Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferential methods for comparing a single case with a control sample: modified t‐tests versus mycroft et al.'s (2002) modified anova

Mycroft, Mitchell, and Kay (2002) have criticised existing inferential methods (e.g., Crawford & Howell, 1998) for comparing a single case with a control sample and propose that such comparisons be made using a modified ANOVA. It is argued that the assumptions made by Mycroft et al. are questionable and, even if they held, would not invalidate Crawford and Howell's method. Crawford and Howell's null hypothesis is that the patient is an observation from the control population whereas Mycroft et al.'s null hypothesis is that the control population and a notional population of patients have a common mean. Even if one accepts Mycroft et al.'s conceptualisation, their arguments only have force if (1) the variance of a notional population of patients was larger than that of the control population, and (2) patients with impaired performance were balanced exactly by patients whose performance had been enhanced relative to controls. Furthermore, the modified ANOVA would have the undesirable consequence of reducing statistical power unnecessarily and it requires users to provide some estimate of the variance of a hypothetical population.
The mitochondrial phosphate‐to‐oxygen ratio is not an integer

For many years, mitochondrial phosphate‐to‐oxygen ratios were believed to be integral values: 3 for ATP/NADH and 2 for ATP/FADH2. The chemiosmotic theory has demonstrated that this need not be the case because coupling sites do not directly synthesize ATP. Coupling between coupling site redox reactions and ATP synthesis occurs via proton pumping and proton flow, respectively. Most recent measurements support phosphate‐to‐oxygen ratios of ∼2.5 ATP/NADH and 1.5 ATP/FADH2; these values match those expected from chemiosmotic calculations. Faculty members who teach metabolism are encouraged to reflect these developments in their lecture notes.
In Vitro synthesis and activity of reporter proteins in an Escherichia coli S30 extract system: An undergraduate experiment *

This undergraduate laboratory experiment integrates multiple techniques (in vitro synthesis, enzyme assays, Western blotting) to determine the production and detection sensitivity of two common reporter proteins (β‐galactosidase and luciferase) within an Escherichia coli S30 transcription/translation extract. Comparison of the data suggests that luciferase is the more suitable reporter for this specific in vitro extract system. Simple modifications in the experimental design allow for flexibility in the use of materials and the time required to perform the study. Furthermore, extension into additional experiments and alternative techniques are also discussed.
Dissociable distal and proximal motor components: Evidence from perseverative errors in three apraxic patients

In the present study we analysed the perseverative behaviour of three apraxic patients (FG, CEO, and VCR) while they were pantomiming the use of common objects and during their real use. The three patients were found to perseverate from one trial to later ones aspects of a given action in the pantomiming and in real use tasks. In particular, our main result was a striking double dissociation between patients in perseverating hand and arm movements. Patients FG and CEO made more perseveration errors involving the hand than VCR did, whereas the perseverative errors made by VCR involving the arm were more numerous than those made by FG and CEO. The patients differed also in other aspects of the perseverations, e.g., their median lags. Results are used to exend previous theories developed in the linguistic domain to that of actions.
Tracheal Traction Exercise Reduces the Occurrence of Postoperative Dysphagia After Anterior Cervical Spine Surgery

