cssi/SciSciGPT-SciSciNet huggingface dataset:
Recruitment of two dyneins to an mRNA-dependent Bicaudal D transport complex

Cytoplasmic dynein is a motor-like protein that uses energy to transport cargo where it is needed within cells. It moves along protein filaments called microtubules, which act like miniature tracks. Once dynein engages with microtubules, it then picks up cargo using adaptor proteins. In fruit flies, this cargo includes a messenger RNA molecule known as K10, which attaches to dynein via adaptors called Egalitarian and BicD (short for “Bicaudal D”). Egalitarian grabs hold of K10, and BicD links Egalitarian to the dynein motor. In the absence of a cargo, full-length BicD does not bind to dynein. But, shortening BicD to remove its link to Egalitarian allows it to bind and activate the motor for transport. Much of our current understanding of dynein comes from studies that use shortened adaptor proteins like these. These proteins cannot bind cargo, so we know little about how the cargo and the adaptors control dynein activity. To address this, Sladewski, Billington, Ali et al. purified the components of the K10 transport system and then recreated it in the laboratory. This revealed that it is BicD that decides when dynein is ready to go. First, imaging techniques showed that empty BicD forms a looped shape that hides the part of its structure that binds to dynein. This essentially switches it “off”, preventing empty dynein motors from moving. When the K10 cargo is ready for transport, it binds to two Egalitarian molecules, which work together to uncurl the BicD loop. This frees up the end of the BicD molecule, allowing it to link up with the dynein motor. The key to uncurling the BicD protein was the presence of two Egalitarian molecules. And it was the cargo, K10, that brought them together, ensuring that the motors only moved when the cargo was ready. What is more, the uncurled BicD could bind not one but two dyneins. This allowed the cargo to move faster, and over longer distances than cargo with one dynein motor. Recreating molecular machines and imaging their molecules provides a way to understand how they work. Studying how dynein moves cargo is key to understanding how molecules are transported within cells. This, in turn, could reveal what happens when the system goes wrong. Transport defects can cause diseases in humans, including neurodegenerative diseases. As such, a better understanding of how the transport system works may one day open new avenues for health research.
Low-mass Tertiary Companions to Spectroscopic Binaries. I. Common Proper Motion Survey for Wide Companions Using 2MASS

We report the first results of a multi-epoch search for wide (separations greater than a few tens of AU), low-mass tertiary companions of a volume-limited sample of 118 known spectroscopic binaries within 30 pc of the Sun, using the Two Micron All Sky Survey Point Source Catalog and follow-up observations with the KPNO and CTIO 4 m telescopes. Note that this sample is not volume complete but volume limited, and, thus, there is incompleteness in our reported companion rates. We are sensitive to common proper motion companions with separations from roughly 200 AU to 10,000 AU (~10ˮ → ~ 10'). From 77 sources followed-up to date, we recover 11 previously known tertiaries, 3 previously known candidate tertiaries, of which 2 are spectroscopically confirmed and 1 rejected, and 3 new candidates, of which 2 are confirmed and 1 rejected. This yields an estimated wide tertiary fraction of 19.5^(+5.2)_(–3.7)%. This observed fraction is consistent with predictions set out in star formation simulations where the fraction of wide, low-mass companions to spectroscopic binaries is >10%.
Three Dimensional Fluorescence Microscopy Image Synthesis and Segmentation

Advances in fluorescence microscopy enable acquisition of 3D image volumes with better image quality and deeper penetration into tissue. Segmentation is a required step to characterize and analyze biological structures in the images and recent 3D segmentation using deep learning has achieved promising results. One issue is that deep learning techniques require a large set of groundtruth data which is impractical to annotate manually for large 3D microscopy volumes. This paper describes a 3D deep learning nuclei segmentation method using synthetic 3D volumes for training. A set of synthetic volumes and the corresponding groundtruth are generated using spatially constrained cycle-consistent adversarial networks. Segmentation results demonstrate that our proposed method is capable of segmenting nuclei successfully for various data sets.
Multi-Collision Resistant Hash Functions and Their Applications

Collision resistant hash functions are functions that shrink their input, but for which it is computationally infeasible to find a collision, namely two strings that hash to the same value (although collisions are abundant).
NOMA-Based Energy-Efficient Wireless Powered Communications

