cssi/SciSciGPT-SciSciNet huggingface dataset:
BeSAT: behavioral SAT-based attack on cyclic logic encryption

Cyclic logic encryption is newly proposed in the area of hardware security. It introduces feedback cycles into the circuit to defeat existing logic decryption techniques. To ensure that the circuit is acyclic under the correct key, CycSAT is developed to add the acyclic condition as a CNF formula to the SAT-based attack. However, we found that it is impossible to capture all cycles in any graph with any set of feedback signals as done in the CycSAT algorithm. In this paper, we propose a behavioral SAT-based attack called BeSAT. Be-SAT observes the behavior of the encrypted circuit on top of the structural analysis, so the stateful and oscillatory keys missed by CycSAT can still be blocked. The experimental results show that BeSAT successfully overcomes the drawback of CycSAT.
Bisperoxovanadium Mediates Neuronal Protection through Inhibition of PTEN and Activation of PI3K/AKT-mTOR Signaling after Traumatic Spinal Injuries

Abstract Although mechanisms involved in progression of cell death in spinal cord injury (SCI) have been studied extensively, few are clear targets for translation to clinical application. One of t...
A Simple Bound on the BER of the Map Decoder for Massive MIMO Systems

The deployment of massive MIMO systems has revived much of the interest in the study of the large-system performance of multiuser detection systems. In this paper, we prove a non-trivial upper bound on the bit-error rate (BER) of the MAP detector for BPSK signal transmission and equal-power condition. In particular, our bound is approximately tight at high-SNR. The proof is simple and relies on Gordon’s comparison inequality. Interestingly, we show that under the assumption that Gordon’s inequality is tight, the resulting BER prediction matches that of the replica method under the replica symmetry (RS) ansatz. Also, we prove that, when the ratio of receive to transmit antennas exceeds 0.9251, the replica prediction matches the matched filter lower bound (MFB) at high-SNR. We corroborate our results by numerical evidence.
Design a Successful Program for Voluntary Carbon Footprint Reduction

A voluntary eco-labeling program acts as “soft” policy instruments to regulate or promote climate change mitigation and carbon footprint reduction. The proper design of an eco-labeling program will likely attract more environmentally cautious companies to participate; it will also demonstrate the authoritativeness and trustfulness to consumers when choosing an eco-labeled product. Ultimately, the environmental consumer behavior will lead to higher market penetration of products with eco-labels. The successful design of an eco-label will: (1) set an appropriate eco-standard accepted by the industry and the participants; (2) offer various degrees of strategic benefits from the participation; (3) ultimately increase the market share of eco-labeling products; and (4) benchmark “green” (described as more environmentally friendly) quality improvement to the environment, reduce carbon footprint, and benefit the society and human beings.
BORDERLINE ACETABULAR DYSPLASIA: INDEPENDENT PREDICTORS OF HIP INSTABILITY VERSUS IMPINGEMENT:

Background:Hips with borderline acetabular dysplasia (lateral center-edge angle, LCEA, between 20° and 25°) are challenging in terms of diagnostic and treatment decision-making. It is accepted that...
Reliability-Based Design of Thermal Protection Systems with Support Vector Machines

The primary objective of this work is to develop a computationally efficient and accurate approach to a reliability analysis of thermal protection systems using support vector machines. An adaptive...
Titer estimation for quality control (TEQC) method: A practical approach for optimal production of protein complexes using the baculovirus expression vector system.

The baculovirus expression vector system (BEVS) is becoming the method of choice for expression of many eukaryotic proteins and protein complexes for biochemical, structural and pharmaceutical studies. Significant technological advancement has made generation of recombinant baculoviruses easy, efficient and user-friendly. However, there is a tremendous variability in the amount of proteins made using the BEVS, including different batches of virus made to express the same proteins. Yet, what influences the overall production of proteins or protein complexes remains largely unclear. Many downstream applications, particularly protein structure determination, require purification of large quantities of proteins in a repetitive manner, calling for a reliable experimental set-up to obtain proteins or protein complexes of interest consistently. During our investigation of optimizing the expression of the Mediator Head module, we discovered that the ‘initial infectivity’ was an excellent indicator of overall production of protein complexes. Further, we show that this initial infectivity can be mathematically described as a function of multiplicity of infection (MOI), correlating recombinant protein yield and virus titer. All these findings led us to develop the Titer Estimation for Quality Control (TEQC) method, which enables researchers to estimate initial infectivity, titer/MOI values in a simple and affordable way, and to use these values to quantitatively optimize protein expressions utilizing BEVS in a highly reproducible fashion.
Fishing rights and colonial government: institutional development in the Bengal Presidency

