Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the Ensemble Kalman Filter for Inverse Problems

The ensemble Kalman filter (EnKF) is a widely used methodology for state estimation in partial, noisily observed dynamical systems, and for parameter estimation in inverse problems. Despite its widespread use in the geophysical sciences, and its gradual adoption in many other areas of application, analysis of the method is in its infancy. Furthermore, much of the existing analysis deals with the large ensemble limit, far from the regime in which the method is typically used. The goal of this paper is to analyze the method when applied to inverse problems with fixed ensemble size. A continuous-time limit is derived and the long-time behavior of the resulting dynamical system is studied. Most of the rigorous analysis is confined to the linear forward problem, where we demonstrate that the continuous time limit of the EnKF corresponds to a set of gradient flows for the data misfit in each ensemble member, coupled through a common pre-conditioner which is the empirical covariance matrix of the ensemble. Numerical results demonstrate that the conclusions of the analysis extend beyond the linear inverse problem setting. Numerical experiments are also given which demonstrate the benefits of various extensions of the basic methodology.
Identification of adulteration in milk by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

The development is described of a rapid, simply and accurate analytical method aimed at evaluating both the presence of cow milk in either raw ewe and water buffalo milk samples employed in industrial processes and the addition of powdered milk to samples of fresh raw milk, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The presence of adulteration is defined by evaluating the protein patterns coming from the most abundant whey proteins, alpha-lactalbumin and beta-lactoglobulin, used as molecular markers. As no pretreatment of the milk samples is required and owing to the speed and ease of use of MALDI-MS the proposed analytical protocol can be used as a routine strategy for the identification of possible adulteration of the raw fresh milk samples that the dairy industry receives from producers every day.
A cost-effectiveness analysis of first-line induction and maintenance treatment sequences in patients with advanced nonsquamous non-small-cell lung cancer in France

Background Comparative effectiveness and cost-effectiveness data for induction–maintenance (I–M) sequences for the treatment of patients with nonsquamous non-small-cell lung cancer (nsqNSCLC) are limited because of a lack of direct evidence. This analysis aimed to compare the cost-effectiveness of I–M pemetrexed with those of other I–M regimens used for the treatment of patients with advanced nsqNSCLC in the French health-care setting. Materials and methods A previously developed global partitioned survival model was adapted to the France-only setting by restricting treatment sequences to include 12 I–M regimens most relevant to France, and incorporating French costs and resource-use data. Following a systematic literature review, network meta-analyses were performed to obtain hazard ratios for progression-free survival (PFS) and overall survival (OS) relative to gemcitabine + cisplatin (induction sequences) or best supportive care (BSC) (maintenance sequences). Modeled health-care benefits were expressed as life-years (LYs) and quality-adjusted LYs (QALYs) (estimated using French EuroQol five-dimension questionnaire tariffs). The study was conducted from the payer perspective (National Health Insurance). Cost- and benefit-model inputs were discounted at an annual rate of 4%. Results Base-case results showed pemetrexed + cisplatin induction followed by (→) pemetrexed maintenance had the longest mean OS and PFS and highest LYs and QALYs. Costs ranged from €12,762 for paclitaxel + carboplatin → BSC to €35,617 for pemetrexed + cisplatin → pemetrexed (2015 values). Gemcitabine + cisplatin → BSC, pemetrexed + cisplatin → BSC, and pemetrexed + cisplatin → pemetrexed were associated with fully incremental cost-effectiveness ratios (ICERs) of €16,593, €80,656, and €102,179, respectively, per QALY gained versus paclitaxel + carboplatin → BSC. All other treatment sequences were either dominated (ie, another sequence had lower costs and better/equivalent outcomes) or extendedly dominated (ie, the comparator had a higher ICER than a more effective comparator) in the model. Sensitivity analyses showed the model to be relatively insensitive to plausible changes in the main assumptions, with none increasing or decreasing the ICER by more than ~€20,000 per QALY gained. Conclusion In the absence of direct comparative trial evidence, this cost-effectiveness analysis indicated that of a large number of I–M sequences used for the treatment of patients with nsqNSCLC in France, pemetrexed + cisplatin → pemetrexed achieved the best clinical outcomes (0.28 incremental QALYs gained) versus paclitaxel + carboplatin → BSC.
A Robust Transmission Strategy for Multi-Cell Interference Networks

