Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence of spintronics behaviour (half-metallicity, spin gapless semiconductor and bipolar magnetic semiconductor) depending on the location of oxygen vacancies in BiFe0.83Ni0.17O3

The current communication signifies the effect of oxygen vacancies (OVs) both qualitatively and quantitatively in multiferroic BiFe0.83Ni0. 17O3 by an in-depth atomic-level investigation of its electronic structure and magnetization properties, and these materials have a variety of applications in spintronics, optoelectronics, sensors and solar energy devices. Depending on the precise location of OVs, all the three types of spintronic material namely half-metallic, spin gapless semiconductor and bipolar magnetic conductor have been established in a single material for the first time and both super-exchange and double-exchange interactions are possible in accordance with the precise location of OVs. We have also calculated the vacancy formation energies to predict their thermodynamic stabilities. These results can highlight the impact and importance of OVs that can alter the multiferroic properties of materials.
Streptococcus mutans: Fructose Transport, Xylitol Resistance, and Virulence

Streptococcus mutans, the primary etiological agent of human dental caries, possesses at least two fructose phosphotransferase systems (PTSs), encoded by fruI and fruCD. fruI is also responsible for xylitol transport. We hypothesized that fructose and xylitol transport systems do not affect virulence. Thus, colonization and cariogenicity of fruI− and fruCD− single and double mutants, their WT (UA159), and xylitol resistance (Xr) of S. mutans were studied in rats fed a high-sucrose diet. A sucrose phosphorylase (gtfA−) mutant and a reference strain (NCTC-10449S) were additional controls. Recoveries of fruI mutant from the teeth were decreased, unlike those for the other strains. The fruCD mutation was associated with a slight loss of cariogenicity on enamel, whereas mutation of fruI was associated with a loss of cariogenicity in dentin. These results also suggest why xylitol inhibition of caries is paradoxically associated with spontaneous emergence of so-called Xr S. mutans in habitual human xylitol users.
Genome Sequence of Avery's Virulent Serotype 2 Strain D39 of Streptococcus pneumoniae and Comparison with That of Unencapsulated Laboratory Strain R6

ABSTRACT Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenesis. To date, the complete genome sequences have been reported for only two S. pneumoniae strains: TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report here the genome sequences and new annotation of two different isolates of strain D39 and the corrected sequence of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only five relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single-base-pair changes, six deletions, and four insertions and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, the relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed.
Hydrolysis of a Broad Spectrum of Extracellular Matrix Proteins by Human Macrophage Elastase*

Macrophage elastase (ME) was originally named when metal-dependent elastolytic activity was detected in conditioned media of murine macrophages. Subsequent cDNA cloning of the mouse and human enzyme demonstrated that ME is a distinct member of the matrix metalloproteinase family. To date, the catalytic parameters that describe the hydrolysis of elastin by ME have not been quantified and its activity against other matrix proteins have not been described. In this report, we have examined the action of purified recombinant human ME (rHME), produced in Escherichia coli, on elastin and other extracellular matrix proteins. On a molar basis, rHME is approximately 30% as active as human leukocyte elastase in solubilizing elastin. rHME also efficiently degrades α1-antitrypsin (α1-AT), the primary physiological inhibitor of human leukocyte elastase. In addition, rHME efficiently degrades fibronectin, laminin, entactin, type IV collagen, chondroitan sulfate, and heparan sulfate. These results suggest that HME may be required for macrophages to penetrate basement membranes and remodel injured tissue during inflammation. Moreover, abnormal expression of HME may contribute to destructive processes such as pulmonary emphysema and vascular aneurysm formation. To further understand the specificity of HME, the initial cleavage sites in α1-AT have been determined. In addition, the hydrolysis of a series of synthetic peptides with different P′1residues has been determined. rHME can accept large and small amino acids at the P′1 site, but has a preference for leucine.
Extraction of $\pi$-Type Substrate Resistance Based on Three-Port Measurement and the Model Verification up to 110 GHz

An analytical parameter-extraction method for pi-type substrate resistance model of RF MOSFETs based on three-port measurement is presented for the first time. The values of substrate resistance components are extracted directly from the three-port S-parameter measurement data, and the output admittance of the MOSFETs is well matched up to 110 GHz. Using a macromodel with extracted substrate components, it is verified that pi-type substrate resistance model is more accurate than other substrate resistance models
Development of maternal and neonatal composite outcomes for trials evaluating management of late-onset pre-eclampsia

