Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-Enhanced Accumulation of FtsN at Division Sites and Roles for Other Proteins with a SPOR Domain (DamX, DedD, and RlpA) in Escherichia coli Cell Constriction

ABSTRACT Of the known essential division proteins in Escherichia coli, FtsN is the last to join the septal ring organelle. FtsN is a bitopic membrane protein with a small cytoplasmic portion and a large periplasmic one. The latter is thought to form an α-helical juxtamembrane region, an unstructured linker, and a C-terminal, globular, murein-binding SPOR domain. We found that the essential function of FtsN is accomplished by a surprisingly small essential domain (EFtsN) of at most 35 residues that is centered about helix H2 in the periplasm. EFtsN contributed little, if any, to the accumulation of FtsN at constriction sites. However, the isolated SPOR domain (SFtsN) localized sharply to these sites, while SPOR-less FtsN derivatives localized poorly. Interestingly, localization of SFtsN depended on the ability of cells to constrict and, thus, on the activity of EFtsN. This and other results suggest that, compatible with a triggering function, FtsN joins the division apparatus in a self-enhancing fashion at the time of constriction initiation and that its SPOR domain specifically recognizes some form of septal murein that is only transiently available during the constriction process. SPOR domains are widely distributed in bacteria. The isolated SPOR domains of three additional E. coli proteins of unknown function, DamX, DedD, and RlpA, as well as that of Bacillus subtilis CwlC, also accumulated sharply at constriction sites in E. coli, suggesting that septal targeting is a common property of SPORs. Further analyses showed that DamX and, especially, DedD are genuine division proteins that contribute significantly to the cell constriction process.
Expression of Political Opinions in Press

In this paper, we present an application designed to analyze news articles from Romanian mass media and extract opinions about political entities relevant to the major political stage. The application was created with the desire to study media polarization around important political events, such as legislative or presidential elections. The application uses different crawlers to extract the data from online newspapers and save it in the database. Then, it uses several Machine Learning techniques for identifying and classifying opinions about given entities over a long span of time. Based on this classification, it generates reports and charts that could be use not only to study political polarization, but also to identify partisan media.
Social Commerce Acceptance : The Role of Trust , Perceived Risk , and Benefit Full papers

Due to the increased popularity of social networking sites, a new platform called social commerce has emerged. Social commerce facilitates online interactions and user contributions to assist them in conducting commercial transactions. In this study, we rely on risk-return strategy in consumers’ decision making to study drivers and deterrents of social commerce use. We study both purchasing and participating behavior; according, we categorized risk and benefit related to each behavior. We also study trust from two insights: trust toward members and trust toward website. Using survey data from 196 users of etsy.com, we found that trust and benefit are important motivators of social commerce use, and perceived risk is a deterrent factor. Trust toward members reduces perceived risks related to both participating and purchasing behaviors. However, trust toward website does not have a significant effect on reducing risk perceptions. Implications for research and practice are discussed.
Ammonia‐based intermittent aeration control optimized for efficient nitrogen removal

This work describes the development of an intermittently aerated pilot‐scale process (V = 0.45 m3) operated for optimized efficient nitrogen removal in terms of volume, supplemental carbon and alkalinity requirements. The intermittent aeration pattern was controlled using a strategy based on effluent ammonia concentration set‐points. The unique feature of the ammonia‐based aeration control was that a fixed dissolved oxygen (DO) set‐point was used and the length of the aerobic and anoxic time (anoxic time ≥25% of total cycle time) were changed based on the effluent ammonia concentration. Unlike continuously aerated ammonia‐based aeration control strategies, this approach offered control over the aerobic solids retention time (SRT) to deal with fluctuating ammonia loading without solely relying on changes to the total SRT. This approach allowed the system to be operated at a total SRT with a small safety factor. The benefits of operating at an aggressive SRT were reduced hydraulic retention time (HRT) for nitrogen removal. As a result of such an operation, nitrite oxidizing bacteria (NOB) out‐selection was also obtained (ammonia oxidizing bacteria [AOB] maximum activity: 400 ± 79 mgN/L/d, NOB maximum activity: 257 ± 133 mgN/L/d, P < 0.001) expanding opportunities for short‐cut nitrogen removal. The pilot demonstrated a total inorganic nitrogen (TIN) removal rate of 95 ± 30 mgN/L/d at an influent chemical oxygen demand: ammonia (COD/NH4+‐N) ratio of 10.2 ± 2.2 at 25°C within the hydraulic retention time (HRT) of 4 h and within a total SRT of 5–10 days. The TIN removal efficiency up to 91% was observed during the study, while effluent TIN was 9.6 ± 4.4 mgN/L. Therefore, this pilot‐scale study demonstrates that application of the proposed on‐line aeration control is capable of relatively high nitrogen removal without supplemental carbon and alkalinity addition at a low HRT. Biotechnol. Bioeng. 2015;112: 2060–2067. © 2015 Wiley Periodicals, Inc.
The design of image processing algorithms on parallel computers

