Miracle-dz/UniFAR-FTUs huggingface dataset:
Four major transcriptional responses in the methionine/threonine biosynthetic pathway of Saccharomyces cerevisiae

Genes encoding enzymes in the threonin/methionine biosynthetic pathwa were cloned and used to investigate their transcriptional response to signals known to affect gene expression on the basis of enzyme specific‐activities. Four major responses were evident: strong repression by methionine of MET3, MET5 and MET14, as previously described for MET3, MET2 and MET25; weak repression by methionine of MET6; weak stimulation by methionine but no response to threonine was seen for THR1, HOM2 and HOM3; no response to any of the signals tested, for HOM6 and MES1. In a BOR3 mutant, THR1, HOM2 and HOM3 mRNA levels were increased slightly. The stimulation of transcription by methionine for HOM2, HOM3 and THR1 is mediated by the GCN4 gene product and hence these genes are under the general amino acid control. In addition to the strong repression by methionine, MET5 is also regulated by the general control.
Action Classification and Highlighting in Videos

Inspired by recent advances in neural machine translation, that jointly align and translate using encoder-decoder networks equipped with attention, we propose an attentionbased LSTM model for human activity recognition. Our model jointly learns to classify actions and highlight frames associated with the action, by attending to salient visual information through a jointly learned soft-attention networks. We explore attention informed by various forms of visual semantic features, including those encoding actions, objects and scenes. We qualitatively show that soft-attention can learn to effectively attend to important objects and scene information correlated with specific human actions. Further, we show that, quantitatively, our attention-based LSTM outperforms the vanilla LSTM and CNN models used by stateof-the-art methods. On a large-scale youtube video dataset, ActivityNet, our model outperforms competing methods in action classification.
Biochemical and immunocytochemical charaterization of olfactory marker protein in the rodent central nervous system

Olfactory marker protein (OMP), previously thought to be expressed only by olfactory receptor neurons and their processes, was localized anatomically with immunocytochemical techniques to a number of brain regions in three rodent species, the mouse, rat, and hamster. In addition, the amount of antigen was quantified by radioimmunoassay (RIA) and characterized by an immunoblot procedure. In all three species the antigen could be detected immunocytochemically in the preoptic region and hypothalamus. The rat did not exhibit immunostaining in any other brain region. However, in the mouse neuronal labelling was observed throughout the neural axis, including cellular labelling in the bed nucleus of the anterior commissure, the median preoptic nucleus, the bed nucleus of the stria terminalis, the periventricular region, the anterior parvicellular subnucleus of the paraventricular nucleus, around the dorsomedial hypothalamic nucleus (pars compacta), the subincertal region, the arcuate nucleus, the anterior cortical nucleus of the amygdala, the suprageniculate nucleus, the lateral lemniscal nuclei, the lateraldorsal and lateralventral central gray, the posterior aspects of the commissural and marginal nuclei of the inferior colliculus, the paragenule nucleus, the A‐5 region, the area postrema, the ventromedial nucleus of the solitary tract, area X, the spinal trigeminal nucleus (pars zonale), and superficial laminae of the spinal cord. The hamster displayed a different pattern of labelling including cells in the periventricular gray, the pontine reticular tegmental nucleus, the A‐5 region, the medial vestibular complex, the prepositus hypoglossal nucleus, the parvicellular reticular nucleus, the lateral paragigantocellular nucleus, the raphe obscuras, the lateral reticular nucleus, and the lateral nucleus of the cerebellum. Immunostaining was seen in fibers within the red nucleus and within mossy fibers of the cerebellum. OMP levels could only be quantified by radioimmunoassay in the olfactory bulb of the three species and in the hamster cerebellum where they were 1/1,000 of those determined in the olfactory bulb. The authenticity of OMP measured in the RIA and detected immunocytochemically was verified by a double‐antibody immunoisolation/immunodetection procedure, which confirmed that the antigen being visualized had the molecular properties expected for OMP. In summary, these experiments demonstrate that authentic OMP exists in small groups of neurons in many areas of the central nervous system.
Brain functional changes in patients with ulcerative colitis: A functional magnetic resonance imaging study on emotional processing

