cssi/SciSciGPT-SciSciNet huggingface dataset:
FluxMarker: Enhancing Tactile Graphics with Dynamic Tactile Markers

For people with visual impairments, tactile graphics are an important means to learn and explore information. However, raised line tactile graphics created with traditional materials such as embossing are static. While available refreshable displays can dynamically change the content, they are still too expensive for many users, and are limited in size. These factors limit wide-spread adoption and the representation of large graphics or data sets. In this paper, we present FluxMaker, an inexpensive scalable system that renders dynamic information on top of static tactile graphics with movable tactile markers. These dynamic tactile markers can be easily reconfigured and used to annotate static raised line tactile graphics, including maps, graphs, and diagrams. We developed a hardware prototype that actuates magnetic tactile markers driven by low-cost and scalable electromagnetic coil arrays, which can be fabricated with standard printed circuit board manufacturing. We evaluate our prototype with six participants with visual impairments and found positive results across four application areas: location finding or navigating on tactile maps, data analysis, and physicalization, feature identification for tactile graphics, and drawing support. The user study confirms advantages in application domains such as education and data exploration.
Trust, Trade, and Moral Progress

Trust is important for a variety of social relationships. Trust facilitates trade, which increases prosperity and induces us to interact with people of different backgrounds on terms that benefit all parties. Trade promotes trustworthiness, which enables us to form meaningful as well as mutually beneficial relationships. In what follows, I argue that when we erect institutions that enhance trust and reward people who are worthy of trust, we create the conditions for a certain kind of moral progress.
Molecular Simulation of Adsorption and Diffusion in Vpi-5 and other Aluminophosphates

Abstract Adsorption isotherms for argon in AlPO 4 -5, AlPO 4 -8 and VPI-5 were simulated at 77K and 87K using the Grand Canonical Monte Carlo method. The shapes of the isotherms were found to be in qualitative agreement with published experimental data; however, the maximum adsorption was overpredicted relative to the experimental observations. We also report isosteric heats of adsorption obtained from the GCMC results, and diffusion coefficients for VPI-5 obtained from Molecular Dynamics.
Canopy soil bacterial communities altered by severing host tree limbs

Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.
SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models

Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-sites models. We propose a statistical inference method for tumor phylogenies from noisy single-cell sequencing data under a finite-sites model. The performance of our method on synthetic and experimental data sets from two colorectal cancer patients to trace evolutionary lineages in primary and metastatic tumors suggests that employing a finite-sites model leads to improved inference of tumor phylogenies.
R&D investments, capital expenditures, and earnings thresholds

Prior studies find that firms cut research and development (R&D) expense in response to earnings considerations. We extend this stream of research by documenting that firms narrowly achieving an earnings threshold also report unusually high capital expenditures. In addition, these firms’ total investments (R&D expense plus capital expenditures) do not vary in response to earnings thresholds, which suggests that, on average, reductions in R&D expense are offset by concurrent increases in capital expenditures. Lastly, our research design allows us to infer that the increased capital expenditures are largely R&D investments that are capitalized instead of non-R&D capital expenditures, suggesting that overall investments in R&D are relatively unchanged.
The causal relationship in North American energy production

Crude oil and natural gas production is examined to investigate the cross‐country causal relationship and interconnectedness of these markets, within the North American context. A vast infrastructure network, consisting of pipelines and railroads that connect the US and Canadian markets, with virtually all of Canada's crude oil and natural gas exports flowing south. The study is undertaken within the context of the recent US shale energy revolution based on technological advancements in drilling and hydraulic fracturing. Unique to this study is the use of production data, rather than the archetypal energy prices, to investigate the presence of bilateral relationships. Monthly, country level data on crude oil and natural gas production, over the period 2002 through 2015, is utilised. The results of standard unit root tests indicate that the production series are non‐stationary in levels, while cointegration test indicate that the markets are integrated. A bidirectional relationship is found for the crude oil market. In contrast, a unidirectional relationship is observed in the gas market – US natural gas production causes Canadian natural gas production.
Distributed camouflage for swarm robotics and smart materials

We present a distributed algorithm for a swarm of active particles to camouflage in an environment. Each particle is equipped with sensing, computation, and communication, allowing the system to take color and gradient information from the environment and self-organize into an appropriate pattern. Current artificial camouflage systems are either limited to static patterns, which are adapted for specific environments, or rely on back-projection, which depend on the viewer’s point of view. Inspired by the camouflage abilities of the cuttlefish, we propose a distributed estimation and pattern formation algorithm that allows to quickly adapt to different environments. We present convergence results both in simulation as well as on a swarm of miniature robots “Droplets” for a variety of patterns.
Deconfined quantum critical point on the triangular lattice

