cssi/SciSciGPT-SciSciNet huggingface dataset:
Conversion of JPG Image into DICOM Image Format with One Click Tagging

DICOM images are the centerpiece of radiological imaging. They contain a lot of metadata information about the patient, procedure, sequence of images, device and location. To modify, annotate or simply anonymize images for distribution, we often need to convert DICOM images to another format like jpeg since there are a number of image manipulation tools available for jpeg images compared to DICOM. As part of a research at our institution to customize radiology images to assess cognitive ability of multiple user groups, we created an open-source tool called Jpg2DicomTags, which is able to extract DICOM metadata tags, convert images to lossless jpg that can be manipulated and subsequently reconvert jpg images to DICOM by adding back the metadata tags. This tool provides a simple, easy to use user-interface for a tedious manual task that providers, researchers and patients might often need to do.
Absence of Landau damping in driven three-component Bose–Einstein condensate in optical lattices

We explore the quantum many-body physics of a three-component Bose-Einstein condensate in an optical lattice driven by laser fields in V and Λ configurations. We obtain exact analytical expressions for the energy spectrum and amplitudes of elementary excitations, and discover symmetries among them. We demonstrate that the applied laser fields induce a gap in the otherwise gapless Bogoliubov spectrum. We find that Landau damping of the collective modes above the energy of the gap is carried by laser-induced roton modes and is considerably suppressed compared to the phonon-mediated damping endemic to undriven scalar condensates
A Virtual Repository Approach to Clinical and Utilization Studies: Application in Mammography as Alternative to a National Database

A national mammography database was proposed, based on a centralized architecture for collecting, monitoring, and auditing mammography data. We have developed an alternative architecture relying on Internet-based distributed queries to heterogeneous databases. This architecture creates a "virtual repository", or a federated database which is constructed dynamically, for each query and makes use of data available in legacy systems. It allows the construction of custom-tailored databases at individual sites that can serve the dual purposes of providing data (a) to researchers through a common mammography repository and (b) to clinicians and administrators at participating institutions. We implemented this architecture in a prototype system at the Brigham and Women's Hospital to show its feasibility. Common queries are translated dynamically into database-specific queries, and the results are aggregated for immediate display or download by the user. Data reside in two different databases and consist of structured mammography reports, coded per BIRADS Standardized Mammography Lexicon, as well as pathology results. We prospectively collected data on 213 patients, and showed that our system can perform distributed queries effectively. We also implemented graphical exploratory analysis tools to allow visualization of results. Our findings indicate that the architecture is not only feasible, but also flexible and scaleable, constituting a good alternative to a national mammography database.
Detecting, Localizing, and Tracking an Unknown Number of Moving Targets Using a Team of Mobile Robots

Target tracking is a fundamental problem in robotics research and has been the subject of detailed studies over the years. In this paper, we introduce a new formulation, based on the mathematical concept of random finite sets, that allows for tracking an unknown and dynamic number of mobile targets with a team of robots. We show how to employ the Probability Hypothesis Density filter to simultaneously estimate the number of targets and their positions. Next, we present a greedy algorithm for assigning trajectories to the robots to actively track the targets. We prove that the greedy algorithm is a 2-approximation for maximizing submodular tracking objective functions. We examine two such functions: the mutual information between the estimated target positions and future measurements from the robots, and the expected number of targets detected by the robot team. We provide extensive simulation evaluations using a real-world dataset.
Simulating fail-stop in asynchronous distributed systems

The fail-stop failure model appears frequently in the distributed systems literature. However, in an asynchronous distributed system, the fail-stop model cannot be implemented. In particular, it is impossible to reliably detect crash failures in an asynchronous system. In this paper, we show that it is possible to specify and implement a failure model that is indistinguishable from the fail-stop model from the point of view of any process within an asynchronous system. We give necessary conditions for a failure model to be indistinguishable from the fail-stop model, and derive lower bounds on the amount of process replication needed to implement such a failure model. We present a simple one-round protocol for implementing one such failure model, which we call simulated fail-stop.
An Aggregate Search Model for Web Search Engines: An Empirical Study.