Objective: Pre-eclampsia is associated with significant maternal and neonatal complications, and delivery is often expedited to minimise complications. For randomised trials evaluating interventions in women with late-onset (>34 weeks) mild to moderate pre-eclampsia, no single outcome has been identified to be the most clinically important. Existing composite outcomes with more than one clinically relevant endpoint to evaluate interventions in pre-eclampsia provide limited justification for selection of the components. Our objective was to develop robust, valid composite maternal and neonatal outcome measures for clinical trials evaluating interventions in women with late-onset mild and moderate pre-eclampsia. Study design: A two-generational Delphi method was used to identify these clinically important maternal and neonatal outcomes. Composite outcomes were developed based on biological plausibility, independence from each other, frequency of occurrence and level of importance. Results: The final maternal composite outcome included maternal death, eclampsia, stroke or reversible ischaemic neurological deficit, pulmonary oedema, major obstetric haemorrhage, need for positive inotropic support, haemolysis, elevated liver enzymes and low platelets syndrome and placental abruption; and the neonatal composite outcome included neonatal death, respiratory distress syndrome needing ventilator support and neurological outcomes as cystic periventricular leukomalacia and grade III/IV intraventricular haemorrhage. Conclusion: The composite outcomes developed will enable clinical trials to provide robust estimates on the effectiveness of the interventions in women with mild to moderate late onset pre-eclampsia to inform clinical practice. Caution is needed in the interpretation of composite outcomes due to variation in the importance of individual components.
THE PRESSURE-VOLUME LOOP REVISITED: IS THE SEARCH FOR A CARDIAC CONTRACTILITY INDEX A FUTILE CYCLE?

ABSTRACT Our previous studies indicate that left ventricular end-systolic pressure-volume relations (ESPVRs) or elastance (Ees) are not reduced in studies where expected reductions of contractility should be found (i.e., heart failure, stunning, and endotoxemia). The present study was done to assess whether this phenomenon is due to a particular load sensitivity of elastance, rendering this index inappropriate as a measurement of contractility in pathologic states in vivo. Methods and Results Analysis of previously generated data revealed an increased ESPVR in stunned hearts, in pigs made endotoxemic, and in hearts rapidly paced. After inducing acute heart failure by microembolization, the ESPVR was increased when assessed using linear relations but reduced when assessing ESPVR by a curvilinear algorithm. To further evaluate the effect of different load alterations on ESPVR, this relation was generated by (i) inferior vena caval occlusions (VCOs); (ii) gradually occluding the descending aorta (pressure interventions); and (iii) rapidly infusing blood (120 mL) into the left atrium (volume increments). The load protocol was applied in 5 pigs, before and after the left ventricle was stunned by 11 brief left main coronary artery occlusions/reperfusions (accumulated ischemia 20 min affecting 81% of the left ventricle). Correlation coefficients for left ventricular elastance ranged from 0.93 to 0.99 in all the 3 types of loading interventions. Despite significant reductions in stroke volume, stroke work, and dP/dtmax, VCO-calculated linear and curvilinear Ees increased 90 min after stunning (55% ± 4% and 94% ± 6%, respectively). Linear Ees during pressure interventions decreased 36% ± 1%, whereas curvilinear Ees decreased 33% ± 3%. During volume infusions, linear Ees decreased 27% ± 2%. We achieved the same results after blocking the baroreceptor reflexes using hexamethonium. Conclusions The Ees is particularly load dependent and will reflect load interventions more than the inotropic state of thecardiac muscle. A VCO-generated Ees increase could be an unmasking of a pronounced preload sensitivity in failing myocardium.
Pyricularia pennisetigena and P. zingibericola from invasive grasses infect signal grass, barley and wheat

Fungal species from the Pyricularia genus are associated with blast disease in plants from the Poaceae family, causing losses in economically important crops such as rice, oat, rye, barley, wheat and triticale. This study aimed at characterizing the pathogenicity spectrum of P. pennisetigena and P. zingibericola to signal grass, barley and wheat, as well as comparing them with those from the species P. grisea and P. oryzae pathotype Triticum, which occur widely in the Brazilian agroecosystem. Twenty isolates of Pyricularia spp. were obtained from infected leaf samples of invasive plant species from wheat fields. The isolates classification into distinct Pyricularia species was done using molecular phylogeny based on actin and calmodulin genes. Pyricularia pennisetigena and P. zingibericola inoculated on plant leaves, at a concentration adjusted to 105 conidia mL-1, were pathogenic to signal grass, barley and wheat, with varying levels of aggressiveness.
Dielectrophoretic detection and quantification of hybridized DNA molecules on nano‐genetic particles

