Miracle-dz/UniFAR-FTUs huggingface dataset:
The diagnostic and therapeutic impact of MRI: an observational multi-centre study.

AIM To provide information about the diagnostic and therapeutic impact of magnetic resonance imaging (MRI) and to compare the findings across diagnostic groups. MATERIALS AND METHODS A prospective, observational study of 2017 consecutive referrals for MRI of the head, spine or knee at four imaging centres. Clinicians completed questionnaires before MRI stating initial diagnoses, diagnostic confidence and treatment plans. After imaging, a second questionnaire evaluated clinicians' revised diagnosis and treatment plans in the light of imaging findings. Patients were grouped into nine diagnostic categories for analysis. Comparison between pre- and post-imaging was used to assess the diagnostic and therapeutic impact of MRI. RESULTS In seven of nine diagnostic groups MRI findings were associated with a diagnostic impact. Diagnoses were revised or discarded following normal MR findings and diagnostic confidence was increased by confirmative MR findings. There was no statistically significant diagnostic impact for suspected pituitary or cerebello-pontine angle lesions. In five of nine diagnostic groups (knee meniscus, knee ligament, multiple sclerosis, lumbar and cervical spine) MRI findings had a clear impact on treatment plans. CONCLUSION This study demonstrates that in most diagnostic categories, MRI influences diagnosis and treatment. However, experimental studies are needed to prove that these diagnostic and therapeutic impacts lead to improved health.Hollingworth (2000). Clinical Radiology55, 825-831.
The Geology and Vertebrate Paleontology of Calvert Cliffs, Maryland, USA

The last comprehensive review of the fossil vertebrates from the Miocene of Calvert Cliffs was published more than 100 years ago. This volume is a collection of papers that updates some of the geological features of Calvert Cliffs and provides reviews of the fossil biota that include representatives from the following taxonomic groups: chondrichthyans (chimaeras, shark, skates, and rays), actinopterygians (ray-finned fishes), crocodilians (crocodiles), and sirenians (sea cows). Peter Vogt, Ralph E. Eshelman, and Stephen J. Godfrey document how the 20–40 m [65–130 ft] high Calvert Cliffs along the western shore of the Chesapeake Bay continue to yield insights into 18–8 mya (Miocene) geology, marine and terrestrial vertebrate fauna, and the origin and evolution of Chesapeake Bay and Calvert Cliffs up to the present. These exposures rank high among the best-known fossiliferous deposits of any age. Bretton W. Kent describes the cartilaginous fish (the chondrichthyan) fauna, consisting of 54 species—3 chimaeras (ratfishes), 39 sharks, and 12 skates and rays—a fauna rich in large macrophagous sharks and large neritic rays. In an addendum to Kent’s chapter, he and David J. Ward describe a new species of giant thresher shark with serrated teeth. Giorgio Carnevale and Stephen J. Godfrey present an account of the 38 actinopterygian taxa known from osteological remains and a diverse otolith assemblage of at least 55 taxa. These actinopterygians show an affinity for well-oxygenated muddy and sandy substrates dominated primarily by shallow-water species characteristic of the inner shelf and secondarily by epipelagic taxa. Robert E. Weems details the crocodilians referable to the tomistomine Thecachampsa. The closest living relative is Tomistoma schlegelii, the false gharial of Southeast Asia. Two species are present: Thecachampsa sericodon and T. antiquus. These tomistomines are found in shallow marine coastal deposits, indicating that they inhabited coastal waters. Daryl P. Domning reports that fossils of the Miocene marine fauna include rare sirenians of the family Dugongidae. Three taxa are known: the halitheriine dugongid Metaxytherium crataegense, the dugongine dugongid Nanosiren sp. , and another dugongine, aff. Corystosiren. The St. Marys Formation contains remains that may be referable to Metaxytherium floridanum, but confirmation awaits the discovery of more complete specimens.
Entamoeba histolytica: a novel cysteine protease and an adhesin form the 112 kDa surface protein

Here, we present evidence that a cysteine protease (EhCP112) and a protein with an adherence domain (EhADH112) form the Entamoeba histolytica 112 kDa adhesin. Immunoelectron microscopy and immunofluorescence assays using monoclonal antibodies (mAbAdh) revealed that, during phagocytosis, the adhesin is translocated from the plasma membrane to phagocytic vacuoles. mAbAdh inhibited 54% adherence, 41% phagocytosis, and 35% and 62% destruction of MDCK cell monolayers by live trophozoites and their extracts respectively. We cloned a 3587 bp DNA fragment (Eh112 ) with two open reading frames (ORFs) separated by a 188 bp non-coding region. The ORF at the 5' end (Ehcp112 ) encodes a protein with a cysteine protease active site, a transmembranal segment and an RGD motif. The second ORF (Ehadh112 ) encodes a protein recognized by mAbAdh with three putative transmembranal segments and four glycosylation sites. Northern blot, primer extension and Southern blot experiments revealed that Ehcp112 and Ehadh112 are two adjacent genes in DNA. Ehcp112 and Ehadh112 genes were expressed in bacteria. The recombinant peptides presented protease activity and inhibited adherence and phagocytosis, respectively, and both were recognized by mAbAdh. The EhCP112 and EhADH112 peptides could be joined by covalent or strong electrostatic forces, which are not broken during phagocytosis.
How to Discount Deep Reinforcement Learning: Towards New Dynamic Strategies

