Miracle-dz/UniFAR-FTUs huggingface dataset:
Thyroid Autoimmunity and Function after Treatment with Biological Antirheumatic Agents in Rheumatoid Arthritis

With the increased pro-inflammatory response in both rheumatoid arthritis and thyroid autoimmune diseases, treatment with biological antirheumatic agents (BAAs) of the former may affect the course of the latter. In hepatitis C and cancer patients, treatment with biological agents substantially increases the risk of developing thyroid autoimmunity. As the use of BAAs in the treatment of rheumatoid arthritis is increasing, this review aimed to investigate if such use affected thyroid status in rheumatoid arthritis patients. We conducted a systematic literature search and included six studies with a total of 311 patients as well as three case reports. The patients were treated with tumor necrosis factor-α inhibitors (infliximab, etanercept, or adalimumab) or the monoclonal CD20-antibody rituximab. There was a non-significant trend of slight improvement of both thyroid function and autoantibody status: a reduction of thyroid peroxidase and thyroglobulin antibody concentrations, and a reduction of thyrotropin levels in hypothyroid patients. Despite the small number of studies, they presented compliant data. The BAAs used in rheumatoid arthritis thus did not seem to negatively affect thyroid status in patients with rheumatoid arthritis and can be considered safe with regard to thyroid autoimmunity. However, the well-established association between rheumatic diseases and thyroid autoimmunity necessitates continued monitoring of thyroid function in patients with rheumatoid arthritis. Each new BAA should be scrutinized for its effect on thyroid as well as other autoimmune diseases in order to establish concise recommendations for patient follow-up for each agent and each disease.
Integrity of human sperm DNA assessed by the neutral comet assay and its relationship to semen parameters and clinical outcomes for the IVF-ET program

Objective To explore potential relationships between sperm DNA integrity and both semen parameters and clinical outcomes. Methods Semen analysis of 498 samples was performed according to the 2010 criteria of the World Health Organization. The sperm DNA fragmentation Index (DFI) of the semen samples was assessed using a neutral comet assay. Results Sperm DFI showed a significant correlation with semen parameters, including the patient's age, sperm viability, motility, morphology, and number of leukocytes (p<0.05). The sperm DFI values for asthenozoospermic (15.2%), oligoteratozoospermic (18.3%), asthenoteratozoospermic (17.5%), and oligoasthenoteratozoospermic semen samples (21.3%) were significantly higher than that observed in normozoospermic semen samples (10.5%, p<0.05). A sperm DFI value of 14% was used as a threshold of sperm DFI in assessing whether DNA was highly damaged. In 114 IVF-ET cycles, the fertilization rate of the sperm DFI <14% group (70 cycles, 61.7%) was significantly higher than that observed for the ≥14% group (44 cycles, 55.3%), but there was no difference in the other clinical outcomes between the two groups. In the ≥14% group, the pregnancy rates of the ICSI cycles (40.0%) and half-ICSI (44.0%) were higher than conventional IVF cycles (30.7%), but the difference was not statistically significant. Conclusion Along with the conventional semen analysis, the sperm DFI assessed using the comet assay was shown to improve the quality of the semen evaluation. To evaluate the precise effect of ICSI on pregnancy rates in the patients who demonstrate high sperm DFI values, further study is necessary.
Psychosocial Outcomes and Health-Related Quality of Life in Adult Childhood Cancer Survivors: A Report from the Childhood Cancer Survivor Study

Purpose: Psychological outcomes, health-related quality of life (HRQOL), and life satisfaction are compared between 7,147 adult childhood cancer survivors and 388 siblings from the Childhood Cancer Survivor Study, examining demographic and diagnosis/treatment outcome predictors. Methods: Psychological distress, HRQOL, and life satisfaction were measured by the Brief Symptom Inventory-18, the Medical Outcomes Survey Short Form-36, and Cantril Ladder of Life, respectively. A self-report questionnaire provided demographic/health information and medical record abstraction provided cancer/treatment data. Siblings' and survivors' scores were compared using generalized linear mixed models, and predictor effects of demographic and cancer/treatment variables were analyzed by multivariate logistic regression. Results: Although survivors report greater symptoms of global distress (mean, 49.17; SE, 0.12) than do siblings (mean, 46.64; SE, 0.51), scores remain below population norms, indicating that survivors and siblings remain psychologically healthy. Survivors scored worse than siblings on overall physical (51.30 ± 0.10 versus 54.98 ± 0.44; P < 0.001) but not emotional aspects of HRQOL, but effect sizes were small, other than in vitality. Most survivors reported present (mean, 7.3; SD, 0.02) and predicted future (mean, 8.6; SD, 0.02) life satisfaction. Risk factors for psychological distress and poor HRQOL were female gender, lower educational attainment, unmarried status, annual household income <$20,000, unemployment, lack of medical insurance, having a major medical condition, and treatment with cranial radiation. Conclusion: Compared with population norms, childhood cancer survivors and siblings report positive psychological health, good HRQOL, and life satisfaction. The findings identify targeted subgroups of survivors for intervention. (Cancer Epidemiol Biomarkers Prev 2008;17(2):435–46)
Kinematics and dynamics identification of a hyper-redundant, electromagnetically actuated manipulator

