A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes.

The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.

Impact of valley degeneracy on the thermoelectric properties of zig-zag graphene nanoribbons with staggered sublattice potentials and transverse electric fields.

This study investigates the band inversion of flat bands in zig-zag graphene nanoribbons (ZGNRs) using a tight-binding model. The band inversion results from symmetry breaking in the transverse direction, achievable through deposition on specific substrates such as separated silicon carbide or hexagonal boron nitride sheets. Upon band inversion, ZGNRs exhibit electronic structures characterized by valley degeneracy and band gap properties, which can be modulated by transverse electric fields. To explore the impact of this level degeneracy on thermoelectric properties, we employ Green's function techniques to calculate thermoelectric quantities in ZGNR segments with staggered sublattice potentials and transverse electric fields. Two carrier transport scenarios are considered: the chemical potential is positioned above and below the highest occupied molecular orbital. We analyze thermionic-assisted transport (TAT) and direct ballistic transport (DBT). Level degeneracy enhances the electric power factors of ZGNRs by increasing electrical conductance, while the Seebeck coefficient remains robust in the TAT scenario. Conversely, in DBT, the enhancement of the power factor primarily stems from improvements in the Seebeck coefficient at elevated temperatures.

Thermal rectification through the topological states of asymmetrical length armchair graphene nanoribbons heterostructures with vacancies.

We present a theoretical investigation of electron heat current in asymmetrical length armchair graphene nanoribbon (AGNR) heterostructures with vacancies, focusing on the topological states (TSs). In particular, we examine the 9-7-9 AGNR heterostructures where the TSs are well-isolated from the conduction and valence subbands. This isolation effectively mitigates thermal noise of subbands arising from temperature fluctuations during charge transport. Moreover, when the TSs exhibit an orbital off-set, intriguing electron heat rectification phenomena are observed, primarily attributed to inter-TS electron Coulomb interactions. To enhance the heat rectification ratio (ηQ), we manipulate the coupling strengths between the heat sources and the TSs by introducing asymmetrical lengths in the 9-AGNRs. This approach offers control over the rectification properties, enabling significant enhancements. Additionally, we introduce vacancies strategically positioned between the heat sources and the TSs to suppress phonon heat current. This arrangement effectively reduces the overall phonon heat current, while leaving the TSs unaffected. Our findings provide valuable insights into the behavior of electron heat current in AGNR heterostructures, highlighting the role of topological states, inter-TS electron Coulomb interactions, and the impact of structural modifications such as asymmetrical lengths and vacancy positioning. These results pave the way for the design and optimization of graphene-based devices with improved thermal management and efficient control of electron heat transport.

Logistic Regression Classification of Primary Vitreoretinal Lymphoma versus Uveitis by Interleukin 6 and Interleukin 10 Levels.

