cssi/SciSciGPT-SciSciNet huggingface dataset:
The effect of partisanship and political advertising on close family ties

Research on growing American political polarization and antipathy primarily studies public institutions and political processes, ignoring private effects, including strained family ties. Using anonymized smartphone-location data and precinct-level voting, we show that Thanksgiving dinners attended by residents from opposing-party precincts were 30 to 50 minutes shorter than same-party dinners. This decline from a mean of 257 minutes survives extensive spatial and demographic controls. Reductions in the duration of Thanksgiving dinner in 2016 tripled for travelers from media markets with heavy political advertising—an effect not observed in 2015—implying a relationship to election-related behavior. Effects appear asymmetric: Although fewer Democratic-precinct residents traveled in 2016 than in 2015, Republican-precinct residents shortened their Thanksgiving dinners by more minutes in response to political differences. Nationwide, 34 million hours of cross-partisan Thanksgiving dinner discourse were lost in 2016 owing to partisan effects.
Adjustment to Negative Price Shocks by a Commodity Exporting Economy: Does Exchange Rate Flexibility Resolve a Balance of Payments Crisis?

Abstract Negative commodity price shocks can induce balance of payments crises in resource dependent economies. Governments often react by intervening against currency depreciation as, for example, in the case of Papua New Guinea in response to the commodity price shocks of 2014. We develop an original theoretical model to analyze the balance of payments impact of a commodity price shock under alternative exchange rate regimes: a flexible rate regime and a fixed rate regime with foreign exchange rationing. The balance of payments consequences are shown to depend on the elasticity of exports and imports with respect to the exchange rate. For the Papua New Guinea case, we estimate export elasticities for a variety of commodities (gold, silver, copper, oil, coffee, cocoa, copra, copra oil, palm oil, rubber, tea, logs, and marine products) as well as for imports. The results indicate that the Marshall-Lerner condition is satisfied for this resource-rich economy, implying that exchange rate flexibility may be practicable. We implement our calibrated model to conduct a counter-factual simulation and find that with a flexible exchange rate, foreign reserves would have been 20 percent higher three years after the shock than they were under the actual policy of exchange rate stabilization. In light of this, we argue the merits of greater exchange rate flexibility.
Type III interferon signaling restricts enterovirus 71 infection of goblet cells

Recent worldwide outbreaks of enterovirus 71 (EV71) have caused major epidemics of hand, foot, and mouth disease with severe neurological complications, including acute flaccid paralysis. EV71 is transmitted by the enteral route, but little is known about the mechanisms it uses to cross the human gastrointestinal tract. Using primary human intestinal epithelial monolayers, we show that EV71 infects the epithelium from the apical surface, where it preferentially infects goblet cells. We found that EV71 infection did not alter epithelial barrier function but did reduce the expression of goblet cell–derived mucins, suggesting that it alters goblet cell function. We also show that the intestinal epithelium responds to EV71 infection through the selective induction of type III interferons (IFNs), which restrict EV71 replication. Collectively, these findings define the early events associated with EV71 infections of the human intestinal epithelium and show that host IFN signaling controls replication in an IFN-specific manner.
Combinatorial Bandits for Incentivizing Agents with Dynamic Preferences.

The design of personalized incentives or recommendations to improve user engagement is gaining prominence as digital platform providers continually emerge. We propose a multi-armed bandit framework for matching incentives to users, whose preferences are unknown a priori and evolving dynamically in time, in a resource constrained environment. We design an algorithm that combines ideas from three distinct domains: (i) a greedy matching paradigm, (ii) the upper confidence bound algorithm (UCB) for bandits, and (iii) mixing times from the theory of Markov chains. For this algorithm, we provide theoretical bounds on the regret and demonstrate its performance via both synthetic and realistic (matching supply and demand in a bike-sharing platform) examples.
Cross-Modality Distillation: A Case for Conditional Generative Adversarial Networks

In this paper, we propose to use a Conditional Generative Adversarial Network (CGAN) for distilling (i.e. transferring) knowledge from sensor data and enhancing low-resolution target detection. In unconstrained surveillance settings, sensor measurements are often noisy, degraded, corrupted, and even missing/absent, thereby presenting a significant problem for multi-modal fusion. We therefore specifically tackle the problem of a missing modality in our attempt to propose an algorithm based on CGANs to generate representative information from the missing modalities when given some other available modalities. Despite modality gaps, we show that one can distill knowledge from one set of modalities to another. Moreover, we demonstrate that it achieves better performance than traditional approaches and recent teacher-student models.
CornerNet: Detecting Objects as Paired Keypoints

We propose CornerNet, a new approach to object detection where we detect an object bounding box as a pair of keypoints, the top-left corner and the bottom-right corner, using a single convolution neural network. By detecting objects as paired keypoints, we eliminate the need for designing a set of anchor boxes commonly used in prior single-stage detectors. In addition to our novel formulation, we introduce corner pooling, a new type of pooling layer that helps the network better localize corners. Experiments show that CornerNet achieves a 42.1% AP on MS COCO, outperforming all existing one-stage detectors.
Combined ab initio and empirical model of the thermal conductivity of uranium, uranium-zirconium, and uranium-molybdenum