We examine the evolution of fishing rights in colonial Bengal through a series of cases heard at the Calcutta High Court in the 1880s and culminating in the passage of legislation in 1889. We posit an implicit relational contract between the colonizing British and the landowning class in colonial Bengal as a way to understand the concurrent evolution of fishing rights and institutions of governance in the region. The system of incentives created by this contract determined the development of fishing rights at a crucial moment in the history of colonial Bengal and, more broadly, became a primary mechanism of institutional change in the region. The analysis also shows the Calcutta High Court to have acted, albeit in vain, as a truly independent judiciary.
Thrombotic Microangiopathy in Cancer.

Thrombotic microangiopathy (TMA) is a rare but often devastating complication of cancer and cancer treatment. The syndrome is defined by thrombocytopenia (i.e., a platelet count of 30% decrease from baseline), microangiopathic hemolytic anemia, and some evidence of organ damage. Among the nine recognized groups of disorders causing TMA, the focus of this article will be on cancer and cancer treatment-related causes of TMA. This review will discuss the pathophysiology of TMA in cancer, chemotherapy-associated TMA, transplant-associated TMA, and newer therapeutic modalities.
Light-induced stress as a primary evolutionary driver of eye origins

Eyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light. While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here, we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including ultraviolet damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.
Menstruation Management in United States Schools and Implications for Attendance, Academic Performance, and Health

Six hundred and ninety-three young women, 18–25 years old, all of whom had attended United States high schools, were surveyed to ask about their need for and the availability of menstrual hygiene p...
Network Effects in Default Clustering for Large Systems

ABSTRACTWe consider a large collection of dynamically interacting components defined on a weighted-directed graph determining the impact of the default of one component to another one. We prove a l...
Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments

Abstract Actin filaments continually assemble and disassemble within a cell. Assembled filaments “age” as a bound nucleotide ATP within each actin subunit quickly hydrolyzes followed by a slower release of the phosphate Pi, leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate-release reactions while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the ultra-coarse-graining model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The model reproduces mechanical properties of the filament and allows us to study whether conformational fluctuations in actin subunits produce cooperative filament aging. We find that the nucleotide states of neighboring subunits modulate the reaction kinetics, implying cooperativity in ATP hydrolysis and Pi release. We further systematically coarse grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and Pi release significantly affects the filament growth dynamics only near the critical G-actin concentration, whereas far from it, both cooperative and random mechanisms show similar growth dynamics. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights, to our knowledge, into the cooperative nature of ATP hydrolysis and Pi release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.
Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations

Integrative networks combine multiple layers of biological data into a model of how genes work together to carry out cellular processes. Such networks become more valuable as they become more context-specific, for example, by capturing how genes work together in a certain tissue or cell type. We discuss the applications of these networks to the study of human disease. Once constructed, these networks provide the means to identify broad biological patterns underlying genes associated with complex traits and diseases. We cover the different types of integrative networks that currently exist, and how such networks that encompass multiple biological layers are constructed. We highlight how specificity can be incorporated into the reconstruction of different types of biomolecular interactions between genes, using tissue specificity as a motivating example. We discuss examples of cases where networks have been applied to study human diseases and opportunities for new applications. Integrative networks with specificity to tissue or other biological features provide new capabilities to researchers engaged in the study of human disease. We expect improved data and algorithms to continue and improve such networks, allowing them to provide more detailed and mechanistic predictions into the context-specific genetic etiology of common diseases.
Oxidative dimerization: Pd(II) catalysis in the presence of oxygen using aqueous media

Reported herein is a method for the formation of symmetric biaryls and dienes via oxidative dimerization of aryl and alkenyl boronic acids. These conditions utilized Pd(II) catalysts under an oxygen atmosphere with water as the solvent. The use of phase transfer catalysts promoted efficient and mild syntheses of a wide range of materials.
Expressing Visual Relationships via Language.