In this paper, we propose a robust transmission strategy for multi-cell networks equipped with multiple-antenna base stations (BSs) under universal frequency reuse and in the presence of channel estimation error. We propose a distributed optimization scheme, where each BS individually minimizes a combination of its total transmit power and its resulting overall interference inflicted on the users of the adjacent cells, subject to maintaining a desired quality of service at its local users. We transform the proposed scheme to a robust optimization problem for the worst case of errors and derive a semidefinite programming (SDP) using rank-relaxation. We prove that the derived SDP always yields exact rank-one optimal solutions. This is in contrast to the standard rank- relaxed SDP technique that requires an additionally high computational complexity to approximate the solutions with sufficient accuracies, required for an effective beamforming. A comparison of simulation results show that the proposed transmission strategy can expand the signal-to-interference-plus-noise-ratio operational range with significantly reduced power consumption levels at BSs and perform closely to its centralized counterpart.
Planar Ku band antenna for perspective telecommunication facilities

The deployment of a new generation of communication systems requires the development of high-frequency ranges of wavelengths. The paper deals with a promising class of millimeter band performed on the basis of different types dielectric wave-guides. The methods of the engineering design of these antennas are presented. It is shown that the considered antenna can serve as the basis for a family of antennas with characteristics suitable for new telecommunications applications.
Self Adaptive Firefly Algorithm based transmission loss minimization using TCSC

This paper presents the use of Thyristor Controlled Series Compensator (TCSC) to minimize the transmission loss in power system network. Self-Adaptive Firefly Algorithm is proposed to identify the optimal location and parameter of TCSC. To validate the proposed algorithm, simulations are performed on IEEE 14-bus and IEEE 30-bus system using MATLAB software package. Analyzing the simulation results the identified location and parameter of TCSC is able to minimize the transmission loss in the power system network.
Improving Knowledge Management Practices in the South African Healthcare System

Knowledge is increasingly recognised in this, the knowledge era, as a strategic resource, by public sector organisations, in view of the public sector reform initiatives. People and knowledge play a vital role in attaining improved organisational performance and high service quality. Many government departments in the public sector have started to realise the importance of knowledge management in streamlining their operations and processes. This study focused on knowledge management in the public healthcare service organisations, where the concept of service provider competitiveness pales to insignificance, considering the huge challenges emanating from the healthcare and public sector reforms. Many government departments are faced with challenges of improving organisational performance and service delivery, improving accountability, making informed decisions, capturing the knowledge of the aging workforce, and enhancing partnerships with stakeholders. The purpose of this paper is to examine the knowledge management practices of the Gauteng Department of Health in South Africa, in order to understand how knowledge management practices influence improvement in organisational performance and healthcare service delivery. This issue is explored through a review of literature on dominant views on knowledge management and healthcare service delivery, as well as results of interviews with, and questionnaire responses from, the general staff of the Gauteng Department of Health. Web-based questionnaires, face-to-face interviews and organisational documents were used to collect data. The data were analysed using both the quantitative and qualitative methods. The central question investigated was: To what extent can the conditions required for successful knowledge management be observed, in order to improve organisational performance and healthcare service delivery in the Gauteng Department of Health. The findings showed that the elements of knowledge management capabilities investigated in this study, namely knowledge creation, knowledge sharing and knowledge application, have a positive, significant relationship with all measures of organisational performance and healthcare service delivery. These findings thus indicate that by employing knowledge management principles, the Gauteng Department of Health could improve its ability to achieve its operational goals and objectives, and solve organisational and healthcare challenges, thereby improving organisational performance and enhancing healthcare service delivery in Gauteng. Keywords—Knowledge Management, Healthcare Service Delivery, Public Healthcare, Public Sector. K. H. Badimo is a PhD candidate with the School of Computing, College of Science, Engineering and Technology, University of South Africa, Sunnyside 0002, RSA (phone: +27 11 467-5842; fax: +27 11467-5849, (email: 35161108@mylife.unisa.ac.za). Prof. S. Buckley is with the Director of the School of Computing, College of Science, Engineering and Technology, University of South Africa, Sunnyside, 0002, RSA(e-mail: bucklsb@unisa.ac.za).
GCDViewer: An online data query, visualization and analysis system for global climatic data

