Miracle-dz/UniFAR-FTUs huggingface dataset:
cAMP protection of pancreatic cancer cells against apoptosis induced by ERK inhibition.

Large increases in cAMP concentration inside the cell are generally growth inhibitory for most cell lines of mesenchymal and epithelial origin. Moreover, recent data suggest a role of cAMP in survival of different cell types. Herein, the ability of forskolin (an adenylyl cyclase activator) and IBMX (3-isobutyl-1-methylxanthine) (a phosphodiesterase inhibitor) to modulate cell cycle progression and survival of human pancreatic cancer cells was evaluated. We showed that forskolin + IBMX inhibited serum-induced ERK activities, Rb hyperphosphorylation, Cdk2 activity, and p27(Kip1) downregulation and caused G1 arrest in MIA PaCa-2 cells. Furthermore, forskolin + IBMX protected pancreatic cells against apoptosis induced by prolonged inhibition of ERK activities by preventing Bcl-X(L) downregulation, activation of caspases 3, 6, 8, and 9, and PARP cleavage and by inducing Bad phosphorylation (ser112). Taken together, our data demonstrate for the first time that cAMP is an inhibitor of cell cycle progression and apoptosis in human pancreatic cancer cells.
Transrectal real-time tissue elastography - an effective way to distinguish benign and malignant prostate tumors.

BACKGROUND To investigate the relationship between extracellular matrix parameters and texture of prostatic lesions evaluated by transrectal real-time tissue elastography (TRTE). METHODS 120 patients suspicious for prostate cancer underwent TRTE. Targeted biopsies were carried out after 12-core systematic biopsy. Epithelia were stained with hematoxylin-eosin, and Victoria blue and Ponceau S were used to stain elastic-collagen fibers, and picric acid-sirius red for visualization of collagen type I (Col1) and III (Col3). Smooth muscles were visualized by immunohistochemistry. All image analyses were performed in a blind manner using Image Pro Plus 6.0, and the area ratios of epithelium, elastic fibers, collagen fibers and Col1/Col3 were determined. RESULTS 42 patients with typical elastograms were included in the final data analysis. Significant differences were detected between the benign and malignant groups in the area ratios of epithelium (P = 0.01), smooth muscles and Col1/Col3 (P = 0.04, P = 0.02, respectively). There were no significant differences in the area ratios of epithelium, smooth muscle and elastic fibers between the stiff and soft lesion groups. The area ratio of Col1 was (0.05 ± 0.03) in the stiff group, and (0.02 ± 0.01) in the soft group (P= 0.00). However, the area ratio of Col3 was (0.03 ± 0.02) in the stiff group, and (0.05 ± 0.04) in the soft group (P = 0.16). Col1/Col3 in the stiff group (1.99 ± 1.59) was greater than in the soft group (0.71 ± 0.64) (P = 0.01). CONCLUSIONS Tissue hardness of prostatic tumors was mainly dependent on the Col1 content, Col1/Col3 being higher in malignant than in benign lesions, so the prostate tissue texture can be used as a target for distinguishing between the two with TRTE.
Hepatitis C Virus Glycoproteins Interact with DC-SIGN and DC-SIGNR

ABSTRACT DC-SIGN and DC-SIGNR are two closely related membrane-associated C-type lectins that bind human immunodeficiency virus (HIV) envelope glycoprotein with high affinity. Binding of HIV to cells expressing DC-SIGN or DC-SIGNR can enhance the efficiency of infection of cells coexpressing the specific HIV receptors. DC-SIGN is expressed on some dendritic cells, while DC-SIGNR is localized to certain endothelial cell populations, including hepatic sinusoidal endothelial cells. We found that soluble versions of the hepatitis C virus (HCV) E2 glycoprotein and retrovirus pseudotypes expressing chimeric forms of both HCV E1 and E2 glycoproteins bound efficiently to DC-SIGN and DC-SIGNR expressed on cell lines and primary human endothelial cells but not to other C-type lectins tested. Soluble E2 bound to immature and mature human monocyte-derived dendritic cells (MDDCs). Binding of E2 to immature MDDCs was dependent on DC-SIGN interactions, while binding to mature MDDCs was partly independent of DC-SIGN, suggesting that other cell surface molecules may mediate HCV glycoprotein interactions. HCV interactions with DC-SIGN and DC-SIGNR may contribute to the establishment or persistence of infection both by the capture and delivery of virus to the liver and by modulating dendritic cell function.
Genetic Variation in PSCA and Risk of Gastric Advanced Preneoplastic Lesions and Cancer in Relation to Helicobacter pylori Infection

