Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Pelvic Floor Disorders on Sleep Quality in Women

Pelvic floor disorders, the impact of their symptoms, and their association with sleep quality and sleep disorders is a little studied area. The aim of this study was to determine if an association exists between pelvic floor disorders in women and sleep disorders. An observational study was conducted among women in Spain during 2021 and 2022. A self-developed questionnaire was used to collect sociodemographic and employment data, previous medical history and health status, lifestyle and habits, obstetric history, and health problems. A validated questionnaire, the Pittsburgh Sleep Quality Index (PSQI), was used to assess the quality of sleep. The presence and impact of pelvic floor problems was assessed with the Pelvic Floor Distress Inventory (PFDI-20). Odds ratios (OR) and adjusted odds ratios (aOR) with their respective 95% confidence intervals were calculated using logistic regression. A total of 1396 women participated in the study. The total PSQI indicated that 75.36% (1052) of women have altered general sleep quality. Women with pelvic floor disorders have a higher probability of developing sleep alterations (aOR: 1.32; 95% CI: 1.22–1.42; for every 20 points). A high BMI (aOR: 1.04; 95% CI: 1.01–1.07; for each point) and the presence of musculoskeletal disorders (aOR: 3.14; 95% CI: 1.20–8.27) are also associated with sleep quality in women. Women with pelvic floor disorders are more likely to develop sleep disorders, probably due to all the discomfort they entail.
Serum Adenosine Deaminase Level in Iraqi Women with Toxoplasmosis with a History of Abortion

Sixty women who had abortion were selected for this study. Serum was collected from the women. ELISA test was used to detect anti-Toxoplasma specific antibodies. Those women were divided into three groups according to the presence or absence of specific anti-Toxoplasma antibodies. These groups included the women with IgG (18), the women with IgM (14) and the women with both IgG and IgM (12). The other 16 women had no antibodies against Toxoplasma. Twenty-four healthy-looking women had been selected as controls. Serum was collected from those women and tested for anti-Toxoplasma antibodies. Those that revealed any antibody titer against Toxoplasma were excluded from the study. The activity of ADA was determined in the serum according to the method of Giusti. The mean concentration of ADA in the women who had anti-Toxoplasma IgM antibody was significantly higher (P0.05). Since a relationship exists between ADA activity and the cell mediated immune response, this result confirms the fact that Toxoplasma antigen induces T-lymphocytes proliferation.
The Toric Geometry of Triangulated Polygons in Euclidean Space

Abstract Speyer and Sturmfels associated Gröbner toric degenerations $\text{G}{{\text{r}}_{2}}{{({{\mathbb{C}}^{n}})}^{\mathcal{T}}}$ of $\text{G}{{\text{r}}_{2}}{{({{\mathbb{C}}^{n}})}^{{}}}$ with each trivalent tree $\mathcal{T}$ having $n$ leaves. These degenerations induce toric degenerations $M_{r}^{\mathcal{T}}$ of ${{M}_{r}}$ , the space of $n$ ordered, weighted (by $\mathbf{r}$ ) points on the projective line. Our goal in this paper is to give a geometric (Euclidean polygon) description of the toric fibers and describe the action of the compact part of the torus as “bendings of polygons”. We prove the conjecture of Foth and Hu that the toric fibers are homeomorphic to the spaces defined by Kamiyama and Yoshida.
N-methyl-d-aspartate antibody encephalitis: temporal progression of clinical and paraclinical observations in a predominantly non-paraneoplastic disorder of both sexes