In this work we developed a practical and general modeling approach for thermal conductivity of metals and metal alloys that integrates ab initio and semiempirical physics-based models to maximize the strengths of both techniques. The approach supports creation of highly accurate, mechanistic, and extensible thermal conductivity modeling of alloys. The model was demonstrated on \ensuremath{\alpha}-U and U-rich U-Zr and U-Mo alloys, which are potential fuels for advanced nuclear reactors. The safe use of U-based fuels requires quantitative understanding of thermal transport characteristics of the fuel. The model incorporated both phonon and electron contributions, displayed good agreement with experimental data over a wide temperature range, and provided insight into the different physical factors that govern the thermal conductivity under different temperatures. This model is general enough to incorporate more complex effects like additional alloying species, defects, transmutation products, and noble gas bubbles to predict the behavior of complex metallic alloys like U-alloy fuel systems under burnup.
Whole Body Protein Synthesis and Turnover in Normal Man and Malnourished Patients With and Without Known Cancer

Plateau enrichment of 15N-ammonia following 24 hour continuous intravenous infusion of 15N-glycine was used to measure total body protein turnover and synthesis in normal volunteers and malnourished patients, with and without cancer. The mean postabsorptive total body protein synthesis rate in three normal controls was 2.5 g protein/kg/day. Protein synthesis and turnover decreased by a mean of 23% following one week of fasting, and returned to baseline levels following one week of refeeding. In three malnourished patients without known tumor, whole body protein synthesis and turnover was similar to controls; following seven to ten days of total parenteral nutrition (TPN) in the nontumor-bearing patients whole body protein synthesis and turnover decreased by 18%. Three of seven malnourished patients with known tumors had marked elevations in total body protein synthesis and turnover; TPN increased protein turnover in five of seven patients with known cancer. This study suggests that some malignant tumors can increase whole body protein synthesis and turnover in both the malnourished and fed state. This increase in protein turnover may represent a direct effect of the tumor, or reflect concomitant illness.
Uncertainty Sampling is Preconditioned Stochastic Gradient Descent on Zero-One Loss

Uncertainty sampling, a popular active learning algorithm, is used to reduce the amount of data required to learn a classifier, but it has been observed in practice to converge to different parameters depending on the initialization and sometimes to even better parameters than standard training on all the data. In this work, we give a theoretical explanation of this phenomenon, showing that uncertainty sampling on a convex (e.g., logistic) loss can be interpreted as performing a preconditioned stochastic gradient step on the population zero-one loss. Experiments on synthetic and real datasets support this connection.
Frontier efficiency, capital structure, and portfolio risk: An empirical analysis of U.S. banks

Firm’ability to effectively allocate capital and manage risks is the essence of their production and performance. This study investigated the relationship between capital structure, portfolio risk ...
TADs pair homologous chromosomes to promote interchromosomal gene regulation

Homologous chromosomes colocalize to regulate gene expression in processes including genomic imprinting and X-inactivation, but the mechanisms driving these interactions are poorly understood. In Drosophila, homologous chromosomes pair throughout development, promoting an interchromosomal gene regulatory mechanism called transvection. Despite over a century of study, the molecular features that facilitate chromosome-wide pairing are unknown. The button model of pairing proposes that specific regions along chromosomes pair with a higher affinity than their surrounding regions, but only a handful of DNA elements that drive homologous pairing between chromosomes have been described. Here, we identify button loci interspersed across the fly genome that have the ability to pair with their homologous sequences. Buttons are characterized by topologically associated domains (TADs), which drive pairing with their endogenous loci from multiple locations in the genome. Fragments of TADs do not pair, suggesting a model in which combinations of elements interspersed along the full length of a TAD are required for pairing. Though DNA-binding insulator proteins are not associated with pairing, buttons are enriched for insulator cofactors, suggesting that these proteins may mediate higher order interactions between homologous TADs. Using a TAD spanning the spineless gene as a paradigm, we find that pairing is necessary but not sufficient for transvection. spineless pairing and transvection are cell-type-specific, suggesting that local buttoning and unbuttoning regulates transvection efficiency between cell types. Together, our data support a model in which specialized TADs button homologous chromosomes together to facilitate cell-type-specific interchromosomal gene regulation.
Deacclimation kinetics as a quantitative phenotype for delineating the dormancy transition and thermal efficiency for budbreak in Vitis species.

