cssi/SciSciGPT-SciSciNet huggingface dataset:
Efficient Expression of Genes in the Drosophila Germline Using a UAS Promoter Free of Interference by Hsp70 piRNAs

Controlling the expression of genes using a binary system involving the yeast GAL4 transcription factor has been a mainstay of Drosophila developmental genetics for nearly 30 years. However, most existing GAL4 expression constructs only function effectively in somatic cells, but not in germ cells during oogenesis, for unknown reasons. A special upstream activation sequence (UAS) promoter, UASp was created that does express during oogenesis, but the need to use different constructs for somatic and female germline cells has remained a significant technical limitation. Here, we show that the expression problem of UASt and many other Drosophila molecular tools in germline cells is caused by their core Hsp70 promoter sequences, which are targeted in female germ cells by Hsp70-directed Piwi-interacting RNAs (piRNAs) generated from endogenous Hsp70 gene sequences. In a genetic background lacking genomic Hsp70 genes and associated piRNAs, UASt-based constructs function effectively during oogenesis. By reducing Hsp70 sequences targeted by piRNAs, we created UASz, which functions better than UASp in the germline and like UASt in somatic cells.
Nearly Optimal Robust Subspace Tracking

In this work, we study the robust subspace tracking (RST) problem and obtain one of the first two provable guarantees for it. The goal of RST is to track sequentially arriving data vectors that lie in a slowly changing low-dimensional subspace, while being robust to corruption by additive sparse outliers. It can also be interpreted as a dynamic (time-varying) extension of robust PCA (RPCA), with the minor difference that RST also requires a short tracking delay. We develop a recursive projected compressive sensing algorithm that we call Nearly Optimal RST via ReProCS (ReProCS-NORST) because its tracking delay is nearly optimal. We prove that NORST solves both the RST and the dynamic RPCA problems under weakened standard RPCA assumptions, two simple extra assumptions (slow subspace change and most outlier magnitudes lower bounded), and a few minor assumptions. Our guarantee shows that NORST enjoys a near optimal tracking delay of $O(r \log n \log(1/\epsilon))$. Its required delay between subspace change times is the same, and its memory complexity is $n$ times this value. Thus both these are also nearly optimal. Here $n$ is the ambient space dimension, $r$ is the subspaces' dimension, and $\epsilon$ is the tracking accuracy. NORST also has the best outlier tolerance compared with all previous RPCA or RST methods, both theoretically and empirically (including for real videos), without requiring any model on how the outlier support is generated. This is possible because of the extra assumptions it uses.
Helping veterans achieve work: A Veterans Health Administration nationwide survey examining effective job development practices in the community.

OBJECTIVE Veterans Health Administration vocational services assist veterans with mental illness to acquire jobs; one major component of these services is job development. The purpose of this study was to characterize the nature of effective job development practices and to examine perceptions and intensity of job development services. METHOD A national mixed-methods online survey of 233 Veterans Health Administration vocational providers collected data regarding frequency of employer contacts, perceptions of job development ease/difficulty, and effective job development practices when dealing with employers. Qualitative responses elucidating effective practices were analyzed using content analysis. RESULTS Vocational providers had a modest number of job development employer contacts across 2 weeks (M = 11.0, SD = 10.6) and fewer were face-to-face (M = 7.6, SD = 8.4). Over 70% of participants perceived job development to be difficult. Six major themes emerged regarding effective job development practices with employers: using an employer-focused approach; utilizing a targeted marketing strategy; engaging in preparation and follow-up; going about the employer interaction with genuineness, resilience, and a strong interpersonal orientation; serving as an advocate for veterans and educator of employers; utilizing specific employer-tailored strategies, such as arranging a one-on-one meeting with a decision maker and touring the business, individualizing a prescripted sales pitch, connecting on a personal level, and engaging in ongoing communication to solidify the working relationship. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE Respondents highlight several potentially effective job development strategies; tools and resources may be developed around these strategies to bolster job development implementation and allow opportunities for fruitful employer interactions. (PsycINFO Database Record
Statistical Estimation of Malware Detection Metrics in the Absence of Ground Truth

The accurate measurement of security metrics is a critical research problem, because an improper or inaccurate measurement process can ruin the usefulness of the metrics. This is a highly challenging problem, particularly when the ground truth is unknown or noisy. In this paper, we measure five malware detection metrics in the absence of ground truth, which is a realistic setting that imposes many technical challenges. The ultimate goal is to develop principled, automated methods for measuring these metrics at the maximum accuracy possible. The problem naturally calls for investigations into statistical estimators by casting the measurement problem as a statistical estimation problem. We propose statistical estimators for these five malware detection metrics. By investigating the statistical properties of these estimators, we characterize when the estimators are accurate, and what adjustments can be made to improve them under what circumstances. We use synthetic data with known ground truth to validate these statistical estimators. Then, we employ these estimators to measure five metrics with respect to a large data set collected from VirusTotal.
Cascading Losses in Reinsurance Networks

