Practicing mentorship: Graduate-student supervision of undergraduate research assistants

Many research universities rely on graduate students to supervise undergraduate research assistants (RAs) who collect data and handle research logistics. This experience can be mutually beneficial, as RAs receive hands-on learning, and graduate students practice mentorship in preparation for assuming a faculty role. However, assistantships must be intentionally designed to meet educational (not just practical) goals. What training and support do graduate students receive to take on this mentorship role? In two surveys, RAs reported on their satisfaction, educational benefit, and desired changes; while graduate students reported on their goals, challenges, and the support they receive

Epithelial Immunization Induces Polyfunctional CD8+ T Cells and Optimal Mousepox Protection.

We assessed several routes of immunization with vaccinia virus (VACV) in protecting mice against ectromelia virus (ECTV). By a wide margin, skin scarification provided the greatest protection. Humoral immunity and resident-memory T cells notwithstanding, several approaches revealed that circulating, memory CD8(+) T cells primed via scarification were functionally superior and conferred enhanced virus control. Immunization via the epithelial route warrants further investigation, as it may also provide enhanced defense against other infectious agents

Cytotoxic polyfunctionality maturation of cytomegalovirus-pp65-specific CD4 + and CD8 + T-cell responses in older adults positively correlates with response size

Cytomegalovirus (CMV) infection is one of the most common persistent viral infections in humans worldwide and is epidemiologically associated with many adverse health consequences during aging. Previous studies yielded conflicting results regarding whether large, CMV-specific T-cell expansions maintain their function during human aging. In the current study, we examined the in vitro CMV-pp65-reactive T-cell response by comprehensively studying five effector functions (i.e., interleukin-2, tumor necrosis factor-α, interferon-γ, perforin, and CD107a expression) in 76 seropositive individuals aged 70 years or older. Two data-driven, polyfunctionality panels (IL-2-associated and cytotoxicity-associated) derived from effector function co-expression patterns were used to analyze the results. We found that, CMV-pp65-reactive CD8 + and CD4 + T cells contained similar polyfunctional subsets, and the level of polyfunctionality was related to the size of antigen-specific response. In both CD8 + and CD4 + cells, polyfunctional cells with high cytotoxic potential accounted for a larger proportion of the total response as the total response size increased. Notably, a higher serum CMV-IgG level was positively associated with a larger T-cell response size and a higher level of cytotoxic polyfunctionality. These findings indicate that CMV-pp65-specific CD4 + and CD8 + T cell undergo simultaneous cytotoxic polyfunctionality maturation during aging

Signaling via interleukin-4, receptor alpha chain is required for successful vaccination against schistosomiasis in BALB/c mice

Radiation-attenuated (RA) schistosome larvae are potent stimulators of innate immune responses at the skin site of exposure (pinna) that are likely to be important factors in the development of Th1-mediated protective immunity. In addition to causing an influx of neutrophils, macrophages, and dendritic cells (DCs) into the dermis, RA larvae induced a cascade of chemokine and cytokine secretion following in vitro culture of pinna biopsy samples. While macrophage inflammatory protein 1 and interleukin-1 (IL-1) were produced transiently within the first few days, the Th1-promoting cytokines IL-12 and IL-18 were secreted at high levels until at least day 14. Assay of C3H/HeJ mice confirmed that IL-12 secretion was not due to lipopolysaccharide contaminants binding Toll-like receptor 4. Significantly, IL-12 p40 secretion was sustained in pinnae from vaccinated mice but not in those from nonprotected infected mice. In contrast, IL-10 was produced from both vaccinated and infected mice. This cytokine regulates IL-12-associated dermal inflammation, since in vaccinated IL-10/ mice, pinna thickness was greatly increased concurrent with elevated levels of IL-12 p40. A significant number of IL-12 p40 cells were detected as emigrants from in vitro-cultured pinnae, and most were within a population of rare large granular cells that were Ia, consistent with their being antigen-presenting cells. Labeling of IL-12 cells for CD11c, CD205, CD8, CD11b, and F4/80 indicated that the majority were myeloid DCs, although a proportion were CD11c F4/80, suggesting that macrophages were an additional source of IL-12 in the skin

