Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism and Consequences of Anaerobic Respiration of Cobalt by Shewanella oneidensis Strain MR-1

ABSTRACT Bacteria from the genus Shewanella are the most diverse respiratory organisms studied to date and can utilize a variety of metals and metal(loid)s as terminal electron acceptors. These bacteria can potentially be used in bioremediation applications since the redox state of metals often influences both solubility and toxicity. Understanding molecular mechanisms by which metal transformations occur and the consequences of by-products that may be toxic to the organism and thus inhibitory to the overall process is significant to future applications for bioremediation. Here, we examine the ability of Shewanella oneidensis to catalyze the reduction of chelated cobalt. We describe an unexpected ramification of [Co(III)-EDTA]− reduction by S. oneidensis: the formation of a toxic by-product. We found that [Co(II)-EDTA]2−, the product of [Co(III)-EDTA]− respiration, inhibited the growth of S. oneidensis strain MR-1 and that this toxicity was partially abolished by the addition of MgSO4. We demonstrate that [Co(III)-EDTA]− reduction by S. oneidensis requires the Mtr extracellular respiratory pathway and associated pathways required to develop functional Mtr enzymes (the c-type cytochrome maturation pathway) and ensure proper localization (type II secretion). The Mtr pathway is known to be required for a variety of substrates, including some chelated and insoluble metals and organic compounds. Understanding the full substrate range for the Mtr pathway is crucial for developing S. oneidensis strains as a tool for bioremediation.
Income-related and educational inequality in small-for-gestational age and preterm birth in Denmark and Finland 1987—2003

Aims: In this paper, we examine income- and education-related inequality in small-for-gestational age (SGA) and preterm birth in Denmark and Finland from 1987 to 2003 using concentration indexes (CIXs). Methods: From the national medical birth registries we gathered information on all births from 1987 to 2003. Information on highest completed maternal education and household income in the year preceding birth of the offspring was obtained for 1,012,400 births in Denmark and 499,390 in Finland. We then calculated CIXs for income- and education-related inequality in SGA and preterm birth. Results: The mean household income-related inequality in SGA was −0.04 (95% confidence interval: −0.05, −0.04) in Denmark and −0.03 (−0.04, −0.02) in Finland. The maternal education-related inequality in SGA was −0.08 (−0.10, −0.06) in Denmark and −0.07 (−0.08, −0.06) in Finland. The income-related inequality in preterm birth was −0.03 (−0.03, −0.02) in Denmark and −0.03 (−0.04, −0.02) in Finland. The education-related inequality in preterm birth was −0.05 (−0.07, −0.04) in Denmark and −0.04 (−0.05, −0.03) in Finland. In Denmark, the income-related and education-related inequity in SGA increased over time. In Finland, the income-related inequality in SGA birth increased slightly, while education-related inequalities remained stable. Inequalities in preterm birth decreased over time in both countries. Conclusions: Denmark and Finland are examples of nations with free prenatal care and publicly financed obstetric care of high quality. During the period of study there were macroeconomic shocks affecting both countries. However, only small income- and education-related inequalities in SGA and preterm births during the period were observed.
Extracting Domain Ontologies from Reference Books

Encyclopedic knowledge bases can be powerful tools for the acquisition of fundamental knowledge for learners. However, the structure and the very nature of these documents can impede learning processes. By extracting domain ontologies from reference books and using this same material to populate an intelligent learning system, we propose a methodology for lifelong learners.
Molecular Analysis of Virulence Profiles and Shiga Toxin Genes in Food-Borne Shiga Toxin-Producing Escherichia coli