Study Design. We designed a novel anterior cervical spine surgery preoperative treatment comprising mechanical trachea/esophagus traction and compared the postoperative outcome regarding dysphagia with nontreated patients. Objective. We investigated whether the newly developed preoperative tracheal/esophageal traction exercise (TTE) treatment has an effect on postoperative dysphagia after anterior cervical spine surgery. Summary of Background Data. Dysphagia is a postoperative complication that occurs after anterior cervical spine surgery, and known treatments are perioperative application of methylprednisolone, monitoring of endotracheal tube cuff pressure, and the use of low-profile plates. Methods. We compared the neck disability index, visual analogue scale scores for arm and neck pain, and Bazaz dysphagia scores, a dysphagia index, of 2 randomized groups, 1 week, 3 weeks, 6 weeks, 3 months, and 6 months after cervical spine surgery. One group received TTE treatment for 3 consecutive days before surgery, whereas the control group did not. Results. In the first week after operation, the Bazaz dysphagia scores for patients with second- to fourth-level fusions in the TTE group were significantly better than that in the control group (P = 0.000 for second- and third-level fusions and P = 0.013 for fourth-level fusion). Also at 3 weeks after surgery, the second- to fourth-level fusion patients in the TTE group had better Bazaz scores than those in the control group (P = 0.000 for second- and third-level fusions and P = 0.004 for fourth-level fusion). There was no significant difference of neck disability index and visual analogue scale scores between the 2 groups. Conclusion. Dysphagia could be reduced in patients with multiple-level fusion after anterior cervical spine surgery by preoperative TTE treatment.
Engagement, exploration, explanation, extension, and evaluation (5E) learning cycle and conceptual change text as learning tools

The purpose of this study is to investigate the effects of the Engagement, Exploration, Explanation, Extension, and Evaluation (5E) learning cycle, conceptual change texts, and traditional instructions on 8th grade students' understanding of photosynthesis and respiration in plants. Students' understanding of photosynthesis and respiration in plants was measured using the test developed by Haslam and Treagust (F. Haslam, D. F. Treagust (1987) Diagnosing secondary students' misconceptions of photosynthesis and respiration in plants using a two‐tier multiple choice instrument, J. Biol. Educ. 21, 203–211). The test was administered as pre‐test and post‐test to a total of 101 8th‐grade students in three intact classes of the same school located in an urban area. The classes were randomly assigned as control and experimental groups. Students in the first experimental group (n = 33) received 5E learning cycle instruction, students in the second experimental group (n = 34) received conceptual change text instruction, and students in the control group (n = 34) received traditional instruction. Attitudes toward science and pre‐test scores were used as covariates. A quasi‐experimental design utilizing the analysis of covariance showed a statistically significant difference between the experimental and control groups in the favor of experimental groups after treatment. However, no statistically significant difference between two experimental groups (5E versus conceptual change text instruction) was found.
Team‐teaching a current events‐based biology course for nonmajors

Rice University has created a team‐taught interactive biology course for nonmajors with a focus on cutting edge biology in the news—advances in biotechnology, medicine, and science policy, along with the biological principles and methodology upon which these advances are based. The challenges inherent to teaching current topics were minimized by team‐teaching the course, providing knowledgeable and enthusiastic lecturers for every topic while distributing the effort required to update material. Postdoctoral associates and advanced graduate students served as lecturers, providing an opportunity for them to develop their teaching skills and learn to communicate effectively with nonscientists on newsworthy topics related to their research. Laboratory tours, in‐class demonstrations, and mock‐ups helped lecturers convey surprisingly advanced ideas with students who lacked a strong theoretical or practical science background. A faculty member and co‐coordinator administer the class, organize class activities, and mentor the speakers on teaching techniques and lecture design. Course design, lecture topics, hands‐on activities, and approaches to successfully solve the difficulties inherent to team teaching are discussed. Course evaluations reflect student involvement in, and enjoyment of, the class.
Lentiviral‐mediated gene delivery reveals distinct roles of nucleus accumbens dopamine D2 and D3 receptors in novelty‐ and light‐induced locomotor activity