Describing images with text is a fundamental problem in vision-language research. Current studies in this domain mostly focus on single image captioning. However, in various real applications (e.g., image editing, difference interpretation, and retrieval), generating relational captions for two images, can also be very useful. This important problem has not been explored mostly due to lack of datasets and effective models. To push forward the research in this direction, we first introduce a new language-guided image editing dataset that contains a large number of real image pairs with corresponding editing instructions. We then propose a new relational speaker model based on an encoder-decoder architecture with static relational attention and sequential multi-head attention. We also extend the model with dynamic relational attention, which calculates visual alignment while decoding. Our models are evaluated on our newly collected and two public datasets consisting of image pairs annotated with relationship sentences. Experimental results, based on both automatic and human evaluation, demonstrate that our model outperforms all baselines and existing methods on all the datasets.
A new asymmetric synthesis of trans-hydroisoquinolones.

A convenient enantioselective synthesis of trans-hydroisoquinolones is described. This synthesis capitalizes on the ready availability of enantioenriched 2-substituted cyclohexenols by exploiting t...
The effects of alcohol and cannabinoid exposure during the brain growth spurt on behavioral development in rats.

Cannabis is the most commonly used illicit drug among pregnant women. Moreover, over half of pregnant women who are consuming cannabis are also consuming alcohol; however, the consequences of combined prenatal alcohol and cannabis exposure on fetal development are not well understood. The current study examined behavioral development following exposure to ethanol (EtOH) and/or CP-55,940 (CP), a cannabinoid receptor agonist. From postnatal days (PD) 4-9, a period of brain development equivalent to the third trimester, Sprague-Dawley rats received EtOH (5.25 g/kg/day) or sham intubation, as well as CP (0.4 mg/kg/day) or vehicle. All subjects were tested on open field activity (PD 18-21), elevated plus maze (PD 25), and spatial learning (PD 40-46) tasks. Both EtOH and CP increased locomotor activity in the open field, and the combination produced more severe overactivity than either exposure alone. Similarly, increases in thigmotaxis in the Morris water maze were caused by either EtOH or CP alone, and were more severe with combined exposure, although only EtOH impaired spatial learning. Finally, developmental CP significantly increased time spent in the open arms on the elevated plus maze. Overall, these data indicate that EtOH and CP produce some independent effects on behavior, and that the combination produces more severe overactivity in the open field. Importantly, these data suggest that prenatal cannabis disrupts development and combined prenatal exposure to alcohol and cannabis may be particularly damaging to the developing fetus, which has implications for the lives of affected individuals and families and also for establishing public health policy.
Total synthesis of peroxyacarnoates A and D: Metal-mediated couplings as a convergent approach to polyunsaturated peroxides

The first syntheses of peroxyacarnoates A and D, members of a family of enyne-containing alkoxydioxanes, have been achieved on the basis of chemoselective ozonolysis within a polyunsaturated framework and Pd-mediated cross-couplings of a functionalized 1,2-dioxane.
Extrinsic Noise Suppression in Micro RNA Mediated Incoherent Feedforward Loops

MicroRNA mediated incoherent feed forward loops (IFFLs) are recurrent network motifs in mammalian cells and have been a topic of study for their noise rejection and buffering properties. Previous work showed that IFFLs can adapt to varying promoter activity and are less prone to noise than similar circuits without the feed forward loop. Furthermore, it has been shown that microRNAs are better at rejecting extrinsic noise than intrinsic noise. This work studies the biological mechanisms that lead to extrinsic noise rejection for microRNA mediated feed forward network motifs. Specifically, we compare the effects of microRNA-induced mRNA degradation and translational inhibition on extrinsic noise rejection, and identify the parameter regimes where noise is most efficiently rejected. In the case of static extrinsic noise, we find that translational inhibition can expand the regime of extrinsic noise rejection. We then analyze rejection of dynamic extrinsic noise in the case of a single-gene feed forward loop (sgFFL), a special case of the IFFL motif where the microRNA and target mRNA are co-expressed. For this special case, we demonstrate that depending on the time-scale of fluctuations in the extrinsic variable compared to the mRN $A$ and microRNA decay rates, the feed forward loop can both buffer or amplify fluctuations in gene product copy numbers.
Phenol derivatized hexahydropyrimidines prepared from Mannich condensations