Using deep neural nets as function approximator for reinforcement learning tasks have recently been shown to be very powerful for solving problems approaching real-world complexity. Using these results as a benchmark, we discuss the role that the discount factor may play in the quality of the learning process of a deep Q-network (DQN). When the discount factor progressively increases up to its final value, we empirically show that it is possible to significantly reduce the number of learning steps. When used in conjunction with a varying learning rate, we empirically show that it outperforms original DQN on several experiments. We relate this phenomenon with the instabilities of neural networks when they are used in an approximate Dynamic Programming setting. We also describe the possibility to fall within a local optimum during the learning process, thus connecting our discussion with the exploration/exploitation dilemma.
Iterative Regularization and MINRES

In this paper we present three theorems which give insight into the regularizing properties of MINRES. While our theory does not completely characterize the regularizing behavior of the algorithm, it provides a partial explanation of the observed behavior of the method. Unlike traditional attempts to explain the regularizing properties of Krylov subspace methods, our approach focuses on convergence properties of the residual rather than on convergence analysis of the harmonic Ritz values. The import of our analysis is illustrated by two examples. In particular, our theoretical and numerical results support the following important observation: in some circumstances the dimension of the optimal Krylov subspace can be much smaller than the number of the components of the truncated spectral solution that must be computed to attain comparable accuracy.
How could preventive therapy affect the prevalence of drug resistance? Causes and consequences

Various forms of preventive and prophylactic antimicrobial therapies have been proposed to combat HIV (e.g. pre-exposure prophylaxis), tuberculosis (e.g. isoniazid preventive therapy) and malaria (e.g. intermittent preventive treatment). However, the potential population-level effects of preventative therapy (PT) on the prevalence of drug resistance are not well understood. PT can directly affect the rate at which resistance is acquired among those receiving PT. It can also indirectly affect resistance by altering the rate at which resistance is acquired through treatment for active disease and by modifying the level of competition between transmission of drug-resistant and drug-sensitive pathogens. We propose a general mathematical model to explore the ways in which PT can affect the long-term prevalence of drug resistance. Depending on the relative contributions of these three mechanisms, we find that increasing the level of coverage of PT may result in increases, decreases or non-monotonic changes in the overall prevalence of drug resistance. These results demonstrate the complexity of the relationship between PT and drug resistance in the population. Care should be taken when predicting population-level changes in drug resistance from small pilot studies of PT or estimates based solely on its direct effects.
Evaluation of the Prognostic Value of IFN-γ Release Assay and Tuberculin Skin Test in Household Contacts of Infectious Tuberculosis Cases in Senegal

Background Chemoprophylaxis of contacts of infectious tuberculosis (TB) cases is recommended for TB control, particularly in endemic countries, but is hampered by the difficulty to diagnose latent TB infection (LTBI), classically assessed through response to the Tuberculin Skin Test (TST). Interferon-gamma release assays (IGRA) are proposed new tools to diagnose LTBI, but there are limited data on their ability to predict the development of active TB disease. To address this, we investigated the response to TST and IGRA in household contacts of infectious TB cases in a TB high-burden country and the potential correlation with development of TB. Methodology/Principal Findings Prospective household contacts study conducted in two health centres in Dakar, Senegal. A total of 2679 household contacts of 206 newly detected smear and/or culture positive index TB cases aged 18 years or greater were identified A TST was performed in each contact and an ESAT6/CFP10 ELISPOT assay performed in a random sample of those. Contacts were followed-up for 24 months. TB was diagnosed in 52 contacts, an incidence rate of 9.27/1000 person-years. In univariable analysis, the presence of positive TST (≥10 mm) and ELISPOT (>32 SFC/million PBMC) responses at baseline were associated with active TB during follow-up: Rate Ratio [RR] = 2.32 (95%CI:1.12–4.84) and RR = 2.09 (95%CI:0.83–5.31), respectively. After adjustment for age, sex and proximity to index case, adjusted RRs were 1.51 (95%CI:0.71–3.19) and 1.98 (95%CI:0.77–5.09), respectively. Restricting analysis to the 40 microbiologically confirmed cases, the adjusted RR for positive ELISPOT was 3.61 (95%CI:1.03–12.65). The median ELISPOT response in contacts who developed TB was 5-fold greater than in those who did not develop TB (p = 0.02). Conclusions/Significance TST and IGRAs are markers of a contact of the immune system with tubercle bacilli. In a TB endemic area, a high ELISPOT response may reflect increased bacterial replication that may subsequently be associated with development of TB disease and may have a prognostic value. Further longitudinal data are needed to assess whether IGRAs are reliable markers to be used for targeting chemoprophylaxis.
Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii

Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.
DNA damage‐inducible origins of DNA replication in Escherichia coli.

