During the last years, several approaches were applied on biomedical data to detect disease specific proteins and genes in order to better target drugs. It was shown that statistical and machine learning based methods use mainly clinical data and improve later their results by adding omics data. This work proposes a new method to discriminate the response of Acute Myeloid Leukemia (AML) patients to treatment. The proposed approach uses proteomics data and prior regulatory knowledge in the form of networks to predict cancer treatment outcomes by finding out the different Boolean networks specific to each type of response to drugs. To show its effectiveness we evaluate our method on a dataset from the DREAM 9 challenge.

The endomembrane system, known as secretory pathway, is responsible for the synthesis and transport of protein molecules in cells. Therefore, genes involved in the secretory pathway are essential for the cellular development and function. Recent scientific investigations show that ER and Golgi apparatus may provide a convenient drug target for cancer therapy. On the other hand, it is known that abundantly expressed genes in different cellular organelles share interconnected pathways and co-regulate each other activities. The cross-talks among these genes play an important role in signaling pathways, associated to the regulation of intracellular protein transport.

Neuroligins are postsynaptic adhesion molecules that are essential for postsynaptic specialization and synaptic function. But the underlying molecular mechanisms of neuroligin functions remain unclear. We found that Drosophila Neuroligin 1 (DNlg1) regulates synaptic structure and function through WAVE regulatory complex (WRC)-mediated postsynaptic actin reorganization. The disruption of DNlg1, DNlg2, or their presynaptic partner neurexin (DNrx) led to a dramatic decrease in the amount of F-actin. Further study showed that DNlg1, but not DNlg2 or DNlg3, directly interacts with the WRC via its C-terminal interacting receptor sequence. That interaction is required to recruit WRC to the postsynaptic membrane to promote F-actin assembly. Furthermore, the interaction between DNlg1 and the WRC is essential for DNlg1 to rescue the morphological and electrophysiological defects in dnlg1 mutants. Our results reveal a novel mechanism by which the DNrx-DNlg1 trans-synaptic interaction coordinates structural and functional properties at the neuromuscular junction.

The volume of genomics and health data is growing rapidly, driven by sequencing for both research and clinical use. However, under current practices, the data is fragmented into many distinct datasets, and researchers must go through a separate application process for each dataset. This is time-consuming both for the researchers and the data stewards, and it reduces the velocity of research and new discoveries that could improve human health. We propose to simplify this process, by introducing a standard Library Card that identifies and authenticates researchers across all participating datasets. Each researcher would only need to apply once to establish their bona fides as a qualified researcher, and could then use the Library Card to access a wide range of datasets that use a compatible data access policy and authentication protocol.

Hippocampus is importantly involved in dopamine-dependent behaviors and dopamine is a significant modulator of synaptic plasticity in the hippocampus. Moreover, the dopaminergic innervation appears to be disproportionally segregated along the hippocampal longitudinal (dorsoventral) axis with unknown consequences for synaptic plasticity. In this study we examined the actions of endogenously released dopamine and the effects of exogenous D1/D5 dopamine receptor agonists on theta-burst stimulation-induced long-term potentiation (LTP) of field excitatory synaptic potential (fEPSP) at Schaffer collateral-CA1 synapses in slices from dorsal (DH) and ventral hippocampus (VH). Furthermore, we quantified D1 receptor mRNA and protein expression levels in DH and VH. We found that blockade of D1/D5 receptors by SCH 23390 (20 μM) significantly reduced the magnitude of LTP in both DH and VH similarly suggesting that dopamine endogenously released during TBS, presumably mimicking low activity of DA neurons, exerts a homogeneous modulation of LTP along the hippocampal long axis. Moderate to high concentrations of the selective partial D1/D5 receptor agonist SKF 38393 (50-150 μM) did not significantly change LTP in either hippocampal segment. However, the full D1 receptor selective agonist SKF 82958 (10 μM) significantly enhanced LTP in VH but not DH. Furthermore, the expression of D1 receptor mRNA and protein was considerably higher in VH compared with DH. These results suggest that the dynamic range of D1/D5 receptor-mediated dopamine effects on LTP may be higher in VH than DH and that VH may be specialized to acquire information about behaviorally relevant strong stimuli signaled by the dopamine system.