In this work we propose a theory for the deconfined quantum critical point (DQCP) for spin-1/2 systems on a triangular lattice, which is a direct unfine-tuned quantum phase transition between the standard ``$\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$'' noncollinear antiferromagnetic order (or the so-called ${120}^{\ensuremath{\circ}}$ state) and the ``$\sqrt{12}\ifmmode\times\else\texttimes\fi{}\sqrt{12}$'' valence solid bond (VBS) order, both of which are very standard ordered phases often observed in numerical simulations. This transition is beyond the standard Landau-Ginzburg paradigm and is also fundamentally different from the original DQCP theory on the square lattice due to the very different structures of both the magnetic and VBS order on frustrated lattices. We first propose a topological term in the effective-field theory that captures the ``intertwinement'' between the $\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$ antiferromagnetic order and the $\sqrt{12}\ifmmode\times\else\texttimes\fi{}\sqrt{12}$ VBS order. Then using a controlled renormalization-group calculation, we demonstrate that an unfine-tuned direct continuous DQCP exists between the two ordered phases mentioned above. This DQCP is described by the ${N}_{f}=4$ quantum electrodynamics (QED) with an emergent PSU(4)=SU(4)/${Z}_{4}$ symmetry only at the critical point. The aforementioned topological term is also naturally derived from the ${N}_{f}=4$ QED. We also point out that physics around this DQCP is analogous to the boundary of a $3d$ bosonic symmetry- protected topological state with only on-site symmetries.
THE MEANING OF MARKET EFFICIENCY

Fama defined an efficient market as one in which prices always “fully reflect” available information. This paper formalizes this definition and provides various characterizations relating to equilibrium models, profitable trading strategies, and equivalent martingale measures. These various characterizations facilitate new insights and theorems relating to efficient markets. In particular, we overcome a well-known limitation in tests for market efficiency, i.e., the need to assume a particular equilibrium asset pricing model, called the joint-hypothesis or bad-model problem. Indeed, we show that an efficient market is completely characterized by the absence of both arbitrage opportunities and dominated securities, an insight that provides tests for efficiency that are devoid of the bad-model problem. Other theorems useful for both the testing of market efficiency and the pricing of derivatives are also provided.
The GCN2-ATF4 Signaling Pathway Induces 4E-BP to Bias Translation and Boost Antimicrobial Peptide Synthesis in Response to Bacterial Infection.

Summary Bacterial infection often leads to suppression of mRNA translation, but hosts are nonetheless able to express immune response genes through as yet unknown mechanisms. Here, we use a Drosophila model to demonstrate that antimicrobial peptide (AMP) production during infection is paradoxically stimulated by the inhibitor of cap-dependent translation, 4E-BP (eIF4E-binding protein; encoded by the Thor gene). We found that 4E-BP is induced upon infection with pathogenic bacteria by the stress-response transcription factor ATF4 and its upstream kinase, GCN2. Loss of gcn2, atf4 , or 4e-bp compromised immunity. While AMP transcription is unaffected in 4e-bp mutants, AMP protein levels are substantially reduced. The 5′ UTRs of AMPs score positive in cap-independent translation assays, and this cap-independent activity is enhanced by 4E-BP. These results are corroborated in vivo using transgenic 5′ UTR reporters. These observations indicate that ATF4-induced 4e-bp contributes to innate immunity by biasing mRNA translation toward cap-independent mechanisms, thus enhancing AMP synthesis.
A Time-Space Lower Bound for a Large Class of Learning Problems

We prove a general time-space lower bound that applies for a large class of learning problems and shows that for every problem in that class, any learning algorithm requires either a memory of quadratic size or an exponential number of samples. As a special case, this gives a new proof for the time-space lower bound for parity learning [R16]. Our result is stated in terms of the norm of the matrix that corresponds to the learning problem. Let X, A be two finite sets. Let M: A &#x00D7; X \rightarrow \{-1,1\} be a matrix. The matrix M corresponds to the following learning problem: An unknown element x &#x220A; X was chosen uniformly at random. A learner tries to learn x from a stream of samples, (a_1, b_1), (a_2, b_2)..., where for every i, a_i &#x220A; A is chosen uniformly at random and b_i = M(a_i,x). Let \sigma be the largest singular value of M and note that always \sigma &#x2264; |A|^{1/2} &#x22C5; |X|^{1/2}. We show that if \sigma &#x2264; |A|^{1/2} &#x22C5; |X|^{1/2 - &#x2265;ilon, then any learning algorithm for the corresponding learning problem requires either a memory of size quadratic in &#x2265;ilon n or number of samples exponential in &#x2265;ilon n, where n = \log_2 |X|.As a special case, this gives a new proof for the memorysamples lower bound for parity learning [14].
Oil-soluble contrast agents for NMR