In this paper, we study the performance of non-orthogonal multiple access (NOMA) schemes in wireless powered communication networks (WPCN) focusing on the system energy efficiency (EE). We consider multiple energy harvesting user equipments (UEs) that operate based on harvest-then-transmit protocol. The uplink information transfer is carried out by using power-domain multiplexing, and the receiver decodes each UE’s data in such a way that the UE with the best channel gain is decoded without interference. In order to determine optimal resource allocation strategies, we formulate optimization problems considering two models, namely half-duplex and asynchronous transmission, based on how downlink and uplink operations are coordinated. In both cases, we have concave-linear fractional problems, and hence Dinkelbach’s method can be applied to obtain the globally optimal solutions. Thus, we first derive analytical expressions for the harvesting interval, and then we provide an algorithm to describe the complete procedure. Furthermore, we incorporate delay-limited sources and investigate the impact of statistical queuing constraints on the energy-efficient allocation of operating intervals. We formulate an optimization problem that maximizes the system effective-EE while UEs are applying NOMA scheme for uplink information transfer. Since the problem satisfies pseudo-concavity, we provide an iterative algorithm using bisection method to determine the unique solution. In the numerical results, we observe that broadcasting at higher power level is more energy efficient for WPCN with uplink NOMA. Additionally, exponential decay quality of service parameter has considerable impact on the optimal solution, and in the presence of strict constraints, more time is allocated for downlink interval under half-duplex operation with uplink time-division multiple access mode.
Codesigned Shared Decision-Making Diabetes Management Plan Tool for Adolescents With Type 1 Diabetes Mellitus and Their Parents: Prototype Development and Pilot Test.

: Adolescents with type 1 diabetes mellitus have difficulty achieving optimal glycemic control, partly due to competing priorities that interfere with diabetes self-care. Often, significant diabetes-related family conflict occurs, and adolescents’ thoughts and feelings about diabetes management may be disregarded. Patient-centered diabetes outcomes may be better when adolescents feel engaged in the decision-making process. : The objective of our study was to codesign a clinic intervention using shared decision making for addressing diabetes self-care with an adolescent patient and parent advisory board. : The patient and parent advisory board consisted of 6 adolescents (teens) between the ages 12 and 18 years with type 1 diabetes mellitus and their parents recruited through our institution’s Pediatric Diabetes Program. Teens and parents provided informed consent and participated in 1 or both of 2 patient and parent advisory board sessions, lasting 3 to 4 hours each. Session 1 topics were (1) patient-centered outcomes related to quality of life, parent-teen shared diabetes management, and shared family experiences; and (2) implementation and acceptability of a patient-centered diabetes care plan intervention where shared decision making was used. We analyzed audio recordings, notes, and other materials to identify and extract ideas relevant to the development of a patient-centered diabetes management plan. These data were visually coded into similar themes. We used the information to develop a prototype for a diabetes management plan tool that we pilot tested during session 2. : Session 1 identified 6 principal patient-centered quality-of-life measurement domains: stress, fear and worry, mealtime struggles, assumptions and judgments, feeling abnormal, and conflict. We determined 2 objectives to be principally important for a diabetes management plan intervention: (1) focusing the intervention on diabetes distress and conflict resolution strategies, and (2) working toward a verbalized common goal. In session 2, we created the diabetes management plan tool according to these findings and will use it in a clinical trial with the aim of assisting with patient-centered goal setting. : Patients with type 1 diabetes mellitus can be effectively engaged and involved in patient-centered research design. Teens with type 1 diabetes mellitus prioritize reducing family conflict and fitting into their social milieu over health outcomes at this time in their lives. It is important to acknowledge this when designing interventions to improve health outcomes in teens with type 1 diabetes mellitus.
Determining the Specificity of Cascade Binding, Interference, and Primed Adaptation In Vivo in the Escherichia coli Type I-E CRISPR-Cas System

In clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) immunity systems, short CRISPR RNAs (crRNAs) are bound by Cas proteins, and these complexes target invading nucleic acid molecules for degradation in a process known as interference. In type I CRISPR-Cas systems, the Cas protein complex that binds DNA is known as Cascade. Association of Cascade with target DNA can also lead to acquisition of new immunity elements in a process known as primed adaptation. Here, we assess the specificity determinants for Cascade-DNA interaction, interference, and primed adaptation in vivo, for the type I-E system of Escherichia coli Remarkably, as few as 5 bp of crRNA-DNA are sufficient for association of Cascade with a DNA target. Consequently, a single crRNA promotes Cascade association with numerous off-target sites, and the endogenous E. coli crRNAs direct Cascade binding to >100 chromosomal sites. In contrast to the low specificity of Cascade-DNA interactions, >18 bp are required for both interference and primed adaptation. Hence, Cascade binding to suboptimal, off-target sites is inert. Our data support a model in which the initial Cascade association with DNA targets requires only limited sequence complementarity at the crRNA 5' end whereas recruitment and/or activation of the Cas3 nuclease, a prerequisite for interference and primed adaptation, requires extensive base pairing.IMPORTANCE Many bacterial and archaeal species encode CRISPR-Cas immunity systems that protect against invasion by foreign DNA. In the Escherichia coli CRISPR-Cas system, a protein complex, Cascade, binds 61-nucleotide (nt) CRISPR RNAs (crRNAs). The Cascade complex is directed to invading DNA molecules through base pairing between the crRNA and target DNA. This leads to recruitment of the Cas3 nuclease, which destroys the invading DNA molecule and promotes acquisition of new immunity elements. We made the first in vivo measurements of Cascade binding to DNA targets. Thus, we show that Cascade binding to DNA is highly promiscuous; endogenous E. coli crRNAs can direct Cascade binding to >100 chromosomal locations. In contrast, we show that targeted degradation and acquisition of new immunity elements require highly specific association of Cascade with DNA, limiting CRISPR-Cas function to the appropriate targets.
Ferroelectric switching of a two-dimensional metal