Grid cells in the entorhinal cortex allow for the precise decoding of position in space. Along with potentially playing an important role in navigation, grid cells have recently been hypothesized to make a general contribution to mental operations. A prerequisite for this hypothesis is that grid cell activity does not critically depend on physical movement. Here, we show that movement of covert attention, without any physical movement, also elicits spatial receptive fields with a triangular tiling of space. In monkeys trained to maintain central fixation while covertly attending to a stimulus moving in the periphery we identified a significant population (20/141, 14% neurons at a FDR <5%) of entorhinal cells with spatially structured receptive fields. This contrasts with recordings obtained in the hippocampus, where grid-like representations were not observed. Our results provide evidence that neurons in macaque entorhinal cortex do not rely on physical movement.

The ability of acupuncture to successfully control pain has been reported in the past. However, currently no systematic reviews exist regarding the effect of acupuncture on trigeminal neuralgia (TN). This proposed review aims to evaluate the current evidence on the efficacy of acupuncture for the management of pain in TN.

No study has investigated the role of pancreatic cancer in the stroke risk using population data. We used claims data obtained from a universal health insurance program of Taiwan to evaluate the stroke risk in pancreatic cancer patients.From the catastrophic disease registry of the insurance, we identified 7479 patients with pancreatic malignancy without stroke history from 2000 to 2009. The comparison cohort consisted of 29,916 individuals identified from 1 million insured people without cancer and stroke history, matching with the cancer cohort by propensity score. We followed each selected individual until stroke was diagnosed or until being censored for death or withdrawal from insurance, or for a maximum of 3 follow-up years, or the end of 2011.The pancreatic cancer cohort had a 2.3-fold greater incident stroke than comparisons had (28.5 vs 12.3 per 1000 person-years), with an adjusted hazard ratio (aHR) of 2.74 (95% confidence interval (CI) = 2.31-3.24) after controlling for covariates, or a subdistribution hazard ratio (SHR) of 2.04 (95% CI = 1.74-2.40) accounting for the competing risk of deaths. During the follow-up period, stroke events occurred constantly in comparisons, but declined rapidly in the cancer cohort. The pancreatic cancer cohort had a stroke incidence of 46.6 per 1000 person-years within 6 months postdiagnosis, with an aHR of 4.37 (95% CI = 3.45-5.54) and a SHR of 3.87 (95% CI = 3.08-4.86), relative to comparisons.Our study suggests that patients with pancreatic cancer are at an elevated risk of stroke, patients deserve sufficient follow-up care, particularly in the first 6 months after the diagnosis of the cancer, and for those with comorbidities.

In recent years, many research groups have synthesized ultra-thin silver nanowires (AgNWs) with diameters below 30 nm by employing Cl- and Br- simultaneously in the polyol process. However, the yield of AgNWs in this method was low, due to the production of Ag nanoparticles (AgNPs) as an unwanted byproduct, especially in the case of high Br- concentration. Here, we investigated the roles of Cl- and Br- in the preparation of AgNWs and then synthesized high aspect ratio (up to 2100) AgNWs in high yield (>85% AgNWs) using a Cl- and Br- co-mediated method. We found that multiply-twinned particles (MTPs) with different critical sizes were formed and grew into AgNWs, accompanied by a small and large amount of AgNPs for the NaCl and NaBr additives, respectively. For the first time, we propose that the growth of AgNWs of different diameters and yields can be understood based on the electron trap distribution (ETD) of the silver halide crystals. For the case of Cl- and Br- co-additives, a mixed silver halide crystal of AgBr1-xClx was formed, rather than the AgBr/AgCl mixture reported previously. In this type of crystal, the ETD is uniform, which is beneficial for the synthesis of AgNWs with small diameter (30~40 nm) and high aspect ratio. AgNW transparent electrodes were prepared in air by rod coating. A sheet resistance of 48 Ω/sq and transmittance of 95% at 550 nm were obtained without any post-treatment.

