Miracle-dz/UniFAR-FTUs huggingface dataset:
A Potent Cell Death Activity Associated with Transient High Level Expression of BCL-2*

The BCL-2 proto-oncogene contains unusually long untranslated 5′ and 3′ sequences. Deletion of the sequences flanking the BCL-2 open reading frame dramatically increases the level of protein expression. Transient high level BCL-2 protein expression mediated by plasmid transfection or by infection with recombinant adenovirus results in potent apoptosis of several cell lines. Detailed mutational (deletion and add-back) analysis reveals that both 5′- and 3′-flanking sequences contribute to the negative modulation of protein expression from the BCL-2 open reading frame. It appears that these sequences exert the negative regulatory effect in an orientation-dependent manner. Analysis of BCL-2RNA levels indicate that elevated levels of mRNA may be the primary cause of elevated levels of protein expression. Apoptosis induced by adenovirus vectors expressing elevated levels of BCL-2 can be readily inhibited by the caspase inhibitor z-VAD-fmk, suggesting that high levels of BCL-2 expression induce apoptosis via the caspase cascade. Mutational analysis of BCL-2 indicates that its pro-apoptotic activity is separable from its anti-apoptosis activity. Our results raise the possibility that oncogenic conversion of BCL-2 may require somatic mutations in the pro-apoptotic activity, in addition to other activating mutations that result in enhanced expression. Consistent with this hypothesis, a somatic mutation of BCL-2 observed in multiple human tumors results in reduced apoptosis activity.
Tissue distribution of CYP3A29 mRNA expression in Bama miniature pig by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR)

Pig or minipig cytochrome P450 (CYP) 3A isozymes have been proven to be a good model of human drug metabolism, and human CYP3A seems to be well modelled by pig or minipig CYP3A29. We studied CYP3A29 mRNA expression in ten tissues (liver, duodenum, kidney, adrenal gland, skin, brain, lung, testis, uterus and ovary) in different age groups of Bama miniature pig by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). In adult pig (4 and 6 months old), the most relative expression by normalization to β-actin of CYP3A29 mRNAs of tissues is in liver; then in duodenum, skin and kidney. Values of CYP3A29 in the extrahepatic tissues except for duodenum are very low compared with that in liver. In new-borns the mean CYP3A29 expression in duodenum was higher than that in liver, and the expression in skin was very low while high in 40 days, 4 months and 6 months age groups. For different ages, the increased CYP3A29 expression in liver and duodenum was detected with age. The effective CYP3A29 induction in liver was also detected by rifampin oral intubation. Apparent interindividual variability of CYP3A29 mRNA expression in Bama miniature pigs was detected. This work will broaden the understanding of the physiological functions of CYP3A29 in miniature pig, and promote Bama miniature pig’s application in pharmacological and toxicological studies.
Full integration and cell characteristics for 64Mb nonvolatile PRAM

We have integrated a 64Mb nonvolatile random access memory using phase transition phenomena. Based on 0.18/spl mu/m-CMOS technologies, the vertical contact typed memory cell is fabricated. The device density can be sharply increased with decreasing the writing current and the GST size. But for reduction of writing current, issues including set and interface resistances should be stabilized. Additionally, our results also show the feasibility of 256Mb nonvolatile PRAM with writing time below 100ns.
Progression of fibrosis in hepatitis C with and without schistosomiasis: Correlation with serum markers of fibrosis

