Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid and Sensitive Method To Identify Mycobacterium avium subsp. paratuberculosis in Cow's Milk by DNA Methylase Genotyping

ABSTRACT Paratuberculosis is an infectious, chronic, and incurable disease that affects ruminants, caused by Mycobacterium avium subsp. paratuberculosis. This bacterium is shed primarily through feces of infected cows but can be also excreted in colostrum and milk and might survive pasteurization. Since an association of genomic sequences of M. avium subsp. paratuberculosis in patients with Crohn's disease has been described; it is of interest to rapidly detect M. avium subsp. paratuberculosis in milk for human consumption. IS900 insertion is used as a target for PCR amplification to identify the presence of M. avium subsp. paratuberculosis in biological samples. Two target sequences were selected: IS1 (155 bp) and IS2 (94 bp). These fragments have a 100% identity among all M. avium subsp. paratuberculosis strains sequenced. M. avium subsp. paratuberculosis was specifically concentrated from milk samples by immunomagnetic separation prior to performing PCR. The amplicons were characterized using DNA methylase Genotyping, i.e., the amplicons were methylated with 6-methyl-adenine and digested with restriction enzymes to confirm their identity. The methylated amplicons from 100 CFU of M. avium subsp. paratuberculosis can be visualized in a Western blot format using an anti-6-methyl-adenine monoclonal antibody. The use of DNA methyltransferase genotyping coupled to a scintillation proximity assay allows for the detection of up to 10 CFU of M. avium subsp. paratuberculosis per ml of milk. This test is rapid and sensitive and allows for automation and thus multiple samples can be tested at the same time.
Comparative Analysis of Two Classes of Quorum-Sensing Signaling Systems That Control Production of Extracellular Proteins and Secondary Metabolites in Erwinia carotovora Subspecies

ABSTRACT In Erwinia carotovora subspecies, N-acyl homoserine lactone (AHL) controls the expression of various traits, including extracellular enzyme/protein production and pathogenicity. We report here that E. carotovora subspecies possess two classes of quorum-sensing signaling systems defined by the nature of the major AHL analog produced as well as structural and functional characteristics of AHL synthase (AhlI) and AHL receptor (ExpR). Class I strains represented by E. carotovora subsp. atroseptica strain Eca12 and E. carotovora subsp. carotovora strains EC153 and SCC3193 produce 3-oxo-C8-HL (N-3-oxooctanoyl-l-homoserine lactone) as the major AHL analog as well as low but detectable levels of 3-oxo-C6-HL (N-3-oxohexanoyl-l-homoserine lactone). In contrast, the members of class II (i.e., E. carotovora subsp. betavasculorum strain Ecb168 and E. carotovora subsp. carotovora strains Ecc71 and SCRI193) produce 3-oxo-C6-HL as the major analog. ExpR species of both classes activate rsmA (Rsm, repressor of secondary metabolites) transcription and bind rsmA DNA. Gel mobility shift assays with maltose-binding protein (MBP)-ExpR71 and MBP-ExpR153 fusion proteins show that both bind a 20-mer sequence present in rsmA. The two ExpR functions (i.e., expR-mediated activation of rsmA expression and ExpR binding with rsmA DNA) are inhibited by AHL. The AHL effects are remarkably specific in that expR effect of EC153, a strain belonging to class I, is counteracted by 3-oxo-C8-HL but not by 3-oxo-C6-HL. Conversely, the expR effect of Ecc71, a strain belonging to class II, is neutralized by 3-oxo-C6-HL but not by 3-oxo-C8-HL. The AHL responses correlated with expR-mediated inhibition of exoprotein and secondary metabolite production.
Multi-fidelity Bayesian Optimisation with Continuous Approximations

Bandit methods for black-box optimisation, such as Bayesian optimisation, are used in a variety of applications including hyper-parameter tuning and experiment design. Recently, multi-fidelity methods have garnered considerable attention since function evaluations have become increasingly expensive in such applications. Multi-fidelity methods use cheap approximations to the function of interest to speed up the overall optimisation process. However, most multi-fidelity methods assume only a finite number of approximations. On the other hand, in many practical applications, a continuous spectrum of approximations might be available. For instance, when tuning an expensive neural network, one might choose to approximate the cross validation performance using less data N and/or few training iterations T. Here, the approximations are best viewed as arising out of a continuous two dimensional space (N, T). In this work, we develop a Bayesian optimisation method, BOCA, for this setting. We characterise its theoretical properties and show that it achieves better regret than than strategies which ignore the approximations. BOCA outperforms several other baselines in synthetic and real experiments.
Continuous Test-Driven Development - A Novel Agile Software Development Practice and Supporting Tool

