Miracle-dz/UniFAR-FTUs huggingface dataset:
Attitudes among students and teachers on vertical integration between clinical medicine and basic science within a problem-based undergraduate medical curriculum

Important elements in the curriculum at the Faculty of Health Sciences in Linköping are vertical integration, i.e. integration between the clinical and basic science sections of the curriculum, and horizontal integration between different subject areas. Integration throughout the whole curriculum is time-consuming for both teachers and students and hard work is required for planning, organization and execution. The aim was to assess the importance of vertical and horizontal integration in an undergraduate medical curriculum, according to opinions among students and teachers. In a questionnaire 102 faculty teachers and 106 students were asked about the importance of 14 different components of the undergraduate medical curriculum including vertical and horizontal integration. They were asked to assign between one and six points to each component (6 points = extremely important for the quality of the curriculum; 1 point = unimportant). Students as well as teachers appreciated highly both forms of integration. Students scored horizontal integration slightly but significantly higher than the teachers (median 6 vs 5 points; p=0.009, Mann-Whitney U-test), whereas teachers scored vertical integration higher than students (6 vs 5; p=0.019, Mann-Whitney U-test). Both students and teachers considered horizontal and vertical integration to be highly important components of the undergraduate medical programme. We believe both kinds of integration support problem-based learning and stimulate deep and lifelong learning and suggest that integration should always be considered deeply when a new curriculum is planned for undergraduate medical education.
Thioredoxin Reductase Is Irreversibly Modified by Curcumin

The thioredoxin reductase (TrxR) isoenzymes, TrxR1 in cytosol or nucleus and TrxR2 in mitochondria, are essential mammalian selenocysteine (Sec)-containing flavoenzymes with a -Gly-Cys-Sec-Gly active site. TrxRs are the only enzymes catalyzing the NADPH-dependent reduction of the active site disulfide in thioredoxins (Trxs), which play essential roles in substrate reductions, defense against oxidative stress, and redox regulation by thiol redox control. TrxRs have been found to be overexpressed by a number of human tumors. Curcumin, which is consumed daily by millions of people, is a polyphenol derived from the plant Curcuma longa. This phytochemical has well known anticancer and antiangiogenic properties. In this study we report that rat TrxR1 activity in Trx-dependent disulfide reduction was inhibited by curcumin. The IC50 value for the enzyme was 3.6 μm after incubation at room temperature for 2 h in vitro. The inhibition occurred with enzyme only in the presence of NADPH and persisted after removal of curcumin. By using mass spectrometry and blotting analysis, we proved that this irreversible inhibition by curcumin was caused by alkylation of both residues in the catalytically active site (Cys496/Sec497) of the enzyme. However, the curcumin-modified enzyme showed a strongly induced NADPH oxidase activity to produce reactive oxygen species. Inhibition of TrxR by curcumin added to cultured HeLa cells was also observed with an IC50 of around 15 μm. Modification of TrxR by curcumin provides a possible mechanistic explanation for its cancer preventive activity, shifting the enzyme from an antioxidant to a prooxidant.
Evaluation of Polymyxa betae Keskin Contaminated by Beet Necrotic Yellow Vein Virus in Soil

The fungus Polymyxa betae Keskin belongs to the family Plasmodiophoraceae and lives in the soil as an obligatory parasite of the roots of the Chenopodiaceae. When contaminated by beet necrotic yellow vein virus, this viruliferous fungus causes a serious disease of sugar beet known as rhizomania, whereas the infection by the fungus alone (aviruliferous fungus) causes only slight damage to the plant with little economic consequence. The manifestation of rhizomania in sugar beet is directly related to the concentration of infecting units of viruliferous P. betae present in the soil. (One infecting unit is a group of one or more sporosori that liberate zoospores capable of visibly infecting a plant.) By using current methods of analysis, it is possible to estimate the total quantity of P. betae present in the soil, but one cannot distinguish quantitatively the infecting units of aviruliferous from viruliferous P. betae. A new method has been developed based on the technique of the most probable number and enzyme-linked immunosorbent assay to estimate the concentration of infecting units of viruliferous P. betae in soil. The method is suitable for the routine analysis of numerous soil samples and allows one to estimate the concentration of viable forms of the fungus P. betae, whether or not contaminated by beet necrotic yellow vein virus, present in a soil affected by rhizomania or presumed healthy. The analyses performed with this method are economical and use a reagent kit and equipment in wide use.
Implementation Cycles, Investment, and Growth