A ferroelectric is a material with a polar structure whose polarity can be reversed (switched) by applying an electric field1,2. In metals, itinerant electrons screen electrostatic forces between ions, which explains in part why polar metals are very rare3–7. Screening also excludes external electric fields, apparently ruling out the possibility of ferroelectric switching. However, in principle, a thin enough polar metal could be sufficiently penetrated by an electric field to have its polarity switched. Here we show that the topological semimetal WTe2 provides an embodiment of this principle. Although monolayer WTe2 is centro-symmetric and thus non-polar, the stacked bulk structure is polar. We find that two- or three-layer WTe2 exhibits spontaneous out-of-plane electric polarization that can be switched using gate electrodes. We directly detect and quantify the polarization using graphene as an electric-field sensor8. Moreover, the polarization states can be differentiated by conductivity and the carrier density can be varied to modify the properties. The temperature at which polarization vanishes is above 350 kelvin, and even when WTe2 is sandwiched between graphene layers it retains its switching capability at room temperature, demonstrating a robustness suitable for applications in combination with other two-dimensional materials9–12. Two- and three-layer WTe2 exhibits spontaneous out-of-plane electric polarization that can be switched electrically at room temperature and is sufficiently robust for use in applications with other two-dimensional materials.
Global-mean vertical tracer mixing in planetary atmospheres i: Theory and fast-rotating planets

Most chemistry and cloud formation models for planetary atmospheres adopt a one-dimensional (1D) diffusion approach to approximate the global-mean vertical tracer transport. The physical underpinning of the key parameter in this framework, eddy diffusivity $K_{zz}$, is usually obscure. Here we analytically and numerically investigate vertical tracer transport in a 3D stratified atmosphere and predict $K_{zz}$ as a function of the large-scale circulation strength, horizontal mixing due to eddies and waves and local tracer sources and sinks. We find that $K_{zz}$ increases with tracer chemical lifetime and circulation strength but decreases with horizontal eddy mixing efficiency. We demarcated three $K_{zz}$ regimes in planetary atmospheres. In the first regime where the tracer lifetime is short compared with the transport timescale and horizontal tracer distribution under chemical equilibrium ($\chi_0$) is uniformly distributed across the globe, global-mean vertical tracer mixing behaves diffusively. But the traditional assumption in current 1D models that all chemical species are transported via the same eddy diffusivity generally breaks down. We show that different chemical species in a single atmosphere should in principle have different eddy diffusion profiles. In the second regime where tracer is short-lived but $\chi_0$ is non-uniformly distributed, a significant non-diffusive component might lead to a negative $K_{zz}$ under the diffusive assumption. In the third regime where the tracer is long-lived, global-mean vertical tracer transport is also largely influenced by non-diffusive effects. Numerical simulations of 2D tracer transport on fast-rotating zonally symmetric planets validate our analytical $K_{zz}$ theory over a wide parameter space.
Differentiation state and invasiveness of human breast cancer cell lines

Eighteen breast cancer cell lines were examined for expression of markers of epithelial and fibroblastic differentiation: E-cadherin, desmoplakins, ZO-1, vimentin, keratin and β1 and β4 integrins. The cell lines were distributed along a spectrum of differentiation from epithelial to fibroblastic phenotypes. The most well-differentiated, epithelioid cell lines contained proteins characteristic of desmosomal, adherens and tight junctions, were adherent to one another on plastic and in the basement membrane matrix Matrigel and were keratin-positive and vimentin-negative. These cell lines were all weakly invasive in anin vitro chemoinvasion assay. The most poorly-differentiated, fibroblastic cell lines were E-cadherin-, desmoplakin- and ZO-1-negative and formed branching structures in Matrigel. They were vimentin-positive, contained only low levels of keratins and were highly invasive in thein vitro chemoinvasion assay. Of all of the markers analyzed, vimentin expression correlated best within vitro invasive ability and fibroblastic differentiation. In a cell line with unstable expression of vimentin, T47DCO, the cells that were invasive were of the fibroblastic type. The differentiation markers described here may be useful for analysis of clinical specimens and could potentially provide a more precise measure of differentiation grade yielding more power for predicting prognosis.
The Disparate Effects of Strategic Manipulation