Continuous testing is a technique in modern software development in which the source code is constantly unit tested in the background and there is no need for the developer to perform the tests manually. We propose an extension to this technique that combines it with well-established software engineering practice called TestDriven Development (TDD). In our practice, that we called Continuous Test-Driven Development (CTDD), software developer writes the tests first and is not forced to perform them manually. We hope to reduce the time waste resulting from manual test execution in highly test driven development scenario. In this article we describe the CTDD practice and the tool that we intend to use to support and evaluate the CTDD practice in a real world software development project.
Magnetic seizure therapy in an adolescent with refractory bipolar depression: a case report

Magnetic seizure therapy (MST) has shown efficacy in adult patients with treatment-resistant depression with limited impairment in memory. To date, the use of MST in adolescent depression has not been reported. Here we describe the first successful use of MST in the treatment of an adolescent patient with refractory bipolar depression. This patient received MST in an ongoing open-label study for treatment-resistant major depression. Treatments employed a twin-coil MST apparatus, with the center of each coil placed over the frontal cortex (ie, each coil centered over F3 and F4). MST was applied at 100 Hz and 100% machine output at progressively increasing train durations. Depressive symptoms were assessed using the 24-item Hamilton Depression Rating Scale and cognitive function was assessed with a comprehensive neuropsychological battery. This adolescent patient achieved full remission of clinical symptoms after an acute course of 18 MST treatments and had no apparent cognitive decline, other than some autobiographical memory impairment that may or may not be related to the MST treatment. This case report suggests that MST may be a safe and well tolerated intervention for adolescents with treatment-resistant bipolar depression. Pilot studies to further evaluate the effectiveness and safety of MST in adolescents warrant consideration.
Effect of Delivered Dosage of Cigarette Smoke Toxins on the Levels of Urinary Biomarkers of Exposure

Urinary metabolites of tobacco smoke toxins are often used as biomarkers for the evaluation of active and passive exposure to cigarette smoke toxins. In a study of healthy smokers, we investigated concentrations of urinary biomarkers in relation to concentrations of selected toxins in mainstream cigarette smoke as determined by machine smoking of cigarettes in a manner that mimics an individual's smoking behavior (topography). Concentrations of nicotine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, and benzo(a)pyrene, in mainstream smoke determined under human smoking conditions, and their urinary metabolites cotinine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol, and 1-hydroxypyrene were established for 257 individuals who smoked low-yield (0.1-0.8 mg Federal Trade Commission nicotine/cigarette; mean, 0.66; n = 87), medium-yield (0.9-1.2 mg nicotine/cigarette; mean, 1.1; n = 109), and high-yield cigarettes (nicotine, >1.3 mg nicotine/cigarette; mean, 1.41; n = 61). Levels of urinary metabolites expressed per unit of delivered parent compounds decreased with increased smoke emissions. In smokers of low-, medium-, and high-yield cigarettes, the respective cotinine (ng/mg creatinine)-to-nicotine (mg/d) ratios were 89.4, 77.8, and 57.1 (low versus high; P = 0.06); the 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (pmol/mg creatinine)-to-4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (ng/d) ratios were 0.81, 0.55, and 0.57 (low versus high; P = 0.05); and the 1-hydroxypyrene (pg/mg creatinine)-to-benzo(a)pyrene (ng/d) ratios were 1.55, 1.13, and 0.97 (low versus high; P = 0.008). Similarly, means of cotinine per unit of delivered nicotine in smokers who consumed <20 cigarettes per day was 3.5-fold higher than in those who smoked >20 cigarettes per day. Likewise, a negative correlation was observed between cotinine-to-nicotine ratios and delivered doses of nicotine in subgroups of smokers who used the identical brand of cigarette, namely a filter tip-vented Marlboro (r = −0.59), which is a popular brand among Euro-Americans, and Newport (r = −0.37), a menthol-flavored cigarette without filter tip vents that is preferred by African-Americans. Thus, the intensity of the exposures significantly affects the levels of urinary biomarkers of exposure and should be taken into account in the evaluation of human exposure to cigarette smoke toxins. (Cancer Epidemiol Biomarkers Prev 2007;16(7):1408–15)
Restricted immunoglobulin variable region gene usage by normal Ly-1 (CD5+) B cells that recognize phosphatidyl choline

