Miracle-dz/UniFAR-FTUs huggingface dataset:
NETT: solving inverse problems with deep neural networks

Recovering a function or high-dimensional parameter vector from indirect measurements is a central task in various scientific areas. Several methods for solving such inverse problems are well developed and well understood. Recently, novel algorithms using deep learning and neural networks for inverse problems appeared. While still in their infancy, these techniques show astonishing performance for applications like low-dose CT or various sparse data problems. However, there are few theoretical results for deep learning in inverse problems. In this paper, we establish a complete convergence analysis for the proposed NETT (network Tikhonov) approach to inverse problems. NETT considers nearly data-consistent solutions having small value of a regularizer defined by a trained neural network. We derive well-posedness results and quantitative error estimates, and propose a possible strategy for training the regularizer. Our theoretical results and framework are different from any previous work using neural networks for solving inverse problems. A possible data driven regularizer is proposed. Numerical results are presented for a tomographic sparse data problem, which demonstrate good performance of NETT even for unknowns of different type from the training data. To derive the convergence and convergence rates results we introduce a new framework based on the absolute Bregman distance generalizing the standard Bregman distance from the convex to the non-convex case.
Understanding Tissue-Specific Gene Regulation

Although all human tissues carry out common processes, tissues are distinguished by gene expres-sion patterns, implying that distinct regulatory programs control tissue-specificity. In this study, we investigate gene expression and regulation across 38 tissues profiled in the Genotype-Tissue Expression project. We find that network edges (transcription factor to target gene connections) have higher tissue-specificity than network nodes (genes) and that regulating nodes (transcription factors) are less likely to be expressed in a tissue-specific manner as compared to their targets (genes). Gene set enrichment analysis of network targeting also indicates that regulation of tissue-specific function is largely independent of transcription factor expression. In addition, tissue-specific genes are not highly targeted in their corresponding tissue-network. However, they do assume bottleneck positions due to variability in transcription factor targeting and the influence of non-canonical regulatory interactions. These results suggest that tissue-specificity is driven by context-dependent regulatory paths, providing transcriptional control of tissue-specific processes.
Assessment of DNA damage in a group of professional dancers during a 10-month dancing season

ABSTRACT Despite the numerous health benefits of physical activity, some studies reported that increased intensity and duration may induce oxidative stress in several cellular components including DNA. The aim of this study was to assess the level of basal DNA damage as well as oxidative DNA damage in a group of professional dancers before and after a 10-month dancing season. A group of individuals from general population was also assessed as a control. The alkaline version of the comet assay was the method selected to measure both basal DNA damage and oxidative stress, since this method quantifies both endpoints. In order to measure oxidative stress, the comet assay was coupled with a lesion-specific endonuclease (formamidopyrimidine glycosylase) to detect oxidized purines. The levels of oxidative DNA damage in dancers were significantly increased after the dancing season. Pre-season levels of oxidative DNA damage were lower in dancers than those obtained from the general population, suggesting an adaptation of antioxidant system in dancers. Results of the present biomonitoring study indicate the need for more effective measures to protect ballet dancers from potentially occupational health risks related to regular intensive physical exercise.
Implicit emotion regulation in adolescent girls: An exploratory investigation of Hidden Markov Modeling and its neural correlates

Numerous data demonstrate that distracting emotional stimuli cause behavioral slowing (i.e. emotional conflict) and that behavior dynamically adapts to such distractors. However, the cognitive and neural mechanisms that mediate these behavioral findings are poorly understood. Several theoretical models have been developed that attempt to explain these phenomena, but these models have not been directly tested on human behavior nor compared. A potential tool to overcome this limitation is Hidden Markov Modeling (HMM), which is a computational approach to modeling indirectly observed systems. Here, we administered an emotional Stroop task to a sample of healthy adolescent girls (N = 24) during fMRI and used HMM to implement theoretical behavioral models. We then compared the model fits and tested for neural representations of the hidden states of the most supported model. We found that a modified variant of the model posited by Mathews et al. (1998) was most concordant with observed behavior and that brain activity was related to the model-based hidden states. Particularly, while the valences of the stimuli themselves were encoded primarily in the ventral visual cortex, the model-based detection of threatening targets was associated with increased activity in the bilateral anterior insula, while task effort (i.e. adaptation) was associated with reduction in the activity of these areas. These findings suggest that emotional target detection and adaptation are accomplished partly through increases and decreases, respectively, in the perceived immediate relevance of threatening cues and also demonstrate the efficacy of using HMM to apply theoretical models to human behavior.
Tuberculosis innovations mean little if they cannot save lives