Abstract Six new phenol derivatized hexahydropyrimidines (1,3-bis-(2-hydroxy-3,5-di(X)benzyl) hexahydropyrimidine and 5,5′-dimethyl-1,3-bis-(2-hydroxy-3,5-di(X)benzyl) hexahydropyrimidine where X = Me, t -Bu, and Cl) were synthesized in one-pot in 33–79% yield using Mannich condensations.
Effective Asymmetric Epoxidation of Styrenes by Chiral Dioxirane

High enantioselectivity (80−92% enantiomeric excess (ee)) has been obtained for the epoxidation of various styrenes using an easily prepared ketone (4) catalyst.
A concise synthetic entry to substituted 2-aminothieno[2,3-d]pyrimidines via a Gewald precursor

Abstract A concise synthesis of substituted 2-aminothieno[2,3- d ]pyrimidines is described based on pyrimidine annulation of tetrasubstituted thiophene precursors assembled by a Gewald thiophene ring synthesis.
Total Synthesis of HUN-7293

The first total synthesis of the cyclic heptadepsipeptide HUN-7293 (1), a potent inhibitor of cell adhesion molecule expression exhibiting anti-inflammatory properties, is detailed. The most effect...
Computational tool to study perturbations in muscle regulation and its application to heart disease

Striated muscle contraction occurs when myosin thick filaments bind to thin filaments in the sarcomere and generate pulling forces. This process is regulated by calcium, and it can be perturbed by pathological conditions (e.g., myopathies), physiological adaptations (e.g., β-adrenergic stimulation), and pharmacological interventions. Therefore, it is important to have a methodology to robustly determine the impact of these perturbations and statistically evaluate their effects. Here, we present an approach to measure the equilibrium constants that govern muscle activation, estimate uncertainty in these parameters, and statistically test the effects of perturbations. We provide a MATLAB-based computational tool for these analyses, along with easy-to-follow tutorials that make this approach accessible. The hypothesis testing and error estimation approaches described here are broadly applicable, and the provided tools work with other types of data, including cellular measurements. To demonstrate the utility of the approach, we apply it to elucidate the biophysical mechanism of a mutation that causes familial hypertrophic cardiomyopathy. This approach is generally useful for studying muscle diseases and therapeutic interventions that target muscle contraction.
Neurons in Primate Entorhinal Cortex Represent Gaze Position in Multiple Spatial Reference Frames

Primates predominantly rely on vision to gather information from the environment, and neurons representing visual space and gaze position are found in many brain areas. Within the medial temporal lobe, a brain region critical for memory, neurons in the entorhinal cortex of macaque monkeys exhibit spatial selectivity for gaze position. Specifically, the firing rate of single neurons reflects fixation location within a visual image (Killian et al., 2012). In the rodents, entorhinal cells such as grid cells, border cells, and head direction cells show spatial representations aligned to visual environmental features instead of the body (Hafting et al., 2005, Solstad et al. 2008, Sargolini et al., 2006, Diehl et al., 2017). However, it is not known whether similar allocentric representations exist in primate entorhinal cortex. Here, we recorded neural activity in the entorhinal cortex in two male rhesus monkeys during a naturalistic, free-viewing task. Our data reveal that a majority of entorhinal neurons represent gaze position, and that simultaneously recorded neurons represent gaze position relative to distinct spatial reference frames, with some neurons aligned to the visual image and others aligned to the monkey9s head position. Our results also show that entorhinal neural activity can be used to predict gaze position with a high degree of accuracy. These findings demonstrate that visuospatial representation is a fundamental property of entorhinal neurons in primates, and suggest that entorhinal cortex may support relational memory and motor planning by coding attentional locus in distinct, behaviorally relevant frames of reference. SIGNIFICANCE STATEMENT The entorhinal cortex, a brain area important for memory, shows striking spatial activity in rodents through grid cells, border cells, head direction cells, and nongrid spatial cells. The majority of entorhinal neurons signal the location of a rodent relative to visual environmental cues, representing the location of the animal relative to space in the world instead of the body. Recently, our laboratory found that entorhinal neurons can signal location of gaze while a monkey visually explores images. Here, we report that spatial entorhinal neurons are widespread in the monkey, and these neurons are capable of showing a world-based spatial reference frame locked to the bounds of explored images. These results help connect the extensive findings in rodents to the primate.
NUCLEOPHILIC AROMATIC SUBSTITUTION WITH THE ANION OF 3,5-DISUBSTITUTED ISOXAZOLE-4-CARBOXYLIC ACIDS