Abstract In well logging applications, nuclear magnetic resonance (NMR) is recognized as a powerful tool to differentiate various fluids inside porous media. However, it can be challenging to do so in complex situations, e.g. when fluid peaks overlap with each other. Water-soluble contrast agents, such as MnCl2 or Gd-EDTA, have been proposed for use to accelerate the water relaxation, thus separating the water signal from those of other fluids. Together with these contrast agents, the log-inject-log method is used and the difference between the two logs is attributed to the doped water phase. This application only works with water-based mud. To extend its use to oil-based mud (OBM), it is desirable to find alternatives to water-soluble contrast agents that are compatible with OBM. In this work, we introduce a new group of doping agents: oil-soluble contrast agents. We selected several iron-based complex compounds that are oil-soluble, and tested and evaluated their effects on oil signal relaxation using a laboratory NMR apparatus. We also tested hydrophobic iron oxide nanoparticles as a contrast agent. The results showed that both the complex compounds and nanoparticles were able to reduce the transverse relaxation time of oil from longer than 2 s to less than 20 ms. To demonstrate their applicability in porous media, we injected doped oil into gas-saturated Berea sandstone and limestone core plugs. With conventional 1D NMR measurements or the use of water-soluble contrast agents, it is not straightforward to discern the gas signal from the OBM signal. Our experiments showed that the gas signal could be easily identified in the presence of doped oil via simple T2 scans. We also performed experiments to demonstrate that the peaks of water and doped oil could be readily differentiated. The use of oil-soluble doping agents can significantly enhance the contrast of the NMR signals originated from different formation fluids, thus facilitating the fluid typing process. It provides a key alternative to the current water-doping technique. It is particularly advantageous when changing the oil relaxation is desired, such as for eliminating signal interferences from OBM invasion and differentiating heavy oil from clay-bound water. It also provides the possibility of speeding up the logging process by dramatically reducing the oil relaxation time. In addition, they can be employed in the laboratory for various purposes such as water saturation determination and fluid displacement monitoring. These contrast agents can also be of useful when oil-soluble contrast agents are desired in other fields, such as medical imaging applications.
mRNA structure determines specificity of a polyQ-driven phase separation

RNA promotes liquid-liquid phase separation (LLPS) to build membraneless compartments in cells. How distinct molecular compositions are established and maintained in these liquid compartments is unknown. Here, we report that secondary structure allows messenger RNAs (mRNAs) to self-associate and determines whether an mRNA is recruited to or excluded from liquid compartments. The polyQ-protein Whi3 induces conformational changes in RNA structure and generates distinct molecular fluctuations depending on the RNA sequence. These data support a model in which structure-based, RNA-RNA interactions promote assembly of distinct droplets and protein-driven, conformational dynamics of the RNA maintain this identity. Thus, the shape of RNA can promote the formation and coexistence of the diverse array of RNA-rich liquid compartments found in a single cell.
Performance characterization of scientific workflows for the optimal use of Burst Buffers

Abstract Scientific discoveries are increasingly dependent upon the analysis of large volumes of data from observations and simulations of complex phenomena. Scientists compose the complex analyses as workflows and execute them on large-scale HPC systems. The workflow structures are in contrast with monolithic single simulations that have often been the primary use case on HPC systems. Simultaneously, new storage paradigms such as Burst Buffers are becoming available on HPC platforms. In this paper, we analyze the performance characteristics of a Burst Buffer and two representative scientific workflows with the aim of optimizing the usage of a Burst Buffer, extending our previous analyses (Daley et al., 2016). Our key contributions are (a) developing a performance analysis methodology pertinent to Burst Buffers, (b) improving the use of a Burst Buffer in workflows with bandwidth-sensitive and metadata-sensitive I/O workloads, (c) highlighting the key data management challenges when incorporating a Burst Buffer in the studied scientific workflows.
Wisconsin Sentencing in the Walker Era: Mass Incarceration as the New Normal