PURPOSE: To assess the diagnostic performance and generalizability of logistic regression in classifying primary vitreoretinal lymphoma (PVRL) versus uveitis from intraocular cytokine levels in a single-center retrospective cohort, comparing a logistic regression model and previously published Interleukin Score for Intraocular Lymphoma Diagnosis (ISOLD) scores against the interleukin 10 (IL-10)-to-interleukin 6 (IL-6) ratio. DESIGN: Retrospective cohort study. PARTICIPANTS: Patient histories, pathology reports, and intraocular cytokine levels from 2339 patient entries in the National Eye Institute Histopathology Core database. METHODS: Patient diagnoses of PVRL versus uveitis and associated aqueous or vitreous IL-6 and IL-10 levels were collected retrospectively. From these data, cytokine levels were compared between diagnoses with the Mann-Whitney U test. A logistic regression model was trained to classify PVRL versus uveitis from aqueous and vitreous IL-6 and IL-10 samples and compared with ISOLD scores and IL-10-to-IL-6 ratios. MAIN OUTCOME MEASURES: Area under the receiver operating characteristic curve (AUC) for each classifier and sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) at the optimal cutoff (maximal Youden index) for each classifier. RESULTS: Seventy-seven lymphoma patients (10 aqueous samples, 67 vitreous samples) and 84 uveitis patients (19 aqueous samples, 65 vitreous samples) treated between October 5, 1999, and September 16, 2015, were included. Interleukin 6 levels were higher and IL-10 levels were lower in uveitis patients compared with lymphoma patients (P < 0.01). For vitreous samples, the logistic regression model, ISOLD score, and IL-10-to-IL-6 ratio achieved AUCs of 98.3%, 97.7%, and 96.3%, respectively. Sensitivity, specificity, PPV, and NPV at the optimal cutoffs for each classifier were 94.2%, 96.9%, 97%, and 94% for the logistic regression model; 92.7%, 100%, 100%, and 92.9% for the ISOLD score; and 94.2%, 95.3%, 95.6%, and 93.9% for the IL-10-to-IL-6 ratio. All models achieved complete separation between uveitis and lymphoma in the aqueous data set. CONCLUSIONS: The accuracy of the logistic regression model and generalizability of the ISOLD score to an independent patient cohort suggest that intraocular cytokine analysis by logistic regression may be a promising adjunct to cytopathologic analysis, the gold standard, for the early diagnosis of primary vitreoretinal lymphoma. Further validation studies are merited.

Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells.

To clarify how smoking leads to heart attack and stroke, we developed an endothelial cell model (iECs) generated from human induced Pluripotent Stem Cells (iPSC) and evaluated its responses to tobacco smoke. These iECs exhibited a uniform endothelial morphology, and expressed markers PECAM1/CD31, VWF/ von Willebrand Factor, and CDH5/VE-Cadherin. The iECs also exhibited tube formation and acetyl-LDL uptake comparable to primary endothelial cells (EC). RNA sequencing (RNA-Seq) revealed a robust correlation coefficient between iECs and EC (R = 0.76), whereas gene responses to smoke were qualitatively nearly identical between iECs and primary ECs (R = 0.86). Further analysis of transcriptional responses implicated 18 transcription factors in regulating responses to smoke treatment, and identified gene sets regulated by each transcription factor, including pathways for oxidative stress, DNA damage/repair, ER stress, apoptosis, and cell cycle arrest. Assays for 42 cytokines in HUVEC cells and iECs identified 23 cytokines that responded dynamically to cigarette smoke. These cytokines and cellular stress response pathways describe endothelial responses for lymphocyte attachment, activation of coagulation and complement, lymphocyte growth factors, and inflammation and fibrosis; EC-initiated events that collectively lead to atherosclerosis. Thus, these studies validate the iEC model and identify transcriptional response networks by which ECs respond to tobacco smoke. Our results systematically trace how ECs use these response networks to regulate genes and pathways, and finally cytokine signals to other cells, to initiate the diverse processes that lead to atherosclerosis and cardiovascular disease.

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.

MOTIVATION: Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed. RESULTS: We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy. AVAILABILITY AND IMPLEMENTATION: RiboDiff webpage http://bioweb.me/ribodiff Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff CONTACTS: zhongy@cbio.mskcc.org or raetsch@inf.ethz.chSupplementary information: Supplementary data are available at Bioinformatics online.

Cost-effectiveness of afatinib and erlotinib as second-line treatments for advanced squamous cell carcinoma of the lung.

AIM: To investigate the cost-effectiveness of afatinib and erlotinib as second-line therapy for advanced squamous cell carcinoma of the lung. MATERIALS & METHODS: A decision-analytic model was developed for projecting the economic outcomes. Clinical parameters and utilities were from the LUX-Lung 8 trial. Costs were mainly estimated from the Chinese health system. The outcome was the incremental cost-effectiveness ratio. RESULTS: The afatinib strategy generated additional 0.154 quality-adjusted life-years compared with erlotinib, with incremental costs of ¥16,852. Relative to erlotinib, afatinib resulted in an incremental cost-effectiveness ratio of ¥109,429 per quality-adjusted life-year gained. The overall survival time of afatinib had a considerable impact on the model outcomes. CONCLUSION: Afatinib is a cost-effective treatment option compared with erlotinib in patients with squamous cell carcinoma.

