Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Production Process for Native Outer Membrane Vesicle Vaccine against Neisseria meningitidis

An improved detergent-free process has been developed to produce vaccine based on native outer membrane vesicles (NOMV) against Neisseria meningitidis serogroup B. Performance was evaluated with the NonaMen vaccine concept, which provides broad coverage based on nine distinct PorA antigens. Scalable aseptic equipment was implemented, replacing undesirable steps like ultracentrifugation, inactivation with phenol, and the use of preservatives. The resulting process is more consistent and gives a higher yield than published reference processes, enabling NOMV production at commercial scale. Product quality met preliminary specifications for 9 consecutive batches, and an ongoing study confirmed real-time stability up to 12 months after production. As the NOMV had low endotoxic activity and induced high bactericidal titres in mice, they are expected to be safe and effective in humans. The production process is not limited to NonaMen and may be applicable for other N. meningitidis serogroups and other gram-negative pathogens. The current results therefore facilitate the late-stage development and clinical evaluation of NOMV vaccines.
BREAKDOWN IN CORRELATIONS DURING LABORATORY EVOLUTION. II. SELECTION ON STRESS RESISTANCE IN DROSOPHILA POPULATIONS

Abstract We trace the evolutionary correlation between stress resistance and longevity in populations of Drosophila melanogaster selected for stress resistance over many generations. Females selected for desiccation resistance and both females and males selected for increasing starvation resistance initially show concurrent increases in longevity, but then begin to decrease in longevity, even as stress resistance continues to increase. We demonstrate that the correlation between two fitness traits can change and that this change is due to sustained selection rather than a genotype-by-environment interaction or inbreeding depression. The breakdown in evolutionary correlation we report underscores the difficulty of extrapolating the results from short-term selection experiments to predictions of long-term evolution.
Clinical Impact of Tumor Regression Grade after Preoperative Chemoradiation for Locally Advanced Rectal Cancer: Subset Analyses in Lymph Node Negative Patients

Background We investigated the prognostic significance of tumor regression grade (TRG) after preoperative chemoradiation therapy (preop-CRT) for locally advanced rectal cancer especially in the patients without lymph node metastasis. Methods One-hundred seventy-eight patients who had cT3/4 tumors were given 5,040 cGy preoperative radiation with 5-fluorouracil/leucovorin chemotherapy. A total mesorectal excision was performed 4-6 weeks after preop-CRT. TRG was defined as follows: grade 1 as no cancer cells remaining; grade 2 as cancer cells outgrown by fibrosis; grade 3 as a minimal presence or absence of regression. The prognostic significance of TRG in comparison with histopathologic staging was analyzed. Results Seventeen patients (9.6%) showed TRG1. TRG was found to be significantly associated with cancer-specific survival (CSS; P = 0.001) and local recurrence (P = 0.039) in the univariate study, but not in the multivariate analysis. The ypN stage was the strongest prognostic factor in the multivariate analysis. Subgroup analysis revealed TRG to be an independent prognostic factor for the CSS of ypN0 patients (P = 0.031). TRG had a stronger impact on the CSS of ypN (-) patients (P = 0.002) than on that of ypN (+) patients (P = 0.521). In ypT2N0 and ypT3N0, CSS was better for TRG2 than for TRG3 (P = 0.041, P = 0.048), and in ypN (-) and TRG2 tumors, CSS was better for ypT1-2 than for ypT3-4 (P = 0.034). Conclusion TRG was found to be the strongest prognostic factor in patients without lymph node metastasis (ypN0), and different survival was observed according to TRG among patients with a specific histopathologic stage. Thus, TRG may provide an accurate prediction of prognosis and may be used for f tailoring treatment for patients without lymph node metastasis.
An assessment of the nonmarket benefits of the Water Framework Directive for households in England and Wales

