Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptococcus neoformans Resides in an Acidic Phagolysosome of Human Macrophages

ABSTRACT Recently, we demonstrated that human monocyte-derived macrophages (MDM) treated with chloroquine or ammonium chloride had markedly increased antifungal activity against the AIDS-related pathogenCryptococcus neoformans. Both of these agents raise the lysosomal pH, which suggested that the increased antifungal activity was a function of alkalinizing the phagolysosome. Moreover, there was an inverse correlation between growth of C. neoformans in cell-free media and pH. These data suggested that C. neoformans was well adapted to survive within acidic compartments. To test this hypothesis, we performed studies to determine the pH of human MDM and neutrophil phagosomes containingC. neoformans. Fungi were labeled with the isothiocyanate derivatives of two pH-sensitive probes: fluorescein and 2′,7′-difluorofluorescein (Oregon Green). These probes have pKas of 6.4 and 4.7, respectively, allowing sensitive pH detection over a broad range. The phagosomal pH averaged approximately 5 after ingestion of either live or heat-killed fungi and remained relatively constant over time, which suggested that C. neoformans does not actively regulate the pH of its phagosome. The addition of 10 and 100 μM chloroquine resulted in increases in the phagosomal pH from a baseline of 5.1 up to 6.5 and 7.3, respectively. Finally, by immunofluorescence, colocalization ofC. neoformans and the MDM lysosomal membrane protein LAMP-1 was demonstrated, establishing that fusion of C. neoformans-laden phagosomes with lysosomal compartments takes place. Thus, unlike many other intracellular pathogens, C. neoformans does not avoid fusion with macrophage lysosomal compartments but rather resides and survives in an acidic phagolysosome.
Exclusive Use of Air as Gas Tamponade in Rhegmatogenous Retinal Detachment

Purpose To investigate outcomes of vitrectomy for rhegmatogenous retinal detachment (RRD) using air exclusively as the gas tamponade. Methods This retrospective, interventional, consecutive case series involved reviewing medical records of patients that underwent vitrectomy and gas tamponade for RRD between January 2013 and December 2015. Patients whose eyes were treated exclusively with air tamponade since July 2014 were assigned to the air group, while those treated with heterogeneous gas agents before June 2014 were assigned to the control group. The primary outcome was the primary reattachment rate. Best-corrected visual acuity (BCVA) and duration to detect redetachments were assigned as the secondary outcomes. Results The air group and the control group included 71 and 72 eyes, respectively. The primary reattachment rate was 94.4% in the air group and there was no significant difference with 94.4% in the control group (p = 0.951). BCVA was significantly better in the air group at 1 month (p = 0.021) but not at 3 months postoperatively (p = 0.561). Redetachments were recognized earlier in the air group (9.3 ± 0.5 days) compared with those in the control group (21.3 ± 7.4 days) (p = 0.041). Conclusions In cases of simple RRD with sufficient removal of subretinal fluid, air could be considered for use as gas tamponade. This trial is registered with KCT0002358.
Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR

Significance Chaperones are integral components of the cellular machinery that assist protein folding and protect against misfolding and aggregation. A bottleneck in understanding how chaperones work is that the relevant functional states are too sparsely populated and dynamic to be observed using conventional biophysical methods. NMR is uniquely suited to detect and provide atomic resolution functional information on such “invisible” states. Here we quantitate the kinetics of the chaperone GroEL binding to a protein substrate that exists in a metastable equilibrium between the native state and a sparsely populated folding intermediate, under conditions where the GroEL-bound states are not directly observable. We show that in the absence of cofactors, GroEL possesses substantial intrinsic un/foldase activity that is mediated by hydrophobic interactions. The prototypical chaperonin GroEL assists protein folding through an ATP-dependent encapsulation mechanism. The details of how GroEL folds proteins remain elusive, particularly because encapsulation is not an absolute requirement for successful re/folding. Here we make use of a metastable model protein substrate, comprising a triple mutant of Fyn SH3, to directly demonstrate, by simultaneous analysis of three complementary NMR-based relaxation experiments (lifetime line broadening, dark state exchange saturation transfer, and Carr–Purcell–Meinboom–Gill relaxation dispersion), that apo GroEL accelerates the overall interconversion rate between the native state and a well-defined folding intermediate by about 20-fold, under conditions where the “invisible” GroEL-bound states have occupancies below 1%. This is largely achieved through a 500-fold acceleration in the folded-to-intermediate transition of the protein substrate. Catalysis is modulated by a kinetic deuterium isotope effect that reduces the overall interconversion rate between the GroEL-bound species by about 3-fold, indicative of a significant hydrophobic contribution. The location of the GroEL binding site on the folding intermediate, mapped from 15N, 1HN, and 13Cmethyl relaxation dispersion experiments, is composed of a prominent, surface-exposed hydrophobic patch.
Recursiveness and Evolvability in a Mutually catalytic reaction System

