Ring oscillator based injection locked clock multiplier

This thesis describes a ring-based injection locked clock multiplier (ILCM) designed with the goal of generating a high-frequency and low-jitter clock. Building on prior research done on injection locking, this design uses a reference frequency doubling technique to push the noise bandwidth of the circuit to Fref/3 to suppress DCO noise to a large extent. A background duty cycle error correction technique is employed to correct errors on the doubled clock that could be detrimental to performance. The design also modifies an existing architecture to achieve type-II suppression of DCO noise in order to fully suppress the flicker noise which becomes prevalent in low process nodes. The prototype ILCM was fabricated in TSMC 65 nm CMOS technology. Thorough testing was performed to characterize the effectiveness of the aforementioned techniques. The circuit achieves 340 fsrms integrated jitter when operating at 5 GHz while only consuming 5.3 mW of power. The ILCM's figure of merit, -242.4 dB, is on par with state-of-the-art ring-based clock multipliers while operating at a much higher output frequency and multiplication factor than previously published work. These results indicate the effectiveness of reference frequency doubling in a ring-based, high-performance clock multiplier design

Monitoring stream stage, channel profile, and aqueous conductivity with time domain reflectometry (TDR).

Time domain reflectometry (TDR) operates by propagating a radar frequency electromagnetic pulse down a transmission line while monitoring the reflected signal. As the electromagnetic pulse propagates along the transmission line, it is subject to impedance by the dielectric properties of the media along the transmission line (e.g., air, water, sediment), reflection at dielectric discontinuities (e.g., air-water or water-sediment interface), and attenuation by electrically conductive materials (e.g., salts, clays). Taken together, these characteristics provide a basis for integrated stream monitoring; specifically, concurrent measurement of stream stage, channel profile and aqueous conductivity. Here, we make novel application of TDR within the context of stream monitoring. Efforts toward this goal followed three critical phases. First, a means of extracting the desired stream parameters from measured TDR traces was required. Analysis was complicated by the fact that interface location and aqueous conductivity vary concurrently and multiple interfaces may be present at any time. For this reason a physically based multisection model employing the S11 scatter function and Cole-Cole parameters for dielectric dispersion and loss was developed to analyze acquired TDR traces. Second, we explored the capability of this multisection modeling approach for interpreting TDR data acquired from complex environments, such as encountered in stream monitoring. A series of laboratory tank experiments were performed in which the depth of water, depth of sediment, and conductivity were varied systematically. Comparisons between modeled and independently measured data indicate that TDR measurements can be made with an accuracy of {+-}3.4x10{sup -3} m for sensing the location of an air/water or water/sediment interface and {+-}7.4% of actual for the aqueous conductivity. Third, monitoring stations were sited on the Rio Grande and Paria rivers to evaluate performance of the TDR system under normal field conditions. At the Rio Grande site (near Central Bridge in Albuquerque, New Mexico) continuous monitoring of stream stage and aqueous conductivity was performed for 6 months. Additionally, channel profile measurements were acquired at 7 locations across the river. At the Paria site (near Lee's Ferry, Arizona) stream stage and aqueous conductivity data were collected over a 4-month period. Comparisons drawn between our TDR measurements and USGS gage data indicate that the stream stage is accurate within {+-}0.88 cm, conductivity is accurate within {+-}11% of actual, and channel profile measurements agree within {+-}1.2 cm

Climate Change and invasibility of the Antarctic benthos

Benthic communities living in shallow-shelf habitats in Antarctica (<100-m depth) are archaic in their structure and function. Modern predators, including fast-moving, durophagous (skeleton-crushing) bony fish, sharks, and crabs, are rare or absent; slow-moving invertebrates are the top predators; and epifaunal suspension feeders dominate many soft substratum communities. Cooling temperatures beginning in the late Eocene excluded durophagous predators, ultimately resulting in the endemic living fauna and its unique food-web structure. Although the Southern Ocean is oceanographically isolated, the barriers to biological invasion are primarily physiological rather than geographic. Cold temperatures impose limits to performance that exclude modern predators. Global warming is now removing those physiological barriers, and crabs are reinvading Antarctica. As sea temperatures continue to rise, the invasion of durophagous predators will modernize the shelf benthos and erode the indigenous character of marine life in Antarctica

Like Mother(-in-Law) Like Daughter? Influence of the Older Generation’s Fertility Behaviours on Women’s Desired Family Size in Bihar, India