Antibodies to the N-methyl-d-aspartate subtype of glutamate receptor have been associated with a newly-described encephalopathy that has been mainly identified in young females with ovarian tumours. However, the full clinical spectrum and treatment responses are not yet clear. We established a sensitive cell-based assay for detection of N-methyl-d-aspartate receptor antibodies in serum or cerebrospinal fluid, and a quantitative fluorescent immunoprecipitation assay for serial studies. Although there was marked intrathecal synthesis of N-methyl-d-aspartate receptor antibodies, the absolute levels of N-methyl-d-aspartate receptor antibodies were higher in serum than in cerebrospinal fluid. N-methyl-d-aspartate receptor antibodies were of the immunoglobulin G1 subclass and were able to activate complement on N-methyl d-aspartate receptor-expressing human embryonic kidney cells. From questionnaires returned on 44 N-methyl-d-aspartate receptor antibody-positive patients, we identified a high proportion without a detected tumour (35/44, 80%: follow-up 3.6–121 months, median 16 months). Among the latter were 15 adult females (43%), 10 adult males (29%) and 10 children (29%), with four in the first decade of life. Overall, there was a high proportion (29%) of non-Caucasians. Good clinical outcomes, as defined by reductions in modified Rankin scores, correlated with decreased N-methyl-d-aspartate receptor antibody levels and were associated with early (<40 days) administration of immunotherapies in non-paraneoplastic patients (P < 0.0001) and earlier tumour removal in paraneoplastic patients (P = 0.02). Ten patients (23%) who were first diagnosed during relapses had no evidence of tumours but had received minimal or no immunotherapy during earlier episodes. Temporal analysis of the onset of the neurological features suggested progression through two main stages. The time of onset of the early features, characterized by neuropsychiatric symptoms and seizures preceded by a median of 10–20 days, the onset of movement disorders, reduction in consciousness and dysautonomia. This temporal dichotomy was also seen in the timing of cerebrospinal fluid, electroencephalographic and in the rather infrequent cerebral imaging changes. Overall, our data support a model in which the early features are associated with cerebrospinal fluid lymphocytosis, and the later features with appearance of oligoclonal bands. The immunological events and neuronal mechanisms underlying these observations need to be explored further, but one possibility is that the early stage represents diffusion of serum antibodies into the cortical grey matter, whereas the later stage results from secondary expansion of the immunological repertoire within the intrathecal compartment acting on subcortical neurons. Four patients, who only had temporal lobe epilepsy without oligoclonal bands, may represent restriction to the first stage.
M5GP: Parallel Multidimensional Genetic Programming with Multidimensional Populations for Symbolic Regression

Machine learning and artificial intelligence are growing in popularity thanks to their ability to produce models that exhibit unprecedented performance in domains that include computer vision, natural language processing and code generation. However, such models tend to be very large and complex and impossible to understand using traditional analysis or human scrutiny. Conversely, Symbolic Regression methods attempt to produce models that are relatively small and (potentially) human-readable. In this domain, Genetic Programming (GP) has proven to be a powerful search strategy that achieves state-of-the-art performance. This paper presents a new GP-based feature transformation method called M5GP, which is hybridized with multiple linear regression to produce linear models, implemented to exploit parallel processing on graphical processing units for efficient computation. M5GP is the most recent variant from a family of feature transformation methods (M2GP, M3GP and M4GP) that have proven to be powerful tools for both classification and regression tasks applied to tabular data. The proposed method was evaluated on SRBench v2.0, the current standard benchmarking suite for Symbolic Regression. Results show that M5GP achieves performance that is competitive with the state-of-the-art, achieving a top-three rank on the most difficult subset of black-box problems. Moreover, it achieves the lowest computation time when compared to other GP-based methods that have similar accuracy scores.
Screening in pregnancy for fetal or neonatal alloimmune thrombocytopenia: systematic review

Please cite this paper as: Kamphuis M, Paridaans N, Porcelijn L, De Haas M, van der Schoot C, Brand A, Bonsel G, Oepkes D. Screening in pregnancy for fetal or neonatal alloimmune thrombocytopenia: systematic review. BJOG 2010;117:1335–1343.
Amplification of cox2 (∼620 bp) from 2 mg of Up to 129 Years Old Herbarium Specimens, Comparing 19 Extraction Methods and 15 Polymerases