In this paper, we study a novel aggregate search model for web search engines. Rather than retrieving individual web pages in the search result, our model aggregates relevant web pages and formulates information groups which may capture user's search intents well. An information group may consist of an individual web page, or a set of hyper-linked web pages that are relevant to user's queries. Several meaningful ranking measures are proposed to rank returned information groups. We evaluate the proposed aggregate search model using a large real search log dataset and an open source web search platform. The empirical study indicates that our model is useful to improve the web search quality.
An Instructional Robotics and Machine Vision Laboratory Station

Abstract In support of several robotics and machine vision courses, the U. S. Naval Academy has assembled a laboratory consisting of 13 identical stations. Each station has a PC AT compatible computer, a five degree-of-freedom robot arm, a video-rate vision system, and a speech synthesis system. The robot arms are capable of teach pendant operation, or control via the attached computer. Programs written in the robot control language (a variant of BASIC) can be downloaded into, stored in, and run from robot RAM. For greater flexibility, move instructions can be generated by the controlling computer (in any desired language) and transmitted to the arm for execution via an RS-232 link. Each joint of the robot (plus the gripper) has a dedicated microprocessor for closed-loop servo operation utilizing incremental drive-motor shaft encoders and dedicated micro-switches for “home” locations. Each vision system includes an arm mounted RS-170-compatible video camera, connected to a dedicated frame-grabber and video memory board in the computer, and a video monitor. This configuration permits utilizing vision feedback in the robot control process. Additionally, machine vision is addressed independent of robot operations, with most of the standard image processing techniques discussed.
Learning the Network Structure of Heterogeneous Data via Pairwise Exponential Markov Random Fields

Markov random fields (MRFs) are a useful tool for modeling relationships present in large and high-dimensional data. Often, this data comes from various sources and can have diverse distributions, for example a combination of numerical, binary, and categorical variables. Here, we define the pairwise exponential Markov random field (PE-MRF), an approach capable of modeling exponential family distributions in heterogeneous domains. We develop a scalable method of learning the graphical structure across the variables by solving a regularized approximated maximum likelihood problem. Specifically, we first derive a tractable upper bound on the log-partition function. We then use this upper bound to derive the group graphical lasso, a generalization of the classic graphical lasso problem to heterogeneous domains. To solve this problem, we develop a fast algorithm based on the alternating direction method of multipliers (ADMM). We also prove that our estimator is sparsistent, with guaranteed recovery of the true underlying graphical structure, and that it has a polynomially faster runtime than the current state-of-the-art method for learning such distributions. Experiments on synthetic and real-world examples demonstrate that our approach is both eﬃcient and accurate at uncovering the structure of heterogeneous data.
Successful Renal Transplantation in Hyperoxaluria. A Report of Two Cases

Two patients with documented primary hyperoxaluria have received renal allografts with successful function for 10 years and 25 months. The patient in case 1 required a ureterolithotomy 6 years post-transplantation to remove a renal calculus of calcium oxalate. This case illustrates that despite recurrence of oxalate stones in the allograft, satisfactory renal function can be maintained by careful follow-up and appropriate interventions. Factors that may be important in successful graft function include the occurrence of acute rejection episodes, avoidance of ischemic graft damage, trials of pyridoxine therapy to decrease oxalate excretion, and frequent evaluation with appropriate interventions as necessary. Renal transplantation is a suitable and possibly the preferred form of therapy of end stage renal disease in patients with primary hyperoxaluria.
Enhanced User Security and Privacy Protection in 4G LTE Network.

Although the Evolved Packet System Authentication and Key Agreement (EPS-AKA) provides security and privacy enhancements in 3rd Generation Partnership Project (3GPP), the International Mobile Subscriber Identity (IMSI) is sent in clear text in order to obtain service. Various efforts to provide security mechanisms to protect this unique private identity have not resulted in methods implemented to protect the disclosure of the IMSI. The exposure of the IMSI brings risk to user privacy, and knowledge of it can lead to several passive and active attacks targeted at specific IMSI's and their respective users. Further, the Temporary Mobile Subscribers Identity (TMSI) generated by the Authentication Center (AuC) have been found to be prone to rainbow and brute force attacks, hence an attacker who gets hold of the TMSI can be able to perform social engineering in tracing the TMSI to the corresponding IMSI of a User Equipment (UE). This paper proposes a change to the EPS-AKA authentication process in 4G Long Term Evolution (LTE) Network by including the use of Public Key Infrastructure (PKI). The change would result in the IMSI never being released in the clear in an untrusted network.
Status of Radiation Treatment of Prostate Cancer at Stanford University