The past decade has seen the emergence of new diagnostics and drugs for tuberculosis, a disease that kills over 1.8 million people each year. However, these new tools are yet to reach scale, and access remains a major challenge for patients in low and middle income countries. Urgent action is needed if we are committed to ending the TB epidemic. This means raising the level of ambition, embracing innovation, increasing financial investments, addressing implementation gaps, and ensuring that new technologies reach those who need them to survive. Otherwise, the promise of innovative technologies will never be realized. DOI: http://dx.doi. org/10.7554/eLife.25956. 001
Evaluation of the Effect of Tofacitinib on the Pharmacokinetics of Oral Contraceptive Steroids in Healthy Female Volunteers

Tofacitinib is an oral Janus kinase inhibitor. Tofacitinib metabolism is primarily mediated by cytochrome P450 3A4. This phase 1 randomized, open‐label, 2‐way crossover study (NCT01137708) evaluated the effect of tofacitinib 30 mg twice daily on the single‐dose pharmacokinetics of combination oral contraceptives ethinylestradiol (EE) and levonorgestrel (LN). EE and LN were administered as a single Microgynon 30® tablet (30 μg EE and 150 μg LN) to 19 healthy women. In the presence of tofacitinib, the area under the curve from time zero to infinity (AUC∞) increased by 6.6% and 0.9% for EE and LN, respectively. Maximal plasma concentrations decreased by 10.4% for EE and increased by 12.2% for LN when coadministered with tofacitinib. The 90% confidence intervals for the adjusted geometric mean ratios for AUC∞ fell within the 80%–125% region for both EE and LN. Mean half‐life was similar in the presence and absence of tofacitinib: 13.8 and 13.3 hours, respectively, for EE; 25.9 and 25.4 hours, respectively, for LN. Tofacitinib had no clinically relevant net inhibitory or inductive effect on the pharmacokinetics of EE and LN. Therefore, there is no evidence to suggest dose adjustments of oral contraceptive drugs containing EE or LN when coadministered with tofacitinib.
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

MOTIVATION Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer and control samples is still required. RESULTS We propose an algorithm that detects significantly differentially methylated regions in data obtained by targeted bisulfite sequencing approaches, such as reduced representation bisulfite sequencing. In a first step, this approach tests all target regions for methylation differences by taking spatial dependence into account. A false discovery rate procedure controls the expected proportion of incorrectly rejected regions. In a second step, the significant target regions are trimmed to the actually differentially methylated regions. This hierarchical procedure detects differentially methylated regions with increased power compared with existing methods. AVAILABILITY R/Bioconductor package BiSeq. SUPPLEMENTARY INFORMATION Supplementary Data are available at Bioinformatics online.
Towards a new speech event detection approach for landmark-based speech recognition

In this work, we present a new approach for the classification and detection of speech units for the use in landmark or event-based speech recognition systems. We use segmentation to model any time-variable speech unit by a fixed-dimensional observation vector, in order to train a committee of boosted decision stumps on labeled training data. Given an unknown speech signal, the presence of a desired speech unit is estimated by searching for each time frame the corresponding segment, that provides the maximum classification score. This approach improves the accuracy of a phoneme classification task by 1.7%, compared to classification using HMMs. Applying this approach to the detection of broad phonetic landmarks inside a landmark-driven HMM-based speech recognizer significantly improves speech recognition.
Weekly cisplatin and radiotherapy for low risk, locoregionally advanced human papillomavirus–positive oropharyngeal squamous cell carcinoma

There is interest in different treatment strategies, including deintensification in good prognosis human papillomavirus‐positive (HPV(+)) oropharyngeal squamous cell carcinoma (SCC). We reviewed our experience with weekly cisplatin in low‐risk, locoregionally advanced HPV(+) oropharyngeal SCC since late 2009.
The Multilayer Connectome of Caenorhabditis elegans

Connectomics has focused primarily on the mapping of synaptic links in the brain; yet it is well established that extrasynaptic volume transmission, especially via monoamines and neuropeptides, is also critical to brain function and occurs primarily outside the synaptic connectome. We have mapped the putative monoamine connections, as well as a subset of neuropeptide connections, in C. elegans based on new and published gene expression data. The monoamine and neuropeptide networks exhibit distinct topological properties, with the monoamine network displaying a highly disassortative star-like structure with a rich-club of interconnected broadcasting hubs, and the neuropeptide network showing a more recurrent, highly clustered topology. Despite the low degree of overlap between the extrasynaptic (or wireless) and synaptic (or wired) connectomes, we find highly significant multilink motifs of interaction, pinpointing locations in the network where aminergic and neuropeptide signalling modulate synaptic activity. Thus, the C. elegans connectome can be mapped as a multiplex network with synaptic, gap junction, and neuromodulator layers representing alternative modes of interaction between neurons. This provides a new topological plan for understanding how aminergic and peptidergic modulation of behaviour is achieved by specific motifs and loci of integration between hard-wired synaptic or junctional circuits and extrasynaptic signals wirelessly broadcast from a small number of modulatory neurons.
Arterial stiffness and peripheral vascular resistance in offspring of hypertensive parents: influence of sex and other confounders

