Miracle-dz/UniFAR-FTUs huggingface dataset:
Psycho-Physiological Associates of Dyspnea in Hospitalized Patients with Interstitial Lung Diseases: A Cross-Sectional Study

Dyspnea has been found to be an independent predictor of mortality among patients with respiratory diseases and is often regarded as a difficult symptom to control in patients with interstitial lung diseases (ILDs). Previous studies have found an association of psychological and physiological factors with dyspnea among patients with chronic obstructive airway diseases. However, symptom management of hospitalized patients with ILDs has been hampered by difficulty in priority, since they are often admitted with multiple psycho-physiological needs. This study examined the prevalence of dyspnea and the psycho-physiological factors associated with it among hospitalized Chinese patients with ILDs. We studied 165 hospitalized patients with ILDs recruited consecutively over three months in a public hospital in Guangzhou, China. Dyspnea and common psycho-physiological factors, including cough symptoms, activity capacity, lung function, physical and mental health status, and anxiety and depression symptoms, were measured. By ordered logistic regression, level of dyspnea statistically significantly affected performance in a six-minute walk test and physical functioning in work or other regular daily activities in hospitalized patients with ILDs. Respiratory rehabilitation with an appropriate intensity of exercise training or other strategies for enhancing the physical functioning of this population with moderate and severe levels of dyspnea should be prioritized.
Matrix Models for Size-Structured Populations: Unrealistic Fast Growth or Simply Diffusion?

Matrix population models are widely used to study population dynamics but have been criticized because their outputs are sensitive to the dimension of the matrix (or, equivalently, to the class width). This sensitivity is concerning for the population growth rate () because this is an intrinsic characteristic of the population that should not depend on the model specification. It has been suggested that the sensitivity of to matrix dimension was linked to the existence of fast pathways (i.e. the fraction of individuals that systematically move up a class), whose proportion increases when class width increases. We showed that for matrix population models with growth transition only from class to class , was independent of the class width when the mortality and the recruitment rates were constant, irrespective of the growth rate. We also showed that if there were indeed fast pathways, there were also in about the same proportion slow pathways (i.e. the fraction of individuals that systematically remained in the same class), and that they jointly act as a diffusion process (where diffusion here is the movement in size of an individual whose size increments are random according to a normal distribution with mean zero). For 53 tree species from a tropical rain forest in the Central African Republic, the diffusion resulting from common matrix dimensions was much stronger than would be realistic. Yet, the sensitivity of to matrix dimension for a class width in the range 1–10 cm was small, much smaller than the sampling uncertainty on the value of . Moreover, could either increase or decrease when class width increased depending on the species. Overall, even if the class width should be kept small enough to limit diffusion, it had little impact on the estimate of for tree species.
Integrating spectral and spatial information into deep convolutional Neural Networks for hyperspectral classification

Deep convolutional neural networks (CNNs) have brought in achievements in image classification and target detection. In this paper, we propose a novel five-layer CNN for hyperspectral classification by encountering recent achievement in deep learning area, such as batch normalization, dropout, Parametric Rectified Linear Unit (PReLu) activation function. By taking advantage of the specific characteristics of hyperspectral images, spatial context and spectral information are elegantly integrated into the framework. Experimental results demonstrate that our proposed CNN out- performs the state-of-the-art methods.
Spatial light modulators in fluorescence microscopy

Spatial light modulators (SLMs) are becoming increasingly important in optical microscopy. These reflective or transmissive devices, based on microdisplays using liquid crystal or micromirror array technology, are used to achieve a variety of useful effects and imaging modes. When placed in an image plane, SLMs can be used to create arbitrary, computer controlled masks. These masks can then be placed in the microscope's illumination pathway, detection pathway, or both. The result is a programmable array microscope (PAM): an optical sectioning microscope with improved speed, sensitivity, and flexibility compared to conventional confocal laser scanning microscopes (CLSMs). Another possibility is structured illumination microscopy (SIM), in which SLMs are used only for illumination. Both high speed optical sectioning and live cell, 3D superresolution can also be achieved via SIM. When placed in an aperture plane, SLMs can manipulate the reflected wavefront. This allows for applications such as adaptive optics.
Parasitoids and hyperparasitoids (Hymenoptera) on aphids (Hemiptera) infesting citrus in east Mediterranean region of Turkey

