Miracle-dz/UniFAR-FTUs huggingface dataset:
What Factors Influence Women’s Perceptions of their Systemic Recurrence Risk after Breast Cancer Treatment?

Background. Breast cancer patients’ misunderstanding of their systemic cancer recurrence risk has consequences on decision-making and quality of life. Little is known about how women derive their risk estimates. Methods. Using Los Angeles and Georgia’s SEER registries (2014–2015), a random sample of early-stage breast cancer patients was sent surveys about 2 to 3 months after surgery (N = 3930; RR, 68%). We conducted an inductive thematic analysis of open-ended responses about why women chose their risk estimates in a uniquely large sub-sample (N = 1,754). Clinician estimates of systemic recurrence risk were provided for patient sub-groups with DCIS and with low-, intermediate-, and high-risk invasive disease. Women’s perceived risk of systemic recurrence (0% to 100%) was categorized as overestimation, reasonably accurate estimation, or underestimation (0% for invasive disease) and was compared across identified factors and by clinical presentation. Results. Women identified 9 main factors related to their clinical experience (e.g., diagnosis and testing; treatment) and non-clinical beliefs (e.g., uncertainty; spirituality). Women who mentioned at least one clinical experience factor were significantly less likely to overestimate their risk (12% v. 43%, P < 0.001). Most women who were influenced by “communication with a clinician” had reasonably accurate recurrence estimates (68%). “Uncertainty” and “family and personal history” were associated with overestimation, particularly for women with DCIS (75%; 84%). “Spirituality, religion, and faith” was associated with an underestimation of risk (63% v. 20%, P < 0.001). Limitations. The quantification of our qualitative results is subject to any biases that may have occurred during the coding process despite rigorous methodology. Conclusions. Patient-clinician communication is important for breast cancer patients’ understanding of their numeric risk of systemic recurrence. Clinician discussions about recurrence risk should address uncertainty and relevance of family and personal history.
A differential expression of uncoupling protein-2 associates with renal damage in stroke-resistant spontaneously hypertensive rat/stroke-prone spontaneously hypertensive rat-derived stroke congenic lines

Objectives: Uncoupling protein-2 (UCP2), a mitochondrial anion transporter involved in mitochondrial uncoupling, limiting reactive oxygen species formation, is significantly downregulated in kidneys of high-salt-fed stroke-prone spontaneously hypertensive rat (SHRSP), where it associates with increased renal damage occurrence. Methods: We aimed at establishing whether UCP2 differential expression associates with renal damage in two stroke-resistant spontaneously hypertensive rat (SHRSR)/SHRSP-derived stroke congenic lines. For this purpose, SHRSR, SHRSP, and two reciprocal stroke congenic lines carrying the (D1Rat134-Mt1pa) segment of chromosome 1 were fed with Japanese style diet for 8 weeks. At 4, 6, and 8 weeks of Japanese diet, kidneys were removed and analyzed for UCP2 gene and protein expression [UCP2 maps within (D1Rat134-Mt1pa)]; nuclear factor kappa-light-chain-enhancer of activated B cells protein expression; oxidized total protein levels; mitochondrial function; gene expression of cubulin, megalin, and nephrin. At 6 and 8 weeks of Japanese diet, histological damage and percentage of high molecular weight urinary proteins excretion were assessed. Results: Introgression of UCP2 in the SHRSP configuration within the SHRSR genome led to UCP2 downregulation upon Japanese diet, as compared with the SHRSR, with significantly reduced ATP levels, increased rate of inflammation, oxidative stress, renal damage, and excretion of high molecular weight proteins. The opposite phenomena were observed in the reciprocal congenic line, compared with the SHRSP. In vitro, high-NaCl medium led to UCP2 downregulation, increased apoptosis/necrosis, and reduced viability in primary renal proximal tubular epithelial cells isolated from SHRSP. Exposure of the SHRSP/proximal tubular epithelial cells to recombinant UCP2 rescued the high-salt-dependent deleterious effects. Conclusion: A differential UCP2 expression associates with different degree of renal damage upon Japanese diet in two SHRSR/SHRSP-derived stroke congenic lines through modulation of mitochondrial function, inflammation, and oxidative stress.
Are Natural Ingredients Effective in the Management of Hyperpigmentation? A Systematic Review.

