Miracle-dz/UniFAR-FTUs huggingface dataset:
The oligomerization of amyloid beta-protein begins intracellularly in cells derived from human brain.

The progressive aggregation and deposition of amyloid beta-protein (Abeta) in brain regions subserving memory and cognition is an early and invariant feature of Alzheimer's disease, the most common cause of cognitive failure in aged humans. Inhibiting Abeta aggregation is therapeutically attractive because this process is believed to be an exclusively pathological event. Whereas many studies have examined the aggregation of synthetic Abeta peptides under nonphysiological conditions and concentrations, we have detected and characterized the oligomerization of naturally secreted Abeta at nanomolar levels in cultures of APP-expressing CHO cells [Podlisny, M. B. , Ostaszewski, B. L. , Squazzo, S. L. , Koo, E. H. , Rydell, R. E. , Teplow, D. B. , and Selkoe, D. J. (1995) J. Biol. Chem. 270, 9564-9570 (1); Podlisny, M. B. , Walsh, D. M. , Amarante, P., Ostaszewski, B. L. , Stimson, E. R. , Maggio, J. E. , Teplow, D. B. , and Selkoe, D. J. (1998) Biochemistry 37, 3602-3611 (2)]. To determine whether similar species occur in vivo, we probed samples of human cerebrospinal fluid (CSF) and detected SDS-stable dimers of Abeta in some subjects. Incubation of CSF or of CHO conditioned medium at 37 degrees C did not lead to new oligomer formation. This inability to induce oligomers extracellularly as well as the detection of oligomers in cell medium very early during the course of pulse-chase experiments suggested that natural Abeta oligomers might first form intracellularly. We therefore searched for and detected intracellular Abeta oligomers, principally dimers, in primary human neurons and in neuronal and nonneural cell lines. These dimers arose intracellularly rather than being derived from the medium by reuptake. The dimers were particularly detectable in neural cells: the ratio of intracellular to extracellular oligomers was much higher in brain-derived than nonbrain cells. We conclude that the pathogenically critical process of Abeta oligomerization begins intraneuronally.
Channeling the Data Flood: Handling Large-Scale Biomolecular Measurements in Silico

The cells of the human body each contain thousands of molecular species,the dynamic interactions of which constitute the biomolecular system underlying cellular function. Many thousands of expressed genes, proteins, and metabolites can be measured simultaneously in a tissue or blood sample, making a scan of most biomolecules possible. This wealth of information causes the bottleneck in biomedical research to shift from making measurements to data integration and analysis. Management of biomolecular information requires efficient data storage and retrieval from integrated databases. Subsequent data analysis has three components: 1) identification of broad molecular "fingerprints" useful for early disease diagnosis and treatment selection; 2) identification of the relatively few molecular signals which change significantly above the high noise level formed by biological variation amongst individuals; and 3) development of a mechanistic understanding of the system by capturing its characteristics in computational models. At present, extensive parts of the biomolecular system are still uncharted. Representation of the entire system in silico presents a great challenge, made more challenging still by great interindividual variation at the molecular level. The prospect of much better control of human disease makes this gigantic enterprise worthwhile.
Infectious Entry Pathway of Adeno-Associated Virus and Adeno-Associated Virus Vectors

ABSTRACT We have investigated the infectious entry pathway of adeno-associated virus (AAV) and recombinant AAV vectors by assessing AAV-mediated gene transfer and by covalently conjugating fluorophores to AAV and monitoring entry by fluorescence microscopy. We examined AAV entry in HeLa cells and in HeLa cell lines which inducibly expressed a dominant interfering mutant of dynamin. The data demonstrate that AAV internalizes rapidly by standard receptor-mediated endocytosis from clathrin-coated pits (half-time <10 min). The lysosomotropic agents ammonium chloride and bafilomycin A1 prevent AAV-mediated gene transfer when present during the first 30 min after the onset of endocytosis, indicating that AAV escapes from early endosomes yet requires an acidic environment for penetration into the cytosol. Following release from the endosome, AAV rapidly moves to the cell nucleus and accumulates perinuclearly beginning within 30 min after the onset of endocytosis. We present data indicating that escape of AAV from the endosome and trafficking of viral particles to the nucleus are unaffected by the presence of adenovirus, the primary helper virus for a productive AAV infection. Within 2 h, viral particles could be detected within the cell nucleus, suggesting that AAV enters the nucleus prior to uncoating. Interestingly, the majority of the intracellular virus particles remain in a stable perinuclear compartment even though gene expression from nuclear AAV genomes can be detected. This suggests that the process of nuclear entry is rate limiting or that AAV entry involves multiple pathways. Nevertheless, these data establish specific points in the AAV infectious entry process and have allowed the generation of a model for future expansion to specific cell types and AAV vector analysis in vivo.
Using tDCS to Explore the Role of the Right Temporo-Parietal Junction in Theory of Mind and Cognitive Empathy

