Maternal HIV-1 envelope-specific antibody responses and reduced risk of perinatal transmission.

Despite the wide availability of antiretroviral drugs, more than 250,000 infants are vertically infected with HIV-1 annually, emphasizing the need for additional interventions to eliminate pediatric HIV-1 infections. Here, we aimed to define humoral immune correlates of risk of mother-to-child transmission (MTCT) of HIV-1, including responses associated with protection in the RV144 vaccine trial. Eighty-three untreated, HIV-1-transmitting mothers and 165 propensity score-matched nontransmitting mothers were selected from the Women and Infants Transmission Study (WITS) of US nonbreastfeeding, HIV-1-infected mothers. In a multivariable logistic regression model, the magnitude of the maternal IgG responses specific for the third variable loop (V3) of the HIV-1 envelope was predictive of a reduced risk of MTCT. Neutralizing Ab responses against easy-to-neutralize (tier 1) HIV-1 strains also predicted a reduced risk of peripartum transmission in secondary analyses. Moreover, recombinant maternal V3-specific IgG mAbs mediated neutralization of autologous HIV-1 isolates. Thus, common V3-specific Ab responses in maternal plasma predicted a reduced risk of MTCT and mediated autologous virus neutralization, suggesting that boosting these maternal Ab responses may further reduce HIV-1 MTCT.

Bioengineered Approaches to Prevent Hypertrophic Scar Contraction

Burn injuries in the United States account for over one million hospital admissions per year, with treatment estimated at four billion dollars. Of severe burn patients, 30-90% will develop hypertrophic scars (HSc). Current burn therapies rely upon the use of bioengineered skin equivalents (BSEs), which assist in wound healing but do not prevent HSc. HSc contraction occurs of 6-18 months and results in the formation of a fixed, inelastic skin deformity, with 60% of cases occurring across a joint. HSc contraction is characterized by abnormally high presence of contractile myofibroblasts which normally apoptose at the completion of the proliferative phase of wound healing. Additionally, clinical observation suggests that the likelihood of HSc is increased in injuries with a prolonged immune response. Given the pathogenesis of HSc, we hypothesize that BSEs should be designed with two key anti-scarring characterizes: (1) 3D architecture and surface chemistry to mitigate the inflammatory microenvironment and decrease myofibroblast transition; and (2) using materials which persist in the wound bed throughout the remodeling phase of repair. We employed electrospinning and 3D printing to generate scaffolds with well-controlled degradation rate, surface coatings, and 3D architecture to explore our hypothesis through four aims.

In the first aim, we evaluate the impact of elastomeric, randomly-oriented biostable polyurethane (PU) scaffold on HSc-related outcomes. In unwounded skin, native collagen is arranged randomly, elastin fibers are abundant, and myofibroblasts are absent. Conversely, in scar contractures, collagen is arranged in linear arrays and elastin fibers are few, while myofibroblast density is high. Randomly oriented collagen fibers native to the uninjured dermis encourage random cell alignment through contact guidance and do not transmit as much force as aligned collagen fibers. However, the linear ECM serves as a system for mechanotransduction between cells in a feed-forward mechanism, which perpetuates ECM remodeling and myofibroblast contraction. The electrospinning process allowed us to create scaffolds with randomly-oriented fibers that promote random collagen deposition and decrease myofibroblast formation. Compared to an in vitro HSc contraction model, fibroblast-seeded PU scaffolds significantly decreased matrix and myofibroblast formation. In a murine HSc model, collagen coated PU (ccPU) scaffolds significantly reduced HSc contraction as compared to untreated control wounds and wounds treated with the clinical standard of care. The data from this study suggest that electrospun ccPU scaffolds meet the requirements to mitigate HSc contraction including: reduction of in vitro HSc related outcomes, diminished scar stiffness, and reduced scar contraction. While clinical dogma suggests treating severe burn patients with rapidly biodegrading skin equivalents, these data suggest that a more long-term scaffold may possess merit in reducing HSc.