Results are presented from a large‐scale stated preference study designed to estimate the nonmarket benefits for households in England and Wales arising from the European Union Water Framework Directive (WFD). Multiple elicitation methods (a discrete choice experiment and two forms of contingent valuation) are employed, with the order in which they are asked randomly varied across respondents, to obtain a robust model for valuing specified WFD implementation programs applied to all of the lakes, reservoirs, rivers, canals, transitional, and coastal waters of England and Wales. The potential for subsequent policy incorporation and value transfer was enhanced by generating area‐based values. These were found to vary from £2,263 to £39,168 per km2 depending on the population density around the location of the improvement, the ecological scope of that improvement, and the value elicitation method employed. While the former factors are consistent with expectations, the latter suggests that decision makers need to be aware of such methodological effects when employing derived values.
Retrospective evidence that the MHC (B haplotype) of chickens influences genetic resistance to attenuated infectious bronchitis vaccine strains in chickens

Infectious bronchitis is a respiratory disease of chickens that is caused by the coronavirus infectious bronchitis virus (IBV). Virtually all broiler and layer breeder flocks are routinely vaccinated against IBV. Two hatches of 1-day-old chicks from four lines were mistakenly vaccinated for infectious bronchitis using a moderately attenuated vaccine designed for chicks of an older age. The vaccination resulted in high mortality, and chicks from three of four lines died with signs typical of infectious bronchitis. The mortality that occurred using this less-attenuated vaccine was significantly influenced by the genetic line, and the MHC (B) haplotype in chickens of three B congenic lines. B congenic chickens possessing the B*15 haplotype were resistant in contrast to chickens possessing the B*13 or B*21 haplotypes. Chicks from two further hatches of the four lines were vaccinated appropriately with a more attenuated IBV vaccine, and only limited chick mortality was seen. These retrospective data from two repeated hatches confirm earlier data indicating chicken genes influence resistance to IBV, and indicate for the first time that genes tightly linked to the B haplotype are relevant in resistance to IBV. Due to extenuating circumstances it was not possible to verify results with chicks from F2 matings. Factors that may enhance definition of the role of the B haplotype in immune response to IBV, and the desirability for further analysis of a B haplotype-linked influence on immunity to IBV are discussed.
Effects of TRH Administration on Orientation Time and Recall After ECT

Summary We investigated the effect of thyrotropin-releasing hormone (TRH) on orientation time and recall, in nine depressed female inpatients undergoing electroconvulsive therapy (ECT). In a balanced order crossover design, an intravenous bolus of 0.4 mg TRH or placebo was administered 20 min before ECT in the first two sessions. Orientation time and retrograde and anterograde components of the memory dysfunction, immediately and 24 h later, were assessed. Administration of TRH did not influence orientation time, word recall, or immediate short story recall compared with placebo. We did find, however, an improvement in the number of short story items recalled after 24 h when patients were given TRH compared with placebo. This indicates that TRH may have a protective role against the specific negative effect of ECT on delayed recall.
A hybrid method for Doppler spread estimation [mobile radio systems]

The Doppler spread estimator presented in this paper solves some problems encountered in some of the previously published solutions. The algorithm consists of two steps, both using the channel autocorrelation function. The first step is a coarse estimate, based on the sign change of the autocorrelation function. Depending on the coarse estimate, either a polynomial fit method (for low Doppler spreads) or a first zero detection method (for high Doppler spreads) is applied. The proposed hybrid Doppler spread estimator provides high estimation accuracy for a wide range of Doppler spreads.
An efficient algorithm for finding a path subject to two additive constraints

One of the key issues in providing end-to-end quality-of-service guarantees in packet networks is how to determine a feasible route that satisfies a set of constraints while simultaneously maintaining high utilization of network resources. In general, finding a path subject to multiple additive constraints (e.g., delay, delay-jitter) is an NP-complete problem that cannot be exactly solved in polynomial time. Accordingly, heuristics and approximation algorithms are often used to address to this problem. Previously proposed algorithms suffer from either excessive computational cost or low performance. In this paper, we provide an efficient approximation algorithm for finding a path subject to two additive constraints. The worst-case computational complexity of this algorithm is within a logarithmic number of calls to Dijkstra's shortest path algorithm. Its average complexity is much lower than that, as demonstrated by simulation results. The performance of the proposed algorithm is justified via theoretical performance bounds. To achieve further performance improvement, several extensions to the basic algorithm are also provided at low extra computational cost. Extensive simulations are used to demonstrate the high performance of the proposed algorithm and to contrast it with other path selection algorithms.
Tracking of vector field singularities in unstructured 3D time-dependent datasets