This thesis is a study of the design of parallel algorithms for low-level digital image processing on Very Large Scale Integration (VLSI) processor arrays which are implemented on both a Sequent Balance (MIMD) via an Occam simulator and a transputer network running the Transputer Development System (TDS). The Occam programming language is used as a tool to simulate and map systolic arrays for the image processing algorithms proposed. [Continues. ]
Genome Sequences of 11 Shiga Toxin-Producing Escherichia coli Strains

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) strains are a common cause of both sporadic infection and outbreaks of enteric disease in humans. Here, we present draft genome sequences of 11 STEC strains of different serotypes (O145, O121, O26, O177, and O-type unknown), that have been isolated from patients with enteric disease of various degrees of severity, in the years 2001 to 2014 at St. Olavs Hospital in Trondheim, Norway.
Des objets qui solidifient une théorie : l'histoire du contrôle statistique de fabrication

Nous proposons ici d'aborder le probleme de la naissance et de la diffusion des savoirs en gestion sous un angle un peu inhabituel : celui des objets a travers lesquels le savoir acquiert une certaine materialite. Dans ce domaine, la tradition consiste plutot a etudier les idees : comment elles naissent, comment on eprouve leur pertinence, en quoi les avantages qu'elles apportent peuvent expliquer leur succes, etc. On se concentre sur le contenu de la pensee, presupposant que c'est dans sa qualite et sa pertinence que reside la valeur des methodes de gestion. Sans vouloir nier l'importance des idees, il est cependant fecond d'examiner le role que jouent les objets materiels, aussi bien dans la construction des idees que dans leur diffusion et dans leur mise en oeuvre dans le monde des entreprises.
The classification of prostaglandin DP‐receptors in platelets and vasculature using BW A868C, a novel, selective and potent competitive antagonist

1 BW A868C, a novel compound, behaved as a simple competitive antagonist in a human washed platelet aggregation assay. Anti‐aggregatory concentration‐effect curves to BW 245C were displaced in a parallel manner. The shifts accorded with a Schild plot slope of unity and a pKB of 9.26. 2 Inhibition of platelet aggregation by prostaglandin D2 (PGD2) was antagonized with a similar potency, as were the relaxation effects of BW 245C and PGD2 in the rabbit jugular vein. BW A868C can, therefore, be classified as a DP‐receptor antagonist. 3 Actions of BW A868C at other prostaglandin receptors (IP, EP1, EP2, TP and FP) were excluded at concentrations up to 1,000 times higher than the DP‐receptor affinity. 4 Analyses of BW 245C‐ and PGD2‐mediated effects were complicated by additional agonist receptor interactions which were revealed by BW A868C. In rabbit jugular vein a resistant phase of agonism was detectable, indicating that both agonists exerted effects through another receptor (possibly EP2). Also, PGD2, in addition to its anti‐aggregatory effect on platelets, demonstrated a pro‐aggregatory action in the presence of BW A868C. 5 The contractile effects of PGD2 in guinea‐pig tracheal strips were resistant to 10 μm BW A868C indicating that they were not mediated through DP‐receptors. 6 To our knowledge this is the first account of a well‐classified competitive antagonist at the DP‐receptor. Its potency and selectivity make it an important new tool in prostanoid receptor classification and identification.
Antiangiogenic tumor treatment: early noninvasive monitoring with USPIO-enhanced MR imaging in mice.