Climatic data are critical in supporting of the agricultural and ecological studies. Traditionally, the way of managing and accessing to the data is locally fulfilled. To demonstrate the value of cyberinfrastructure and to ease the access to the data, this paper presented a case study of managing, visualizing and analyzing the global multi-station climatic data in a Web-based environment. This study took 1961-1990 global standard climate normals data published by World Meteorological Organization as an exemplar. It proposed a relational data model to store the climate normals data. It utilized SQL Server to store and manage the data as Web-accessible data services, ArcGIS Server as GIS Server to enable on-demand accessuser operation map and presented an ASP.Net-based web portal for scientists to fulfill data search, data visualization and data analysis functions. The system design and the implementation details of this prototype are introduced. This case study clearly shows that the unstructured climatic text data could be transformed to be structured database, which further enables the on-demand data sharing, search, retrieval and online analysis functions. GCDViewer's design principle and system architecture could apply to many other types of scientific data. It clearly shows the advantage of building cyberinfrastructure to improve the overall research efficiency.
Validation of the Brief International Cognitive Assessment for Multiple Sclerosis in Japan

Background The Brief International Cognitive Assessment for MS (BICAMS) is a practical battery for measuring cognitive function in multiple sclerosis (MS). Objectives We aimed to validate a Japanese version of the BICAMS in patients with MS and healthy controls. Methods The Symbol Digit Modalities Test (SDMT), the California Verbal Learning Test-Second Edition (CVLT2) and the Brief Visuospatial Memory Test Revised (BVMTR) were administered to 156 patients with MS and 126 healthy controls (HCs). The BICAMS was re-administered in a subset of 27 MS patients and 30 HCs. Results The mean (±SD) raw scores in the MS and HC groups were as follows: SDMT: MS 47.9 ± 14.0, HC 61.0 ± 9.5; CVLT2: MS 48.6 ± 12.6, HC 55.7 ± 10.5; BVMTR: MS 23.5 ± 8.4, HC 28.3 ± 5.4, respectively, and significant differences were found between the two groups on all tests (p < 0.0001). Cohen’s d values were 1.07, 0.60, and 0.67 in SDMT, CVLT2, and BVMTR, respectively. The test-retest reliability coefficients for each test were as follows: SDMT: r = 0.93; CVLT2: r = 0.82; and BVMTR: r = 0.77 (p < 0.0001). Conclusions This study provides results that support the reliability and validity of the BICAMS in Japan.
Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray

Background: A custom phylogenetic microarray composed of small subunit ribosomal RNA probes, representing ≈500 bacterial species from the human and animal gut, was developed and evaluated for analysis of gut microbial diversity using fecal samples from healthy subjects and Crohn's disease (CD) patients. Methods: Oligonucleotide probes (≈40 mer) used on the microarray were selected from published articles or designed with the “GoArray” microarray probe design program using selected bacterial 16S rRNA sequences. Fecal 16S rDNA from individual samples of six healthy subjects and six CD patients were used as template to generate fluorescently labeled cRNA that was hybridized to the microarray. Differences revealed by the microarray in relative abundance of microbial populations between healthy and diseased patients were verified using quantitative real‐time polymerase chain reaction (PCR) with species‐specific primer sets. Results: The microarray analyses showed that Eubacterium rectale, Bacteroides fragilis group, B. vulgatus, Ruminococcus albus, R. callidus, R. bromii, and Faecalibacterium prausnitzii were 5–10‐fold more abundant in the healthy subjects than in the CD patients, while Enterococcus sp. , Clostridium difficile, Escherichia coli, Shigella flexneri, and Listeria sp. were more abundant in the CD group. Conclusions: The microarray detected differences in abundance of bacterial populations within the phylum Firmicutes that had been reported previously for the same samples based on phylogenetic analysis of metagenomic clone libraries. In addition, the microarray showed that Enterococcus sp. was in higher abundance in the CD patients. This microarray should be another useful tool to examine the diversity and abundance of human intestinal microbiota. (Inflamm Bowel Dis 2010)
Accuracy of LHC proton loss rate determination by the BLM system

Most of the monitors of the LHC beam loss monitoring (BLM) system are installed on the outside of the magnet cryostats, around the quadrupole magnets. Their aim is to prevent quenches and to protect the superconducting magnets from damage. The lost beam particles initiate hadronic showers through the magnets and deposit energy in the coils. The gas filled BLM ionization chambers probe the very far transverse tail of the showers. The BLM system relies on GEANT simulations and control measurements to determine the relation between the chamber signal, the number of lost beam particles and the energy deposited in the magnet coil. The specification of the BLM system includes a factor of two in absolute precision on the final prediction of the quench levels. As the shower tails are not necessarily well represented by particle simulation codes, it is crucial to experimentally determine the accuracy of these simulations. An LHC type BLM system was installed at the internal beam dump of HERA at DESY since 2005. The hadronic showers created by the impacting 39 GeV and 920 GeV protons have been simulated with GEANT4. The far transverse tails of the showers on the outside of the dump have been measured by ionization chambers. This paper will present the comparison of simulation to measurement and the conclusions drawn for the LHC BLM system.
Experimental Demonstration of Amplified Feedback DFB Laser With Modulation Bandwidth Enhancement Based on the Reconstruction Equivalent Chirp Technique

A novel amplified feedback DFB laser with extended modulation bandwidth is experimentally demonstrated in this paper. All the three sections of laser cavity, including DFB section, phase section, and amplified feedback section, have the same active layer, which can avoid the butt-joint regrowth process. The gratings in both DFB section and amplified feedback section are fabricated by the reconstruction equivalent chirp technique, which can significantly decrease the difficulties in realizing precise grating structure. An enhanced −3 dB bandwidth of 19 GHz is achieved by means of a normal low-frequency wafer. Modulation linearity and relative intensity noise characteristics are experimentally investigated. 20 MSymbol/s 32-QAM signal with 19 GHz carrier is transmitted via 25-km radio-over-fiber link using the as-fabricated directly modulated DFB laser, and the average error vector magnitude of the whole link is 3.91%.
Long-path supercontinuum absorption spectroscopy for measurement of atmospheric constituents.

A supercontinuum source has been proposed as a new tool for measurement of minor species concentrations on long paths through the atmosphere. The present work describes results from recent experiments that demonstrate the potential for Differential Absorption Spectroscopy (DAS) and Spectral Pattern Recognition Differential Absorption Lidar (SPR-DIAL) measurements utilizing a supercontinuum source. As an initial example of this measurement approach, the results include the quantification of water vapor concentration through indoor and outdoor path absorption measurements using a collimated supercontinuum source. Experimental spectra are compared with equivalent simulations from MODTRAN? versions 4 and 5 to examine the water vapor band between 1300 and 1500 nm to demonstrate the feasibility of the approach.
Exploring the conformational space of protein loops using a mean field technique with MOLS sampling