We develop a model for contagion in reinsurance networks by which primary insurers’ losses are spread through the network. Our model handles general reinsurance contracts, such as typical excess of...
What are consumers willing to pay for a broad network health plan?: Evidence from covered California

Health Insurance Marketplaces have received considerable attention for their narrow network health plans. Yet, little is known about consumer tastes for network breadth and how they affect plan selection. I estimate demand for health plans in California's Marketplace, Covered California. Using 2017 individual enrollment data and provider network directories, I develop a geospatial measure of network breadth that reflects the physical locations of households and network providers. I find that households are sensitive to network breath in their plan choices. Mean willingness to pay for a broad network plan relative to a narrow network plan, defined as a two standard deviation, 17.44 percentage point increase in network breadth, is $45.83 in post-subsidy monthly premiums. Variation in WTP indicates a selection mechanism exists whereby older households sort into broader network plans. I also find that households are highly premium sensitive, which may be a result of plan standardization in Covered California.
Laws for Metaphysical Explanation

I argue that, just like causal explanation requires laws of nature, so metaphysical explanation requires laws of metaphysics. I offer a minimal rendition of the argument for laws of metaphysics, assuming nothing about grounding or essences, and little about explanation. And I offer a positive and minimal functional conception of the laws of metaphysics, coupled with an argument that some laws of metaphysics are fundamental.
Track Xplorer: A System for Visual Analysis of Sensor-based Motor Activity Predictions

With the rapid commoditization of wearable sensors, detecting human movements from sensor datasets has become increasingly common over a wide range of applications. To detect activities, data scientists iteratively experiment with different classifiers before deciding which model to deploy. Effective reasoning about and comparison of alternative classifiers are crucial in successful model development. This is, however, inherently difficult in developing classifiers for sensor data, where the intricacy of long temporal sequences, high prediction frequency, and imprecise labeling make standard evaluation methods relatively ineffective and even misleading. We introduce Track Xplorer, an interactive visualization system to query, analyze, and compare the predictions of sensor-data classifiers. Track Xplorer enables users to interactively explore and compare the results of different classifiers, and assess their accuracy with respect to the ground-truth labels and video. Through integration with a version control system, Track Xplorer supports tracking of models and their parameters without additional workload on model developers. Track Xplorer also contributes an extensible algebra over track representations to filter, compose, and compare classification outputs, enabling users to reason effectively about classifier performance. We apply Track Xplorer in a collaborative project to develop classifiers to detect movements from multisensor data gathered from Parkinson's disease patients. We demonstrate how Track Xplorer helps identify early on possible systemic data errors, effectively track and compare the results of different classifiers, and reason about and pinpoint the causes of misclassifications.
Fast Algorithms for Displacement and Low-Rank Structured Matrices

This tutorial provides an introduction to the development of fast matrix algorithms based on the notions of displacement and various low-rank structures.
Critical Role of the Surgeon–Anesthesiologist Relationship for Patient Safety

Teamwork is now recognized as important for safe, high-quality perioperative care. The relationship in each surgeon-anesthesiologist dyad is perhaps the most critical element of overall team performance. A well-functioning relationship is conducive to safe, effective care. A dysfunctional relationship can promote unsafe conditions and contribute to an adverse outcome. Yet, there is little research about this relationship, about what works well or not well, what can be done to optimize it. This article explores functional and dysfunctional aspects of the relationship, identifies some negative stereotypes each profession has of the other and calls for research to better characterize and understand how to improve working relationships. Suggestions are given for what an ideal relationship might be and actions that surgeons and anesthesiologists can take to improve how they work together. The goal is safer care for patients, and more joy and meaning in work for surgeons and anesthesiologists.
EviHunter: Identifying Digital Evidence in the Permanent Storage of Android Devices via Static Analysis

Crimes, both physical and cyber, increasingly involve smartphones due to their ubiquity. Therefore, digital evidence on smartphones plays an increasingly important role in crime investigations. Digital evidence could reside in the memory and permanent storage of a smartphone. While we have witnessed significant progresses on memory forensics recently, identifying evidence in the permanent storage is still an underdeveloped research area. Most existing studies on permanent-storage forensics rely on manual analysis or keyword-based scanning of the permanent storage. Manual analysis is costly, while keyword matching often misses the evidentiary data that do not have interesting keywords. In this work, we develop a tool called EviHunter to automatically identify evidentiary data in the permanent storage of an Android device. There could be thousands of files on the permanent storage of a smartphone. A basic question a forensic investigator often faces is which files could store evidentiary data. EviHunter aims to answer this question. Our intuition is that the evidentiary data were produced by apps; and an app's code has rich information about the types of data the app may write to a permanent storage and the files the data are written to. Therefore, EviHunter first pre-computes an App Evidence Database (AED) via static analysis of a large number of apps. The AED includes the types of evidentiary data and files that store them for each app. Then, EviHunter matches the files on a smartphone's permanent storage against the AED to identify the files that could store evidentiary data. We evaluate EviHunter on benchmark apps and 8,690 real-world apps. Our results show that EviHunter can precisely identify both the types of evidentiary data and the files that store them.
Assessing the impact of health system organizational structure on hospital electronic data sharing.