The preparation of the anion of a series of protected 3,5-disubstituted 4-isoxazolecarboxylic acids and the resulting addition of the anion to 9-chloroacridine is described. The addition-elimination reaction proceeds to give the expected acridinylmethylisoxazoles and has been justified based on calculated molecular mechanics energies and solvent effects.
Coupling of autonomic and central events during sleep benefits declarative memory consolidation.

Abstract While anatomical pathways between forebrain cognitive and brainstem autonomic nervous centers are well-defined, autonomic–central interactions during sleep and their contribution to waking performance are not understood. Here, we analyzed simultaneous central activity via electroencephalography (EEG) and autonomic heart beat-to-beat intervals (RR intervals) from electrocardiography (ECG) during wake and daytime sleep. We identified bursts of ECG activity that lasted 4–5 s and predominated in non-rapid-eye-movement sleep (NREM). Using event-based analysis of NREM sleep, we found an increase in delta (0.5–4 Hz) and sigma (12–15 Hz) power and an elevated density of slow oscillations (0.5–1 Hz) about 5 s prior to peak of the heart rate burst, as well as a surge in vagal activity, assessed by high-frequency (HF) component of RR intervals. Using regression framework, we show that these Autonomic/Central Events (ACE) positively predicted post-nap improvement in a declarative memory task after controlling for the effects of spindles and slow oscillations from sleep periods without ACE. No such relation was found between memory performance and a control nap. Additionally, NREM ACE negatively correlated with REM sleep and learning in a non-declarative memory task. These results provide the first evidence that coordinated autonomic and central events play a significant role in declarative memory consolidation.
Elevated Conformational Rigidity in Dipeptides Incorporating Piperazic Acid Derivatives

N-Acyl derivatives of piperazic acids display an unusual degree of conformational rigidity. As a consequence, α-N-coupling of a piperazic acid of given configuration (d or l) with an α-aminoacyl unit of opposite configuration (l or d) produces a “heterochiral” dipeptide that exists in a conformation conducive to the formation of a peptide turn. Piperazic acids and related compounds may thus be regarded as conformationally rigid analogues of proline, and because they are readily available in either antipodal form by synthesis, they should become of great interest in the study of peptide turns.
EDGE STATES IN 4d AND THEIR 3d GROUPS AND FIELDS

It is known that the Lagrangian for the edge states of a Chern-Simons theory describes a coadjoint orbit of a Kac-Moody (KM) group with its associated Kirillov symplectic form and group representation. It can also be obtained from a chiral sector of a non-chiral field theory. We study the edge states of the Abelian BF system in four dimensions (4D) and show the following results in almost exact analogy: 1) The Lagrangian for these states is associated with a certain 2D generalization of the KM group. It describes a coadjoint orbit of this group as a Kirillov symplectic manifold and also the corresponding group representation. 2) It can be obtained from with a "self-dual" or "anti-self-dual" sector of a Lagrangian describing a massless scalar and a Maxwell field (the phrase "self-dual" here being used essentially in its sense in monopole theory). There are similar results for the non-Abelian BF system as well. These shared features of edge states in 3D and 4D suggest that the edge Lagrangians for BF systems are certain natural generalizations of field theory Lagrangians related to KM groups.
On the choice of instruments in mixed frequency specification tests

Time averaging has been the traditional approach to handle mixed sampling frequencies. However, it ignores information possibly embedded in high frequency. Mixed data sampling (MIDAS) regression mo...
A ring-closing metathesis strategy to phosphonosugars.