Over 900 patients have been treated with radiation therapy in the 30-year Stanford prostate study. Overall survival, i.e., scoring death due to all causes, was 45%, 35%, 33%, 20%, and 10% for Stanford stages T0, T1, T2, T3, and T4 (nominal stages A, B1, B2, C) at 15 years; lymph node status was unknown. Disease-specific survival at 15 years was 85%, 64%, 45%, 33%, and 15%, respectively, for the same patients. In 141 patients with restricted nodular disease (lymph node status unknown) equal to or less than one-half of one lobe involved (stage B1), the 15-year overall survival was 50% and identical to the expected survival of an age-matched cohort of males. Potency was preserved in 86% of the patients at 15 months posttreatment, and 50% of the patients maintained erectile potency for 7 years posttherapy. Other sequelae and complications are analyzed. The incidence of second neoplasms did not exceed expectations for an age-matched population.
Cytogenetic, Flow Cytometric, and Ultrastructural Studies of Twenty-Nine Nonfamilial Human Renal Carcinomas

Multifactorial analysis, including cytogenetic studies, flow cytometry, and light and electron microscopic evaluation, was performed on 29 primary renal cell carcinomas and short-term cultures derived from them. Eleven of the 21 cases that yielded cytogenetic results demonstrated clonal chromosomal aberrations which included trisomy 7 in 8 cases, loss of the Y chromosome in 7, trisomy 12 in 2, and 16q- in 1. Flow cytometry showed that there was preferential growth of near-diploid populations and loss of aneuploid clones in culture with standard media. The ultrastructural features of both the primary and cultured tumors were remarkably similar. They included cytoplasmic vacuolization, reticulated dense nucleoli, and cell surface microvilli. Thus, morphological evidence supported the epithelial and, specifically, the renal tubular origin of the cultured cells. The development of chromosomal abnormalities seemed linked to advanced tumor stage, but the number of such cases was too small to analyze for statistical significance. No other correlations could be made between karyotypic change, DNA analysis, tumor histology, grade, and stage at this point in the patient follow-up.
Chasing ghosts: How an SRAM detected the subtle impact of stray light

The ever-shrinking world of semiconductors has always challenged the interplay of tool capability, process integration, and characterization. The fine line between structural or electrical success and failure has steadily been redefined from microns to nanometers with leading edge technology using terms with the likes of angstroms and layers of atoms. Failure modes at these nodes become increasing difficult at times to even grasp, let alone “visualize” with electrical and physical analytical techniques. The complexity of these state-of-the-art problem sets demand adaptive and robust problem solving methodologies tailored to uncover and drive root cause understanding. Assembling and organizing diverse teams covering a broad range of expertise becomes paramount. In this case study, we were able to make use of a unique low voltage static random access memory fail mode and spatial fingerprint to chase down a 1 nanometer change in transistor gate line widths; the sleuthing effort concluded with the unlikely combination of mask chrome frame and stray light from lithography as the ultimate root cause.
New Insights into Genome Structure: Genes of a Feather Stick Together.

DNA structuring proteins such as CTCF facilitate DNA loop formation and are presumed to be among the major determinants of eukaryotic genome structure. Recent studies, including Rowley et al. (2017), suggest that gene activation and repression play fundamentally important roles in structuring the genome independently of CTCF.
Multicenter prevalence of anaphylaxis in clinic-based oral food challenges.

Abstract Background Although previous single-center studies report the rate of anaphylaxis for oral food challenges (OFCs) as 9% to 11%, little is known regarding the epidemiology of clinical OFCs across multiple centers in the United States. Objective To examine the epidemiology, symptoms, and treatment of clinical low-risk OFCs in the nonresearch setting. Methods Data were obtained from 2008 to 2013 through a physician survey in 5 food allergy centers geographically distributed across the United States. Allergic reaction rates and the association of reaction rates with year, hospital, and demographics were determined using a linear mixed model. Meta-analysis was used to pool the proportion of reactions and anaphylaxis with inverse-variance weights using a random-effects model with exact confidence intervals (CIs). Results A total of 6,377 OFCs were performed, and the pooled estimate of anaphylaxis was 2% (95% CI, 1%-3%). The rate of allergic reactions was 14% (95% CI, 13%-16%) and was consistent during the study period ( P = .40). Reaction rates ranged from 13% to 33%. Males reacted 16% more frequently than females (95% CI, 4%-37.5%; P = .04). Foods challenged in 2013 varied geographically, with peanut as the most challenged food in the Northeast, Midwest, and West and egg as the most challenged in the South. Conclusion As the largest national survey of allergic reactions of clinical open OFCs in a nonresearch setting in the United States, this study found that performing clinical nonresearch open low-risk OFCs results in few allergic reactions, with 86% of challenges resulting in no reactions and 98% without anaphylaxis.
Semantic coherence in psychometric schizotypy: An investigation using Latent Semantic Analysis