Objective Horizontal consolidation in the hospital industry has gained momentum in the United States despite concerns over rising costs and lower quality. Hospital systems frequently point to potential gains in interoperability and electronic exchange of patient information as consolidation benefits. We sought to assess whether hospitals in different health system structures varied in their interoperable data sharing. Materials and methods We created a cross-sectional national hospital sample from the 2014 AHA Annual Survey and 2015 IT Supplement. We combined the existing taxonomy of health system organizational forms and the ONC's functionality-based, technology-agnostic definition of interoperability. We used logistic regression models to assess the relationship between health systems' organizational forms and interoperability engagement, controlling for hospital characteristics. Results We found that interoperability engagement varied greatly across hospitals in different health system structures, with facilities in more centralized health systems more likely to be interoperable. Hospitals in one system type, featuring centralized insurance product development but diverse service offerings across member organizations, had significantly higher odds of being engaged in interoperable data sharing in our multivariate regression results. Discussion The heterogeneity in health system interoperability engagement indicates that incentives to share data vary greatly across organizational strategies and structures. Our results suggest that horizontal consolidation in the hospital industry may not bring significant gains in interoperability progress unless that consolidation takes a specific business alignment form. Conclusion Policymakers should be wary of claims that horizontal consolidation will lead to interoperability gains. Future research should explore the specific mechanisms that lead to greater interoperability in certain health system organizational structures.
Some nontrivial properties of a formula for compound interest

Abstract We analyze the classical model of compound interest with a constant per-period payment and interest rate. We examine the outstanding balance function as well as the periodic payment function and show that the outstanding balance function is not generally concave in the interest rate, but instead may be initially convex on its domain and then concave.
Threatcasting: a framework and process to model future operating environments

Threatcasting, a new foresight methodology, draws from futures studies and military strategic thinking to provide a novel method to model the future. The methodology fills gaps in existing military...
Structural and Functional Insights into Human Nuclear Cyclophilins

The peptidyl prolyl isomerases (PPI) of the cyclophilin type are distributed throughout human cells, including eight found solely in the nucleus. Nuclear cyclophilins are involved in complexes that regulate chromatin modification, transcription, and pre-mRNA splicing. This review collects what is known about the eight human nuclear cyclophilins: peptidyl prolyl isomerase H (PPIH), peptidyl prolyl isomerase E (PPIE), peptidyl prolyl isomerase-like 1 (PPIL1), peptidyl prolyl isomerase-like 2 (PPIL2), peptidyl prolyl isomerase-like 3 (PPIL3), peptidyl prolyl isomerase G (PPIG), spliceosome-associated protein CWC27 homolog (CWC27), and peptidyl prolyl isomerase domain and WD repeat-containing protein 1 (PPWD1). Each “spliceophilin” is evaluated in relation to the spliceosomal complex in which it has been studied, and current work studying the biological roles of these cyclophilins in the nucleus are discussed. The eight human splicing complexes available in the Protein Data Bank (PDB) are analyzed from the viewpoint of the human spliceophilins. Future directions in structural and cellular biology, and the importance of developing spliceophilin-specific inhibitors, are considered.
The benefits and costs of writing a POSIX kernel in a high-level language

This paper presents an evaluation of the use of a high-level language (HLL) with garbage collection to implement a monolithic POSIX-style kernel. The goal is to explore if it is reasonable to use an HLL instead of C for such kernels, by examining performance costs, implementation challenges, and programmability and safety benefits.The paper contributes Biscuit, a kernel written in Go that implements enough of POSIX (virtual memory, mmap, TCP/IP sockets, a logging file system, poll, etc.) to execute significant applications. Biscuit makes liberal use of Go's HLL features (closures, channels, maps, interfaces, garbage collected heap allocation), which subjectively made programming easier. The most challenging puzzle was handling the possibility of running out of kernel heap memory; Biscuit benefited from the analyzability of Go source to address this challenge.On a set of kernel-intensive benchmarks (including NGINX and Redis) the fraction of kernel CPU time Biscuit spends on HLL features (primarily garbage collection and thread stack expansion checks) ranges up to 13%. The longest single GC-related pause suffered by NGINX was 115 microseconds; the longest observed sum of GC delays to a complete NGINX client request was 600 microseconds. In experiments comparing nearly identical system call, page fault, and context switch code paths written in Go and C, the Go version was 5% to 15% slower.
Psychological Issues in Medically Underserved Patients