Abstract The aphids, aphid parasitoids, and hyperparasitoids found in citrus orchards, the parasitoids’ and hyperparasitoids’ seasonal abundance, and the plant–aphid–parasitoid relationships in Hatay, Osmaniye, Adana, and Mersin provinces of the east Mediterranean region of Turkey are presented in the present 2-yr study. Aphidius colemani Viereck, Binodoxys angelicae (Haliday), and Lysiphlebus confusus Tremblay and Eady (Hymenoptera: Braconidae: Aphidiinae) were encountered as the most common parasitoids among 10 identified aphidiine and aphelinid taxa on different citrus species. Hyperparasitoids belonging to the genera Alloxysta , Phaenoglyphis , Asaphes , Pachyneuron , Syrphophagus , and Dendrocerus are reported for the first time emerging from aphids feeding on citrus in Turkey. Among them, Asaphes spp. , Pachyneuron spp. , and Syrphophagus spp. were recorded as the most common ones. Citrus reticulata Blanco and Citrus limon (L.) Burm. fil. were recorded as main hosts for the aphid parasitoids and their hyperparasitoids.
Can We Tell the Site of Origin of Metastatic Squamous Cell Carcinoma? An Immunohistochemical Tissue Microarray Study of 194 Cases

To the workup of metastatic squamous cell carcinoma (SCC) of unknown primary, we studied an immunohistochemical panel including thyroid transcription factor (TTF-1), napsin A, villin, CDX-2, K903, CK5/6, p63, p16, CK7, and CK20. Using tissue microarray, we compared 194 SCC cases from the following sites: 35 lung, 34 skin, 14 cervix, 4 vagina, 16 vulva, 8 penis, 9 anus, 3 rectum, 10 esophagus, 4 bladder/urethra, and 57 SCC from various head and neck sites. p63 and K903 stained positively in 100% of cases, and CK5/6 in nearly 100% of cases, with the exception of 1 lung. CK7 was positive in 31.6% of all cases, with varying positivity according to the site. CK20 was negative in all cases except 1 lung. Napsin A was positive in 25.8% of lung, 7.7% of skin, 37.5% of penis, and 13.3% of tongue, and negative in all other sites. TTF-1 was positive only in 1 lung. p16 positivity ranged from 21.43% in vulva, to 75% in vagina and anus, and it was negative in lung, penis, bladder/urethra, and some head and neck. CDX-2 was negative in all cases except 1 vulva. Villin was negative in all cases. We conclude that immunohistochemistry has very limited value in determining the primary site of metastatic SCC. If lung is in the differential versus head and neck, esophagus, anorectal, or genital SCC, a panel including TTF-1, napsin A and p16 may be helpful, since positive TTF-1 and/or napsin A would favor lung primary, and positive p16 would favor an extrapulmonary site.
Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells

Significance Because structures in the developing embryo are organized by secreted signals, embryonic cells must integrate multiple inputs to turn on the target genes necessary for proper development. Little is known about how multiple signals can work together to regulate such target genes in an embryological context. In this work, we use cultured limb bud mesenchymal cells to investigate how two such signals, Sonic hedgehog (Shh) and fibroblast growth factor 8 (Fgf8), work together to control the activity of Hoxd genes, a set of transcription factors necessary for the patterning of developing tetrapod limbs. During embryonic development, fields of progenitor cells form complex structures through dynamic interactions with external signaling molecules. How complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. In the early limb bud, for instance, Sonic hedgehog (Shh) is expressed in the distal posterior mesenchyme, where it acts as a mediator of anterior to posterior (AP) patterning, whereas fibroblast growth factor 8 (Fgf8) is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud to direct outgrowth along the proximal to distal (PD) axis. Here we use cultured limb mesenchyme cells to assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to activate Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is only partially achieved under these in vitro conditions, suggesting an additional requirement for other factors.
Change in psychotropic drug use in Norwegian nursing homes between 2004 and 2011