To overcome restrictions of passive, flexible endoscopes in technical tasks (e. g. inspection jobs) as well as in medical interventions, such as minimally invasive surgery, a hyper-redundant active shaft concept is proposed. Due to its unique binary, electromagnetic actuation concept it features good resistance with respect to manipulation forces. Thanks to an active control of each element of the hyper-redundant shaft, different shapes (configurations) can be commanded easily. As a matter of fact, the resulting shape and end effector errors highly depend on the accuracy of the kinematic model. Furthermore, a dynamic model - including a description of the electromagnetic behavior - is required to determine necessary individual poweron durations for the capacity discharge in the tilting circuit of the electromagnetic actuators. In this paper, the dynamics and kinematics for the hyperredundant manipulator are determined. A simplified model for the tilting actuator torque is deduced from the electromagnetic behavior. Subsequently, model parameters are identified and evaluated for a prototypical manipulator based on measurements of the end effector movements.
Immunohistochemical analysis of EGFR and HER-2 in patients with metastatic squamous cell carcinoma of the skin.

BACKGROUND Metastatic squamous cell carcinoma (SCC) of the skin often raise difficult therapeutic problems. Few data are available about the expression of EGFR and HER-2 in SCC of the skin. Overexpression of EGFR and of HER-2 proteins has been reported. The purpose of this study was to investigate the expression of EGFR and HER-2 in a series of metastatic SCC of the skin. PATIENTS AND METHODS EGFR and HER-2 expression was studied by immunochemistry on 13 specimens of metastatic recurrence and on 2 primary lesions of these tumours. RESULTS EGFR had a strong membranous expression in all specimens. HER-2 was weakly expressed in 4 specimens, with a membrane expression in 2 cases. CONCLUSION In the present study, EGFR was overexpressed in all samples of metastatic SCCs of the skin. Therefore, these metastatic tumours appear to be suitable targets for treatment with tyrosine kinase inhibitors. Additional studies are warranted to establish whether or not HER-2 is expressed in SCC of the skin.
Mission Optimisation and Multi-Disciplinary Design of Hybrid Unmanned Aerial Systems (UAS) using Advanced Numerical Techniques

This paper describes the theory and practical application of Hierarchical Asynchronous Parallel Multi-objective Evolutionary Algorithms (HAPMOEA) for mission optimisation of Unmanned Aerial Systems (UAS). Optimisation has emerged as a new discipline for UAS in recent years and most of the optimisation efforts are focused on the use of gradient-based techniques. One drawback of these methods is that they are mostly suitable when there is only one objective to be met with or when the objectives are differentiable. A real design or simulation will have more than one objective such as minimising fuel consumption, drag or time to complete the mission. It is usually the case that the problem is highly non-linear and non-differentiable. New techniques are required, and one of such techniques, even though computationally more intensive than gradient-based methods, are Evolutionary Algorithms (EAs). This paper describes an advanced EA methodology and its coupling with simulation analysis tools. Results will indicate the practicality and robustness of the method in finding optimal solutions and Pareto trade-offs between fuel consumption and time to complete the mission of a hybrid UAS by producing a set of non-dominated trajectories and mission from which the designer can choose.
Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)

Abstract Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome‐wide levels of divergence that are comparable among allopatric populations (F st estimate = 0.0042) and sympatric species (F st estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (F st estimate ≈ 0), a very small proportion of F st outlier loci (0.05–0.07%), and remarkably few repeated outliers (1–3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation.
Evaluative Meanings and Disciplinary Values: A Corpus-based Study of Adjective Patterns in Research Articles in Applied Linguistics and Business Studies

The purpose of this study is to investigate disciplinary variation in academic writing, focusing in particular on the use of adjective patterns followed by prepositions. The analysis proceeds through a detailed quantitative and qualitative analysis of these patterns in two large corpora of authentic texts. The analysis focuses not only on the specific adjectives found in the patterns themselves, but also on collocations within and around each pattern. The empirical focus of the study will be on two ‘soft-applied’ disciplines (Becher and Trowler 2001), applied linguistics and business studies, as represented by two corpora of research articles drawn from 16 leading journals in each field. Comparison of the results for each corpus shows that there are many differences in form and meaning between the two disciplines: it is argued that the features revealed by my analysis are indicative of the epistemological characteristics of these two different disciplinary discourses. These differences reveal the particular culture and norm of applied linguistics and business studies.
Genome-Wide Association Study of Septoria tritici Blotch Resistance in Ethiopian Durum Wheat Landraces

