coined for this novel paradigm, called, fog computing. In this paper, we propose a privacy-preserving protocol for enhancing security in vehicular crowdsensing-based road surface condition monitoring system using fog computing. At the onset, this paper proposes a certificateless aggregate signcryption scheme that is highly efficient. On the basis of the proposed scheme, a data transmission protocol for monitoring road surface conditions is designed with security aspects such as information confidentiality, mutual authenticity, integrity, privacy, as well as anonymity. In analyzing the system, the ability of the proposed protocol to achieve the set objectives and exercise higher efficiency with respect to computational and communication abilities in comparison to existing systems is also considered.
Heavy smoking in midlife and long-term risk of Alzheimer disease and vascular dementia.

BACKGROUND Smoking is a risk factor for several life-threatening diseases, but its long-term association with dementia is controversial and somewhat understudied. Our objective was to investigate the long-term association of amount of smoking in middle age on the risk of dementia, Alzheimer disease (AD), and vascular dementia (VaD) several decades later in a large, diverse population. METHODS We analyzed prospective data from a multiethnic population-based cohort of 21,123 members of a health care system who participated in a survey between 1978 and 1985. Diagnoses of dementia, AD, and VaD made in internal medicine, neurology, and neuropsychology were collected from January 1, 1994, to July 31, 2008. Multivariate Cox proportional hazards models were used to investigate the association between midlife smoking and risk of dementia, AD, and VaD. RESULTS A total of 5367 people (25.4%) were diagnosed as having dementia (including 1136 cases of AD and 416 cases of VaD) during a mean follow-up period of 23 years. Results were adjusted for age, sex, education, race, marital status, hypertension, hyperlipidemia, body mass index, diabetes, heart disease, stroke, and alcohol use. Compared with nonsmokers, those smoking more than 2 packs a day had an elevated risk of dementia (adjusted hazard ratio [HR], 2.14; 95% CI, 1.65-2.78), AD (adjusted HR, 2.57; 95% CI, 1.63-4.03), and VaD (adjusted HR, 2.72; 95% CI, 1.20-6.18). CONCLUSIONS In this large cohort, heavy smoking in midlife was associated with a greater than 100% increase in risk of dementia, AD, and VaD more than 2 decades later. These results suggest that the brain is not immune to long-term consequences of heavy smoking.
High-speed Rail Network and Changing Industrial Dynamics in Chinese Regions

High-speed railway (HSR) network can significantly reduce the transport cost of people and facilitate interregional knowledge spillovers. It may thus affect regional industrial dynamics. By employing the industrial relatedness indicator, this article shows that regional industrial dynamics is path dependent in China. It further adopts several classical accessibility indicators to capture the network characteristics of transport infrastructure and the accessibility of Chinese cities in the HSR network. In response to the endogeneity issue, we design an instrumental variable based on historic transport network. Another econometric strategy is to include only two groups of cities in the sample: cities with existing HSR stations and cities with planned HSR stations. The empirical results suggest that high accessibility in the HSR network not only pushes forward new industry creation but also enables regions to be more pathbreaking and diversify into less related industries.
Public Estimates of Cancer Frequency: Cancer Incidence Perceptions Mirror Distorted Media Depictions

Compared with incidence rates, certain cancers are over- or underrepresented in news coverage. Past content analytic research has consistently documented these news distortions, but no study has examined whether they are related to public perception of cancer incidence. Adults (N = 400) completed a survey with questions about perceived cancer incidence, news consumption, and attention to health news. Cancer incidence perceptions paralleled previously documented news distortions. Overrepresented cancers were overestimated (e.g., blood, head/brain) and underrepresented cancers were underestimated (e.g., male reproductive, lymphatic, thyroid, and bladder). Self-reported news consumption was related to perceptual distortions such that heavier consumers were more likely to demonstrate distorted perceptions of four cancers (bladder, blood, breast, and kidney). Distortions in risk perception and news coverage also mirrored discrepancies in federal funding for cancer research. Health care professionals, journalists, and the public should be educated about these distortions to reduce or mitigate potential negative effects on health behavior and decision making.
Persistent Productivity Failure in the UK: Is the EU Really to Blame?

On average, UK productivity performance in the decades leading up to the financial crisis was quite disappointing. Joining the EU was not to blame. Indeed, EU membership, which was an integral part of the Thatcher reform programme, had a significant positive impact. Over the long run, UK supply-side policies have been badly designed in various different ways. These design faults have not been the result of constraints imposed by EU membership but rather the consequence of domestic government failure. There is no reason to think that EU exit will lead, either directly or indirectly, to improvements in UK productivity outcomes.