Miracle-dz/UniFAR-FTUs huggingface dataset:
Wrong biochemistry results: two case reports and observational study in 5310 patients on potentially misleading thyroid-stimulating hormone and gonadotropin immunoassay results.

BACKGROUND Immunoassays are used in almost all medical and surgical specialties, but they suffer from interference from proteins such as antibodies in some patients' sera. Such interferences are usually reported in the literature only as case reports after the introduction of a new assay. METHODS We undertook a prospective observational study on 5310 patients for whom the common immunoassay tests for thyroid-stimulating hormone (TSH) and/or gonadotropins were requested. All TSH and gonadotropin results were critically assessed for a mismatch between the clinical details and analytical results to identify samples suspected of analytical unreliability. These were tested further by three approaches to screen for interference. RESULTS From the 5310 sets of results, 59 patients' samples were identified as suspect and were tested further. Analytically incorrect results were found in 28 (0.53% of the total studied). The magnitude of interference varied, but in 23 of 28 patients (82%), it was considered large enough to have a potentially adverse effect on cost and/or the clinical care of these patients. Two cases, described in detail, illustrate the adverse effect of error on patient care and cost, and the second highlights the difficulties and limitations of current approaches for identifying interference and inaccuracy in immunoassays. CONCLUSIONS Because millions of TSH/gonadotropin tests are carried out in UK hospital laboratories alone, our data suggest that thousands of patients could be adversely affected by errors from interferences. Early identification of interference in cases with unusual results could be valuable.
Factors related to professional development of English language university teachers in Thailand

Professional development is deemed necessary for university teachers at all levels, as it helps to enhance teaching quality. However, the extent of English language university teachers’ professional development might depend on a number of factors. This paper reports on a study investigating English language university teachers’ professional development in Thailand, the factors related to their development, the activities they used and the obstacles they encountered. The study was conducted through the use of a questionnaire to collect data from 217 full-time English language university teachers at 14 universities in Bangkok metropolis, selected through the multi-stage sampling technique. The results indicate that the overall mean score of Thai university teachers’ professional development was at a moderate level, and the factors of gender, academic title, degree and job responsibility were not related to professional development. Only one factor, university type, was found to be related to their development. This means that private university teachers had more professional development than those in Rajabhat and government universities. Discussing or sharing knowledge with colleagues was the activity they used to develop themselves most, with heavy teaching loads being the main obstacle. In addition, students’ background knowledge was the main obstacle to implementation of the received knowledge in teaching.
Effects of feed supplementation with manganese from its different sources on performance and egg parameters of laying hens

The objective of this study was to compare the effects of feed supplementation of laying hens with manganese from its inorganic and organic sources on performance and some parameters of egg quality. Ninety-six hens at 20 weeks of age were randomly allocated to 4 dietary treatments, each consisting of 6 rep- licates (4 birds per replicate). The control group was fed unsupplemented basal diet (BD) with only natural background Mn level of 46.4 mg/kg feed. For the three experimental treatments, the BD was supplemented with 120 mg Mn/kg either from Mn-sulphate or Mn-chelate of protein hydrolysate (Mn-Pro) or Mn-chelate of glycine hydrate (Mn-Gly). After 8 weeks of dietary treatments the egg production, egg weight, feed intake, and feed efficiency were not affected by dietary treatments. Regardless of the sources, Mn supplementation to feed resulted in significantly decreased percentages of cracked eggs compared to the unsupplemented con- trol group. The thickness, weight, proportion, and index of eggshell were significantly elevated in all groups supplemented with Mn. The intake of Mn-Gly resulted in considerably increased Mn deposition in egg yolk compared to the control eggs. In the control and Mn-sulphate groups yolk malondialdehyde (MDA) started to increase after 20 and 30 days of egg storage respectively, whereas in eggs from hens given organic Mn-sources this parameter was not affected up to 40 days. Although there were no significant differences in MDA values between the treatments until 20 days of storage, the Mn-sulphate group showed significantly higher MDA concentration in yolks compared to the control group after 30 days of storage. These results demonstrate that supplementation of hens' diet with Mn has positive effects on eggshell quality. Feed supplementation with Mn from organic sources appears to be more effective in preventing yolk lipid oxidation during cold storage of eggs than that from Mn-sulphate.
Changes in Chromosomal Localization of Heterochromatin-binding Proteins during the Cell Cycle in Drosophila