We have recently developed a computational technique that uses mutually orthogonal Latin square sampling to explore the conformational space of oligopeptides in an exhaustive manner. In this article, we report its use to analyze the conformational spaces of 120 protein loop sequences in proteins, culled from the PDB, having the length ranging from 5 to 10 residues. The force field used did not have any information regarding the sequences or structures that flanked the loop. The results of the analyses show that the native structure of the loop, as found in the PDB falls at one of the low energy points in the conformational landscape of the sequences. Thus, a large portion of the structural determinants of the loop may be considered intrinsic to the sequence, regardless of either adjacent sequences or structures, or the interactions that the atoms of the loop make with other residues in the protein or in neighboring proteins. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Administration of a Peroxynitrite Decomposition Catalyst Into the Bronchial Artery Attenuates Pulmonary Dysfunction After Smoke Inhalation and Burn Injury in Sheep

ABSTRACT Reactive nitrogen species such as peroxynitrite play a significant role in burn and smoke inhalation injury. The bronchial circulation increases more than 10-fold in response to this combination injury. We hypothesized that direct delivery of low-dose WW-85, a peroxynitrite decomposition catalyst, into the bronchial artery would attenuate burn- and smoke inhalation–induced acute lung injury. In adult female sheep (n = 17), the bronchial artery was cannulated in preparation surgery. After a 5- to 7-day recovery period, sheep were subjected to a burn (40% total body surface area, third degree) and inhalation injury (48 breaths of cotton smoke, <40°C). The animals were divided into three groups following the injury: (i) WW-85 group: 1 h after injury, WW-85 (0.002 mg/kg per hour) was continuously infused into the bronchial artery, n = 5; (ii) control group: 1 h after injury, an equivalent amount of saline was injected into the bronchial artery, n = 6; (iii) sham group: no injury, no treatment, same operation and anesthesia, n = 6. All animals were mechanically ventilated and fluid resuscitated equally. In the control group, the injury induced a severe deterioration of pulmonary oxygenation and shunting and an increase in pulmonary microvascular permeability toward sham. The injury was further associated with an increase in reactive nitrogen species in lung tissues of the control group. All these alterations were significantly attenuated in the WW-85 group. We demonstrated that a low dosage of WW-85 directly administered into the bronchial artery attenuated pulmonary dysfunction to the same extent as higher systemically administered doses in previous experiments. Our data strongly suggest that local airway production of peroxynitrite contributes to pulmonary dysfunction following smoke inhalation and burn injury.
Detection of Mycoplasma genitalium by PCR Amplification of the 16S rRNA Gene

ABSTRACT In order to develop a species-specific PCR for the detection of Mycoplasma genitalium, the sequence of 1,490 bases of the 16S rRNA gene was determined for M. genitalium G37 (type strain) and four Danish isolates of M. genitalium. The sequences of the four Danish strains, mutually different with respect to their MgPa gene, were 100% homologous, although they carried a single common base substitution compared to the type strain. Among members of the Mycoplasma pneumoniae phylogenetic cluster, M. genitalium showed the most-prominent homology to the 16S rRNA sequence of M. pneumoniae (98% homology). From regions showing the least homology to the M. pneumoniae 16S rRNA gene sequence, primers were chosen to amplify DNA from M. genitalium only. Two sets of primers were selected for their ability to detect <10 to 50 M. genitalium genome copies without cross-reactions with M. pneumoniae. The performance of these primers was compared to the performance of two pairs of primers amplifying parts of the MgPa adhesin gene; 1,030 randomly selected specimens submitted for Chlamydia trachomatis culture were screened with one of the 16S rRNA gene primer sets. A total of 41 specimens were found to be positive for this gene; 40 of these could be confirmed by one of the MgPa primer sets, whereas the other MgPa primer set detected only 21 positive specimens out of 40. These results indicate that estimates of the prevalence of M. genitalium in various populations using MgPa PCR primers could be incorrectly low if the PCR primers are located in variable regions of the MgPa gene.