Serial liver biopsies are the gold standard by which the progression of fibrosis is evaluated. This longitudinal cohort study assessed the different rates in the progression of fibrosis using serial liver biopsies and serum fibrosis markers YKL‐40 and PIIINP and the cytokines, transforming growth factor beta (TGF‐β) and tumor necrosis factor alpha (TNF−α). A 10‐year cohort study was performed in patients with hepatitis C virus (HCV) alone or HCV and schistosomiasis. Patients were enrolled at the time of acute HCV infection and prospectively evaluated with two liver biopsies (at entry and end of follow‐up), and true rates in the progression of fibrosis were calculated per year. Serum YKL‐40, N‐terminal propeptide of collagen III (PIIINP), TGF‐β, and TNF‐α were measured, as well as the expression of TGF‐β, TNF‐α, and YKL‐40 mRNA in liver tissue. A significant increase in the progression rates of fibrosis occurred in the coinfected group (0.61 ± 0.13) compared with the HCV monoinfection group (0.1 ± 0.06; P < .001)). The progression of fibrosis rate/year had a direct linear correlation for YKL‐40 (r = 0.892, P < .001) and for PIIINP (r = 0.577, P < .01). YKL‐40 showed a linear correlation with TGF‐β (r = 0.897, P < .001). Hepatic mRNA levels of YKL‐40 and TGF‐β correlated with the serum levels, confirming a hepatic source for the elevated serum levels. In conclusion, serial cytokine and fibrosis markers can accurately determine the rate at which fibrosis is progressing, identifying both those with rapid fibrosis and those with stable disease. (HEPATOLOGY 2006;43:771–779.)
Dephosphorylation of the Calcium Pump Coupled to Counterion Occlusion

P-type ATPases extract energy by hydrolysis of adenosine triphosphate (ATP) in two steps, formation and breakdown of a covalent phosphoenzyme intermediate. This process drives active transport and countertransport of the cation pumps. We have determined the crystal structure of rabbit sarcoplasmic reticulum Ca2+ adenosine triphosphatase in complex with aluminum fluoride, which mimics the transition state of hydrolysis of the counterion-bound (protonated) phosphoenzyme. On the basis of structural analysis and biochemical data, we find this form to represent an occluded state of the proton counterions. Hydrolysis is catalyzed by the conserved Thr-Gly-Glu-Ser motif, and it exploits an associative nucleophilic reaction mechanism of the same type as phosphoryl transfer from ATP. On this basis, we propose a general mechanism of occluded transition states of Ca2+ transport and H+ countertransport coupled to phosphorylation and dephosphorylation, respectively.
Comparison between resource reservation protocol and next steps in signalling in mobile IP networks

Providing an acceptable level of quality of service (QoS) for critical applications is one of the interesting topics in next generation wireless networks. Confronting the major criticisms of resource reservation protocol (RSVP), the next steps in signalling (NSIS) was introduced as a general framework to include not only the RSVP but other signalling services in IP-based networks. It attempts to address the RSVP shortcomings and to offer additional features. It is widely believed that NSIS can be considered as a suitable alternative for RSVP. However, it worsens the scalability issue in the RSVP operation, inherits the RSVP problem in mobile environments and its appealing features come with a significant cost. This study develops an analytical framework to evaluate the RSVP and NSIS performances in proxy mobile IPv6 (PMIPv6) environment. The results obtained showed a significant increase in network signalling cost, more bandwidth consumption by resource reservation signalling messages and a high resource re-establishment latency in NSIS operations. The authors believe these outcomes raise doubts over the NSIS eligibility as a suitable replacement for RSVP.
Cbfa1 Contributes to the Osteoblast-specific Expression of type I collagen Genes*

