Miracle-dz/UniFAR-FTUs huggingface dataset:
Harmonin in the murine retina and the retinal phenotypes of Ush1c-mutant mice and human USH1C.

PURPOSE To investigate the expression of harmonin in the mouse retina, test for ultrastructural and physiological mutant phenotypes in the retina of an Ush1c mutant mouse, and define in detail the retinal phenotype in human USH1C. METHODS Antibodies were generated against harmonin. Harmonin isoform distribution was examined by Western blot analysis and immunocytochemistry. Retinas of deaf circler (dfcr) mice, which possess mutant Ush1c, were analyzed by microscopy and electroretinography (ERG). Two siblings with homozygous 238_239insC (R80fs) USH1C mutations were studied with ERG, perimetry, and optical coherence tomography (OCT). RESULTS Harmonin isoforms a and c, but not b are expressed in the retina. Harmonin is concentrated in the photoreceptor synapse where the majority is postsynaptic. Dfcr mice do not undergo retinal degeneration and have normal synaptic ultrastructure and ERGs. USH1C patients had abnormal rod and cone ERGs. Rod- and cone-mediated sensitivities and retinal laminar architecture were normal across 50 degrees -60 degrees of visual field. A transition zone to severely abnormal function and structure was present at greater eccentricities. CONCLUSIONS The largest harmonin isoforms are not expressed in the retina. A major retinal concentration of harmonin is in the photoreceptor synapses, both pre- and post-synaptically. The dfcr mouse retina is unaffected by its mutant Ush1c. Patients with USH1C retained regions of normal central retina surrounded by degeneration. Perhaps the human disease is simply more aggressive than that in the mouse. Alternatively, the dfcr mouse may be a model for nonsyndromic deafness, due to the nonpathologic effect of its mutation on the retinal isoforms.
Gene expression profiles of the meniscus avascular phenotype: A guide for meniscus tissue engineering

Avascular (Avas) meniscus regeneration remains a challenge, which is partly a consequence of our limited knowledge of the cells that maintain this tissue region. In this study, we utilized microarrays to characterize gene expression profiles of intact human Avas meniscus tissue and of cells following culture expansion. Using these data, we examined various 3D culture conditions to redifferentiate Avas cells toward the tissue phenotype. RNA was isolated from either the tissue directly or following cell isolation and 2 weeks in monolayer culture. RNA was hybridized on human genome arrays. Differentially expressed (DE) genes were identified by ranking analysis. DAVID pathway analysis was performed and visualized using STRING analysis. Quantitative PCR (qPCR) on additional donor menisci (tissues and cells) were used to validate array data. Avas cells cultured in 3D were subjected to qPCR to compare with the array‐generated data. A total of 387 genes were DE based on differentiation state (>3‐fold change; p < 0.01). In Avas‐cultured cells, the upregulated pathways included focal adhesion, ECM‐receptor interaction, regulation of actin cytoskeleton, and PDGF Signaling. In 3D‐cultured Avas cells, TGFβ1 or combinations of TGFβ1 and BMP6 were most effective to promote an Avas tissue phenotype. THBS2 and THBS4 expression levels were identified as a means to denote meniscus cell phenotype status. We identified the key gene expression profiles, new markers and pathways involved in characterizing the Avas meniscus phenotype in the native state and during in vitro dedifferentiation and redifferentiation. These data served to screen 3D conditions to generate meniscus‐like neotissues. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1947–1958, 2018.
Characteristics and outcomes of lymphoblastic lymphoma – the University of Miami experience

Juan Pablo Alderuccio, Pooja Amarapurkar, Jennifer R. Chapman, Francisco Vega and Izidore S. Lossos Department of Medicine, Division of Hematology–Oncology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Medicine, Division of Internal Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Pathology and Laboratory Medicine, Division of Hematopathology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
HDAC inhibitors show differential epigenetic regulation and cell survival strategies on p53 mutant colon cancer cells

