Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrinsic laminar lattice connections in primate visual cortex

Intracortical injections of horseradish peroxidase (HRP) reveal a system of periodically organized intrinsic connections in primate striate cortex. In layers 2 and 3 these connections form a reticular or latticelike pattern, extending for about 1.5–2.0 mm around an injection. This connectional lattice is composed of HRP‐labeled walls (350–450 μm apart in Saimiri and about 500–600 μm in macaque) surrounding unlabeled central lacunae. Within the lattice walls there are regularly arranged punctate loci of particularly dense HRP label, appearing as isolated patches as the lattice wall labeling thins further from the injection site. A periodic organization has also been demonstrated for the intrinsic connections in layer 4B, which are apparently in register with the supragranular periodicities, although separated from these by a thin unlabeled region. The 4B lattice is particularly prominent in squirrel monkey, extending for 2–3 mm from an injection. In both layers, these intrinsic connections are demonstrated by orthogradely and retrogradely transported HRP and seem to reflect a system of neurons with long horizontal axon collaterals, presumably with arborizations at regularly spaced intervals. The intrinsic connectional lattice in layers 2 and 3 resembles the repetitive array of cytochrome oxidase activity in these layers; but despite similarities of dimension and pattern, the two systems do not appear identical. In primate, as previously described in tree shrews (Rockland et al., 1982), the HRP‐labeled anatomical connections resemble the pattern of 2‐deoxy‐glucose accumulation resulting from stimulation with oriented lines, although the functional importance of these connections remains obscure.
Cyclin G1 associates with MDM2 and regulates accumulation and degradation of p53 protein

Background: Cyclin G1 is a transcriptional target of p53 and is induced by DNA damage in a p53 dependent manner. Analysis of cyclin G1 disrupted mice demonstrated that cyclin G1 is involved in many of the functions regulated by p53 such as apoptosis, growth control and check point regulation in response to DNA damage. The results suggest that the main role of cyclin G1 is to mediate or regulate the function of p53.
Vietnamese boat refugees: the influence of war and flight traumatization on mental health on arrival in the country of resettlement

A consecutive cohort of 145 adult Vietnamese refugees were personally interviewed and completed the Symptom Checklist 90 R self‐rating scale on arrival in Norway. Sixty‐two percent had witnessed bombing, fires and shooting, 48% had witnessed other people being wounded or killed and 36% had been involved in life‐threatening situations or had been wounded in the war. Nearly all war trauma variables but none of the escape or refugee camp variables were significantly related to mental health 7 years after the end of the war. War trauma was significantly associated with mental health, also when age, gender and previous mental problems were controlled for. These results and our clinical experience indicate that clinicians treating refugees should address such traumatic experiences specifically.
Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.

The N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY, revealed non-standard positioning for both peptide termini. To investigate whether these deviations are indeed related to the length of the nef-peptide, we have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A resolution. A comparison of HLA-B*3501/peptide complexes with structures of other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well as peptide-induced structural changes. Independent of the length of the bound peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the alpha1-helix and nearer to the A pocket than observed for other HLA class I/peptide complexes. This reorientation is accompanied by a shift within the N-terminal part of the alpha2-helix towards the middle of the binding groove. Due to the short distance between the N and C termini, the nona-peptide is compressed and forced to zig-zag vertically within the binding groove. Its conformation rather resembles that of a deca-peptide than of other nona-peptides bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes additionally reveals a significant, peptide-dependent deviation between the N-terminal parts of the alpha1-helices which might be due to different positioning of the peptide N termini. Taken together, these data illustrate the strong interdependence between the HLA class I molecule and the bound peptide.
Fledging in the common swift,
 Apus apus
 : weight-watching with a difference