Bud dormancy and cold hardiness are critical adaptations for surviving winter cold stress for temperate perennial plant species. In grapevine, acquisition of cold hardiness requires dormancy induction in the early winter and careful maintenance of dormancy state throughout winter. With sufficient exposure to low, non-freezing temperatures (chilling requirement), grapevine buds transition between early (endodormant) and late winter (ecodormant) states. The objective of this study was to uncover the relationship between fulfilment of the chilling requirement and the effects of various temperatures on loss of cold hardiness (deacclimation). The relationship between chilling requirement and temperature as it affects the rate of deacclimation (kdeacc) was examined for dormant cuttings of Vitis vinifera, V. aestivalis, V. amurensis and V. riparia. The effect of temperature on kdeacc was exponential at low and logarithmic at high temperatures. Deacclimation rates also increased in magnitude as chilling accumulated demonstrating a change in deacclimation potential (Ψdeacc), following a logarithmic response. The combination of Ψdeacc and kdeacc indicates genotype-specific thermal efficiency for deacclimation and growth in Vitis that may be overlooked by simple growing degree-day computations. The Ψdeacc and kdeacc parameters are genotype-specific and will greatly increase the refinement of models predicting effects of climate change on phenology. Deacclimation rates represent a quantitative determinant of dormancy transition and budbreak in grapevine and will assist researchers in selecting germplasm for differences in chilling requirement and thermal efficiency.
Concurrent reaction and diffusion in photo-responsive hydrogels

Abstract A hydrogel is a polymer network dispersed in an aqueous solvent. A hydrogel with photo-reactive molecules bonded on the polymer network can change its volume in response to light. The light triggers a chemical reaction of the photo-reactive molecules, for example the photo-isomerization of spirobenzopyran, and alters the interaction parameter between the polymer network and the solvent molecules, which drives the diffusion of the solvent molecules, inducing a volumetric change of the hydrogel. The photo-response kinetics of the hydrogel is governed by concurrent reaction and diffusion. In this paper, we establish a theoretical framework to describe the constitutive behavior of photo-responsive hydrogels based on non-equilibrium thermodynamics. The framework, coupling deformation of hydrogels with diffusion of solvent molecules and reaction of photo-reactive molecules, allows us to predict the spatiotemporal response of photo-responsive hydrogels under light and in the dark. We show the significantly different photo-response kinetics, including reaction-limited, diffusion-limited, and reaction-diffusion coupling processes, with constrained and free swelling of a hydrogel thin film as examples. Particularly, we demonstrate how slow diffusion postpones the onset of post-illumination kinetic response of a photo-responsive hydrogel in the dark. This framework provides us understanding and design guidelines for photo-responsive hydrogels.
Optimal Terrain Construction Problems and Applications in Intensity-Modulated Radiation Therapy

In this paper we study several rectilinear terrain construction problems, which model the leaf sequencing problems in intensity-modulated radiation therapy (IMRT). We present a novel unified approach based on geometric techniques for solving these terrain construction problems. Our ideas include formulating the terrain construction problems as computing shortest paths in a weighted directed graph and building the graph by computing optimal bipartite matchings on various geometric objects subject to specific constraints of each of the problems. Further, since we need to compute optimal bipartite matchings on many sets of geometric objects, we use techniques for computing such matchings in a batch fashion to speed up these matching computations. Our approach leads to the first algorithms for several leaf sequencing problems in IMRT that are practically fast and guarantee an output which is optimal for a large sub-class of solutions. The previously known leaf sequencing algorithms which are currently used in radiation therapy practice are all heuristics that do not guarantee any good quality of the output solutions and may run in a long time. Our implementation results show that our terrain construction algorithms run very fast on real medical data (all under few seconds).
Technologies and Operations for High Voltage Corona Detection with UAVs

Autonomous UAV transmission line inspection served as a reference mission for NASA demonstration of UAV deployment for economic benefit; this paper reports corona sensing advances in development of that reference mission. Unmanned aerial vehicles can serve as a platform for autonomous sensing and location of high voltage coronal discharge. Simple processing of commercial corona camera imagery can automate discharge localization and documentation. Inexpensive ultraviolet point sensors can sense discharge when carried close to the defect with a UAV. Augmented with a parabolic mirror, point sensor range can be increased to a safe inspection standoff distance, at the cost of a narrowed field of view. Results from a test flight of an augmented UV sensor are described. The imaging approach is superior in sensitivity and acquisition time, while the point sensor approach has superior size, weight, cost and durability advantages.
Biased Sampling of Cohorts

Selection biases can distort findings from cohort studies. Self-selection into a study cohort can yield results that are not representative of the target population. Screening a population to detect persons with high blood pressure, for example, can lead to misleading estimates of the effects of antihypertensive medication, in the absence of a control group, because subsequent blood pressure measurements will tend to be lower solely by virtue of the selection process. Studying a selected group of workers who were healthy before hiring can obscure the effects of occupational exposures in comparison to a study of the general population. Incomplete follow-up of cohort members can also lead to biased estimates of cumulative risk and relative risk. Some time-related biases can affect cohort studies. Left truncation arises when one only studies subjects who have survived to a certain time; the analysis must take left truncation into account to avoid bias. Prevalent cohorts consist of subjects who have a prevalent disease at the time of enrollment. Because the age at disease onset is often unknown in prevalent cohorts, estimates of cumulative and relative risks are subject to various biases. Keywords: selection bias; regression to the mean; prevalent cohort; left truncation; healthy worker effect; loss to follow-up
Early-Life Adversity, but Not Suicide, Is Associated With Less Prefrontal Cortex Gray Matter in Adulthood.