The US population has a subset of those that are underserved who are in need of primary care and also suffer from mental health disorders. In this article, categories of underserved populations are described. Each section defines the population being presented, identifies the mental health problems each is likely to encounter, explores the barriers that prevent access to care, and identifies potential methods to minimize such barriers. The ways in which psychiatric issues vary in underserved settings compared with the general population are differentiated. Recommendations are offered for primary care physicians to support improved recognition and management of psychosocial stressors and psychiatric illness among the underserved.
Advertising for consideration

Abstract We analyze markets where firms competing on price advertise to increase the probability of entering consumers’ consideration sets. We find that moderately costly advertising allows firms to raise prices and possibly profits by reducing the fraction of price-conscious consumers, and by segmenting the market according to whether or not consumers consider the lower priced firm. However, when the cost of advertising is sufficiently low, advertising leads to a prisoners’ dilemma that adversely impacts profits without affecting expected prices.
Donors change both their level and pattern of giving in response to contests among charities

Abstract This paper examines two previously unexplored techniques for increasing charitable giving, both motivated by the contest literature. One is a fixed bonus that is paid to the organization receiving the most donations, akin to an all-pay auction. The other is a raffle-based bonus, akin to a Tullock contest. These two techniques are compared to a one-to-one matching program and a baseline condition in a within-subject laboratory experiment. The results reveal that all three bonus techniques lead to similar increases in donations to organizations eligible for the promotion. However, when only some organizations are eligible for the bonuses, the increases in giving to eligible organizations are primarily driven by a reallocation of donations away from ineligible organizations.
Predictors of psychological distress and sleep quality in former family caregivers of people with dementia.

AbstractObjectives: The stress-related psychological symptoms experienced by informal family caregivers do not always improve or resolve after the death of the care recipient. The purpose of this s...
A High-Frequency Inverter for Variable-Load Operation

This paper presents a new inverter architecture suitable for driving widely varying load impedances at high frequency (HF, 3–30 MHz) and above. We present the underlying theory and design considerations for the proposed architecture along with a physical prototype and efficiency optimizing controller. The HF variable-load inverter (HFVLI) architecture comprises two HF inverters with independently controllable amplitude and phase connected together and to the load via a lossless power combining network, implemented here as an immittance converter. By controlling the amplitudes and relative phase of the two constituent inverters, the loading seen by each constituent inverter can be kept in a desirable range even for wide variations in load impedance. This allows for the use of highly efficient zero-voltage switching inverters that would otherwise be precluded or limited in applications presenting wide impedance ranges, such as wireless power transfer and RF plasma generation. The prototype HFVLI system demonstrates the benefits of the proposed approach. It operates at 13.56 MHz and can supply a maximum output power of 1 kW into a 21.8 + 0.3j load at an efficiency of 95.4% and is able to drive a wide range of capacitive and inductive loads at high power with high efficiency.
Aicardi-Goutières syndrome gene Rnaseh2c is a metastasis susceptibility gene in breast cancer.

Breast cancer is the second leading cause of cancer-related deaths in the United States, with the majority of these deaths due to metastatic lesions rather than the primary tumor. Thus, a better understanding of the etiology of metastatic disease is crucial for improving survival. Using a haplotype mapping strategy in mouse and shRNA-mediated gene knockdown, we identified Rnaseh2c, a scaffolding protein of the heterotrimeric RNase H2 endoribonuclease complex, as a novel metastasis susceptibility factor. We found that the role of Rnaseh2c in metastatic disease is independent of RNase H2 enzymatic activity, and immunophenotyping and RNA-sequencing analysis revealed engagement of the T cell-mediated adaptive immune response. Furthermore, the cGAS-Sting pathway was not activated in the metastatic cancer cells used in this study, suggesting that the mechanism of immune response in breast cancer is different from the mechanism proposed for Aicardi-Goutieres Syndrome, a rare interferonopathy caused by RNase H2 mutation. These results suggest an important novel, non-enzymatic role for RNASEH2C during breast cancer progression and add Rnaseh2c to a panel of genes we have identified that together could determine patients with high risk for metastasis. These results also highlight a potential new target for combination with immunotherapies and may contribute to a better understanding of the etiology of Aicardi-Goutieres Syndrome autoimmunity.
Compound-V formations in shorebird flocks.