ABSTRACT In this study, 75 Shiga toxin (Stx)-producing Escherichia coli (STEC) strains originating from foods (n = 73) and drinking water (n = 2) were analyzed for their stx genotype, as well as for further chromosome-, phage-, and plasmid-encoded virulence factors. A broad spectrum of stx genes was detected. Fifty-three strains (70.7%) contained stx2 or stx2 variants, including stx2d, mucus-activatable stx2d, stx2e, and stx2g. Seven strains (9.3%) harbored stx1 or stx1c, and 15 strains (20.0%) carried both stx2 and/or stx2 variants and stx1 or stx1c. Beside stx, the most abundant accessory virulence markers in STEC food isolates were iha (57.3%), ehxA (40.0%), espP (28.0%), and subAB (25.3%). Only four strains were eae positive; three of these belonged to the serogroups O26, O103, and O157 and contained a typical enterohemorrhagic E. coli virulence spectrum. The results of this study show that a number of STEC strains that occur in foods appear to be pathogenic for humans, based on their virulence profiles. Analysis of stx subtypes and detection of additional virulence factors in eae-negative strains may help to better assess the risk of such strains for causing human infection.
Diversity, Structures, and Collagen-Degrading Mechanisms of Bacterial Collagenolytic Proteases

ABSTRACT Bacterial collagenolytic proteases are important because of their essential role in global collagen degradation and because of their virulence in some human bacterial infections. Bacterial collagenolytic proteases include some metalloproteases of the M9 family from Clostridium or Vibrio strains, some serine proteases distributed in the S1, S8, and S53 families, and members of the U32 family. In recent years, there has been remarkable progress in discovering new bacterial collagenolytic proteases and in investigating the collagen-degrading mechanisms of bacterial collagenolytic proteases. This review provides comprehensive insight into bacterial collagenolytic proteases, especially focusing on the structures and collagen-degrading mechanisms of representative bacterial collagenolytic proteases in each family. The roles of bacterial collagenolytic proteases in human diseases and global nitrogen cycling, together with the biotechnological and medical applications for these proteases, are also briefly discussed.
Communications in Early Detection and Intervention Programs: Legal and Risk Management Perspectives*

—Since the introduction of newborn screening, public health pol icy making has addressed the twin goals of providing organized preventive health care and achieving universal access to these services. Simultaneously, consumer rights movements have led to the expectation that medical rights will be understood and respected whether a test or treatment is voluntary or mandatory. Although universal identification and intervention programs have become feasible with the development of reliable screening methods, the tran sition from screening to follow-up presents challenges. To ensure timely follow-up while balancing social goals with individual rights, effective clinical commu nication is essential. Legal and risk management considerations surrounding informed consent, notification of results, and confidentiality assist the clinician in developing policy and procedural guidelines for quality assurance in this cru cial area.
The number of persons with alcohol problems in the Danish population

Aims: A) To qualify the existing estimates of the prevalence of heavy drinking, harmful alcohol use and alcohol dependency by applying adjustment for non-participation. B) To describe socio-demographic correlates of heavy drinkers. Methods: Data came from the Danish Health Interview Survey 2005, which included a personal interview of 14,566 individuals (response rate 66.7 %), and of 5,552 individuals who completed a self-administered questionnaire containing the Alcohol Use Disorder Test (AUDIT) (response rate 50.9%). Heavy drinkers were defined as consuming >14/21 drinks/week (women/men). Identification of harmful alcohol users and dependent drinkers was based on the score of specific AUDIT questions (harmful alcohol use a score of ≥4 in questions 7—10, dependent drinkers ≥4 in questions 4—6). Adjustment for non-participation was performed using data from the Danish National Patient Registry. Results: In the Danish population, 20% were heavy drinkers (862,876 persons 95% confidence interval (95% CI): 672,002—1,195,069), 14% had harmful alcohol use (620,301 persons 95% CI: 439,221—944,992), 3% were dependent drinkers (147,528 persons 95% CI: 118,196—188,384). Being male was associated with heavy drinking (odds ratio (OR): 1.70; 95% CI: 1.53—1.89), as was being a single male (OR: 1.27; 95% CI: 1.01—1.61) and being a smoker (men: OR: 1.96; 95% CI: 1.67—2.30 / women: OR: 2.08; 95% CI: 1.72—2.52). Conclusions: The number of heavy drinkers in the Danish population and the number of people with harmful alcohol use is considerably higher than earlier prevalence estimates. The number of dependent drinkers is similar to earlier estimates.
A Review of In Vitro Drug Release Test Methods for Nano-Sized Dosage Forms