SNPs in the Prostate Stem Cell Antigen (PSCA) gene have been found associated with gastric cancer (GC) risk in a genome-wide association study. This association has been replicated in several populations. In this study we assessed the impact of PSCA genotype on the risk of advanced gastric precancerous lesions and GC. We used baseline gastric histopathology data and DNA from frozen gastric biopsies of 2045 subjects enrolled in a chemoprevention trial for gastric precancerous lesions in Venezuela, and 180 cases of GC from the same area. We analyzed 3 SNPs in the PSCA gene (rs2294008, rs9297976 and rs12155758) which were previously found to be associated with GC risk in Europeans. The T allele of rs2294008 was found to be associated with a higher prevalence of atrophic gastritis (OR = 1.44; 95% CI 1.03–2.01 for the dominant model) and intestinal metaplasia (OR = 1.50; 95% CI 1.13–1.98 for the dominant model). We also confirmed the association with higher risk of gastric cancer (OR = 2.34; 95% CI 1.36–4.01 for the allele carriers). SNP rs12155758 was not associated with risk of gastric preneoplastic lesions, but we confirmed its association with higher GC risk (OR 1.95; 95% CI 1.29–2.97 for dominant model). We tested the relevance of the presence of the Helicobacter pylori cagA gene, which is known to increase the risk of more severe gastric lesions, but we did not find any clearcut interaction with PSCA SNPs in defining risk of gastric precancerous lesions or cancer.
Transcriptomic Analysis of Staphylococcus epidermidis Biofilm-Released Cells upon Interaction with Human Blood Circulating Immune Cells and Soluble Factors

This study was funded by the Portuguese Foundation for Science and Technology (FCT) by the project with the reference FCOMP-01-012014-FEDER-041246 (EXPL/BIA-MIC/0101/2013), the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01-0145-FEDER-006684), BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by European Regional Development Fund under the. scope of Norte2020 - Programa Operational Regional do Norte. NC is an Investigador FCT. AT is supported by the FCT fellowship SFRH/BPD/99961/2014. The hinders had no role in study design, data collection and interpretation, or decision to submit the work for publication.
Meat physical quality and muscle fibre properties of rabbit meat as affected by the sire breed, season, parity order and gender in an organic production system

The aim of the study was to evaluate some meat physical quality and muscle fibre properties of rabbit meat when considering 2 sire breeds (SB: Vienna Blue [VB]; Burgundy Fawn [BF]; both coloured and slow-growing breeds), several parity orders (P: 1, 2, ≥3), gender (G), and 2 slaughter seasons (SS: spring, summer) in an organic production system. The effect of storage time (ST) at frozen state (2 mo at –20°C) of Longissimus lumborum (LL) meat was also evaluated. Animals were slaughtered when they reached 2.8 kg of live weight. Then, pH and L*a*b* colour values of Biceps femoris (BF) and LL muscles, water loss and Warner-Bratzler shear force of LL and hind leg (HL) meat, and the fibre typing and enzymatic activity of LL muscle were analysed. LL meat from females showed higher b* values than males (0.04 vs. –1.25; P<0.05). Significant (P<0.05) SB×P, SB×G and P×G interactions were observed for the b* value of LL: VB and BF crossbreds presented a higher b* value when born as P≥3 and P2 respectively, VB females showed higher b* value than VB males, and P2 and P≥3 produced males with a significantly lower b* value. HL thawing losses were significantly (P<0.05) higher in rabbits slaughtered in summer than in those slaughtered in spring, whereas the opposite result was obtained for LL meat (P<0.01). Cooking loss of LL meat was significantly lower in P2 group than P≥3 group (P<0.05). The lactate dehydrogenase activity in LL muscle was higher in VB than in BF crossbreds (930 vs. 830 IU; P<0.05), albeit not supported by differences in fibre type distribution. The ST significantly (P<0.01) reduced pH, a* and b* colour values, and increased lightness of LL meat. It was concluded that the crossbreeds derived from VB and BF genotypes and farmed organically did not show remarkable sexual dimorphism, considering their elder slaughter age than rabbits reared under intensive conditions. Physical quality of meat was mainly affected by slaughter season, indicating that in the organic rearing system, specific attention needs to be paid to the farming environmental conditions.
Robust Server Consolidation: Coping with Peak Demand Underestimation

