Miracle-dz/UniFAR-FTUs huggingface dataset:
Adhesive durability of bone cements containing gentamicin or gentamicin/clindamycin-based antibiotics on titanium used for oral implants

Abstract This study investigated the durability of adhesion of bone cements containing antibiotics to titanium. Titanium plates (15 mm × 15 mm × 1 mm) (N = 80, n = 10 per group) were obtained representing oral implants. Half of the titanium plates were air-abraded (30 μm CoJet) (distance: 10 mm; pressure: 2.8 bar; duration: 15 s/cm2) and silanized. They were then randomly divided into two subgroups and chemically polymerized bone cements containing either (a) gentamicin (Refobacin Bone Cement R, Biomet) (GT) or (b) gentamicin/clindamycin (Refobacin Bone Cement Revision, Biomet) (GTC) were bonded to the substrates. Half of the specimens were kept dry and the other half were thermocycled (5–55 °C, 6000 cycles). Shear force was applied to the adhesive interface until failure occurred (0.5 mm/min). Failure types were categorized considering the amount of cement on the substrate. Data (MPa) were analysed using one-, three-way ANOVAs and K-N-S tests (α = 0.05). Two-parameter Weibull modulus, scale (m) and shape (0) were calculated. Surface conditioning (p < 0.01) and ageing (p < 0.01) significantly affected the results, but bone cement did not (p > 0.05). In dry conditions, GT (without: 19.5 ± 2, with: 31.6 ± 1) showed higher bond strength than that of GTC (without: 14.1 ± 1.6, with: 20.4 ± 2.9) (p < 0.01). Thermocycling significantly increased the results for both cements without (GT: 50 ± 3; GTC: 48.6 ± 5.6) and with air-abrasion (GT: 74 ± 1.6; GTC: 76.1 ± 2.4) (p < 0.01). Weibull distribution presented the highest shape (0) for GT (Dry: 12.65; Thermocyled: 17.22). Failure types were predominantly Type 2 (46/80) (Mixed, cement remnants <¼ left on the substrate). Bone cements containing gentamicin may adhere to titanium surface more reliable but both cements benefited from air abrasion and silanization.
Neutral dynamics and cell renewal of colonic crypts in homeostatic regime

The self renewal process in colonic crypts is the object of several studies. We present here a new compartment model with the following characteristics: (a) we distinguish different classes of cells: stem cells, six generations of transit amplifying cells and the differentiated cells; (b) in order to take into account the monoclonal character of crypts in homeostatic regimes we include symmetric divisions of the stem cells. We first consider the dynamic differential equations that describe the evolution of the mean values of the populations, but the small observed value of the total number of cells involved plus the huge dispersion of experimental data found in the literature leads us to study the stochastic discrete process. This analysis allows us to study fluctuations, the neutral drift that leads to monoclonality, and the effects of the fixation of mutant clones.
Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism.
Stochastic Variance Reduced Multiplicative Update for Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF), a dimensionality reduction and factor analysis method, is a special case in which factor matrices have low-rank nonnegative constraints. Considering the stochastic learning in NMF, we specifically address the multiplicative update (MU) rule, which is the most popular, but which has slow convergence property. This present paper introduces on the stochastic MU rule a variance-reduced technique of stochastic gradient. Numerical comparisons suggest that our proposed algorithms robustly outperform state-of-the-art algorithms across different synthetic and real-world datasets.
CALL FOR PAPERS Ion Channels and Transporters in Lung Function and Disease Increased susceptibility of Cftr (cid:2) / (cid:2) mice to LPS-induced lung remodeling

mice ﬁbrosis (CF) is caused by homozygous mutations of the CF transmembrane conductance regulator (CFTR) Cl (cid:2) channel, which result in chronic pulmonary infection and inﬂammation, the major cause of morbidity and mortality. Although these processes are clearly related to each other, each is likely to contribute to the pathology differently. Understanding the contribution of each of these processes to the overall pathology has been difﬁcult, because they are usually so intimately connected. Various CF mouse models have demonstrated abnormal immune responses compared with wild-type (WT) littermates when challenged with live bacteria or bacterial products acutely. However, these studies have not investigated the consequences of persistent inﬂammation on lung tissue in CF mice, which may better model the lung pathology in patients. We characterized the lung pathology and immune response of Cftr (cid:2) / (cid:2) (CF) and Cftr (cid:3) / (cid:3) (WT) mice to chronic administration of Pseudomonas aeruginosa lipopolysaccharide (LPS). We show that, after long-term repeated LPS exposure, CF mice develop an abnormal and persistent immune response, which is associated with more robust structural changes in the lung than those observed in WT mice. Although CF mice and their WT littermates develop lung pathology after chronic exposure to LPS, the inﬂammation and damage resolve in WT mice. However, CF mice do not recover efﬁciently, and, as a consequence of their chronic inﬂammation, CF mice are more susceptible to morphological changes and lung remodeling. This study shows that chronic inﬂammation alone contributes signiﬁcantly to aspects of CF lung pathology.
Effect of material variation on the biomechanical behaviour of orthodontic fixed appliances: a finite element analysis.