We present an approach for monitoring the positions of vector field singularities and related structural changes in time-dependent datasets. The concept of singularity index is discussed and extended from the well-understood planar case to the more intricate three-dimensional setting. Assuming a tetrahedral grid with linear interpolation in space and time, vector field singularities obey rules imposed by fundamental invariants (Poincare index), which we use as a basis for an efficient tracking algorithm. We apply the presented algorithm to CFD datasets to illustrate its purpose. We examine structures that exhibit topological variations with time and describe some of the insight gained with our method. Examples are given that show a correlation in the evolution of physical quantities that play a role in vortex breakdown.
Resection of Obstructing Inferior Turbinates Following Rhinoplasty

Total inferior turbinectomy was carried out in 38 patients who complained of nasal obstruction following rhinoplasty or rhinoseptoplasty and in whom hypertrophied inferior turbinates were found to be the cause of obstruction. Postoperatively, relief of nasal obstruction was reported by 84 percent of patients, while rhinoscopy showed wide, clean nasal airways in 92 percent. Nasal airflow measurements in 32 tested patients showed increased patency in all of them, including 3 who still complained of nasal obstruction postoperatively. The follow-up period ranged from 1 to 7 years (mean 2.8 years). Atrophic changes of the nasal mucosa or chronic purulent infection was not observed in any of the patients. Because the results of partial procedures on the inferior turbinates are often unsatisfactory, I suggest performing total inferior turbinectomy in patients with obstructing inferior turbinates following rhinoplasty.
Fabrication and characterization of hollow needle array for electrokinetic intracellular delivery of biomolecules

Delivering molecules into a single cell is a key technology for differentiation of cells and analyze cell functions. This study aims to develop a method for massive intracellular delivery of biomolecules in a precise manner using electrokinetic forces. We fabricated an array of hollow needles by MEMS technologies to establish a high-throughput cellular delivery method. Dimensional change of the fabricated needle array was investigated. A method to integrate a needle array, PDMS flow channels, and electrodes was developed. We applied a voltage between electrodes placed inside and outside the needle substrate and observed electrokinetic ejection of fluorescent dyes from the fabricated hollow needle array.
A Unified Framework of QoS-Based Web Service Recommendation with Neighborhood-Extended Matrix Factorization

QoS-based Web service recommendation is a widely employed way of selecting proper candidate services that can provide better QoS to users. In this paper, based on Matrix Factorization (MF) model, at first, we propose the service neighborhood extended MF model (SN-EMF) and user neighborhood-extended MF model (UN-EMF), in which we integrate two types of valuable information respectively. One is the historical QoS records of the k most similar neighbors, and the other is the geographical location information. Then, with aggregating the results together, we unify the two models into a unified service recommending framework (U-EMF), which can be divided into two parts of offline and online. Moreover, we also discuss some strategies about model selection and simplification. In the end, we conduct sufficient experiments, showing the effectiveness of our three models, especially the relatively large performance improvement of U-EMF model.
The comprehensive effect of surface texture and roughness under hydrodynamic and mixed lubrication conditions

A theoretical study is carried out to investigate the comprehensive effect of the machined roughness and fabricated textures, by solving the average Reynolds equation coupled with a mass-conservative cavitation algorithm and taking into account asperity contact. We analyzed the influence of surface roughness, which is represented by the combined root-mean-square roughness σ and surface pattern parameter γ on the optimum texture parameters including the dimple depth-over-diameter ratio and area density under hydrodynamic and mixed lubrication conditions. The results show that the effect of surface roughness on load-carrying capacity can be ignored under hydrodynamic lubrication condition. Furthermore, the optimum texture parameters under hydrodynamic lubrication condition and the optimum dimple depth-over-diameter ratio under mixed lubrication condition are determined at minimized friction coefficient, which can be taken as the same for smooth-textured surface and rough-textured surface. The corresponding minimum friction coefficient increases with increasing σ and γ, and decreasing dimple area density under mixed lubrication condition.
Potent Neutralization of Hendra and Nipah Viruses by Human Monoclonal Antibodies