First elected Wisconsin’s governor in 2010, Republican Scott Walker came to office with a tough-on-crime reputation. Consistent with campaign promises, Walker and his legislative allies swiftly repealed an ambitious set of “earned release” reforms that had been adopted just two years earlier. Since then, however, there have been few notable changes in Wisconsin sentencing law. Tight budgets and chronically overcrowded prisons have helped to keep punitive instincts in check. At the same time, a set of leaders in various counties and agencies around the state have quietly embraced the “evidence-based decision making” model for criminal justice. This may prove a transformative development over the long run, but there has yet to be any discernible impact on Wisconsin’s imprisonment rate, which remains at a record-high level.
Enhancing the Value of Cover Crops through Utilization by Beef Stocker Cattle: Progress Report (Year 2)

The increase in cover crops across Iowa presents a substantial amount of potential forage available to the beef industry that would otherwise go unutilized. While the benefits of improved soil health and nutrient retention through cover crops are well known, limited data are available on utilization by beef cattle. Thus, a study was designed to measure cattle performance while spring grazing cereal rye and to evaluate the impact grazing had on the soil profile. Preliminary data suggests that with proper supplementation, cattle grazing cereal rye may achieve average daily gains of 1.5 to 3.0 lb/d. Initial analysis of soil bulk density indicates minimal negative changes in compaction due to grazing. Because many variables impact the successful integration of cover crops and livestock into row crops, this is a four-year study summarizing data from year two.
Shared Decision Making in Neurocritical Care

Shared decision making is a collaborative decision-making process between health care providers and patients or their surrogates, taking into account the best scientific evidence available while considering the patient's values, goals, and preferences. Decision aids are tools enabling SDM. This article discusses shared decision making in general and in the intensive care unit in particular and facilitators and barriers for the creation and implementation of International Patient Decision Aids Standards Collaboration-compliant decision aids for the intensive care unit and neuro-intensive care unit.
Current and future needs and research for composite materials NDE

The use of composite materials continues to increase in the aerospace community due to the potential benefits of reduced weight, increased strength, and manufacturability. The ability to characterize damage in carbon fiber reinforced polymer composite components is required to enable damage progression models capable of yielding accurate remaining life predictions. As these composite structures become larger and more complex, nondestructive evaluation (NDE) techniques capable of quantifying and fully characterizing the material state are needed. This paper will present an overview of current NDE research activities for quantitative characterization of aerospace composites as well as a discussion of future directions in NDE research.
A variation on bisecting the binomial coefficients

Abstract In this paper, we present an algorithm which allows us to search for all the bisections for the binomial coefficients { n k } k = 0 , … , n and include a table with the results for all n ≤ 154 . Connections with previous work on this topic are included. We conjecture that the probability of having only trivial solutions is 5 ∕ 6 .
Inverse regression for ridge recovery: a data-driven approach for parameter reduction in computer experiments

Parameter reduction can enable otherwise infeasible design and uncertainty studies with modern computational science models that contain several input parameters. In statistical regression, techniques for sufficient dimension reduction (SDR) use data to reduce the predictor dimension of a regression problem. A computational scientist hoping to use SDR for parameter reduction encounters a problem: a computer prediction is best represented by a deterministic function of the inputs, so data comprised of computer simulation queries fail to satisfy the SDR assumptions. To address this problem, we interpret SDR methods sliced inverse regression (SIR) and sliced average variance estimation (SAVE) as estimating the directions of a ridge function, which is a composition of a low-dimensional linear transformation with a nonlinear function. Within this interpretation, SIR and SAVE estimate matrices of integrals whose column spaces are contained in the ridge directions’ span; we analyze and numerically verify convergence of these column spaces as the number of computer model queries increases. Moreover, we show example functions that are not ridge functions but whose inverse conditional moment matrices are low-rank. Consequently, the computational scientist should beware when using SIR and SAVE for parameter reduction, since SIR and SAVE may mistakenly suggest that truly important directions are unimportant.
Field-effect transistors made from solution-grown two-dimensional tellurene

