Human CD4+ T Cell Epitopes from Vaccinia Virus Induced by Vaccination or Infection

Despite the importance of vaccinia virus in basic and applied immunology, our knowledge of the human immune response directed against this virus is very limited. CD4+ T cell responses are an important component of immunity induced by current vaccinia-based vaccines, and likely will be required for new subunit vaccine approaches, but to date vaccinia-specific CD4+ T cell responses have been poorly characterized, and CD4+ T cell epitopes have been reported only recently. Classical approaches used to identify T cell epitopes are not practical for large genomes like vaccinia. We developed and validated a highly efficient computational approach that combines prediction of class II MHC-peptide binding activity with prediction of antigen processing and presentation. Using this approach and screening only 36 peptides, we identified 25 epitopes recognized by T cells from vaccinia-immune individuals. Although the predictions were made for HLA-DR1, eight of the peptides were recognized by donors of multiple haplotypes. T cell responses were observed in samples of peripheral blood obtained many years after primary vaccination, and were amplified after booster immunization. Peptides recognized by multiple donors are highly conserved across the poxvirus family, including variola, the causative agent of smallpox, and may be useful in development of a new generation of smallpox vaccines and in the analysis of the immune response elicited to vaccinia virus. Moreover, the epitope identification approach developed here should find application to other large-genome pathogens

Dynamic bonding of metallic nanocontacts: Insights from experiments and atomistic simulations

The conductance across an atomically narrow metallic contact can be measured by using scanning tunneling microscopy. In certain situations, a jump in the conductance is observed right at the point of contact between the tip and the surface, which is known as “jump to contact” (JC). Such behavior provides a way to explore, at a fundamental level, how bonding between metallic atoms occurs dynamically. This phenomenon depends not only on the type of metal but also on the geometry of the two electrodes. For example, while some authors always find JC when approaching two atomically sharp tips of Cu, others find that a smooth transition occurs when approaching a Cu tip to an adatom on a flat surface of Cu. In an attempt to show that all these results are consistent, we make use of atomistic simulations; in particular, classical molecular dynamics together with density functional theory transport calculations to explore a number of possible scenarios. Simulations are performed for two different materials: Cu and Au in a [100] crystal orientation and at a temperature of 4.2 K. These simulations allow us to study the contribution of short- and long-range interactions to the process of bonding between metallic atoms, as well as to compare directly with experimental measurements of conductance, giving a plausible explanation for the different experimental observations. Moreover, we show a correlation between the cohesive energy of the metal, its Young's modulus, and the frequency of occurrence of a jump to contact.W. Dednam acknowledges support from the National Research Foundation of South Africa through the Scarce Skills Masters scholarship funding programme (Grant Unique Number 92138). This work is supported by the Generalitat Valenciana through Grant Reference PROMETEO2012/011 and MINECO under Grant No. FIS2013-47328, by European Union structural funds and the Comunidad de Madrid Programs S2013/MIT-3007 and P2013/MIT-2850. This work is also part of the research programme of the Foundation for Fundamental Research on Matter (FOM), which is financially supported by the Netherlands Organisation for Scientific Research (NWO)

Directional bonding explains the high conductance of atomic contacts in bcc metals

Atomic-sized contacts of iron, created in scanning tunneling microscope break junctions, present unusually high values of conductance compared to other metals. This result is counterintuitive since, at the nanoscale, body-centered-cubic metals are expected to exhibit lower coordination than face-centered-cubic metals. In this work we first perform classical molecular dynamics simulations of the contact rupture, using two different interatomic potentials. The first potential is isotropic, and produces mostly single-atom prerupture contacts. The second potential accounts for the directional bonding in the materials, and produces mostly highly coordinated prerupture structures, generally consisting of more than one atom in contact. To compare the two different types of structures with experiments, we use them as input to density functional theory electronic transport calculations of the conductance. We find that the highly coordinated structures, obtained from the anisotropic potential, yield higher conductances which are statistically in better agreement with those measured for body-centered-cubic iron. We thus conclude that the directional bonding plays an important role in body-centered-cubic metals.This work was supported by the Generalitat Valenciana through PROMETEO2017/139 and GENT (CDEIGENT2018/028), the Spanish government through Grants No. MAT2016-78625-C2-1-P and No. FIS2016-80434-P, and the Spanish Ministry of Science and Innovation, through the “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000805-M), by Comunidad Autónoma de Madrid through Grant No. S2018/NMT-4321 (NanomagCOST-CM), by the Fundación Ramón Areces, and by the European Union Graphene Flagship under Grant No. 604391