BACKGROUND: Hyperpigmentation disorders are commonly encountered in dermatology clinics. Botanical and natural ingredients have gained popularity as alternative depigmenting products. OBJECTIVE: We sought to review clinical studies evaluating the use of different natural products in treating hyperpigmentation so clinicians are better equipped to educate their patients. Specific ingredients reviewed include azelaic acid, aloesin, mulberry, licorice extracts, lignin peroxidase, kojic acid, niacinamide, ellagic acid, arbutin, green tea, turmeric, soy, and ascorbic acid. METHODS: Systematic searches of PubMed and SCOPUS databases were performed in March 2016 using the various ingredient names, "melasma"and "hyperpigmentation. " Two reviewers independently screened titles, leading to the selection of 30 clinical studies. RESULTS: Review of the literature revealed few clinical trials that evaluated the treatment of hyperpigmentation with natural ingredients. Despite the limited evidence-based research, several natural ingredients did show efficacy as depigmenting agents, including azelaic acid, soy, lignin peroxidase, ascorbic acid iontophoresis, arbutin, ellagic acid, licorice extracts, niacinamide, and mulberry. CONCLUSION: The aforementioned ingredients show promise as natural treatments for patients with hyperpigmentation disorders. These agents might also provide clinicians and researchers with a way to further characterize the pathogenesis of dyschromia. However, the paucity of clinical studies is certainly a limitation. Additionally, many of the in-vivo studies are limited by the short length of the trials, and questions remain about the long-term efficacy and safety of the ingredients used in these studies. Lastly, we suggest a standardized objective scoring system be implemented in any further comparative studies.
Telomere Length in the Newborn

Telomere length is similar in different organs of the human fetus but variable among fetuses. During extrauterine life telomere length is highly variable among individuals and longer in women than men. In the present work we addressed the following questions:1) Are there sex-related differences in telomere length at birth? 2) Is there synchrony (i.e. correlation in length) of telomeres in tissues within the newborn? 3) Is the variability in telomere length among newborns as large as that in adults? We studied normal male and female newborns who donated DNA samples from three sources: white blood cells, umbilical artery, and foreskin. Telomere length was measured by the mean length of the terminal restriction fragments (TRF). TRF length was not different between male and female newborns. It was highly synchronized among the DNA samples from white blood cells, umbilical artery and skin within individual donors but exhibited a high variability among donors. We conclude that there is no evidence for the effect of sex on telomere length at birth, suggesting that longer telomeres in women than men arise from a slower rate of telomeric attrition in women. The variability in telomere length among newborns and synchrony in telomere length within organs of the newborn are consistent with the concept that variations in telomere length among adults are in large part attributed to determinants (genetic and environmental) that start exerting their effect in utero.
Reservoir Computing Approaches for Representation and Classification of Multivariate Time Series

Classification of multivariate time series (MTS) has been tackled with a large variety of methodologies and applied to a wide range of scenarios. Reservoir computing (RC) provides efficient tools to generate a vectorial, fixed-size representation of the MTS that can be further processed by standard classifiers. Despite their unrivaled training speed, MTS classifiers based on a standard RC architecture fail to achieve the same accuracy of fully trainable neural networks. In this article, we introduce the reservoir model space, an unsupervised approach based on RC to learn vectorial representations of MTS. Each MTS is encoded within the parameters of a linear model trained to predict a low-dimensional embedding of the reservoir dynamics. Compared with other RC methods, our model space yields better representations and attains comparable computational performance due to an intermediate dimensionality reduction procedure. As a second contribution, we propose a modular RC framework for MTS classification, with an associated open-source Python library. The framework provides different modules to seamlessly implement advanced RC architectures. The architectures are compared with other MTS classifiers, including deep learning models and time series kernels. Results obtained on the benchmark and real-world MTS data sets show that RC classifiers are dramatically faster and, when implemented using our proposed representation, also achieve superior classification accuracy.
The ecology of the microbiome: Networks, competition, and stability