Characterization of three human cell line models for high-throughput neuronal cytotoxicity screening.

More than 75 000 man-made chemicals contaminate the environment; many of these have not been tested for toxicities. These chemicals demand quantitative high-throughput screening assays to assess them for causative roles in neurotoxicities, including Parkinson's disease and other neurodegenerative disorders. To facilitate high throughput screening for cytotoxicity to neurons, three human neuronal cellular models were compared: SH-SY5Y neuroblastoma cells, LUHMES conditionally-immortalized dopaminergic neurons, and Neural Stem Cells (NSC) derived from human fetal brain. These three cell lines were evaluated for rapidity and degree of differentiation, and sensitivity to 32 known or candidate neurotoxicants. First, expression of neural differentiation genes was assayed during a 7-day differentiation period. Of the three cell lines, LUHMES showed the highest gene expression of neuronal markers after differentiation. Both in the undifferentiated state and after 7 days of neuronal differentiation, LUHMES cells exhibited greater cytotoxic sensitivity to most of 32 suspected or known neurotoxicants than SH-SY5Y or NSCs. LUHMES cells were also unique in being more susceptible to several compounds in the differentiating state than in the undifferentiated state; including known neurotoxicants colchicine, methyl-mercury (II), and vincristine. Gene expression results suggest that differentiating LUHMES cells may be susceptible to apoptosis because they express low levels of anti-apoptotic genes BCL2 and BIRC5/survivin, whereas SH-SY5Y cells may be resistant to apoptosis because they express high levels of BCL2, BIRC5/survivin, and BIRC3 genes. Thus, LUHMES cells exhibited favorable characteristics for neuro-cytotoxicity screening: rapid differentiation into neurons that exhibit high level expression neuronal marker genes, and marked sensitivity of LUHMES cells to known neurotoxicants. Copyright © 2016 John Wiley & Sons, Ltd.

Novel quorum-quenching agents promote methicillin-resistant Staphylococcus aureus (MRSA) wound healing and sensitize MRSA to ß-lactam antibiotics.

The dwindling repertoire of antibiotics to treat methicillin-resistant Staphylococcus aureus (MRSA) calls for novel treatment options. Quorum-quenching agents offer an alternative or an adjuvant to antibiotic therapy. Three biaryl hydroxyketone compounds discovered previously (F1, F12, and F19; G. Yu, D. Kuo, M. Shoham, and R. Viswanathan, ACS Comb Sci 16:85-91, 2014) were tested for efficacy in MRSA-infected animal models. Topical therapy of compounds F1 and F12 in a MRSA murine wound infection model promotes wound healing compared to the untreated control. Compounds F1, F12, and F19 afford significant survival benefits in a MRSA insect larva model. Combination therapy of these quorum-quenching agents with cephalothin or nafcillin, antibiotics to which MRSA is resistant in monotherapy, revealed additional survival benefits. The quorum-quenching agents sensitize MRSA to the antibiotic by a synergistic mode of action that also is observed in vitro. An adjuvant of 1 µg/ml F1, F12, or F19 reduces the MIC of nafcillin and cephalothin about 50-fold to values comparable to those for vancomycin, the antibiotic often prescribed for MRSA infections. These findings suggest that it is possible to resurrect obsolete antibiotic therapies in combination with these novel quorum-quenching agents.

Quantum interference and electron correlation in charge transport through triangular quantum dot molecules.