During the past years an increasing number of studies have focussed on the use of herbarium specimens for molecular phylogenetic investigations and several comparative studies have been published. However, in the studies reported so far usually rather large amounts of material (typically around 100 mg) were sampled for DNA extraction. This equals an amount roughly equivalent to 8 cm2 of a medium thick leaf. For investigating the phylogeny of plant pathogens, such large amounts of tissue are usually not available or would irretrievably damage the specimens. Through systematic comparison of 19 DNA extraction protocols applied to only 2 mg of infected leaf tissue and testing 15 different DNA polymerases, we could successfully amplify a mitochondrial DNA region (cox2; ∼620 bp) from herbarium specimens well over a hundred years old. We conclude that DNA extraction and the choice of DNA polymerase are crucial factors for successful PCR amplification from small samples of historic herbarium specimens. Through a combination of suitable DNA extraction protocols and DNA polymerases, only a fraction of the preserved plant material commonly used is necessary for successful PCR amplification. This facilitates the potential use of a far larger number of preserved specimens for molecular phylogenetic investigation and provides access to a wealth of genetic information in preserved in specimens deposited in herbaria around the world without reducing their scientific or historical value.
Dissociable Temporal Lobe Activations during Emotional Episodic Memory Retrieval

The richness of human recollective experience is, in part, related to evocation of previously experienced emotions. An extensive functional neuroimaging literature has provided a description of brain regions involved in retrieving emotionally neutral episodic memories. Whether similar or distinct systems are involved in retrieving emotional memories is unresolved. This question motivated the present functional neuroimaging study, using 0-15 positron emission tomography (PET), where we compared patterns of brain activation associated with retrieving previously studied emotional and neutral pictorial material. By varying task requirements and item density we characterized two distinct neural response patterns during emotional memory retrieval. First, we identified an anterior temporal pole activation that reflected the psychological set associated with emotional memory retrieval. Second, we identified a left amygdala response sensitive to actual retrieval of emotional items. These data suggest distinct functional roles for temporal lobe regions during emotional memory retrieval involving context-related tonic anterior temporal pole activation and a phasic item-related amygdala response. We conclude that brain regions involved in episodic memory retrieval reflect not only physical attributes of stimulus material, for example, their verbal or visual qualities, but also their affective significance.
Dissociable effects of surprising rewards on learning and memory

The extent to which rewards deviate from learned expectations is tracked by a signal known as a “reward prediction error”, but it is unclear how this signal interacts with episodic memory. Here, we investigated whether learning in a high-risk environment, with frequent large prediction errors, gives rise to higher fidelity memory traces than learning in a low-risk environment. In Experiment 1, we showed that higher magnitude prediction errors, positive or negative, improved recognition memory for trial-unique items. Participants also increased their learning rate after large prediction errors. In addition, there was an overall higher learning rate in the low-risk environment. Although unsigned prediction errors enhanced memory and increased learning rate, we did not find a relationship between learning rate and memory, suggesting that these two effects were due to separate underlying mechanisms. In Experiment 2, we replicated these results with a longer task that posed stronger memory demands and allowed for more learning. We also showed improved source and sequence memory for high-risk items. In Experiment 3, we controlled for the difficulty of learning in the two risk environments, again replicating the previous results. Moreover, equating the range of prediction errors in the two risk environments revealed that learning in a high-risk context enhanced episodic memory above and beyond the effect of prediction errors to individual items. In summary, our results across three studies showed that (absolute) prediction error magnitude boosted both episodic memory and incremental learning, but the two effects were not correlated, suggesting distinct underlying systems.
Monte Carlo simulation of large electron fields