PURPOSE To prospectively investigate steady-state blood volume measurements for early quantitative monitoring of antiangiogenic treatment with ultrasmall superparamagnetic iron oxide (USPIO)-enhanced magnetic resonance (MR) imaging. MATERIALS AND METHODS The institutional animal care committee approved all experiments. HT-1080 fibrosarcoma-bearing nude mice were injected with a thrombogenic vascular targeting agent (VTA) (11 nude mice, 20 tumors) or saline (12 nude mice, 20 tumors). USPIO-enhanced (SH U 555C) MR imaging was performed after the VTA was administered. USPIO-induced changes in tissue R2* (DeltaR2*) were measured with a T2-weighted dual-echo echo-planar imaging sequence, and the vascular volume fraction (VVF) was calculated. Parametric DeltaR2* maps were analyzed with respect to tumor perfusion patterns. Correlative histologic analysis was performed for grading of tissue thrombosis, and tissue perfusion was quantified with fluorescent microbeads. Unpaired Student t test and Spearman nonparametric correlation coefficient were used for statistical analysis. RESULTS The DeltaR2* values were significantly (P < .001) reduced shortly after treatment initiation (mean DeltaR2*, 0.017 msec(-1) +/- 0.0014 [standard error] in control animals vs 0.005 msec(-1) +/- 0.0007 in animals that received VTA), which was also reflected by a decrease in the VVF (2.47% +/- 0.18 vs 0.41% +/- 0.48, P < .001). Histologic analysis revealed various degrees of tumor thrombosis after VTA treatment that correlated inversely with the DeltaR2* values (r = -0.83). Moreover, tumor perfusion measurements corroborated the MR results, indicating a significant reduction in tissue perfusion after VTA treatment (mean tissue fluorescence, 570.4 arbitrary units [au] per gram +/- 27 vs 161.7 au/g +/- 17; P < .05). CONCLUSION USPIO-enhanced MR imaging enables early monitoring of antiangiogenic treatment of tumors.
A Review on Specification Mining Architecture

To aid program testing efforts and help program verification tools to find bugs and ensure correctness of systems the mined specifications can be used. Mining of specification process starts with a program under analysis and/or a set of test cases. By applying static or dynamic analysis method traces should be produced from the program. Techniques employing dynamic analysis require the running of the test cases to produce a set of traces which is later analyzed. Program traces are often long and involve several phases. Semantic clustering can be used to split the traces vertically into phases based on comments or annotations on source code. This paper shows a review on the architecture of the automaton based specification mining process.
Red Cell Transfusion–Associated Hemolysis in Cardiac Surgery: An Observational Cohort Study

BACKGROUND: Red cell viability is impaired during storage, resulting in excess hemolysis during storage and after transfusion. As a result, transfusions may oversaturate the hemoglobin clearance pathways, resulting in cell-free hemoglobin and iron toxicity in susceptible patients, such as those undergoing cardiac surgery with cardiopulmonary bypass. To explore this hypothesis, we assessed the relationship of red cell transfusions with cell-free hemoglobin and transferrin saturation levels in a consecutive cohort of cardiac surgical patients. METHODS: Laboratory measures of hemolysis were obtained in consecutive cardiac surgical patients 15 to 30 minutes after bypass. Multivariable regression models controlling for important confounders were constructed to determine the independent relationship of red cell transfusions during bypass with cell-free hemoglobin and transferrin saturation levels post-bypass, analyzed as continuous variables (linear regression) and categorized at the 90th percentiles (logistic regression). RESULTS: Of the 543 included patients, 82 (15.1%) received red cell transfusions during bypass (median 1; interquartile range 1–2 units). Cell-free hemoglobin was detected in all patients (mean 11.3; standard deviation ± 9.3; 90th percentile 18 &mgr;mol/L), and transferrin saturations were relatively high (mean 41 ± 19%; 90th percentile 66%). After controlling for confounders, transfusions were not associated with cell-free hemoglobin (P > .25 in linear and logistic regression) but were directly associated with transferrin saturation levels (P < .001 in linear and logistic regression). Transfused patients had a 6.2-fold (95% confidence interval: 2.4–16.1) risk-adjusted increase in the odds of having high (>66%) transferrin saturation levels. CONCLUSIONS: The findings support the hypothesis that transfusion-related adverse events may be in part caused by the excessive hemolysis of transfused red cells, which can lead to acute iron overload and related toxicity. This suggests that strategies aimed at avoiding or mitigating transfusion-related acute iron overload may improve the safety of red cell transfusions.
Effects of an Alien Ant Invasion on Abundance, Behavior, and Reproductive Success of Endemic Island Birds