Fledging in the common swift involves young having to switch suddenly and completely from the sedentary lifestyle of a nestling to continuous flight with no post-fledging care. Using manipulations of brood size and the contrasting resource conditions in different breeding seasons, I observed fledging under a range of chick states. Poorly fed chicks took longer to fledge, and had lower body mass and short wing length at fledging. Despite this, maximum body mass of nestlings always exceeded those of adults and fledged young. Under all conditions, nestlings lost mass for 1 week prior to fledging, and at fledging they had similar wing loadings. I suggest that in their last days in the nest young swifts use up the fat stores that insured them against irregular parental provisioning as well as losing water from the drying out of feathers. Reductions in body mass associated with increases in wing length before fledging will affect flight efficiency by increasing the lift:drag ratio. This is interpreted as 'slimming' down to the optimal body mass which would improve the lift:drag ratio and set fledgings up for their life on the wing.
Allais for the poor

This paper complements evidence on the Allais paradox from advanced countries and educated people by a novel investigation in a poor rural area. The share of Allais-type behavior is indeed high and related to characteristics of 'lacking ability', such as poor education, unemployment, and little financial sophistication. Based on prospective reference theory, we extend these characteristics by biased processing of probabilistic information. Finally, we reveal that Allais-type behavior is linked to risk-related characteristics, such as risk tolerance and optimism. This indicates a potential problem as exactly the more dynamic among the poor tend to make inconsistent decisions under uncertainty.
[Quantitative analysis of adenosine and cordycepin in Cordyceps sinensis and its substitutes with LC-MS-MS].

OBJECTIVE To develop a LC-MS-MS method for determination of adenosine and cordycepin in Cordyceps sinensis and it's substitutes. METHOD The sawple was extracted with. 90% methanol. Multi-reactions monitoring (MRM) technique was adopted. RESULT The regression equations and coefficients were Y = 89.04X + 506.85 (r = 0.999 7) for adenosine, Y = 99.66X + 1 251.34 (r = 0.998 8) for cordycepin respectively. The linear range was 5.0-1 000.0 microg x L(-1) for adenosine and cordycepin. The limits of detection (LOD) were 0. 44 microg x L(-1) for adenosine and 0.31 microg x L(-1) for cordycepin, respectively. The average recoveries of adenosine and cordycepin were 98.1% and 97.9%, respectively. CONCLUSION The method was highly sensitive, selective and fast, which can be used for the determination of adenosine and cordycepin in C. sinensis and it's substitutes. This method can also be applied for the quality control of the medicinal materials.
Examination of cognitive function during six months of calorie restriction: results of a randomized controlled trial.

BACKGROUND Calorie restriction increases longevity in many organisms, and calorie restriction or its mimetic might increase longevity in humans. It is unclear if calorie restriction/dieting contributes to cognitive impairment. During this randomized controlled trial, the effect of 6 months of calorie restriction on cognitive functioning was tested. METHODS Participants (n = 48) were randomized to one of four groups: (1) control (weight maintenance), (2) calorie restriction (CR; 25% restriction), (3) CR plus structured exercise (CR + EX, 12.5% restriction plus 12.5% increased energy expenditure via exercise), or (4) low-calorie diet (LCD; 890 kcal/d diet until 15% weight loss, followed by weight maintenance). Cognitive tests (verbal memory, visual memory, attention/concentration) were conducted at baseline and months 3 and 6. Mixed linear models tested if cognitive function changed significantly from baseline to months 3 and 6, and if this change differed by group. Correlation analysis was used to determine if average daily energy deficit (quantified from change in body energy stores) was associated with change in cognitive test performance for the three dieting groups combined. RESULTS No consistent pattern of verbal memory, visual retention/memory, or attention/concentration deficits emerged during the trial. Daily energy deficit was not significantly associated with change in cognitive test performance. CONCLUSIONS This randomized controlled trial suggests that calorie restriction/dieting was not associated with a consistent pattern of cognitive impairment. These conclusions must be interpreted in the context of study limitations, namely small sample size and limited statistical power. Previous reports of cognitive impairment might reflect sampling biases or information processing biases.
Identification of a novel protein isoform derived from cancer‐related splicing variants using combined analysis of transcriptome and proteome