Besides inactivating tumour suppressor activity in cells, mutations in p53 confer significant oncogenic functions and promote metastasis and resistance to anticancer therapy. A variety of therapies involving genetic and epigenetic signalling events regulate tumorogenesis and progression in such cases. Pharmacological interventions with HDAC inhibitors have shown promise in therapy. This work explores the changes in efficacy of the four HDAC inhibitors SAHA, MS-275, valproic acid and sodium butyrate on a panel of colon cancer cell lines – HCT116 (p53 wt), HCT116 p53-/-, HT29 and SW480 (with mutations in p53). Clonogenic assays, gene profiling and epigenetic expression done on these cells point to p53 dependent differential activity of the 4 HDAC inhibitors which also elevate methylation levels in p53 mutant cell lines. In silico modelling establishes the alterations in interactions that lead to such differential activity of valproic acid, one of the inhibitors considered for the work. Molecular Dynamic simulations carried out on the valproic acid complex ensure stability of the complex. This work establishes a p53 dependent epigenetic signalling mechanism triggered by HDAC inhibition expanding the scope of HDAC inhibitors in adjuvant therapy for p53 mutant tumours.
Effectiveness of a 16-Week High-Intensity Cardioresistance Training Program in Adults

Abstract Greenlee, TA, Greene, DR, Ward, NJ, Reeser, GE, Allen, CM, Baumgartner, NW, Cohen, NJ, Kramer, AF, Hillman, CH, and Barbey, AK. Effectiveness of a 16-week high-intensity cardioresistance training program in adults. J Strength Cond Res 31(9): 2528–2541, 2017—The purpose of this study was to determine the efficacy of a novel, 16-week high-intensity cardioresistance training (HICRT) program on measures of aerobic fitness, agility, aerobic power, muscular endurance, lower-body explosive power, and self-reported activity level. The intervention group (N = 129; 63 f, 24.65 ± 5.55 years) had a baseline V̇o2max of 39.83 ± 9.13. These individuals participated in 26, 70-minute exercise sessions, and 4 fitness testing sessions. Participants were matched with a nonexercise control group, paired by sex, age, and baseline V̇o2max. Matched controls (N = 129, 63 f, 24.26 ± 5.59 years) had a baseline V̇o2max of 39.86 ± 8.59 and completed preintervention and postintervention V̇o2max testing only. The results demonstrate that participants in the fitness intervention group significantly increased their V̇o2max (2.72 ± 0.31, Mdiff ± SE; p < 0.001) and reported being more physically active (0.42 ± 0.11, Mdiff ± SE; p < 0.001) after the intervention. The matched control group showed no significant pre–post intervention changes. Participants in the fitness intervention showed a significant improvement in 3 of 5 components of the fitness field tests. Specifically, significant improvements were observed for the 1-minute rower (5.32 ± 0.505, Mdiff ± SE; p < 0.001), 1-minute push-up (8.168 ± 0.709, Mdiff ± SE; p < 0.001), and 1.5-mile run tests (1.79 ± 0.169, Mdiff ± SE; p < 0.001). No significant improvements were observed for the shuttle run (p = 0.173) or standing long jump (p = 0.137). These findings demonstrate the efficacy of a novel, HICRT intervention across multiple dimensions of fitness for young- and middle-aged adults. High-intensity cardioresistance training affords flexibility for tailoring to meet desired health and fitness outcomes and makes perceivably daunting high-intensity functional training and multimodal sports training more accessible to general, traditionally nonathletic, populations.
MRI findings of neuronal ceroid lipofuscinosis in a cat

Case summary A 2-year-old male domestic shorthair cat presented to the University of Liverpool Small Animal Teaching Hospital with a 2 week history of altered mentation, blindness and focal epileptic seizures. MRI examination revealed generalised cerebral and cerebellar atrophy, diffuse T2-weighted hyperintensity of the white matter and meningeal thickening. Neuronal ceroid lipofuscinosis was confirmed on post-mortem examination. Relevance and novel information This is the first report of the MRI findings of neuronal ceroid lipofuscinosis in a cat.
Reduction of the Instrument Model Error in Aperture Synthesis Radiometers