INTRODUCTION Biomechanical analysis of orthodontic tooth movement is complex, as many different tissues and appliance components are involved. The aim of this finite element study was to assess the relative effect of material alteration of the various components of the orthodontic appliance on the biomechanical behaviour of tooth movement. METHODS A three-dimensional finite element solid model was constructed. The model consisted of a canine, a first, and a second premolar, including the surrounding tooth-supporting structures and fixed appliances. The materials of the orthodontic appliances were alternated between: (1) composite resin or resin-modified glass ionomer cement for the adhesive, (2) steel, titanium, ceramic, or plastic for the bracket, and (3) β-titanium or steel for the wire. After vertical activation of the first premolar by 0.5mm in occlusal direction, stress and strain calculations were performed at the periodontal ligament and the orthodontic appliance. RESULTS The finite element analysis indicated that strains developed at the periodontal ligament were mainly influenced by the orthodontic wire (up to +63 per cent), followed by the bracket (up to +44 per cent) and the adhesive (up to +4 per cent). As far as developed stresses at the orthodontic appliance are concerned, wire material had the greatest influence (up to +155 per cent), followed by bracket material (up to +148 per cent) and adhesive material (up to +8 per cent). LIMITATIONS The results of this in silico study need to be validated by in vivo studies before they can be extrapolated to clinical practice. CONCLUSION According to the results of this finite element study, all components of the orthodontic fixed appliance, including wire, bracket, and adhesive, seem to influence, to some extent, the biomechanics of tooth movement.
Applying the Longitudinal Model from Item Response Theory to Assess Health-Related Quality of Life in the PRODIGE 4/ACCORD 11 Randomized Trial

Introduction. A new longitudinal statistical approach was compared to the classical methods currently used to analyze health-related quality-of-life (HRQoL) data. The comparison was made using data in patients with metastatic pancreatic cancer. Methods. Three hundred forty-two patients from the PRODIGE4/ACCORD 11 study were randomly assigned to FOLFIRINOX versus gemcitabine regimens. HRQoL was evaluated using the European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30. The classical analysis uses a linear mixed model (LMM), considering an HRQoL score as a good representation of the true value of the HRQoL, following EORTC recommendations. In contrast, built on the item response theory (IRT), our approach considered HRQoL as a latent variable directly estimated from the raw data. For polytomous items, we extended the partial credit model to a longitudinal analysis (longitudinal partial credit model [LPCM]), thereby modeling the latent trait as a function of time and other covariates. Results. Both models gave the same conclusions on 11 of 15 HRQoL dimensions. HRQoL evolution was similar between the 2 treatment arms, except for the symptoms of pain. Indeed, regarding the LPCM, pain perception was significantly less important in the FOLFIRINOX arm than in the gemcitabine arm. For most of the scales, HRQoL changes over time, and no difference was found between treatments in terms of HRQoL. Discussion. The use of LMM to study the HRQoL score does not seem appropriate. It is an easy-to-use model, but the basic statistical assumptions do not check. Our IRT model may be more complex but shows the same qualities and gives similar results. It has the additional advantage of being more precise and suitable because of its direct use of raw data.
Identifying Dyscalculia Symptoms Related to Magnocellular Reasoning Using Smartphones

This paper presents a study that has developed a mobile software application for assisting diagnosis of learning disabilities in mathematics, called dyscalculia, and measuring correlations between dyscalculia symptoms and magnocellular reasoning. Usually, software aids for dyscalculic individuals are focused on both assisting diagnosis and teaching the material. The software developed in this study however maintains a specific focus on the former, and in the process attempts to capture alleged correlations between dyscalculia symptoms and possible underlying causes of the condition. Classification of symptoms is performed by k-Nearest Neighbor algorithm classifying five parameters evaluating user's skills, returning calculated performance in each category as well as correlation strength between detected symptoms and magnocellular reasoning abilities. Expert evaluations has found the application to be appropriate and productive for its intended purpose, proving that mobile software is a suitable and valuable tool for assisting dyscalculia diagnosis and identifying root causes of developing the condition.
Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

Significance Ammonia-oxidizing archaea (AOA), key players in global biogeochemical cycles, represent a heterogeneous group with a broad environmental distribution. Understanding their activity and physiology is of great importance due to the impact of the overuse of agricultural fertilizers on the N cycle and the production of the greenhouse gas N2O during nitrification. Despite their prominent ecological role, little is known about the fundamental metabolic processes of AOA. Here, we show that AOA of marine and terrestrial environments share unique and well-conserved pathways of carbon and nitrogen metabolism, and we raise hypotheses about missing steps in these pathways. Our approach also highlights the extensive environmental adaptations of the soil clade, including the capacity for cell surface modifications, carbohydrate conversions, detoxification, and biofilm formation. Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile “Ca. Nitrosotalea devanaterra” revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and “Ca. Nitrosopelagicus brevis” proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
Care and Feeding of the Endocannabinoid System: A Systematic Review of Potential Clinical Interventions that Upregulate the Endocannabinoid System