Birds often fly in flocks ranging from very structured V-formations to unstructured clusters. Many studies have tried to prove what causes birds to flock and how it benefits them. Flocks, for example, may help birds to avoid predators and to navigate. Flying in a V-shaped formation likely also gives aerodynamic benefits that can make it easier to fly long distances. Few studies, however, have measured how the positions of birds in a flock relate to things like flying speed or the frequency of wing flaps. This is because it was difficult to take such measurements in large flocks of moving birds. Advances in cameras and computers are now making it easier to track individual birds flying in large flocks. The technology allows scientists to measure how birds position themselves in relation to other birds, or how flock-positioning varies by bird size, species, ecology, and behaviors. Such measurements may help scientists better understand why and how birds flock. Corcoran and Hedrick now show that four different types of shorebirds position themselves in the same way when flying in a flock. In the experiments, digital cameras recorded video of 18 cluster-like flocks of four different species of birds flying over a bird sanctuary or agricultural fields. The flocks ranged in size from a hundred to a thousand birds. Some flocks had two types of bird. The four types of birds – dunlin, short-billed dowitcher, American avocet, and marbled godwit – live in similar environments but greatly vary in size and fly at different speeds. Corcoran and Hedrick measured individual bird positions using three-dimensional computer reconstructions of the flocks. Each bird – regardless of size or species – most commonly flew about one wingspan to the side and between a half to one-and-a-half wingspans back from the bird in front of it. Birds flying in simple V-shaped formations follow similar rules. This suggests that birds flying in clusters may also gain aerodynamic benefits.
Identification of exon skipping events associated with Alzheimer’s disease in the human hippocampus

At least 90% of human genes are alternatively spliced. Alternative splicing has an important function regulating gene expression and miss-splicing can contribute to risk for human diseases, including Alzheimer’s disease (AD). We developed a splicing decision model as a molecular mechanism to identify functional exon skipping events and genetic variation affecting alternative splicing on a genome-wide scale by integrating genomics, transcriptomics, and neuroimaging data in a systems biology approach. In this study, we analyzed RNA-Seq data of hippocampus brain tissue from Alzheimer’s disease (AD; n = 24) and cognitively normal elderly controls (CN; n = 50) and identified three exon skipping events in two genes (RELN and NOS1) as significantly associated with AD (corrected p-value 1.5). Next, we identified single-nucleotide polymorphisms (SNPs) affecting exon skipping events using the splicing decision model and then performed an association analysis of SNPs potentially affecting three exon skipping events with a global cortical measure of amyloid-β deposition measured by [18F] Florbetapir position emission tomography (PET) scan as an AD-related quantitative phenotype. A whole-brain voxel-based analysis was also performed. Two exons in RELN and one exon in NOS1 showed significantly lower expression levels in the AD participants compared to CN participants, suggesting that the exons tend to be skipped more in AD. We also showed the loss of the core protein structure due to the skipped exons using the protein 3D structure analysis. The targeted SNP-based association analysis identified one intronic SNP (rs362771) adjacent to the skipped exon 24 in RELN as significantly associated with cortical amyloid-β levels (corrected p-value < 0.05). This SNP is within the splicing regulatory element, i.e., intronic splicing enhancer. The minor allele of rs362771 conferred decreases in cortical amyloid-β levels in the right temporal and bilateral parietal lobes. Our results suggest that exon skipping events and splicing-affecting SNPs in the human hippocampus may contribute to AD pathogenesis. Integration of multiple omics and neuroimaging data provides insights into possible mechanisms underlying AD pathophysiology through exon skipping and may help identify novel therapeutic targets.
Evidence From EELS of Oxygen in the Nucleation Layer of a MBE Grown III-N HEMT

The presence of oxygen throughout the nominally AlN nucleation layer of a RF assisted MBE grown III-N HEMT was revealed upon examination by Electron Energy Loss Spectroscopy (EELS) in a Scanning Transmission Electron Microscope (STEM). The nucleation layer generates the correct polarity (gallium face) required for producing a piezoelectric induced high mobility two dimensional electron gas at the AlGaN/GaN heterojunction. Only AlN or AlGaN nucleation layers have provided gallium face polarity in RF assisted MBE grown III-N’s on sapphire. The sample was grown at Cornell University in a Varian GenII MBE using an EPI Uni-Bulb nitrogen plasma source. The nucleation layer was examined in the Cornell University STEM using Annular Dark Field (ADF) imaging and Parallel Electron Energy Loss Spectroscopy (PEELS). Bright Field TEM reveals a relatively crystallographically sharp interface, while the PEELS reveal a chemically diffuse interface. PEELS of the nitrogen and oxygen K-edges at approximately 5-Angstrom steps across the GaN/AlN/sapphire interfaces reveals the presence of oxygen in the AlN nucleation layer. The gradient suggests that the oxygen has diffused into the nucleation region from the sapphire substrate forming this oxygen containing AlN layer. Based on energy loss near edge structure (ELNES), oxygen is in octahedral interstitial sites in the AlN and Al is both tetrahedrally and octahedrally coordinated in the oxygen rich region of the AlN.
MOVPE Growth of Quaternary (Al,Ga,In)N for UV Optoelectronics

We report the growth and characterization of quaternary AlGaInN. A combination of photoluminescence (PL), high-resolution x-ray diffraction (XRD), and Rutherford backscattering spectrometry (RBS) characterizations enables us to explore the contours of constant- PL peak energy and lattice parameter as functions of the quaternary compositions. The observation of room temperature PL emission at 351nm (with 20% Al and 5% In) renders initial evidence that the quaternary could be used to provide confinement for GaInN (and possibly GaN). AlGaInN/GaInN MQW heterostructures have been grown; both XRD and PL measurements suggest the possibility of incorporating this quaternary into optoelectronic devices.
Efficiently Exploring Ordering Problems through Conflict-Directed Search.