We study the charge transport properties of triangular quantum dot molecules (TQDMs) connected to metallic electrodes, taking into account all correlation functions and relevant charging states. The quantum interference (QI) effect of TQDMs resulting from electron coherent tunneling between quantum dots is revealed and well interpreted by the long distance coherent tunneling mechanism. The spectra of electrical conductance of TQDMs with charge filling from one to six electrons clearly depict the many-body and topological effects. The calculated charge stability diagram for conductance and total occupation numbers matches well with the recent experimental measurements. We also demonstrate that the destructive QI effect on the tunneling current of TQDMs is robust with respect to temperature variation, making the single electron QI transistor feasible at higher temperatures.

Quantum interference and structure-dependent orbital-filling effects on the thermoelectric properties of quantum dot molecules.

The quantum interference and orbital filling effects on the thermoelectric (TE) properties of quantum dot (QD) molecules with high figure of merit are illustrated via the full solution to the Hubbard-Anderson model in the Coulomb blockade regime. It is found that under certain conditions in the triangular QD molecule (TQDM), destructive quantum interference (QI) can occur, which leads to vanishingly small electrical conductance, while the Seebeck coefficient is modified dramatically. When the TQDM is in the charge localization state due to QI, the Seebeck coefficient is seriously suppressed at low temperature, but is highly enhanced at high temperature. Meanwhile, the behavior of the Lorenz number reveals that it is easier to block charge transport via destructive QI than the electron heat transport at high temperatures. The maximum power factor (PF) in the TQDM occurs under full-filling conditions. Nevertheless, low-filling conditions are preferred for getting the maximum PF in serially coupled triple QDs in general. In double QDs, the maximum PF can be achieved either with orbital-depletion or orbital-filling as a result of electron-hole symmetry. Our theoretical work provides a useful guideline for the advancement of the nanoscale TE technology.

Integration of nanoimprint lithography with block copolymer directed self-assembly for fabrication of a sub-20 nm template for bit-patterned media.

We propose a novel strategy to integrate the nanoimprint lithography (NIL) technique with directed self-assembly (DSA) of block copolymer (BCP) for providing a robust, high-yield, and low-defect-density path to sub-20 nm dense patterning. Through this new NIL-DSA method, UV nanoimprint resist is used as the DSA copolymer pre-pattern to expedite the DSA process. This method was successfully used to fabricate a 1.0 Td in(-2) servo-integrated nanoimprint template for bit-patterned media (BPM) application. The fabricated template was used for UV-cure NIL on a 2.5-inch disk. The imprint resist patterns were further transferred into the underlying CoCrPt magnetic layer through a carbon hard mask using ion beam etching. The successful integration of the NIL technique with the DSA process provides us with a new route to BPM nanofabrication, which includes the following three major advantages: (1) a simpler and faster way to implement DSA for high-density BPM patterning; (2) a novel method for fabricating a high-quality dot pattern template through an iterative imprint-DSA-template procedure; and (3) an uncomplicated integration scheme for implementing non-periodic servo features with BCP patterns, thus accelerating the transition of moving the DSA technique from laboratory research to the BPM manufacturing environment.

Thermoelectric properties of armchair graphene nanoribbons with array characteristics.

The thermoelectric properties of armchair graphene nanoribbons (AGNRs) with array characteristics are investigated theoretically using the tight-binding model and Green's function technique. The AGNR structures with array characteristics are created by embedding a narrow boron nitride nanoribbon (BNNR) into a wider AGNR, resulting in two narrow AGNRs. This system is denoted as w-AGNR/n-BNNR, where 'w' and 'n' represent the widths of the wider AGNR and narrow BNNR, respectively. We elucidate the coupling effect between two narrow symmetrical AGNRs on the electronic structure of w-AGNR/i-BNNR. A notable discovery is that the power factor of the 15-AGNR/5-BNNR with the minimum width surpasses the quantum limitation of power factor for 1D ideal systems. The energy level degeneracy observed in the first subbands of w-AGNR/n-BNNR structures proves to be highly advantageous in enhancing the electrical power outputs of graphene nanoribbon devices.