Identification of Importin 8 (IPO8) as the most accurate reference gene for the clinicopathological analysis of lung specimens

<p>Abstract</p> <p>Background</p> <p>The accurate normalization of differentially expressed genes in lung cancer is essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin have been widely used in the past, their accuracy as reference genes for lung tissues has not been proven.</p> <p>Results</p> <p>We have conducted a thorough analysis of a panel of 16 candidate reference genes for lung specimens and lung cell lines. Gene expression was measured by quantitative real time RT-PCR and expression stability was analyzed with the softwares <it>GeNorm </it>and <it>NormFinder</it>, mean of |ΔCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic comparison between candidates led us to the identification of a subset of suitable reference genes for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had a very low mean of |ΔCt| (0.70 ± 0.09), with no statistically significant differences between normal and malignant samples and with excellent expression stability.</p> <p>Conclusion</p> <p>Our data show that IPO8 is the most accurate reference gene for clinical lung specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are inappropriate to normalize data derived from lung biopsies, although they are suitable as reference genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples.</p

Business cycles, international trade and capital flows: Evidence from Latin America

This paper adopts a flexible framework to assess both short- and long-run business cycle linkages between six Latin American (LA) countries and the four largest economies in the world (namely the US, the Euro area, Japan and China) over the period 1980:I-2011:IV. The result indicate that within the LA region there are considerable differences between countries, success stories coexisting with extremely vulnerable economies. They also show that the LA region as a whole is largely dependent on external developments, especially in the years after the great recession of 2008 and 2009. The trade channel appears to be the most important source of business cycle comovement, whilst capital flows are found to have a limited role, especially in the very short run

Anti-vascular endothelial growth factor for proliferative diabetic retinopathy.