The right temporo-parietal junction (rTPJ) is thought to be closely related to theory of mind (ToM) and cognitive empathy. In the present study, we investigated whether these socio-cognitive abilities could be modulated with non-invasive transcranial direct current stimulation (tDCS) of the rTPJ. Participants received anodal (excitatory), cathodal (inhibitory), or sham stimulation before performing a social cognitive task which included inferring other’s intention (the ToM condition) and inferring other’s emotion (the cognitive empathy condition). Our results showed that the accuracy of both ToM and cognitive empathy decreased after receiving the cathodal stimulation, suggesting that altering the cortical excitability in the rTPJ could influence human’s socio-cognitive abilities. The results of this study emphasize the critical role of the rTPJ in ToM and cognitive empathy and demonstrate that these socio-cognitive abilities could be modulated by the tDCS.
Grain Size Effect on the Microhardness of BCC Metal Vapor Deposits

The physical vapor deposition methods of evaporation and sputtering are used to prepare foils of the body-centered-cubic metals, vanadium and tantalum. A two-fold increase in the micro-hardness is measured as the grain size decreases to the sub-micron scale. The micro-hardness of vanadium increases to 2.7 GPa and for tantalum to 2.9 GPa.
Integration of PLSA into Probabilistic CLIR Model - Yokohama National University at NTCIR4 CLIR

In this paper, we propose a method of CrossLanguage Information Retrieval based on an integration of a probabilistic CLIR model and Probabilistic Latent Semantic Analysis (PLSA). PLSA is adopted to extract the information of translation probability from a parallel corpus. The information is utilized in a probabilistic CLIR model. Although the probabilistic CLIR model with PLSA is quite effective, it takes very long time in the processing. We therefore introduce an approximation method based on a two-phased retrieval model in order to reduce the computational cost. Using the model, we submitted runs for Japaneseto-English bilingual retrieval in CLIR task of NTCIR4.
On the approximability of some network design problems

Consider the following classical network design problem: a set of terminals <i>T</i> = [<i>t<inf>i</inf></i> wants to send traffic to a "root" <i>r</i> in an <i>n</i>-node graph <i>G</i> = (<i>V,E</i>). Each terminal <i>t<inf>i</inf></i> sends <i>d<inf>i</inf></i> units of traffic, and enough bandwidth has to be allocated on the edges to permit this. However, bandwidth on an edge <i>e</i> can only be allocated in <i>integral</i> multiples of some base capacity <i>u<inf>e</inf></i> --- and hence provisioning <i>k</i> x <i>u<inf>e</inf></i> bandwidth on edge <i>e</i> incurs a cost of [<i>k</i>] times the cost of that edge. The objective is a minimum-cost feasible solution.This is one of many network design problems widely studied where the bandwidth allocation being governed by side constraints: edges may only allow a subset of cables to be purchased on them, or certain quality-of-service requirements may have to be met.In this work, we show that the above problem, and in fact, several basic problems in this general network design framework, cannot be approximated better than Ω(log log <i>n</i>) unless <b>NP</b> ⊆ <b>DTIME</b> (<i>n</i><sup><i>O</i>(log log log <i>n</i>). </sup> In particular, we show that this inapproximability threshold holds for (i) the Priority-Steiner Tree problem [7], (ii) the Cost-Distance problem [31], and the single-sink version of an even more fundamental problem, (iii) <b>Fixed Charge Network Flow</b> [33]. Our results provide a further breakthrough in the understanding of the level of complexity of network design problems. These are the first non-constant hardness results known for all these problems.
Evaluation of MMA and MAG arc welding process data