The reliable production of two-dimensional (2D) crystals is essential for the development of new technologies based on 2D materials. However, current synthesis methods suffer from a variety of drawbacks, including limitations in crystal size and stability. Here, we report the fabrication of large-area, high-quality 2D tellurium (tellurene) using a substrate-free solution process. Our approach can create crystals with process-tunable thickness, from a monolayer to tens of nanometres, and with lateral sizes of up to 100 µm. The chiral-chain van der Waals structure of tellurene gives rise to strong in-plane anisotropic properties and large thickness-dependent shifts in Raman vibrational modes, which is not observed in other 2D layered materials. We also fabricate tellurene field-effect transistors, which exhibit air-stable performance at room temperature for over two months, on/off ratios on the order of 106, and field-effect mobilities of about 700 cm^2 V^(−1) s^(−1). Furthermore, by scaling down the channel length and integrating with high-k dielectrics, transistors with a significant on-state current density of 1 A mm^(−1) are demonstrated.
Ordinal Approximation for Social Choice, Matching, and Facility Location Problems Given Candidate Positions

In this work, we consider general facility location and social choice problems, in which sets of agents A and facilities F are located in a metric space, and our goal is to assign agents to facilities (as well as choose which facilities to open) to optimize the social cost. We form new algorithms to do this in the presence of only ordinal information, i.e., when the true costs or distances of the agents from the facilities are unknown, and only the ordinal preferences of the agents for the facilities are available. The main difference between our work and previous work in this area is that, while we assume that only ordinal information about agent preferences is known, we also know the exact locations of the possible facilities F. Due to this extra information about the facilities, we are able to form powerful algorithms that have small distortion, i.e., perform almost as well as omniscient algorithms (which know the true numerical distances between agents and facilities) but use only ordinal information about agent preferences. For example, we present natural social choice mechanisms for choosing a single facility to open with distortion of at most 3 for minimizing both the total and the median social cost; this factor is provably the best possible. We analyze many general problems including matching, k-center, and k-median, and we present black-box reductions from omniscient approximation algorithms with approximation factor β to ordinal algorithms with approximation factor 1+2β doing this gives new ordinal algorithms for many important problems and establishes a toolkit for analyzing such problems in the future.
CuH‐Catalyzed Asymmetric Hydroamidation of Vinylarenes

A CuH-catalyzed enantioselective hydroamidation reaction of vinylarenes has been developed using readily accessible 1,4,2-dioxazol-5-ones as electrophilic amidating reagents. This method provides a straightforward and efficient approach to synthesize chiral amides in good yields with high levels of enantiopurity under mild conditions. Moreover, this transformation tolerates substrates bearing a broad range of functional groups.
The Effect of Single Pyramidal Neuron Firing Within Layer 2/3 and Layer 4 in Mouse V1.

The influence of cortical cell spiking activity on nearby cells has been studied extensively in vitro. Less is known, however, about the impact of single cell firing on local cortical networks in vivo. In a pioneering study, Kwan and Dan (Kwan and Dan, 2012) reported that in mouse layer 2/3 (L2/3), under anesthesia, stimulating a single pyramidal cell recruits ~2.1% of neighboring units. Here we employ two-photon calcium imaging in layer 2/3 of mouse V1, in conjunction with single-cell patch clamp stimulation in layer 2/3 or layer 4, to probe, in both the awake and lightly anesthetized states, how (i) activating single L2/3 pyramidal neurons recruits neighboring units within L2/3 and from layer 4 (L4) to L2/3, and whether (ii) activating single pyramidal neurons changes population activity in local circuit. To do this, it was essential to develop an algorithm capable of quantifying how sensitive the calcium signal is at detecting effectively recruited units ("followers"). This algorithm allowed us to estimate the chance of detecting a follower as a function of the probability that an epoch of stimulation elicits one extra action potential (AP) in the follower cell. Using this approach, we found only a small fraction (<0.75%) of L2/3 cells to be significantly activated within a radius of ~200 μm from a stimulated neighboring L2/3 pyramidal cell. This fraction did not change significantly in the awake vs. the lightly anesthetized state, nor when stimulating L2/3 vs. underlying L4 pyramidal neurons. These numbers are in general agreement with, though lower than, the percentage of neighboring cells (2.1% pyramidal cells and interneurons combined) reported by Kwan and Dan to be activated upon stimulating single L2/3 pyramidal neurons under anesthesia (Kwan and Dan, 2012). Interestingly, despite the small number of individual units found to be reliably driven, we did observe a modest but significant elevation in aggregate population responses compared to sham stimulation. This underscores the distributed impact that single cell stimulation has on neighboring microcircuit responses, revealing only a small minority of relatively strongly connected partners. One sentence summary Patch-clamp stimulation in conjunction with 2-photon imaging shows that activating single layer-2/3 or layer-4 pyramidal neurons produces few (<1% of local units) reliable single-cell followers in L2/3 of mouse area V1, either under light anesthesia or in quiet wakefulness: instead, single cell stimulation was found to elevate aggregate population activity in a weak but highly distributed fashion.
Numeracy and Preventive Health Care Service Utilization among Middle-Aged and Older Adults in the U.S.