Energy consumption in data centres accounts for a significant proportion of national energy usage in many countries. One approach for reducing energy consumption is to improve the server usage efficiency via workload consolidation. However, there are two primary reasons why this is not done to a large extent. The first reason is that greater consolidation could result in violations of Service Level Agreements (SLAs) if resources are over-utilised. The second reason is that users specify the requirements of a virtual machine (VM) based on the maximum estimated usage for each resource over the whole life span of the VM, and usually over-estimate these maximum values to avoid possible contract violations. Typically, the VM will have significantly lower resource usage in most time periods. Recently, a number of methods have been proposed to predict resource usage of VMs. We show that although these prediction techniques are efficient when their performances are measured using well known metrics, a low prediction error can still result in significant violations of SLAs if not handled properly during workload allocation. Our results emphasise the importance of analysing workload prediction in conjunction with workload allocation techniques. We examine the impact of using predicted resource usage for optimal server consolidation. We investigate the occurrences of over-utilised resources on servers due to under-predicted resource usage. We propose methods to reduce the likelihood of such occurrences, both through the enforcement of safety capacities on the server side, and through biasing towards over-prediction on the VM side. The results indicate that an appropriate balance can be found between energy savings and non-violation of SLAs.
Great expectations? Pre-transplant quality of life expectations and distress after kidney transplantation: a prospective study.

OBJECTIVES Previous research suggests that prior to kidney transplantation, patients overestimate their post-transplant quality of life (QoL). The current study aimed to corroborate these findings, identify determinants of QoL overestimation, examine its association with subsequent distress, and clarify the role of optimism. DESIGN Prospective observational study. METHODS Physical, psychological, and social QoL expectations, actual QoL, and distress (GHQ-12) of participants (56% male) were prospectively assessed before (T0; n = 228) and 3 (T1; n = 149), 6 (T2; n = 146), and 12 (T3; n = 114) months after successful transplantation. RESULTS Patients who were treated with haemodialysis before transplantation reported greater physical QoL overestimation than those who received treatment with peritoneal dialysis. Neither physical nor social QoL overestimation at T1 was prospectively associated with increased distress at T2 or T3. The interaction between optimism and social QoL overestimation at T1 (β = -.56, p < .001) for distress at T2 was significant, with patients low in optimism experiencing more distress after QoL overestimation. CONCLUSIONS QoL overestimation is not associated with subsequent distress. Findings suggest that patients low in optimism are more vulnerable to distress following QoL overestimation. STATEMENT OF CONTRIBUTION What is already known on this subject? Kidney transplantation improves patients' quality of life. Prior to kidney transplantation, patients overestimate the scale of this improvement. What does this study add? Quality of life overestimation is not associated with subsequent distress. When optimism is low, kidney transplant recipients experience higher distress following quality of life overestimation.
Hemagglutinin of swine influenza virus: a single amino acid change pleiotropically affects viral antigenicity and replication.