When consequential decisions are informed by algorithmic input, individuals may feel compelled to alter their behavior in order to gain a system's approval. Models of agent responsiveness, termed "strategic manipulation," analyze the interaction between a learner and agents in a world where all agents are equally able to manipulate their features in an attempt to "trick" a published classifier. In cases of real world classification, however, an agent's ability to adapt to an algorithm is not simply a function of her personal interest in receiving a positive classification, but is bound up in a complex web of social factors that affect her ability to pursue certain action responses. In this paper, we adapt models of strategic manipulation to capture dynamics that may arise in a setting of social inequality wherein candidate groups face different costs to manipulation. We find that whenever one group's costs are higher than the other's, the learner's equilibrium strategy exhibits an inequality-reinforcing phenomenon wherein the learner erroneously admits some members of the advantaged group, while erroneously excluding some members of the disadvantaged group. We also consider the effects of interventions in which a learner subsidizes members of the disadvantaged group, lowering their costs in order to improve her own classification performance. Here we encounter a paradoxical result: there exist cases in which providing a subsidy improves only the learner's utility while actually making both candidate groups worse-off---even the group receiving the subsidy. Our results reveal the potentially adverse social ramifications of deploying tools that attempt to evaluate an individual's "quality" when agents' capacities to adaptively respond differ.
One-Shot Relational Learning for Knowledge Graphs

Knowledge graphs (KG) are the key components of various natural language processing applications. To further expand KGs’ coverage, previous studies on knowledge graph completion usually require a large number of positive examples for each relation. However, we observe long-tail relations are actually more common in KGs and those newly added relations often do not have many known triples for training. In this work, we aim at predicting new facts under a challenging setting where only one training instance is available. We propose a one-shot relational learning framework, which utilizes the knowledge distilled by embedding models and learns a matching metric by considering both the learned embeddings and one-hop graph structures. Empirically, our model yields considerable performance improvements over existing embedding models, and also eliminates the need of re-training the embedding models when dealing with newly added relations.
Chapter 14 – * Life Testing

Publisher Summary This chapter deals with problems related to life testing. The exponential rather than the normal distribution play a key role here. A population of items having lifetimes that are assumed to be independent random variables with a common distribution that is specified up to an unknown parameter is considered. The problem of interest will use whatever data are available to estimate this parameter. The concept of the hazard rate function—a useful engineering concept that can be utilized to specify lifetime distributions is introduced. The underlying life distribution is exponential and shows how to obtain estimates of its mean under a variety of sampling plans. A test of the hypothesis that two exponentially distributed populations have a common mean is developed. Two approaches to estimate the parameters of a Weibull distribution are also considered in the chapter.
Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning

Pathway and cell type signatures are patterns present in transcriptome data that are associated with biological processes or phenotypic consequences. These signatures result from specific cell type...
Distributed Multi-Stream Beamforming in MIMO Multi-Relay Interference Networks

In this paper, multi-stream transmission in interference networks aided by multiple amplify-and-forward (AF) relays in the presence of direct links is considered. The objective is to minimize the sum power of transmitters and relays by beamforming optimization under the stream signal-to-interference-plus-noise-ratio (SINR) constraints. For transmit beamforming optimization, the problem is a well-known non-convex quadratically constrained quadratic program (QCQP) that is NP-hard to solve. After semi-definite relaxation (SDR), the problem can be optimally solved via alternating direction method of multipliers (ADMM) algorithm for distributed implementation. Analytical and extensive numerical analyses demonstrate that the proposed ADMM solution converges to the optimal centralized solution. The convergence rate, computational complexity, and message exchange load of the proposed algorithm outperforms the existing solutions. Furthermore, by SINR approximation at the relay side, distributed joint transmit and relay beamforming optimization is also proposed that further improves the total power saving at the cost of increased complexity.
GRIBCG: a software for selection of sgRNAs in the design of balancer chromosomes

Balancer chromosomes are tools used by fruit fly geneticists to prevent meiotic recombination. Recently, CRISPR/Cas9 genome editing has been shown capable of generating inversions similar to the chromosomal rearrangements present in balancer chromosomes. Extending the benefits of balancer chromosomes to other multicellular organisms could significantly accelerate biomedical and plant genetics research. Here, we present GRIBCG (Guide RNA Identifier for Balancer Chromosome Generation), a tool for the rational design of balancer chromosomes. GRIBCG identifies single guide RNAs (sgRNAs) for use with Streptococcus pyogenes Cas9 (SpCas9). These sgRNAs would efficiently cut a chromosome multiple times while minimizing off-target cutting in the rest of the genome. We describe the performance of this tool on six model organisms and compare our results to two routinely used fruit fly balancer chromosomes. GRIBCG is the first of its kind tool for the design of balancer chromosomes using CRISPR/Cas9. GRIBCG can accelerate genetics research by providing a fast, systematic and simple to use framework to induce chromosomal rearrangements.
Transferable Natural Language Interface to Structured Queries Aided by Adversarial Generation