IFNAR1-Signalling Obstructs ICOS-mediated Humoral Immunity during Non-lethal Blood-Stage Plasmodium Infection

Funding: This work was funded by a Career Development Fellowship (1028634) and a project grant (GRNT1028641) awarded to AHa by the Australian National Health & Medical Research Council (NHMRC). IS was supported by The University of Queensland Centennial and IPRS Scholarships. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Target and beam-target spin asymmetries in exclusive pion electroproduction for Q2>1GeV2 . I. ep→eπ+n

Beam-target double-spin asymmetries and target single-spin asymmetries were measured for the exclusive π + electroproduction reaction γ ∗ p → n π + . The results were obtained from scattering of 6-GeV longitudinally polarized electrons off longitudinally polarized protons using the CEBAF Large Acceptance Spectrometer at Jefferson Laboratory. The kinematic range covered is 1.1 < W < 3 GeV and 1 < Q 2 < 6 GeV 2 . Results were obtained for about 6000 bins in W ,   Q 2 ,   cos ( θ ∗ ) , and ϕ ∗ . Except at forward angles, very large target-spin asymmetries are observed over the entire W region. Reasonable agreement is found with phenomenological fits to previous data for W < 1.6 GeV, but very large differences are seen at higher values of W . A generalized parton distributions (GPD)-based model is in poor agreement with the data. When combined with cross-sectional measurements, the present results provide powerful constraints on nucleon resonance amplitudes at moderate and large values of Q 2 , for resonances with masses as high as 2.4 GeV

Near-threshold Photoproduction of Phi Mesons from Deuterium

We report the first measurement of the differential cross section on $\phi$-meson photoproduction from deuterium near the production threshold for a proton using the CLAS detector and a tagged-photon beam in Hall B at Jefferson Lab. The measurement was carried out by a triple coincidence detection of a proton, $K^+$ and $K^-$ near the theoretical production threshold of 1.57 GeV. The extracted differential cross sections $\frac{d\sigma}{dt}$ for the initial photon energy from 1.65-1.75 GeV are consistent with predictions based on a quasifree mechanism. This experiment establishes a baseline for a future experimental search for an exotic $\phi$-N bound state from heavier nuclear targets utilizing subthreshold/near-threshold production of $\phi$ mesons

Comment on the narrow structure reported by Amaryan et al

The CLAS Collaboration provides a comment on the physics interpretation of the results presented in a paper published by M. Amaryan et al. regarding the possible observation of a narrow structure in the mass spectrum of a photoproduction experiment.Comment: to be published in Physical Review

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Differential cross sections and recoil polarizations for the reaction gamma p -> K+ Sigma0

High-statistics measurements of differential cross sections and recoil polarizations for the reaction $\gamma p \rightarrow K^+ \Sigma^0$ have been obtained using the CLAS detector at Jefferson Lab. We cover center-of-mass energies ($\sqrt{s}$) from 1.69 to 2.84 GeV, with an extensive coverage in the $K^+$ production angle. Independent measurements were made using the $K^{+}p\pi^{-}$($\gamma$) and $K^{+}p$($\pi^-, \gamma$) final-state topologies, and were found to exhibit good agreement. Our differential cross sections show good agreement with earlier CLAS, SAPHIR and LEPS results, while offering better statistical precision and a 300-MeV increase in $\sqrt{s}$ coverage. Above $\sqrt{s} \approx 2.5$ GeV, $t$- and $u$-channel Regge scaling behavior can be seen at forward- and backward-angles, respectively. Our recoil polarization ($P_\Sigma$) measurements represent a substantial increase in kinematic coverage and enhanced precision over previous world data. At forward angles we find that $P_\Sigma$ is of the same magnitude but opposite sign as $P_\Lambda$, in agreement with the static SU(6) quark model prediction of $P_\Sigma \approx -P_\Lambda$. This expectation is violated in some mid- and backward-angle kinematic regimes, where $P_\Sigma$ and $P_\Lambda$ are of similar magnitudes but also have the same signs. In conjunction with several other meson photoproduction results recently published by CLAS, the present data will help constrain the partial wave analyses being performed to search for missing baryon resonances.Comment: 23 pages, 17 figure