We develop a model of "intrinsic" cycles, driven by the decentralized behavior of entrepreneurs and firms making continuous, divisible improvements in their productivity. We show that when the introduction of productivity improvements is endogenous, implementation cycles arise even in the presence of reversible investment and consumption smoothing. The implied cyclical equilibrium is unique within its class and shares several features in common with actual business cycles. In particular, its predictions are qualitatively consistent with the joint behavior of the investment rate and Tobin's Q during U.S. recessions. Copyright © 2008 the Economics Department of the University of Pennsylvania and the Osaka University Institute of Social and Economic Research Association.
Chemical‐Shift Magnetic Resonance Imaging of Two‐Line Spectra by Gradient Reversal

A method of chemical‐shift imaging is described using the invariance of chemical shifts to changes in magnetic field gradients used for frequency encoding of position in imaging. This enables separation of the effects on the observed signal of chemical shift from the effects of different positions along the imaging gradient when the signal is observed with different gradients. A simple implementation for a two‐line spectrum is presented using signals observed with normal and reversed imaging gradients. This is used to create “fat” and “water” images of the thigh. © 1985 Academic Press,Inc.
Quorum Sensing Enhances the Stress Response in Vibrio cholerae

ABSTRACT Vibrio cholerae lives in aquatic environments and causes cholera. Here, we show that quorum sensing enhances V. cholerae viability under certain stress conditions by upregulating the expression of RpoS, and this regulation acts through HapR, suggesting that a quorum-sensing-enhanced stress response plays a role in V. cholerae environmental survival.
Different structure-function relationships for alpha-factor-induced morphogenesis and agglutination in Saccharomyces cerevisiae

Eight synthetic analogs of the mating pheromone alpha-factor-induced morphogenesis and increased agglutinability in a cells. Most analogs induced increased agglutinability at lower concentrations than those at which they induced morphogenesis, but the ratio of the potencies for the two effects varied 140-fold among different analogs. Morphological response to pheromone required exposure for at least 90 min, but increased agglutinability followed exposures of 20 s. Two synthetic analogs induced neither response. In competition experiments, both of these analogs prevented induction of increased agglutinability and morphogenesis by active alpha factor. The inactive peptides blocked increased agglutinability at lower concentrations than those at which they blocked morphogenesis. alpha factors exhibited different structure-function relationships for morphogenesis as compared with agglutinability. Thus, response of Saccharomyces cerevisiae to alpha factor is complex and may be mediated by more than one receptor.
Pathogenesis of experimental neonatal woodchuck hepatitis virus infection: Chronicity as an outcome of infection is associated with a diminished acute hepatitis that is temporally deficient for the expression of interferon gamma and tumor necrosis factor‐alpha messenger RNAs

Surgical biopsies of the liver were obtained from woodchuck hepatitis virus (WHV)‐infected neonatal woodchucks at 2 time points before the self‐limited or chronic outcomes became obvious by serologic criteria. Following segregation of outcomes, livers were analyzed for intrahepatic type 1 cytokine messenger RNAs (mRNAs) (interleukin 2 [IL‐2], interferon gamma [IFN‐γ], tumor necrosis factor‐alpha [TNF‐α]) and leukocyte inflammatory phenotype (IgG+ plasma cells, lysozyme+ macrophages, CD3+ T cells). Baselines were assessed using age‐matched uninfected control livers. At week 8 (early acute phase), intrahepatic type 1 cytokine mRNAs were similarly low in both outcome settings and no different from age‐matched uninfected controls. This was consistent with the minimal initial viral loads and lack of histologic inflammation at this time. At week 14 (mid‐acute phase), changes in viral load between outcome groups related inversely to the intrahepatic inflammatory responses. Animals that eventually became resolved had increased intrahepatic expression of IFN‐γ and TNF‐α mRNAs and robust inflammation by CD3+ T cells, plasma cells, and macrophages. At the same time point of infection, animals that eventually became chronic carriers had an acute hepatitis involving the same cell types, but at diminished levels, and markedly deficient intrahepatic expression of IFN‐γ and TNF‐α mRNAs. IL‐2 mRNA remained at baseline control levels in both outcome groups. These cotemporal comparisons map a critical deviation in host response to the acute stage of an evolving chronic infection. They strongly suggest that increasing viral load and chronicity as an outcome of neonatal WHV infection result from a temporal deficiency in the acute intrahepatic effector mechanisms mediated by IFN‐γ and TNF‐α.
RBE for carbon track-segment irradiation in cell lines of differing repair capacity.