BACKGROUND Suicide and major depression are prevalent in individuals reporting early-life adversity. Prefrontal cortex volume is reduced by stress acutely and progressively, and changes in neuron and glia density are reported in depressed suicide decedents. We previously found reduced neurotrophic factor brain-derived neurotrophic factor in suicide decedents and with early-life adversity, and we sought to determine whether cortex thickness or neuron or glia density in the dorsolateral prefrontal and anterior cingulate cortex are associated with early-life adversity or suicide. METHODS A total of 52 brains, constituting 13 quadruplets of nonpsychiatric controls and major depressive disorder suicide decedents with and without early-life adversity, were matched for age, sex, race, and postmortem interval. Brains were collected at autopsy and frozen, and dorsolateral prefrontal cortex and anterior cingulate cortex were later dissected, postfixed, and sectioned. Sections were immunostained for neuron-specific nuclear protein (NeuN) to label neurons and counterstained with thionin to stain glial cell nuclei. Cortex thickness, neuron and glial density, and neuron volume were measured by stereology. RESULTS Cortical thickness was 6% less with early-life adversity in dorsolateral prefrontal cortex and 12% less in anterior cingulate cortex (P < .05), but not in depressed suicide decedents in either region. Neuron density was not different in early-life adversity or with suicide, but glial density was 17% greater with early-life adversity in dorsolateral prefrontal cortex and 15% greater in anterior cingulate cortex, but not in suicides. Neuron volume was not different with early-life adversity or suicide. CONCLUSIONS Reported early-life adversity, but not the stress associated with suicide, is associated with thinner prefrontal cortex and greater glia density in adulthood. Early-life adversity may alter normal neurodevelopment and contribute to suicide risk.
A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.

To detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare “more evolved” to “less evolved” entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer. To be retained during evolution, a protein must not only have a function, but must also avoid toxic dysfunction such as protein aggregation. There is conflict between the two requirements: hydrophobic amino acids form the cores of protein folds, but also promote aggregation. Young genes avoid strongly hydrophobic amino acids, which is presumably the simplest solution to the aggregation problem. Here we show that young genes’ few hydrophobic residues are clustered near one another along the primary sequence, presumably to assist folding. The higher aggregation risk created by the higher hydrophobicity of older genes is counteracted by more subtle effects in the ordering of the amino acids, including a reduction in the clustering of hydrophobic residues until they eventually become more interspersed than if distributed randomly. This interspersion has previously been reported to be a general property of proteins, but here we find that it is restricted to old genes. Quantitatively, the index of dispersion delineates a gradual trend, i.e. , a decrease in the clustering of hydrophobic amino acids over billions of years.
Prescription Writing 1971

To the Editor.— A hundred years ago, as is apparent in Fig 1, the individual prescription ordered a multiplicity of drugs, and was compounded in a neighborhood drug store. Today, a prescription is often fractionated into two to eight separate drug orders. Fractionation into individual drug orders has resulted in an increased burden of paper work, in that the physician must write his name, the date, and the patient's name many times for one therapeutic regimen. The mushrooming lists of useful available drugs have added further to the number of prescriptions, and to the paper work. To meet medicolegal requirements, the physician must next write all the drugs again into his office records. Because of the responsibility, these are duties he cannot easily delegate. A common cause of drug-induced death over many years has been cardiac arrhythmias in patients given digitalis, resulting from low potassium states secondary to diuretic therapy.
Employment Discrimination against Indigenous Peoples in the United States: Evidence from a Field Experiment

We conducted an audit study - a resume correspondence experiment - to measure discrimination in hiring faced by Indigenous Peoples in the United States (Native Americans, Alaska Natives, and Native Hawaiians). We sent employers 13,516 realistic resumes of Indigenous or white applications for common jobs in 11 cities. We signalled Indigenous status in one of four different ways. Interview offer rates do not differ by race, which holds after an extensive battery of robustness checks. We discuss multiple concerns such as the saliency of signals, selection of cities and occupations, and labour market tightness that could affect the results of our audit study and those of others. We also conduct decompositions of wages, unemployment rates, unemployment durations, and employment durations to explore if discrimination might exist in contexts outside our experiment. We conclude by highlighting the essential tests and considerations that are important for future audit studies, regardless of if they find discrimination or not.
The Power of the IUD: Effects of Expanding Access to Contraception Through Title X Clinics