Type I collagen is composed of two chains, α1(I) and α2(I), encoded by two distinct genes, the α1(I) and α2(I) collagen genes, that are highly expressed in osteoblasts. In most physiological situations, α1(I) and α2(I) collagen expression is coregulated, suggesting that identical transcription factors control their expression. Here, we studied the role of Cbfa1, an osteoblast-specific transcription factor, in the control of α1(I) and α2(I) collagen expression in osteoblasts. A consensus Cbfa1-binding site, termed OSE2, is present at the same location in the α1(I) collagen promoter at approximately −1347 base pairs (bp) of the rat, mouse, and human genes. Cbfa1 can bind to this site, as demonstrated by electrophoretic mobility shift assay (EMSA) and supershift experiments using an anti-Cbfa1 antibody. Mutagenesis of the α1(I) collagenOSE2 at −1347 bp reduced the activity of a α1(I) collagen promoter fragment 2- to 3-fold. Moreover, multimers of this OSE2 at −1347bp confer osteoblast-specific activity to a minimum α1(I) collagen promoter fragment in DNA transfection experiments as well as in transgenic mice. An additional Cbfa1-binding element is present in the α1(I) collagen promoter of mouse, rat, and human at approximately position −372. This site binds Cbfa1 only weakly and does not act as a cis-acting activator of transcription when tested in DNA transfection experiments. Similar to α1(I) collagen, the mouse α2(I) collagen gene contains multiple OSE2 sites, of which one is conserved across multiple species. In EMSA, Cbfa1 binds to this site and multimers of this α2(I) OSE2 element confer osteoblast-specific activity to the minimum α1(I) collagen promoter in DNA transfection experiments. Thus, our results suggest that Cbfa1 is one of the positive regulators of the osteoblast-specific expression of both type I collagengenes.
Evaluating Genetic Algorithms for selection of similarity functions for record linkage

Machine learning algorithms have been successfully employed in solving the record linkage problem. Machine learning casts the record linkage problem as a classification problem by training a classifier that classifies 2 records as duplicates or unique. Irrespective of the machine learning algorithm used, the initial step in training a classifier involves selecting a set of similarity functions to be applied to each attribute to get a similarity measure. Usually this is done manually with input from a domain expert. We evaluate an approach in which the optimal combination of similarity function for a given type of input data records is searched using Genetic Algorithms.
Probing RNA Folding Pathways by RNA Fingerprinting

This unit provides protocols for using native polyacrylamide gel electrophoresis to distinguish folding and unfolding conformers of RNA. It is useful for studying conformers that can exchange in a period of minutes or seconds, and that are thus difficult to study by solution‐based methods. Conformers that have been separated and immobilized in the gel matrix can be used to studying catalytic activity with or without being eluted from the gel. The method can be applied to a wide varied of catalytic RNAs and RNA‐protein complexes.
N‐terminal region of ZW10 serves not only as a determinant for localization but also as a link with dynein function

ZW10 interacts with dynamitin, a subunit of the dynein accessory complex dynactin, and functions in termination of the spindle checkpoint during mitosis and in membrane transport between the endoplasmic reticulum (ER) and Golgi apparatus during interphase. Its associations with kinetochores and ER membranes are mediated by Zwint‐1 and RINT‐1, respectively. A previous yeast two‐hybrid study showed that the C‐terminal region of ZW10 interacts with dynamitin, and part of this region has been used as an inhibitor of ZW10 function. In the present study, we reinvestigated the interaction between ZW10 and dynamitin, and showed that the N‐terminal region of ZW10 is the major binding site for dynamitin and, like full‐length ZW10, could potentially move along microtubules to the centrosomal area in a dynein‐dynactin‐dependent manner. Competitive binding experiments demonstrated that dynamitin and RINT‐1 occupy the same N‐terminal region of ZW10 in a mutually exclusive fashion. Consistent with this, over‐expression of RINT‐1 interfered with the dynein‐dynactin‐mediated movement of ZW10 to the centrosomal area. Given that the N‐terminal region of ZW10 also interacts with Zwint‐1, this region may be important for switching partners; one partner is a determinant for localization (kinetochore and ER) and the other links ZW10 to dynein function.
An “elite hacker”