Two Monte Carlo systems, EGSnrc and Geant4, the latter with two different ‘physics lists,’ were used to calculate dose distributions in large electron fields used in radiotherapy. Source and geometry parameters were adjusted to match calculated results to measurement. Both codes were capable of accurately reproducing the measured dose distributions of the six electron beams available on the accelerator. Depth penetration matched the average measured with a diode and parallel-plate chamber to 0.04 cm or better. Calculated depth dose curves agreed to 2% with diode measurements in the build-up region, although for the lower beam energies there was a discrepancy of up to 5% in this region when calculated results are compared to parallel-plate measurements. Dose profiles at the depth of maximum dose matched to 2–3% in the central 25 cm of the field, corresponding to the field size of the largest applicator. A 4% match was obtained outside the central region. The discrepancy observed in the bremsstrahlung tail in published results that used EGS4 is no longer evident. Simulations with the different codes and physics lists used different source energies, incident beam angles, thicknesses of the primary foils, and distance between the primary and secondary foil. The true source and geometry parameters were not known with sufficient accuracy to determine which parameter set, including the energy of the source, was closest to the truth. These results underscore the requirement for experimental benchmarks of depth penetration and electron scatter for beam energies and foils relevant to radiotherapy.
Willingness and ability to pay for health care: a selection of methods and issues.

Willingness to pay (WTP) is a concept which is being used increasingly to inform policy decisions in the health sector. This paper briefly reviews the reasons why there is more interest in WTP studies and provides some examples of how they have been conducted. The final section of the paper emphasizes the need for caution in interpreting results as the WTP method is still in an experimental stage of development.
Splitting schemes for nonlinear parabolic problems

This thesis is based on five papers, which all analyse different aspects of splitting schemes when applied to nonlinear parabolic problems. These numerical methods are frequently used when a problem has a natural decomposition into two or more parts, as the computational cost may then be significantly decreased compared to other methods. There are two prominent themes in the thesis; the first concerns convergence order analysis, while the second focuses on structure preservation. To motivate the first theme, we note that even if a method has been shown to converge it might be that the speed of convergence is arbitrarily slow. As such a method is unusable in practice we see that it is essential to prove convergence orders. However, those studies that present such error analyses in the fully nonlinear setting typically assume more regularity of the solution than what should be expected. In this context, we present a convergence order analysis for a class of splitting schemes which, importantly, does not require any artificial regularity assumptions. This analysis is carried out in the setting of m-dissipative operators, which includes a large number of interesting problem classes. As demonstrated by the first three papers, the theory can be applied to such diverse problems as nonlinear reaction-diffusion systems, nonlinear parabolic problems with delay, as well as differential Riccati equations. Within the second theme of structure preservation, an in-depth study of operator-valued differential Riccati equations has been carried out. In such equations it is desirable for a numerical method to produce positive semi-definite approximations. Further, it is essential that an implementation can utilize the problem-inherent property of low rank. As shown in the last three papers, both these features are readily satisfied for various splitting schemes. Since these are additionally less costly than existing comparable methods, they constitute a particularly competitive choice for such problems.
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

The advent of next generation sequencing (NGS) has enabled investigations of the gut microbiome with unprecedented resolution and throughput. This has stimulated the development of sophisticated bioinformatics tools to analyze the massive amounts of data generated. Researchers therefore need a clear understanding of the key concepts required for the design, execution and interpretation of NGS experiments on microbiomes. We conducted a literature review and used our own data to determine which approaches work best. The two main approaches for analyzing the microbiome, 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses. Several methods for taxonomic classification of bacterial sequences are discussed. We present simulations to assess the number of sequences that are required to perform reliable appraisals of bacterial community structure. To the extent that fluctuations in the diversity of gut bacterial populations correlate with health and disease, we emphasize various techniques for the analysis of bacterial communities within samples (α-diversity) and between samples (β-diversity). Finally, we demonstrate techniques to infer the metabolic capabilities of a bacteria community from these 16S and shotgun data.
Clathrin Hub Expression Dissociates the Actin‐Binding Protein Hip1R from Coated Pits and Disrupts Their Alignment with the Actin Cytoskeleton