The present study demonstrates an economical and eco-friendly method for the synthesis of silver nanoparticles (AgNPs) using the wild mushroom Ganoderma sessiliforme. The synthesis of AgNPs was confirmed and the products characterized by UV-visible spectroscopy, dynamic light scattering spectroscopy and X-ray diffraction analysis. Furthermore, Fourier transform infrared spectroscopy (ATR-FTIR) analysis was performed to identify the viable biomolecules involved in the capping and active stabilization of AgNPs. Moreover, the average sizes and morphologies of AgNPs were analyzed by field emission scanning electron microscopy (FE-SEM). The potential impacts of AgNPs on food safety and control were evaluated by the antimicrobial activity of the synthesized AgNPs against common food-borne bacteria, namely, Escherichia coli, Bacillus subtilis, Streptococcus faecalis, Listeria innocua and Micrococcus luteus. The results of this study revealed that the synthesized AgNPs can be used to control the growth of food-borne pathogens and have potential application in the food packaging industry. Moreover, the AgNPs were evaluated for antioxidant activity (aDPPH), for biocompatibility (L-929, normal fibroblast cells), and for cytotoxic effects on human breast adenosarcoma cells (MCF-7 & MDA-MB231) to highlight their potential for use in a variety of bio-applications.

Shoot and root apical meristems (SAM and RAM, respectively) are crucial to provide cells for growth and organogenesis and therefore need to be maintained throughout the life of a plant. However, plants lacking the mitochondrial protease AtFTSH4 exhibit an intriguing phenotype of precocious cessation of growth at both the shoot and root apices when grown at elevated temperatures. This is due to the accumulation of internal oxidative stress and progressive mitochondria dysfunction. To explore the impacts of the internal oxidative stress on SAM and RAM functioning, we study the expression of selected meristem-specific (STM, CLV3, WOX5) and cell cycle-related (e.g., CYCB1, CYCD3;1) genes at the level of the promoter activity and/or transcript abundance in wild-type and loss-of-function ftsh4-1 mutant plants grown at 30 °C. In addition, we monitor cell cycle progression directly in apical meristems and analyze the responsiveness of SAM and RAM to plant hormones. We show that growth arrest in the ftsh4-1 mutant is caused by cell cycle dysregulation in addition to the loss of stem cell identity. Both the SAM and RAM gradually lose their proliferative activity, but with different timing relative to CYCB1 transcriptional activity (a marker of G2-M transition), which cannot be compensated by exogenous hormones.

Plant viruses are inducers and targets of antiviral RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressor proteins that interfere with antiviral RNA silencing. The NSs protein is an RNA silencing suppressor in orthotospoviruses, such as the tomato spotted wilt virus (TSWV). The mechanism of RNA silencing suppression by NSs and its role in virus infection and movement are poorly understood. Here, we cloned and tagged TSWV NSs and expressed it from a GFP-tagged turnip mosaic virus (TuMV-GFP) carrying either a wild-type or suppressor-deficient (AS9) helper component proteinase (HC-Pro). When expressed in cis, NSs restored pathogenicity and promoted systemic infection of suppressor-deficient TuMV-AS9-GFP in Nicotiana benthamiana and Arabidopsis thaliana. Inactivating mutations were introduced in NSs RNA-binding domain one. A genetic analysis with active and suppressor-deficient NSs, in combination with wild-type and mutant plants lacking essential components of the RNA silencing machinery, showed that the NSs insert is stable when expressed from a potyvirus. NSs can functionally replace potyviral HC-Pro, condition virus susceptibility, and promote systemic infection and symptom development by suppressing antiviral RNA silencing through a mechanism that partially overlaps that of potyviral HC-Pro. The results presented provide new insight into the mechanism of silencing suppression by NSs and its effect on virus infection.

We investigated whether β-adrenergic antagonists attenuates dietary fat absorption through the regulation of pancreatic lipase (PNLIP) expression in pancreatic acinar cells in the context of high fat diet feeding. Male six-week-old C57BL/6 mice were assigned into an ad libitum fed control diet (CON) and a high fat diet (HIGH). Within each diet group, subgroups of mice were treated with vehicle (VEH) or propranolol, a β-adrenergic antagonist (BB). Over 12 weeks, body weight gain observed in HIGHVEH was mitigated in HIGHBB (+103% vs. +72%). Increase in fecal fat amount observed in HIGHVEH was further increased in HIGHBB. Increase in PNLIP expressions observed in HIGHVEH pancreatic tissues was abolished in HIGHBB. PNLIP expression in mouse primary pancreatic acinar cells and 266-6 cell lines increased with isoproterenol treatment, which was blocked by propranolol. Isoproterenol increased PNLIP expression in a cAMP/protein kinase A/ cyclic AMP response element binding protein (CREB)-dependent manner. CREB directly bound to the CRE on the mouse PNLIP promoter and transactivated PNLIP expression. These results suggest that sympathetic activation increases dietary fat absorption through the upregulation of PNLIP expression and that a β-adrenergic antagonist attenuates obesity development partly through the downregulation of PNLIP expression and inhibition of dietary fat absorption in the context of high fat diet feeding.