Charge transport through the multiple end zigzag edge states of armchair graphene nanoribbons and heterojunctions.

This comprehensive study investigates charge transport through the multiple end zigzag edge states of finite-size armchair graphene nanoribbons/boron nitride nanoribbons (n-AGNR/w-BNNR) junctions under a longitudinal electric field, where n and w denote the widths of the AGNRs and the BNNRs, respectively. In 13-atom wide AGNR segments, the edge states exhibit a blue Stark shift in response to the electric field, with only the long decay length zigzag edge states showing significant interaction with the red Stark shift subband states. Charge tunneling through such edge states assisted by the subband states is elucidated in the spectra of the transmission coefficient. In the 13-AGNR/6-BNNR heterojunction, notable influences on the energy levels of the end zigzag edge states of 13-AGNRs induced by BNNR segments are observed. We demonstrate the modulation of these energy levels in resonant tunneling situations, as depicted by bias-dependent transmission coefficient spectra. Intriguing nonthermal broadening of tunneling current shows a significant peak-to-valley ratio. Our findings highlight the promising potential of n-AGNR/w-BNNR heterojunctions with long decay length edge states in the realm of GNR-based single electron transistors at room temperature.

Alternative Pre-mRNA Splicing, Cell Death, and Cancer.

Alternative splicing is one of the most powerful mechanisms for generating functionally distinct products from a single genetic loci and for fine-tuning gene activities at the post-transcriptional level. Alternative splicing plays important roles in regulating genes critical for cell death. These cell death genes encode death ligands, cell surface death receptors, intracellular death regulators, signal transduction molecules, and death executor enzymes such as caspases and nucleases. Alternative splicing of these genes often leads to the formation of functionally different products, some of which have antagonistic effects that are either cell death-promoting or cell death-preventing. Differential alternative splicing can affect expression, subcellular distribution, and functional activities of the gene products. Molecular defects in splicing regulation of cell death genes have been associated with cancer development and resistance to treatment. Studies using molecular, biochemical, and systems-based approaches have begun to reveal mechanisms underlying the regulation of alternative splicing of cell death genes. Systematic studies have begun to uncover the multi-level interconnected networks that regulate alternative splicing. A global picture of the complex mechanisms that regulate cell death genes at the pre-mRNA splicing level has thus begun to emerge.

Thermoelectric properties of a quantum dot array connected to metallic electrodes.

The thermoelectric properties of a quantum dot array (QDA) embedded in a nanowire connected to metallic electrodes are investigated theoretically via the extended Hubbard model in the Coulomb blockade regime. Coupled quantum dots (QDs) with dot number N = 2-5 are considered. It is found that the thermoelectric properties converge to almost the same results when N approaches 5, indicating that our results are applicable for a QDA with a large number of QDs. Our studies indicate that in order to achieve the optimal figure of merit (ZT), it is preferable to have the QD energy levels above the Fermi energy (EF) of the electrodes of the QDA junction. The effects of QD energy level and interdot coupling variations (due to the QD size and position fluctuation) on the thermoelectric properties are also examined. We find that the QD size fluctuation significantly suppresses the maximum ZT in the weak interdot hopping strength (tℓ,j). We also find that the Seebeck coefficient is insensitive to tℓ,j and the tunneling rates when the QD energy levels are far above EF. For a given tℓ,j and large on-site Coulomb interactions, increasing the QD number N in the QDA would suppress the maximum ZT value. It is possible to achieve an optimal ZT larger than 3 by tailoring the physical parameters of the QDA junction system.

Effects of metallic electrodes on the thermoelectric properties of zigzag graphene nanoribbons with periodic vacancies.