Objectives: Determine whether a specific numeracy skill cut-point(s) reflects an empirical threshold in the context of preventive health service utilization, and identify associations between numer...
Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing mice

Catch-up growth after insults to growing organs is paramount to achieving robust body proportions. In fly larvae, injury to individual tissues is followed by local and systemic compensatory mechanisms that allow the damaged tissue to regain normal proportions with other tissues. In vertebrates, local catch-up growth has been described after transient reduction of bone growth, but the underlying cellular responses are controversial. We developed an approach to study catch-up growth in foetal mice in which mosaic expression of the cell cycle suppressor p21 is induced in the cartilage cells (chondrocytes) that drive long-bone elongation. By specifically targeting p21 expression to left hindlimb chondrocytes, the right limb serves as an internal control. Unexpectedly, left-right limb symmetry remained normal, revealing deployment of compensatory mechanisms. Above a certain threshold of insult, an orchestrated response was triggered involving local enhancement of bone growth and systemic growth reduction that ensured that body proportions were maintained. The local response entailed hyperproliferation of spared left limb chondrocytes that was associated with reduced chondrocyte density. The systemic effect involved impaired placental function and IGF signalling, revealing bone-placenta communication. Therefore, vertebrates, like invertebrates, can mount coordinated local and systemic responses to developmental insults that ensure that normal body proportions are maintained.
Cold agglutinin-mediated autoimmune haemolytic anaemia associated with diffuse large B cell lymphoma

Cold agglutinin-mediated autoimmune haemolytic anaemia is associated with the development of autoantibodies that can agglutinate red blood cells at cold temperatures. While primary cold agglutinin disease is an idiopathic lymphoproliferative disorder, secondary cold agglutinin syndrome (CAS) complicates other diseases such as infections, autoimmune diseases and cancers, mostly low-grade lymphomas. Early recognition, treatment of CAS and treatment of its associated underlying diseases are crucial to a successful outcome. We report a case of CAS in a setting of diffuse large B cell lymphoma, in which the treatment course was complicated by worsened anaemia due to chemotherapy-induced myelosuppression. We reviewed previously reported cases and discussed diagnosis and treatment strategies, including novel complement inhibitors, as potential future therapy.
Augmenting Physical Simulators with Stochastic Neural Networks: Case Study of Planar Pushing and Bouncing

An efficient, generalizable physical simulator with universal uncertainty estimates has wide applications in robot state estimation, planning, and control. In this paper, we build such a simulator for two scenarios, planar pushing and ball bouncing, by augmenting an analytical rigid-body simulator with a neural network that learns to model uncertainty as residuals. Combining symbolic, deterministic simulators with learnable, stochastic neural nets provides us with expressiveness, efficiency, and generalizability simultaneously. Our model outperforms both purely analytical and purely learned simulators consistently on real, standard benchmarks. Compared with methods that model uncertainty using Gaussian processes, our model runs much faster, generalizes better to new object shapes, and is able to characterize the complex distribution of object trajectories.
Choosing between Growth and Glory

Prior work has established that the financing environment can impact firm strategy. We argue that this influence can shape the earliest strategic choices of a new venture by creating a potential tr...
Bessel Decomposition of Temperature Profiles in Film Deposition Reactors

Among the three process pillars of adding, patterning, and removing actions in the fabrications of semiconductor devices, film deposition takes up the central position in the construction flow of structure formation. Film uniformity of the deposition processes has significant impacts on the distributions of the electrical functions of the fabricated devices. Achieving good final uniformity of the film thickness depends critically on profiles of the thermal fields inside the film deposition chambers. Constructing simple, efficient, and yet accurate enough models of the temperature fields is therefore crucial in effective fault detection and eventually, for film thickness uniformity controls. Instead of solving systems of nonlinear partial differential field equations or conducting large-scale simulation runs, we explored one decomposition method of the temperature fields using a zeroth order Bessel function of the first kind for applications of fault detection and classification.
Large-Scale Validation of Hypothesis Generation Systems via Candidate Ranking