The microprocessor-controlled system for real-time collection and display of welding parameters was designed, implemented and tested. The system records up to 4 digital or analog signals collected from welding process and display their run on the LCD display. The aim of the research was to examine the possibility of detecting welding imperfections by recording the instant values of welding parameters. Tests of the device performed during manual metal arc welding and metal active gas welding revealed that the occurrence of some welding imperfections is followed by changes of the welding parameters. In this case, they can be detected by the analysis of the instant values of the welding parameters. Experiments show that monitoring of gas metal arc welding and a simple statistical approach to welding parameters can help in evaluation of weld quality. (Received 15 April 2006; Accepted 8 February 2007)
Irreversible electroporation of lung neoplasm: A case series

Summary Background Percutaneous irreversible electroporation (IRE) of lung tumors is a new minimally invasive technique which has recently been used in the treatment of soft tissue tumors. Case Reports The case histories are presented of two patients with unresectable malignancies in the lung, who underwent irreversible electroporation as a treatment attempt. The procedure was performed under CT guidance and was uneventful. Conclusions At follow up 6 months later, the tumors both appeared to have recurred. To our knowledge, no similar cases have previously been reported in the literature.
The Effect of Variations in Gold and Oil Prices on BIST 100 Index

It is commonly known that the factors that are affecting stock prices are macroeconomic variables, returns on alternative investment means, political and social stability, developments in other countries, risk preferences of domestic and foreign investors, information regarding companies and manipulations. Due to the effect of financial globalization and as local capital has transformed into an international quality, individual country economies are now more fragile against not only internal dynamics but external factors as well. Under these circumstances, the Borsa Istanbul is a stock market which has recently been popular for investors who carefully chase and direct their investments toward this spot. The present study, except the generally adopted economical factors, investigates the effect of variations in gold and oil prices on BIST 100 index econometrically. The reason for analyzing the effect of gold prices is that the global interest toward gold metal has increased overwhelmingly which caused major central banks of both developing and developed world countries increased their gold reserves. This tendency created a serious increased demand for gold which accordingly has led increased prices in the global market and affected other macro economical variables. The reason for analyzing oil prices is that fluctuation in oil prices affects economical factors both directly and indirectly. Whereas the BIST 100 index has positive relationship with oil prices; it has negative relationship with gold prices. DOI: 10.5901/mjss.2013. v4n10p726
Dynamically encoded actions based on spacetime saliency

Human actions typically occur over a well localized extent in both space and time. Similarly, as typically captured in video, human actions have small spatiotemporal support in image space. This paper capitalizes on these observations by weighting feature pooling for action recognition over those areas within a video where actions are most likely to occur. To enable this operation, we define a novel measure of spacetime saliency. The measure relies on two observations regarding foreground motion of human actors: They typically exhibit motion that contrasts with that of their surrounding region and they are spatially compact. By using the resulting definition of saliency during feature pooling we show that action recognition performance achieves state-of-the-art levels on three widely considered action recognition datasets. Our saliency weighted pooling can be applied to essentially any locally defined features and encodings thereof. Additionally, we demonstrate that inclusion of locally aggregated spatiotemporal energy features, which efficiently result as a by-product of the saliency computation, further boosts performance over reliance on standard action recognition features alone.
Efficient Multi-Point Local Decoding of Reed-Muller Codes via Interleaved Codex