This review summarizes the methods used to study real-time (37°C) drug release from nanoparticulate drug delivery systems and establish an IVIVC. Since no compendial standards exist, drug release is currently assessed using a variety of methods including sample and separate (SS), continuous flow (CF), dialysis membrane (DM) methods, and a combination thereof, as well as novel techniques like voltametry and turbidimetry. This review describes the principle of each method along with their advantages and disadvantages, including challenges with set-up and sampling. The SS method allows direct measurement of drug release with simple set-up requirements, but sampling is cumbersome. With the CF method, sampling is straightforward but the set-up is time consuming. Set-up as well as sampling is easier with the DM, but it may not be suitable for drugs that bind to the membrane. Novel methods offer the possibility of real-time drug release measurement but may be restricted to certain types of drugs. Of these methods, Level A IVIVCs have been obtained with dialysis, alone or in combination with the sample and separate technique. Future efforts should focus on developing mathematical models that describe drug release mechanisms as well as facilitate formulation development of nano-sized dosage forms.
Pathways and mechanisms in adolescence contribute to adult health inequalities

Aims: This paper presents a model that encompasses pathways and mechanisms working over adolescence that contribute to adult health inequalities. We review evidence on the four mechanisms: socially differential exposure, tracking, socially differential tracking, and socially differential vulnerability. Methods: We conducted literature searches in English-language peer-reviewed journals using PubMed (from 1966 to May 2009) and PsycINFO, and combined these with hand-searches of reference lists, journals, and authors of particular relevance. Results: Most health indicators are socially patterned in adolescence and track into adulthood, with higher risks of adverse outcomes among individuals from lower socioeconomic positions. Adolescent health behaviours track into adulthood. Smoking, physical activity, and especially fruit and vegetable intake are socially patterned, while evidence for social patterning of alcohol use is less consistent. Relational dimensions like lone parenthood and bullying are socially patterned and track over time, and there are indications of a socially differential vulnerability to the effects of these types of relational strain. Very little research has investigated the social patterning of the above indicators over time or studied social vulnerability of these indicators from adolescence to adulthood. However, all four mechanisms seem to be active in establishing social differences in adult educational attainment. Conclusions: We find the Adolescent Pathway Model useful for providing an overview of what elements and mechanisms in adolescence may be of special importance for adult health inequalities. There is a lack of knowledge of how social patterns of health, health behaviours, and social relations in adolescence transfer into adulthood and to what extent they reflect themselves in adult health.
Gold Nanoprisms as Optical Coherence Tomography Contrast Agents in the Second Near Infrared Window for Enhanced Angiography in Live Animals

Optical coherence tomography angiography (OCTA) is an important tool for investigating vascular networks and microcirculation in living tissue. Traditional OCTA detects blood vessels via intravascular dynamic scattering signals derived from the movements of red blood cells (RBCs). However, the low hematocrit and long latency between RBCs in capillaries makes these OCTA signals discontinuous, leading to incomplete mapping of the vascular networks. OCTA imaging of microvascular circulation is particularly challenging in tumors due to the abnormally slow blood flow in angiogenic tumor vessels and strong attenuation of light by tumor tissue. Here we demonstrate in vivo that gold nanoprisms (GNPRs) can be used as OCT contrast agents working in the second near infrared window, significantly enhancing the dynamic scattering signals in microvessels and improving the sensitivity of OCTA in skin tissue and melanoma tumors in live mice. This is the first demonstration that nanoparticle-based OCT contrast agent work in vivo in the second near infrared window, which allows deeper imaging depth by OCT. With GNPRs as contrast agents, the post-injection OCT angiograms showed 41% and 59% more microvasculature than pre-injection angiograms in healthy mouse skin and melanoma tumors, respectively. By enabling better characterization of microvascular circulation in vivo, GNPR-enhanced OCTA could lead to better understanding of vascular functions during pathological conditions, more accurate measurements of therapeutic response, and improved patient prognoses.
Occupational mortality