5-15% of lymphocytes in the peritoneums of normal adult B10.H-2aH- 4bp/Wts (2a4b) mice are CD5+ (Ly-1) B cells that recognize phosphatidyl choline (PtC), a phospholipid component of all mammalian cells. We produced a set of IgM-secreting hybridomas from the peritoneal cells of normal, adult 2a4b mice. We found that this set of hybridomas shows a similarly high frequency of antibodies specific for PtC (21 of 86) that also react with bromelain-treated mouse erythrocytes. Restriction fragment analysis of Ig gene rearrangements and analysis of expressed Ig idiotypes reveal that these cells use a restricted set of variable region genes to generate the PtC-specific antibodies. The Ig genes used by the PtC-specific hybridomas appear to be the same as those found in the PtC-specific Ly-1 B cell lymphomas, CH27 and CH34.
Dynamic Distributed Cooperative Control of Multiple Heterogeneous Resources

Abstract : This research is concerned with dynamically determining appropriate flight patterns for a set of autonomous UAVs in an urban environment, with multiple mission goals. The UAVs are tasked with searching the urban region for targets of interest, and tracking those targets that have been detected. We assume that there are limited communication capabilities between the UAVs, and that there exist possible line of sight constraints between the UAVs and the targets. Each UAV (i) operates its own dynamic feedback loop, in a receding horizon framework, incorporating local information (from the perspective of UAV i) as well as remote information (from the perspective of the neighbor' UAVs) to determine the tasks to perform and the optimal trajectory of UAV i (and neighbor UAVs) over the planning horizon. This results in a decentralized and more realistic model of the real-world situation. As the coupled task assignment and flight route optimization formulation is NP-hard, a hybrid heuristic for continuous global optimization is developed to solve for the flight plan and tasking over the planning horizon. Metrics capturing the price of anarchy and price of decentralization are developed, and experimental results are discussed.
Preinspiratory calcium rise in putative pre‐Bötzinger complex astrocytes

• Autonomic respiratory rhythm is essential to maintain lives and is generated in the lower brainstem. The ventrolateral medullary region, called the pre‐Bötzinger complex (preBötC), is the kernel for respiratory rhythm generation. Despite previous extensive studies focusing on neurons, the mechanism of how respiratory rhythm is generated has not been fully understood. • Here we show that non‐neuronal glial cells (a subset of putative astrocytes) in the preBötC are periodically activated preceding inspiratory neuronal activity, periodic activity of putative astrocytes persists during blockade of neuronal activity, and stimulation of astrocytes in the preBötC induces inspiratory neuronal firings. • These findings together with the previous report that blockade of astrocytic metabolism abolishes inspiratory neural output suggest that astrocytes are functionally involved in respiratory rhythm generation. • These results will help us better understand how respiratory rhythm is generated and how respiratory output is disturbed in various pathological conditions.
Disconnected Objects : Reconciliation in a Nested Object Transaction Environment

A mechanism for handling inconsistencies created when replicated objects are updated during disconnected operations on a mobile host is described. By exploiting the encapsulation property of objects, analysis of object behaviours is employed to derive \reconciliation procedures" so con icting concurrent updates made on di erent copies of objects may be rendered mutually consistent. The process of generating and applying reconciliation procedures is discussed.
Chronic Maternal Dietary Chromium Restriction Modulates Visceral Adiposity