The year 2011 marked the 40 year anniversary of Richard Nixon signing the National Cancer Act, thus declaring the beginning of the “War on Cancer” in the United States. Whereas we have made tremendous progress toward understanding the genetics of tumors in the past four decades, and in developing enabling technology to dissect the molecular underpinnings of cancer at unprecedented resolution, it is only recently that the important role of the stromal microenvironment has been studied in detail. Cancer is a tissue-specific disease, and it is becoming clear that much of what we know about breast cancer progression parallels the biology of the normal breast differentiation, of which there is still much to learn. In particular, the normal breast and breast tumors share molecular, cellular, systemic and microenvironmental influences necessary for their progression. It is therefore enticing to consider a tumor to be a “rogue hacker”—one who exploits the weaknesses of a normal program for personal benefit. Understanding normal mammary gland biology and its “security vulnerabilities” may thus leave us better equipped to target breast cancer. In this review, we will provide a brief overview of the heterotypic cellular and molecular interactions within the microenvironment of the developing mammary gland that are necessary for functional differentiation, provide evidence suggesting that similar biology—albeit imbalanced and exaggerated—is observed in breast cancer progression particularly during the transition from carcinoma in situ to invasive disease. Lastly we will present evidence suggesting that the multigene signatures currently used to model cancer heterogeneity and clinical outcome largely reflect signaling from a heterogeneous microenvironment—a recurring theme that could potentially be exploited therapeutically.
A System-On-Chip Approach in Designing a Dedicated RISC Microcontroller Unit Using the Field-Programmable Gate Array

Standard processors have logical resources necessary for implementing various calculating platforms, capable to execute applications in different fields such as communication, command and control or signal processing. However, the sequential aspect of executing the instructions, the speed limit given by the access to the memory block and the standard architecture of the processors, dictate some of the systems limitations regarding its performance. A solution that can increase the performance for a specified application, is the hardware implementation of the calculating platform using the Field Programmable Gate Array. This paper presents a principle on how performance can be improved in the context of Microcontroller Units applications, using the Instruction Set Architecture of a conventional Reduced Instruction Set Computer, over Field Programmable Gate Array. It concludes how this idea could be suggested as a principle at a higher scale, in designing dedicated System-On-Chip with the Field Programmable Gate Array.
A Novel Algorithm for Optimizing Multiple Services Resource Allocation

Resource provisioning becomes more and more challenging problem in cloud computing environment since cloudbased services become more numerous and dynamic. The problem of scheduling multiple tasks for multiple users on a given number of resources is considered NP-Complete problem, and therefore, several heuristic based research methods were proposed, yet, there are still many improvements can be done, since the problem has several optimization parameters. In addition, most proposed solutions are built on top of several assumptions and simplifications by applying computational methods such as game theory, fuzzy logic, or evolutionary computing. This paper presents an algorithm to address the problem of resource allocation across a cloud-based network, where several resources are available, and the cost of computational service depends on the amount of computation. The algorithm is applicable without restrictions on cost vector or compaction time matrix as opposed to methods in the literature. In addition, the execution of the algorithm shows better utility compared to methods applied on similar problems
Significance of the vertical profile of the Indonesian Throughflow transport to the Indian Ocean

Using an ocean general circulation model, we find that the vertical profile of the Indonesian Throughflow (ITF) transport is important in regulating the stratification and surface heat fluxes of the Indian Ocean. With the same total ITF transport, a thermocline‐intensified ITF, relative to a surface‐intensified ITF, not only cools the surface layer of the Indian Ocean while warming the Indian Ocean below the thermocline, but also induces negative temperature anomalies at the sea surface throughout the Indian basin. As a consequence of this surface effect the net heat gain of the Indian Ocean is increased. The results suggest that it is necessary to properly represent the vertical profile of ITF transport within ocean and climate numerical models.
The relationship between phytoplankton biovolume and chlorophyll in a deep oligotrophic lake: decoupling in their spatial and temporal maxima