We examined the heterochromatic binding of GAGA factor and proliferation disrupter (Prod) proteins during the cell cycle in Drosophila melanogaster and sibling species. GAGA factor binding to the brownD ominant AG-rich satellite sequence insertion was seen at metaphase, however, no binding of GAGA factor to AG-rich sequences was observed at interphase in polytene or diploid nuclei. Comparable mitosis-specific binding was found for Prod protein to its target satellite in pericentric heterochromatin. At interphase, these proteins bind numerous dispersed sites in euchromatin, indicating that they move from euchromatin to heterochromatin and back every cell cycle. The presence of Prod in heterochromatin for a longer portion of the cell cycle than GAGA factor suggests that they cycle between euchromatin and heterochromatin independently. We propose that movement of GAGA factor and Prod from high affinity sites in euchromatin occurs upon condensation of metaphase chromosomes. Upon decondensation, GAGA factor and Prod shift from low affinity sites within satellite DNA back to euchromatic sites as a self-assembly process.
Hill's Criteria for Causality

Despite philosophic criticisms of inductive inference, inductively oriented causal criteria have commonly been used to make such inferences. If a set of necessary and sufficient causal criteria could be used to distinguish causal from noncausal associations in observational studies, the job of the scientist would be eased considerably. With such criteria, all the concerns about the logic or lack thereof in causal inference could be forgotten: it would only be necessary to consult the checklist of criteria to see if a relation were causal. We know from philosophy that a set of sufficient criteria does not exist [3, 6]. Nevertheless, lists of causal criteria have become popular, possibly because they seem to provide a road map through complicated territory. A commonly used set of criteria was proposed by Sir Austin Bradford Hill [1]; it was an expansion of a set of criteria offered previously in the landmark Surgeon General’s report on Smoking and Health [11], which in turn were anticipated by the inductive canons of John Stuart Mill [5] and the rules of causal inference given by Hume [3]. Hill suggested that the following aspects of an association be considered in attempting to distinguish causal from noncausal associations: strength, consistency, specificity, temporality, biologic gradient, plausibility, coherence, experimental evidence, and analogy. The popular view that these criteria should be used for causal inference makes it necessary to examine them in detail:
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam

Transport systems comprise roughly 10% of all proteins in a cell, playing critical roles in many processes. Improving and expanding their classification is an important goal that can affect studies ranging from comparative genomics to potential drug target searches. It is not surprising that different classification systems for transport proteins have arisen, be it within a specialized database, focused on this functional class of proteins, or as part of a broader classification system for all proteins. Two such databases are the Transporter Classification Database (TCDB) and the Protein family (Pfam) database. As part of a long-term endeavor to improve consistency between the two classification systems, we have compared transporter annotations in the two databases to understand the rationale for differences and to improve both systems. Differences sometimes reflect the fact that one database has a particular transporter family while the other does not. Differing family definitions and hierarchical organizations were reconciled, resulting in recognition of 69 Pfam ‘Domains of Unknown Function’, which proved to be transport protein families to be renamed using TCDB annotations. Of over 400 potential new Pfam families identified from TCDB, 10% have already been added to Pfam, and TCDB has created 60 new entries based on Pfam data. This work, for the first time, reveals the benefits of comprehensive database comparisons and explains the differences between Pfam and TCDB.
Frequency and Course of Pure Motor Hemiparesis: A Clinical Study