Heavy metal pollution of croplands is a major environmental problem worldwide. Methods for accurately and quickly monitoring heavy metal stress have important practical significance. Many studies have explored heavy metal stress in rice in relation to physiological function or physiological factors, but few studies have considered phenology, which can be sensitive to heavy metal stress. In this study, we used an integrated Normalized Difference Vegetation Index (NDVI) time-series image set to extract remote sensing phenology. A phenological indicator relatively sensitive to heavy metal stress was chosen from the obtained phenological periods and phenological parameters. The Dry Weight of Roots (WRT), which directly affected by heavy metal stress, was simulated by the World Food Study (WOFOST) model; then, a feature space based on the phenological indicator and WRT was established for monitoring heavy metal stress. The results indicated that the feature space can distinguish the heavy metal stress levels in rice, with accuracy greater than 95% for distinguishing the severe stress level. This finding provides scientific evidence for combining rice phenology and physiological characteristics in time and space, and the method is useful to monitor heavy metal stress in rice.

BackgroundDepression and/or anxiety during pregnancy have been associated with impaired fetal growth and neurodevelopment. Because placental imprinted genes play a central role in fetal development and respond to environmental stressors, we hypothesized that imprinted gene expression would be affected by prenatal depression and anxiety.MethodsPlacental gene expression was compared between mothers with prenatal depression and/or anxiety/obsessive compulsive disorder/panic and control mothers without psychiatric history (n=458) in the Rhode Island Child Health Study.ResultsTwenty-nine genes were identified as being significantly differentially expressed between placentae from infants of mothers with both depression and anxiety (n=54), with depression (n=89), or who took perinatal psychiatric medications (n=29) and control mother/infant pairs, with most genes having decreased expression in the stressed group. Among placentae from infants of mothers with depression, we found no differences in expression by medication use, indicating that our results are related to the stressor rather than the treatments. We did not find any relationship between the stress-associated gene expression and neonatal neurodevelopment, as measured using the Neonatal Intensive Care Unit Network Neurobehavioral Scale.ConclusionsThis variation in expression may be part of an adaptive mechanism by which the placenta buffers the infant from the effects of maternal stress.

Locally sustainable resource extraction activities, at times, transform into ecologically detrimental enterprises. Understanding such transitions is a primary challenge for conservation and management of many ecosystems. In marine systems, over-exploitation of small-scale fisheries creates problems such as reduced biodiversity and lower catches. However, long-term documentation of how governance and associated changes in fishing gears may have contributed to such declines is often lacking. Using fisher interviews, we characterized fishing gear dynamics over 60 years (1950-2010) in a coral reef ecosystem in the Philippines subject to changing fishing regulations. In aggregate fishers greatly diversified their use of fishing gears. However, most individual fishers used one or two gears at a time (mean number of fishing gears < 2 in all years). Individual fishing effort (days per year) was fairly steady over the study period, but cumulative fishing effort by all fishers increased 240%. In particular, we document large increases in total effort by fishers using nets and diving. Other fishing gears experienced less pronounced changes in total effort over time. Fishing intensified through escalating use of non-selective, active, and destructive fishing gears. We also found that policies promoting higher production over sustainability influenced the use of fishing gears, with changes in gear use persisting decades after those same policies were stopped. Our quantitative evidence shows dynamic changes in fishing gear use over time and indicates that gears used in contemporary small-scale fisheries impact oceans more than those used in earlier decades.