Aperture synthesis radiometers measure the visibilities of the scene under observation by an antenna array, and based on these visibility measurements, inverse algorithm is employed to reconstruct the brightness temperature of the observed scene. The instrument model plays a key role in the inverse problem and its error will degrade the reconstruction accuracy. This work provides an analysis of the impact of the instrument model error on the reconstruction accuracy and a method regarding how to reduce its impact. It will be demonstrated in this work that the point spread functions (PSFs) of the imaging system at different spatial locations are highly correlated with each other, but the PSF errors are not. Benefit from this fact, the PSF can be represented as a sum of basis functions obtained from principal component analysis of PSF. It can be observed that most of the energy of the true PSF is concentrated on the first <inline-formula> <tex-math notation="LaTeX">$L$ </tex-math></inline-formula> principal components, and the last <inline-formula> <tex-math notation="LaTeX">$N$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">$L$ </tex-math></inline-formula> principal components can be neglected due to that they are dominated by the noise. Numerical studies are carried out using the data obtained from the Soil Moisture and Ocean Salinity (SMOS) official website, and the corresponding results validate that the proposed method is effective in reducing the instrument model error.
Leveraging antimicrobial stewardship into improving rates of carbapenem-resistant Enterobacteriaceae

ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are among the most critical threats facing our healthcare system and account for significant patient mortality. There is considerable interest in the development of new treatment strategies. However, less attention has been paid to reducing CRE infection rates. Antibiotic stewardship programs can be uniquely empowered to reduce widespread pathogen resistance and by extension, optimize patient care and lower healthcare costs.
Deletion of Running-Induced Hippocampal Neurogenesis by Irradiation Prevents Development of an Anxious Phenotype in Mice

Recent evidence postulates a role of hippocampal neurogenesis in anxiety behavior. Here we report that elevated levels of neurogenesis elicit increased anxiety in rodents. Mice performing voluntary wheel running displayed both highly elevated levels of neurogenesis and increased anxiety in three different anxiety-like paradigms: the open field, elevated O-maze, and dark-light box. Reducing neurogenesis by focalized irradiation of the hippocampus abolished this exercise-induced increase of anxiety, suggesting a direct implication of hippocampal neurogenesis in this phenotype. On the other hand, irradiated mice explored less frequently the lit compartment of the dark-light box test irrespective of wheel running, suggesting that irradiation per se induced anxiety as well. Thus, our data suggest that intermediate levels of neurogenesis are related to the lowest levels of anxiety. Moreover, using c-Fos immunocytochemistry as cellular activity marker, we observed significantly different induction patterns between runners and sedentary controls when exposed to a strong anxiogenic stimulus. Again, this effect was altered by irradiation. In contrast, the well-known induction of brain-derived neurotrophic factor (BDNF) by voluntary exercise was not disrupted by focal irradiation, indicating that hippocampal BDNF levels were not correlated with anxiety under our experimental conditions. In summary, our data demonstrate to our knowledge for the first time that increased neurogenesis has a causative implication in the induction of anxiety.
The Effect on Fisher-KPP Propagation in a Cylinder with Fast Diffusion on the Boundary

In this paper we consider a reaction-diffusion equation of Fisher-KPP type inside an infinite cylindrical domain in $\mathbb{R}^{N+1}$, coupled with a reaction-diffusion equation on the boundary of the domain, where potentially fast diffusion is allowed. We will study the existence of an asymptotic speed of propagation for solutions of the Cauchy problem associated with such system, as well as the dependence of this speed on the diffusivity at the boundary and the amplitude of the cylinder. When $N=1$ the domain reduces to a strip between two straight lines. This models the effect of two roads with fast diffusion on a strip-shaped field bounded by them.
Optomechanical control of molecular motors