What makes the gut microbiome stable? Classically, we think of our microbiome as stable, benign, and cooperative. Recent experimental work is beginning to unpick essential functions that can be attributed to the stable microbiota of humans. To be able to manipulate the microbiome to improve health, we need to understand community structure and composition and we need models to quantify and predict stability. Coyte et al. applied concepts and tools from community ecology to gut microbiome assembly. Independently developed models converged on a surprising answer: A high diversity of species is likely to coexist stably when the system is dominated by competitive, rather than cooperative, interactions. Science, this issue p. 663 Diversity and competition are more likely than cooperation to lead to gut microbial community stability. The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods. This stability is considered critical for good health but is poorly understood. Here we develop a body of ecological theory to help us understand microbiome stability. Although cooperating networks of microbes can be efficient, we find that they are often unstable. Counterintuitively, this finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability. More generally, stability is promoted by limiting positive feedbacks and weakening ecological interactions. We have analyzed host mechanisms for maintaining stability—including immune suppression, spatial structuring, and feeding of community members—and support our key predictions with recent data.
Distance and Sex Determine Host Plant Choice by Herbivorous Beetles

Background Plants respond to herbivore damage with the release of volatile organic compounds (VOCs). This indirect defense can cause ecological costs when herbivores themselves use VOCs as cues to localize suitable host plants. Can VOCs reliably indicate food plant quality to herbivores? Methodology We determined the choice behavior of herbivorous beetles (Chrysomelidae: Gynandrobrotica guerreroensis and Cerotoma ruficornis) when facing lima bean plants (Fabaceae: Phaseolus lunatus) with different cyanogenic potential, which is an important constitutive direct defense. Expression of inducible indirect defenses was experimentally manipulated by jasmonic acid treatment at different concentrations. The long-distance responses of male and female beetles to the resulting induced plant volatiles were investigated in olfactometer and free-flight experiments and compared to the short-distance decisions of the same beetles in feeding trials. Conclusion Female beetles of both species were repelled by VOCs released from all induced plants independent of the level of induction. In contrast, male beetles were repelled by strongly induced plants, showed no significant differences in choice behavior towards moderately induced plants, but responded positively to VOCs released from little induced plants. Thus, beetle sex and plant VOCs had a significant effect on host searching behavior. By contrast, feeding behavior of both sexes was strongly determined by the cyanogenic potential of leaves, although females again responded more sensitively than males. Apparently, VOCs mainly provide information to these beetles that are not directly related to food quality. Being induced by herbivory and involved in indirect plant defense, such VOCs might indicate the presence of competitors and predators to herbivores. We conclude that plant quality as a food source and finding a potentially enemy-free space is more important for female than for male insect herbivores, whereas the presence of a slightly damaged plant can help males to localize putative mating partners.
Cost-effectiveness of enhanced liver fibrosis test to assess liver fibrosis in chronic hepatitis C virus and alcoholic liver disease patients

AIM To assess liver fibrosis (LF) in hepatitis C virus (HCV) and alcoholic liver disease (ALD), estimate health outcomes and costs of new noninvasive testing strategies METHODS A Markov model was developed to simulate LF progression in HCV and ALD for a cohort of 40-year-old men with abnormal levels of transaminases. Three different testing alternatives were studied: a single liver biopsy; annual Enhanced liver fibrosis (ELF™) followed by liver stiffness measurement (LSM) imaging as a confirmation test if the ELF test is positive; and annual ELF test without LSM. The analysis was performed from the perspective of a university hospital in Spain. Clinical data were obtained from published literature. Costs were sourced from administrative databases of the hospital. Deterministic and probabilistic sensitivity analyses were performed. RESULTS In HCV patients, annual sequential ELF test/LSM and annual ELF test alone prevented respectively 12.9 and 13.3 liver fibrosis-related deaths per 100 persons tested, compared to biopsy. The incremental cost-effectiveness ratios (ICERs) were respectively €13400 and €11500 per quality-adjusted life year (QALY). In ALD, fibrosis-related deaths decreased by 11.7 and 22.1 per 100 persons tested respectively with sequential ELF test/LSM and annual ELF test alone. ICERs were €280 and €190 per QALY, respectively. CONCLUSION The use of the ELF test with or without a confirmation LSM are cost-effective options compared to a single liver biopsy for testing liver fibrosis in HCV and ALD patients in Spain.
GnRH agonist pre-treatment for microwave endometrial ablation in women with less than 1 centimetre myometrial thickness