The actin cytoskeleton has been implicated in the maintenance of discrete sites for clathrin‐coated pit formation during receptor‐mediated endocytosis in mammalian cells, and its function is intimately linked to the endocytic pathway in yeast. Here we demonstrate that staining for mammalian endocytic clathrin‐coated pits using a monoclonal antibody against the AP2 adaptor complex revealed a linear pattern that correlates with the organization of the actin cytoskeleton. This vesicle organization was disrupted by treatment of cells with cytochalasin D, which disassembles actin, or with 2,3‐butanedione monoxime, which prevents myosin association with actin. The linear AP2 staining pattern was also disrupted in HeLa cells that were induced to express the Hub fragment of the clathrin heavy chain, which acts as a dominant‐negative inhibitor of receptor‐mediated endocytosis by direct interference with clathrin function. Additionally, Hub expression caused the actin‐binding protein Hip1R to dissociate from coated pits. These findings indicate that proper function of clathrin is required for coated pit alignment with the actin cytoskeleton and suggest that the clathrin–Hip1R interaction is involved in the cytoskeletal organization of coated pits.
Assessment of ischemic penumbra in patients with hyperacute stroke using amide proton transfer (APT) chemical exchange saturation transfer (CEST) MRI

Chemical exchange saturation transfer (CEST)‐derived, pH‐weighted, amide proton transfer (APT) MRI has shown promise in animal studies for the prediction of infarction risk in ischemic tissue. Here, APT MRI was translated to patients with acute stroke (1–24 h post‐symptom onset), and assessments of APT contrast, perfusion, diffusion, disability and final infarct volume (23–92 days post‐stroke) are reported. Healthy volunteers (n = 5) and patients (n = 10) with acute onset of symptoms (0–4 h, n = 7; uncertain onset <24 h, n = 3) were scanned with diffusion‐ and perfusion‐weighted MRI, fluid‐attenuated inversion recovery (FLAIR) and CEST. Traditional asymmetry and a Lorentzian‐based APT index were calculated in the infarct core, at‐risk tissue (time‐to‐peak, TTP; lengthening) and final infarct volume. On average (mean ± standard deviation), control white matter APT values (asymmetry, 0.019 ± 0.005; Lorentzian, 0.045 ± 0.006) were not significantly different (p > 0.05) from APT values in normal‐appearing white matter (NAWM) of patients (asymmetry, 0.022 ± 0.003; Lorentzian, 0.048 ± 0.003); however, ischemic regions in patients showed reduced (p = 0.03) APT effects compared with NAWM. Representative cases are presented, whereby the APT contrast is compared quantitatively with contrast from other imaging modalities. The findings vary between patients; in some patients, a trend for a reduction in the APT signal in the final infarct region compared with at‐risk tissue was observed, consistent with tissue acidosis. However, in other patients, no relationship was observed in the infarct core and final infarct volume. Larger clinical studies, in combination with focused efforts on sequence development at clinically available field strengths (e.g. 3.0 T), are necessary to fully understand the potential of APT imaging for guiding the hyperacute management of patients. Copyright © 2013 John Wiley & Sons, Ltd.
Timing optimization of interconnect by simultaneous net-ordering, wire sizing and spacing

This paper addresses the problem of ordering and sizing parallel wires in a single metal layer within an interconnect channel of a given width, such that cross-capacitances are optimally shared for circuit timing optimization. Using an Elmore delay model including cross capacitances for a bundle of wires, we show that an optimal wire ordering is uniquely determined, such that best timing can be obtained by proper allocation of wire widths and inter-wire spaces. The optimal order, called BMI (balanced monotonic interleaved) depends only on the size of drivers for a wide range of cases. Heuristics are presented for simultaneous ordering, sizing and spacing of wires. Examples for 90-nanometer technology are analyzed and discussed
Reoptimization With the Primal-Dual Interior Point Method

Reoptimization techniques for an interior point method applied to solving a sequence of linear programming problems are discussed. Conditions are given for problem perturbations that can be absorbed in merely one Newton step. The analysis is performed for both short-step and long-step feasible path-following methods. A practical procedure is then derived for an infeasible path-following method. It is applied in the context of crash start for several large-scale structured linear programs. Numerical results with OOPS, a new object-oriented parallel solver, demonstrate the efficiency of the approach. For large structured linear programs, crash start leads to about 40% reduction in the number of iterations and translates into a 25% reduction of the solution time. The crash procedure parallelizes well, and speed-ups between 3.1--3.8 on four processors are achieved.