Abstract: Biological invaders can reconfigure ecological networks in communities, which changes community structure, composition, and ecosystem function. We investigated whether impacts caused by the introduced yellow crazy ant (Anoplolepis gracilipes), a pantropical invader rapidly expanding its range, extend to higher‐order consumers by comparing counts, behaviors, and nesting success of endemic forest birds in ant‐invaded and uninvaded rainforest on Christmas Island (Indian Ocean). Point counts and direct behavioral observations showed that ant invasion altered abundances and behaviors of the bird species we examined: the Island Thrush (Turdus poliocephalus erythropleurus), Emerald Dove (Chalcophaps indica natalis), and Christmas Island White‐eye (Zosterops natalis). The thrush, which frequents the forest floor, altered its foraging and reproductive behaviors in ant‐invaded forest, where nest‐site location changed, and nest success and juvenile counts were lower. Counts of the dove, which forages exclusively on the forest floor, were 9–14 times lower in ant‐invaded forest. In contrast, counts and foraging success of the white‐eye, a generalist feeder in the understory and canopy, were higher in ant‐invaded forest, where mutualism between the ant and honeydew‐secreting scale insects increased the abundance of scale‐insect prey. These complex outcomes involved the interplay of direct interference by ants and altered resource availability and habitat structure caused indirectly by ant invasion. Ecological meltdown, rapidly unleashed by ant invasion, extended to these endemic forest birds and may affect key ecosystem processes, including seed dispersal.
The decomposition of 1-chloro- and 1-bromonaphthalene by soil bacteria.

Two species of naphthalene-utilizing bacteria from soil were able to metabolize 1-chloro- and 1-bronionaphthalene. From cultures in which 1-chloro-naphthalene was the sole source of organic carbon, d-8-chIoro-l:2-dihydro-1:2-di-hydroxynaphthalene and 3-chlorosalicylic acid were isolated. 3-Bromosalicylic acid was isolated from cultures with 1-bromonaphthalene and evidence of the formation of a ‘diol’ compound obtained. The course of the metabolic pathways is discussed.
Nanomedical system for nucleic acid drugs created with the biodegradable nanoparticle platform

Nanomedical applications of biodegradable poly(DL-lactide-co-glycolide) (PLGA) nanoparticles (NPs) developed are discussed in this review. A surface-functionalized PLGA NP platform for drug delivery was established to encapsulate a number of macromolecular drugs such as peptides and nucleic acids as well as low-molecular-weight drugs by the emulsion solvent diffusion method. The interaction of PLGA NPs with cells and tissues could be controlled by changing the surface properties of NPs, suggesting their potential utility for the intracellular drug delivery of nucleic acid-based drugs. Furthermore, orally administered NF-κB decoy oligonucleotide-loaded CS-PLGA NPs are also useful in treating experimental colitis. These approaches using surface-modified PLGA NPs could be able to open new possibilities for nucleic acid-based drug delivery via noninvasive administration method.
4‐Methylcatechol‐induced cell damage in TM4 Sertoli cells

4‐Methylcatechol (4‐MC) is one of the metabolites of quercetin, which is a potential drug for neuroprotection and tumorigenesis inhibition. This study was performed to investigate the cytotoxic effect of 4‐MC in mouse TM4 Sertoli cells. TM4 Sertoli cell viability was significantly inhibited by 4‐MC in a time‐ and dose‐dependent manner. The number of apoptotic and dead cells was significantly increased after 4‐MC treatment. Caspase 3 activity increased by prolonged exposure of TM4 Sertoli cells to 200 μM 4‐MC. The 4‐MC significantly upregulated the mRNA level of Bax gene and considerably downregulated the Bcl‐2 gene expression in a concentration‐dependent manner. Results showed that 4‐MC could induce TM4 Sertoli cell apoptosis, and the cytotoxic effect of 4‐MC on TM4 Sertoli cells may be associated with upregulated Bax gene expression, which induced caspase cascade activation.
Performance evaluation of parallel packet processing architectures using systemC based modeling and refinement