This paper investigates the associations between preferred family size of women in rural Bihar, India and the fertility behaviours of their mother and mother-in-law. Scheduled interviews of 440 pairs of married women aged 16–34 years and their mothers-in-law were conducted in 2011. Preferred family size is first measured by Coombs scale, allowing us to capture latent desired number of children and then categorized into three categories (low, medium and high). Women’s preferred family size is estimated using ordered logistic regression. We find that the family size preferences are not associated with mother’s fertility but with mother’s education. Mother-in-law’s desired number of grandchildren is positively associated with women’s preferred family size. However, when the woman has higher education than her mother-in-law, her preferred family size gets smaller, suggesting that education provides women with greater autonomy in their decision-making on childbearing

Range expansion and the origin of USA300 north american epidemic methicillin-resistant Staphylococcus aureus

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. IMPORTANCE The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread

Effects of Intracellular Calcium and Actin Cytoskeleton on TCR Mobility Measured by Fluorescence Recovery

Background: The activation of T lymphocytes by specific antigen is accompanied by the formation of a specialized signaling region termed the immunological synapse, characterized by the clustering and segregation of surface molecules and, in particular, by T cell receptor (TCR) clustering. Methodology/Principal Findings: To better understand TCR motion during cellular activation, we used confocal microscopy and photo-bleaching recovery techniques to investigate the lateral mobility of TCR on the surface of human T lymphocytes under various pharmacological treatments. Using drugs that cause an increase in intracellular calcium, we observed a decrease in TCR mobility that was dependent on a functional actin cytoskeleton. In parallel experiments measurement of filamentous actin by FACS analysis showed that raising intracellular calcium also causes increased polymerization of the actin cytoskeleton. These in vitro results were analyzed using a mathematical model that revealed effective binding parameters between TCR and the actin cytoskeleton. Conclusion/Significance: We propose, based on our results, that increase in intracellular calcium levels leads to actin polymerization and increases TCR/cytoskeleton interactions that reduce the overall mobility of the TCR. In a physiological setting, this may contribute to TCR re-positioning at the immunological synapse

A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen

Experimental work has shown that T cells of the immune system rapidly and specifically respond to antigenic molecules presented on the surface of antigen-presenting-cells and are able to discriminate between potential stimuli based on the kinetic parameters of the T cell receptor-antigen bond. These antigenic molecules are presented among thousands of chemically similar endogenous peptides, raising the question of how T cells can reliably make a decision to respond to certain antigens but not others within minutes of encountering an antigen presenting cell. In this theoretical study, we investigate the role of localized rebinding between a T cell receptor and an antigen. We show that by allowing the signaling state of individual receptors to persist during brief unbinding events, T cells are able to discriminate antigens based on both their unbinding and rebinding rates. We demonstrate that T cell receptor coreceptors, but not receptor clustering, are important in promoting localized rebinding, and show that requiring rebinding for productive signaling reduces signals from a high concentration of endogenous pMHC. In developing our main results, we use a relatively simple model based on kinetic proofreading. However, we additionally show that all our results are recapitulated when we use a detailed T cell receptor signaling model. We discuss our results in the context of existing models and recent experimental work and propose new experiments to test our findings

Impact of Upadacitinib on laboratory parameters and related adverse events in patients with RA: Integrated data up to 6.5 years

Introduction: Upadacitinib (UPA) is a Janus kinase inhibitor that has demonstrated efficacy in moderate-to-severe rheumatoid arthritis (RA) with an acceptable safety profile. We investigated laboratory parameter changes in UPA RA clinical trials. Methods: Pooled data from six randomized trials in the SELECT phase 3 program were included. Key laboratory parameters and safety data were measured for UPA 15 and 30 mg once daily (QD), adalimumab (ADA) 40 mg every other week + methotrexate (MTX), and MTX monotherapy. Exposure-adjusted event rates (EAERs) of adverse events were calculated. Results: A total of 3209 patients receiving UPA 15 mg QD (10 782.7 patient-years [PY]), 1204 patients receiving UPA 30 mg QD (3162.5 PY), 579 patients receiving ADA + MTX (1573.2 PY), and 314 patients receiving MTX monotherapy (865.1 PY) were included, representing up to 6.5 years of total exposure. Decreases in mean levels of hemoglobin, neutrophils, and lymphocytes, and increases in mean levels of liver enzymes and creatinine phosphokinase were observed with UPA, with grade 3 or 4 changes observed in some patients. Mean low- and high-density lipoprotein cholesterol ratios remained stable for patients receiving UPA 15 mg QD. EAERs of anemia and neutropenia occurred at generally consistent rates between UPA and active comparators (3.1–4.3 and 1.7–5.0 events [E]/100 PY across treatment groups, respectively). Rates of hepatic disorder were higher with MTX monotherapy, UPA 15 mg and UPA 30 mg (10.8, 9.7, and 11.0 E/100 PY, respectively) versus ADA + MTX (6.4 E/100 PY). Rates of lymphopenia were highest with MTX monotherapy (3.2 E/100 PY). Treatment discontinuations due to laboratory-related events were rare, occurring in 1.1% and 2.2% of patients treated with UPA 15 and 30 mg QD, respectively. Conclusions: The results of this integrated long-term analysis of laboratory parameters continue to support an acceptable safety profile of UPA 15 mg QD for moderate-to-severe RA