In planning and scheduling, solving problems with both state and temporal constraints is hard since these constraints may be highly coupled. Judicious orderings of events enable solvers to efficiently make decisions over sequences of actions to satisfy complex hybrid specifications. The ordering problem is thus fundamental to planning. Promising recent works have explored the ordering problem as search, incorporating a special tree structure for efficiency. However, such approaches only reason over partial order specifications. Having observed that an ordering is inconsistent with respect to underlying constraints, prior works do not exploit the tree structure to efficiently generate orderings that resolve the inconsistency. In this paper, we present Conflict-directed Incremental Total Ordering (CDITO), a conflict-directed search method to incrementally and systematically generate event total orders given ordering relations and conflicts returned by sub-solvers. Due to its ability to reason over conflicts, CDITO is much more efficient than Incremental Total Ordering. We demonstrate this by benchmarking on temporal network configuration problems that involve routing network flows and allocating bandwidth resources over time.
Salience and social choice

The axioms of expected utility and discounted utility theory have been tested extensively. In contrast, the axioms of social welfare functions have only been tested in a few questionnaire studies involving choices between hypothetical income distributions. In a controlled experiment with 100 subjects placed in the role of social planners, we test five fundamental properties of social welfare functions to determine the efficacy of traditional social choice models in predicting social planner allocations when presented with choice sets designed to test the axioms of the theory. We find that three properties of the standard social welfare functions tested are systematically violated, producing an Allais paradox, a common ratio effect, and a framing effect in social choice. We find support for scale invariance and a preference for tail-increasing transfers. Our experiment also enables us to test a model of salience-based social choice which predicts the systematic deviations and highlights the close relationship between these anomalies and the classical paradoxes for risk and time.
Book Review: Robotics in STEM Education: Redesigning the Learning Experience

This book review critiques Robotics in STEM Education: Redesigning the Learning Experience by Myint Swe Khine. The review will give the reader insight into the chapter authors' ideas, strategies, and research on how educational robotics can help transform the way students learn in the classroom. The review also provides a critique on the overall purpose of the book, author strengths and suggestions, and the books' overall impact on the field of STEM education.
Selective aldol condensation or cyclotrimerization reactions catalyzed by FeCl3

The inexpensive and commercially available FeCl3 catalyzes the selective homo-aldol condensation of aldehydes into the corresponding α–β unsaturated aldehydes, presumably through an unobserved aldol intermediate. Surprisingly the reaction course can be diverted to produce 1,3,5-trioxanes via aldehyde cyclotrimerization. Selectivity for trioxanes is achieved at lower temperatures and is enhanced by the presence of water, contrary to prior reports. A broad range of aliphatic and aromatic aldehydes are capable of undergoing these transformations; short reaction times, high yields, scalability, and easy purification processes are also described.
Highly Efficient 1,4-Additions of Electron-Deficient Aryl Boronic Acids with a Novel Rhodium(I) Quinonoid Catalyst§

Rhodium(I) quinonoid catalysts are a remarkably efficient new class of reagents for the conjugate addition of aryl boronic acids. Herein, we describe the use of these reagents in catalyzing the highly efficient addition of a broad range of boronic acids, including heteroaromatic and the first example of trihalogenated aryl boronic acids.
THE FIRST ASYMMETRIC TOTAL SYNTHESES OF (+)-LYCORINE AND (+)-1-DEOXYLYCORINE

The first asymmetric total syntheses of (+)-1-deoxylycorine (2a) and (+)-lycorine (2b), the unnatural enantiomer of lycorine (1), are described. Construction of lactam 12, a key intermediate in the synthesis of both 2a and 2b, began by Birch reduction-alkylation of the chiral benzamide 3 with 2-bromoethyl acetate followed by ester saponification to give the 6-(2-hydroxyethyl)-1-methoxy-1,4-cyclohexadiene 6a in 96% yield as a single diastereomer. This material was converted to the radical cyclization substrates 11a and 11b. Both 11a and 11b gave 12 and the reduced enamide 11c on treatment with AIBN and Bu3SnH in refluxing benzene solution. Lactam 12 also was obtained by photocyclization of enamide 11c. The allylic alcohol unit characteristic of the C ring of the lycorine alkaloids was fashioned by a radical induced decarboxylation-epoxide fragmentation of the N-hydroxy-2-thiazoline ester 21b. The resulting (+)-2-epi-deoxylycorine (22) was subjected to Mitsunobu inversion followed by LiAlH4 reduction to giv...
HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures.

