Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways

This article has been made available through the Brunel Open Access Publishing Fund. Copyright @ 2013 Pey et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling. Results: We present here an in-silico framework to infer relevant metabolic pathways for a particular phenotype under study based on its gene/protein expression data. This framework is based on the Carbon Flux Path (CFP) approach, a mixed-integer linear program that expands classical path finding techniques by considering additional biophysical constraints. In particular, the objective function of the CFP approach is amended to account for gene/protein expression data and influence obtained paths. This approach is termed integrative Carbon Flux Path (iCFP). We show that gene/protein expression data also influences the stoichiometric balancing of CFPs, which provides a more accurate picture of active metabolic pathways. This is illustrated in both a theoretical and real scenario. Finally, we apply this approach to find novel pathways relevant in the regulation of acetate overflow metabolism in Escherichia coli. As a result, several targets which could be relevant for better understanding of the phenomenon leading to impaired acetate overflow are proposed. Conclusions: A novel mathematical framework that determines functional pathways based on gene/protein expression data is presented and validated. We show that our approach is able to provide new insights into complex biological scenarios such as acetate overflow in Escherichia coli.Basque Governmen

Protein stability, folding and misfolding in human PGK1 deficiency

Conformational diseases are often caused by mutations, altering protein folding and stability in vivo. We review here our recent work on the effects of mutations on the human phosphoglycerate kinase 1 (hPGK1), with a particular focus on thermodynamics and kinetics of protein folding and misfolding. Expression analyses and in vitro biophysical studies indicate that disease-causing mutations enhance protein aggregation propensity. We found a strong correlation among protein aggregation propensity, thermodynamic stability, cooperativity and dynamics. Comparison of folding and unfolding properties with previous reports in PGKs from other species suggests that hPGK1 is very sensitive to mutations leading to enhance protein aggregation through changes in protein folding cooperativity and the structure of the relevant denaturation transition state for aggregation. Overall, we provide a mechanistic framework for protein misfolding of hPGK1, which is insightful to develop new therapeutic strategies aimed to target native state stability and foldability in hPGK1 deficient patients. © 2013 by the authors; licensee MDPI, Basel, Switzerland

Structural Characterization of Rapid Thermal Oxidized Si\u3csub\u3e1−x−y\u3c/sub\u3eGe\u3csub\u3ex\u3c/sub\u3eC\u3csub\u3ey\u3c/sub\u3e Alloy Films Grown by Rapid Thermal Chemical Vapor Deposition

The structural properties of as-grown and rapid thermal oxidized Si1−x−yGexCy epitaxial layers have been examined using a combination of infrared, x-ray photoelectron, x-ray diffraction, secondary ion mass spectroscopy, and Raman spectroscopy techniques. Carbon incorporation into the Si1−x−yGexCy system can lead to compressive or tensile strain in the film. The structural properties of the oxidized Si1−x−yGexCy film depend on the type of strain (i.e., carbon concentration) of the as-prepared film. For compressive or fully compensated films, the oxidation process drastically reduces the carbon content so that the oxidized films closely resemble to Si1−xGex films. For tensile films, two broad regions, one with carbon content higher and the other lower than that required for full strain compensation, coexist in the oxidized films

Workfunction Tuning of n-Channel MOSFETs Using Interfacial Yttrium Layer in Fully Silicided Nickel Gate

Continual scaling of the CMOS technology requires thinner gate dielectric to maintain high performance. However, when moving into the sub-45 nm CMOS generation, the traditional poly-Si gate approach cannot effectively reduce the gate thickness further due to the poly-depletion effect. Fully silicided Ni metal gate (FUSI) has been proven to be a promising solution. Ni FUSI metal gate can significantly reduce gate-line sheet resistance, eliminate boron penetration to channels and has good process compatibility with high-k gate dielectric. But Ni FUSI has a mid-gap workfunction which is not suitable for high-performance CMOS applications where the band-edge workfunction is required. In this paper, we propose to tune the nickel (Ni) fully silicided metal gate (FUSI) workfunction via an yttrium/Si/Ni gate stack structure. The workfunction of such structure indicates that the Y interlayer can effectively tune the Ni FUSI workfunction from the mid gap to the conduction band edge of silicon by controlling the interlayer thickness. The gate stack workfunction starts to saturate to the pure yttrium value when the yttrium interlayer is >1.6 nm. This indicates the chemical potential of the material adjacent to gate electrode/gate insulator plays an important role in the determination of the workfunction.Singapore-MIT Alliance (SMA