DNA–DNA hybridization reactions on 100 nm oligonucleotide‐functionalized silica nanoparticles are found to sensitively affect the amplitude and direction of the dielectrophoretic mobility of the particles at nanomolar target ssDNA concentrations. Such sensitivity permits visual detection of the hybridization event without fluorescent labeling and confocal microscopy by imaging the cross‐over frequency (cof) of the particle suspension on a quadrupole electrode array. Strong correlation with effective particle radius and zeta‐potential measurements suggests that the dielectrophoretic cof offers not just sensitive signatures for successful functionalization and hybridization but also those for three distinct DNA surface conformations that appear at different surface densities of hybridized DNA. A properly normalized cof calibration chart allows simplified quantification of the target ssDNA concentrations. These results provide a simple, rapid and portable genetic detection method compatible for use outside the laboratory.
Laminin Receptor Involvement in the Anti-angiogenic Activity of Pigment Epithelium-derived Factor*♦

Pigment epithelium-derived factor (PEDF) is a multifunctional protein with neurotrophic, anti-oxidative, and anti-inflammatory properties. It is also one of the most potent endogenous inhibitors of angiogenesis, playing an important role in restricting tumor growth, invasion, and metastasis. Studies show that PEDF binds to cell surface proteins, but little is known about how it exerts its effects. Recently, research identified phospholipase A2/nutrin/patatin-like phospholipase domain-containing 2 as one PEDF receptor. To identify other receptors, we performed yeast two-hybrid screening using PEDF as bait and discovered that the non-integrin 37/67-kDa laminin receptor (LR) is another PEDF receptor. Co-immunoprecipitation, His tag pulldown, and surface plasmon resonance assays confirmed the interaction between PEDF and LR. Using the yeast two-hybrid method, we further restricted the LR-interacting domain on PEDF to a 34-amino acid (aa) peptide (aa 44–77) and the PEDF-interacting domain on LR to a 91-aa fragment (aa 120–210). A 25-mer peptide named P46 (aa 46–70), derived from 34-mer, interacts with LR in surface plasmon resonance assays and binds to endothelial cell (EC) membranes. This peptide induces EC apoptosis and inhibits EC migration, tube-like network formation in vitro, and retinal angiogenesis ex vivo, like PEDF. Our results suggest that LR is a real PEDF receptor that mediates PEDF angiogenesis inhibition.
Spatial fragment distribution from a therapeutic pencil-like carbon beam in water

The latest heavy ion therapy tends to require information about the spatial distribution of the quality of radiation in a patient's body in order to make the best use of any potential advantage of swift heavy ions for the therapeutic treatment of a tumour. The deflection of incident particles is described well by Molière's multiple-scattering theory of primary particles; however, the deflection of projectile fragments is not yet thoroughly understood. This paper reports on our investigation of the spatial distribution of fragments produced from a therapeutic carbon beam through nuclear reactions in thick water. A ΔE–E counter telescope system, composed of a plastic scintillator, a gas-flow proportional counter and a BGO scintillator, was rotated around a water target in order to measure the spatial distribution of the radiation quality. The results revealed that the observed deflection of fragment particles exceeded the multiple scattering effect estimated by Molière's theory. However, the difference can be sufficiently accounted for by considering one term involved in the multiple-scattering formula; this term corresponds to a lateral ‘kick’ at the point of production of the fragment. This kick is successfully explained as a transfer of the intra-nucleus Fermi momentum of a projectile to the fragment; the extent of the kick obeys the expectation derived from the Goldhaber model.
LIT at TREC 2002: Web Track

In Trec-2002, we participated in the Web Trec (named page finding task). There are two kinds of information that can be used while finding the expected page, content information and link information. We exploited both of them. That is to say, our system is content-based and link-based. As to link information, we only used anchor text and connections, and topology between pages is ignored. We submitted two runs. One is based on traditional contented-based retrieval, the other try to combine content-based retrieval and link-based retrieval to get better result.
Ecotoxicology of antifouling biocides - with special focus on the novel antifoulant medetomidine and microbial communities