Histone modifications play important roles in gene regulation, heredity, imprinting, and many human diseases. The histone code is complex and consists of more than 100 marks. Therefore, biologists need computational tools to characterize general signatures representing the distributions of tens of chromatin marks around thousands of regions. To this end, we developed a software tool, HebbPlot, which utilizes a Hebbian neural network in learning a general chromatin signature from regions with a common function. Hebbian networks can learn the associations between tens of marks and thousands of regions. HebbPlot presents a signature as a digital image, which can be easily interpreted. Moreover, signatures produced by HebbPlot can be compared quantitatively. We validated HebbPlot in six case studies. The results of these case studies are novel or validating results already reported in the literature, indicating the accuracy of HebbPlot. Our results indicate that promoters have a directional chromatin signature; several marks tend to stretch downstream or upstream. H3K4me3 and H3K79me2 have clear directional distributions around active promoters. In addition, the signatures of high- and low-CpG promoters are different; H3K4me3, H3K9ac, and H3K27ac are the most different marks. When we studied the signatures of enhancers active in eight tissues, we observed that these signatures are similar, but not identical. Further, we identified some histone modifications — H3K36me3, H3K79me1, H3K79me2, and H4K8ac — that are associated with coding regions of active genes. Other marks — H4K12ac, H3K14ac, H3K27me3, and H2AK5ac — were found to be weakly associated with coding regions of inactive genes. This study resulted in a novel software tool, HebbPlot, for learning and visualizing the chromatin signature of a genetic element. Using HebbPlot, we produced a visual catalog of the signatures of multiple genetic elements in 57 cell types available through the Roadmap Epigenomics Project. Furthermore, we made a progress toward a functional catalog consisting of 22 histone marks. In sum, HebbPlot is applicable to a wide array of studies, facilitating the deciphering of the histone code.
Cross-population analysis for functional characterization of type II diabetes variants

As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Polymorphisms (SNPs) that are associated with the same disease. Using Type II Diabetes (T2D) as a test case, we develop measures and methods to characterize the functional overlap of SNPs associated with the same disease across populations. We introduce the notion of an Overlap Matrix as a general means of characterizing the functional overlap between different SNP sets at different genomic and functional granularities. Using SNP-to-gene mapping, functional annotation databases, and functional association networks, we assess the degree of functional overlap across nine populations from Asian and European ethnic origins. We further assess the generalizability of the method by applying it to a dataset for another complex disease – Prostate Cancer. Our results show that more overlap is captured as more functional data is incorporated as we go through the pipeline, starting from SNPs and ending at network overlap analyses. We hypothesize that these observed differences in the functional mechanisms of T2D across populations can also explain the common use of different prescription drugs in different populations. We show that this hypothesis is concordant with the literature on the functional mechanisms of prescription drugs. Our results show that although the etiology of a complex disease can be associated with distinct processes that are affected in different populations, network-based annotations can capture more functional overlap across populations. These results support the notion that it can be useful to take ethnicity into account in making personalized treatment decisions for complex diseases.
First total synthesis of xestobergsterol A and active structural analogues of the xestobergsterols

Abstract The novel pentacyclic polyhydroxylated sterol, xestobergsterol A 1a , a strong inhibitor of histamine release from rat mast cells induced by anti-IgE, has been synthesized in 24 steps and good overall yield from stigmasterol 7 . The Breslow remote functionalization process has been extended to several more highly functionalized steroid derivatives, especially those with oxygen functionality in the B-ring. The key steps of the synthesis of xestobergsterol A 1a and its analogues, 7-deoxyxestobergsterol A 1d and 16,23- seco -23-deoxyxestobergsterol A 73 , are the Breslow remote functionalization of oxygenated steroids and for compounds 1a and 1d , a novel base-catalyzed epimerization-aldol condensation of a dione to give the desired CD- cis ring structure of the xestobergsterols. Thus the known alcohol 75 , prepared from stigmasterol 7 , was taken to the tetraacetate 107 which was then converted via a Breslow remote functionalization into the alkene aldehyde 114 which was transformed in 5 steps to xestobergsterol A 1a . Testing of the synthetic materials showed that the two analogues, 7-deoxyxestobergsterol A 1b and 16,23- seco -23-deoxyxestobergsterol A 73 , are also potent inhibitors of histamine release with IC 50 values (IC 50 500 nM and 750 nM, respectively) being only 1015 times less than that of xestobergsterol A itself (50 nM).
(+)‐3‐Oxoglycyrrhetinic acid: catemeric hydrogen bonding in a non‐racemic triterpenoid diketo acid