A natural language interface (NLI) to structured query is intriguing due to its wide industrial applications and high economical values. In this work, we tackle the problem of domain adaptation for NLI with limited data on target domain. Two important approaches are considered: (a) effective general-knowledge-learning on source domain semantic parsing, and (b) data augmentation on target domain. We present a Structured Query Inference Network (SQIN) to enhance learning for domain adaptation, by separating schema information from NL and decoding SQL in a more structural-aware manner; we also propose a GAN-based augmentation technique (AugmentGAN) to mitigate the issue of lacking target domain data, by generating NL texts from recombined target-domain SQL queries. We report solid results on Geoquery, Overnight, and WIKISQL to demonstrate state-of-the-art performances for both in-domain and domain-transfer tasks. Our experiment is promising to significantly reduce human labor for transfer learning tasks.
ORACLE: Optimized Radio clAssification through Convolutional neuraL nEtworks

This paper describes the architecture and performance of ORACLE, an approach for detecting a unique radio from a large pool of bit-similar devices (same hardware, protocol, physical address, MAC ID) using only IQ samples at the physical layer. ORACLE trains a convolutional neural network (CNN) that balances computational time and accuracy, showing 99% classification accuracy for a 16-node USRP X310 SDR testbed and an external database of >100 COTS WiFi devices. Our work makes the following contributions: (i) it studies the hardware-centric features within the transmitter chain that causes IQ sample variations; (ii) for an idealized static channel environment, it proposes a CNN architecture requiring only raw IQ samples accessible at the front-end, without channel estimation or prior knowledge of the communication protocol; (iii) for dynamic channels, it demonstrates a principled method of feedback-driven transmitter-side modifications that uses channel estimation at the receiver to increase differentiability for the CNN classifier. The key innovation here is to intentionally introduce controlled imperfections on the transmitter side through software directives, while minimizing the change in bit error rate. Unlike previous work that imposes constant environmental conditions, ORACLE adopts the ‘train once deploy anywhere’ paradigm with near-perfect device classification accuracy.
The exchange rate and export variety: A cross-country analysis with long panel estimators

Abstract This paper studies how the number of categories exported by countries is related to the level and the volatility of the exchange rate. The results show that export variety is positively related to a weaker exchange rate and negatively related to exchange rate volatility. These relationships appear to be stronger for goods with higher technological intensity. Using data for a long panel of countries, the paper investigates these relationships using a methodology that allows for heterogeneous coefficients across countries and discusses two sources of bias that are often overlooked.
Healing the poor: The influence of patient socioeconomic status on physician supply responses.

Abstract A longstanding literature explores how altruism affects the way physicians respond to incentives and provide care. We analyze how patient socioeconomic status mediates these responses. We show theoretically that patient socioeconomic status systematically influences the way physicians respond to reimbursement changes, and we identify the channels through which these effects operate. We use two Medicare reimbursement changes to investigate these insights empirically. We confirm that a given physician facing an increase in reimbursement boosts utilization by more when treating richer patients. We show that average supply price elasticities vary from 0.02 to 0.18 for a given physician, depending on the patient’s socioeconomic status. Finally, we show that the Medicare reforms we study led to overall reimbursement increases that raised healthcare utilization by 10% more for high-income patients compared to their low-income peers.
Understanding the Loss of Maternal Care in Avian Brood Parasites Using Preoptic Area Transcriptome Comparisons in Brood Parasitic and Non-parasitic Blackbirds

Parental care is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, we compared brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region known to play a critical role in parental behavior across vertebrates. Using comparative transcriptomic approaches, we identified gene expression patterns associated with brood parasitism. We evaluated three non-mutually exclusive alternatives for the evolution of brood parasitism: (1) retention of juvenile-like (neotenic) gene expression, (2) reduced expression of maternal care-related genes in the POA, and/or (3) increased expression of genes inhibiting maternal care. We find evidence for neotenic expression patterns in both species of parasitic cowbirds as compared to maternal, non-parasites. In addition, we observed differential expression in a number of genes with previously established roles in mediating maternal care. Together, these results provide the first insight into transcriptomic and genetic mechanisms underlying the loss of maternal behavior in avian brood parasites.
On the Values of Vehicle-to-Grid Electricity Selling in Electric Vehicle Sharing

Problem definition: We study electric vehicle (EV) sharing systems and explore the opportunity for incorporating vehicle-to-grid (V2G) electricity selling in EV sharing. Academic/practical relevanc...
Neural Joint Source-Channel Coding

For reliable transmission across a noisy communication channel, classical results from information theory show that it is asymptotically optimal to separate out the source and channel coding processes. However, this decomposition can fall short in the finite bit-length regime, as it requires non-trivial tuning of hand-crafted codes and assumes infinite computational power for decoding. In this work, we propose to jointly learn the encoding and decoding processes using a new discrete variational autoencoder model. By adding noise into the latent codes to simulate the channel during training, we learn to both compress and error-correct given a fixed bit-length and computational budget. We obtain codes that are not only competitive against several separation schemes, but also learn useful robust representations of the data for downstream tasks such as classification. Finally, inference amortization yields an extremely fast neural decoder, almost an order of magnitude faster compared to standard decoding methods based on iterative belief propagation.
Uterine Epithelial Development and Enhancer of Zeste Homolog 2: It Is Important for More than Just Cancer.