BACKGROUND: Proliferative diabetic retinopathy (PDR) is a complication of diabetic retinopathy that can cause blindness. Although panretinal photocoagulation (PRP) is the treatment of choice for PDR, it has secondary effects that can affect vision. An alternative treatment such as anti-vascular endothelial growth factor (anti-VEGF), which produces an inhibition of vascular proliferation, could improve the vision of people with PDR. OBJECTIVES: To assess the effectiveness and safety of anti-VEGFs for PDR. SEARCH METHODS: We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (2014, Issue 3), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE (January 1946 to April 2014), EMBASE (January 1980 to April 2014), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 28 April 2014. SELECTION CRITERIA: We included randomised controlled trials (RCTs) comparing anti-VEGFs to another active treatment, sham treatment or no treatment for people with PDR. We also included studies that assessed the combination of anti-VEGFs with other treatments. DATA COLLECTION AND ANALYSIS: Two review authors independently selected studies for inclusion, extracted data and assessed risk of bias for all included trials. We calculated the risk ratio (RR) or the mean difference (MD), and 95% confidence intervals (CI). MAIN RESULTS: We included 18 RCTs with 1005 participants (1131 eyes) of whom 57% were men. The median number of participants per RCT was 40 (range 15 to 261). The studies took place in Asia (three studies), Europe (two studies), the Middle East (seven studies), North America (three studies) and South America (three studies). Eight RCTs recruited people eligible for PRP, nine RCTs enrolled people with diabetes requiring vitrectomy and one RCT recruited people undergoing cataract surgery. The median follow-up was six months (range one to 12 months). Seven studies were at high risk of bias and the remainder were unclear risk of bias in one or more domains.Very low quality evidence from one study of 61 people showed that people treated with bevacizumab and PRP were less likely to lose 3 or more lines of visual acuity at 12 months compared with people treated with PRP alone (RR 0.19, 95% CI 0.05 to 0.81). People treated with anti-VEGF had an increased chance of gaining 3 or more lines of visual acuity but the effect was imprecise and compatible with no effect or being less likely to gain vision (RR 6.78, 95% CI 0.37 to 125.95). No other study reported these two outcomes. On average, people treated with anti-VEGF (bevacizumab, pegaptanib or ranibizumab) had better visual acuity at 12 months compared with people not receiving anti-VEGF (MD -0.07 logMAR, 95% CI -0.12 to -0.02; 5 RCTs, 373 participants, low quality evidence). There was some evidence to suggest a regression of PDR with smaller leakage on fluorescein angiography but it was difficult to estimate a pooled result from the two trials reporting this outcome. People receiving anti-VEGF were less likely to have vitreous or pre-retinal haemorrhage at 12 months (RR 0.32, 95% CI 0.16 to 0.65; 3 RCTs, 342 participants, low quality evidence). No study reported on fluorescein leakage or quality of life.All of the nine trials of anti-VEGF before or during vitrectomy investigated bevacizumab; most studies investigated bevacizumab before vitrectomy, one study investigated bevacizumab during surgery.People treated with bevacizumab and vitrectomy were less likely to lose 3 or more lines of visual acuity at 12 months compared with people given vitrectomy alone but the effect was imprecise and compatible with no effect or being more likely to lose vision (RR 0.49, 95% CI 0.08 to 3.14; 3 RCTs, 94 participants, low quality evidence). People treated with bevacizumab were more likely to gain 3 or more lines of visual acuity (RR 1.62, 95% CI 1.20 to 2.17; 3 RCTs, 94 participants, low quality evidence). On average, people treated with bevacizumab had better visual acuity at 12 months compared with people not receiving bevacizumab but there was uncertainty in the estimate (the CIs included 0; i.e. were compatible with no effect, and there was considerable inconsistency between studies; MD -0.24 logMAR, 95% CI -0.50 to 0.01; 6 RCTs, 335 participants, I(2) = 67%; low quality evidence). People receiving bevacizumab were less likely to have vitreous or pre-retinal haemorrhage at 12 months (RR 0.30, 95% CI 0.18 to 0.52; 7 RCTs, 393 participants, low quality evidence). No study reported on quality of life.Reasons for downgrading the quality of the evidence included risk of bias in included studies, imprecision of the estimates, inconsistency of effect estimates and indirectness (few studies reported at 12 months).Adverse effects were rarely reported and there was no evidence for any increased risk with anti-VEGF but given the relatively few studies that reported these, and the low event rate, the power of the analysis to detect any differences was low. AUTHORS' CONCLUSIONS: There was very low or low quality evidence from RCTs for the efficacy and safety of anti-VEGF agents when used to treat PDR over and above current standard treatments. However, the results suggest that anti-VEGFs can reduce the risk of intraocular bleeding in people with PDR. Further carefully designed clinical trials should be able to improve this evidence

Photoluminescence Enhancement by Band Alignment Engineering in MoS2/FePS3 van der Waals Heterostructures

Single-layer semiconducting transition metal dichalcogenides (2H-TMDs) display robust excitonic photoluminescence emission, which can be improved by controlled changes to the environment and the chemical potential of the material. However, a drastic emission quench has been generally observed when TMDs are stacked in van der Waals heterostructures, which often favor the nonradiative recombination of photocarriers. Herein, we achieve an enhancement of the photoluminescence of single-layer MoS2 on top of van der Waals FePS3. The optimal energy band alignment of this heterostructure preserves light emission of MoS2 against nonradiative interlayer recombination processes and favors the charge transfer from MoS2, an n-type semiconductor, to FePS3, a p-type narrow-gap semiconductor. The strong depletion of carriers in the MoS2 layer is evidenced by a dramatic increase in the spectral weight of neutral excitons, which is strongly modulated by the thickness of the FePS3 underneath, leading to the increase of photoluminescence intensity. The present results demonstrate the potential for the rational design of van der Waals heterostructures with advanced optoelectronic properties.The authors acknowledge funding from Generalitat Valenciana through grants IDIFEDER/2020/005, IDIFEDER/2018/061, PROMETEO Program and PO FEDER Program, the APOSTD/2020/249 fellowship for M.R., and support from the Plan Gen-T of Excellence for J.J.B. (CDEIGENT/ 2019/022), J.C.-F. (CIDEGENT/2018/005), and M.R.C (CideGenT2018004); from the Spanish MCINN through grants PLASTOP PID2020-119124RB-I00, 2D-HETEROS PID2020-117152RB-100, and Excellence Unit “María de Maeztu” CEX2019-000919-M; and from the European Union (ERC-2021-StG-101042680 2D-SMARTiES and ERC AdG Mol-2D 788222)