Introduction: This paper aims to present the methods and main results from the Danish occupational mortality studies, and to set the Danish studies into the international context of occupational mortality studies. Research topics: The first Danish occupational mortality study from 1970—1975 revealed a considerable social class gradient in male mortality where university teachers and farmers had a 40% lower mortality and waiters and seamen had an about 100% higher mortality than the average for economically active men. The social class gradient was less steep for women. A similar pattern was found in 1996— 2005. Conclusion: In view of the considerable societal changes which have taken place from the beginning of the 1970s to the turn of the century, surprisingly small changes have taken place in the mortality pattern across social groups.
Covert channels analysis in TCP/IP networks

Covert channels use stealth communications to compromise the security policies of systems. They constitute an important security threat since they can be used to exfiltrate confidential data from networks. TCP/IP protocols are used everyday and are subject to covert channels problems. The aim of this paper is to give an overview of covert channels in TCP/IP networks. We briefly describe the TCP and IP protocols, present the different types of covert channels and the methods to set them up in TCP/IP networks; then we study the existing methods to detect and avoid covert channels. Statistical methods, neural networks, support vectors machines and traffic normalizer are presented. Some new insights on packet sorting techniques, counting covert channels and traffic normalizers evasion are given.
Genomic Sequence and Characterization of the Virulent Bacteriophage φCTP1 from Clostridium tyrobutyricum and Heterologous Expression of Its Endolysin

ABSTRACT The growth of Clostridium tyrobutyricum in developing cheese leads to spoilage and cheese blowing. Bacteriophages or their specific lytic enzymes may provide a biological control method for eliminating such undesirable organisms without affecting other microflora. We isolated the virulent bacteriophage φCTP1 belonging to the Siphoviridae and have shown that it is effective in causing lysis of sensitive strains. The double-stranded DNA genome of φCTP1 is 59,199 bp, and sequence analysis indicated that it has 86 open reading frames. orf29 was identified as the gene coding for the phage endolysin responsible for cell wall degradation prior to virion release. We cloned and expressed the ctp1l gene in E. coli and demonstrated that the partially purified protein induced lysis of C. tyrobutyricum cells and reduced viable counts both in buffer and in milk. The endolysin was inactive against a range of clostridial species but did show lysis of Clostridium sporogenes, another potential spoilage organism. Removal of the C-terminal portion of the endolysin completely abolished lytic activity.
Removal of Antibiotic Resistance Gene-Carrying Plasmids from Lactobacillus reuteri ATCC 55730 and Characterization of the Resulting Daughter Strain, L. reuteri DSM 17938

ABSTRACT The spread of antibiotic resistance in pathogens is primarily a consequence of the indiscriminate use of antibiotics, but there is concern that food-borne lactic acid bacteria may act as reservoirs of antibiotic resistance genes when distributed in large doses to the gastrointestinal tract. Lactobacillus reuteri ATCC 55730 is a commercially available probiotic strain which has been found to harbor potentially transferable resistance genes. The aims of this study were to define the location and nature of β-lactam, tetracycline, and lincosamide resistance determinants and, if they were found to be acquired, attempt to remove them from the strain by methods that do not genetically modify the organism before subsequently testing whether the probiotic characteristics were retained. No known β-lactam resistance genes was found, but penicillin-binding proteins from ATCC 55730, two additional resistant strains, and three sensitive strains of L. reuteri were sequenced and comparatively analyzed. The β-lactam resistance in ATCC 55730 is probably caused by a number of alterations in the corresponding genes and can be regarded as not transferable. The strain was found to harbor two plasmids carrying tet(W) tetracycline and lnu(A) lincosamide resistance genes, respectively. A new daughter strain, L. reuteri DSM 17938, was derived from ATCC 55730 by removal of the two plasmids, and it was shown to have lost the resistances associated with them. Direct comparison of the parent and daughter strains for a series of in vitro properties and in a human clinical trial confirmed the retained probiotic properties of the daughter strain.
Equitable access to elective hospital services: The introduction of patient choice in a decentralised healthcare system