ABSTRACT Hendra virus (HeV) and Nipah virus (NiV) are closely related emerging viruses comprising the Henipavirus genus of the Paramyxovirinae. Each has a broad species tropism and can cause disease with high mortality in both animal and human hosts. These viruses infect cells by a pH-independent membrane fusion event mediated by their attachment (G) and fusion (F) envelope glycoproteins (Envs). Seven Fabs, m101 to -7, were selected for their significant binding to a soluble form of Hendra G (sG) which was used as the antigen for panning of a large naïve human antibody library. The selected Fabs inhibited, to various degrees, cell fusion mediated by the HeV or NiV Envs and virus infection. The conversion of the most potent neutralizer of infectious HeV, Fab m101, to immunoglobulin G1 (IgG1) significantly increased its cell fusion inhibitory activity: the 50% inhibitory concentration was decreased more than 10-fold to approximately 1 μg/ml. The IgG1 m101 was also exceptionally potent in neutralizing infectious HeV; complete (100%) neutralization was achieved with 12.5 μg/ml, and 98% neutralization required only 1.6 μg/ml. The inhibition of fusion and infection correlated with binding of the Fabs to full-length G as measured by immunoprecipitation and less with binding to sG as measured by enzyme-linked immunosorbent assay and Biacore. m101 and m102 competed with the ephrin-B2, which we recently identified as a functional receptor for both HeV and NiV, indicating a possible mechanism of neutralization by these antibodies. The m101, m102, and m103 antibodies competed with each other, suggesting that they bind to overlapping epitopes which are distinct from the epitopes of m106 and m107. In an initial attempt to localize the epitopes of m101 and m102, we measured their binding to a panel of 11 G alanine-scanning mutants and identified two mutants, P185A and Q191 K192A, which significantly decreased binding to m101 and one, G183, which decreased binding of m102 to G. These results suggest that m101 to -7 are specific for HeV or NiV or both and exhibit various neutralizing activities; they are the first human monoclonal antibodies identified against these viruses and could be used for treatment, prophylaxis, and diagnosis and as research reagents and could aid in the development of vaccines.
Molecular characterization of Rhodococcus equi Isolates of horse breeding farms from an endemic region in South of Brazil by multiplex PCR

Rhodococcus equi is a gram-positive coco-bacillus and an intracellular opportunistic pathogen which causes pneumonia in foals. It is widely detected in environment and has been isolated from several sources, as soil, feces and gut from health and sick foals. The goal of this study was to characterize the epidemiological status (endemic, sporadic or no infection) of horse breeding farms from Bage County in South of Brazil, using a multiplex PCR. One hundred and eighteen R. equi isolates were identified by biochemical tests and submitted to a specie-specific and vapA multiplex PCR. These isolates were obtained from: three farms where the R. equi infection has been noticed, two farms where the disease has been not reported and one farm where the disease is frequent. All clinical isolates from horse breeding farms where the disease is endemic and/or sporadic were vapA-positive. None environmental isolates were vapA-positive. In three horse breeding farms with sporadic R. equi infection, 11.54% of the isolates from adult horse feces were vapA-positive. The multiplex PCR technique has proven to be effective for the molecular and epidemiological characterization of the R. equi isolates in horse breeding farms. An important finding in this study was the isolation of vapApositive R. equi from adult horse feces, which is an evidence for other routes of dissemination of this pathogen in the farms.
Culture Method and PCR for the Detection of Helicobacter pylori in Drinking Water in Basrah Governorate Iraq