Marine biofouling, growth on submerged surfaces, is a problem for the commercial shipping industry but also for recreational boat owners. It leads to increased fuel consumption, loss of maneuverability and is a source of invasive species. The common solution to avoid biofouling is to use antifouling paints containing biocides which hinder the fouling organisms from growing on the ship hull. Medetomidine (4-[1-(2,3dimethylphenyl)ethyl]-1-H-imidazole, also known as Selektope) is used in antifouling paint due to its ability to inhibit settlement of barnacle cyprid larvae. Exposure to medetomidine hinders settlement and metamorphosis to an adult barnacle at 0.2 μg/l (1 nM), a concentration one hundred thousand times lowers than the lethal concentration. Several studies of possible environmental effects have been performed during the developmental phase of medetomidine as an antifoulant, both on invertebrates and vertebrates. This thesis focuses on the effects on marine microbial communities with studies on short-term toxicity, toxicant-induced succession after intermediate time exposure, long-term microcosm exposure and bioaccumulation. The predicted environmental concentrations (PEC) of medetomidine in different environments have also been established using the MAMPEC model. A worst-case prediction for a Baltic marina generated a water concentration of 0.057 μg/l (0.28 nM). The conclusion for this thesis is that microalgal and bacterial metabolic functions are not affected by medetomidine until very high concentrations (2 mg/l, 10 μM). The same conclusion can be drawn for direct effects on species composition although there is an indication that grazing organisms in the microbial community could be affected, changing their grazing pattern and hence the microalgal species composition. Long-term effects of medetomidine on microbial communities from an antifouling paint were unfortunately surpassed by effects of zinc which was also present in the paint. It can therefore also be concluded that zinc affects both metabolic functions and species composition in microbial communities to a larger extent than does medetomidine.
Modeling and optimizing Ultra Wideband antennas for microwave breast cancer detection

In this paper, two compact Ultra Wideband (UWB) antennas have been proposed to be in touch with skin for microwave breast cancer detection. The UWB techniques allow for a good shape-identification and allow sensing of dielectric properties differences among tissue types over a very wide frequency band. The UWB antennas are designed and analyzed using CST simulation tool in transient mode to verify antenna parameters improvements. The simulation results indicated the improvement of the antenna response by properly selecting antenna dimensions and antenna shape.
Distributed predictive control of grid-connected solar PV generation based on data-driven subspace approach

The scale of a distributed grid-connected solar photovoltaic (PV) generation system keeps growing, which is naturally composed of many subsystems interacting with each other. In this paper, a novel distributed predictive control based on data-driven subspace approach is proposed to design the predictive controller of the grid-connected inverter in the distributed solar PV generation system. The control performance of the whole system is improved by minimizing the interaction between solar PV generation subsystems and the grid, as well as the interactions within subsystems. Each solar PV generation subsystem has its own inverter which converts the induced energy into the power in utility grid and exchanges the input and output information with each other through network. The application of data-driven predictive method in the grid-connected solar PV generation system is analyzed in detail in this paper. The simulation model of the distributed grid-connected solar PV generation system is established in Matlab/Simulink, which validates the good performance of the approach. The results demonstrate the effectiveness of the proposed control method.
Neuro-fuzzy decision trees for content popularity model and multi-genre movie recommendation system over social network

In this paper, we propose a framework of multi-genre movie recommender system based on neuro-fuzzy decision tree (NFDT) methodology. The system is capable of recommending list of movies in descending order of preference in response to user queries and profiles. The system also takes care of attempt to vote stuffing using novel application of fuzzy c-means clustering algorithm. Typical user query and profiles consists of content ratings for multiple genres like Action, Comedy, Drama, Music and many others. The distinctive point of the proposed approach is to handle recommender system generation as a supervised pattern classification problem, where in user reviews for multiple genres are conditions and overall star ratings are decisions. The entire recommender system is represented in the form of NFDT. Rules represented by NFDT also acts as a tool for understanding the combinations of contents driving popularity (and unpopularity) over certain social network. We have also proposed a modified inference mechanism based on matching and ordering of firing strength of each fuzzy decision tree path in response to user queries. The computational experiments have been presented on a sample real-world movie review database to judge the efficiency of the proposed recommender system.
Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 (JAK1), in 9.1% of patients and provides a path toward therapeutic intervention of the disease.
Analysis of Failure Time Data with Multilevel Clustering, with Application to the Child Vitamin A Intervention Trial in Nepal

Summary We consider the problem of estimating covariate effects in the marginal Cox proportional hazard model and multilevel associations for child mortality data collected from a vitamin A supplementation trial in Nepal, where the data are clustered within households and villages. For this purpose, a class of multivariate survival models that can be represented by a functional of marginal survival functions and accounts for hierarchical structure of clustering is exploited. Based on this class of models, an estimation strategy involving a within‐cluster resampling procedure is proposed, and a model assessment approach is presented. The asymptotic theory for the proposed estimators and lack‐of‐fit test is established. The simulation study shows that the estimates are approximately unbiased, and the proposed test statistic is conservative under extremely heavy censoring but approaches the size otherwise. The analysis of the Nepal study data shows that the association of mortality is much greater within households than within villages.