A review of 850 acute unselected stroke cases at Harlem Hospital found only 25 (3%) who met a clinical definition of pure motor hemiparesis. Compared to other cerebral infarction survivors, the 23 pure motor syndrome survivors were slightly younger, not much more often hypertensive and did not make a faster recovery. The degree of motor deficit a year later was nearly the same in both groups. Brain scans were positive in one-third of the pure motor patients, which suggests that this clinical picture may be associated with larger brain lesions than had been suspected before, as well as with lacunar infarction.
Differential geometric modelling and robust path following control of snake robots using sliding mode techniques

This paper considers straight line path following control of wheel-less planar snake robots using sliding mode techniques. We first derive the Poincaré representation of the equations of motion of the robot using the techniques of differential geometry. Furthermore, we use partial feedback linearization to linearize the directly actuated part of the system dynamics. Subsequently, we propose an analytical solution to the robust path following control problem in two steps. In the first step, we use sliding mode techniques to design a robust tracking controller for the joints of the robot to track a desired gait pattern. In the second step, we stabilize an appropriately defined sliding manifold for the underactuated configuration variables of the robot, thereby guaranteeing convergence of the robot to the desired straight path. The paper presents simulation results which validate the theoretical results.
Protein 3D Structure Computed from Evolutionary Sequence Variation

The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues. , including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.
Graph Based Verification of Software Evolution Requirements

Due to market demands and changes in the environment, software systems have to evolve. However, the size and complexity of the current software systems make it time consuming to incorporate changes. During our collaboration with the industry, we observed that the developers spend much time on the following evolution problems: designing runtime reconfigurable software, obeying software design constraints while coping with evolution, reusing old software solutions for new evolution problems. This thesis presents 3 processes and tool suits that aid the developers/designers when tackling these problems. The first process and tool set allow early verification of runtime reconfiguration requirements. In this process the UML models are converted into a graph-based model. The execution semantics of UML are modeled by graph transformation rules. Using these graph transformation rules, the execution of the UML models is simulated. The simulation generates a state-space showing all possible reconfigurations. The runtime reconfiguration requirements are expressed by computational tree logic or with a visual state-based language, which are verified over the generated state-space. When the verification fails a feedback on the problem is provided. The second process and tool set are developed for computer aided detection of static program constraint violations. We developed a modeling language called Source Code Modeling Language (SCML) in which program elements from the source code can be represented. In the proposed process for constraint violation detection, the source code is converted into SCML models. The constraint detection is realized by graph transformation rules. The rules detect the violation and extract information from the SCML model to provide feedback on the location of the problem. The third process and tool set provide computer aided verification of whether a design idiom can be used to implement a change request. The developers tend to implement evolution requests using software structures that are familiar to them; called design idioms. Graph transformations are used for detecting whether the constraints of the design idiom are satisfied or not. For a given design idiom and given source files in SCML, the implementation of the idiom is simulated. If the simulation succeeds, then the models are converted to source code.
Subjective Well-Being: An Intersection between Economics and Psychology

This thesis uses subjective well-being data to understand the impact that an individual’s economic circumstances have on their well-being. Chapters 2, 3, 4 and 5 look specifically at the role of income on well-being; whilst Chapters 6 and 7 focus on the effect of employment status. This thesis draws heavily on psychological concepts and ideas; highlighting that an interdisciplinary approach to subjective well-being data can have substantial benefits to the study of well-being. Chapter 2 seeks to understand how people compare their incomes with one another. Relative judgment models from psychology are explored and the evidence suggests that individuals may be concerned with their rank position rather than their absolute position or how they compare relative to a mean level. Applying this idea to relative income studies it is shown that an individual’s rank income provides a better explanation of life satisfaction than either absolute income or their income relative to the mean income of those around them. Chapter 3 highlights that although more money may reduce psychological distress it is a relatively inefficient way to do so. This chapter provides medical evidence to suggest that psychological therapy is a more efficient way to reduce psychological distress. Income growth does not appear to increase national well-being in developed countries so this chapter suggests that increasing access to mental health care could be a better way to raise national well-being. Personality, although appropriately controlled for, is mostly ignored by economists researching subjective well-being data. Chapters 4, 5 and 6 therefore explore the use of personality measures in economic subjective well-being research. Chapter 4 proposes a new methodological technique that incorporates personality measures. Chapters 5 and 6 then show that personality interacts with important economic variables. These chapters show that personality is an important aspect to be understood by economists. Chapter 7 demonstrates the importance of using longitudinal data to understand causal effects on well-being. Improvements to occupational status have been argued to lead directly to improvements to health. This argument has been based solely on the cross-sectional association that individuals with high occupational status tend to have better health. Chapter 7 shows that improvements to occupational status actually tend to increase mental strain. Taken altogether these studies suggest that subjective well-being data provides a useful arena in which interdisciplinary research can be conducted.
Conserved and Divergent Patterns of DNA Methylation in Higher Vertebrates