This commentary highlights the article by Fang et al that describes the role of enhancer of zeste homolog 2 in endometrial development.
Context-Aware Resiliency: Unequal Message Protection for Random-Access Memories

A common way to protect data stored in DRAM and related memory systems is through the use of an error-correcting code such as the extended Hamming code. Traditionally, these error-correcting codes provide equal protection guarantees to all messages. In this paper, we focus on unequal message protection (UMP), in which a subset of messages is deemed as special, and is afforded additional error-correction protection while maintaining the same number of redundancy bits as the baseline code. UMP is a powerful approach when the special messages are chosen based on the knowledge of data patterns in context. Our objective is to construct deterministic, algebraic codes with guaranteed UMP properties, derive their cardinality bounds using novel combinatorial techniques, and to demonstrate their efficacy for realistic memory benchmarks. We first introduce a UMP alternative to the single-bit parity-check code, and then we generalize to a broader UMP code family, including a UMP alternative to the extended Hamming code, offering full double-error correction protection to special messages. Our UMP constructions, applied to main memory in high-performance computing applications, could lead to significant system-level benefits such as less frequent checkpoints in supercomputers and decreased risk of catastrophic failure from erroneous special messages.
Addressing the “black box” of focused deterrence: an examination of the mechanisms of change in Chicago’s Project Safe Neighborhoods

Chicago’s Project Safe Neighborhoods focused deterrence program is an effective crime reduction policy. However, similar to other focused deterrence programs, prior evaluations have not empirically established the mechanisms of change believed to underlie the program. The purpose of this paper was to address this gap by examining the influence of offender notification meetings—a key component of the program—on three mechanisms: perceptions of risks associated with future offending, perceptions of police legitimacy, and adherence to community norms. Over a 1-year period, parolees attending the notification meetings were randomly assigned to complete surveys assessing each of the mechanisms immediately before the meeting (control) or immediately after (treatment). Parolees in the treatment condition had higher perceptions of risk and police legitimacy compared to those in the control condition. Additionally, they were more likely to judge police as procedurally fair. The groups did not differ with respect to adherence to community norms. Within both groups, perception of risk was positively associated with motivation to stay out of prison. Police legitimacy was also positively associated with motivation for the treatment group, while community norm adherence was positively associated with motivation for those in the control condition. This study indicates that the offender notification meetings are working as intended with respect to the underlying mechanisms of change embedded in Chicago’s Project Safe Neighborhoods.
CDK phosphorylation of Xenopus laevis M18BP1 promotes its metaphase centromere localization

Abstract Chromosome segregation requires the centromere, the site on chromosomes where kinetochores assemble in mitosis to attach chromosomes to the mitotic spindle. Centromere identity is defined epigenetically by the presence of nucleosomes containing the histone H3 variant CENP‐A. New CENP‐A nucleosome assembly occurs at the centromere every cell cycle during G1, but how CENP‐A nucleosome assembly is spatially and temporally restricted remains poorly understood. Centromere recruitment of factors required for CENP‐A assembly is mediated in part by the three‐protein Mis18 complex (Mis18α, Mis18β, M18BP1). Here, we show that Xenopus M18BP1 localizes to centromeres during metaphase—prior to CENP‐A assembly—by binding to CENP‐C using a highly conserved SANTA domain. We find that Cdk phosphorylation of M18BP1 is necessary for M18BP1 to bind CENP‐C and localize to centromeres in metaphase. Surprisingly, mutations which disrupt the metaphase M18BP1/CENP‐C interaction cause defective nuclear localization of M18BP1 in interphase, resulting in defective CENP‐A nucleosome assembly. We propose that M18BP1 may identify centromeric sites in metaphase for subsequent CENP‐A nucleosome assembly in interphase.
Preparation of 1H‐pyrazole‐5‐carboxamides from dilithiated C(α), N‐phenylhydrazones and lithiated ethyl oxanilates or lithiated ethyl oxamate

Dilithiated C(α), N-phenylhydrazones were prepared in excess lithium diisopropylamide and condensed with either ethyl oxanilate, ethyl 4′-chlorooxanilate, or ethyl oxamate to give intermediates that were quenched and acid cyclized to substituted lH-pyrazole-5-carboxamides.
Synthesis of a new C32H12 bowl-shaped aromatic hydrocarbon