OBJECTIVE We demonstrated previously that chronic maternal micronutrient restriction altered the body composition in rat offspring and may predispose offspring to adult-onset diseases. Chromium (Cr) regulates glucose and fat metabolism. The objective of this study is to determine the long-term effects of maternal Cr restriction on adipose tissue development and function in a rat model. RESEARCH DESIGN AND METHODS Female weanling WNIN rats received, ad libitum, a control diet or the same with 65% restriction of Cr (CrR) for 3 months and mated with control males. Some pregnant CrR mothers were rehabilitated from conception or parturition and their pups weaned to control diet. Whereas some CrR offspring were weaned to control diet, others continued on CrR diet. Various parameters were monitored in the offspring at three monthly intervals up to 15–18 months of age. RESULTS Maternal Cr restriction significantly increased body weight and fat percentage, especially the central adiposity in both male and female offspring. Further, the expression of leptin and 11 β-hydroxysteroid dehydrogenase 1 genes were significantly increased in CrR offspring of both the sexes. Adipocytokine levels were altered in plasma and adipose tissue; circulating triglyceride and FFA levels were increased, albeit in female offspring only. Rehabilitation regimes did not correct body adiposity but restored the circulating levels of lipids and adipocytokines. CONCLUSIONS Chronic maternal Cr restriction increased body adiposity probably due to increased stress and altered lipid metabolism in WNIN rat offspring, which may predispose them to obesity and associated diseases in later life.
Reevaluation of the primary motor cortex connections with the thalamus in primates

Six injections (∼1 mm in diameter) of biotinylated dextran amine (BDA) were placed in different locations of the primary motor cortex of the rhesus monkey. Anterograde and retrograde labeling patterns in the thalamus were charted and individual labeled axons traced in continuous serial sections. Both anterograde and retrograde labeling in the thalamus was extensive, spanning several millimeters mediolaterally and including ventral lateral, ventral anterior, centromedian, and centrolateral nuclei. Paracentral, mediodorsal, lateral posterior, and medial pulvinar nuclei were also labeled. Two basic types of corticothalamic axons were identified: small to medium‐width, type 1 axons that formed large terminal fields with small boutons, and thick, type 2 axons that formed small terminal fields with large boutons. Within each group, subtypes were identified based on specific features of the axons and terminals: two subtypes of type 1 axons and four subtypes of type 2 axons. The results revealed multiple modes of corticothalamic connectivity: sparsely distributed type 1 axons, dense plexuses of type 1 axons, type 2 axon terminal fields either singly or in clusters, and mixed plexuses of type 1 and type 2 axons. Only some cells in the plexuses were retrogradely labeled; some plexuses did not contain any labeled neurons, and many retrogradely labeled neurons were in the regions devoid of anterograde labeling. These connectivity patterns differed between thalamic nuclei. The results revealed much more complex relationships between M1 and thalamus than were previously thought to exist. It is suggested that this connectivity is neither of exclusively a feedback nature nor perfectly reciprocal but is subserved by a multitude of channels, most likely originating from different populations of cortical neurons, and feeding into a variety of functionally different neuronal networks, with each processing specific information. J. Comp. Neurol. 457:133–158, 2003. © 2003 Wiley‐Liss, Inc.
Role for the outer membrane ferric siderophore receptor PupB in signal transduction across the bacterial cell envelope.

The outer membrane protein PupB of Pseudomonas putida WCS358 facilitates transport of iron complexed to the siderophores pseudobactin BN8 and pseudobactin BN7 into the cell. Its synthesis is induced by the presence of these specific siderophores under iron limitation. The signal transduction pathway regulating siderophore‐dependent expression of pupB was shown to consist of two regulatory proteins, PupI and PupR, and the PupB receptor itself. Mutational analysis of the regulatory genes suggested that PupI acts as a positive regulator of pupB transcription, whereas PupR modifies PupI activity dependent on the presence of pseudobactin BN8. PupI and PupR do not share homology with the classical bacterial two‐component systems but display significant similarity to the FecI and FecR proteins of Escherichia coli involved in regulation of ferric dicitrate transport. The function of the PupB receptor in pupB regulation was studied by the use of chimeric receptor proteins composed of PupB and the ferric pseudobactin 358 receptor PupA. This experiment revealed that PupB is involved in the initiation of the signal transduction pathway, implying a so far unique role for an outer membrane protein in signal transduction.
Power-efficient real-time solution for adaptive vision algorithms