We discuss how recursive production of a proto-cell consisting of a mutually catalytic reaction network is possible. It is shown that a minority molecule species plays an essential role in carrying heredity, in the sense that the molecule is preserved well and controls replication of the cell. The cell state controlled by such a minority molecule is shown to have evolvability. Successive switches over quasi-recursive states are found, caused by extinction of minority molecules. Experimental demonstration of the theory is also discussed.
On the thermal behaviour of small iron grains

The optical properties of small spherical iron grains are derived using a Kramers-Kronig-consistent model of the dielectric function including its dependence on temperature and size. Especially discussed is the effect of the size dependence, which results from the limitation of the free path of the free electrons in the metal by the size of the grain, on the absorption behaviour of small iron spheres and spheroids. The estimated absorption properties are applied to study the temperature behaviour of spherical and spheroidal grains which are heated by the interstellar radiation field.
Origin Analysis and Elimination of Obtuse Triangular Defects in 4° Off 4H-SiC Epitaxy

The obtuse triangular defects would result in higher leakage currents and the preferential gate oxide breakdown of SiC devices. The formation and structural features of obtuse triangular defects on the 4° off 4H-SiC epilayers were investigated by confocal microscope and photoluminescence image. Two structrures of obtuse triangular defects were found. By optimizing the growth process, obtuse triangular defect free epitaxial layers were abtained on SiC substrate with serveral stacking fault. The number of triangular SFs defects was less than 0.5/cm2.
Coenzyme Q10 Protects Astrocytes from ROS-Induced Damage through Inhibition of Mitochondria-Mediated Cell Death Pathway

Coenzyme Q10 (CoQ10) acts by scavenging reactive oxygen species to protect neuronal cells against oxidative stress in neurodegenerative diseases. The present study was designed to examine whether CoQ10 was capable of protecting astrocytes from reactive oxygen species (ROS) mediated damage. For this purpose, ultraviolet B (UVB) irradiation was used as a tool to induce ROS stress to cultured astrocytes. The cells were treated with 10 and 25 μg/ml of CoQ10 for 3 or 24 h prior to the cells being exposed to UVB irradiation and maintained for 24 h post UVB exposure. Cell viability was assessed by MTT conversion assay. Mitochondrial respiration was assessed by respirometer. While superoxide production and mitochondrial membrane potential were measured using fluorescent probes, levels of cytochrome C (cyto-c), cleaved caspase-9, and caspase-8 were detected using Western blotting and/or immunocytochemistry. The results showed that UVB irradiation decreased cell viability and this damaging effect was associated with superoxide accumulation, mitochondrial membrane potential hyperpolarization, mitochondrial respiration suppression, cyto-c release, and the activation of both caspase-9 and -8. Treatment with CoQ10 at two different concentrations started 24 h before UVB exposure significantly increased the cell viability. The protective effect of CoQ10 was associated with reduction in superoxide, normalization of mitochondrial membrane potential, improvement of mitochondrial respiration, inhibition of cyto-c release, suppression of caspase-9. Furthermore, CoQ10 enhanced mitochondrial biogenesis. It is concluded that CoQ10 may protect astrocytes through suppression of oxidative stress, prevention of mitochondrial dysfunction, blockade of mitochondria-mediated cell death pathway, and enhancement of mitochondrial biogenesis.
Rare incidence of a diffuse brain metastatic carcinoma: A case report

Brain metastases generally present in the parenchyma of the brain. In the current report, a very rare case of brain metastasis, which simultaneously invaded the subgaleal region, the skull, and the dural and cavernous sinuses is presented. The patient, a 54-year-old female, complained of a progressive headache and exhibited the symptoms of intracranial hypertension. Coronal contrast-enhanced T1-weighted magnetic resonance imaging (MRI) showed high intensity signals in the subgaleal tissue of the left frontoparietal area, as well as in the dural and the cavernous sinuses. The patient was initially diagnosed with an intracranial infection, however, the administered treatment was ineffective. The patient subsequently underwent a biopsy and the pathological diagnosis was determined as a metastatic adenocarcinoma; a primary tumor was not identified during the examinations. Surgical removal of certain metastases and a decompressive craniectomy were performed to relieve the intracranial hypertension. However, the prognosis was unsatisfactory. The patient’s neurological condition progressively worsened and an axial computed tomography scan with a bone window demonstrated a bulging growth in the brain tissue. The patient succumbed after one month due to the widespread metastasis. Thus, this case presents the unusual clinical development of this type of metastatic adenocarcinoma. In addition, due to the intracranial hypertension, the unusual sites of the high intensity signals in the MRI and the lack of a primary tumor, the patient was misdiagnosed with an intracranial infection. Furthermore, this case highlights the necessity for conducting a biopsy as soon as possible and demonstrates the poor prognosis associated with this type of patient.
ZCluster: A Zynq-based Hadoop cluster