Background: Ulcerative colitis (UC) is associated with psychological stress and poor emotional functioning. The neural emotional processing involves the complex integration of several cortical and subcortical brain structures. The amygdala plays a fundamental role in the neural processing of emotional stimuli and is a core structure of the brain–gut axis (BGA) that represents the anatomo‐functional substrate for the bidirectional influences between emotions and gastrointestinal functions. The aim of this study was to investigate the brain emotional processing in UC patients compared to healthy people. Methods: Ten UC patients in remission and 10 matched healthy controls underwent a functional magnetic resonance imaging (fMRI) scan while performing a task involving emotional visual stimuli. A set of negative, positive, and neutral pictures were used to study brain‐related emotional responses. Results: A significantly reduced blood oxygen level‐dependent (BOLD) signal in UC patients relative to controls was found in the amygdala, thalamic regions, and cerebellar areas (P < 0.05 corrected for multiple comparisons). The group‐related differences were detected in the brain activity in response to positive emotional stimuli. Conclusions: UC is associated with an emotional dysfunction characterized by decreased sensitivity to emotions with a positive content. The previous intestinal inflammatory activity in UC patients might have contributed to determine the functional changes of the amygdala that we found. On the other hand, the dysfunction of the amygdala may influence the course of the disease. (Inflamm Bowel Dis 2010;)
In vitro and in vivo therapeutic efficacy of the PPAR‐γ agonist troglitazone in combination with cisplatin against malignant pleural mesothelioma cell growth

Malignant pleural mesothelioma (MPM), an aggressive and refractory tumor type, is increasing in frequency throughout the world. Peroxisome proliferator activated receptor‐γ (PPAR‐γ) agonists have anticancer activity against several cancer cell lines in vitro and in vivo. However, there have been no reports that PPAR‐γ agonists induce growth inhibition of MPM cell lines. In this study, we investigated the inhibitory effect of a PPAR‐γ agonist in combination with an anticancer agent on MPM cell growth in vitro and in vivo. We examined the therapeutic efficacy of the PPAR‐γ agonist troglitazone (TGZ) in combination with cisplatin against a human MPM cell line, both in vitro and orthotopically inoculated into severe combined immunodeficient (SCID) mice. Troglitazone (TGZ) alone inhibited MPM cell growth in vitro in a dose‐dependent manner via induction of G1 cell cycle arrest and apoptosis. The combination of TGZ and cisplatin showed an additive inhibitory effect on MPM cell growth compared to treatment with either individual drug. Treatment with 500 mg/kg or 1000 mg/kg TGZ effectively inhibited the production of thoracic tumors and pleural effusion in EHMES‐10 cell‐bearing SCID mice. Moreover, treatment with 500 mg/kg TGZ in combination with 3 mg/kg cisplatin more effectively prolonged survival compared to treatment with either individual drug. These results suggest that TGZ in combination with cisplatin may become a novel therapy for MPM. (Cancer Sci 2010)
Mechanism of kidney injury caused by bevacizumab in rats.

OBJECTIVE We investigate kidney injury caused by high dose bevacizumab to uncover the possible mechanisms involving in this process. METHODS Forty rats were divided into four groups: cisplation group (treated with 1 mg/kg cisplation), Bev-high group (treated with 5 mg/kg bevacizumab); Bev-low group (treated with 2.5 mg/kg bevacizumab) and control group (treated with saline). The urine microalbumin, serum cystatin C, blood urea nitrogen and serum creatinine were detected in the four group rats, respectively. The immunoglobulin of IgG, IgA and IgM and protein of VEGF (vascular endothelial growth factor) and nephrin were detected by immunohistochemical methods. RESULTS All the levels of microalbumin, cystatin C, serum creatinine and blood urea nitrogen in Bev-high group were significantly higher than those in normal control group (P < 0.05). The cystatin C was much more increased in kidney Bev-high group than cisplatin and Bev-low groups (P < 0.05). The light microscope showed a normal glomerular morphology in the four groups, while the electronic microscopy showed the podocytes were extensively fused in cisplatin group and Bev-high group. The two groups were found IgG and IgM deposition as well. The VEGF in kidney amples were down regulated in high dose bevacizumab group, whereas the nephrin and IgA showed no significant expression changes at all. CONCLUSION Bevacizumab increases the risk of injury in glomerular filtration barrier in a dose dependent model. The injury may not only associate with the rising level of proteinuria but also with podocyte-dependent membrane structures.
In Vitro and In Vivo Evaluation of Proniosomes Containing Celecoxib for Oral Administration