Spinal motoneurones (Mns) constitute the final output for the execution of motor tasks. In addition to innervating muscles, Mns project excitatory collateral connections to Renshaw cells (RCs) and other Mns, but the latter have received little attention. We show that Mns receive strong synaptic input from other Mns throughout development and into maturity, with fast-type Mns systematically receiving greater recurrent excitation than slow-type Mns. Optical recordings show that activation of Mns in one spinal segment can propagate to adjacent segments even in the presence of intact recurrent inhibition. While it is known that transmission at the neuromuscular junction is purely cholinergic and RCs are excited through both acetylcholine and glutamate receptors, here we show that neurotransmission between Mns is purely glutamatergic, indicating that synaptic transmission systems are differentiated at different postsynaptic targets of Mns.

We performed a retrospective analysis to identify risk factors and survival outcome for central nervous system (CNS) relapse of peripheral T-cell lymphoma (PTCL) by histologic type. Records of 600 PTCL patients diagnosed between 1999 and 2014 were analyzed including PTCL not otherwise specified (PTCL-NOS, 174 patients), angoimmunoblastic T-cell lymphoma (AITL, 144), ALK+anaplastic large cell lymphoma (ALCL, 74), ALK-ALCL (103), extranodal NK-cell lymphoma (ENKL, 54), or others (51). With a median follow up of 57 months, 13 patients (4 PTCL-NOS, 1 AITL, 4 ALK+ALCL, 2 ALK-ALCL, 2 ENKL) experienced CNS relapse. One-year and 5-year cumulative incidence of CNS relapse were 1.5% (95%CI: 0.7-2.8%) and 2.1% (95%CI: 1.1-3.5%), respectively. The 5-year cumulative incidence of CNS relapse was 1.8% in PTCL-NOS, 0.7% in AITL, 5.4% in ALK+ALCL, 2.1% in ALK-ALCL and 3.7% in ENKL. Extranodal involvement >1 site was the only significant factor associated with higher chance of CNS relapse (HR: 4.9, 95%CI: 1.6-15.0, p = 0.005). Patients with ALK+ALCL who had extranodal involvement >1 (N = 19) had very high risk of CNS relapse with one year cumulative incidence of 17% (95%CI: 4%-37%), all occurring within six months after diagnosis. All patients with CNS relapse eventually died (median, 1.5 months; range, 0.1-10.1 months). CNS relapse in patients with PTCL is rare event but the risk varies by subtype. ALK+ALCL patients with extranodal involvement >1 site have a very high risk of early CNS relapse, and thus evaluation of CNS involvement at the time of diagnosis and possible CNS-directed prophylaxis may be considered.

Handgrip strength, a measure of muscular fitness, is associated with cardiovascular (CV) events and CV mortality but its association with cardiac structure and function is unknown. The goal of this study was to determine if handgrip strength is associated with changes in cardiac structure and function in UK adults.

Monocyte activation and polarization play essential roles in many chronic inflammatory diseases. An imbalance of M1 and M2 macrophage activation (pro-inflammatory and alternatively activated, respectively) is believed to be a key aspect in the etiology of these diseases, thus a therapeutic approach that regulates macrophage activation could be of broad clinical relevance. Methylglyoxal-bis-guanylhydrazone (MGBG), a regulator of polyamine metabolism, has recently been shown to be concentrated in monocytes and macrophages, and interfere with HIV integration into the DNA of these cells in vitro. RNA expression analysis of monocytes from HIV+ and control donors with or without MGBG treatment revealed the only gene to be consistently down regulated by MGBG to be osteopontin (OPN). The elevated expression of this pro-inflammatory cytokine and monocyte chemoattractant is associated with various chronic inflammatory diseases. We demonstrate that MGBG is a potent inhibitor of secreted OPN (sOPN) in cultured monocytes with 50% inhibition achieved at 0.1 μM of the drug. Furthermore, inhibition of OPN RNA transcription in monocyte cultures occurs at similar concentrations of the drug. During differentiation of monocytes into macrophages in vitro, monocytes express cell surface CD16 and the cells undergo limited DNA synthesis as measured by uptake of BrdU. MGBG inhibited both activities at similar doses to those regulating OPN expression. In addition, monocyte treatment with MGBG inhibited differentiation into both M1 and M2 classes of macrophages at non-toxic doses. The inhibition of differentiation and anti-OPN effects of MGBG were specific for monocytes in that differentiated macrophages were nearly resistant to MGBG activities. Thus MGBG may have potential therapeutic utility in reducing or normalizing OPN levels and regulating monocyte activation in diseases that involve chronic inflammation.