The importance of the dopaminergic system for proper brain activity is demonstrated by findings that alterations in this system lead to severe disabilities, including motor impairment observed in various neurological and psychiatric disorders. Although the roles of specific dopamine receptors in behaviour have been extensively investigated using pharmacological agents and knockout mice, non‐specificity of ligands and compensatory molecular adaptations in mutated animals restrict the interpretation of the results. To overcome these limitations and further explore the role of the dopamine D2 and D3 receptors (D2R and D3R) in rats, we used lentivirus‐mediated gene knockdown and overexpression to specifically manipulate expression levels of these genes in the rat nucleus accumbens (NAcc), a brain area important for spontaneous and induced locomotor responses. Lentiviruses, inducing expression of rat D2R or D3R, or efficient knockdown of either receptor by small hairpin (sh)RNAs, were stereotaxically injected into the NAcc. While knockdown of either receptor significantly reduced spontaneous locomotor activity in a novel but not in a habituated environment, D2R and D3R appeared to contribute in opposite ways to light‐induced locomotor activity. D2R knockdown increased while D3R knockdown decreased locomotor activity in this test. Altogether, our findings suggest that D2R and D3R, expressed in the NAcc, have both shared and non‐overlapping roles in transduction of alerting signals elicited by potentially important sensory and environmental cues.
From gene mutation to protein characterization

A seven‐week “gene to protein” laboratory sequence is described for an undergraduate biochemistry laboratory course. Student pairs were given the task of introducing a point mutation of their choosing into the well studied protein, enhanced green fluorescent protein (EGFP). After conducting literature searches, each student group chose the mutation they wanted to introduce into EGFP. Students designed their sequence‐specific mutagenic primers and constructed their desired mutation. The resulting EGFP mutant proteins were expressed in E. coli, purified and characterized. This laboratory sequence connected the major concepts of molecular biology and biochemistry, while incorporating the thrill of novel discovery in an undergraduate‐level biochemistry laboratory course.
Food Skills of People with a Chronic Mental Illness: The Need for Intervention

This study quantified the food skills of people with a mental illness living in hospital-based care and the community using the Functional Needs Assessment — Nutritional Management Program (Dombrowski 1990). There were clear and marked food skills deficits among people living in hospital-based care. There were no significant differences between the food skills of male and female participants. The deficits that were identified may place patients at nutritional risk if they are moved into community accommodation without appropriate support mechanisms for the provision of food. Recommendations are made for intervention through the implementation of food skills training and incidental learning.
Altered spatial learning, cortical plasticity and hippocampal anatomy in a neurodevelopmental model of schizophrenia‐related endophenotypes

Adult rats exposed to the DNA‐methylating agent methylazoxymethanol on embryonic day 17 show a pattern of neurobiological deficits that model some of the neuropathological and behavioral changes observed in schizophrenia. Although it is generally assumed that these changes reflect targeted disruption of embryonic neurogenesis, it is unknown whether these effects generalise to other antimitotic agents administered at different stages of development. In the present study, neurochemical, behavioral and electrophysiological techniques were used to determine whether exposure to the antimitotic agent Ara‐C later in development recapitulates some of the changes observed in methylazoxymethanol (MAM)‐treated animals and in patients with schizophrenia. Male rats exposed to Ara‐C (30 mg/kg/day) at embryonic days 19.5 and 20.5 show reduced cell numbers and heterotopias in hippocampal CA1 and CA2/3 regions, respectively, as well as cell loss in the superficial layers of the pre‐ and infralimbic cortex. Birth date labeling with bromodeoxyuridine reveals that the cytoarchitectural changes in CA2/3 are a consequence rather that a direct result of disrupted cortical neurogenesis. Ara‐C‐treated rats possess elevated levels of cortical dopamine and DOPAC (3,4‐didyhydroxypheylacetic acid) but no change in norepinephrine or serotonin. Ara‐C‐treated rats are impaired in their ability to learn the Morris water maze task and showed diminished synaptic plasticity in the hippocampocortical pathway. These data indicate that disruption of neurogenesis at embryonic days 19.5 and 20.5 constitutes a useful model for the comparative study of deficits observed in other gestational models and their relationship to cognitive changes observed in schizophrenia.
The use of an active learning approach to teach metabolism to students of nutrition and dietetics