PURPOSE The LET position of the RBE maximum and its dependence on the cellular repair capacity was determined for carbon ions. Hamster cell lines of differing repair capacity were irradiated with monoenergetic carbon ions. RBE values for cell inactivation at different survival levels were determined and the differences in the RBE-LET patterns were compared with the individual sensitivity to photon irradiation of the different cell lines. MATERIAL AND METHODS Three hamster cell lines, the wild-type cell lines V79 and CHO-K1 and the radiosensitive CHO mutant xrs5, were irradiated with carbon ions of different energies (2.4-266.4 MeV/u) and LET values (13.7-482.7 keV/microm) and inactivation data were measured in comparison to 250 kV x-rays. RESULTS For the repair-proficient cell lines a RBE maximum was found at LET values between 150 and 200 keV/microm. For the repair-deficient cell line the RBE failed to show a maximum and decreased continuously for LET values above 100 keV/microm. CONCLUSIONS The carbon RBE LET relationship for inactivation is shifted to higher LET values compared with protons and alpha-particles. RBE correlated with the repair capacity of the cells.
Variation among Pathologists in the Histologic Grading of Canine Cutaneous Mast Cell Tumors with Uniform Use of a Single Grading Reference

Ten veterinary pathologists independently assigned histologic grades to the same 60 canine cutaneous mast cell tumors using the Patnaik classifications. The degree of agreement in grading among the pathologists was compared with the degree of agreement among the same pathologists in a previous study, in which each pathologist used the reference for grading that he/she uses routinely. Mean agreement improved significantly from 50.3% to 62.1% with uniform use of the Patnaik classifications (P = 0.00001), suggesting that there is value in uniform application of a single grading scheme for canine cutaneous mast cell tumors. Agreement among pathologists was still not 100%, suggesting that a more objective grading scheme should be developed and that other histologic indicators of prognosis should be investigated.
Investigation of optics behind N719 dye in dye-sensitized solar cells by using molecular dynamics simulation

A molecular dynamics simulation based on density functional theory is used to study the mechanism for the regeneration of the cis-di(thiocyanato)-bis(2, 2'-bipyridyl-4-carboxylate 4'carboxylic acid)-ruthenium (II) sensitizing dye (N719) by I in acetonitrile. The regeneration process includes the formation of barrier-free complex of the oxidized dye with both I- and I2-, and the dissociation of I2- and I3- from the reduced dye. In addition to this, simulations of the electrolyte electrode interface are also presented which suggests the role of solvent in lowering the recombination process through redox mediator, thereby favoring swift dye regeneration. The results are validated using FTIR-ATR (Fourier Transform Infra Red- Attenuated Total Reflection) spectra.
Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer

Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencing (WES) of cell‐free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, “differential presence of exons” (DPE). We determined differences in levels of 379 exons in plasma cfDNA and used DPE analysis to cluster and classify patients with disseminated and localized disease. The resultant bioinformatics analysis pipeline allowed us to design a predictive DPE algorithm in a small subset of patients that could not be initially classified based on the selection criteria. This DPE suggests that these nucleic acids could be actively released by both tumor and nontumor cells as a means of intercellular communication and might thus play a role in the process of malignant transformation. DPE is a new technique for the study of plasma cfDNA by WES that might have predictive and prognostic value in patients with CRC.
Mollified Impulse Methods for Highly Oscillatory Differential Equations

We introduce a family of impulselike methods for the integration of highly oscillatory second-order differential equations whose forces can be split into a fast part and a slow part. Methods of this family are specified by two weight functions $\phi$, $\psi$; one is used to average positions and the other to mollify the force. When the fast forces are conservative and $\phi=\psi$, the methods here coincide with the mollified impulse methods introduced by Garcia-Archilla, Sanz-Serna, and Skeel. On the other hand, the methods here extend to nonlinear situations a well-known class of exponential integrators introduced by Hairer and Lubich for cases of linear fast forces. A convergence analysis is presented that provides insight into the role played by the processes of mollification and averaging in avoiding order reduction. A simple condition on the weight functions is shown to be both necessary and sufficient to avoid order reduction.
Role of glucotoxicity and lipotoxicity in the pathophysiology of Type 2 diabetes mellitus and emerging treatment strategies

Type 2 diabetes mellitus is a disease characterized by persistent and progressive deterioration of glucose tolerance. Both insulin resistance and impaired insulin secretion contribute to development of Type 2 diabetes. However, whilst insulin resistance is fully apparent in the pre‐diabetic condition, impairment of insulin secretion worsens over the time, being paralleled by a progressive decline in both pancreatic B‐cell function and B‐cell mass. Intense research has identified a number of genetic variants that may predispose to impaired B‐cell function, but such predisposition can be precipitated and worsened by toxic effects of hyperglycaemia (glucotoxicity) and elevated levels of free fatty acids (lipotoxicity). All these aspects of the pathogenesis of Type 2 diabetes are discussed in this review. Moreover, treatments that target reduction in glucotoxicity or lipotoxicity are outlined, including emerging strategies that target the role of glucagon‐like peptide 1 and sodium glucose co‐transporter 2.
Reflective writing as a tool for assessing teamwork in bioscience: Insights into student performance and understanding of teamwork