In the second aim, we further investigate the impact of scaffold longevity on HSc contraction by studying a degradable, elastomeric, randomly oriented, electrospun micro-fibrous scaffold fabricated from the copolymer poly(l-lactide-co-ε-caprolactone) (PLCL). PLCL scaffolds displayed appropriate elastomeric and tensile characteristics for implantation beneath a human skin graft. In vitro analysis using normal human dermal fibroblasts (NHDF) demonstrated that PLCL scaffolds decreased myofibroblast formation as compared to an in vitro HSc contraction model. Using our murine HSc contraction model, we found that HSc contraction was significantly greater in animals treated with standard of care, Integra, as compared to those treated with collagen coated-PLCL (ccPLCL) scaffolds at d 56 following implantation. Finally, wounds treated with ccPLCL were significantly less stiff than control wounds at d 56 in vivo. Together, these data further solidify our hypothesis that scaffolds which persist throughout the remodeling phase of repair represent a clinically translatable method to prevent HSc contraction.

In the third aim, we attempt to optimize cell-scaffold interactions by employing an anti-inflammatory coating on electrospun PLCL scaffolds. The anti-inflammatory sub-epidermal glycosaminoglycan, hyaluronic acid (HA) was used as a coating material for PLCL scaffolds to encourage a regenerative healing phenotype. To minimize local inflammation, an anti-TNFα monoclonal antibody (mAB) was conjugated to the HA backbone prior to PLCL coating. ELISA analysis confirmed mAB activity following conjugation to HA (HA+mAB), and following adsorption of HA+mAB to the PLCL backbone [(HA+mAB)PLCL]. Alican blue staining demonstrated thorough HA coating of PLCL scaffolds using pressure-driven adsorption. In vitro studies demonstrated that treatment with (HA+mAB)PLCL prevented downstream inflammatory events in mouse macrophages treated with soluble TNFα. In vivo studies using our murine HSc contraction model suggested positive impact of HA coating, which was partiall impeded by the inclusion of the TNFα mAB. Further characterization of the inflammatory microenvironment of our murine model is required prior to conclusions regarding the potential for anti-TNFα therapeutics for HSc. Together, our data demonstrate the development of a complex anti-inflammatory coating for PLCL scaffolds, and the potential impact of altering the ECM coating material on HSc contraction.

In the fourth aim, we investigate how scaffold design, specifically pore dimensions, can influence myofibroblast interactions and subsequent formation of OB-cadherin positive adherens junctions in vitro. We collaborated with Wake Forest University to produce 3D printed (3DP) scaffolds with well-controlled pore sizes we hypothesized that decreasing pore size would mitigate intra-cellular communication via OB-cadherin-positive adherens junctions. PU was 3D printed via pressure extrusion in basket-weave design with feature diameter of ~70 µm and pore sizes of 50, 100, or 150 µm. Tensile elastic moduli of 3DP scaffolds were similar to Integra; however, flexural moduli of 3DP were significantly greater than Integra. 3DP scaffolds demonstrated ~50% porosity. 24 h and 5 d western blot data demonstrated significant increases in OB-cadherin expression in 100 µm pores relative to 50 µm pores, suggesting that pore size may play a role in regulating cell-cell communication. To analyze the impact of pore size in these scaffolds on scarring in vivo, scaffolds were implanted beneath skin graft in a murine HSc model. While flexural stiffness resulted in graft necrosis by d 14, cellular and blood vessel integration into scaffolds was evident, suggesting potential for this design if employed in a less stiff material. In this study, we demonstrate for the first time that pore size alone impacts OB-cadherin protein expression in vitro, suggesting that pore size may play a role on adherens junction formation affiliated with the fibroblast-to-myofibroblast transition. Overall, this work introduces a new bioengineered scaffold design to both study the mechanism behind HSc and prevent the clinical burden of this contractile disease.

Together, these studies inform the field of critical design parameters in scaffold design for the prevention of HSc contraction. We propose that scaffold 3D architectural design, surface chemistry, and longevity can be employed as key design parameters during the development of next generation, low-cost scaffolds to mitigate post-burn hypertrophic scar contraction. The lessening of post-burn scarring and scar contraction would improve clinical practice by reducing medical expenditures, increasing patient survival, and dramatically improving quality of life for millions of patients worldwide.