Aim: During the 1980s and 1990s, increased waiting times for elective surgery was perceived to be a major accessibility problem in many countries. In an attempt to improve access, hospital choice reforms were introduced in a number of countries. In Norway, a nationwide reform to improve access came into effect in 2001. At the same time, renewed support was expressed for the long-standing political aim of ensuring equal access to healthcare services for all citizens regardless of their social position. The current aim is to analyse the relationship of the hospital choice reform and the goal of equitable access to hospital services. Method: A survey conducted among Norwegian patients in 2004 provided information about whether a choice of hospital had been made. Information from the survey was merged with administrative data from the hospital that performed the treatment. The survey provided data on patients’ socioeconomic position. Demographics, medical need, and prior use of healthcare services were controlled for to determine the effect of socioeconomic position on hospital choice. Results: The patient’s socioeconomic position, measured by education, was found to be significantly associated with hospital choice. The relationship resembled that of a social gradient. Patients with a primary education were less likely to have made a choice, followed by those with secondary education or a lower university degree. Patients with higher university education were most likely to have chosen. Conclusions: Hospital selection is a demanding task for many patients. Policymakers should therefore focus on crafting and implementing tools necessary for supporting uptake of choice in disadvantaged groups.
A Delta–Sigma Modulator for Low-Power Analog Front Ends in Biomedical Instrumentation

This paper presents a high-resolution dual-integrating delta-sigma modulator (DI-DSM) for low-power analog front-end (AFE) circuits in biomedical instrumentation. The AFE contains a preamplifier and a switched-capacitor DS analog-to-digital converter. The proposed DI-DSM adopts two kinds of clock frequencies: one is the same as the conventional frequency and the other is one-half of the conventional frequency, which provides sufficient settling time for critical blocks. The proposed structure reduces harmonic distortions at the output of the preamplifier, since the preamplifier is given sufficient time to charge the sampling capacitor in the DSM. The use of a lower switching frequency at the critical blocks results in a significant reduction in the power consumption of both the preamplifier and the modulator. The proposed AFE chip is fabricated in a 65-nm CMOS process. The measurement results of the modulator show a peak signal-to-noise ratio (SNR) of 81.4 dB and a peak signal-to-noise-plus-distortion ratio (SNDR) of 80.4 dB, with a power consumption of 24.8 μW at a supply voltage of 1 V and a signal bandwidth of 10 kHz. The complete AFE chip [which includes a preamplifier, a DI-DSM, a low-dropout (LDO) regulator, and a bandgap reference circuit (BGR)] shows a measured peak SNR of 79.3 dB and a measured peak SNDR of 77.0 dB with a preamplifier power of only 46.8 μW (and 22.3 μW for LDO, and 36.3 μW for BGR).
Design and Development of an Electro-Optic Type-Flow Transmitter Using Mach–Zehnder Interferometer

The rotameter, the widely used flow meter, is generally used as a local indicator. Therefore, for industrial use, some necessary technique is required to transmit float displacement to remote location. Direct transmission of electrical signal through connecting wires is generally prohibited in an inflammable region. In this paper, an electro-optic system is developed using a modified inductive-type rotameter, which produces an electrical signal according to float movement of the rotameter. The electrical signal is then converted into an optical signal using the Mach-Zhender interferometer. Necessary equations along with the developed theory of operation are presented in this paper. An experiment is performed on the proposed transmitter and the experimental and simulation results are reported in this paper. Very good linearity and repeatability with a very small uncertainty in the measurement of the transducer characteristic have been observed. The graphical abstract is shown.