Abstract Technological advancements have led to the development of automated methods for assessing semantic coherence in psychiatric populations. Latent Semantic Analysis (LSA) is an automated method that has been used to quantify semantic coherence in schizophrenia-spectrum disorders. The current study examined whether: 1) Semantic coherence reductions extended to psychometrically-defined schizotypy and 2) Greater cognitive load further reduces semantic coherence. LSA was applied to responses generated during category fluency tasks in baseline and cognitive load conditions. Significant differences between schizotypy and non-schizotypy groups were not observed. Findings suggest that semantic coherence may be relatively preserved at this point on the schizophrenia-spectrum.
Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory

Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We use a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we demonstrate that the optimal design varies as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible design-space analysis we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.
Alternative methodology for assessing cracking resistance of hot mix asphalt mixtures with overlay tester

Several highway agencies have either implemented or considered implementing performance tests to predict the cracking potential of asphalt concrete (AC) mixes in the laboratory setting. One such te...
Planning parenthood: the Affordable Care Act young adult provision and pathways to fertility

This paper investigates the effect of the Affordable Care Act young adult provision on fertility and related outcomes. The expected effect of the provision on fertility is not clear ex ante. By expanding insurance coverage to young adults, the provision may affect fertility directly through expanded options for obtaining contraceptives as well as through expanded options for obtaining pregnancy-, birth-, and infant-related care, and these may lead to decreased or increased fertility, respectively. In addition, the provision may also affect fertility indirectly through marriage or labor markets, and the direction and magnitude of these effects is difficult to determine. This paper considers the effect of the provision on fertility as well as the contributing channels by applying difference-in-differences type methods using the 2008–2010 and 2012–2013 American Community Survey, 2006–2009 and 2012–2013 Centers for Disease Control and Prevention abortion surveillance data, and 2006–2010 and 2011–2013 National Survey of Family Growth. Results suggest that the provision is associated with decreases in the likelihood of having given birth and abortion rates and an increase in the likelihood of using long-term hormonal contraceptives.
Association of vitamin E intake at early childhood with alanine aminotransferase levels at mid-childhood.

The extent to which vitamin E (alpha-tocopherol) intake early in childhood is associated with alanine aminotransferase (ALT) level later in childhood is unknown. The objective of this research is to test the hypothesis that higher alpha-tocopherol intake during early childhood is associated with lower odds of elevated ALT levels during mid-childhood and to examine how body mass index (BMI) influences these relationships. We studied 528 children in Project Viva. Mothers reported child dietary intake at early childhood visits (median 3.1 years) using a validated food frequency questionnaire. At mid-childhood (median 7.6 years), we collected child blood and anthropometric data. The main outcome was elevated sex-specific mid-childhood ALT level (≥22.1 U/L for female children and ≥25.8 U/L for male children). In multivariable logistic regression models, we assessed the association of energy-adjusted alpha-tocopherol intake with ALT levels, adjusting for child age, sex, race/ethnicity, diet, and age-adjusted sex-specific BMI z-score at mid-childhood. Among children in this study, 48% were female, 63% were non-Hispanic white, 19% were non-Hispanic black, and 4% were Hispanic/Latino. Mean alpha-tocopherol intake was 3.7 ± 1.0 mg/day (range, 1.4-9.2) at early childhood. At mid-childhood, mean BMI z-score was 0.41 ± 1.0 units and 22% had an elevated ALT level. In multivariable-adjusted logistic regression models, children with higher early childhood vitamin E intake had lower odds of elevated mid-childhood ALT (adjusted odds ratio [AOR], 0.62; 95% confidence interval [CI], 0.39, 0.99) for quartiles 2-4 compared with the lowest quartile of intake. Findings persisted after accounting for early childhood diet (AOR, 0.62; 95% CI, 0.36, 1.08) and were strengthened after additionally accounting for mid-childhood BMI z-score (AOR, 0.56; 95% CI, 0.32, 0.99). CONCLUSION In this cohort, higher early childhood intake of alpha-tocopherol was associated with lower odds of elevated mid-childhood ALT level. (Hepatology 2018;67:1339-1347).
Foreign and domestic divestment and investment decisions: like or unlike?