Helicobacter pylori is recognized by the World Health Organization to be the primary cause of peptic ulcers, chronic gastritis, and stomach cancer, though the source of human infection is not well understood. One of the problems in understanding the source of human contamination is the difficulty in isolating the organism from the environment. However, the combination of PCR results with those of culturing of 471 drinking water samples can provide a more accurate picture of H. pylori detection. In this method 78 presumptive H. pylori colonies out of 266 tap water samples were obtained in the preliminary detection on modified Columbia agar (MCUA) slant relying on urease positivity with a rate of 29.3%. However, only 11 out of them were confirmed by Gram staining and biochemical tests reducing the rate to 4.13% whereas only 3 (1.46%) from 205 reverse osmosis (RO) water samples. Furthermore, only 6 (54.5%) out of the 11 isolates from tap water and 1 (33.3%) of the 3 RO isolates were confirmed by 16SrRNA PCR. Thus PCR confirmation reduced the rate to 2.2%. In addition, only 4 (4%) of 100 tap water samples negative for H. pylori by culture method were H. pylori positive by 16SrRNA. Water samples were collected from 24 districts of Basrah Governorate from February–December 2009. The direct recovery of H. pylori from drinking water is both alarming and scientifically exciting in terms of the investigation of its epidemiology.
SUBMILLIMETER LINE SPECTRUM OF THE SEYFERT GALAXY NGC 1068 FROM THE HERSCHEL-SPIRE FOURIER TRANSFORM SPECTROMETER

The first complete submillimeter spectrum (190–670 μm) of the Seyfert 2 galaxy NGC 1068 has been observed with the SPIRE Fourier transform spectrometer on board the Herschel Space Observatory. The sequence of CO lines (Jup = 4–13), lines from H2O, the fundamental rotational transition of hydrogen fluoride, two o-H2O+ lines, and one line each from CH+ and OH+ have been detected, together with the two [C i] lines and the [N ii] 205 μm line. The observations in both single pointing mode with sparse image sampling and in mapping mode with full image sampling allow us to disentangle two molecular emission components, one due to the compact circumnuclear disk (CND) and one from the extended region encompassing the star-forming ring (SF-ring). Radiative transfer models show that the two CO components are characterized by densities of n(H2) = 104.5 and 102.9 cm−3 and temperatures of Tkin = 100 K and 127 K, respectively. A comparison of the CO line intensities with the photodissociation region (PDR) and X-ray-dominated region (XDR) models, together with the other observational constraints, such as the observed CO surface brightness and the radiation field, indicates that the best explanation for the CO excitation of the CND is an XDR with a density of n(H2) ∼ 104 cm−3 and an X-ray flux of 9 erg s−1 cm−2, consistent with illumination by the active galactic nucleus, while the CO lines in the SF-ring are better modeled by a PDR. The detected water transitions, together with those observed with the Herschel PACS spectrometer, can be modeled by a large velocity gradient model with low temperature (Tkin ∼ 40 K) and high density (n(H2) in the range 106.7–107.9 cm−3). The emission of H2O+ and OH+ are in agreement with PDR models with cosmic-ray ionization. The diffuse ionized atomic component observed through the [N ii] 205 μm line is consistent with previous photoionization models of the starburst.
TNF-α and Microalbuminuria in Patients with Type 2 Diabetes Mellitus

Aim. Recent evidence suggests that chronic subclinical inflammation plays a key role in the pathogenesis and progression of diabetic nephropathy. Aim of the present study was to investigate possible correlation between the presence and degree of microalbuminuria and markers of inflammation in patients with type 2 diabetes mellitus (DM). Patients-Methods. Eighty patients were enrolled and clinical and laboratory data were recorded. Albumin-creatinine ratio (ACR) was calculated in first-morning urine samples. Serum and urinary tumor necrosis factor-α (TNF-α) levels were determined by ELISA. Results. Forty-five patients had normoalbuminuria, 33 microalbuminuria, and 2 macroalbuminuria. Patients with microalbuminuria were older, with higher glycosylated hemoglobin levels (HbA1c) and they more frequently had diabetic retinopathy, neuropathy, and cardiovascular disease and were on treatment with angiotensin converting enzyme inhibitors (ACEi) and/or angiotensin receptor blockers (ARBs). ACR was significantly correlated with the presence of cardiovascular disease, hypertension, and HbA1c levels and the administration of clopidogrel and ACEi or ARBs. ACR was not correlated with C-reactive protein, fibrinogen, or serum TNF-α levels but had a strong correlation with urinary TNF-α levels. Conclusions. In patients with type 2 DM, urinary, but not serum, TNF-α levels are associated with the presence and severity of microalbuminuria.