Emulsion-Based RIR-MAPLE Deposition of Conjugated Polymers: Primary Solvent Effect and Its Implications on Organic Solar Cell Performance.

Emulsion-based, resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) has been demonstrated as an alternative technique to deposit conjugated polymer films for photovoltaic applications; yet, a fundamental understanding of how the emulsion target characteristics translate into film properties and solar cell performance is unclear. Such understanding is crucial to enable the rational improvement of organic solar cell (OSC) efficiency and to realize the expected advantages of emulsion-based RIR-MAPLE for OSC fabrication. In this paper, the effect of the primary solvent used in the emulsion target is studied, both experimentally and theoretically, and it is found to determine the conjugated polymer cluster size in the emulsion as well as surface roughness and internal morphology of resulting polymer films. By using a primary solvent with low solubility-in-water and low vapor pressure, the surface roughness of deposited P3HT and PCPDTBT polymer films was reduced to 10 nm, and the efficiency of P3HT:PC61BM OSCs was increased to 3.2% (∼100 times higher compared to the first MAPLE OSC demonstration [ Caricato , A. P. ; Appl. Phys. Lett. 2012 , 100 , 073306 ]). This work unveils the mechanism of polymer film formation using emulsion-based RIR-MAPLE and provides insight and direction to determine the best ways to take advantage of the emulsion target approach to control film properties for different applications.

Nanowires for 3d silicon interconnection – low temperature compliant nanowire-polymer film for z-axis interconnect

Semiconductor chip packaging has evolved from single chip packaging to 3D heterogeneous system integration using multichip stacking in a single module. One of the key challenges in 3D integration is the high density interconnects that need to be formed between the chips with through-silicon-vias (TSVs) and inter-chip interconnects. Anisotropic Conductive Film (ACF) technology is one of the low-temperature, fine-pitch interconnect method, which has been considered as a potential replacement for solder interconnects in line with continuous scaling of the interconnects in the IC industry. However, the conventional ACF materials are facing challenges to accommodate the reduced pad and pitch size due to the micro-size particles and the particle agglomeration issue. A new interconnect material - Nanowire Anisotropic Conductive Film (NW-ACF), composed of high density copper nanowires of ~ 200 nm diameter and 10-30 µm length that are vertically distributed in a polymeric template, is developed in this work to tackle the constrains of the conventional ACFs and serves as an inter-chip interconnect solution for potential three-dimensional (3D) applications.

Seawater carbonate chemistry, length, mass and otholith development of spiny damselfish Acanthochromis polyacanthus during experiments, 2011

Determining which marine species are sensitive to elevated CO2 and reduced pH, and which species tolerate these changes, is critical for predicting the impacts of ocean acidification on marine biodiversity and ecosystem function. Although adult fish are thought to be relatively tolerant to higher levels of environmental CO2, very little is known about the sensitivity of juvenile stages, which are usually much more vulnerable to environmental change. We tested the effects of elevated environmental CO2 on the growth, survival, skeletal development and otolith (ear bone) calcification of a common coral reef fish, the spiny damselfish Acanthochromis polyacanthus. Newly hatched juveniles were reared for 3 wk at 4 different levels of PCO2(seawater) spanning concentrations already experienced in near-reef waters (450 µatm CO2) to those predicted to occur over the next 50 to 100 yr in the IPCC A2 emission scenario (600, 725, 850 µatm CO2). Elevated PCO2 had no effect on juvenile growth or survival. Similarly, there was no consistent variation in the size of 29 different skeletal elements that could be attributed to CO2 treatments. Finally, otolith size, shape and symmetry (between left and right side of the body) were not affected by exposure to elevated PCO2, despite the fact that otoliths are composed of aragonite. This is the first comprehensive assessment of the likely effects of ocean acidification on the early life history development of a marine fish. Our results suggest that juvenile A. polyacanthus are tolerant of moderate increases in environmental CO2 and that further acidification of the ocean will not, in isolation, have a significant effect on the early life history development of this species, and perhaps other tropical reef fishes

Seawater carbonate chemistry and biological processes during experiments with barnacle Semibalanus balanoides, 2010