Reed-Muller codes are among the most important classes of locally correctable codes. Currently local decoding of Reed-Muller codes is based on decoding on lines or quadratic curves to recover one single coordinate. To recover multiple coordinates simultaneously, the naive way is to repeat the local decoding for recovery of a single coordinate. This decoding algorithm might be more expensive, i.e., require higher query complexity. In this paper, we focus on Reed-Muller codes with usual parameter regime, namely, the total degree of evaluation polynomials is <inline-formula> <tex-math notation="LaTeX">$d=\Theta ({q})$ </tex-math></inline-formula>, where <inline-formula> <tex-math notation="LaTeX">$q$ </tex-math></inline-formula> is the code alphabet size (in fact, <inline-formula> <tex-math notation="LaTeX">$d$ </tex-math></inline-formula> can be as big as <inline-formula> <tex-math notation="LaTeX">$q/4$ </tex-math></inline-formula> in our setting). By introducing a novel variation of codex, i.e., interleaved codex (the concept of codex has been used for arithmetic secret sharing), we are able to locally recover arbitrarily large number <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> of coordinates of a Reed-Muller code simultaneously with error probability <inline-formula> <tex-math notation="LaTeX">$\exp (-\Omega (k))$ </tex-math></inline-formula> at the cost of querying merely <inline-formula> <tex-math notation="LaTeX">$O(q^{2}k)$ </tex-math></inline-formula> coordinates. It turns out that our local decoding of Reed-Muller codes shows (<italic>perhaps surprisingly</italic>) that accessing <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> locations is in fact cheaper than repeating the procedure for accessing a single location for <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> times. Precisely speaking, to get the same success probability by repeating the local decoding algorithm of a single coordinate, one has to query <inline-formula> <tex-math notation="LaTeX">$\Omega (qk^{2})$ </tex-math></inline-formula> coordinates. Thus, the query complexity of our local decoding is smaller for <inline-formula> <tex-math notation="LaTeX">$k=\Omega (q)$ </tex-math></inline-formula>. If we impose the same query complexity constraint on both algorithm, our local decoding algorithm yields smaller error probability when <inline-formula> <tex-math notation="LaTeX">$k=\Omega (q^{q})$ </tex-math></inline-formula>. In addition, our local decoding is efficient, i.e., the decoding complexity is <inline-formula> <tex-math notation="LaTeX">${\mathrm{ Poly}}(k,q)$ </tex-math></inline-formula>. Construction of an interleaved codex is based on concatenation of a codex with a multiplication friendly pair, while the main tool to realize codex is based on algebraic function fields (or more precisely, algebraic geometry codes).
A Flexible Framework for View-Based 3 D Model Retrieval

-View-based method is one of the important approaches for 3D model retrieval. In this paper, we propose a flexible framework for view-based 3D model retrieval. The framework provides users the ability to configure three components: the number of views, the type of views, and the 2D shape descriptors used to distinguish views. Because the three components are closely related to the performance of a view-based 3D model retrieval system and usually application-dependent, it is necessary to make them configurable. To achieve this goal, the framework employs a new view polyhedron positioning algorithm and provides an adaptable interface to its 3D shape feature extraction module. We build a demo 3D model retrieval system based on the framework. Experiment shows that the performance of the demo system is satisfactory. Key-Words: 3D model retrieval, information retrieval, 3D shape analysis, model feature extraction, view-based models
Long term performance of atomic layer deposition coatings for corrosion protection of stainless steel

The use of atomic layer deposition (ALD) for the corrosion protection of metallic substrates was speculated for the first time in the 1990 s. Since then, a lot of research has been carried on to investigate the application limits of this technique. ALD has been efficiently used to deposit conformal oxide layers on different metallic substrates, which were used as insulators and diffusion barriers to prevent contact between aggressive electrolytes and metal. In this work, a complete morphological and compositional characterization of some ALD coatings has been carried out using atomic force microscopy and glow discharge optical emission spectrometry. Electrochemical impedance spectroscopy and potentiodynamic polarizations have been used to evaluate the over‐time performance of three different ALD deposits on AISI 316 stainless steel, namely TiO2, Al2O3 and AlN, and the results have been compared to previous literature data. It has been observed that, in contrast with the previous literature results, Al2O3 layers deposited on AISI 316 do not suffer premature failure. On the contrary, a lower and time‐dependent corrosion protection was observed when using TiO2 coatings and a decrease of corrosion protection over time due to oxidative phenomena of the protective layer has been observed in the case of the AlN coatings.
5-Lipoxygenase compartmentalization in granulocytic cells is modulated by an internal bipartite nuclear localizing sequence and nuclear factor kappa B complex formation.