ARM-based servers are garnering increasing interest in big data processing for their low power consumption. However, they are ill-suited for compute-intensive tasks due to their poor processing capability compared to the CPUs used in a traditional server. This paper describes our early efforts to integrate the processing power of the FPGA with the ARM processor inside the Xilinx Zynq SoC. An eight-slave Zynq-based Hadoop cluster is built and a customized hardware accelerator for a standard FIR filter is implemented to demonstrate the effectiveness of hardware acceleration. The Xillybus is used for communication between the ARM processor and the FPGA fabric, achieving a bandwidth of 103MB/s. The Hadoop cluster is proved to be linearly scalable with different input sizes and numbers of slaves. Overall, the cluster achieves a 3.3-fold speedup compared to a native pure software implementation on a single ARM processor and about a 20% improvement compared to an ARM-based cluster without hardware accelerators.
Quantitative measurement of multifunctional quantum dot binding to cellular targets using flow cytometry

Semiconductor nanocrystals such as quantum dots (QDs) are a potentially powerful resource in the fields of flow cytometry and fluorescence microscopy. QD size and fluorescence characteristics offer attractive features for use in targeted delivery systems and detection by flow cytometry. While quantitative measurements of a variety of fluorescent molecules are routinely performed, fluorophores for which no calibration standards exist, such as QDs, pose a problem for quantitation in flow cytometry. Our goal was to develop a targeted nanoparticle delivery platform as well as a corresponding method to accurately and quantitatively assess the performance of this system. We synthesized surface‐modified QD probes targeted to cellular surface receptors and measured the MFI of the resulting cell‐probe conjugates by flow cytometry. MFI was converted to mean equivalent R‐PE intensity (MEPE) using standard calibration microspheres. Known concentrations of both R‐PE and QD probes were measured by fluorometry to relate R‐PE and QD fluorescence. Fluorometry results were then used to translate MEPE measurements to the number of bound QD probes. The targeted probes exhibited superior binding characteristics over unmodified and untargeted particles. This binding interaction was shown to be specific and mediated by the NGR targeting peptide tethered to the QD surface. The calibration method developed to assess this system proved successful at converting raw fluorescence data to quantitative probe binding values. We demonstrate the synthesis and performance of a highly modular nanoparticle system capable of targeted binding and fluorescent imaging. The calibration method implemented to quantify the performance of this system represents a potentially powerful tool to utilize truly quantitative flow cytometry measurements with an array of fluorescent molecules, including QDs. © 2008 International Society for Advancement of Cytometry
Fault-Tolerant Wavelength Allocations in All-optical Hypercubes

Motivated by wavelength division multiplexing in all-optical networks, we consider the problem of finding an optimal (with respect to the least possible number of wavelengths) set of f +1 internally node disjoint dipaths for every pair of distinct nodes in the binary r-dimensional hypercube, where 0 f < r. This system of dipaths serves as a routing protocol that remains functional in the presence of up to f faults (nodes and/or links) in the hypercube. The importance of such protocols follows from the fact that the major applications for all-optical networks require connections that last for relatively long periods once set up. In this model, we give nearly optimal All-to-All protocols, in terms of number of wavelengths, for the hypercube network.
Adaptive Framework for Network Intrusion Detection by Using Genetic-Based Machine Learning Algorithm

Summery Computer networks have expanded significantly in use and in numbers. This expansion makes them target to different attacks. Intrusion Detection System (IDS) is used to identify unknown or new type of attacks or in dynamic environments as mobile networks. As a result, it is necessary to find a ways to implement and operate IDSs. Among different techniques, Genetic-based machine learning algorithm (GBML) which offers a good ability to be adapted to changing environments, robustness to noise and ability to identify unknown attacks. The objective of this paper is to incorporate different techniques into classifier system to detect and classify intrusion from normal network packet. Among several techniques, steady state genetic-based machine leaning algorithm (SSGBML) which will be used to detect intrusions. Steady State Genetic Algorithm (SSGA) and Zeroth Level Classifier system (ZCS) are investigated. SSGA is used as a discovery mechanism for classifiers, while ZCS plays the role of detector by matching incoming environment message with classifiers to determine whether it is normal or intrusion. As a feedback, the environment will make a decision on whether to take action or not. In order to attain the best results, modifying SSGA will enhance our discovery engine. The experiments and evaluations of the proposed method were performed with the KDD 99 intrusion detection dataset.
Association between Parent and Child Dietary Sodium and Potassium Intakes as Assessed by 24-h Urinary Excretion