The Arctic Ocean and its associated ecosystems face numerous challenges over the coming century. Increasing atmospheric CO2 is causing increasing warming and ice melting as well as a concomitant change in ocean chemistry ("ocean acidification"). As temperature increases it is expected that many temperate species will expand their geographic distribution northwards to follow this thermal shift; however with the addition of ocean acidification this transition may not be so straightforward. Here we investigate the potential impacts of ocean acidification and climate change on populations of an intertidal species, in this case the barnacle Semibalanus balanoides, at the northern edge of its range. Growth and development of metamorphosing post-larvae were negatively impacted at lower pH (pH 7.7) compared to the control (pH 8.1) but were not affected by elevated temperature (+4 °C). The mineral composition of the shells did not alter under any of the treatments. The combination of reduced growth and maintained mineral content suggests that there may have been a change in the energetic balance of the exposed animals. In undersaturated conditions more mineral is expected to dissolve from the shell and hence more energy would be required to maintain the mineral integrity. Any energy that would normally be invested into growth could be reallocated and hence organisms growing in lowered pH grow slower and end up smaller than individuals grown in higher pH conditions. The idea of reallocation of resources under different conditions of pH requires further investigation. However, there could be long-term implications on the fitness of these barnacles, which in turn may prevent them from successfully colonising new areas.

Investigation of escape response of Norwegian Pecten maximus

The ongoing process of ocean acidification already affects marine life and, according to the concept of oxygen- and capacity limitation of thermal tolerance (OCLTT), these effects may be exacerbated at the boarders of the thermal tolerance window. We studied the effects of elevated CO2 concentrations on clapping performance and energy metabolism of the commercially important scallop Pecten maximus. Individuals were exposed for at least 30 days to 4°C (winter) or to 10°C (spring/summer) at either ambient (0.04 kPa, normocapnia) or predicted future PCO2 levels (0.11 kPa, hypercapnia). Cold (4°C) exposed groups revealed thermal stress exacerbated by PCO2 indicated by a high mortality overall and its increase from 55% under normocapnia to 90% under hypercapnia. We therefore excluded the 4°C groups from further experimentation. Scallops at 10°C showed impaired clapping performance following hypercapnic exposure. Force production was significantly reduced although the number of claps was unchanged between normo- and hypercapnia exposed scallops. The difference between maximal and resting metabolic rate (aerobic scope) of the hypercapnic scallops was significantly reduced compared to normocapnic animals, indicating a reduction in net aerobic scope. Our data confirm that ocean acidification narrows the thermal tolerance range of scallops resulting in elevated vulnerability to temperature extremes and impairs the animal's performance capacity with potentially detrimental consequences for its fitness and survival in the ocean of tomorrow.

Appendix A: LA-ICP-MS results (Laser-ablation inductively coupled plasma mass spectrometer) from monazite Moacir standard

Three samples of garnet-kyanite paragneiss from the Variscan Ulten Zone (Northern Italy) were studied in detail for U-Th-Pb monazite dating. Monazite in these gneisses is abundant, shows highly variable grain size and occupies different textural positions: within the matrix, as inclusion in garnet and kyanite, within apatite aggregates. Monazite shows different deformation features as a function of the textural position: enclosed (shielded) monazite is generally more fractured than matrix (unshielded) monazite. The integration of textural information with deformation features and in situ U-Th-Pb analyses by LA-ICP-MS indicates that there is no direct correlation between textural site and monazite ages. Old ages of 351-343 Ma, determined on portions of large matrix (unshielded) monazite and on rare domains of monazite shielded by garnet, have been related to a prograde stage of the Variscan metamorphic evolution of the Ulten Zone. Ages of 330-326 Ma, which are related to the thermal peak, are recorded by small matrix monazite, external domains of large matrix monazite, and by (domains of) fractured monazite enclosed in garnet and kyanite. Large, old unshielded grains formed as blasts during the prograde metamorphic history and survived the peak metamorphism during which crystallisation/re-crystallisation partially occurred.