We theoretically analyze the thermoelectric properties of graphene quantum dot arrays (GQDAs) with line- or surface-contacted metal electrodes. Such GQDAs are realized as zigzag graphene nanoribbons (ZGNRs) with periodic vacancies. Gaps and minibands are formed in these GQDAs, which can have metallic and semiconducting phases. The electronic states of the first conduction (valence) miniband with nonlinear dispersion may have long coherent lengths along the zigzag edge direction. With line-contacted metal electrodes, the GQDAs have the characteristics of serially coupled quantum dots (SCQDs) if the armchair edge atoms of the ZGNRs are coupled to the electrodes. By contrast, the GQDAs have the characteristics of parallel quantum dots if the zigzag edge atoms are coupled to the electrodes. The maximum thermoelectric power factors of SCQDs with line-contacted electrodes of Cu, Au, Pt, Pd, or Ti at room temperature were similar or greater than 0.186 nW K-1; their figures of merit were greater than three. GQDAs with line-contacted metal electrodes have much better thermoelectric performance than surface contacted metal electrodes.

Effects of Coulomb Blockade on the Charge Transport through the Topological States of Finite Armchair Graphene Nanoribbons and Heterostructures.

In this study, we investigate the charge transport properties of semiconducting armchair graphene nanoribbons (AGNRs) and heterostructures through their topological states (TSs), with a specific focus on the Coulomb blockade region. Our approach employs a two-site Hubbard model that takes into account both intra- and inter-site Coulomb interactions. Using this model, we calculate the electron thermoelectric coefficients and tunneling currents of serially coupled TSs (SCTSs). In the linear response regime, we analyze the electrical conductance (Ge), Seebeck coefficient (S), and electron thermal conductance (κe) of finite AGNRs. Our results reveal that at low temperatures, the Seebeck coefficient is more sensitive to many-body spectra than electrical conductance. Furthermore, we observe that the optimized S at high temperatures is less sensitive to electron Coulomb interactions than Ge and κe. In the nonlinear response regime, we observe a tunneling current with negative differential conductance through the SCTSs of finite AGNRs. This current is generated by electron inter-site Coulomb interactions rather than intra-site Coulomb interactions. Additionally, we observe current rectification behavior in asymmetrical junction systems of SCTSs of AGNRs. Notably, we also uncover the remarkable current rectification behavior of SCTSs of 9-7-9 AGNR heterostructure in the Pauli spin blockade configuration. Overall, our study provides valuable insights into the charge transport properties of TSs in finite AGNRs and heterostructures. We emphasize the importance of considering electron-electron interactions in understanding the behavior of these materials.

Determination of exciton binding energy using photocurrent spectroscopy of Ge quantum-dot single-hole transistors under CW pumping.

We reported exciton binding-energy determination using tunneling-current spectroscopy of Germanium (Ge) quantum dot (QD) single-hole transistors (SHTs) operating in the few-hole regime, under 405-1550 nm wavelength (λ) illumination. When the photon energy is smaller than the bandgap energy (1.46 eV) of a 20 nm Ge QD (for instance, λ = 1310 nm and 1550 nm illuminations), there is no change in the peak voltages of tunneling current spectroscopy even when the irradiation power density reaches as high as 10 µW/µm2. In contrast, a considerable shift in the first hole-tunneling current peak towards positive VG is induced (ΔVG ≈ 0.08 V at 0.33 nW/µm2 and 0.15 V at 1.4 nW/µm2) and even additional photocurrent peaks are created at higher positive VG values (ΔVG ≈ 0.2 V at 10 nW/µm2 irradiation) by illumination at λ = 850 nm (where the photon energy matches the bandgap energy of the 20 nm Ge QD). These experimental observations were further strengthened when Ge-QD SHTs were illuminated by λ = 405 nm lasers at much lower optical-power conditions. The newly-photogenerated current peaks are attributed to the contribution of exciton, biexciton, and positive trion complexes. Furthermore, the exciton binding energy can be determined by analyzing the tunneling current spectra.