Abstract We estimate the effect of Colorado's Family Planning Initiative, which provided funds to Title X clinics to offer long-acting reversible contraceptives to low-income women. We find substantial effects on childbearing, concentrated among women in zip codes within 7 miles of clinics: the initiative reduced births by approximately 20% for 15–19 year olds. We also estimate effects of extensive media coverage in 2014 and 2015, and find a substantial increase in LARC insertions, extended effects on births among 15–17 year olds living greater than 7 miles from clinics, and significant reductions in births among 20–24 and 25–29 year olds.
Unimodality-Constrained Matrix Factorization for Non-Parametric Source Localization

In this paper, the problem of simultaneous localization of multiple sources given a number of energy samples at different locations is examined. The strategies do not require knowledge of the signal propagation models, nor do they exploit the spatial signatures of the source. A non-parametric source localization framework based on a matrix observation model is developed. It is shown that the source location can be estimated by localizing the peaks of a pair of location signature vectors extracted from the incomplete energy observation matrix. A robust peak localization algorithm is developed and shown to decrease the source localization mean squared error (MSE) faster than $\mathcal {O}(1/M^{1.5})$ with $M$ samples, when there is no measurement noise. To extract the source signature vectors from a matrix with mixed energy from multiple sources, a unimodality-constrained matrix factorization (UMF) problem is formulated, and two rotation techniques are developed to solve the UMF efficiently. Our numerical experiments demonstrate that the proposed scheme achieves similar performance as the kernel regression baseline using only $1/5$ energy measurement samples in detecting a single source, and the performance gain is more significant in the cases of detecting multiple sources.
Coherent TEA laser rangefinder transmitter

A new design for the transmitter/local oscillator portion of a coherent CO2 TEA laser rangefinder is described. The transmitter is a hybrid laser design in which single-longitudinal-mode operation is obtained by operating two transversely excited pulsed gain sections in the same optical resonator. One gain section is operated at atmospheric pressure to provide high gain; the other is operated at low pressure to provide additional gain only to the axial mode nearest line center. Thus the central axial mode sees the highest gain and lases first before the other modes reach threshold.
An Assessment of Student Learning and Instructional Methods in a Golf Skills Physical Education Course at a Public University

Inquiries have shown that students enroll in sport skills courses in college to learn a new activity, have fun, improve skills, and increase physical activity. However, physical education course requirements at 4-year universities have hit an all-time low. This study assessed learning in and student perceptions of a university golf physical education course. Student goals, instructor feedback, and course structure were examined. Twenty-one students enrolled in a university beginner golf class were surveyed about their knowledge and experience in the course. Participants were given a survey related to basic golf knowledge that featured questions that were derived from material in the course textbook and created in collaboration with the course instructor. Participants also completed a survey related to instructional methods. It was developed in collaboration with motor learning experts and assessed perceptions of instruction. Primary student goals included improving swing technique and ball flight. To improve the class, participants suggested a smaller class with more individual instruction, an increased focus on driving, and an allocation of time for playing rather than solely practicing. This assessment provided evidence that a golf skills class significantly increased basic golf knowledge, along with self-ratings of knowledge and interest in the sport. These findings provide evidence for benefits of participating in golf skills courses, suggest that such activity courses can be effective at increasing a person’s disposition toward participation, and elucidate areas for improvement.Subscribe to TPE
Utility of thromboelastography for the diagnosis of von Willebrand disease

Von Willebrand disease (VWD) is an inherited bleeding disorder that is caused by a quantitative or qualitative deficiency of von Willebrand factor (VWF). The National Heart, Lung, and Blood Institute (NHLBI) guidelines for the diagnosis of VWD state that a VWF activity (VWF:RCo) of <30 IU/dL or <50 IU/dL with symptoms of clinical bleeding are consistent with the diagnosis of VWD. However, current gold-standard diagnostic testing takes days to have complete results. Thromboelastography (TEG) is a testing method that provides a graphical trace that represents the viscoelastic changes seen with fibrin polymerization in whole blood, therefore providing information on all phases of the coagulation process. This study describes the TEG characteristics in 160 patients who presented for workup of a bleeding disorder and a subset of those were subsequently diagnosed with VWD. The TEG parameters, K-time (representing the dynamics of clot formation) and the maximal rate of thrombus generation (MRTG), were found to be sensitive in detecting patients with VWF:RCo <30 IU/dL. The TEG, unlike VWF:RCo, can be done in real time, and results are available to the clinician within an hour. This will definitely be beneficial in acute situations such as evaluation of and management of acute bleeding in patients with acquired deficiencies of VWF and may play an important role in the surgical management of patients with VWD.
Facilitating Inclusive Global Trade: Evidence from a Field Experiment

How can we make global trade inclusive for smaller sellers and firms? I present causal evidence that a major e-commerce platform increases on-site exports from small sellers through integrating an ...
Attention is not Explanation.