ABSTRACT Background: We aimed to assess whether there were any changes in the use of psychotropic drugs in Norwegian nursing homes between 2004 and 2011. Also, we investigated whether the predictors of use of specific psychotropic drug groups have changed. Methods: We conducted a secondary analysis of two cohort studies of two Norwegian nursing home samples (2004/05 and 2010/11). Multivariate models were applied. Results: We found a significant decrease in the prescription of antipsychotic drugs between 2004 and 2011 (0.63 OR, 95%CI = 0.49–0.82, p < 0.001) even after adjusting for relevant demographic and clinical variables. There are only minor changes for the other psychotropic drugs. We found that (1) the use of specific psychotropic drug groups as well as the number of psychotropic drugs used was associated with more affective symptoms and (2) the use of specific psychotropic drug groups as well as the number of psychotropic drugs used was associated with lower scores on the Physical Self-Maintenance scale. Conclusion: This is the first study to show a robust decrease in antipsychotic drug use in nursing home patients with dementia unrelated to possible changes in case mix. The change might be explained by treatment recommendations against its use except in the most severe conditions of aggression or psychosis. Our findings indicate that it takes several years to implement scientific knowledge in clinical practice in nursing homes.
Brain-Behavior Mechanisms for the Transfer of Neuromuscular Training Adaptions to Simulated Sport: Initial Findings From the Train the Brain Project.

CONTEXT A limiting factor for reducing anterior cruciate ligament injury risk is ensuring that the movement adaptions made during the prevention program transfer to sport-specific activity. Virtual reality provides a mechanism to assess transferability, and neuroimaging provides a means to assay the neural processes allowing for such skill transfer. OBJECTIVE To determine the neural mechanisms for injury risk-reducing biomechanics transfer to sport after anterior cruciate ligament injury prevention training. DESIGN Cohort study. SETTING Research laboratory. PARTICIPANTS Four healthy high school soccer athletes. INTERVENTIONS Participants completed augmented neuromuscular training utilizing real-time visual feedback. An unloaded knee extension task and a loaded leg press task were completed with neuroimaging before and after training. A virtual reality soccer-specific landing task was also competed following training to assess transfer of movement mechanics. MAIN OUTCOME MEASURES Landing mechanics during the virtual reality soccer task and blood oxygen level-dependent signal change during neuroimaging. RESULTS Increased motor planning, sensory and visual region activity during unloaded knee extension and decreased motor cortex activity during loaded leg press were highly correlated with improvements in landing mechanics (decreased hip adduction and knee rotation). CONCLUSION Changes in brain activity may underlie adaptation and transfer of injury risk-reducing movement mechanics to sport activity. Clinicians may be able to target these specific brain processes with adjunctive therapy to facilitate intervention improvements transferring to sport.
A novel pH-triggered in situ gel for sustained ophthalmic delivery of ketorolac tromethamine