This study focuses on embedded realisation of adaptive vision algorithms, and illustrates the challenges using mixture of Gaussian (MoG) background subtraction. MoG is a frequently used adaptive vision kernel, for example, for surveillance applications. It involves massive computation and communication demands, which renders a software approach infeasible considering a 1 W power budget. To address these challenges, the authors employ a systematic system-level design approach and first analyse the demands at high-level, explore opportunities for bandwidth reduction, and derive a customised system-level specification. Based on the system-level exploration, this study then proposes a communication-centric architecture template that simplifies implementing embedded adaptive vision algorithms. To achieve high efficiency, they propose to separate steaming and algorithm-intrinsic traffic. This allows customising the traffic handling based on role of the data, as well as simplifying interconnecting multiple heterogeneous nodes. The authors demonstrate the benefits of traffic separation and the communication-centric architecture template based on MoG. They realise MoG on the Zynq-7000 SoC processing 1080p 30 Hz stream in real-time. The MoG processing kernel consists of 77 pipeline stages operating at 148.5 MHz. The authors' solution is more than 600 × faster than an ARM Cortex-A9 with 666 MHz. It only consumes 151 mW of on-chip power operating in real-time.
Embedding research activities to enhance student learning

Purpose – The purpose of this paper's novel, research‐oriented approach is to embed research‐based activities in a core second‐year course of a university business degree program to support and develop student research capabilities.Design/methodology/approach – The design draws on Boud and Prosser's work to foster participation in a learner‐centred, discipline‐based approach. Activities rely on technology supports and mixed delivery modes to combine diverse theoretical perspectives and research methodologies.Findings – The initial implementations of the design generated improved student learning experiences compared to the previous year. Voluntary participation was high and informal evidence suggested that research activities were a core‐contributing element to positive student outcomes.Research limitations/implications – A formal evaluation study is required to measure precisely the extent to which research activities like those described in this paper have an effect on students' learning experiences.Pra.
Three faces of police referral: Welfare, Justice and business perspectives on multi‐agency work with drug arrestees

There are a series of loosely connected debates in Britain about forms of punishment, diversion and case disposal that might be financially economical, fair in terms of justice, and in the welfare interest of persons caught up in the criminal justice system. This paper describes and analyses schemes in which arresting police officers and/or custody officers offer to arrested persons an opportunity for referral to specialist drugs advice and/or wider forms of services (debt advice, housing advice, health services, etc). Such schemes have variously been piloted, abandoned, forgotten and proposed afresh, in many areas of Britain from the mid‐1980s onwards. The application of three perspectives upon police referral ‐ welfare, justice and business ‐ illuminates some quite problematic aspects of police referral and, it is suggested, pinpoints some possible ways forward for police and other practitioners. A summary checklist of suggested police referral ‘dos and donts’ is offered for those contemplating or manag.
Catalase and superoxide dismutase activities after heat injury of Listeria monocytogenes

Four strains of Listeria monocytogenes were examined for catalase (CA) and superoxide dismutase (SOD) activities. The two strains having the highest CA activities (LCDC and Scott A) also possessed the highest SOD activities. The CA activity of heated cell extracts of all four strains examined decreased sharply between 55 and 60 degrees C. SOD was more heat labile than CA. Two L. monocytogenes strains demonstrated a decline in SOD activity after heat treatment at 45 degrees C, whereas the other two strains demonstrated a decline at 50 degrees C. Sublethal heating of the cells at 55 degrees C resulted in increased sensitivity to 5.5% NaCl. Exogenous hydrogen peroxide was added to suspensions of L. monocytogenes; strains producing the highest CA levels showed the greatest H2O2 resistance.
Primary central nervous system diffuse large B‐cell lymphoma has poorer immune cell infiltration and prognosis than its peripheral counterpart

Primary central nervous system (CNS) diffuse large B‐cell lymphoma (PCNSL) is an ominous disease with a poor prognosis. The brain is an immune‐privileged sanctuary, and this may contribute to an ineffective host immune response and thus a poorer outcome. The aim of this study was therefore to study the difference in the immune composition in PCNSL and non‐CNS diffuse large B‐cell lymphoma (DLBCL), and the role of the immune response in PCNSL prognosis.