Aim: Established essential hypertension is associated with increased arterial stiffness and peripheral resistance, but the extent of vascular changes in persons genetically predisposed for essential hypertension is uncertain. Methods: Participants from the Danish Hypertension Prevention Project (DHyPP) (both parents hypertensive) (n = 95, 41 ± 1 years, 53% men) were compared with available spouses (n = 45, 41 ± 1 years) using measurements of ambulatory blood pressure (BP), left ventricular mass index (LVMI), pulse wave velocity, central BP and augmentation index (AIx) in addition to forearm resting and minimal resistance [forearm resting vascular resistance (Rrest) and forearm minimal vascular resistance (Rmin)]. Results: DHyPP patients with participating spouses had higher 24-h mean BP (94 ± 1 vs. 88 ± 1 mmHg, P < 0.01), LVMI (94 ± 3 vs. 80 ± 2 g/m2, P < 0.01), central SBP (121 ± 2 vs. 111 ± 2 mmHg, P < 0.01) and AIx (16.0 ± 1.2 vs. 10.5 ± 1.7%, P < 0.01), but similar carotid–femoral pulse wave velocity (7.5 ± 0.2 vs. 7.1 ± 0.2 m/s), Rrest (53 ± 3 vs. 51 ± 3 mmHg/ml/min/100 ml) and log Rmin (0.58 ± 0.02 vs. 0.55 ± 0.02 mmHg/ml/min/100 ml) when compared with spouses. Using multiple linear regression analysis (adjusting for sex, age, BMI, creatinine clearance and 24-h BP, heart rate and sodium excretion) AIx and LVMI remained elevated in DHyPP patients [4.2% (0.7; 7.7), P = 0.02 and 6.3 g/m2 (0.7; 11.9), P = 0.03]. For the entire DHyPP cohort AIx, Rrest and Rmin were higher in women than men (P < 0.01), and the same was true for AIx and Rmin among spouses (P < 0.05). Furthermore, AIx was linearly associated with Rrest and Rmin. Conclusion: Young to middle-aged individuals genetically predisposed for essential hypertension display increased AIx and LVMI, although vascular stiffness and peripheral resistance are still normal.
Sodium and chloride requirements of young broiler chickens fed corn-soybean diets (one to twenty-one days of age).

Sodium (Na+) and chloride (Cl-) nutritional requirements, dietary electrolyte balance (DEB), and their effects on acid-base balance, litter moisture, and tibial dyschondroplasia (TD) incidence for young broiler chickens were evaluated in two trials. One-day-old Cobb broilers were distributed in a completely randomized design with six treatments, five replicates, and 50 birds per experimental unit. Treatments used in both experiments were a basal diet with 0.10% Na+ (Experiment 1) or Cl- (Experiment 2) supplemented to result in diets with Na+ or Cl- levels of 0.10, 0.15, 0.20, 0.25, 0.30, or 0.35%, respectively. In Experiment 1, results indicated an optimum Na+ requirement of 0.26%. Sodium levels caused a linear increase in arterial blood gas parameters, indicating an alkalogenic effect of Na+. The hypertrophic area of growth plate in the proximal tibiotarsi decreased with Na+ levels. The TD incidence decreased with increases in dietary Na+. Litter moisture increased linearly with sodium levels. In Experiment 2, the Cl- requirement was estimated as 0.25%. Chloride levels caused a quadratic effect (P < or = 0.01) on blood gas parameters, with an estimated equilibrium [blood base excess (BE) = 0] at 0.30% of dietary Cl-. No Cl- treatment effects (P > or = 0.05) were observed on litter moisture or TD incidence. The best DEB for maximum performance was 298 to 315 mEq/kg in Experiment 1 and 246 to 264 mEq/kg in Experiment 2. We concluded that the Na+ and Cl- requirements for optimum performance of young broiler chickens were 0.28 and 0.25%, respectively.
Increased bone strength in coop-reared broilers provided flouridated water.