The majority of mechanisms that can be deployed for optical micromanipulation are not especially amenable for extension into the nanoscale. At the molecular level, the rich variety of schemes that have been proposed to achieve mechanical effect using light commonly exploit specific chemical structures; familiar examples are compounds that can fold by cis-trans isomerization, or the mechanically interlocked architectures of rotaxanes. However, such systems are synthetically highly challenging, and few of them can realistically form the basis for a true molecular motor. Developing the basis for a very different strategy based on programmed electronic excitation, this paper explores the possibility of producing controlled mechanical motion through optically induced modifications of intermolecular force fields, not involving the limitations associated with using photochemical change, nor the high intensities required to produce and manipulate optical binding forces between molecules. Calculations reveal that significant, rapidly responsive effects can be achieved in relatively simple systems. By the use of suitable laser pulse sequences, the possibilities include the generation of continuous rotary motion, the ultimate aim of molecular motor design.
Report f Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians

Helena Malmström,1,2 M.Thomas P. Gilbert,2 Mark G. Thomas,3 Mikael Brandström,4 Jan Storå,5 Petra Molnar,5 Pernille K. Andersen,6 Christian Bendixen,6 Gunilla Holmlund,7 Anders Götherström,1,8,* and Eske Willerslev2,8,* 1Department of Evolutionary Biology, Uppsala University, SE-11863 Uppsala, Sweden 2Centre for GeoGenetics, University of Copenhagen, DK-2100 Copenhagen, Denmark 3Research Department of Genetics, Evolution and Environment, and the AHRC Centre for the Evolution of Cultural Diversity, University College London, Gower Street, London WC1E 6BT, UK 4Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, SE-10691 Uppsala, Sweden 5Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden 6Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, PO Box 50, DK-8830 Tjele, Denmark 7National Board of Forensic Medicine, Department of Forensic Genetics and Forensic Toxicology, SE-58758 Linköping, Sweden
News Flow, Web Attention and Extreme Returns in the European Financial Crisis

We examine the existence of stock market contagion effects among three groups of countries: the Euro-periphery countries (Portugal, Ireland, Italy, Greece, Spain), the Euro-core countries (Germany, France, the Netherlands, Finland, Belgium), and the major European Union - but not euro-countries (Sweden, UK, Poland, Czech Republic, Denmark). Using daily stock market data from January 2004 till March 2013, contagion effects for the tails of the marginal distributions are present for the Pre-crisis and the Euro-crisis periods within the Euro-periphery countries and from the Euro-periphery group to the Non-Euro and the Euro-core groups. We do not find a significant change in the contagion transmission mechanism when comparing the two periods, but for the Euro-crisis periods the extreme returns have a higher magnitude. Finally, we propose a connection between extreme stock market returns, the Web Attention index and two News Flow factors. The Euro-periphery Web Attention and News Flow variables significantly affect the probabilities of extreme bottom returns for the Euro-periphery, the Non-euro and the Euro-core groups. The effect is asymmetric in most of the cases since the Euro-periphery Web Attention and News Flow factors do not affect the probabilities of extreme top returns, with a few exceptions. More Web Attention and more bad news for the Euro-periphery in times of crisis are associated with higher probabilities of extreme bottom returns within and across groups. Granger-causality tests show that the News Pessimism and the News Relevance factors exhibit a two-way causality with the stock market movements while the Web Search Volume Index (SVI) one-way Granger-causes stock markets and extreme bottom returns in the three country groups.
Feed intake, digestibility and energy partitioning in beef cattle fed diets with cassava pulp instead of rice straw