Attention mechanisms have seen wide adoption in neural NLP models. In addition to improving predictive performance, these are often touted as affording transparency: models equipped with attention provide a distribution over attended-to input units, and this is often presented (at least implicitly) as communicating the relative importance of inputs. However, it is unclear what relationship exists between attention weights and model outputs. In this work we perform extensive experiments across a variety of NLP tasks that aim to assess the degree to which attention weights provide meaningful “explanations” for predictions. We find that they largely do not. For example, learned attention weights are frequently uncorrelated with gradient-based measures of feature importance, and one can identify very different attention distributions that nonetheless yield equivalent predictions. Our findings show that standard attention modules do not provide meaningful explanations and should not be treated as though they do.
Dual Sensing of Physiologic pH and Calcium by EFCAB9 Regulates Sperm Motility

Varying pH of luminal fluid along the female reproductive tract is a physiological cue that modulates sperm motility. CatSper is a sperm-specific, pH-sensitive calcium channel essential for hyperactivated motility and male fertility. Multi-subunit CatSper channel complexes organize linear Ca2+ signaling nanodomains along the sperm tail. Here, we identify EF-hand calcium-binding domain-containing protein 9 (EFCAB9) as a bifunctional, cytoplasmic machine modulating the channel activity and the domain organization of CatSper. Knockout mice studies demonstrate that EFCAB9, in complex with the CatSper subunit, CATSPERζ, is essential for pH-dependent and Ca2+-sensitive activation of the CatSper channel. In the absence of EFCAB9, sperm motility and fertility is compromised, and the linear arrangement of the Ca2+ signaling domains is disrupted. EFCAB9 interacts directly with CATSPERζ in a Ca2+-dependent manner and dissociates at elevated pH. These observations suggest that EFCAB9 is a long-sought, intracellular, pH-dependent Ca2+ sensor that triggers changes in sperm motility.
Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures

Understanding how an organism's phenotypic traits are conditioned by genetic and environmental variation is a central goal of biology. Root systems are one of the most important but poorly understood aspects of plants, largely due to the three-dimensional (3D), dynamic, and multiscale phenotyping challenge they pose. A critical gap in our knowledge is how root systems build in complexity from a single primary root to a network of thousands of roots that collectively compete for ephemeral, heterogeneous soil resources. We used time-lapse 3D imaging and mathematical modeling to assess root system architectures (RSAs) of two maize (Zea mays) inbred genotypes and their hybrid as they grew in complexity from a few to many roots. Genetically driven differences in root branching zone size and lateral branching densities along a single root, combined with differences in peak growth rate and the relative allocation of carbon resources to new versus existing roots, manifest as sharply distinct global RSAs over time. The 3D imaging of mature field-grown root crowns showed that several genetic differences in seedling architectures could persist throughout development and across environments. This approach connects individual and system-wide scales of root growth dynamics, which could eventually be used to predict genetic variation for complex RSAs and their functions.
The Neural Representational Space of Social Memory.

Social functioning involves learning about the social networks in which we live and interact; knowing not just our friends, but also who is friends with our friends. This study utilized an incident...
A highly convergent approach for the synthesis of disaccharide repeating units of peptidoglycan

A highly convergent strategy has been developed for the synthesis of the two possible saccharide-repeating units of peptidoglycan using TBDMS and PMB ethers as orthogonal protecting groups and a two-directional glycosylation strategy for the efficient assembly of the spacer containing disaccharides.
Synthesis of a model for C7-C13 of lankamycin.

A convenient method is reported for construction of the C7−C13 segment of the macrolide antiobiotic lankamycin.
Chemistry of Conversions of [o-[1-Halo-1-(p-tolylsulfonyl)alkyl]benzyl]trimethylsilanes to o-Quinodimethanes and Benzocyclobutenes

Trimethyl[o-[bromo(p-tolylsulfonyl)methyl]benzyl]silane (10) is prepared from o-[(trimethylsilyl)methyl]benzyl p-tolyl sulfone (9), n-BuLi, and bromine. Sulfone 9 eliminates trimethylsilyl bromide upon reaction with TBAF in acetonitrile to give the presumed intermediate, α-sulfonyl-o-quinodimethane 11, which (1) dimerizes to disulfone 12 and (2) is trapped by alkyl fumarates to yield (p-tolylsulfonyl)tetrahydronaphthalenes 17a,b and 18a,b, respectively. Sulfone 9 is converted by n-BuLi and alkyl halides to α-alkyl-α-bromosulfones 19a−f which react with TBAF to give α-sulfonylbenzocyclobutenes 21a−f and vinyl sulfones 23a−f, apparently upon ring closure and upon 1,5-sigmatropic rearrangements of hydrogen in α-sulfonyl-o-quinodimethane intermediates 20a−f and 22a−f. Further, sulfone 9, n-BuLi, and tert-butyl hypochlorite yield α-chlorosulfone 26 and α,α-dichlorosulfone 27. TBAF effects dechlorotrimethylsilation of 27 to chloro(p-tolylsulfonyl)cyclobutene 28 presumably upon formation and cyclization of o-qui...
Synthetic studies toward bioactive cyclic peroxides from the marine sponge Plakortis angulospiculatus.