Purpose: Most eye diseases are treated with topical application of eye drops. The poor bioavailability and therapeutic response exhibited by these conventional eye drops due to rapid precorneal elimination of the drug may be overcome by the use of in situ gelling systems that are instilled as drops into the eye and undergo a sol-to-gel transition in the cul-de-sac. Hence, the purpose of the present work was to formulate and evaluate an ophthalmic delivery system for a nonsteroidal anti-inflammatory drug, ketorolac tromethamine, based on the concept of pH-triggered in situ gelation. Methods: Polyacrylic acid (Carbopol ® 934) was used as the gelling agent in combination with hydroxypropylmethylcellulose (Methocel K4M) which acted as a viscosity enhancing agent. Compatibility studies of the drug excipients were carried out using differential scanning calorimetry (DSC). The prepared formulations were characterized for clarity, pH, drug content, sol-to-gel transition by scanning electron microscopy (SEM), in vitro and in vivo drug release, ocular irritation and stability. Results: The clarity, pH and drug content of the developed formulation were found to be satisfactory. The developed formulation was therapeutically efficacious, stable, non-irritant, and provided sustained drug release over an 8-h period. The formulation with benzalkonium chloride and edetate disodium improved the rate of corneal absorption but not the extent. Conclusions: The developed formulation is a viable alternative to conventional eye drops by virtue of its ability to enhance bioavailability through its longer precorneal residence time and ability to produce sustained drug release. Also important factor is the ease of instillation and the reduced frequency of instillation resulting in better patient acceptance.
Implementation of a disability management policy in a large healthcare employer: a quasi-experimental, mixed-methods evaluation

Objective This study describes the process and outcomes of the implementation of a strengthened disability management policy in a large Canadian healthcare employer. Key elements of the strengthened policy included an emphasis on early contact, the training of supervisors and the integration of union representatives in return-to-work (RTW) planning. Design The study applied mixed methods, combining a process evaluation within the employer and a quasi-experimental outcome evaluation between employers for a 3-year period prior to and following policy implementation in January 2012. Participants Staff in the implementation organisation (n=4000) and staff in a peer group of 29 large hospitals (n=1 19 000). Outcomes Work disability episode incidence and duration. Results Both qualitative and quantitative measures of the implementation process were predominantly positive. Over the 6-year observation period, there were 624 work disability episodes in the organisation and 8604 in the comparison group of 29 large hospitals. The annual per cent change in episode incidence in the organisation was −5.6 (95% CI −9.9 to −1.1) comparable to the annual per cent change in the comparison group: −6.2 (-7.2 to –5.3). Disability episode durations also declined in the organisation, from a mean of 19.4 days (16.5, 22.3) in the preintervention period to 10.9 days (8.7, 13.2) in the postintervention period. Reductions in disability durations were also observed in the comparison group: from a mean of 13.5 days (12.9, 14.1) in the 2009–2011 period to 10.5 days (9.9, 11.1) in the 2012–2014 period. Conclusion The incidence of work disability episodes and the durations of work disability declined strongly in this hospital sector over the 6-year observation period. The implementation of the organisation’s RTW policy was associated with larger reductions in disability durations than observed in the comparison group.
Translating weight loss and physical activity programs into the community to preserve mobility in older, obese adults in poor cardiovascular health.

BACKGROUND Limitations in mobility are common among older adults with cardiovascular and cardiometabolic disorders and have profound effects on health and well-being. With the growing population of older adults in the United States, effective and scalable public health approaches are needed to address this problem. Our goal was to determine the effects of a physical activity and weight loss intervention on 18-month change in mobility among overweight or obese older adults in poor cardiovascular health. METHODS The study design was a translational, randomized controlled trial of physical activity (PA) and weight loss (WL) on mobility in overweight or obese older adults with cardiovascular disease (CVD) or at risk for CVD. The study was conducted within the community infrastructure of Cooperative Extension Centers. Participants were randomized to 1 of 3 interventions: PA, WL + PA, or a successful aging (SA) education control arm. The primary outcome was time to complete a 400-m walk in seconds (400MWT). RESULTS A significant treatment effect (P = .002) and follow-up testing revealed that the WL + PA group improved their 400MWT (adjusted mean [SE], 323.3 [3.7] seconds) compared with both PA (336.3 [3.9] seconds; P = .02) and SA (341.3 [3.9] seconds; P < .001). Participants with poorer mobility at baseline benefited the most (P < .001). CONCLUSION Existing community infrastructures can be effective in delivering lifestyle interventions to enhance mobility in older adults in poor cardiovascular health with deficits in mobility; attention should be given to intervening on both weight and sedentary behavior since weight loss is critical to long-term improvement in mobility. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00119795.
Mechanisms Influencing the Spread of a Native Marine Alga