DNA methylation in the genome plays a fundamental role in the regulation of gene expression and is widespread in the genome of eukaryotic species. For example, in higher vertebrates, there is a “global” methylation pattern involving complete methylation of CpG sites genome-wide, except in promoter regions that are typically enriched for CpG dinucleotides, or so called “CpG islands. ” Here, we comprehensively examined and compared the distribution of CpG sites within ten model eukaryotic species and linked the observed patterns to the role of DNA methylation in controlling gene transcription. The analysis revealed two distinct but conserved methylation patterns for gene promoters in human and mouse genomes, involving genes with distinct distributions of promoter CpGs and gene expression patterns. Comparative analysis with four other higher vertebrates revealed that the primary regulatory role of the DNA methylation system is highly conserved in higher vertebrates.
Appropriate global ontology construction: a domain-reference-ontology based approach

Data integration involves combining data residing in different sources and providing users with a unified view of these data through what is called a "global schema". We address here the problem of automatic construction of this global schema in the semantic Web context, where data sources are annotated with ontologies. We aim in other words to automatically build a common vocabulary (ontology) that will serve as a shared conceptual level for several heterogeneous data sources needing to share their data in a specific application domain. We propose a solution based on the use of a domain reference ontology (or "background knowledge") as a mediation support.
ICT and Academic Rigour in Middle Schools: An Australian case study

This project investigated the question: Does using Information and Communication Technology (ICT) as a teaching and learning tool in middle schools make a difference to academic rigour, and if so how? The project on society and environment was conducted at a Perth, Australia metropolitan middle school with two classes each completing two open-ended tasks (in digital and print mode) over two school terms, with the same teacher. Analysis of data showed that students displayed high quality intellectual work using both digital and print modes of learning. Overall the print mode provided greater academic rigour for students than the digital mode. This finding stands in contrast, if not contradiction, to another finding of the study; namely, that students working in digital mode engaged in more social and collaborative interaction and demonstrated more independent problem-solving ability than students working in print mode.
Isolation And Identification Of Active Compound Of Ethylacetate Fraction Of Kasturi ( Mangifera casturi Konsterm . ) Fruit From South Kalimantan Indonesia

Kasturi (Mangifera casturi Konsterm.) is a native plant of Kalimantan and has a chemical compound of potential as a drug. A test was conducted for isolation and identification of the active compound from ethyl acetate fraction of M. casturi fruit. The ethyl acetate fraction was obtained from methanolic extract of M. casturi that was extracted using n-hexane; n-hexane insoluble extract was re-extracted using ethyl acetate (ethyl acetate soluble extract is called ethyl acetate fraction). Isolation and identification of active compound from ethyacetate fraction of M. casturi fruit had been done using liquid liquid extraction method followed by column chromatography. The compound was isolated using column chromatography with n-hexane-ethyl acetate as solvents at gradients of (10:1, 8:2, 6:4, 5:5, 4:6, 2:8) v/v and 100% ethyl acetate. The isolate was white crystal with melting point ranging from 189 190C. Identification of the isolate was conducted with spectroscopic analyses of UV-Vis, FT-IR, HNMR, CNMR, DEPT, and LCMS. The identification found a polyphenol compound, namely, 3,4,5-trihydroxy-benzoic acid methyl ester (methyl gallate).