The crystal structure of the title compound, (+)-10,13-dioxo-2α,4aβ,6aα,6bβ,9,9,12aβ-heptamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8aα,9,10,11,12,12a,12bα,13,14bβ-icosahydropicene-2β-carboxylic acid, C 30 H 44 O 4 , involves carboxyl-to-ketone hydrogen-bonding catemers. Distorted hydrogen bonds progress from the carboxyl H atom of one molecule to the remote-ring ketone O atom of a screw-related neighbor [O...O = 2.975 (5) A], yielding helical hydrogen-bonding chains which proceed in the b direction. Two C-H...O close contacts were found, connecting the unsaturated ketone (2.71 A) and the acid carbonyl (2.55 A) to separate screw-related neighbors.
Functional dissection of the ARGONAUTE7 promoter

ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA-guided manner. Arabidopsis thaliana has 10 ARGONAUTE (AGO) genes, with specialized roles in RNA-directed DNA methylation, post-transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO1,AGO10, and AGO7 using yeast 1-hybrid assays. A ranked list of candidate DNA-binding TFs revealed binding of the AGO7 promoter by a number of proteins in two families: the miR156-regulated SPL family and the miR319-regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO7, nor for the function of AGO7 in leaf shape. Normal AGO7 transcription levels and function appear to depend instead on an adjacent 124-bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO7-triggered TAS3 pathway functions in timing and polarity.
An improved synthesis of the C,D-ring pyrromethenone of phytochrome and phytochromobilin

Pyrromethenone 1b, the C,D-ring segment of both phytochrome (Pr) and phytochromobilin (PΦB) has been prepared in a highly efficient fashion beginning with 2-acetyl-butyrolactone (8). The key steps involved conversion of 8 to the Z-enol triflate 9, followed by Pdo catalyzed coupling with trimethylsilylacetylene, p-chlorophenylselenide ring opening, and amidation, to afford ring-D synthon 11 having the proper geometry and oxidation state for conversion to 1b.
25 Years of Molecular Biology Databases: A Study of Proliferation, Impact, and Maintenance

Online resources enable unfettered access to and analysis of scientific data and are considered crucial for the advancement of modern science. Despite the clear power of online data resources, including web-available databases, proliferation can be problematic due to challenges in sustainability and long-term persistence. As areas of research become increasingly dependent on access to collections of data, an understanding of the scientific community’s capacity to develop and maintain such resources is needed. The advent of the Internet coincided with expanding adoption of database technologies in the early 1990s, and the molecular biology community was at the forefront of using online databases to broadly disseminate data. The journal Nucleic Acids Research has long published articles dedicated to the description of online databases, as either debut or update articles. Snapshots throughout the entire history of online databases can be found in the pages of Nucleic Acids Research’s “Database Issue.” Given the prominence of the Database Issue in the molecular biology and bioinformatics communities and the relative rarity of consistent historical documentation, database articles published in Database Issues provide a particularly unique opportunity for longitudinal analysis. To take advantage of this opportunity, the study presented here first identifies each unique database described in 3055 Nucleic Acids Research Database Issue articles published between 1991-2016 to gather a rich dataset of databases debuted during this time frame, regardless of current availability. In total, 1727 unique databases were identified and associated descriptive statistics were gathered for each, including year debuted in a Database Issue and the number of all associated Database Issue publications and accompanying citation counts. Additionally, each database identified was assessed for current availability through testing of all associated URLs published. Finally, to assess maintenance, database websites were inspected to determine the last recorded update. The resulting work allows for an examination of the overall historical trends, such as the rate of database proliferation and attrition as well as an evaluation of citation metrics and on-going database maintenance.
Sulfide ion transfer from a vicinal dithiolate. A new route for the synthesis of mesocyclic trithiaethers

Abstract Four mesocyclic and one macrocyclic trithiaethers have been synthesized using a sulfide ion transfer from a vicinal dithiolate. The mechanism of the sulfide ion transfer is discussed. An improved method for synthesizing 2-hydroxymethyl-1,4,8,11-tetrathiacyclotetradecane is also reported.
Flowtrace: simple visualization of coherent structures in biological fluid flows.

ABSTRACT We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results with more experimentally difficult and mathematically sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential ‘middle ground’ allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques. In addition to being informative, the visualizations generated by our tool are often striking and elegant, illustrating coherent structures directly from videos without the need for computational overlays. Our tool is available as fully documented open-source code for MATLAB, Python or ImageJ at www.flowtrace.org.
1-Bromo-3,3- bis (2-bromoethyl)alkanes: Precursors to 4-Substituted Quinuclidines and 1-Phosphabicyclo[2.2.2]octanes

Abstract 1-Bromo-3,3-bis(2-bromoethyl)octane has been synthesized from tetrahydro-4H-pyran-4-one in 6 steps and 18% overall yield. This method is more convenient, gives higher overall yields and is potentially more general than those previously reported for related tribromides.