This article describes the transition from a traditional instructor‐centered course, based on lectures, to a student‐centered course based on active learning methodologies as part of the reform of the Spanish higher education system within the European Higher Education Area (EHEA). Specifically, we describe the use of active learning methodologies to teach metabolism to students of nutrition and dietetics during the first year of their professional training in a 4‐year undergraduate degree (Bachelor of Human Nutrition and Dietetics). In the new course design, the number of didactic lectures was largely reduced and complemented with a series of activities (problems/case studies, discussion workshops, self‐assessment quizzes) aimed to get students actively engaged, to encourage self‐learning, and to promote sustained work throughout the length of the course. The article presents quantitative data demonstrating a clear and significant improvement in students' performance when an active approach was implemented. Importantly, the improved performance was achieved without work overload. Finally, students' responses to this new teaching methodology have been very positive and overall satisfaction high. In summary, our results strongly argue in favor of the teaching model described herein. © 2013 by The International Union of Biochemistry and Molecular Biology, 41(3):131–138, 2013
Human Mitochondrial Genetics

The field of human mitochondrial genetics has advanced way beyond where the Hunlan Genome Project hopes to be by the year 2003, the projected year for completing the sequence of the entire human nuclear DNA genome. Not only has the mitochondrial DNA (JntDNA) been completely sequenced, the regions that code for genes and those that are noncoding have been distinguished, the function of all the genes have been determined, the nltDNA genetic code has been shown to differ in some ways from the Universal Genetic Code of nuclear DNA, and a Ilutnber of diseases have been correlated with specific mitochondrial DNA mutations (http:// infinity.gen.emory.edu/mitomap.htmI). Some of the current areas of research interest with regard to mitochondrial genetics are: examining the variability among individuals or within a single individual (heteroplasmy); distinguishing between polymorphisms and disease-producing mutations; detecting mutations present in low concentrations in an individual; analysing the effects of chemical or physical agents and the mechanisms which lead
Advances in the use of nanoscale bilayers to study membrane protein structure and function

Within the last decade, nanoscale lipid bilayers have emerged as powerful experimental systems in the analysis of membrane proteins (MPs) for both basic and applied research. These discoidal lipid lamellae are stabilized by annuli of specially engineered amphipathic polypeptides (nanodiscs) or polymers (SMALPs/Lipodisqs®). As biomembrane mimetics, they are well suited for the reconstitution of MPs within a controlled lipid environment. Moreover, because they are water-soluble, they are amenable to solution-based biochemical and biophysical experimentation. Hence, due to their solubility, size, stability, and monodispersity, nanoscale lipid bilayers offer technical advantages over more traditional MP analytic approaches such as detergent solubilization and reconstitution into lipid vesicles. In this article, we review some of the most recent advances in the synthesis of polypeptide- and polymer-bound nanoscale lipid bilayers and their application in the study of MP structure and function.
A molecular genetic lab to generate inclusive and exclusive forensic evidence: Two suspects, a victim, and a bloodstained T‐shirt

Molecular genetic laboratory exercises can be ineffective due the student's lack of connection to the complex and sequential protocols. In this inquiry‐based molecular genetic laboratory exercise, we harness students' fascination with human forensics and provide a real‐life scenario using biomolecular techniques to identify “whose blood is on the t‐shirt. ” We use fish blood to create realistic blood stains on clothing and challenge the students to use DNA analyses to clear or implicate suspects. Safety concerns are minimized through the use of fish blood, while maximizing both realism and the likelihood of student success due to fishes' nucleated red blood cells. The goal in designing this laboratory exercise was to create a feasible protocol for large (over 300 students) second year university courses. During two 3 hour laboratory sessions, students learn and apply clean/sterile technique, DNA extraction, polymerase chain reaction, restriction fragment length polymorphisms, and agarose gel electrophoresis. The students also learn to interpret the resulting gel bands in terms of inclusive or exclusive evidence. Students have consistently ranked this lab as their favorite of five taken as part of a second year Genetics course. © 2013 by The International Union of Biochemistry and Molecular Biology, 42(3):XXXXX–XXXXX, 2014.
An undergraduate study of two transcription factors that promote lateral root formation