Microwave Plasma Assisted ALD Development for the Deposition of Gate Oxides & ALD of High-k Dielectrics

The semiconductor industry's urge towards faster, smaller and cheaper integrated circuits has lead the industry to smaller node devices. The integrated circuits that are now under volume production belong to 22 nm and 14 nm technology nodes. In 2007 the 45 nm technology came with the revolutionary high- /metal gate structure. 22 nm technology utilizes fully depleted tri-gate transistor structure. The 14 nm technology is a continuation of the 22 nm technology. Intel is using second generation tri-gate technology in 14 nm devices. After 14 nm, the semiconductor industry is expected to continue the scaling with 10 nm devices followed by 7 nm. Recently, IBM has announced successful production of 7 nm node test chips. This is the fashion how nanoelectronics industry is proceeding with its scaling trend. For the present node of technologies selective deposition and selective removal of the materials are required. Atomic layer deposition and the atomic layer etching are the respective techniques used for selective deposition and selective removal. Atomic layer deposition still remains as a futuristic manufacturing approach that deposits materials and lms in exact places. In addition to the nano/microelectronics industry, ALD is also widening its application areas and acceptance. The usage of ALD equipments in industry exhibits a diversi cation trend. With this trend, large area, batch processing, particle ALD and plasma enhanced like ALD equipments are becoming prominent in industrial applications. In this work, the development of an atomic layer deposition tool with microwave plasma capability is described, which is a ordable even for lightly funded research labs.

Kinetics and coverage dependent reaction mechanisms of the copper atomic layer deposition from copper dimethylamino-2-propoxide and diethylzinc

Atomic layer deposition (ALD) has been recognized as a promising method to deposit conformal and uniform thin film of copper for future electronic devices. However, many aspects of the reaction mechanism and the surface chemistry of copper ALD remain unclear. In this paper, we employ plane wave density functional theory (DFT) to study the transmetalation ALD reaction of copper dimethylamino-2-propoxide [Cu(dmap)2] and diethylzinc [Et2Zn] that was realized experimentally by Lee et al. [ Angew. Chem., Int. Ed. 2009, 48, 4536−4539]. We find that the Cu(dmap)2 molecule adsorbs and dissociates through the scission of one or two Cu–O bonds into surface-bound dmap and Cu(dmap) fragments during the copper pulse. As Et2Zn adsorbs on the surface covered with Cu(dmap) and dmap fragments, butane formation and desorption was found to be facilitated by the surrounding ligands, which leads to one reaction mechanism, while the migration of ethyl groups to the surface leads to another reaction mechanism. During both reaction mechanisms, ligand diffusion and reordering are generally endothermic processes, which may result in residual ligands blocking the surface sites at the end of the Et2Zn pulse, and in residual Zn being reduced and incorporated as an impurity. We also find that the nearby ligands play a cooperative role in lowering the activation energy for formation and desorption of byproducts, which explains the advantage of using organometallic precursors and reducing agents in Cu ALD. The ALD growth rate estimated for the mechanism is consistent with the experimental value of 0.2 Å/cycle. The proposed reaction mechanisms provide insight into ALD processes for copper and other transition metals.

A III-V channel field effect transistor for non-classical CMOS: process optimisation for improved gate stack function