Four experiments were conducted to determine the feasibility of using fluoride to mitigate bone fragility (osteoporosis) that develops in cage-reared broilers. The treatments consisted of adding sodium fluoride to the drinking water at the levels of 100, 150, 200, and 200 p.p.m. of fluoride in the four experiments, respectively. Birds were transferred from starting batteries at four weeks of age into six coops. Birds in three coops served as controls; birds in the other three coops were provided the fluoridated water ad libitum from four to eight weeks of age. No significant differences were observed in the final body weights between treated and control birds in the four experiments. The percentage of bone ash was usually greater from the treated birds than from the controls. These differences were significant (P less than or equal to 0.01) in the 150 and 200 p.p.m. treatments. At all levels of fluoridation, the strengths of humeri were significantly (P less than or equal to 0.01) increased. However, at the lowest level of fluoridation, 100 p.p.m. , the increase was significant only in the females. Tibia strength was significantly (P less than 0.01) increased only at the 200 p.p.m. level. The increase in bone strength from fluoridation may be sufficiently great enough to result in a decrease in the incidence of bone breakage during the processing of coop-reared boilers.
Influence of virginiamycin on growth and efficiency of large white turkeys.

Efficacy of virginiamycin (22 mg/kg) in combination with no drug, amprolium, carbarsone, halofuginone, or monensin, was studied. Male and female turkeys were raised to market age in five experiments conducted from 1983 to 1987. Body weights and feed:gain responses to virginiamycin for males and females were positive and significant (P less than .05). Virginiamycin resulted in mean 5.2 and 6.3% body weight responses and 3.3 and 2.2% feed:gain responses for males at 19 or 20 wk of age and for females at 16 or 17 wk of age, respectively. Mortality rates were low in all studies, and were not influenced by virginiamycin. In a processing study, virginiamycin in combination with halofuginone did not affect shrinkage, yield, or market grade. Feed was utilized by males and females 3.9 and 3.0%, respectively, more efficiently than expected with dietary virginiamycin, compared with results predicted by a simulation modeling technique. Profitability was considerably greater with dietary virginiamycin using actual data than with simulated feed consumption data.
The Probability Distribution Modeling of Surface Heat Flux Density on Metal Material

In order to get the energy consumption relationship in the heating process of metal material, the probability and statistics law between the temperature distribution and surface heat flux density of heating metal material is established in this paper. Moreover the surface heat flux density distribution of heating metal material is used to associate with its energy consumption. And it builds a new technology method for saving energy control decisions.
Early health technology assessment of future clinical decision rule aided triage of patients presenting with acute chest pain in primary care

The objective of the paper is to estimate the number of patients presenting with chest pain suspected of acute coronary syndrome (ACS) in primary care and to calculate possible cost effects of a future clinical decision rule (CDR) incorporating a point-of-care test (PoCT) as compared with current practice. The annual incidence of chest pain, referrals and ACS in primary care was estimated based on a literature review and on a Dutch and Belgian registration study. A health economic model was developed to calculate the potential impact of a future CDR on costs and effects (ie, correct referral decisions), in several scenarios with varying correct referral decisions. One-way, two-way, and probabilistic sensitivity analyses were performed to test robustness of the model outcome to changes in input parameters. Annually, over one million patient contacts in primary care in the Netherlands concern chest pain. Currently, referral of eventual ACS negative patients (false positives, FPs) is estimated to cost €1,448 per FP patient, with total annual cost exceeding 165 million Euros in the Netherlands. Based on ‘international data’, at least a 29% reduction in FPs is required for the addition of a PoCT as part of a CDR to become cost-saving, and an additional €16 per chest pain patient (ie, 16.4 million Euros annually in the Netherlands) is saved for every further 10% relative decrease in FPs. Sensitivity analyses revealed that the model outcome was robust to changes in model inputs, with costs outcomes mainly driven by costs of FPs and costs of PoCT. If PoCT-aided triage of patients with chest pain in primary care could improve exclusion of ACS, this CDR could lead to a considerable reduction in annual healthcare costs as compared with current practice.
Augmented Reality for teaching spatial relations

unchen, Germany Abstract: This paper describes an approach for increasing the understanding and ease the learning of chemistry for students by visualizing and controlling virtual models of molecules in a intuitive way. With the Help of Augmented Reality, we developed a tool with the name Augmented Chemical Reactions. This program visualizes models of molecules rendered to a camera picture at the position of special markers hold in the hands of the users. The intuitive controlling of the position and orientation of the molecules is done by moving and rotating the markers in front of a camera, so the virtual objects behave as they would have been manipulated themselves. For a better understanding of the subject of chemistry, Augmented Chemical Reactions also shows the dynamic deformation of molecules when they come close to each other. Here the users can have a better view on certain behaviours between molecules. This program has the potential to increase the understanding and ease learning chemistry because of its intuitive controlling of the 3D structure of molecules. In the same way that Augmented Chemical Reactions can help students, it also has the potential to speed up the process of designing new molecules. Scientists can inspect the created molecules and see, if they meet the spatial requirements for specific reactions. This approach prevents time consuming reactions in the laboratory to create those molecules and test them for their desired attributes.