We present a lab that enables students to test the role of genes involved in the regulation of lateral roots growth in the model plant Arabidopsis thaliana. Here, students design an experiment that follows the effects of the hormone auxin on the stimulation of genes involved in the formation of lateral root initials. These genes, known as lateral organ boundary domain containing protein (LBD) genes, are upregulated in the presence of auxin as part of a multistep molecular and biochemically controlled pathway. Depending on which LBD gene is tested, and the stage of root development, expression patterns are localized in a discrete and punctate fashion at the site of lateral root initials (LBD33), or reveal a broader localization pattern (LBD16). Students view expression using the reporter gene GUS (beta‐glucuronidase). Before GUS staining, students view root growth in a “pseudo‐aseptic” agar‐based environment that allows complete visualization of whole root development to determine the proper stage to test molecular expression. © 2014 by The International Union of Biochemistry and Molecular Biology, 42(3):XXXXX–XXXXX, 2014.
Development of a lateral flow immunoassay strip for screening of sulfamonomethoxine residues

A rapid lateral flow immunoassay screening method has been developed for the determination of sulfamonomethoxine (SMM) residues in swine urine. For this purpose, a specific monoclonal antibody (mAb), SMM4B9 for SMM, was generated and characterized. The mAb showed low cross-reactivity (not larger than 0.3%) to other sulfonamides and other potentially occurring analytes. Based on the competitive immunoassay principle, the strip was developed with the mAb SMM4B9 and applied to the screening of SMM residues. The test strip is made up of a sample pad, a gold-conjugate SMM4B9 reagent pad, a blotted test membrane containing a test line, a control line (a nitrocellulose membrane spotted with SMM-BSA and goat anti-mouse antibody, respectively), and an absorbent pad. The test could be accomplished within 8–10 min. It was shown that the sensitivity of the test strip was as low as 5 ng ml−1 of SMM and the half of maximal inhibition concentration (IC50) was calculated to be 10.78 ± 0.22 ng ml−1 by relative optical density. In unaided visual assessment the detection limit of the strip was 15 ng ml−1. For samples spiked at 20 and 30 ng ml−1 the coefficient of variation (CV (%)) was between 2.3 and 7.1%. When the test strip was compared with high-performance liquid chromatography (HPLC) analysis for naturally contaminated swine urine samples, the difference in results was less than 6.1%. The data suggest that the method has advantages of high sensitivity, specificity, simplicity and speed of performance, as well as the characteristics of repeatability, reproducibility or accuracy and assurance. Therefore, the test strip is suitable to determine SMM residues in swine urine rapidly and reliably by quantitative, semi-quantitative or qualitative detection.
Mycotoxin analysis: An update

Mycotoxin contamination of cereals and related products used for feed can cause intoxication, especially in farm animals. Therefore, efficient analytical tools for the qualitative and quantitative analysis of toxic fungal metabolites in feed are required. Current methods usually include an extraction step, a clean-up step to reduce or eliminate unwanted co-extracted matrix components and a separation step with suitably specific detection ability. Quantitative methods of analysis for most mycotoxins use immunoaffinity clean-up with high-performance liquid chromatography (HPLC) separation in combination with UV and/or fluorescence detection. Screening of samples contaminated with mycotoxins is frequently performed by thin layer chromatography (TLC), which yields qualitative or semi-quantitative results. Nowadays, enzyme-linked immunosorbent assays (ELISA) are often used for rapid screening. A number of promising methods, such as fluorescence polarization immunoassays, dipsticks, and even newer methods such as biosensors and non-invasive techniques based on infrared spectroscopy, have shown great potential for mycotoxin analysis. Currently, there is a strong trend towards the use of multi-mycotoxin methods for the simultaneous analysis of several of the important Fusarium mycotoxins, which is best achieved by LC–MS/MS (liquid chromatography with tandem mass spectrometry). This review focuses on recent developments in the determination of mycotoxins with a special emphasis on LC–MS/MS and emerging rapid methods.