Septoria tritici blotch (STB) is a devastating fungal disease affecting durum and bread wheat cultivation worldwide. The identification, development, and employment of resistant wheat genetic material is the key to overcoming costs and limitations of fungicide treatments. The search for resistance sources in untapped genetic material may speed up the deployment of STB genetic resistance in the field. Ethiopian durum wheat landraces represent a valuable source of such diversity. In this study, 318 Ethiopian durum wheat genotypes, for the most part traditional landraces, were phenotyped for resistance to different aspects of STB infection. Phenology, yield and yield component traits were concurrently measured the collection. Here we describe the distribution of STB resistance traits in modern varieties and in landraces, and the relation existing between STB resistance and other agronomic traits. STB resistance sources were found in landraces as well as in modern varieties tested, suggesting the presence of alleles of breeding relevance. The genetic material was genotyped with more than 16 thousand genome-wide polymorphic markers to describe the linkage disequilibrium and genetic structure existing within the panel of genotypes, and a genome-wide association (GWA) study was run to allow the identification of genomic loci involved in STB resistance. High diversity and low genetic structure in the panel allowed high efficiency GWA. The GWA scan detected five major putative QTL for STB resistance, only partially overlapping those already reported in the wheat literature. We report four putative loci for Septoria resistance with no match in previous literature: two highly significant ones on Chr 3A and 5A, and two suggestive ones on Chr 4B and 5B. Markers underlying these QTL explained as much as 10% of the phenotypic variance for disease resistance. We found three cases in which putative QTL for agronomic traits overlapped marker trait association deriving from STB GWA. Our results show that the Ethiopian untapped allelic diversity bears a great value in studying the molecular basis of STB resistance and in breeding for resistance in local and international material.
Normwerte und altersabhängige Veränderungen magnetoelektrisch evozierter Muskelsummenpotentiale

A number of 57 normal subjects was investigated using transcranial magnetic stimulation of the motor cortex and transcutaneous magnetic stimulation of the spinal nerve root in order to obtain normative data for central and peripheral motor latencies. Under standardized conditions (site of stimulation, stimulus intensity, degree of voluntary tonic background activation) muscle compound action potentials were recorded from different muscles of the upper and lower extremity: M. biceps brachii, M. extensor carpi radialis, M. interosseus dorsalis I, M. vastus medialis, M. tibialis anterior, and M. extensor digitorum brevis. Onset latency, peak to peak amplitude (% of maximal M-wave), duration and configuration of the muscle compound action potentials were evaluated (Fig. 1 and Tab. 1-6). Central and peripheral motor latencies were determined by stimulation over two different points of the neuraxis (cortex/cervical or lumbar nerve roots). Central motor latencies were calculated by subtracting the peripheral conduction time from the onset latency of the fastest cortically evoked muscle response. Not only the peripheral but also the central motor latencies were found to increase in higher ages (Tab. 6). This has to be taken into account when elderly patients are examined for diagnosis of disorders of the descending motor tracts.
AEROTRIANGULATION AND DEM/ORTHOPHOTO GENERATION FROM HIGH-RESOLUTION STILL-VIDEO IMAGERY

This paper presents two practical studies on the helicopter-based use of a high-resolution digital still-video camera for digital aerotriangulation and the automatic generation of digital elevation models and orthophotos. Test regions were an alpine village and a landslide area in Switzerland. The current performance and future developments of solid-state matrix sensors are shown, and the advantages and disadvantages of the use of digital cameras in aerial applications are discussed. Using self-calibration techniques, externally verified accuracies of 2 cm for planimetry coordinates and 5 to 6 cm for height coordinates were obtained in digital aerotriangulation using imagery of 1.20,000 scale, and a precision of 0.03 percent of the flying height above ground could be achieved for digital elevation models.
What do Neural Machine Translation Models Learn about Morphology?