Splicing variation enhances proteome diversity and modulates cancer‐associated proteins. Thus, the identification of alternative splice forms is significant for discovery of new cancer‐related biomarkers. However, relatively few screening approaches of alternative splicing via proteomics have been reported. In the present study, we describe a combined analysis with proteome and transcriptome to simultaneously identify cancer‐related splicing variants and splicing variant‐derived protein fragments that are differentially expressed in a highly metastatic gastric cancer cell line MKN45P versus its parental cell line MKN45. We found three potential alternative‐spliced genes using MS‐based shotgun method and two different microarray platforms. Among them, aldolase C, fructose‐bisphosphate (ALDOC) was predicted to have novel alternative splice forms. We successfully identified and validated novel splice forms of ALDOC gene by RT‐PCR and DNA sequencing analyses, the expression level of which were higher in MKN45P than in MKN45. Furthermore, the protein fragment derived from the validated splicing variant was identified using custom‐built data set including sequences of ALDOC variants in MS/MS analysis. Our combined analysis will be a promising technique for screening of cancer‐related splicing variants and their protein isoforms.
Promoter methylation of the bone morphogenetic protein‐6 gene in association with adult T‐cell leukemia

Bone morphogenetic proteins (BMP), belonging to the transforming growth factor‐β superfamily, are multifunctional regulators of cell proliferation, differentiation and apoptosis in various types of malignant cells. In this study, we investigated BMP‐6 promoter methylation in patients with various types of leukemias. The BMP‐6 methylation was found preferentially in adult T‐cell leukemia (ATL) (49 of 60, 82%) compared with other types of leukemias studied including acute myeloid leukemia (3 of 67, 5%), acute lymphoblastic leukemia (6 of 38, 16%) and chronic lymphocytic leukemia (1 of 21, 5%). Among subtypes of ATL, the BMP‐6 gene was more frequently methylated in aggressive ATL forms of acute (96%) and lymphoma (94%) types than less malignant chronic ATL (44%) and smoldering ATL (20%). We also analyzed the methylation status of peripheral blood mononuclear cells from healthy donors and nonmalignant lymph nodes with reactive lymphadenopathy, none of which showed detectable BMP‐6 methylation in this study. The BMP‐6 methyaltion was correlated with decreased mRNA transcript and protein expression. Expression of BMP‐6 was restored by the demethylating agent 5‐aza‐2′‐deoxycytidine, suggesting that methylation was associated with the transcriptional silencing. Serial analysis demonstrated an increasing methylation of CpG sites in the BMP‐6 promoter and the resultant suppression of BMP‐6 expression as ATL progressed. These findings suggested that BMP‐6 promoter methylation is likely to be a common epigenetic event at later stages of ATL and that the methylation profiles may be useful for the staging of ATL as well as for evaluation of the individual risk of developing the disease. © 2008 Wiley‐Liss, Inc.
A multi-network control framework based on industrial internet of things

In the industrial internet of things (IIoT), the coexistence of great deal of intelligent equipment and traditional network devices is universally found. Network has been transforming from single form into large-scale, heterogeneous networks. On such circumstance, traditional network standards and protocols fail to cope with the differences of the equipment. Moreover, there are inconveniences being found in the communication networks among multi-networks. This paper proposed a multi-network control framework based on industrial internet of things by the techniques of the software defined network and the virtualization. In this research, the differences of the equipment are masked. In addition, the flexible extension of network scale is realized through the dynamic extension and the collaborative sharing of virtual switches. A case shows the feasibility of the proposed framework.
An Exposed KID-Like Domain in Human T-Cell Lymphotropic Virus Type 1 Tax Is Responsible for the Recruitment of Coactivators CBP/p300