Effect of Oxygen on Ni-Silicided FUSI Metal Gate

Continual evolution of the CMOS technology requires thinner gate dielectric to maintain high performance. However, when moving into the sub-65 nm CMOS generation, the traditional poly-Si gate approach cannot effectively reduce the gate thickness further due to the poly-depletion effect. Fully silicided metal gate (FUSI) has been proven to be a promising solution. FUSI metal gate can significantly reduce gate-line sheet resistance, eliminate boron penetration to channels and has good process compatibility with high-k gate dielectric. In this paper, the effect of oxygen introduced by the process of conventional furnace annealing in FUSI metal gate is investigated. A 120 nm amorphous Si layer was sputtered on dielectric oxides of various thicknesses grown using a standard oxidation process. Raman spectra showed that the 120 nm thick pre-sputtered amorphous Si recrystallized after annealing in a conventional furnace at 900°C. Secondary ion mass spectrometry (SIMS) revealed that the annealed Si film contained traces of oxygen which were incorporated into the film during the furnace annealing process. It is suspected that the oxygen was originated from a few ppm of impurities present in the high-purity annealing gas (N2). When a 100 nm of Ni was deposited using a DC sputterer on such sample and was rapid thermal annealed (RTA) at 400°C to form a fully silicide film, the transmission electron micrograph showed the existence of unreacted oxygen-rich Si layer along the interface of the NiSi/SiO2, leading to areal non-uniformity in the workfunction. It is suggested that the presence of oxygen can effectively retard the Ni diffusion into the Si film during the silicidation process such that the FUSI process is delayed, and the equivalent oxide thickness (EOT) increased as shown by capacitance-voltage (C-V) measurements. The workfunction of Ni-silicided FUSI film determined by C-V measurement on MOS structures was found to increase compared to the as-deposited amorphous Si film (the control sample).Singapore-MIT Alliance (SMA

Effects of Platinum on NiPtSiGe/n-SiGe and NiPtSi/n-Si Schottky Contacts

Solid phase reaction of NiPt/Si and NiPt/SiGe is one of the key issues for silicide (germanosilicide) technology. Especially, the NiPtSiGe, in which four elements are involved, is a very complex system. As a result, a detailed study is necessary for the interfacial reaction between NiPt alloy film and SiGe substrate. Besides using traditional material characterization techniques, characterization of Schottky diode is a good measure to detect the interface imperfections or defects, which are not easy to be found on large area blanket samples. The I-V characteristics of 10nm Ni(Pt=0, 5, 10 at.%) germanosilicides/n-Si₀/₇Ge₀.₃ and silicides/n-Si contact annealed at 400 and 500°C were studied. For Schottky contact on n-Si, with the addition of Pt in the Ni(Pt) alloy, the Schottky barrier height (SBH) increases greatly. With the inclusion of a 10% Pt, SBH increases ~0.13 eV. However, for the Schottky contacts on SiGe, with the addition of 10% Pt, the increase of SBH is only ~0.04eV. This is explained by pinning of the Fermi level. The forward I-V characteristics of 10nm Ni(Pt=0, 5, 10 at.%)SiGe/SiGe contacts annealed at 400°C were investigated in the temperature range from 93 to 300K. At higher temperature (>253K) and larger bias at low temperature (<253K), the I-V curves can be well explained by a thermionic emission model. At lower temperature, excess currents at lower forward bias region occur, which can be explained by recombination/generation or patches due to inhomogenity of SBH with pinch-off model or a combination of the above mechanisms.Singapore-MIT Alliance (SMA

Effect of Pt on agglomeration and Ge out-diffusion in Ni(Pt) germanosilicide

The effect of Ni and Ni(Pt) alloy with ~5 and 10 at. % Pt on the agglomeration and Ge out-diffusion in Nickel germanosilicide formed on Si&#x2080;.&#x2087;&#x2085;Ge&#x2080;.&#x2082;&#x2085;(100) has been studied. A remarkable improvement in the agglomeration behavior with increasing Pt atomic percentage is observed by sheet resistance measurements and scanning electron microscopy (SEM). In addition, x-ray diffraction (XRD) shows that only NiSiGe or Ni(Pt)SiGe phase exists from 400 to 800°C. However, Ge out-diffusion from the monogermanosilicide grains is obvious at 600°C and 700°C for Ni/SiGe and Ni(Pt)(Pt at.%~10%)/SiGe, respectively, evident by XRD and micro-Raman spectroscopy. The improved melting temperature of Ni(Pt)SiGe solution compared to that of NiSiGe is the likely reason of seeing better surface morphology and suppressing Ge out-diffusion of the germanosilicide grains observed.Singapore-MIT Alliance (SMA

Recent key developments in nanoscale reliability and failure analysis techniques for advanced nanoelectronics devices