Abstract We evaluated the efficacy of gonadotropin-releasing hormone agonist (GnRHa) therapy for improving the myometrial thickness in women with thin (less than 1 cm) uterine walls, a contraindication for microwave endometrial ablation (MEA). The normal myometrium thickness was 0.5 cm, 0.7 cm and 0.9 cm. After the third GnRHa dose, the myometrial thickness increased to over 1 cm in all the three patients, and all were able to undergo MEA. The VAS score for menorrhagia improved in all the cases. The patient satisfaction levels were 10 in 2 of the 3 patients, and 5 in the other. There was no symptom recurrence, and no adjuvant therapy was administered. GnRHa therapy in women with submucous leiomyomata and a myometrial thickness of less than 1 cm could effectively thicken the myometrium, allowing for the use of MEA.
THE BALTEX BRIDGE CAMPAIGN: An Integrated Approach for a Better Understanding of Clouds

Clouds affect our daily life in many ways. They dominate our perception of weather and, thus, have an enormous influence on our everyday activities and our health. This fact is completely at odds with our knowledge about clouds, their representation in climate and weather forecast models, and our ability to predict clouds. It is their high variability in time and space that makes clouds both hard to monitor and to model. Clouds are the major concern in the climate modeling community, as stated by the Intergovernmental Panel on Climate Change (IPCC; information available online at www.ipcc.ch) the most urgent scientific problems requiring attention to determine the rate and magnitude of climate change and sea level rise are the factors controlling the distribution of clouds and their radiative characteristics.  A similar conclusion was obtained within the Atmospheric Model Intercomparison Project (AMIP; e.g., Gates et al. 1999). The great challenge of climate research is to correctly account for the fact that the global state of our climate system is largely driven by various small-scale processes and their interaction with each other. Clouds are the most visible examples of this situation. On a global scale, clouds have a strong cooling effect on our climate: more solar radiation is reflected back to space than thermal surface radiation is trapped in the atmosphere. However, because radiation reacts on the instantaneous cloudy atmosphere and not on some climatological mean, the physical processes leading to the overall radiative effect strongly depend on the spatial distribution and structure of clouds.
Convergent and concurrent validity of a report- versus performance-based evaluation of everyday functioning in the diagnosis of cognitive disorders in a geriatric population

ABSTRACT Background: Several methods have been developed to evaluate activities of daily living (ADLs) in mild cognitive impairment (MCI) and mild dementia. This study evaluated the convergent and concurrent validity between (1) two report-based methods (the advanced (a)- and instrumental (i)-ADL tools) and (2) a performance-based method (the Naturalistic Action Test (NAT)) to check if their ability to differentiate between cognitively healthy comparisons (HCs), persons with MCI, and persons with mild Alzheimer's disease (AD) are comparable to each other. Method: This was a cross-sectional study, undertaken in a geriatric day hospital. The participants comprised community-dwelling HCs (n = 21, median age 78.0 years, 61.9% female), MCI (n = 20, median age 79.5 years, 55.0% female), and AD (n = 20, median age 80.0 years, 85.0% female) adults. A diagnostic procedure for neurocognitive disorders was employed. In addition, the a- and i-ADL tools and the NAT were administered separately by blinded raters. Results: The NAT and both the a- and i-ADL tools showed significant differences between HCs, MCI, and AD participants. Convergent validity showed moderate to strong significant correlations between the NAT, and a- and i-ADL tools (range −0.583 to −0.663; p < 0.01). Concurrent validity showed that the NAT (AUC 0.809–1.000) and the a- and i-ADL tools (AUC 0.739–0.964) presented comparable discriminatory accuracy (p = 0.0588). Conclusions: In contrast to prior studies comparing report-based and performance-based methods of assessing ADL, this study indicates that the NAT and the a- and i-ADL tools have strong convergent and concurrent validity, and appear to have similar discriminatory power in differentiating between HCs, MCI, and AD.
Experimental evolution heals the scars of genome-scale recoding