A region of basic amino acids spanning residues 639-656 in the human 5-lipoxygenase sequence resembles a consensus bipartite nuclear localizing sequence. A synthetic peptide consisting of the Kaposi fibroblast growth factor signal sequence fused to the 5-lipoxygenase639-656 bipartite nuclear localizing sequence has a prominent inhibitory effect on 5-lipoxygenase catalysis in granulocytic HL-60 cells activated by calcium ionophor A23187. Recombinant 5-lipoxygenase was not affected by the peptide. The peptide also inhibited redistribution of 5-lipoxygenase from the cytosol to the nuclear membrane of HL-60 cells stimulated by A23187. 5-Lipoxygenase protein was detected in nuclear factor kappaB (NF-kappaB) p65 subunit immunoprecipitate fractions prepared from HL-60 cell lysates. The amount of 5-lipoxygenase protein coimmunoprecipitated by NF-kappaB antiserum was increased following A23187 stimulation. In cells treated with agents that block 5-lipoxygenase translocation to the nucleus, 5-lipoxygenase protein appearing in the NF-kappaB immunoprecipitate was diminished. Our results implicate an internal bipartite nuclear localizing sequence as a regulatory domain that modulates 5-lipoxygenase redistribution and catalysis in granulocytic cells. Additionally, our results suggest that molecular determinants which govern 5-lipoxygenase and NF-kappaB redistribution to the nucleus may be coordinately controlled in granulocytic cells.
Production, Properties, and Some New Applications of Chitin and Its Derivatives

Chitin is a polysaccharide composed from N-acetyl-D-glucosamine units. It is the second most abundant biopolymer on Earth and found mainly in invertebrates, insects, marine diatoms, algae, fungi, and yeasts. Recent investigations confirm the suitability of chitin and its derivatives in chemistry, biotechnology, medicine, veterinary, dentistry, agriculture, food processing, environmental protection, and textile production. The development of technologies based on the utilization of chitin derivatives is caused by their polyelectrolite properties, the presence of reactive functional groups, gel-forming ability, high adsorption capacity, biodegradability and bacteriostatic, and fungistatic and antitumour influence. Resources of chitin for industrial processing are crustacean shells and fungal mycelia. Fungi contain also chitosan, the product of N-deacetylation of chitin. Traditionally, chitin is isolated from crustacean shells by demineralization with diluted acid and deproteinization in a hot base solution. Furthermore, chitin is converted to chitosan by deacetylation in concentrated NaOH solution. It causes changes in molecular weight and a degree of deacetylation of the product and degradation of nutritionally valuable proteins. Thus, enzymatic procedures for deproteinization of the shells or mold mycelia and for chitin deacetylation were investigated. These studies show that chitin is resistant to enzymatic deacetylation. However, chitin deacetylated partially by chemical treatment can be processed further by deacetylase. Efficiency of enzymatic deproteinization depends on the source of crustacean offal and the process conditions. Mild enzymatic treatment removes about 90% of the protein and carotenoids from shrimp-processing waste, and the carotenoprotein produced is useful for feed supplementation. In contrast, deproteinization of shrimp shells by Alcalase led to the isolation of chitin containing about 4.5% of protein impurities and recovery of protein hydrolysate. Referee: Dr. Norman F. Haard, Professor, Institute of Marine Resources, Department of Food Science & Technology, University of California, Davis, CA 95616
Time Perspective, Depression, and Substance Misuse Among the Homeless

Using the Zimbardo Time Perspective Inventory (ZTPI; P. G. Zimbardo & J. N. Boyd, 1999), the authors found that homeless people, in comparison with a control group, had a significantly more negative outlook concerning their past and present as evinced by high Past-Negative and Present-Fatalistic scores and low Past-Positive scores on the ZTPI. However, the homeless individuals were almost indistinguishable from control participants on measures of Present-Hedonism and Future thinking. The homeless individuals had significantly higher levels of depression, with 31 out of 50 (62%) reaching criteria for probable depression. However, this finding was unrelated to their atypical time perspective. There was no significant relation between substance misuse and time perspective. Despite their current difficulties, including depression and drug abuse, the homeless individuals maintained a propensity toward future thinking characterized by striving to achieve their goals.