Upon induction of the SOS response in Escherichia coli, the mode of initiation of DNA replication is altered such that it can occur in the absence of normally required protein synthesis. This type of DNA replication has been termed induced stable DNA replication (iSDR). We examined the origin usage during iSDR and found that the initiation of iSDR occurs primarily in the oriC and terC regions of the chromosome in a manner completely independent of transcription, translation and DnaA protein. Minichromosomes (oriC plasmids) pOC23 and pOC81 were induced to replicate in the absence of DnaA protein and transcription after SOS induction. The results localized one of the iSDR origin activities in a 596 bp region which includes the minimal oriC.
Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites

A typical homing endonuclease initiates mobility of its group I intron by recognizing DNA both upstream and downstream of the intron insertion site of intronless alleles, preventing the endonuclease from binding and cleaving its own intron-containing allele. Here, we describe a GIY-YIG family homing endonuclease, I-BmoI, that possesses an unusual recognition sequence, encompassing 1 base pair upstream but 38 base pairs downstream of the intron insertion site. I-BmoI binds intron-containing and intronless substrates with equal affinity but can nevertheless discriminate between the two for cleavage. I-BmoI is encoded by a group I intron that interrupts the thymidylate synthase (TS) gene (thyA) of Bacillus mojavensis s87-18. This intron resembles one inserted 21 nucleotides further downstream in a homologous TS gene (td) of Escherichia coli phage T4. I-TevI, the T4 td intron-encoded GIY-YIG endonuclease, is very similar to I-BmoI, but each endonuclease gene is inserted within a different position of its respective intron. Remarkably, I-TevI and I-BmoI bind a homologous stretch of TS-encoding DNA and cleave their intronless substrates in very similar positions. Our results suggest that each endonuclease has independently evolved the ability to distinguish intron-containing from intronless alleles while maintaining the same conserved recognition sequence centered on DNA-encoding active site residues of TS.
The irritant potential of n‐propanol (nonanoic acid vehicle) in cumulative skin irritation: a validation study of two different human in vivo test models

Background/purpose: Human in vivo cumulative irritation tests with low‐grade irritants simulate real‐life exposure to skin irritants. The test outcome depends not only on the substance tested but also on the design of the assay. More than one experimental irritant is usually used because chemicals have diverse mechanisms of action on the skin. We used sodium lauryl sulfate (SLS) and nonanoic acid (NON) in three different concentrations plus their vehicles, water and n‐propanol, respectively, to validate our test models and to optimize test concentrations.
Successfully implementing it outsourcing strategy in German banks: the role of contract design and risk analysis

From the outsourcer’s perspective, the IS outsourcing literature emphasizes the importance of contracts and risk awareness for managing outsourcing ventures. However, there is a lack of proven and tested outsourcing management concepts in theory and practise incorporating contractual designs to effectively counter risk. By extending the risk model of Bahli and Rivard (2001) we investigate the influence of risk analysis on contract quality and their interrelation with outsourcing success. Using multiple case studies within the German banking industry our Research-In-Progress paper aims at answering the following questions: (1) ‘How does the contract contribute to outsourcing success from a risk mitigation perspective? ’ and (2) ‘How does risk analysis affect the risk mitigation quality of the contract? ’. Our research provides insights on how the conduction of a thorough risk analysis can improve contract quality. We show that involving business staff as well as IT staff in an outsourcing project helps to optimize contract clauses. In addition, we demonstrate how the design of contract contents such as pricing schemes, service level agreements, and penalty-reward-systems can ensure the expected cost savings and thereby contribute to outsourcing success.
Augmentation of the Antibody Response of Atlantic Salmon by Oral Administration of Alginate-Encapsulated IPNV Antigens