Much of the dramatic plot of Mary Shelley’s Frankenstein resulted from the apparent scars and imperfections of the creature her hero brought to life. Similarly, organisms highly modified by synthetic biologists suffer from scars and imperfect functioning that their creators had not intended. However, as presented in PNAS by Wannier et al. (1), synthetic biologists can use experimental evolution to rapidly heal some of these scars, as they have performed on a highly recoded Escherichia coli strain modified to incorporate efficiently nonstandard amino acids (nsAA). One of the aims of synthetic biology is to expand the range of functions natural organisms can perform. While chemists have created myriads of new molecules over the last centuries, their ability to create complex molecules is surpassed by the biochemistry that evolved within living organisms during billions years of evolution. However, organisms too have their limits, and a large one is that their proteins use a limited set of amino acids. The needs for robust protein encoding and historical contingencies have limited this set to 20 canonical amino acids. However, there appear to be no short-term constraints to have a more diverse pool of amino acids. Synthetic biologists have, therefore, proposed that protein’s biochemical creativity could be unleashed with the incorporation of nsAA (2, 3). These nsAA can provide a finer understanding of protein functions and structures, a precise control on protein activity, or a larger range of functions (4). Several steps are required to introduce a nsAA to the existing set of standard amino acids. For translation to occur, amino acids are charged to their cognate tRNA by aminoacyl-tRNA synthetases (aaRS). Then, when the codon complementary to the anticodon part of the tRNA is exposed in the ribosome, the charged tRNA is loaded and the amino acid is transferred from the … [↵][1]1Email: olivier.tenaillon{at}inserm.fr. [1]: #xref-corresp-1-1
Ultrafiltration of the waste plasma effluent from cardiopulmonary bypass circuit contents processed with a cell-washing device.

Blood conservation methods are commonly practiced throughout most hospitals that conduct cardiothoracic surgery. In an effort to reduce patients' exposure to homologous blood products and due to cost effectiveness of blood conservation techniques, this present study combines autotransfusion of the remaining blood in the extracorporeal circuit and ultrafiltration of the plasma effluent, and describes the resulting product. Seven patients, greater than 19 years of age, requiring cardiopulmonary bypass (CPB) were incorporated into this study. Exclusion criteria included age limitation. At termination of CPB, the remaining blood in the circuit was transferred to an autotransfusion machine and processed. Plasma (1054 +/- 206 ml) effluent was collected directly from the centrifugal bowl and processed through a ultrafiltrator, with a constant flow rate and negative pressure, until the plasma effluent concentrated down to an end processed volume of approximately 150 ml. The following variables were either measured or calculated: plasma-concentrate volumes per three minute interval, inlet/outlet pressures of an ultrafiltrator, transmembrane pressure (TMP), plasma free hemoglobin, fibrinogen, total protein, and colloid osmotic pressure. The average ultrafiltrate volume taken off from the plasma effluent was 828 +/- 237 ml, with an average ultrafiltrate volume of 115 ml in every three minute interval. The TMP did not change over the first 15 minutes of processing but became significantly elevated at the 18th minute interval and continued to increase and reach a maximum TMP of 286.5 +/- 2.1 mmHg at the end of concentration. Fibrinogen levels increased from pre-concentration values of 118.2 +/- 64 to 317 +/- 177 mg/dl (p = .03) along with increases in plasma free hemoglobin from 97.7 +/- 46 to 402.1 +/- 180 mg/dl (p = .0002). The total protein concentration increased by over 330% from baseline values. Ultrafiltrating plasma effluent from autotransfused cell salvaged CPB circuit contents could prove beneficial, but further study is required to discover ways to separate unfavorable products, such as activated platelet-leukocyte products and reduced plasma free hemoglobin, and to lower heparin concentrations of the plasma-concentrate.