The managerial literature on foreign investment and divestment is much less developed than the economic literature on foreign direct investment theory. Nevertheless, surveyed with the purpose of better understanding foreign divestment decisions, the research to date reveals some noticeable differences between investment and divestment divisions—whether foreign or domestic—and even more substantial differences between foreign divestment and domestic divestment decisions. Additional research, however, is clearly in order.
Childhood Stroke and Vision: A Review of the Literature

Abstract Objective Here we review the current literature regarding visual outcome after perinatal and childhood stroke. Background Visual deficits following stroke in adults are common and have been previously reviewed. Less is known about visual deficits following stroke in neonates and older children. Most of the literature regarding this subject has focused on preterm infants, or on other types of brain injury. This review summarizes the types of visual deficits seen in term infants following perinatal stroke and children following childhood stroke and predictors of outcome. This review suggests areas for future research. Methods We performed Ovid MEDLINE searches regarding visual testing in children, vision after childhood stroke, neuroplasticity of vision, treatment of visual impairment after stroke, and driving safety concerns after stroke. Results Visual field defects were the most commonly reported visual deficits after perinatal and childhood stroke. There is a significant lack of literature on this subject, and most is in the form of case reports and case series. Children can experience significant visual morbidity after stroke, and have the potential to show some recovery, but guidelines on assessment and treatment of this population are lacking. Conclusions There were limitations to this study, given the small amount of literature available. Although stroke in children can result in severe visual deficits, most children regain at least a portion of their vision. However, more research is needed regarding visual assessment of this population, long-term visual outcomes, specific predictors of recovery, and treatment options.
Assessing the Necessity of Stopping Antithrombotic Agents Before Wide-Awake Hand Surgery.

This review of 304 carpal tunnel release procedures examines the necessity of stopping antithrombotic medications prior to carpal tunnel release surgery.
Multiple Myeloma and Bone: The Fatal Interaction

Multiple myeloma (MM) is the second-most-common hematologic malignancy and the most frequent cancer to involve bone. MM bone disease (MMBD) has devastating consequences for patients, including dramatic bone loss, severe bone pain, and pathological fractures that markedly decrease the quality of life and impact survival of MM patients. MMBD results from excessive osteoclastic bone resorption and persistent suppressed osteoblastic bone formation, causing lytic lesions that do not heal, even when patients are in complete and prolonged remission. This review discusses the cellular and molecular mechanisms that regulate the uncoupling of bone remodeling in MM, the effects of MMBD on tumor growth, and potential therapeutic approaches that may prevent severe bone loss and repair damaged bone in MM patients.
Using barcoded Zika virus to assess virus population structure in vitro and in Aedes aegypti mosquitoes

Arboviruses such as Zika virus (ZIKV, Flaviviridae; Flavivirus) must replicate in both mammalian and insect hosts possessing strong immune defenses. Accordingly, transmission between and replication within hosts involves genetic bottlenecks, during which viral population size and genetic diversity may be significantly reduced. To help quantify these bottlenecks and their effects, we constructed 4 "barcoded" ZIKV populations that theoretically contain thousands of barcodes each. After identifying the most diverse barcoded virus, we passaged this virus 3 times in 2 mammalian and mosquito cell lines and characterized the population using deep sequencing of the barcoded region of the genome. C6/36 maintain higher barcode diversity, even after 3 passages, than Vero. Additionally, field-caught mosquitoes exposed to the virus to assess bottlenecks in a natural host. A progressive reduction in barcode diversity occurred throughout systemic infection of these mosquitoes. Differences in bottlenecks during systemic spread were observed between different populations of Aedes aegypti.
Optimal planning of plant flexibility: Problem formulation and performance analysis

Manufacturing systems are becoming more and more flexible to confront uncertainty in demands of multiple product types. In this paper, we study the properties of flexible manufacturing systems from the perspective of demand shortfall and service level as functions of setup time, nonhomogeneous capacities and demand distributions. Closed-form bounds as well as an accurate estimate of the service level are obtained. Sensitivity analyses of service level with respect to reductions in setup time, downtime and cycle time are carried out, and the impact of new product launch and product correlation on system flexibility is investigated. Note to Practitioners: The strategic decision-making issues in flexible production system management are critical. Questions facing plant or enterprise teams are how manufacturers should plan and evaluate their system flexibility profile in order to wisely invest in and upgrade their flexible equipments? Or which factory out of many they should choose from to launch a new product given different flexibilities of the plants? In order to answer these questions, we study production system flexibility measures in terms of matching production capacities and demands. Accurate estimates of demand shortfall and the service level are obtained. The results lead to measurements on how much demand shortfall a manufacturer generates when confronting its demand and production uncertainty. By taking advantage of such metrics, one can compare distinct improvement plans. To further understand such measurement, sensitivity analyses of service level with respect to reductions in setup time, downtime and cycle time are carried out, and the impact of new product launch and product correlation on system flexibility is investigated. The results can be used to guide strategic system flexibility planning.
A Pattern Analysis of Daily Electric Vehicle Charging Profiles: Operational Efficiency and Environmental Impacts