The first step of many research projects is to define and rank a short list of candidates for study. In the modern rapidity of scientific progress, some turn to automated hypothesis generation (HG) systems to aid this process. These systems can identify implicit or overlooked connections within a large scientific corpus, and while their importance grows alongside the pace of science, they lack thorough validation. Without any standard numerical evaluation method, many validate general-purpose HG systems by rediscovering a handful of historical findings, and some wishing to be more thorough may run laboratory experiments based on automatic suggestions. These methods are expensive, time consuming, and cannot scale. Thus, we present a numerical evaluation framework for the purpose of validating HG systems that leverages thousands of validation hypotheses. This method evaluates a HG system by its ability to rank hypotheses by plausibility; a process reminiscent of human candidate selection. Because HG systems do not produce a ranking criteria, specifically those that produce topic models, we additionally present novel metrics to quantify the plausibility of hypotheses given topic model system output. Finally, we demonstrate that our proposed validation method aligns with real-world research goals by deploying our method within MOLIERE, our recent topic-driven HG system, in order to automatically generate a set of candidate genes related to HIV-associated neurodegenerative disease (HAND). By performing laboratory experiments based on this candidate set, we discover a new connection between HAND and Dead Box RNA Helicase 3 (DDX3).Reproducibility: code, validation data, and results can be found at sybrandt.com/2018/validation.
Bio-Informatics & Bio-Statistics for the Third Millennium

The author promotes application of biostatistics and bioinformatics, ICT and IoT technologies in support of environment protection, modern agriculture and healthcare. The author also promotes further research and creation of global multidisciplinary research teams to build future sustainable bioinformatics solutions that will support healthy environment and food production for all mankind for many generations to come.
Researcher, Analyze Thyself

This article attempts to answer the phenomenological question, “What does it mean to be a qualitative researcher?” and an ancillary question, “What does ‘making meaning’ mean?” The author, in colla...
The Fiat-Shamir Zoo: Relating the Security of Different Signature Variants

The Fiat-Shamir paradigm encompasses many different ways of turning a given identification scheme into a signature scheme. Security proofs pertain sometimes to one variant, sometimes to another. We systematically study three variants that we call the challenge (signature is challenge and response), commit (signature is commitment and response), and transcript (signature is challenge, commitment and response) variants. Our framework captures the variants via transforms that determine the signature scheme as a function of not only the identification scheme and hash function (to cover both standard and random oracle model hashing), but also what we call a signing algorithm, to cover both classical and with-abort signing. We relate the security of the signature schemes produced by these transforms, giving minimal conditions under which uf-security of one transfers to the other. To apply this comprehensively, we formalize linear identification schemes, show that many schemes in the literature are linear, and show that any linear scheme meets our conditions for the signature schemes given by the three transforms to have equivalent uf-security. Our results give a comprehensive picture of the Fiat-Shamir zoo and allow proofs of security in the literature to be transferred automatically from one variant to another.
Repeat radiographic imaging in patients with long bone fractures transferred to a pediatric trauma center.

This study sought to determine the proportion of children with long bone fractures who undergo duplicate radiographic imaging after transfer to a pediatric trauma center (PTC) for further management. The secondary objective was to explore provider rationale and diagnostic yield of repeat X-rays. This was a single-site, retrospective cohort study conducted at a PTC. All patients, aged 0–21 years, who were transferred to the PTC for management of a long bone fracture were included. Electronic medical records were reviewed to determine the proportion of children who had repeat radiographic imaging and the provider rationale for obtaining this. T-test and Χ2 analyses were used to compare patients who had repeat X-rays with those who did not. During the study period, 309 patients (63% male, mean age 7.2±4.3 years) were transferred from 30 referring hospitals. Of these, 43% (n=133) underwent repeat radiographs. Patient age (p=0.9), gender (p=0.7), fracture location (p=0.19), and type of referring emergency department (pediatric vs general, p=0.3) were not significantly associated with repeat imaging. Rationale for repeat imaging could be ascertained in 31% of cases (n=41); the most common reasons were request by orthopedist (17%, n=23) and suboptimal original imaging (10%, n=13). Repeat imaging at the PTC did not reveal new or additional diagnoses in any case. Nearly half of the children in our study population undergo repeat and likely unnecessary imaging. Strategies to reduce repeat radiographs should be developed, as redundant imaging exposes patients to additional radiation and increases medical expense.
Voyager 2 Observations of Plasma and Pressure Pulses