The objectives of this research were to prepare celecoxib proniosomes and evaluate the influence of proniosomal formulation on the oral bioavailability of the drug in human volunteers. A new proniosomal delivery system for a poorly water-soluble drug such as celecoxib was developed and subjected to in vitro and in vivo studies. Proniosomes were prepared by sequential spraying method, which consisted of cholesterol, span 60, and dicetyl phosphate in a molar ratio of 1:1: 0.1, respectively. The average entrapment percent of celecoxib proniosome-derived niosomes was about 95%. The prepared proniosomes showed marked enhancement in the dissolution of celecoxib as compared to pure drug powder. The bioavailability of 200 mg single dose of both celecoxib proniosomal formulation and a conventional marketed celecoxib capsule was studied in human volunteers. The obtained results show that the proniosomal formulation significantly improved the extent of celecoxib absorption than conventional capsule. The mean relative bioavailability of the proniosomal formulation to the conventional capsule was 172.06 ± 0.14%. The mean Tmax for celecoxib was prolonged when given as proniosomal capsule. There was no significant difference between the values of Kel and t1/2 for both celecoxib preparations. In conclusion, the proniosomal oral delivery system of celecoxib with improved bioavailability was established.
The effect of entacapone (OR‐611) on brain [18F]‐6‐L‐fluorodopa metabolism

We used PET and [18F]-6-L-fluorodopa ([18F]dopa) to measure the effect of a peripheral COMT inhibitor, entacapone, on the extracerebral metabolism and subsequent striatal uptake of [18F]dopa. Four parkinsonian patients and six age-matched normal controls were each scanned twice, once after carbidopa (150 mg) plus placebo and once after carbidopa (150 mg) plus entacapone (400 mg or 800 mg). Without entacapone premedication, by 90 minutes from injection, only 22% of the [18F] signal in plasma represented unmetabolized [18F]dopa (the balance being 3-0-methyl[18F]dopa). After entacapone medication, this fraction increased to 56% of the [18F] signal (p < 0.0001). We did not find any significant differences between the changes observed in patients versus controls or between those subjects who received 400 mg entacapone versus 800 mg in either this or any of the other reported measures. PET image contrast increased in all cases, reflecting an increase in the specific striatal signal ([striatum-oceipitalhoccipital ratio increased 38% [p < 0.0001]). Entacapone did not alter the rate of striatal uptake and decarboxylation of [18F]dopa as estimated using a graphic approach with metabolite-corrected plasma as input function to calculate the influx constant, Ki(p) (p = NS). This confirms that such an analytic approach adequately corrects for the effect of extracerebral [18F]dopa methylation. In contrast, the influx constant Ki(o) (calculated using occipital counts as the input function) increased 45% after entacapone (p < 0.0001). This demonstrates the sensitivity of this analytic approach to the presence of peripheral 3-O-methyl[18F]dopa and provides an estimate of the percentage increase in brain free [18F]dopa resulting from entacapone premedication.
Vitamin D deficiency predicts decline in kidney allograft function: a prospective cohort study.

CONTEXT Vitamin D, often deficient in kidney transplant (KTx) recipients, has potential immunomodulatory effects. OBJECTIVE This study aimed to evaluate whether vitamin D status affects the rate of decline in kidney allograft function. DESIGN, SETTING, AND PATIENTS The study included a prospective cohort of 264 ambulatory KTx recipients at a single Japanese center. MAIN OUTCOME MEASURES We measured the baseline 25-hydroxyvitamin D (25D) concentration and examined its association with annual decline in estimated glomerular filtration rate (eGFR). Secondary outcome was rescue treatment with iv methylprednisolone (IV-MP) as an index of rejection episodes. RESULTS The mean serum 25D concentration was 17.1 (SD 6.5) ng/mL, and 68.4% patients had vitamin D inadequacy or deficiency. Time after KTx was a significant effect modifier for the association of serum 25D concentration with annual eGFR change and need for IV-MP (P for interaction < .1). We divided patients according to the median time after KTx (10 y) and found that low vitamin D was significantly associated with a rapid eGFR decline at less than 10 years after KTx but not at 10 or more years after KTx. The same was true for rescue treatment with IV-MP. Overall, propensity score matching showed independent associations of low vitamin D with both outcomes. Stratified matching confirmed pronounced associations at less than 10 years after KTx. CONCLUSIONS Vitamin D deficiency predicts a rapid decline in eGFR and need for IV-MP at less than 10 years after KTx. Future studies are warranted to evaluate the clinical efficacy of vitamin D supplementation.
PmrB Mutations Promote Polymyxin Resistance of Pseudomonas aeruginosa Isolated from Colistin-Treated Cystic Fibrosis Patients

