Miracle-dz/UniFAR-FTUs huggingface dataset:
Establishment of a retinal hypoxia organ culture model

ABSTRACT Hypoxia plays an important role in several retinal diseases, especially in central retinal artery occlusion (CRAO). Although CRAO has been known for over a hundred years, no cure or sufficient treatment is available. Potential therapies are being evaluated in several in vivo models or primary cultures. However, in vivo models or primary cultures are very time-consuming, expensive, and furthermore several therapies or agents cannot be tested. Therefore, we aimed to develop a standardized organotypic ex vivo retinal hypoxia model. A chamber was developed in which rat retinal explants were incubated for different hypoxia durations. Afterwards, the retinas were adjusted to normal air and incubated for 24, 48 or 72 h under standard conditions. To analyze the retinal explants, and in particular the retinal ganglion cells (RGC) immunohistology, western blot and optical coherence tomography (OCT) measurements were performed. To compare our model to a standardized degeneration model, additional retinal explants were treated with 0.5 and 1 mM glutamate. Depending on hypoxia duration and incubation time, the amount of RGCs decreased and accordingly, the amount of TUNEL-positive RGCs increased. Furthermore, β-III-tubulin expression and retinal thickness significantly decreased with longer-lasting hypoxia. The reduction of RGCs induced by 75 min of hypoxia was comparable to the one of 1 mM glutamate treatment after 24 h (20.27% versus 19.69%) and 48 h (13.41% versus 14.41%) of incubation. We successfully established a cheap, standardized, easy-to-use organotypic culture model for retinal hypoxia. We selected 75 min of hypoxia for further studies, as approximately 50% of the RGC died compared to the control group after 48 h. Summary: An easy-to-use ex vivo retinal hypoxia model is introduced that reliably induced retinal damage on a morphological (retinal thickness), and molecular (protein expression and apoptotic markers) level.
Achieving MAC layer fairness in wireless packet networks

Link-layer fairness models that have been proposed for wireline and packet cellular networks cannot be generalized for shared channel wireless networks because of the unique characteristics of the wireless channel, such as location-dependent contention, inherent conflict between optimizing channel utilization and achieving fairness, and the absence of any centralized control. In this paper, we propose a general analytical framework that captures the unique characteristics of shared wireless channels and allows the modeling of a large class of system-wide fairness models via the specification of per-flow utility functions. We show that system-wide fairness can be achieved without explicit global coordination so long as each node executes a contention resolution algorithm that is designed to optimize its local utility function. We present a general mechanism for translating a given fairness model in our framework into a corresponding contention resolution algorithm. Using this translation, we derive the backoff algorithm for achieving proportional fairness in wireless shared channels, and compare the fairness properties of this algorithm with both the ideal proportional fairness objective, and state-of-the-art backoff-based contention resolution algorithms. We believe that the two aspects of the proposed framework, i.e. the ability to specify arbitrary fairness models via local utility functions, and the ability to automatically generate local contention resolution mechanisms in response to a given utility function, together provide the path for achieving flexible service differentiation in future shared channel wireless networks.
Viruses in type 1 diabetes

Environmental factors play an important role in the pathogenesis of type 1 diabetes and can determine if a genetically susceptible individual develops the disease. Increasing evidence suggest that among other exogenous agents certain virus infections can contribute to the beta‐cell damaging process. Possible viral etiology of type 1 diabetes has been explored extensively but the final proof for causality is still lacking. Currently, the group of enteroviruses (EVs) is considered as the strongest candidate. These viruses have been found in the pancreas of type 1 diabetic patients, and epidemiological studies have shown more EV infections in diabetic patients than in controls. Prospective studies, such as the Type 1 Diabetes Prediction and Prevention (DIPP) study in Finland, are of fundamental importance in the evaluation viral effects as they can cover all stages of the beta‐cell damaging process, including those preceding the initiation of the process. DIPP study has carried out the most comprehensive virological analyses ever done in prospective cohorts. This article summarizes the findings from these analyses and discuss them in the context of the existing other knowledge and the prospects for intervention studies with EV vaccines or antiviral drugs.
SNOC: A Monte-Carlo simulation package for high-z supernova observations