The total synthesis of two stereoisomers of a bioactive cyclic peroxide isolated from the marine sponge Plakortis angulospiculatus has been achieved in 18 steps with an overall yield of 2.8%. Diels−Alder addition of singlet oxygen to an acyclic triene carboxylic acid precursor was used to construct the 3,6-dihydro-1,2-dioxin ring. By comparing spectral data of the synthesized compounds and the natural material, we tentatively assign the absolute stereochemistry for the natural product as 3S,6R,8S,10R.
The Structure of GeS2-P2S5 Glasses

Structural models of (GeS2)1-x(P2S5)x glasses were developed and used to explain bulk properties of the glasses, including density, glass transition temperature, and refractive index. The models we...
Computational Model of Chimeric Antigen Receptors Explains Site-Specific Phosphorylation Kinetics

Abstract Chimeric antigen receptors (CARs) have recently been approved for the treatment of hematological malignancies, but our lack of understanding of the basic mechanisms that activate these proteins has made it difficult to optimize and control CAR-based therapies. In this study, we use phosphoproteomic mass spectrometry and mechanistic computational modeling to quantify the in vitro kinetics of individual tyrosine phosphorylation on a variety of CARs. We show that each of the 10 tyrosine sites on the CD28-CD3ζ CAR is phosphorylated by lymphocyte-specific protein-tyrosine kinase (LCK) with distinct kinetics. The addition of CD28 at the N-terminal of CD3ζ increases the overall rate of CD3ζ phosphorylation. Our computational model identifies that LCK phosphorylates CD3ζ through a mechanism of competitive inhibition. This model agrees with previously published data in the literature and predicts that phosphatases in this system interact with CD3ζ through a similar mechanism of competitive inhibition. This quantitative modeling framework can be used to better understand CAR signaling and T cell activation.
Monocyclopentadienyltitanium aryloxide complexes: Preparation, characterization, and application in cyclization reactions

A variety of monocyclopentadienyltitanium aryloxide complexes were prepared, characterized by X-ray crystallography, and used to catalyze or mediate cyclization reactions. Structural characterization allowed for the comparison of steric parameters of various 2,6-disubstituted aryloxide ligands. Transformations of dienes and enynesincluding the catalysis of a 1,6-diene cycloisomerization and the intramolecular Pauson−Khand reactionwere investigated. A titanium metallacycle was prepared from a sterically hindered enyne containing a trisubstituted olefin. The Pauson−Khand reaction of trimethylsilyl-substituted enynes was promoted to generate α-silylcyclopentenones.
Estimating drivers of cell state transitions using gene regulatory network models.

Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks. Here we describe MONSTER, MOdeling Network State Transitions from Expression and Regulatory data, a regression-based method for inferring transcription factor drivers of cell state conditions at the gene regulatory network level. As a demonstration, we apply MONSTER to four different studies of chronic obstructive pulmonary disease to identify transcription factors that alter the network structure as the cell state progresses toward the disease-state. We demonstrate that MONSTER can find strong regulatory signals that persist across studies and tissues of the same disease and that are not detectable using conventional analysis methods based on differential expression. An R package implementing MONSTER is available at github.com/QuackenbushLab/MONSTER.
Total synthesis of 2′-deoxycadeguomycin, a new pyrrolo[2,3-d]pyrimidine nucleotide analogue

Abstract This paper describes an efficient synthetic route to a novel pyrrolo[2,3- d ]pyrimidine nucleotide analogue, 2′-deoxycadeguomycin 4a . The key transformation involves the conversion of the differentially protected pyrrolo[2,3- d ]pyrimidin-2,4-dione base portion in 1a into a protected 2-amino-pyrrolo[2,3- d ]pyrimidin-4-one 3a .
An in situ approach for nickel-catalyzed cycloaddition.

A convenient method for preparing pyridines from air-stable, commercially available catalyst precursors is described. The addition of n-BuLi to Ni(acac)2 and an NHC salt (such as IPr·HCl or SIPr·HCl) rapidly generates an active Ni(0)/NHC catalyst for the cycloaddition of diynes and nitriles that affords pyridines without a decrease in observed yields. The in situ method also converts diynes and carbon dioxide to the corresponding pyrones.
Synthesis of terphenyl oligomers as molecular electronic device candidates

Six functionalized bis(phenylene ethynylene)-p,p-terphenyls (BPETs) have been synthesized as potential molecular electronic devices. The molecules containing mono- and dinitro terphenyl cores, were rationally designed based on the electronic properties recently found in oligo(phenylene ethynylene)s (OPEs). From our understanding of the conductance properties in OPEs, improvement of electronic properties may be possible by using BPETs due to a higher rotational barrier between the central aromatic rings of the compounds prepared here. BPETs cores were functionalized with nitro groups and with different metallic adhesion moieties (alligator clips) to provide new compounds for testing in the nanopore and planar testbed structures.
Hydrophobically directed selective reduction of ketones.