ABSTRACT Pseudomonas aeruginosa can develop resistance to polymyxin and other cationic antimicrobial peptides. Previous work has shown that mutations in the PmrAB and PhoPQ regulatory systems can confer low to moderate levels of colistin (polymyxin E) resistance in laboratory strains and clinical isolates of this organism (MICs of 8 to 64 mg/liter). To explore the role of PmrAB in high-level clinical polymyxin resistance, P. aeruginosa isolates from chronically colistin-treated cystic fibrosis patients, most with colistin MICs of >512 mg/liter, were analyzed. These cystic fibrosis isolates contained probable gain-of-function pmrB alleles that conferred polymyxin resistance to strains with a wild-type or pmrAB deletion background. Double mutant pmrB alleles that contained mutations in both the periplasmic and dimerization-phosphotransferase domains markedly augmented polymyxin resistance. Expression of mutant pmrB alleles induced transcription from the promoter of the arnB operon and stimulated addition of 4-amino-l-arabinose to lipid A, consistent with the known role of this lipid A modification in polymyxin resistance. For some highly polymyxin-resistant clinical isolates, repeated passage without antibiotic selection pressure resulted in loss of resistance, suggesting that secondary suppressors occur at a relatively high frequency and account for the instability of this phenotype. These results indicate that pmrB gain-of-function mutations can contribute to high-level polymyxin resistance in clinical strains of P. aeruginosa.
Adaptive divided difference filter for nonlinear systems with unknown noise

An Adaptive Divided Difference filter has been proposed for joint estimation of parameter and states of nonlinear systems in situations with unknown process noise statistics. The proposed filter, which is based on the innovation sequence, ensures improved estimation performance adapting the unknown process noise covariance. The performance of the filter is assessed with a benchmark nonlinear problem. Simulation results demonstrate that the performance of the proposed filter is superior compared to a non adaptive Divided Difference filter when the process noise covariance is unknown.
T Lymphocyte Activation Signals for Interleukin-2 Production Involve Activation of MKK6-p38 and MKK7-SAPK/JNK Signaling Pathways Sensitive to Cyclosporin A*

p38/CSBP, a subgroup member of mitogen-activated protein kinase (MAPK) superfamily molecules, is known to be activated by proinflammatory cytokines and environmental stresses. We report here that p38 is specifically activated by signals that lead to interleukin-2 (IL-2) production in T lymphocytes. A p38 activator MKK6 was also markedly activated by the same stimulation. Pretreatment of cells with SB203580, a specific inhibitor of p38, as well as expression of a dominant-negative mutant of MKK6, suppressed the transcriptional activation of the IL-2 promoter. We also demonstrated that MKK7, a recently described MAPK kinase family member, plays a major role in the activation of stress-activated protein kinase (SAPK)/c-Jun NH2-terminal kinase (JNK) in T lymphocytes. Moreover, a dominant-negative mutant of MKK7 abrogated the transcriptional activation of the distal nuclear factor of activated T cells response element in the IL-2 promoter. Cyclosporin A, a potent immunosuppressant, inhibited activation of both p38 and SAPK/JNK pathways but not the MAPK/extracellular signal-regulated kinase (ERK) pathway. Our results indicate that both MKK6 to p38 and MKK7 to SAPK/JNK signaling pathways are activated in a cyclosporin A-sensitive manner and contribute to IL-2 gene expression in T lymphocytes.
The Open Language Archives Community: An Infrastructure for Distributed Archiving of Language Resources