The complete nucleotide sequence has been obtained of the H1 hemagglutinin (HA) gene of a high-yielding (H) mutant of the A/NJ/11/76(H1N1) strain of swine influenza virus in studies of a viral reassortant (X-53a) bearing this gene. This determination has permitted comparison with human influenza H1N1 prototype viruses A/WSN/33 and A/PR/8/34, with which 80% and 94% amino acid homology was found between HA1 and HA2, respectively. Partial sequences have been determined for other viral reassortants containing either H or L (low-yielding phenotype) genes derived from A/NJ/11/76. Sequence of the HA1 region of an L mutant prototype was virtually completed and differed from that of the H mutant by only four amino acid changes. Sequence analysis of four other viruses was restricted to regions of the HA with which monoclonal antibodies capable of distinguishing L and H mutants are presumed to react. Therefore, changes in these sequences are relevant to changes in viral phenotype. Change at residue 155 from Gly to Glu is associated with change from L to H HA phenotype. This site, structurally equivalent to amino acid 158 on the Wiley et al. HA model [Wiley, D. C. , Wilson, I. A. & Skehel, J. J. (1981) Nature (London) 289, 373-378] is near the tip of the HA monomer adjacent to the proposed receptor binding site and therefore credibly could influence both viral antigenicity and replication. Because both L and H variants exist in nature and because revertants may be selected in the laboratory as replication variants in the absence of immunoselection, these studies provide evidence for fortuitous antigenic change in association with change in biological function, which is determined by a single base change.
Adaptive MIMO Systems in 2 x 2 Uncorrelated Rayleigh Fading Channel

Adaptive MQAM modulation is used to maximize spectral efficiency while keeping bit error rate (BER) under a target level. The closed-form expressions of the average spectral efficiency of adaptive modulation system are derived for beamforming (BF), singular value decomposition (SVD), space-time block coding (STBC) and spatial multiplexing with zero-forcing (ZF) receiver in uncorrelated flat Rayleigh fading channel. Further, a low-complexity adaptive scheme that switches across BF and SVD in closed loop systems, STBC and ZF in open loop systems is suggested to enhance the spectral efficiency on the basis of the closed form expressions.
Effect of a Broad-Specificity Chemokine-Binding Protein on Brain Leukocyte Infiltration and Infarct Development

Background and Purpose— Expression of numerous chemokine-related genes is increased in the brain after ischemic stroke. Here, we tested whether post-stroke administration of a chemokine-binding protein (CBP), derived from the parapoxvirus bovine papular stomatitis virus, might reduce infiltration of leukocytes into the brain and consequently limit infarct development. Methods— The binding spectrum of the CBP was evaluated in chemokine ELISAs, and binding affinity was determined using surface plasmon resonance. Focal stroke was induced in C57Bl/6 mice by middle cerebral artery occlusion for 1 hour followed by reperfusion for 23 or 47 hours. Mice were treated intravenously with either bovine serum albumin (10 &mgr;g) or CBP (10 &mgr;g) at the commencement of reperfusion. At 24 or 48 hours, we assessed plasma levels of the chemokines CCL2/MCP-1 and CXCL2/MIP-2, as well as neurological deficit, brain leukocyte infiltration, and infarct volume. Results— The CBP interacted with a broad spectrum of CC, CXC, and XC chemokines and bound CCL2/MCP-1 and CXCL2/MIP-2 with high affinity (pM range). Stroke markedly increased plasma levels of CCL2/MCP-1 and CXCL2/MIP-2, as well as numbers of microglia and infiltrating leukocytes in the brain. Increases in plasma chemokines were blocked in mice treated with CBP, in which there was reduced neurological deficit, fewer brain-infiltrating leukocytes, and ≈50% smaller infarcts at 24 hours compared with bovine serum albumin–treated mice. However, CBP treatment was no longer protective at 48 hours. Conclusions— Post-stroke administration of CBP can reduce plasma chemokine levels in association with temporary atten uation of brain inflammation and infarct volume development.
Comparative assessment of the leprosy antibody absorption test, Mycobacterium leprae extract enzyme-linked immunosorbent assay, and gelatin particle agglutination test for serodiagnosis of lepromatous leprosy