Objective This study was conducted to assess the effects of replacing rice straw with different proportions of cassava pulp on growth performance, feed intake, digestibility, rumen microbial population, energy partitioning and efficiency of metabolizable energy utilization in beef cattle. Methods Eighteen yearling Thai native beef cattle (Bos indicus) with an average initial body weight (BW) of 98.3±12.8 kg were allocated to one of three dietary treatments and fed ad libitum for 149 days in a randomized complete block design. Three dietary treatments using different proportions of cassava pulp (100, 300, and 500 g/kg dry matter basis) instead of rice straw as a base in a fermented total mixed ration were applied. Animals were placed in a metabolic pen equipped with a ventilated head box respiration system to determine total digestibility and energy balance. Results The average daily weight gain, digestible intake and apparent digestibility of dry matter, organic matter and non-fiber carbohydrate, total protozoa, energy intake, energy retention and energy efficiency increased linearly (p<0.05) with an increasing proportion of cassava pulp in the diet, whereas the three main types of fibrolytic bacteria and energy excretion in the urine (p<0.05) decreased. The metabolizable energy requirement for the maintenance of yearling Thai native cattle, determined by a linear regression analysis, was 399 kJ/kg BW0.75, with an efficiency of metabolizable energy utilization for growth of 0.86. Conclusion Our results demonstrated that increasing the proportion of cassava pulp up to 500 g/kg of dry matter as a base in a fermented total mixed ration is an effective strategy for improving productivity in zebu cattle.
Solid-Liquid Interdiffusion Bonding of Silicon Carbide to Steel for High Temperature MEMS Sensor Packaging and Bonding

Complex engineering systems ranging from automobile engines to geothermal wells require specialized sensors to monitor conditions such as pressure, acceleration and temperature in order to improve efficiency and monitor component lifetime in what may be high temperature, corrosive, harsh environments. Microelectromechanical systems (MEMS) have demonstrated their ability to precisely and accurately take measurements under such conditions. The systems being monitored are typically made from metals, such as steel, while the MEMS sensors used for monitoring are commonly fabricated from silicon, silicon carbide and aluminum nitride, and so there is a sizable thermal expansion mismatch between the two. For these engineering applications the direct bonding of MEMS sensors to the components being monitored is often required. This introduces several challenges, namely the development of a bond that is capable of surviving high temperature harsh environments while mitigating the thermally induced strains produced during bonding.This project investigates the development of a robust packaging and bonding process, using the gold-tin metal system and the solid-liquid interdiffusion (SLID) bonding process, to join silicon carbide substrates directly to type-316 stainless steel. The SLID process enables bonding at lower temperatures while producing a bond capable of surviving higher temperatures. Finite element analysis was performed to model the thermally induced strains generated in the bond and to understand the optimal way to design the bond. The cross-sectional composition of the bonds has been analyzed and the bond strength has been investigated using die shear testing. The effects of high temperature aging on the bond's strength and the metallurgy of the bond were studied. Additionally, loading of the bond was performed at temperatures over 415 °C, more than 100 °C, above the temperature used for bonding, with full survival of the bond, thus demonstrating the benefit of SLID bonding for high temperature applications.Lastly, this dissertation provides recommendations for improving the strength and durability of the bond at temperatures of 400 °C and provides the framework for future work in the area of high temperature harsh environment MEMS packaging that would take directly bonded MEMS to temperatures of 600 °C and beyond.
The Long-Run Impact of Biofuels on Food Prices

More than 40% of US grain is now used to produce biofuels, which are used as substitutes for gasoline in transportation. Biofuels have been blamed universally for recent increases in world food prices. Many studies have shown that these energy mandates in the US and EU may have a large (30-60%) impact on food prices. In this paper we show that demand-side effects - in the form of population growth and income-driven preferences for meat and dairy products rather than cereals - may play as much of a role in raising food prices as biofuel policy. By specifying a Ricardian model with differential land quality, we show that a significant amount of new land will be converted to farming which is likely to cause a modest increase in food prices. However, biofuels may increase aggregate world carbon emissions, due to leakage from lower oil prices and conversion of pasture and forest land for farming.