Plug-in Electric Vehicles (PEVs) are considered one solution to reducing GHG emissions from private transport. Additionally, PEV adopters often have free access to public charging facilities. Through a pattern analysis, this study identifies five distinct clusters of daily PEV charging profiles observed at the public charging stations. Empirically observed patterns indicate a significant amount of operational inefficiency, where 54% of the total parking duration PEVs do not consume electricity, preventing other users from charging. This study identifies the opportunity cost in terms of GHG emissions savings if gasoline vehicles are replaced with potential PEV adopters. The time spent in parking without charging by current PEV users can be used by these potential PEV users to charge their PEVs and replace the use of gasoline. The results suggest that reducing inefficient station use leads to significant reductions in emissions. Overall, there is significant variability in outcomes depending on the specific cluster membership.
Integrating statistical rock physics and pressure and thermal history modeling to map reservoir lithofacies in the deepwater Gulf of Mexico

ABSTRACTWe have developed an approach integrating statistical rock physics with pressure and thermal history modeling for quantitative seismic interpretation (QSI). Extending the training data for ...
The Development of an Undergraduate Data Curriculum: A Model for Maximizing Curricular Partnerships and Opportunities

The article provides the motivations and foundations for creating an interdisciplinary program between a Library and Information Science department and a Human-Centered Computing department. The program focuses on data studies and data science concepts, issues, and skill sets. In the paper, we analyze trends in Library and Information Science curricula, the emergence of data-related Library and Information Science curricula, and interdisciplinary data-related curricula. Then, we describe the development of the undergraduate data curriculum and provide the institutional context; discuss collaboration and resource optimization; provide justifications and workforce alignment; and detail the minor, major, and graduate opportunities. Finally, we argue that the proposed program holds the potential to model interdisciplinary, holistic data-centered curriculum development by complimenting Library and Information Science traditions (e.g., information organization, access, and ethics) with scholarly work in data science, specifically data visualization and analytics. There is a significant opportunity for Library and Information Science to add value to data science and analytics curricula, and vice versa.
Biomechanic and Energetic Effects of a Quasi-Passive Artificial Gastrocnemius on Transtibial Amputee Gait

State-of-the-art transtibial prostheses provide only ankle joint actuation and thus do not provide the biarticular function of the amputated gastrocnemius muscle. We develop a prosthesis that actuates both knee and ankle joints and then evaluate the incremental effects of this prosthesis as compared to ankle actuation alone. The prosthesis employs a quasi-passive clutched-spring knee orthosis, approximating the largely isometric behavior of the biological gastrocnemius, and utilizes a commercial powered ankle-foot prosthesis for ankle joint functionality. Two participants with unilateral transtibial amputation walk with this prosthesis on an instrumented treadmill, while motion, force, and metabolic data are collected. Data are analyzed to determine differences between the biarticular condition with the activation of the knee orthosis and the monoarticular condition with the orthosis behaving as a free-joint. As hypothesized, the biarticular system is shown to reduce both affected-side knee and hip moment impulse and positive mechanical work in both participants during the late stance knee flexion phase of walking, compared to the monoarticular condition. The metabolic cost of walking is also reduced for both participants. These very preliminary results suggest that biarticular functionality may provide benefits beyond even those of the most advanced monoarticular prostheses.
Primate fetal hepatic responses to maternal obesity: epigenetic signalling pathways and lipid accumulation

Key points Maternal obesity (MO) and exposure to a high-fat, high-simple-carbohydrate diet during pregnancy predisposes offspring to obesity, metabolic and cardiovascular disorders in later life. Underlying molecular pathways and potential epigenetic factors that are dysregulated in MO were identified using unbiased transcriptomic methods. There was increased lipid accumulation and severe steatosis in the MO baboon fetal liver suggesting that these offspring are on an early trajectory of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis. Abstract Maternal obesity (MO) increases offspring cardiometabolic disease risk. Altered fetal liver development in response to the challenge of MO has metabolic consequences underlying adverse offspring life-course health outcomes. Little is known about the molecular pathways and potential epigenetic changes regulating primate fetal liver responses to MO. We hypothesized that MO would induce fetal baboon liver epigenetic changes resulting in dysregulation of key metabolic pathways that impact lipid metabolism. MO was induced prior to pregnancy by a high-fat, high-fructose diet. Unbiased gene and microRNA (small RNA Seq) abundance analyses were performed on fetal baboon livers at 0.9 gestation and subjected to pathway analyses to identify fetal liver molecular responses to MO. Fetal baboon liver lipid and glycogen content were quantified by the Computer Assisted Stereology Toolbox. In response to MO, fetal livers revealed dysregulation of TCA cycle, proteasome, oxidative phosphorylation, glycolysis and Wnt/β-catenin signalling pathways together with marked lipid accumulation supporting our hypothesis that multiple pathway dysregulation detrimentally impacts lipid management. This is the first study of MO programming of the non-human primate fetal liver using unbiased transcriptome analysis to detect changes in hepatic gene expression levels and identify potential microRNA epigenetic regulators of metabolic disruption.
Arcjet Tests and Thermal Response Analysis for Dual-Layer Woven Carbon Phenolic