Background The “classic” endocannabinoid (eCB) system includes the cannabinoid receptors CB1 and CB2, the eCB ligands anandamide (AEA) and 2-arachidonoylglycerol (2-AG), and their metabolic enzymes. An emerging literature documents the “eCB deficiency syndrome” as an etiology in migraine, fibromyalgia, irritable bowel syndrome, psychological disorders, and other conditions. We performed a systematic review of clinical interventions that enhance the eCB system—ways to upregulate cannabinoid receptors, increase ligand synthesis, or inhibit ligand degradation. Methodology/Principal Findings We searched PubMed for clinical trials, observational studies, and preclinical research. Data synthesis was qualitative. Exclusion criteria limited the results to 184 in vitro studies, 102 in vivo animal studies, and 36 human studies. Evidence indicates that several classes of pharmaceuticals upregulate the eCB system, including analgesics (acetaminophen, non-steroidal anti-inflammatory drugs, opioids, glucocorticoids), antidepressants, antipsychotics, anxiolytics, and anticonvulsants. Clinical interventions characterized as “complementary and alternative medicine” also upregulate the eCB system: massage and manipulation, acupuncture, dietary supplements, and herbal medicines. Lifestyle modification (diet, weight control, exercise, and the use of psychoactive substances—alcohol, tobacco, coffee, cannabis) also modulate the eCB system. Conclusions/Significance Few clinical trials have assessed interventions that upregulate the eCB system. Many preclinical studies point to other potential approaches; human trials are needed to explore these promising interventions.
High Resolution LTCC Laser Processing in the Green and Fired State for Future Technologies

Abstract In this publication the results of laser structuring processes of LTCC substrates, screen printed and laser structured gold thick film lines and the processing procedures are presented. To investigate the compatibility of the laser processes into the conventional LTCC process chain the laser structuring was done in green as well as in fired state. Typical easy electrical patterns like miniaturized interdigital structures and meanders serve as examples of the reached resolution and geometrical borders of the laser structuring techniques at the Center of Micro- and Nanotechnologies of the TU Ilmenau (IMN Macro Nano®). The lateral precision and the topological shape are determined by laser scanning microscopy. The aimed structures have lines and spaces of 30 μm. A statistical evaluation is done to show the possibilities and the limits of the new laser structuring processes with picosecond UV laser ablation systems.
Classroom sound can be used to classify teaching practices in college science courses

Significance Although the United States needs to expand its STEM (science, technology, engineering, mathematics) workforce, United States postsecondary institutions struggle to retain and effectively teach students in STEM disciplines. Using teaching techniques beyond lecture, such as pair discussions and reflective writing, has been shown to boost student learning, but it is unknown what proportion of STEM faculty use these active-learning pedagogies. Here we describe DART: Decibel Analysis for Research in Teaching, a machine-learning–derived algorithm that analyzes classroom sound to predict with high accuracy the learning activities used in classrooms, and its application to thousands of class session recordings. DART can be used for large-scale examinations of STEM teaching practices, evaluating the extent to which educators maximize opportunities for effective STEM learning. Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning–derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.
Evolution and Design Principles of the Diverse Chloroplast Transit Peptides

Chloroplasts are present in organisms belonging to the kingdom Plantae. These organelles are thought to have originated from photosynthetic cyanobacteria through endosymbiosis. During endosymbiosis, most cyanobacterial genes were transferred to the host nucleus. Therefore, most chloroplast proteins became encoded in the nuclear genome and must return to the chloroplast after translation. The N-terminal cleavable transit peptide (TP) is necessary and sufficient for the import of nucleus-encoded interior chloroplast proteins. Over the past decade, extensive research on the TP has revealed many important characteristic features of TPs. These studies have also shed light on the question of how the many diverse TPs could have evolved to target specific proteins to the chloroplast. In this review, we summarize the characteristic features of TPs. We also highlight recent advances in our understanding of TP evolution and provide future perspectives about this important research area.
Frequency of Chromosomal Abnormalities in Products of Conception

Abstract Purpose To describe the frequencies of chromosomal abnormalities found in abortion material, and to observe its correlation to maternal age. Methods A retrospective study was conducted based on data obtained from the databank of a medical genetics laboratory in Belo Horizonte, MG, Brazil. A total of 884 results from products of conception analysis were included, 204 of which were analyzed by cytogenetics, and 680 by molecular biology based on quantitative fluorescence polymerase chain reaction (QF-PCR). The frequency of individual chromosomal aberrations and the relationship between the presence of anomalies and maternal age were also evaluated. Results The conventional cytogenetics technique was able to detect 52% of normal and 48% of abnormal results in the analyzed material. Quantitative fluorescence polymerase chain reaction revealed 60% of normal and 40% of abnormal results from the samples evaluated by this method. The presence of trisomy 15 was detected only by cytogenetics, as it was not included in the QF-PCR routine investigation in the laboratory. A significant increase in abnormal results was observed among women aged 35 years or older compared with younger women (p = 0.02). Conclusion Chromosomal aberrations are still a major cause of spontaneous abortion, and the conventional cytogenetics technique is efficient for miscarriage material analysis, but molecular methods such as QF-PCR are adequate complementary strategies to detect the major chromosomal anomalies, leading to technical reports with reliable results.