New ways of documenting and describing language via electronic media coupled with new ways of distributing the results via the World -Wide Web offer a degree of access to language resources that is unparalleled in history. At the same time, the proliferation of approaches to using these new technologies is causing serious problems relating to resource discovery and resource creation. This article describes the infras tructure that the Open Language Archives Community (OLAC) has built in order to address these problems. Its technical and usage infrastructures address problems of resource discovery by constructing a single virtual library of distributed resources. Its go vernance infrastructure addresses problems of resource creation by providing a mechanism through which the language-resource community can express its consensus on recommended best practices.
Characterization of low-temperature SU-8 photoresist processing for MEMS applications

In this paper, negative SU-8 photoresist processed at low-temperature has been characterized in terms of delamination. Based on a 3/sup 3/ factorial designed experiment, 27 samples are fabricated and the degree of delamination is measured. In addition, nine samples are fabricated for the purpose of verification. Employing a neural network modeling technique, a process model is established, and response surfaces are generated to investigate the degree of delamination associated with three process parameters: post exposure bake (PEB) temperature, PEB time, and exposure energy. From the response surfaces generated, two significant parameters associated with delamination are identified, and their effects on delamination are analyzed. The higher the post exposure bake (PEB) temperature at a fixed PEB time, the more delamination occurred. In addition, the higher the dose of exposure energy, the lower the temperature at which the delamination begins and the larger the degree of delamination. The results identify acceptable ranges of the three process variables to avoid the delamination of SU-8 film, which in turn might lead to potential defects in MEMS device fabrication.
Leaders and elites: portrayals of smoking in popular films

Objective: To study frequency and traits of characters that smoke in films and to document on-screen consequences of tobacco use. Design: This study conducted a content analysis of the top 100 grossing films in 2002, with a total global gross of US$12.4 billion. Outcome measures: Three outcome measures were frequency of smoking incidents, traits of characters who smoke, and consequences of tobacco use. Results: 6% of characters smoked in 453 incidents, including 3% of children. In 92% of incidences, smoking had no consequences. The most frequent consequence was a verbal reprimand. Although tobacco is a leading cause of preventable deaths globally, only 0.4% of tobacco incidences resulted in death. No deaths were caused by disease. Characters who smoked tended to be major characters playing leadership roles. They tended to be from privileged elites: male, white, and mature. Conclusions: Films portray characters that smoke as leaders from privileged elites, making smoking more attractive to audience members. Because 99.6% of characters suffer no life threatening consequences from smoking on screen, smokers seem invincible, belying tobacco’s role as a leading cause of preventable deaths.
Combined MR, fluorescence and histology imaging strategy in a human breast tumor xenograft model

Applications of molecular imaging in cancer and other diseases frequently require the combination of in vivo imaging modalities, such as MR and optical imaging, with ex vivo optical, fluorescence, histology and immunohistochemical imaging to investigate and relate molecular and biological processes to imaging parameters within the same region of interest. We have developed a multimodal image reconstruction and fusion framework that accurately combines in vivo MRI and MRSI, ex vivo brightfield and fluorescence microscopic imaging and ex vivo histology imaging. Ex vivo brightfield microscopic imaging was used as an intermediate modality to facilitate the ultimate link between ex vivo histology and in vivo MRI/MRSI. Tissue sectioning necessary for optical and histology imaging required the generation of a three‐dimensional reconstruction module for two‐dimensional ex vivo optical and histology imaging data. We developed an external fiducial marker‐based three‐dimensional reconstruction method, which was able to fuse optical brightfield and fluorescence with histology imaging data. The registration of the three‐dimensional tumor shape was pursued to combine in vivo MRI/MRSI and ex vivo optical brightfield and fluorescence imaging data. This registration strategy was applied to in vivo MRI/MRSI, ex vivo optical brightfield/fluorescence and histology imaging datasets obtained from human breast tumor models. Three‐dimensional human breast tumor datasets were successfully reconstructed and fused with this platform. Copyright © 2012 John Wiley & Sons, Ltd.
Acceleration "G" compensated for VCOCXO based on digital controller

The paper proposes a digital compensation by imposing real-time compensation voltage to Vin Pin of VCOXCO while device vibrating. The embedded digital compensating circuit includes a MEMS three-axes acceleration sensor, a FPGA and a D/A converter. G-sensitivity vector can be computed based on the MEMS sensor. A proportion digital compensation model is built to generate voltage which can compensate frequency drift and perturbation caused by acceleration.