A new dual-layer carbon phenolic manufactured from a three-dimensional woven substrate was tested in three arcjet facilities over a range of environments up to heat flux of approximately 6 kW/cm2 ...
Epigenetic and Transcriptomic Profiling of Mammary Gland Development and Tumor Models Disclose Regulators of Cell State Plasticity

Cell state reprogramming during tumor progression complicates accurate diagnosis, compromises therapeutic effectiveness, and fuels metastatic dissemination. We used chromatin accessibility assays and transcriptional profiling during mammary development as an agnostic approach to identify factors that mediate cancer cell state interconversions. We show that fetal and adult basal cells share epigenetic features consistent with multi-lineage differentiation potential. We find that DNA-binding motifs for SOX transcription factors are enriched in chromatin that is accessible in stem/progenitor cells and inaccessible in differentiated cells. In both mouse and human tumors, SOX10 expression correlates with stem/progenitor identity, dedifferentiation, and invasive characteristics. Strikingly, we demonstrate that SOX10 binds to genes that regulate neural crest cell identity, and that SOX10-positive tumor cells exhibit neural crest cell features.
Fine-Pruning: Defending Against Backdooring Attacks on Deep Neural Networks

Deep neural networks (DNNs) provide excellent performance across a wide range of classification tasks, but their training requires high computational resources and is often outsourced to third parties. Recent work has shown that outsourced training introduces the risk that a malicious trainer will return a backdoored DNN that behaves normally on most inputs but causes targeted misclassifications or degrades the accuracy of the network when a trigger known only to the attacker is present. In this paper, we provide the first effective defenses against backdoor attacks on DNNs. We implement three backdoor attacks from prior work and use them to investigate two promising defenses, pruning and fine-tuning. We show that neither, by itself, is sufficient to defend against sophisticated attackers. We then evaluate fine-pruning, a combination of pruning and fine-tuning, and show that it successfully weakens or even eliminates the backdoors, i.e., in some cases reducing the attack success rate to 0% with only a \(0.4\%\) drop in accuracy for clean (non-triggering) inputs. Our work provides the first step toward defenses against backdoor attacks in deep neural networks.
Aging, Output Per Capita, and Secular Stagnation

This paper re-examines the relationship between population aging and economic growth. We confirm previous research such as Cutler et al. (1990) and Acemoglu and Restrepo (2017) that show positive correlation between population aging and per capita output growth. Our contribution is demonstrating that this relationship breaks down when the adjustment of interest rates is inhibited by a lower bound on nominal rates, as during the Great Financial Crisis decade. Indeed, during the "secular stagnation regime" of 2008–2015 that prevailed in a number of countries, aging had a negative impact on living standards, consistent with the secular stagnation hypothesis.
Robot Learning in Homes: Improving Generalization and Reducing Dataset Bias

Data-driven approaches to solving robotic tasks have gained a lot of traction in recent years. However, most existing policies are trained on large-scale datasets collected in curated lab settings. If we aim to deploy these models in unstructured visual environments like people's homes, they will be unable to cope with the mismatch in data distribution. In such light, we present the first systematic effort in collecting a large dataset for robotic grasping in homes. First, to scale and parallelize data collection, we built a low cost mobile manipulator assembled for under 3K USD. Second, data collected using low cost robots suffer from noisy labels due to imperfect execution and calibration errors. To handle this, we develop a framework which factors out the noise as a latent variable. Our model is trained on 28K grasps collected in several houses under an array of different environmental conditions. We evaluate our models by physically executing grasps on a collection of novel objects in multiple unseen homes. The models trained with our home dataset showed a marked improvement of 43.7% over a baseline model trained with data collected in lab. Our architecture which explicitly models the latent noise in the dataset also performed 10% better than one that did not factor out the noise. We hope this effort inspires the robotics community to look outside the lab and embrace learning based approaches to handle inaccurate cheap robots.
Anisotropic thermal conductivity measurement using a new Asymmetric-Beam Time-Domain Thermoreflectance (AB-TDTR) method