We present a Monte-Carlo package for simulation of high-redshift supernova data, SNOC. Optical and near-infrared photons from supernovae are ray-traced over cosmological distances from the simulated host galaxy to the observer at Earth. The distances to the sources are calculated from user provided cosmological parameters in a Friedmann-Lemaˆ itre universe, allowing for arbitrary forms of "dark energy". The code takes into account gravitational interactions (lensing) and extinction by dust, both in the host galaxy and in the line-of-sight. The user can also choose to include exotic eects like a hypothetical attenuation due to photon-axion oscillations. SNOC is primarily useful for estimations of cosmological parameter uncertainties from studies of apparent brightness of type Ia supernovae vs redshift, with special emphasis on potential systematic eects. It can also be used to compute standard cosmological quantities like luminosity distance, lookback time and age of the universe in any Friedmann-Lemaˆ itre model with or without quintessence.
Non‐enzymatic glycation of chondrocyte‐seeded collagen gels for cartilage tissue engineering

Collagen glycated with ribose (250 mM) in solution (pre‐glycation) and as a gel (post‐glycation) was seeded with chondrocytes and the effects of glycation on chondrocyte matrix assembly in culture were determined. Pre‐glycation enhanced GAG accumulation significantly over controls at both 2 and 4 weeks (p < 0.05), although at both time points there were no statistical differences in cell number between pre‐glycated and control gels. The increased proteoglycan accumulation was shown to be in part due to significantly increased GAG retention by the pre‐glycated constructs (p < 0.05). Total collagen content in these pre‐glycated gels was also significantly higher than unglycated gels at 4 weeks (p < 0.05). With post‐glycation of collagen gels, chondrocyte number and GAG accumulation were all significantly lower than controls (p < 0.05). Post‐glycation also inhibited GAG retention by the constructs (p < 0.05). Given these results, pre‐glycation may be an improved processing method for collagen gels for tissue engineering techniques. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1434–1439, 2008
Behavior of structural concrete members strengthened by composite fabrics

BEHAVIOR OF STRUCTURAL CONCRETE MEMBERS STRENGTHENED BY COMPOSITE FABRICS by Jian Chen The new technique of using Fiber Reinforced Polymer (FRP) materials to repair and strengthen various concrete members is becoming more and more popular in structural retrofitting field. Among all the confining materials, Carbon Fiber Reinforced Polymer (CFRP) fabric jackets are identified as an effective way to enhance the strength and ductility of concrete members due to its superior mechanical properties. This study investigates the detailed structural behavior of confined concrete members using CFRP fabric jackets by both analytical and experimental approaches. A series of CFRP wrapped concrete cylinder tests were conducted to study the compressive stress-strain behavior for CFRP confined concrete members, Based on the test results, the CFRP system can significantly increase the ductility and ultimate compressive strength of normal concrete specimens. Also, a complete stress-strain equation was derived to model the fabric-confined concrete and verified by various experimental tests results. In order to fully apply this new technique to structural engineering, more experiments were conducted by wrapping CFRP fabric to the large structure members such as beams and columns in this study. The flexural behavior of the large concrete beams wrapped by CFRP fabrics was investigated based on the experiments at the NJIT Structures Laboratory. Different wrapping methods were applied. Test results show that the CFRP confinement can significantly increase the ultimate flexural strength of Reinforced Concrete (RC) beams. However, the contribution of fabrics may vary due to the different wrapping methods applied. Experimental results are compared with the finite element modeling using the ANSYS computer program. A practical design method similar to ACI strength method is also proposed to predict the ultimate strength of the beam specimens. Good agreements are achieved for both methods. Structural behavior of the RC slender columns wrapped with CFRP fabrics under combined axial load and biaxial bending were also investigated in this research. Seven slender columns with different wrapping methods were tested and analyzed. It can be concluded that both longitudinal and transverse fabric do help increase the load capacity of the column specimens, although the longitudinal fabric tends to decrease the deformability of the columns. The columns with both wrapping methods applied achieve a better strength and ductility performance. A modified computer program accounting for the proposed stress-strain equation for fabric-confined concrete has been used to verify the present experimental results. A satisfactory agreement is attained for both ascending and descending branches of the load-deformation curves. BEHAVIOR OF STRUCTURAL CONCRETE MEMBERS STRENGTHENED BY COMPOSITE FABRICS
DNA Modifications: Function and Applications in Normal and Disease States

Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone, and non-histone chromosomal proteins, which establish a complex regulatory network that controls genome function. Methylation of DNA at the fifth position of cytosine in CpG dinucleotides (5-methylcytosine, 5mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5hmC), which is a product of the ten-eleven translocation (TET) proteins converting 5mC to 5hmC. In this review, we will highlight current studies on the role of 5mC and 5hmC in regulating gene expression (using some aspects of brain development as examples). Further the roles of these modifications in detection of pathological states (type 2 diabetes, Rett syndrome, fetal alcohol spectrum disorders and teratogen exposure) will be discussed.
Colon cancer stem cells