Like invasive macrophytes, some native macrophytes are spreading rapidly with consequences for community structure. There is evidence that the native alga Caulerpa filiformis is spreading along intertidal rocky shores in New South Wales, Australia, seemingly at the expense of native Sargassum spp. We experimentally investigated the role physical disturbance plays in the spread of C. filiformis and its possible consequences for Sargassum spp. Cleared patches within beds of C. filiformis (Caulerpa habitat) or Sargassum spp. (Sargassum habitat) at multiple sites showed that C. filiformis had significantly higher recruitment (via propagules) into its own habitat. The recruitment of Sargassum spp. to Caulerpa habitat was rare, possibly due in part to sediment accretion within Caulerpa habitat. Diversity of newly recruited epibiotic assemblages within Caulerpa habitat was significantly less than in Sargassum habitat. In addition, more C. filiformis than Sargassum spp. recruited to Sargassum habitat at some sites. On common boundaries between these two macroalgae, the vegetative growth of adjacent C. filiformis into cleared patches was significantly higher than for adjacent Sargassum spp. In both experiments, results were largely independent of the size of disturbance (clearing). Lastly, we used PAM fluorometry to show that the photosynthetic condition of Sargassum spp. fronds adjacent to C. filiformis was generally suppressed relative to those distant from C. filiformis. Thus, physical disturbance, combined with invasive traits (e.g. high levels of recruitment and vegetative growth) most likely facilitate the spread of C. filiformis, with the ramifications being lower epibiotic diversity and possibly reduced photosynthetic condition of co-occurring native macrophytes.
X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification.

X! TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X! TandemPipeline allows the users to launch X! tandem identification, to inspect spectra and to manually validate their assignment to peptides, to launch the grouping program, and to visualize elementary data as well as grouping and redundancy information. Identification results obtained from other search engines can also be processed. X! TandemPipeline results can be exported as ready-to-use tabulated files or as XML files that can be directly used by the PROTICdb database or by the MassChroQ quantification software. X! TandemPipeline runs fast, is easy to use, and can process hundreds of samples simultaneously. It is freely available under the GNU General Public License v3.0 at http://pappso.inra. fr/bioinfo/xtandempipeline/ .
Nutrition activation and dietary intake disparities among US adults

Abstract Objective To introduce the concept ‘nutrition activation’ (the use of health and nutrition information when making food and diet decisions) and to assess the extent to which nutrition activation varies across racial/ethnic groups and explains dietary disparities. Design Cross-sectional sample representative of adults in the USA. Primary outcome measures include daily energy intake and consumption of sugar-sweetened beverages (SSB), fast foods and sit-down restaurant foods as determined by two 24 h dietary recalls. We use bivariate statistics and multiple logistic and linear regression analyses to assess racial/ethnic disparities in nutrition activation and food behaviour outcomes. Setting USA. Subjects Adult participants (n 7825) in the 2007–2010 National Health and Nutrition Examination Survey. Results Nutrition activation varies across racial/ethnic groups and is a statistically significant predictor of SSB, fast-food and restaurant-food consumption and daily energy intake. Based on the sample distribution, an increase from the 25th to 75th percentile in nutrition activation is associated with a decline of about 377 kJ (90 kcal)/d. Increased nutrition activation is associated with a larger decline in SSB consumption among whites than among blacks and foreign-born Latinos. Fast-food consumption is associated with a larger ‘spike’ in daily energy intake among blacks (+1582 kJ (+378 kcal)/d) than among whites (+678 kJ (+162 kcal)/d). Conclusions Nutrition activation is an important but understudied determinant of energy intake and should be explicitly incorporated into obesity prevention interventions, particularly among racial/ethnic minorities.