Reactivation of tectonics, crustal underplating, and uplift after 60 Myr of passive subsidence, Raukumara Basin, Hikurangi-Kermadec fore arc, New Zealand: implications for global growth and recycling of continents

We use seismic reflection and refraction data to determine crustal structure, to map a fore-arc basin containing 12 km of sediment, and to image the subduction thrust at 35 km depth. Seismic reflection megasequences within the basin are correlated with onshore geology: megasequence X, Late Cretaceous and Paleogene marine passive margin sediments; megasequence Y, a similar to 10,000 km(3) submarine landslide emplaced during subduction initiation at 22 Ma; and megasequence Z, a Neogene subduction margin megasequence. The Moho lies at 17 km beneath the basin center and at 35 km at the southern margin. Beneath the western basin margin, we interpret reflective units as deformed Gondwana fore-arc sediment that was thrust in Cretaceous time over oceanic crust 7 km thick. Raukumara Basin has normal faults at its western margin and is uplifted along its eastern and southern margins. Raukumara Basin represents a rigid fore-arc block > 150 km long, which contrasts with widespread faulting and large Neogene vertical axis rotations farther south. Taper of the western edge of allochthonous unit Y and westward thickening and downlap of immediately overlying strata suggest westward or northwestward paleoslope and emplacement direction rather than southwestward, as proposed for the correlative onshore allochthon. Spatial correlation between rock uplift of the eastern and southern basin margins with the intersection between Moho and subduction thrust leads us to suggest that crustal underplating is modulated by fore-arc crustal thickness. The trench slope has many small extensional faults and lacks coherent internal reflections, suggesting collapse of indurated rock, rather than accretion of > 1 km of sediment from the downgoing plate. The lack of volcanic intrusion east of the active arc, and stratigraphic evidence for the broadening of East Cape Ridge with time, suggests net fore-arc accretion since 22 Ma. We propose a cyclical fore-arc kinematic: rock moves down a subduction channel to near the base of the crust, where underplating drives rock uplift, oversteepens the trench slope, and causes collapse toward the trench and subduction channel. Cyclical rock particle paths led to persistent trench slope subsidence during net accretion. Existing global estimates of fore-arc loss are systematically too high because they assume vertical particle paths. Citation: Sutherland, R., et al. (2009), Reactivation of tectonics, crustal underplating, and uplift after 60 Myr of passive subsidence, Raukumara Basin, Hikurangi-Kermadec fore arc, New Zealand: Implications for global growth and recycling of continents, Tectonics, 28, TC5017, doi: 10.1029/2008TC002356

Federated Learning for Breast Density Classification: A Real-World Implementation

Building robust deep learning-based models requires large quantities of diverse training data. In this study, we investigate the use of federated learning (FL) to build medical imaging classification models in a real-world collaborative setting. Seven clinical institutions from across the world joined this FL effort to train a model for breast density classification based on Breast Imaging, Reporting & Data System (BI-RADS). We show that despite substantial differences among the datasets from all sites (mammography system, class distribution, and data set size) and without centralizing data, we can successfully train AI models in federation. The results show that models trained using FL perform 6.3% on average better than their counterparts trained on an institute's local data alone. Furthermore, we show a 45.8% relative improvement in the models' generalizability when evaluated on the other participating sites' testing data.Comment: Accepted at the 1st MICCAI Workshop on "Distributed And Collaborative Learning"; add citation to Fig. 1 & 2 and update Fig.