Colorectal cancer (CRC) is the third most common form of cancer and the second cause of cancer-related death in the Western world, leading to 655,000 deaths worldwide per year (Jemal et al. in CA Cancer J Clin 56:106–130, 2006). Despite the emergence of new targeted agents and the use of various therapeutic combinations, none of the treatment options available is curative in patients with advanced cancer. A growing body of evidence is increasingly supporting the idea that human cancers can be considered as a stem cell disease. According to the cancer stem cell model, malignancies originate from a small fraction of cancer cells that show self-renewal and pluripotency and are capable of initiating and sustaining tumor growth (Boman and Wicha in J Clin Oncol 26:2795–2799, 2008). The cancer-initiating cells or “cancer stem cells” were first identified in hematologic malignancies and most recently in several solid tumors, including CRC. The hypothesis of stem cell-driven tumorigenesis in colon cancer raises questions as to whether current treatments are able to efficiently target the tumorigenic cell population that is responsible for tumor growth and maintenance. This review will focus on the different aspects of stem cell biology in the context of CRC, which might help to understand the mechanisms that give rise to tumor development and resistance to therapy. First, we will briefly revise the knowledge available on normal intestinal stem cells and recent advances in understanding crypt biology, which have led to new theory on the origins of colon adenomas and cancers. Then, we will summarize the evidence and current status on colon cancer stem cells, focusing on their relevance and promises for the treatment of colorectal carcinoma.
Hydrodynamic and Thermal Effects of Sub-critical Heating on Superhydrophobic Surfaces and Microchannels

Hydrodynamic and Thermal Effects of Sub-Critical Heating on Superhydrophobic Surfaces and Microchannels Adam M. Cowley Department of Mechanical Engineering, BYU Doctor of Philosophy This dissertation focuses on the effects of heating on superhydrophobic (SHPo) surfaces. The work is divided into two main categories: heat transfer without mass transfer and heat transfer in conjunction with mass transfer. Numerical methods are used to explore the prior while experimental methods are utilized for the latter. The numerical work explores convective heat transfer in SHPo parallel plate microchannels and is separated into two stand-alone chapters that have been published archivally. The first considers surfaces with a rib/cavity structure and the second considers surfaces patterned with a square lattice of square posts. Laminar, fully developed, steady flow with constant fluid properties is considered where the tops of the ribs and posts are maintained at a constant heat flux boundary condition and the gas/liquid interfaces are assumed to be adiabatic. For both surface configurations the overall convective heat transfer is reduced. Results are presented in the form of average Nusselt number as well as apparent temperature jump length (thermal slip length). The heat transfer reduction is magnified by increasing cavity fraction, decreasing Peclet number, and decreasing channel size relative to the micro-structure spacing. Axial fluid conduction is found to be substantial at high Peclet numbers where it is classically neglected. The parameter regimes where prior analytical works found in the literature are valid are delineated. The experimental work is divided into two stand-alone chapters with one considering chan-nel flow and the other a pool scenario. The channel work considers high aspect ratio microchannels with one heated SHPo wall. If water saturated with dissolved air is used, the airfilled cavities of SHPo surfaces act as nucleation sites for mass transfer. As the water heats it becomes supersatu-rated and air can effervesce onto the SHPo surface forming bubbles that align to the underlying micro-structure if the cavities are comprised of closed cells. The large bubbles increase drag in the channel and reduce heat transfer. Once the bubbles grow large enough, they are expelled from the channel and the nucleation and growth cycle begins again. The pool work considers submerged, heated SHPo surfaces such that the nucleation behavior can be explored in the absence of forced fluid flow. The surface is maintained at a constant temperature and a range of temperatures (40 – 90 oC) are explored. Similar nucleation behavior to that of the microchannels is observed; however, the bubbles are not expelled. Natural convection coefficients are computed. The surfaces with the greatest amount of nucleation show a significant reduction in convection coefficient, relative to a smooth hydrophilic surface, due to the insulating bubble layer.
Maximizable routing metrics

We develop a theory for deciding, for any routing metric and any network, whether the messages in this network can be routed along paths whose metric values are maximum. In order for the messages in a network to be routed along paths whose metric values are maximum, the network needs to have a rooted spanning tree that is maximal with respect to the routing metric. We identify two important properties of routing metrics: boundedness and monotonicity, and show that these two properties are both necessary and sufficient to ensure that any network has a maximal tree with respect to any (bounded and monotonic) metric. We also discuss how to combine two (or more) routing metrics into a single composite metric such that if the original metrics are bounded and monotonic, then the composite metric is bounded and monotonic. Finally we show that the composite routing metrics used in IGRP (inter-gateway routing protocol) and EIGRP (enhanced IGRP) are bounded but not monotonic.
Cavitary Lung Disease: Not Always due to Tuberculosis! Primary Lung Cancer with Smear Positive Pulmonary Tuberculosis- A Case Report