Last decade has witnessed an aggressive scaling of CMOS technology nodes pushing it all the way down to sub-10nm and this scaling trend looks positive for the next two-three nodes as well down to 5nm. This push for scaling of the technology node has created a need for using material characterization techniques with (sub)nanometer probe resolution to characterize these advanced nanoelectronic devices - to observe and understand the underlying thermodynamics and kinetics of the physical phenomenon at the nanometer scale in real-time. Among these advanced characterization techniques, transmission election microscopy (TEM) and scanning probe microscopy (SPM), as well as the techniques derived from these, have become critical and instrumental to failure analysis and for evaluation of key design metrics for reliability studies. In this work, we present the different case studies using these two techniques which we have employed for studying both advanced logic and memory devices. High resolution TEM (HRTEM) has been used for both RRAM and gate oxide reliability studies due to its multiple compositional characterization capabilities with sub-nm resolution. TEM can routinely achieve a resolution around 0.1nm and thus can provide tremendous information related to structure (Diffraction Pattern) and composition (Electron Energy Loss Spectroscopy). Ex-situ TEM techniques (supported by Focused Ion Beam (FIB)) have allowed us to perform diverse electrical and thermal testing on devices. We have found concrete evidence of FinFET device degradation recently [1]. We have also employed in-situ TEM techniques (facilitated by scanning tunneling microscopy (STM) and the thermal holder) to observe the degradation behavior of metal-dielectric stacks in real-time [2]. The in-situ TEM technique has provided insight into the direct and solid time sequential evolution of failure behavior in RRAM devices. Additionally, 3D tomography characterization of the defect and failure spot has been acquired by tilting the sample and collecting the sequential images at different angles [3]. This technique of 3D tomography is a very powerful one for defect reorganization and for root cause analysis of failure mechanism. Conductive atomic force microscopy (CAFM) and STM are two techniques, belonging to a large pool of available SPM tools, which we have used for breakdown studies in ultra-thin HfO2 and other high-κ dielectrics as well as multi-layered fluorinated graphene (FG) stacks. With a resolution, down to ~10nm and ~0.1nm for CAFM and STM respectively under ultra-high vacuum (UHV) conditions, we have applied these tools to measure electrical properties (I-V and dI/dV) at grain and grain boundary spots in ultra-thin polycrystalline HfO2 dielectrics [4] as well as to understand the breakdown mechanism in FG stacks [5]. We have also explored the local spectroscopy capabilities (of both STM and CAFM) for the measurement of random telegraph noise (RTN) in blanket HfO2 films. Using bias dependent RTN measurements, it has been possible to quantify the position of the defect in the probed location of the dielectric. Interestingly, these dielectric breakdowns and RTN measurements at the nanoscale have also provided experimental evidence of defect clustering in polycrystalline dielectrics and possible existence of the metastable nature of oxygen vacancy (VO) defect in HfO2 respectively [6]. CAFM has also been explored to study the role of VO in HfO2 based RRAM stacks for ultra-low power memory applications where the signature of sub-quantum conductance based resistive switching has been experimentally observed [7]. We strongly believe that these tools and techniques would play an indispensable role in unveiling the underlying physics of the nanoscale physical phenomenon for existing as well as emerging materials and 2D/3D devices. References: [1] S. Mei et al., IEDM (2016). [2] K. L. Pey et al., IRPS (2010). [3] S. Mei et al., Unpublished. [4] K. Shubhakar et al., Micro. Engineering (2013). [5] A. Ranjan et al., IRPS (2017, Accepted). [6] A. Ranjan et al., IRPS (2016

Imaging features of retroperitoneal extra-adrenal paragangliomas in 10 dogs

Retroperitoneal paragangliomas are rare tumors of the neuroendocrine system. Only a few canine case reports are available with rare descriptions of their imaging features. The objectives of this multi-center, retrospective case series study were to describe the diagnostic imaging features of confirmed retroperitoneal paragangliomas and specify their location. Medical records and imaging studies of 10 affected dogs with cytological or histopathologic results concordant with retroperitoneal paragangliomas were evaluated. Dogs had a median age of 9 years. Four of them had clinical signs and laboratory reports compatible with excessive production of catecholamines. Six ultrasound, four CT, four radiographic, and one MRI studies were included. The paragangliomas did not have a specific location along the aorta. They were of various sizes (median 33&nbsp;mm, range: 9–85&nbsp;mm of length). Masses had heterogeneous parenchyma in six of 10 dogs, regardless of the imaging modality. Strong contrast enhancement was found in all CT studies. Encircling of at least one vessel was detected in six of 10 masses, clear invasion of a vessel was identified in one of 10 masses. In five of 10 cases, the masses were initially misconstrued as lymph nodes by the on-site radiologist. Retroperitoneal paragangliomas appear along the abdominal aorta, often presenting heterogeneous parenchyma, possibly affecting the local vasculature, and displaying strong contrast enhancement on CT. Clinical signs can be secondary to mass effects or excessive catecholamine production. Underdiagnosis and misdiagnosis of this tumor are suspected as they can be silent, of small size, or confused with other structures