This thesis describes a collection of studies into the electrical response of a III-V MOS stack comprising metal/GaGdO/GaAs layers as a function of fabrication process variables and the findings of those studies. As a result of this work, areas of improvement in the gate process module of a III-V heterostructure MOSFET were identified. Compared to traditional bulk silicon MOSFET design, one featuring a III-V channel heterostructure with a high-dielectric-constant oxide as the gate insulator provides numerous benefits, for example: the insulator can be made thicker for the same capacitance, the operating voltage can be made lower for the same current output, and improved output characteristics can be achieved without reducing the channel length further. It is known that transistors composed of III-V materials are most susceptible to damage induced by radiation and plasma processing. These devices utilise sub-10 nm gate dielectric films, which are prone to contamination, degradation and damage. Therefore, throughout the course of this work, process damage and contamination issues, as well as various techniques to mitigate or prevent those have been investigated through comparative studies of III-V MOS capacitors and transistors comprising various forms of metal gates, various thicknesses of GaGdO dielectric, and a number of GaAs-based semiconductor layer structures. Transistors which were fabricated before this work commenced, showed problems with threshold voltage control. Specifically, MOSFETs designed for normally-off (VTH > 0) operation exhibited below-zero threshold voltages. With the results obtained during this work, it was possible to gain an understanding of why the transistor threshold voltage shifts as the gate length decreases and of what pulls the threshold voltage downwards preventing normally-off device operation. Two main culprits for the negative VTH shift were found. The first was radiation damage induced by the gate metal deposition process, which can be prevented by slowing down the deposition rate. The second was the layer of gold added on top of platinum in the gate metal stack which reduces the effective work function of the whole gate due to its electronegativity properties. Since the device was designed for a platinum-only gate, this could explain the below zero VTH. This could be prevented either by using a platinum-only gate, or by matching the layer structure design and the actual gate metal used for the future devices. Post-metallisation thermal anneal was shown to mitigate both these effects. However, if post-metallisation annealing is used, care should be taken to ensure it is performed before the ohmic contacts are formed as the thermal treatment was shown to degrade the source/drain contacts. In addition, the programme of studies this thesis describes, also found that if the gate contact is deposited before the source/drain contacts, it causes a shift in threshold voltage towards negative values as the gate length decreases, because the ohmic contact anneal process affects the properties of the underlying material differently depending on whether it is covered with the gate metal or not. In terms of surface contamination; this work found that it causes device-to-device parameter variation, and a plasma clean is therefore essential. This work also demonstrated that the parasitic capacitances in the system, namely the contact periphery dependent gate-ohmic capacitance, plays a significant role in the total gate capacitance. This is true to such an extent that reducing the distance between the gate and the source/drain ohmic contacts in the device would help with shifting the threshold voltages closely towards the designed values. The findings made available by the collection of experiments performed for this work have two major applications. Firstly, these findings provide useful data in the study of the possible phenomena taking place inside the metal/GaGdO/GaAs layers and interfaces as the result of chemical processes applied to it. In addition, these findings allow recommendations as to how to best approach fabrication of devices utilising these layers.

A randomised controlled trial comparing weight adjusted dose versus fixed dose prophylactic phenylephrine infusion on maintaining systolic blood pressure during caesarean section under spinal anaesthesia.

Background: Spinal anaesthesia is the standard of care for elective caesarean delivery. It has advantages over general anaesthesia. However the sympathetic blockade induced by spinal anaesthesia results in an 80 percent incidence of hypotension without prophylactic management. Current evidence supports co-loading with intravenous fluids in conjunction with the use of vasopressors as the most effective way to prevent and treat the hypotension. Phenylephrine is the accepted vasopressor of choice in the parturient. A prophylactic phenylephrine infusion combined with a fluid co-load is proven to be an effective and safe method of maintaining maternal hemodynamic stability. While most published studies have assessed the effectiveness of a prophylactic phenylephrine fixed dose infusion, few studies have assessed the effect of a prophylactic phenylephrine weight adjusted dose infusion on maintaining maternal hemodynamic stability following spinal anesthesia for a cesarean delivery. Objective: To compare the incidence of hypotension between women undergoing elective caesarean section under spinal anaesthesia, receiving prophylactic phenylephrine infusion at a fixed dose of 37.5 micrograms per minute versus a weight adjusted dose of 0.5 micrograms per kilogram per minute. Methods: One hundred and eight patients scheduled for non-urgent caesarean section under spinal anaesthesia were randomized into 2 groups; control group and intervention group using a computer generated table of numbers. Control group; Received prophylactic phenylephrine fixed dose infusion at 37.5 micrograms per minute. Intervention group; Received prophylactic phenylephrine weight adjusted dose infusion at 0.5 micrograms per kilogram per minute Results: The two groups had similar baseline characteristics in terms of ; Age, sex, weight and height. There was a 35.2% incidence of hypotension in the fixed dose group and an 18.6% incidence of hypotension in the weight adjusted dose group. This difference was found to be of borderline statistical significance p-value 0.05, and the difference in the incidence rates between the two groups was found to be statistically significant p= 0.03. The difference in the incidence of reactive hypertension and bradycardia between the two groups was not statistically significant: p-value of 0.19 for reactive hypertension and p-value of 0.42 for the incidence of bradycardia. There was also no statistically significant difference in the use of phenylephrine boluses, use of atropine, intravenous fluid used and the number of times the infusion was stopped. Conclusion: Among this population, the incidence of hypotension was significantly less in the weight adjusted dose group than in the fixed dose group. There was no difference in the number of physician interventions required to keep the blood pressure within 20% of baseline, and no difference in the proportion of reactive hypertension or bradycardia between the two groups. Administering prophylactic phenylephrine infusion at a weight adjusted dose of 0.5 micrograms per kilogram per minute results in a lower incidence of hypotension compared to its administration at a fixed dose of 37.5 micrograms per minute.