Three hydrophobic borohydrides carrying phenyl, pentafluorophenyl, and β-naphthyl groups were used to reduce ketones in water and in methanol. With ketones carrying phenyl, naphthyl, or biphenyl substituents, there was preferential reduction in methanol of competing acetyl groups, either intermolecular or intramolecular, but preferential reduction of the aryl ketones in water. In the most extreme case, there was a 40-fold selectivity reversal. Lithium borohydride showed no such change in selectivity and favored acetyl reduction in both solvents. Salt and cosolvent effects indicate that hydrophobic packing is involved in the reaction of hydrophobic reagents with the aryl ketones. Some special interaction of the pentafluorophenyl group with aryl rings was also detected.
Polynomial-Time, Semantically-Secure Encryption Achieving the Secrecy Capacity

In the wiretap channel setting, one aims to get information-theoretic privacy of communicated data based only on the assumption that the channel from sender to adversary is noisier than the one from sender to receiver. The secrecy capacity is the optimal (highest possible) rate of a secure scheme, and the existence of schemes achieving it has been shown. For thirty years the ultimate and unreached goal has been to achieve this optimal rate with a scheme that is polynomial-time. (This means both encryption and decryption are proven polynomial time algorithms.) This paper finally delivers such a scheme. In fact it does more. Our scheme not only meets the classical notion of security from the wiretap literature, called MIS-R (mutual information security for random messages) but achieves the strictly stronger notion of semantic security, thus delivering more in terms of security without loss of rate. 1 Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. Email: mihir@cs.ucsd.edu. URL: http://www.cs.ucsd.edu/users/mihir. Supported in part by NSF grants CNS-0904380 and CCF-0915675. 2 Department of Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. Email: stessaro@cs.ucsd.edu. URL: http://www.cs.ucsd.edu/users/stessaro. Supported in part by Calit2 and NSF grant CNS-0716790.
PROPOSED BORON NANOTUBES

In the search for boron nanotubes, the geometrical duals of carbon nanotubes, we employ the Euler−Poincare formula for a cylinder, P − C + F = 0. As may be seen in the attached figure, boron nanotubes may be imagined as arising from a correspondence between a boron atom and the center of each of the faces in a carbon nanotube.
Intramolecular cyclization of alkylimidazoles

Abstract 1,2-Dialkylimidazoles can be converted to nucleophilic 2-alkylidene imidazolines upon treatment with (BOC)2O under mild conditions. Incorporation of a β-keto amide carbonyl electrophile in the 2-alkylimidazole side chain results in intramolecular aldol-like cyclization to afford imidazole-functionalized γ-lactams. Positioning of a ketone electrophile in a 1-alkyl side chain results in cyclization at the 2-position to afford fused ring imidazoles through a similar reaction manifold. Efficient transfer of a BOC group from an intermediate N-acyl imidazolium species to a nucleophilic center in the cyclized product appears to be an important feature of these reactions.
N-Alkyl-4-boronopyridinium Salts as Thermally Stable and Reusable Amide Condensation Catalysts

N-Alkyl-4-boronopyridinium salts are highly effective and reusable catalysts for the dehydrative amide condensation reaction between equimolar mixtures of carboxylic acids and amines. N-Alkylboronopyridinium salts are thermally stabilized in the order N-alkyl-2-boronopyridinium salt ≪ N-alkyl-3-boronopyridinium salt < N-alkyl-4-boronopyridinium salt. Homogeneous catalysts, such as 4-borono-N-methylpyridinium iodide, are more effective in the presence of ionic liquid and can be recovered by extraction with ionic liquid. In contrast, heterogeneous catalysts, such as polystyrene-bound 4-boronopyridinium salts, are effective even in the absence of ionic liquid and can be recovered by filtration.
An FeLoBAL Binary Quasar

In an ongoing infrared imaging survey of quasars at the Keck Observatory, we have discovered that the z = 1.285 quasar SDSS J233646.2-010732.6 comprises two point sources with a separation of 167. Resolved spectra show that one component is a standard quasar with a blue continuum and broad emission lines; the other is a broad absorption line (BAL) quasar, specifically, a BAL QSO with prominent absorption from Mg II and metastable Fe II, making it a member of the "FeLoBAL" class. The number of known FeLoBALs has recently grown dramatically from a single example to more than a dozen, including a gravitationally lensed example and the binary member presented here, suggesting that this formerly rare object may be fairly common. Additionally, the presence of this BAL quasar in a relatively small separation binary adds to the growing evidence that the BAL phenomenon is not due to viewing a normal quasar at a specific orientation but rather that it is an evolutionary phase in the life of many, if not all, quasars and is particularly associated with conditions found in interacting systems.