The aim of this study was to assess the association between parent and child sodium (Na) and potassium (K) intake as assessed by 24-h urinary excretion (24hUE). Primary school children and their parent(s) provided one 24-h urine sample and information on cooking and children’s discretionary salt use. Valid urine samples were provided by 108 mothers (mean age 41.8 (5.1) (SD) years, Na 120 (45) mmol/day) (7.0 g/day salt equivalent) and 40 fathers (44.4 (4.9) years, Na 152 (49) mmol/day (8.9 g/day salt), and 168 offspring (51.8% male, age 9.1 (2.0) years, Na 101 (47) mmol/day (5.9 g/day salt). When adjusted for parental age, child age and gender a 17 mmol/day Na (1 g/day salt) increase in mother’s 24hUE was associated with a 3.4 mmol/day Na (0.2 g/day salt) increase in child’s salt 24hUE (p = 0.04) with no association observed between father and child. Sixty-seven percent of parents added salt during cooking and 37% of children added salt at the table. Children who reported adding table salt had higher urinary excretion than those who did not (p = 0.01). The association between mother and child Na intake may relate to the consumption of similar foods and highlights the importance of the home environment in influencing total dietary sodium intake.
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 108 synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
Analysis of spectral-domain optical coherence tomography in preterm children: retinal layer thickness and choroidal thickness profiles.

PURPOSE To compare retinal layer thickness and choroidal thickness profiles in preterm and full-term children using spectral-domain optical coherence tomography (SD-OCT). METHODS We performed horizontal and vertical SD-OCT crosshair scans through the fovea with and without an enhanced depth technique in 31 premature and 30 full-term children. Retinal layer and choroidal thicknesses were measured at various locations including the fovea and 1.0 and 3.0 mm nasal, temporal, superior, and inferior to the fovea. After adjusting for age and the child's axial length, we compared retinal layer and choroidal thicknesses at the measurement points. RESULTS Total retinal thickness and outer nuclear layer (ONL) thickness at the foveal center in preterm children (256.00 ± 30.71 μm, 141.87 ± 28.75 μm, respectively) were larger than those in full-term children (217.57 ± 10.64 μm, 101.22 ± 10.90 μm, respectively, P < 0.001). Gestational age at birth was inversely correlated with both total retinal and ONL thicknesses (P < 0.001). Choroidal thickness 3.0 mm temporal to the fovea in preterm children (283.75 ± 60.47 μm) was significantly less than that in full-term children (339.89 ± 90.32, P = 0.010). Retinopathy of prematurity staging showed a marginal inverse correlation with choroidal thickness 3.0 mm temporal to the fovea (P = 0.053). Visual acuity in preterm children was not correlated with retinal thickness or choroidal thickness. CONCLUSIONS Our SD-OCT data demonstrated an increased total retinal thickness and ONL thickness at the foveal center and decreased choroidal thickness 3.0 mm temporal to the fovea in preterm children. Further studies are needed to better understand the association between these structural changes and visual functions in preterm children.
Cell Growth Pattern and Wall Microfibrillar Arrangement

In cylindrical cells growing throughout their length, over-all transverse reinforcement of the wall by microfibrils is believed to be required for cell elongation. The multinet theory states that in such cells microfibrils are deposited at the inner surface of the wall with transverse orientation and are then passively reoriented toward the longitudinal direction by the predominant longitudinal strain (surface expension). In the present study young Nitella cells were physically forced to grow in highly abnormal patterns: in length only, in girth only, or with localized suppression of growth. Subsequent gradients of microfibrillar arrangement within the wall cross-section were measured with polarized light and interference microscopes. The novel wall structures produced were in all cases explainable by passive reorientation, i.e. by the multinet theory. The study also showed that orientation of synthesis remains insensitive to several of the physical manipulations that strongly influence the passive behavior of wall microfibrils. Only the localized complete suppression of surface growth led to the deposition of nontransverse cellulose. These results suggest that the presence of strain is needed for continued oriented synthesis, but that the directional aspect of strain is not an "instructional" agent continuously guiding the orientation of synthesis, once this orientation has been established.