The objective of the present study was to assess the effect of alginate-encapsulated infectious pancreatic necrosis virus antigens in inducing the immune response of Atlantic salmon as booster vaccines. One year after intraperitoneal injection with an oil-adjuvanted vaccine, post-smolts were orally boosted either by 1) alginate-encapsulated IPNV antigens (ENCAP); 2) soluble antigens (UNENCAP) or 3) untreated feed (control). This was done twice, seven weeks apart. Sampling was done twice, firstly at 7 weeks post 1st oral boost and the 2nd, at 4 weeks after the 2nd oral boost. Samples included serum, head kidney, spleen and hindgut. Serum antibodies were analyzed by ELISA while tissues were used to assess the expression of IgM, IgT, CD4, GATA3, FOXP3, TGF-β and IL-10 genes by quantitative PCR. Compared to controls, fish fed with ENCAP had a significant increase (p<0.04) in serum antibodies following the 1st boost but not after the 2nd boost. This coincided with significant up-regulation of CD4 and GATA3 genes. In contrast, serum antibodies in the UNENCAP group decreased both after the 1st and 2nd oral boosts. This was associated with significant up-regulation of FOXP3, TGF-β and IL-10 genes. The expression of IgT was not induced in the hindgut after the 1st oral boost but was significantly up-regulated following the 2nd one. CD4 and GATA3 mRNA expressions exhibited a similar pattern to IgT in the hindgut. IgM mRNA expression on the other hand was not differentially regulated at any of the times examined. Our findings suggest that 1) Parenteral prime with oil-adjuvanted vaccines followed by oral boost with ENCAP results in augmentation of the systemic immune response; 2) Symmetrical prime and boost (mucosal) with ENCAP results in augmentation of mucosal immune response and 3) Symmetrical priming and boosting (mucosal) with soluble antigens results in the induction of systemic immune tolerance.
Relative Radiometric Normalisation - performance testing of selected techniques and impact analysis on vegetation and water bodies

Abstract In this paper, six image-based Relative Radiometric Normalization (RRN) techniques were applied to normalize the bi-temporal Landsat 5 TM data-set. RRN techniques do not require any atmospheric and ground information at the time of image acquisition. The target image for the year 2009 was normalized in such a way that it resembled the atmospheric and sensor conditions similar to those under which the reference image of the same season for the year 1990 was acquired. Among the selected methods applied, it was found that the Iteratively Reweighted Multivariate Alteration Detection (IR-MAD) method performed better, based on the error statistic. The IR-MAD technique was found to be advantageous as it identified a large set of true time-invariant pixels automatically from the change background using iterative canonical component analysis. The technique also stretches the values of Normalized Difference Vegetation Index and Normalized Difference Water Index and may help to distinguish different vegetation and water bodies better.
Protective Role of Toll-like Receptor 3-Induced Type I Interferon in Murine Coronavirus Infection of Macrophages

Toll-like Receptors (TLRs) sense viral infections and induce production of type I interferons (IFNs), other cytokines, and chemokines. Viral recognition by TLRs and other pattern recognition receptors (PRRs) has been proven to be cell-type specific. Triggering of TLRs with selected ligands can be beneficial against some viral infections. Macrophages are antigen-presenting cells that express TLRs and have a key role in the innate and adaptive immunity against viruses. Coronaviruses (CoVs) are single-stranded, positive-sense RNA viruses that cause acute and chronic infections and can productively infect macrophages. Investigation of the interplay between CoVs and PRRs is in its infancy. We assessed the effect of triggering TLR2, TLR3, TLR4, and TLR7 with selected ligands on the susceptibility of the J774A.1 macrophage cell line to infection with murine coronavirus (mouse hepatitis virus, [MHV]). Stimulation of TLR2, TLR4, or TLR7 did not affect MHV production. In contrast, pre-stimulation of TLR3 with polyinosinic-polycytidylic acid (poly I:C) hindered MHV infection through induction of IFN-β in macrophages. We demonstrate that activation of TLR3 with the synthetic ligand poly I:C mediates antiviral immunity that diminishes (MHV-A59) or suppresses (MHV-JHM, MHV-3) virus production in macrophages.
Haptic Stylus and Empirical Studies on Braille, Button, and Texture Display

This paper presents a haptic stylus interface with a built-in compact tactile display module and an impact module as well as empirical studies on Braille, button, and texture display. We describe preliminary evaluations verifying the tactile display's performance indicating that it can satisfactorily represent Braille numbers for both the normal and the blind. In order to prove haptic feedback capability of the stylus, an experiment providing impact feedback mimicking the click of a button has been conducted. Since the developed device is small enough to be attached to a force feedback device, its applicability to combined force and tactile feedback display in a pen-held haptic device is also investigated. The handle of pen-held haptic interface was replaced by the pen-like interface to add tactile feedback capability to the device. Since the system provides combination of force, tactile and impact feedback, three haptic representation methods for texture display have been compared on surface with 3 texture groups which differ in direction, groove width, and shape. In addition, we evaluate its capacity to support touch screen operations by providing tactile sensations when a user rubs against an image displayed on a monitor.