Anisotropic thermal properties are of both fundamental and practical interests, but remain challenging to characterize using conventional methods. In this work, a new metrology based on asymmetric beam time-domain thermoreflectance (AB-TDTR) is developed to measure three-dimensional anisotropic thermal transport by extending the conventional TDTR technique. Using an elliptical laser beam with controlled elliptical ratio and spot size, the experimental signals can be exploited to be dominantly sensitive to measure thermal conductivity along the cross-plane or any specific in-plane directions. An analytic solution for a multi-layer system is derived for the AB-TDTR signal in response to the periodical pulse, elliptical laser beam, and heating geometry to extract the anisotropic thermal conductivity from experimental measurement. Examples with experimental data are given for various materials with in-plane thermal conductivity from 5 W/m K to 2000 W/m K, including isotropic materials (silicon, boron phosphide, and boron nitride), transversely isotropic materials (graphite, quartz, and sapphire), and transversely anisotropic materials (black phosphorus). Furthermore, a detailed sensitivity analysis is conducted to guide the optimal setting of experimental configurations for different materials. The developed AB-TDTR metrology provides a new approach to accurately measure anisotropic thermal phenomena for rational materials design and thermal applications.
Mks6 mutations reveal tissue- and cell type-specific roles for the cilia transition zone

The transition zone (TZ) is a domain at the base of the cilium that is involved in maintaining ciliary compartment-specific sensory and signaling activity by regulating cilia protein composition. M...
On Centro-Affine Curves and Bäcklund Transformations of the KdV Equation

We continue the study of the Korteweg-de Vries equation in terms of cento-affine curves, initiated by Pinkall. A centro-affine curve is a closed parametric curve in the affine plane such that the determinant made by the position and the velocity vectors is identically one. The space of centro-affine curves is acted upon by the special linear group, and the quotient is identified with the space of Hill’s equations with periodic solutions. It is known that the space of centro-affine curves carries two pre-symplectic structures, and the KdV flow is identified with is a bi-Hamiltonian dynamical system therein. We introduce a one-parameter family of transformations on centro-affine curves, prove that they preserve both presymplectic structures, commute with the KdV flow, and share the integrals with it. Furthermore, the transformation commute with each other (Bianchi permutability). We also describe integrals of the KdV equation as arising from the monodromy of Riccati equations associated with centro-affine curves. We are motivated by our work (joint with M. Arnold, D. Fuchs, and I. Izmenstiev), concerning the cross-ratio dynamics on ideal polygons in the hyperbolic plane and hyperbolic space, whose continuous version is studied in the present paper.
Extreme variation in rates of evolution in the plastid Clp protease complex

Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.
Biogeochemical properties of eddies in the California Current System

Author(s): Chenillat, F; Franks, PJS; Combes, V | Abstract: The California Current System (CCS) has intense mesoscale activity that modulates and exports biological production from the coastal upwelling system. To characterize and quantify the ability of mesoscale eddies to affect the local and regional planktonic ecosystem of the CCS, we analyzed a 10 year-long physical-biological model simulation, using eddy detection and tracking to isolate the dynamics of cyclonic and anticyclonic eddies. As they propagate westward across the shelf, cyclonic eddies efficiently transport coastal planktonic organisms and maintain locally elevated production for up to 1 year (800 km offshore). Anticyclonic eddies, on the other hand, have a limited impact on local production over their ~6 month lifetime as they propagate 400 km offshore. At any given time ~8% of the model domain was covered by eddy cores. Though the eddies cover a small area, they explain ~50 and 20% of the transport of nitrate and plankton, respectively.
Identification and Estimation of Causal Effects from Dependent Data

The assumption that data samples are independent and identically distributed (iid) is standard in many areas of statistics and machine learning. Nevertheless, in some settings, such as social networks, infectious disease modeling, and reasoning with spatial and temporal data, this assumption is false. An extensive literature exists on making causal inferences under the iid assumption [12, 8, 21, 16], but, as pointed out in [14], causal inference in non-iid contexts is challenging due to the combination of unobserved confounding bias and data dependence. In this paper we develop a general theory describing when causal inferences are possible in such scenarios. We use segregated graphs [15], a generalization of latent projection mixed graphs [23], to represent causal models of this type and provide a complete algorithm for non-parametric identification in these models. We then demonstrate how statistical inferences may be performed on causal parameters identified by this algorithm, even in cases where parts of the model exhibit full interference, meaning only a single sample is available for parts of the model [19]. We apply these techniques to a synthetic data set which considers the adoption of fake news articles given the social network structure, articles read by each person, and baseline demographics and socioeconomic covariates.