Pulmonary Tuberculosis is the leading cause of cavitary lung disease globally. Although clinical scenario of majority of the disorders causing cavitation and hemoptysis are overlapping, special emphasis should be given on smoking history and concomitant clubbing especially in elderly population. CT thorax will differentiate probability of malignancy as cause of cavity by delineating its pericavitary nodularity, irregular wall, thickness and size. Bronchoscopy is must in all the cases, will help to confirm the diagnosis and ruling out underlying malignancy. Squamous cell carcinoma is known to cause cavitation and the only histological lung cancer type causing such radiological abnormality. In this case report we described a elderly male patient presented with persistent intermittent hemoptysis with chest pain and clubbing on clinical evaluation. Initially diagnosed as a case of smear positive pulmonary tuberculosis finally we confirmed as Primary Lung cancer of Squamous cell origin. High index of suspicion is must in such cases, with bronchoscopy and cytopathology expertise in lung histopathology will be crucial in confirming diagnosis.
Molecular epidemiology of enteric viruses in children with sporadic gastroenteritis in Valencia, Venezuela

The epidemiology and clinical symptoms in infants and young children with acute sporadic viral gastroenteritis due to viral etiologies other than rotaviruses have not been studied thoroughly in developing countries. Fecal specimens from 480 children <5 years of age who were admitted to a large children's hospital in the city of Valencia, Venezuela, with acute diarrhea during January to December 2003 were collected and screened by ELISA and RT‐PCR for rotavirus, adenovirus, norovirus, sapovirus, and astrovirus. Viral isolates were partially characterized by phylogenetic analysis. Norovirus viral load was determined by qRT‐PCR. Viruses were identified in 205 (43%) of the 480 stool samples collected. Rotavirus was the virus detected most frequently (21%), followed by norovirus (13%), adenovirus (5%), sapovirus (3%), and astrovirus (2%). Viral infection rates were highest in the 6‐ to 11‐month‐old group (49%) and lowest in children >24 months old. Norovirus GII was more prevalent (90%) than GI (10%). Enteric adenovirus (serotypes 40/41) was present in 43% of the adenovirus‐positive samples. Rotavirus infection caused more severe clinical symptoms than the other viruses detected, with more vomiting (84%) and dehydration (11%) that led to hospital admission of 20% of the children with acute gastroenteritis. Rotavirus and norovirus showed marked and opposite seasonal patterns. No association was observed between disease severity and viral load in children infected with norovirus. These results not only confirm the impact of rotavirus infection in Venezuela but also indicate that other enteric viruses, especially noroviruses, contribute significantly to sporadic acute gastroenteritis and to the burden of disease. J. Med. Virol. 83:1972–1982, 2011. © 2011 Wiley‐Liss, Inc.
Vascular risk factors and cognitive function among 3763 participants in the Hypertension in the Very Elderly Trial (HYVET): a cross-sectional analysis

ABSTRACT Background: It is well known that the global population is aging and that those over the age of 80 are the fastest growing part of this expansion. Also known is that prevalence of hypertension and cognitive decline both increase with increasing age. Method: The Hypertension in the Very Elderly Trial (HYVET) was a double blind placebo-controlled trial of antihypertensive treatment (indapamide SR 1.5 mg ± perindopril 2–4 mg) and recruited only those hypertensives who were aged 80 or over and were without a diagnosis of dementia at baseline. Systolic blood pressure had to be in the range 160–199 mmHg and diastolic pressure <110 mmHg. Cognitive function was assessed at baseline using the Mini-mental State Examination prior to randomization into the trial. Also collected at baseline was information relating to sociodemographic, clinical, cardiovascular and biochemical factors which may impact upon cognitive function. This paper reports on the baseline cognitive function data from the HYVET trial and its relationship to these factors. Results: The mean age of the 3763 HYVET participants who had full cognitive function data at baseline was 83.6 years; 60 percent were female. The median MMSE score at baseline was 26 and, in multivariate analyses, higher at younger age, with male gender, higher educational level, having higher creatinine, higher total cholesterol and lower high-density lipoprotein cholesterol. Conclusions: This is the first such study to examine a large number of very elderly hypertensives and it shows some similar patterns to those seen in younger elderly groups.