Abstract 7,10-Bis(2-bromophenyl)benzo[k]fluoranthene undergoes pyrolysis to afford a number of polynuclear aromatics including a new bowl-shaped C32H12 hydrocarbon having a carbon framework that can be identified on the buckminsterfullerene surface.
Absolute Asymmetric Synthesis: A Commentary

Absolute asymmetric synthesis, i.e. , the formation of enantiomerically enriched products from achiral precursors without the intervention of chiral chemical reagents or catalysts, is in practice unavoidable on statistical grounds alone. That random chance, combined with suitable amplification mechanisms, might ultimately account for biomolecular homochirality in Nature was recognized more than a century ago. Soai and collaborators have recently developed an asymmetric autocatalysis reaction that is capable of amplifying a tiny enantiomeric excess of far below 1% to yield a nearly enantiopure product. Although there is no easy way to tell the difference between an asymmetric autocatalysis reaction initiated by the tiny enantiomeric excess due to random chance and one initiated by minuscule quantities of unidentified chiral impurities, it is nevertheless all but certain that the Soai reaction is capable of producing optically active compounds by an absolute asymmetric synthesis, starting from nominally achiral reagents free of chiral contaminants and run under achiral conditions, e.g. , without the intervention of chiral physical forces.
Connectivity Problems on Heterogeneous Graphs

Network connectivity problems are abundant in computational biology research, where graphs are used to represent a range of phenomena: from physical interactions between molecules to more abstract relationships such as gene co-expression. One common challenge in studying biological networks is the need to extract meaningful, small subgraphs out of large databases of potential interactions. A useful abstraction for this task turned out to be the Steiner Network problems: given a reference “database” graph, find a parsimonious subgraph that satisfies a given set of connectivity demands. While this formulation proved useful in a number of instances, the next challenge is to account for the fact that the reference graph may not be static. This can happen for instance, when studying protein measurements in single cells or at different time points, whereby different subsets of conditions can have different protein milieu. We introduce the condition Steiner Network problem in which we concomitantly consider a set of distinct biological conditions. Each condition is associated with a set of connectivity demands, as well as a set of edges that are assumed to be present in that condition. The goal of this problem is to find a minimal subgraph that satisfies all the demands through paths that are present in the respective condition. We show that introducing multiple conditions as an additional factor makes this problem much harder to approximate. Specifically, we prove that for C conditions, this new problem is NP-hard to approximate to a factor of $$C - \epsilon $$ , for every $$C \ge 2$$ and $$\epsilon > 0$$ , and that this bound is tight. Moving beyond the worst case, we explore a special set of instances where the reference graph grows monotonically between conditions, and show that this problem admits substantially improved approximation algorithms. We also developed an integer linear programming solver for the general problem and demonstrate its ability to reach optimality with instances from the human protein interaction network. Our results demonstrate that in contrast to most connectivity problems studied in computational biology, accounting for multiplicity of biological conditions adds considerable complexity, which we propose to address with a new solver. Importantly, our results extend to several network connectivity problems that are commonly used in computational biology, such as Prize-Collecting Steiner Tree, and provide insight into the theoretical guarantees for their applications in a multiple condition setting.
Extensive horizontal gene transfer in cheese-associated bacteria

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.
Antiinflammatory 1-phenylpyrazole-4-heteroarylalkanoic acids

A series of antiinflammatory agents, based on the structural integration of fentiazac and lonazolac, was synthesized.
Asymmetric synthesis of optically pure β-isopropylphenylalanine: A new β-branched unusual amino acid

Abstract All four optically pure isomers of a highly conformationally constrained unusual amino acid, β-isopropylphenylalanine, have been asymmetrically synthesized.
Verifying, Challenging, and Discovering New Synapses Among Fully EM-Reconstructed Neurons in the Leech Ganglion.

Neural circuits underpin the production of animal behavior, largely based upon the precise pattern of synaptic connectivity among the neurons involved. For large numbers of neurons, determining such “connectomes” by direct physiological means is difficult, as physiological accessibility is ultimately required to verify and characterize the function of synapses. We collected a volume of images spanning an entire ganglion of the juvenile leech nervous system via serial blockface electron microscopy (SBEM). We validated this approach by reconstructing a well-characterized circuit of motor neurons involved in the swimming behavior of the leech by locating the synapses among them. We confirm that there are multiple synaptic contacts between connected pairs of neurons in the leech, and that these synapses are widely distributed across the region of neuropil in which the neurons’ arbors overlap. We verified the anatomical existence of connections that had been described physiologically among longitudinal muscle motor neurons. We also found that some physiological connections were not present anatomically. We then drew upon the SBEM dataset to design additional physiological experiments. We reconstructed an uncharacterized neuron and one of its presynaptic partners identified from the SBEM dataset. We subsequently interrogated this cell pair via intracellular electrophysiology in an adult ganglion and found that the anatomically-discovered synapse was also functional physiologically. Our findings demonstrate the value of combining a connectomics approach with electrophysiology in the leech nervous system
Functional deficits may be explained by plantarflexor remodeling following Achilles tendon rupture repair: Preliminary findings.