ABSTRACT Human T-cell lymphotropic virus type 1 (HTLV-1) transcriptional activation is mediated by the viral transactivator, Tax, and three 21-bp repeats (Tax response element [TxRE]) located in the U3 region of the viral long terminal repeat (LTR). Each TxRE contains a core cyclic AMP response element (CRE) flanked by 5′ G-rich and 3′ C-rich sequences. The TxRE binds CREB (CRE-binding protein) and Tax to form a ternary complex and confers Tax-dependent transactivation. Recent data indicate that Tax functions as a specific link to connect CREB-binding protein (CBP)/p300 in a phosphorylation-independent manner to CREB/ATF-1 assembled on the viral 21-bp repeats. GlutathioneS-transferase pull-down performed with Tax deletion mutants and peptide competition have localized the site in Tax critical for binding CBP/p300 to a highly protease-sensitive region around amino acid residues 81 to 95 (81QRTSKTLKVLTPPIT95) which lies between the domains previously proposed to be important for CREB binding and Tax subunit dimerization. Amino acid residues around the trypsin- and chymotrypsin-sensitive sites (88KVL90) of Tax bear resemblance to those in the kinase-inducible domain of CREB (129SRRPSYRKILNE140) surrounding Ser-133, which undergoes signal-induced phosphorylation to recruit CBP/p300. Site-directed mutagenesis of residues in this domain (R82A, K85A, K88A, and V89A) resulted in proteins which failed to transactivate from the HTLV-1 LTR in vivo. These mutants (K85A, K88A, and V89A) bind CREB with similar affinities as wild-type Tax, yet interaction with CBP/p300 is abrogated in various biochemical assays, indicating that the recruitment of CBP/p300 is crucial for Tax transactivation. A Tax mutant, M47, defective in the COOH-terminal transactivation domain, continued to interact with CBP/p300, suggesting that interactions with additional cellular factors are required for proper Tax function.
A Model System of the Dynamic Loading Occurring in Synovial Joints: The Biological Effect of Plowing on Pristine Cartilage

Mechanical stress is listed as a main risk factor for cartilage degradation. The aim of this study was to investigate the biological response of cartilage to dynamic loading such as plowing. Cartilage strips harvested from bovine nasal septum were submitted to plowing using a cylindrical indenter, applying a constant normal force in the vertical axis and moving at constant speed in the horizontal axis. After plowing, cell viability, gene expression and glycosaminoglycan (GAG) release were measured with conventional assays. The cell-viability assay and qRT-PCR showed that plowing induces cell death and matrix metalloproteinase 3 (MMP-3) upregulation. The addition of actinomycin D, before or after plowing, confirmed that plowing was responsible for the observed MMP-3 upregulation. Even if the transcriptions of the tissue inhibitor of metalloproteinase (TIMP-1), aggrecan (Agg), collagen type I (Coll1), collagen type II (Coll2) and fibronectin (Fn) were not significantly affected by plowing, actinomycin D treatment revealed that plowing induces a strong increase in TIMP-1 and Coll1 messenger RNA content and influences the gene regulation of Agg, Coll2 and Fn. Furthermore, plowed cartilage explants exhibited enhanced GAG release. Application of hydroxamate MMP inhibitor after loading showed that plowing induces GAG release via the activation of catabolic enzymes. Plowing causes cell death of the chondrocytes closer to the surface as well as matrix damage, observed as GAG loss. Moreover, in healthy chondrocytes, plowing promotes the production and activation of catabolic enzymes like MMP-3.
The integrity of the stem structure of human immunodeficiency virus type 1 Tat-responsive sequence of RNA is required for interaction with the interferon-induced 68,000-Mr protein kinase