This paper provides the latest data from Voyager 2 on plasma characteristics in the heliosheath including the observations of pressure waves in the plasma and particle data. Models and observations show that solar transients drive pressure waves through the heliosphere. Pressure pulses that could drive heliosheath waves are observed near the previous solar maximum upstream of the termination shock. We show that the most recent data is consistent with the presence of pressure waves and compare the heliosheath waves with the pressure increases in the heliosheath. The magnetic field is better correlated with density and galactic cosmic ray intensities in the supersonic solar wind than in the heliosheath. The galactic cosmic rays are correlated with the plasma and particles with a ~30-day lag in both the supersonic wind and heliosheath.
Classes of order 4 in the strict class group of number fields and remarks on unramified quadratic extensions of unit type

Let K be a number field of degree n over $$\mathbb {Q}$$ . Then the 4-rank of the strict class group of K is at least $$\text {rank}_2 \, ( E_{K}^{+} / E_K^2) - \lfloor n /2 \rfloor $$ where $$E_K$$ and $$ E_{K}^{+} $$ denote the units and the totally positive units of K, respectively, and $$\text {rank}_2$$ is the dimension as an elementary abelian 2-group. In particular, the strict class group of a totally real field K with a totally positive system of fundamental units contains at least $$(n-1)/2$$ (n odd) or $$n/2 -1$$ (n even) independent elements of order 4. We also investigate when units in K are sums of two squares in K or are squares mod 4 in K.
Safe Deferred Memory Reclamation with Types

Memory management in lock-free data structures remains a major challenge in concurrent programming. Design techniques including read-copy-update (RCU) and hazard pointers provide workable solutions, and are widely used to great effect. These techniques rely on the concept of a grace period: nodes that should be freed are not deallocated immediately, and all threads obey a protocol to ensure that the deallocating thread can detect when all possible readers have completed their use of the object. This provides an approach to safe deallocation, but only when these subtle protocols are implemented correctly.
Critical Service-Learning as a Vehicle for Change in Higher Education Courses

Our story begins with us, two female faculty members of Color, meeting through a faculty fellowship program focused on service-learning. Through this program, we soon discovered that the work in wh...
Nonsingular group actions and stationary S alpha S random fields

This paper deals with measurable stationary symmetric stable random fields indexed by R^d and their relationship with the ergodic theory of nonsingular R^d-actions. Based on the phenomenal work of Rosinski(2000), we establish extensions of some structure results of stationary S alpha S processes to S\alpha S fields. Depending on the ergodic theoretical nature of the underlying action, we observe different behaviors of the extremes of the field.
Miniaturization and optimization of 384-well compatible RNA sequencing library preparation

Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved cost savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.
“Dorsal–Ventral” Genes Are Part of an Ancient Axial Patterning System: Evidence from Trichoplax adhaerens (Placozoa)

Placozoa are a morphologically simplistic group of marine animals found globally in tropical and subtropical environments. They consist of two named species, Trichoplax adhaerens and more recently Hoilungia hongkongensis, both with roughly six morphologically distinct cell types. With a sequenced genome, a limited number of cell types, and a simple flattened morphology, Trichoplax is an ideal model organism from which to explore the biology of an animal with a cellular complexity analagous to that of the earliest animals. Using a new approach for identification of gene expression patterns, this research looks at the relationship of Chordin/TgfΒ signaling and the axial patterning system of Placozoa. Our results suggest that placozoans have an oral-aboral axis similar to cnidarians and that the parahoxozoan ancestor (common ancestor of Placozoa and Cnidaria) was likely radially symmetric.
Forecasting U.S. Domestic Migration Using Internet Search Queries

Roughly one in ten Americans move every year, bringing significant social and economic impact to both the places they move from and places they move to. We show that migration intent mined from internet search queries can forecast domestic migration and provide new insights beyond government data. We extract from a major search engine (Bing.com) 120 million raw queries with migration intent from 2014 to 2016, including origin and destination geographies, and the specific intent for migration such as whether the potential migration is housing or employment related. Using these queries, we map U.S. state level migration flows, validate them against government data, and demonstrate that adding search query-based metrics explains variance in migration prediction above robust baseline models. In addition, we show that the specific migration intent extracted from these queries unpack the differential demands of migrants with different demographic backgrounds and geographic interests. Examples include interactions between age, education, and income, and migration attributes such as buying versus renting housing and employment in technology versus manual labor job sectors. We discuss how local government, policy makers, and computational social scientists can benefit from this information.