Neural machine translation (MT) models obtain state-of-the-art performance while maintaining a simple, end-to-end architecture. However, little is known about what these models learn about source and target languages during the training process. In this work, we analyze the representations learned by neural MT models at various levels of granularity and empirically evaluate the quality of the representations for learning morphology through extrinsic part-of-speech and morphological tagging tasks. We conduct a thorough investigation along several parameters: word-based vs. character-based representations, depth of the encoding layer, the identity of the target language, and encoder vs. decoder representations. Our data-driven, quantitative evaluation sheds light on important aspects in the neural MT system and its ability to capture word structure.
Polymicrobial Sepsis Alters Antigen-Dependent and -Independent Memory CD8 T Cell Functions

Mortality from sepsis frequently results from secondary infections, and the extent to which sepsis affects pathogen-specific memory CD8 T cell responses remains unknown. Using the cecal ligation and puncture model of polymicrobial sepsis, we observed rapid apoptosis of pre-existing memory CD8 T cells after sepsis induction that led to a loss in CD8 T cell–mediated protection. Ag sensitivity (functional avidity) and Ag-driven secondary expansion of memory CD8 T cells were decreased after sepsis, further contributing to the observed loss in CD8 T cell–mediated immunity. Moreover, Ag-independent bystander activation of memory CD8 T cells in response to heterologous infection was also significantly impaired early after sepsis induction. The reduced sensitivity of pre-existing memory CD8 T cells to sense inflammation and respond to heterologous infection by IFN-γ production was observed in inbred and outbred hosts and controlled by extrinsic (but not cell-intrinsic) factors, suggesting that sepsis-induced changes in the environment regulate innate functions of memory CD8 T cells. Taken together, the data in this study revealed a previously unappreciated role of sepsis in shaping the quantity and functionality of infection- or vaccine-induced memory CD8 T cells and will help further define the decline in T cell–mediated immunity during the sepsis-induced phase of immunosuppression.
Structural and functional correlates of synaptic transmission in the vertebrate neuromuscular junction.

Because vertebrate neuromuscular junctions are readily accessible for experimental manipulation, they have provided a superb model in which to examine and test functional correlates of chemical synaptic transmission. In the neuromuscular synapse, acetylcholine receptors have been localized to the crests of the junctional folds and visualized by a variety of ultrastructural techniques. By using ultrarapid freezing techniques with a temporal resolution of less than 1 msec, quantal transmitter release has been correlated with synaptic vesicle exocytosis at discrete sites called "active zones. " Mechanisms for synaptic vesicle membrane retrieval and recycling have been identified by using immunological approaches and correlated with endocytosis via coated pits and coated vesicles. In this review, available ultrastructural, physiological, immunological, and biochemical data have been used to construct an ultrastructural model of neuromuscular synaptic transmission that correlates structure and function at the molecular level.
Ion Mobility Spectrometry–Mass Spectrometry Analysis for the Site of Aromatic Hydroxylation

Hydroxylated metabolites often retain the pharmacological activity of parent compound, and the position of hydroxylation determines the formation of chemically reactive intermediates, such as quinones and analogs, from para- and/or ortho-hydroxylation of phenols or arylamines. Therefore, the identification of exact position of hydroxylation is often required at the early development stage of new drug candidates. In many cases, liquid chromatography–tandem mass spectrometry (LC-MS/MS) provides identical MS/MS spectra among isomeric hydroxylated metabolites, and therefore, it alone cannot unequivocally identify the exact position(s) of hydroxylation. Ion mobility spectrometry (IMS), integrated with LC-MS/MS, recently showed the capability of separating isomeric species based on differences in their drift times from IMS, which are linearly proportional to the collision cross-section (CCS) reflecting physical size and shape. In the present study, a chemical derivatization of isomeric hydroxylated metabolites with 2-fluoro-N-methyl pyridinium p-toluenesulfonate was found to confer distinct theoretical CCS value on each isomer by forming corresponding N-methyl pyridine (NMP) derivative. The regression lines established by the comparison between theoretical CCS values and observed drift times from IMS for each set of parent compound (labetalol, ezetimibe, atorvastatin, and warfarin) and its MS/MS product ions accurately and selectively projected the actual drift times of NMP derivatives of corresponding aromatic or isomeric hydroxylated metabolites. The established method was used for the accurate assignment of predominant formation of 2-hydroxylated metabolite from imipramine in NADPH- fortified human liver microsomes. The present application expands the versatility of LC-IMS-MS technique to the structure identification of isomeric hydroxylated metabolites at the early stage for drug development.
How meta-analysis increases statistical power.

One of the most frequently cited reasons for conducting a meta-analysis is the increase in statistical power that it affords a reviewer. This article demonstrates that fixed-effects meta-analysis increases statistical power by reducing the standard error of the weighted average effect size (T.) and, in so doing, shrinks the confidence interval around T. Small confidence intervals make it more likely for reviewers to detect nonzero population effects, thereby increasing statistical power. Smaller confidence intervals also represent increased precision of the estimated population effect size. Computational examples are provided for 3 effect-size indices: d (standardized mean difference), Pearson's r, and odds ratios. Random-effects meta-analyses also may show increased statistical power and a smaller standard error of the weighted average effect size. However, the authors demonstrate that increasing the number of studies in a random-effects meta-analysis does not always increase statistical power.