To ensure a modern bioscience curriculum that responds to the current needs of stakeholders, there is a need to embed a range of generic capabilities that enables graduates to succeed in and contribute to a rapidly changing world, as well as building strong bioscience skills and knowledge. The curriculum must also prepare students for a rapidly evolving competitive work place and align with the needs of industry. This creates a challenge, how do we develop generic capabilities without losing discipline content. This report analyses teamwork projects embedded in an undergraduate Biotechnology degree designed to promote teamwork skills along with a deeper understanding of the underpinning biochemistry. Student reflective writing was used to capture students' understanding and experience of teamwork as well as provide insight into their metacognition. The analysis demonstrates that 73% of Year 3 and 93% of Year 4 students were capable of learning about teamwork through reflective writing. While the importance of frequent high quality communication was a common theme, evidence suggests that many students were unsophisticated in their use of communication software. The analysis also highlighted the depth of metacognition that underpins successful team function and the significant weaknesses in self‐insight some students possess. These findings challenge assumptions regarding student capacity for leadership and the ability of some students to contribute to successful team outcomes. It is essential for the design of teamwork experiences to fully understand the competencies that underlie teamwork, the metacognitive processes required, and ensure that assessments are fair and measure individual academic performance.
Samara: Biologically Inspired Self-Deploying Sensor Networks

The early detection of wildfires with monitoring sensors can improve the effectiveness of fire responders, decreasing the destruction of property and saving lives. However, distributing these sensors across a wide area is an expensive and laborsome task. Furthermore, the cost of the sensors themselves may be high, limiting their practicality in instrumenting large wilderness areas. By integrating aerodynamic structures into the sensor module printed circuit board, a reliable aerial deployment mechanism may be constructed.
Total energy expenditure in underweight patients with severe chronic obstructive pulmonary disease living at home.

AIM The aim of the study was to assess total daily energy expenditure (TDE), as measured by doubly labelled water (DLW), and describe its components in home-living underweight patients with severe chronic obstructive pulmonary disease (COPD). METHODS Basal metabolic rate (BMR) was measured prior to the study. Ten patients received DLW, followed by urine analysis by isotope ratio mass spectrometry from 10 standardised occasions during 15 days. Dietary intake was registered by each patient the first 7 days of the study. The patients were also interviewed about their physical activity pattern. RESULTS Measured BMR was higher than predicted in five of the 10 patients using equations from WHO. Using disease-specific equations, estimated BMR was higher for male, but not for female COPD patients. The best estimation of BMR resulted from prediction including fat-free mass. TDE varied considerably between 5200 and 11,100 kJ. Physical activity level (PAL) ranged from 1.15 to 1.80. Energy intake varied between 4500 and 9100 kJ. In underweight patients with severe COPD, TDE is highly variable, ranging from 110 to 200 kJ/kg body weight. CONCLUSIONS This is the first study assessing and describing total energy expenditure in underweight patients with severe COPD living at home. Energy requirement in the patient group cannot solely be calculated from prediction equations. BMR should be measured and physical activity level assessed.
Automatic Algorithm for Extracting an Ontology for a Specific Domain Name

Scientists use knowledge representation techniques to transfer knowledge from humans to machines. Ontology is the well-known representation technique of transferring knowledge to machines. Creating a new knowledge ontology is a complex task, and most proposed algorithms for creating an ontology from documents have problems in detecting complex concepts and their non-taxonomic relationships. Moreover, previous algorithms are not able to analyze multidimensional context, where each concept might have different meanings. This study proposes a framework that separates the process of finding important concepts from linguistic analysis to extract more taxonomic and non-taxonomic relationships. In this framework, we use a modified version of Term Frequency – Inverse Document Frequency (TF-IDF) weight to extract important concepts from an online encyclopedia. Data mining algorithms like labeling semantic classes are used to connect concepts, categorize attributes, and label them and an online encyclopedia is used to create a structure for the knowledge of the given domain. Part Of Speech tagging (POS) and dependency tree of sentences are used to extract concepts and their relationships (i.e. taxonomic and non-taxonomic). We then evaluate this framework by comparing the results of our framework with an existing ontology in the area of “biochemy”. The results show that the proposed method can detect more detailed information and has better