Abstract Achilles tendon ruptures are common injuries that often lead to long-term functional deficits. Despite the prevalence of these injuries, the mechanism responsible for limited function has not yet been established. Therefore, the purpose of this study was to present preliminary findings that support a hypothesis that skeletal muscle remodeling is the driving factor of poor outcomes in some patients. Biomechanical and ultrasonography assessments were performed on a patient that presented with poor functional outcomes 2.5 years after a surgically-repaired acute Achilles tendon rupture. Single-leg heel raise height was decreased by 75% in the affected limb (3.0 cm compared to 11.9 cm) while walking mechanics showed no deficits. Ultrasonography revealed that the affected medial gastrocnemius muscle was less thick and had shorter, more pennate fascicles compared to the unaffected limb. A simple computational model of a maximal-effort plantarflexion contraction was employed to test the implications of changes in muscle architecture on single-leg heel raise function. Subject-specific measurements of fascicle length and pennation were input into the model, which supported these architectural parameters as being drivers of heel raise function. These preliminary findings support the hypothesis that an Achilles tendon rupture elicits changes in skeletal muscle architecture, which reduces the amount of work and power the joint can generate. This multidisciplinary framework of biomechanical, imaging, and computational modeling provides a unique platform for studying the complex interactions between structure and function in patients recovering from Achilles tendon injuries.
Selective N-Arylation of Aminobenzanilides under Mild Conditions Using Triarylbismuthanes

Diarylamines are prepared selectively in good yields under mild conditions by treatment of aminobenzanilides with triarylbismuthanes in the presence of copper(II) acetate and triethylamine. Arylation under these conditions occurs preferentially at the amino- rather than the amide-nitrogen of the benzanilide. Thus, heating an aminobenzanilide in dichloromethane under reflux in the presence of 1 equiv each of a triarylbismuthane, triethylamine, and copper(II) acetate affords the diarylamine in good yields. This method thereby provides a mild and expeditious route to functionalized diarylamines.
Chiral diazaborolidine-mediated enantioselective aldol reactions of phenylthioacetate esters

Abstract Methodology is described for the enantioselective conversion of achiral aldehydes by anti-selective aldol reaction to chiral β-hydroxy-α-phenylthio esters and aldehydes.
Palladium-bisimidazol-2-ylidene complexes as catalysts for general and efficient Suzuki cross-coupling reactions of aryl chlorides with arylboronic acids

A series of bisimidazolium salts 1–6 were synthesized and evaluated as precursors to bisimidazol-2-ylidene ligands in palladium-catalyzed Suzuki cross-coupling reactions with aryl chlorides and arylboronic acids. The bisimidazolium salt 6 was found to be superior over imidazolium and other bisimidazolium salts affording high yields of biaryl products employing a wide variety of substrates.
Bilingual Lexicon Induction with Semi-supervision in Non-Isometric Embedding Spaces

Recent work on bilingual lexicon induction (BLI) has frequently depended either on aligned bilingual lexicons or on distribution matching, often with an assumption about the isometry of the two spaces. We propose a technique to quantitatively estimate this assumption of the isometry between two embedding spaces and empirically show that this assumption weakens as the languages in question become increasingly etymologically distant. We then propose Bilingual Lexicon Induction with Semi-Supervision (BLISS) — a semi-supervised approach that relaxes the isometric assumption while leveraging both limited aligned bilingual lexicons and a larger set of unaligned word embeddings, as well as a novel hubness filtering technique. Our proposed method obtains state of the art results on 15 of 18 language pairs on the MUSE dataset, and does particularly well when the embedding spaces don’t appear to be isometric. In addition, we also show that adding supervision stabilizes the learning procedure, and is effective even with minimal supervision.
Palladium-catalyzed picolinamide-directed halogenation of ortho C–H bonds of benzylamine substrates

Abstract We report a new set of methods for the halogenation of the ortho C–H bonds of N -benzyl picolinamides under palladium-catalyzed conditions. These reactions feature the use of a unique combination of K(Na)XO 3 and K 2 S 2 O 8 reagents, which enables the installation of iodo, bromo, and chloro groups onto the ortho position of N -benzyl picolinamides in a unified fashion. A variety of benzylamine products bearing complex halogen substitution can be quickly prepared from much simpler precursors in good yield and selectivity.
A METAL MEDIATED 6+3 CYCLOADDITION REACTION. COUPLING OF AZIRINES AND CYCLOHEPTATRIENE

Abstract UV irradiation of tricarbonyl(cycloheptatriene)chromium(0) and 2-phenyl-1-azirines through pyrex at 0° C leads to 7-aza-8-phenylbicyclo[4.3.1]deca-2,4,7-trienes via a [6 + 3] cycloaddition of the azirine to the cycloheptatriene ring.