A number of eucaryotic viruses have devised strategies to minimize the deleterious effects on protein synthesis caused by activation of the interferon-induced, double-stranded-RNA-activated protein kinase, P68. In a recent report, we described the down regulation of the P68 protein kinase in cells infected by human immunodeficiency virus type 1 (HIV-1) (S. Roy, M. G. Katze, N. T. Parkin, I. Edery, A. G. Hovanessian, and N. Sonenberg, Science 247:1216-1219, (1990). We now present evidence that such a decrease in amounts of P68 could be essential for HIV-1 replication because of the presence of the Tat-responsive sequence (TAR sequence) present in the 5' untranslated region of HIV-1 mRNAs, which activates the P68 kinase. We found that poly(A)+ mRNAs prepared from HIV-1-infected cells efficiently activated the protein kinase as did mRNAs from stably transformed cell lines constitutively expressing the TAR region. Furthermore, we found that TAR-containing RNAs complexed with purified P68 protein kinase in vitro by two independent assays and could be cross-linked to P68 kinase present in a HeLa cell extract. Experiments using in vitro-synthesized wild-type and mutant TAR RNAs revealed that both the efficient binding to and the activation of P68 kinase were dependent on the TAR RNA stem structure. The TAR-P68 complex could be competed out by a synthetic RNA that bound to and activated the protein kinase but not by a synthetic RNA that bound with low affinity and did not activate P68. The possible biological consequences of a P68-TAR interaction that may include the switch from latent to active virus replication are discussed.
Noncontact ECG Recording System With Real Time Capacitance Measurement for Motion Artifact Reduction

A system for noncontact ECG recording is proposed that measures the real time electrode-body capacitance concurrently with the ECG as a reference signal for motion artifact reduction. Simultaneous recordings of these two signals from the human body in the presence of electrode motion artifacts are shown and an adaptive least-mean-squares (LMS) filtering algorithm run on these signals is demonstrated to be able to reduce the severity of certain types of electrode motion artifacts.
Late autumn to spring changes in the inorganic and organic carbon dissolved in the water column at Scholaert Channel, West Antarctica

Abstract The temporal changes in dissolved inorganic (DIC) and organic carbon concentrations (DOC) were monitored from late autumn to spring 2006 in the Scholaert Channel, West Antarctic Peninsula. Surface DIC spanned a small range (2163.3 to 2194.5 μmol kg-1), increasing from late autumn to winter and then decreasing in spring. An excess of DOC (7.0–63.6 μmol l-1), against a deepwater background concentration of 44 μmol l-1, existed in the surface mixed layer throughout the sampling period. Mass-balance budgeting indicates that the DIC dynamics were primarily governed by remineralization in winter and by primary production in spring despite very low biomass of both autotrophic and heterotrophic organisms. The net community production (7.3 mmol C m-2 d-1) in spring was mainly partitioned to DOC accumulation (3.6 mmol m-2 d-1) and downward export of particulate organic carbon (POC) (2.9 mmol m-2 d-1) rather than POC accretion (0.8 mmol m-2 d-1) in the surface mixed layer. The study area acted as a source of CO2 to the atmosphere in winter (∼0.8 mmol m-2 d-1) and a sink in spring (2.3–5.3 mmol m-2 d-1), and hence was not a one-way CO2 sink as had been previously hypothesized for marginal sea ice zones.
Construction of Protease-deficient Candida boidinii Strains Useful for Recombinant Protein Production: Cloning and Disruption of Proteinase A Gene (PEP4) and Proteinase B Gene…

The yeast Candida boidinii PEP4 and PRB1 genes, encoding proteinase A (PrA) and proteinase B (PrB), respectively, have been cloned and their primary structures were analyzed. The open reading frames of the PEP4 gene (1263 bp encoding a protein of 420 amino acids) and the PRB1 gene (1683 bp encoding a protein of 560 amino acids) were found. The deduced amino acid sequences of PrA and PrB are very similar to Saccharomyces cerevisiae PrA and PrB (64% and 61% identities, respectively). Both PEP4 and PRB1 genes were disrupted in the C. boidinii genome by one-step gene disruption. The resultant pep4Δ and the pep4Δ prb1Δ strains lost protease activity when compared with the wild-type original strain. The constructed C. boidinii strains are expected to be useful hosts for heterologous protein production.