A comparative assessment of three serological methods for leprosy diagnosis (the fluorescent leprosy antibody absorption [FLA-ABS] test, the Mycobacterium leprae soluble-extract enzyme-linked immunosorbent assay [ELISA], and the M. leprae particle agglutination [MLPA] test) was carried out. The objective was to identify their performance in clinical and epidemiological diagnosis of leprosy. The study group included 45 lepromatous leprosy patients under treatment. Specificity was > 95% for all three assays, and sensitivity was 95, 58, and 74% for the FLA-ABS test, the MLPA test, and the ELISA, respectively. The only cross-reactivity for M. tuberculosis-infected patients was with the soluble-extract ELISA. Although the FLA-ABS test displayed the highest specificity and sensitivity values, it can only be used in well-developed laboratories, and the patient's clinical and epidemiological background must be considered when results are interpreted because the test remains positive after therapeutic success and could be positive for some household contacts. The MLPA test is easier to perform and interpret, and it is adequate for small laboratories and epidemiological studies intended to detect active untreated or irregularly treated leprosy cases. Therefore, the FLA-ABS and MLPA tests are complementary, and both should be used for serodiagnosis of leprosy.
Rapid BAC selection for tol2-mediated transgenesis in zebrafish

The generation of zebrafish transgenic lines that express specific fluorophores in a cell- or tissue-specific manner is an important technique that takes full advantage of the optical clarity of the embryo. Identifying promoter fragments that faithfully recapitulate endogenous expression patterns and levels is often difficult and using large genomic DNA fragments, such as bacterial artificial chromosomes (BACs), makes the process of transgenesis less reliable. Here we provide a detailed protocol that allows for BAC selection and subsequent rapid modification through recombineering in Escherichia coli, resulting in BACs that can be injected into zebrafish embryos and, aided by tol2-mediated transgenesis, reliably yield stable transgenic lines. A number of BACs can be prepared in parallel, and injection of the BACs containing CFP/YFP/RFP or Gal4 cassettes allows for immediate testing of whether a particular BAC will yield the desired result. Furthermore, since injected embryos often show widespread expression, recombineered BACs provide an alternative to two-color in situ hybridizations: BACs injected into embryos of a different transgenic reporter line thus enable in vivo colocalization studies. Using this protocol, we have generated 66 stable lines for 23 different genes, with an average transgenesis rate above 10%. Importantly, we provide evidence that BAC size shows no apparent correlation to the transgenesis rate achieved and that there are no severe position effects.
Power Waves and Conjugate Matching

The concept of power waves gives more natural relations between incident and reflected power in a microwave network than the typically used traveling waves. The reflection coefficient for power waves directly describes the reflection of power whereas the reflection coefficient of traveling waves describes the reflection of the waves themselves. In this brief, new physical reasoning of power waves is given starting from the principle of conjugate matching. In addition, a new formula for the reference impedances for a two-port system is given such that the system is simultaneously conjugate matched for both ports.
Adding psychotherapy to pharmacotherapy in the treatment of depressive disorders in adults: a meta-analysis.

OBJECTIVE A considerable number of studies has examined whether adding psychotherapy to pharmacotherapy results in stronger effects than pharmacotherapy alone. However, earlier meta-analyses in this field have included only a limited number of available studies and did not conduct extended subgroup analyses to examine possible sources of heterogeneity. DATA SOURCES We used a database derived from a comprehensive literature search in PubMed, PsycINFO, EMBASE, and the Cochrane Central Register of Controlled Trials for studies published from 1966 to January 2008 that examined the psychological treatment of depression. The abstracts of these studies were identified by combining terms indicative of psychological treatment and depression. STUDY SELECTION We included randomized trials in which the effects of a pharmacologic treatment were compared to the effects of a combined pharmacologic and psychological treatment in adults with a depressive disorder. DATA EXTRACTION For each of the studies, we calculated a standardized mean effect size indicating the difference between pharmacotherapy and the combined treatment at posttest. We also coded major characteristics of the population, the interventions, and the quality and design of the study. DATA SYNTHESIS Twenty-five randomized trials, with a total of 2,036 patients, were included. A mean effect size of d = 0.31 (95% CI, 0.20 approximately 0.43) was found for the 25 included studies, indicating a small effect in favor of the combined treatment over pharmacotherapy alone. Studies aimed at patients with dysthymia resulted in significantly lower effect sizes compared to studies aimed at patients with major depression, a finding that suggests that the added value of psychotherapy is less in patients with dysthymia. The dropout rate was significantly lower in the combined treatment group compared to the pharmacotherapy only group (OR = 0.65; 95% CI, 0.50 approximately 0.83). CONCLUSIONS Psychotherapy seems to have an additional value compared to pharmacotherapy alone for depression.