Network nodes, such as broadband access components, are facing new design challenges due to recent trends in applications and technologies. Stringent constraints on platform costs, performance, and power dissipation increasingly require novel programmable application-specific multi-processor architectures to be deployed. Early design space exploration is required to build a proper hardware platform. Multiple processing elements and on-chip interconnects need to be integrated. As complexity grows there is a demand to efficiently evaluate the performance of the complete system. Due to the complexity and heterogeneity it is no longer feasible to start with a model at the register-transfer level. Abstractions must be found to allow performance evaluation even in the concept phase of the design flow. A system-level performance evaluation framework is required to explore multi-processor architectures and to quantitatively evaluate different design alternatives. Due to a lack of these frameworks, today’s architectures exhibit overprovisioning of resources instead of configurability in general or reconfigurability at run-time. This leads to systems that are either designed too pessimistically in order to meet all traffic requirements or too optimistically due to inaccurate approximations of resource utilizations caused by non-deterministic real-life workload. Multi-processor architectures can address non-deterministic workload by reconfigurability that can be expressed, e. g. , by load balancing. Thereby, workload is distributed among a number of processing resources. Several approaches exist to exploit load balancing of computing resources within a System-on-Chip (SoC). However, complex network nodes consist of several SoCs and their complexity prevents a quantitative evaluation of system-level load balancing at low abstractions. The above issues are concerned with two main contributions that can be summarized as follows: 1. A system-level performance evaluation framework, named SystemQ, is introduced that provides a high abstraction, i. e. performance abstraction. SystemQ is based on queuing theory and implemented using SystemC. It therefore provides modeling at multiple abstractions and enables a refinement path between these abstractions. 2. A disciplined approach to system-level load balancing in systems consisting of several systems-on-chip is motivated. The advantages of this approach are compared quantitatively with SoC-local load balancing by using the SystemQ framework. This thesis reveals how to use the performance evaluation framework in order to efficiently model and simulate load balancing of multi-SoC platforms. The results of this work will eventually influence the design of future SoC platform architectures by means of improved performance and economical deployment of resources.
Systematic Review With Meta-Analyses and Critical Appraisal of Clinical Prediction Rules for Pulmonary Tuberculosis in Hospitals

Objective To systematically review studies evaluating clinical prediction rules (CPRs) for adult inpatients suspected to have pulmonary tuberculosis. Design Systematic review with meta-analyses. Setting Hospitals. Patients Inpatients at least 15 years of age admitted to acute care. Methods A search was conducted in 5 indexed electronic databases with no language or year of publication restrictions. We performed a meta-analysis for those CPRs with at least 2 validation studies. Results were reported according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Results Of the 461 abstracts selected, 36 articles were fully analyzed and 11 articles were included, yielding 8 CPRs derived in 4 countries. Broad validation studies were identified for 2 CPRs. The most frequent clinical predictors were fever and weight loss. All CPRs included chest imaging signs. Most CPRs were derived in countries with a low prevalence of pulmonary tuberculosis and included homeless, immigrants, and those who reacted to the purified protein derivative test. Both of the CPRs derived in countries with a high prevalence of pulmonary tuberculosis strongly relied on chest radiograph predictors. Accuracy of the different CPRs was high (area under receiver operating characteristic curve, 0.79–0.91). Meta-analysis of 4 validation studies for Wisnivesky´s CPR indicates optimistic pooled results: sensitivity, 94.1% (95% CI, 89.7%–96.7%); negative likelihood ratio, 0.22 (95% CI, 0.12–0.40). Conclusion On the basis of a critical appraisal of the 2 best validated CPRs, the presence of weight loss and/or fever in inpatients warrants obtaining a chest radiograph, regardless of the presence of productive cough. If the chest radiograph is abnormal, the patient should be placed in isolation until more specific test results are available. Validation in different settings is required to maximize external generalization of existing CPRs. Infect Control Hosp Epidemiol 2014;00(0): 1–10
ZnO–ZnMgO Multiple Quantum-Well Ridge Waveguide Lasers

ZnO-ZnMgO multiple quantum-well (MQW) thin-film waveguides with ridge structures have been fabricated on quartz substrates. Low-temperature deposition of high-quality ZnO-ZnMgO MQW thin films was achieved by filtered cathodic vacuum arc technique. A ridge is defined on the thin film by plasma etching. Room-temperature lasing with a peak wavelength at 378 nm of 1.5-nm well width was observed under 355-nm optical excitation. Exciton-exciton scattering was attributed to the amplified spontaneous emission observed from the MQW waveguide. The net optical gain can be larger than 80 cm-1 at a pump intensity of 2 MW/cm2 .