The seasonal distributions of phytoplankton biovolume and chlorophyll a content were monitored for 14 months in a deep oligotrophic, high mountain lake (Redo, Pyrenees). An allomet- ric relationship of chlorophyll with biovolume was found throughout the period studied, with a corre- lation coefficient of 0.66. However, the relationship changed with season and the taxonomic composition of the phytoplankton. Both parameters showed a similar seasonal pattern, but differ- ences in space and time were observed. The chlorophyll maximum was recorded deeper and later than that of phytoplankton biovolume. While the biovolume maximum was related to an improve- ment in conditions for growth (nutrient input during column mixing periods), and reflected an increase in biomass, the chlorophyll maximum was related to changes in cell pigment content, and to spatial or successional trends in species dominance. Flagellated chrysophytes predominated at the chlorophyll maxima. Chlorophyll content per unit of phytoplankton biovolume fluctuated greatly throughout the year, depending on light intensity, temperature and phytoplankton composition. Of the main groups of phytoplankton in the lake, the dinoflagellates, which dominated the summer epil- imnion phytoplankton community, recorded the lowest pigment content per biovolume (which is consistent with their size). Higher chlorophyll contents per biovolume were found in the deep hypolimnion and during the winter cover period associated with small cells such as some species of chlorococcales chlorophytes. When flagellated chrysophytes were predominant, a broad range of chlorophyll values per biovolume was found and there was no significant correlation between the two biomass indices. These findings reaffirm the need to treat phytoplankton biomass estimates with caution, in particular when conducting primary production studies. While our results show that changes in chlorophyll content per cell occur as a photoacclimation response along a vertical profile, they also point out a component of the successional trends which appear in a phytoplankton growth phase in a lake.
Vocabulary acquisition for deaf readers using augmented technology

Learning how to read for deaf and hard-of-hearing children poses a few challenges that have been explored over the years by various researchers [13]. We propose an innovative solution that may enhance the way deaf and hard-of-hearing children learn to read through the use of a head-mounted-display (HMD). Through the HMD, deaf and hard-of-hearing children will be able look up unfamilar printed words from a varity of sources and have an American Sign Language (ASL) video definition play back for them.
Anisotropic cooperative structural rearrangements in sheared supercooled liquids.

A supercooled liquid generally exhibits marked shear-thinning behavior, but its detailed mechanism remains elusive. Here we study the dynamics of structural rearrangements in supercooled liquids under shear, using two-dimensional (2D) molecular dynamics simulation. To elucidate the relationship between heterogeneous dynamics and the rheological behavior, we extend the four-point correlation function, which has been used for analyzing "dynamic heterogenity" in a quiescent condition, to a system under steady shear. In the Newtonian regime, the rearrangement dynamics is strongly heterogeneous in space, but remains isotropic. Contrary to this, in the non-Newtonian regime, where marked shear-thinning behavior appears, we find a novel dynamic effect: The mobile region tends to form anisotropic "fluidized bands. " This finding suggests a link between nonlinear rheology and inhomogeneization of flow.
Converting Treebank Annotations to Language Neutral Syntax

We describe the automatic conversion of English Penn Treebank (PTB) annotations into Language Neutral Syntax (LNS) (Campbell and Suzuki, 2002a,b). In this paper, we describe LNS and why it is useful, describe the conversion algorithm, present an evaluation of the conversion, and discuss some uses of the converted annotations and the potential for extending the coverage to other languages. The work described here is in the spirit of other automatic re-annotations of PTB trees (e.g. Frank, 2000 and Meyers, 2001), but differs in the nature of the output.
School-Based Educational Intervention to Improve Children’s Oral Health–Related Knowledge

Objective. To evaluate a brief oral health promotion intervention delivered in schools by a primary care dental practice, aimed at changing oral health care knowledge and oral health–related behaviors in children. Design. Cohort study with pretest–posttest design. Setting. Three primary schools. Participants. One hundred and fifty children (aged 9-12 years). Intervention. Children received a 60-minute theory-driven classroom-based interactive educational session delivered by a dental care professional and received take-home literature on oral health. Main Outcome Measures. All children completed a questionnaire on oral health–related knowledge and self-reported oral health–related behaviors before, immediately after, and 6 weeks following the intervention. Results. Children’s dental knowledge significantly improved following the intervention, with improvement evident at immediate follow-up and maintained 6 weeks later. Significantly more children reported using dental floss 6 weeks after the intervention compared with baseline. No significant differences were detected in toothbrushing or dietary behaviors. Conclusions. School-based preventative oral health education delivered by primary care dental practices can generate short-term improvements in children’s knowledge of oral health and some aspects of oral hygiene behavior. Future research should engage parents/carers and include objective clinical and behavioral outcomes in controlled study designs.