Molecular chaperone accumulation as a function of stress evidences adaptation to high hydrostatic pressure in the piezophilic archaeon Thermococcus barophilus

The accumulation of mannosyl-glycerate (MG), the salinity stress response osmolyte of Thermococcales, was investigated as a function of hydrostatic pressure in Thermococcus barophilus strain MP, a hyperthermophilic, piezophilic archaeon isolated from the Snake Pit site (MAR), which grows optimally at 40 MPa. Strain MP accumulated MG primarily in response to salinity stress, but in contrast to other Thermococcales, MG was also accumulated in response to thermal stress. MG accumulation peaked for combined stresses. The accumulation of MG was drastically increased under sub-optimal hydrostatic pressure conditions, demonstrating that low pressure is perceived as a stress in this piezophile, and that the proteome of T. barophilus is low-pressure sensitive. MG accumulation was strongly reduced under supra-optimal pressure conditions clearly demonstrating the structural adaptation of this proteome to high hydrostatic pressure. The lack of MG synthesis only slightly altered the growth characteristics of two different MG synthesis deletion mutants. No shift to other osmolytes was observed. Altogether our observations suggest that the salinity stress response in T. barophilus is not essential and may be under negative selective pressure, similarly to what has been observed for its thermal stress response. Introduction

High Precision Plasma Etch for Pattern Transfer: Towards Fluorocarbon Based Atomic Layer Etching

A basic requirement of a plasma etching process is fidelity of the patterned organic materials. In photolithography, a He plasma pretreatment (PPT) based on high ultraviolet and vacuum ultraviolet (UV/VUV) exposure was shown to be successful for roughness reduction of 193nm photoresist (PR). Typical multilayer masks consist of many other organic masking materials in addition to 193nm PR. These materials vary significantly in UV/VUV sensitivity and show, therefore, a different response to the He PPT. A delamination of the nanometer-thin, ion-induced dense amorphous carbon (DAC) layer was observed. Extensive He PPT exposure produces volatile species through UV/VUV induced scissioning. These species are trapped underneath the DAC layer in a subsequent plasma etch (PE), causing a loss of adhesion. Next to stabilizing organic materials, the major goals of this work included to establish and evaluate a cyclic fluorocarbon (FC) based approach for atomic layer etching (ALE) of SiO2 and Si; to characterize the mechanisms involved; and to evaluate the impact of processing parameters. Periodic, short precursor injections allow precise deposition of thin FC films. These films limit the amount of available chemical etchant during subsequent low energy, plasma-based Ar+ ion bombardment, resulting in strongly time-dependent etch rates. In situ ellipsometry showcased the self-limited etching. X-ray photoelectron spectroscopy (XPS) confirms FC film deposition and mixing with the substrate. The cyclic ALE approach is also able to precisely etch Si substrates. A reduced time-dependent etching is seen for Si, likely based on a lower physical sputtering energy threshold. A fluorinated, oxidized surface layer is present during ALE of Si and greatly influences the etch behavior. A reaction of the precursor with the fluorinated substrate upon precursor injection was observed and characterized. The cyclic ALE approach is transferred to a manufacturing scale reactor at IBM Research. Ensuring the transferability to industrial device patterning is crucial for the application of ALE. In addition to device patterning, the cyclic ALE process is employed for oxide removal from Si and SiGe surfaces with the goal of minimal substrate damage and surface residues. The ALE process developed for SiO2 and Si etching did not remove native oxide at the level required. Optimizing the process enabled strong O removal from the surface. Subsequent 90% H2/Ar plasma allow for removal of C and F residues.

High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes

Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.