Syntheses of cyclic phosphonate (phostone) analogues of carbohydrates containing a phosphorus atom at the anomeric position are described. The ring-closing metathesis reaction of mixed allylic phenyl esters of allylphosphonic acid 2 and 22 generates the six-membered allylic phosphonates 3 and 23 in excellent yields. Introduction of the polyhydroxy functionality in these cyclic phosphonates provides facile entry into an array of phostone sugar analogues.
Synthesis, structure, and acidic properties of MCM-41 functionalized with phosphate and titanium phosphate groups.

Mesoporous molecular sieves Si-MCM-41 (purely siliceous) and Ti-MCM-41 (partly covered with a surface layer of TiO2) were functionalized with phosphate groups by treatment with POCl3 (denoted -MCM-41(P) and Ti-MCM-41(P), respectively). With the use of TEM, X-ray diffraction, and N2 adsorption, it was shown that the initial hexagonal structure, the high specific surface area, and porosity are retained in the functionalized materials but are not as good as in the starting materials. 1H MAS NMR and 31P MAS NMR revealed that the surface of Si-MCM-41(P) consists of silicon phosphate and pyrophosphate species. That of Ti-MCM-41(P) additionally contains titanium dihydro-, hydro-, and pyrophosphate species, the latter being predominant. TPD of adsorbed ammonia for Si-MCM-41(P) and Ti-MCM-41(P) showed that functionalization leads to the creation of moderate and strong acid sites. A combination of mesoporous structure with acidic properties makes the MCM-41 functionalized with phosphate groups promising for use as ...
Synthesis of oxepanes and trans-fused bisoxepanes via biomimetic, endo-regioselective tandem oxacyclizations of polyepoxides.

This communication describes the first examples of tandem endo-regioselective and stereospecific oxacyclizations of 1,5-diepoxides to oxepane products and a similar tandem oxacyclization of 1,5,9-triepoxides to fused bisoxepane cyclic carbonates. A mechanism for these biomimetic oxacyclizations is proposed in which the epoxides act as both electrophilic and nucleophilic reaction partners.
Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure.

The most internal part of the human ear, the inner ear, is essential for us to hear and have a sense of balance. It is formed by a complex series of connected cavities filled by a liquid. When sound waves and changes in the position of the body make this liquid move, specialized ‘hair’ cells can detect these subtle movements; neurons then relay this information to the brain where it is decoded and interpreted. For the inner ear to work properly, the body needs to finely regulate the pressure created by the liquid inside the cavities. For example, people with unstable pressure in their ears can experience deafness or problems with balance. A structure known as the endolymphatic sac, which is a balloon-like chamber connected to the rest of the inner ear by a thin tube, helps with this regulation. However, scientists are still unsure about how exactly the sac performs its role. One problem is that the inner ear is difficult to study because it is encased in one of the densest bones in the body. Many other animals also have inner ears, from fish to birds and mammals. Here, Swinburne et al. examine the inner ear of zebrafish embryos because, in this fish, the ear starts working before the bones around it form; the structure is therefore accessible for injections and microscopy. Experiments show that when the pressure in the inner ear rises, the endolymphatic sac slowly fills up with the ear liquid, and then it rapidly deflates. Fish with mutations that stop the sac from deflating have overinflated sacs, which is a symptom also found in certain patients with hearing and balance disorders. Looking into the details of these inflation-deflation cycles, Swinburne et al. found that the cells that form the sac have gaps between them, unlike a normal sheet of cells. A flap covers these gaps to keep the liquid in, but under pressure, the flap opens and the liquid can escape. These results show that the endolymphatic sac works as a pressure relief valve for the inner ear. Ultimately, understanding how pressure is regulated in the ear could help patients with inner ear disorders. It could also serve as a template to investigate how eyes, kidneys and the brain, which all have liquid-filled cavities, control their internal pressure.
Substructure in the lens HE 0435−1223

We investigate the properties of dark matter substructure in the gravitational lens HE 0435-1223 (z_l=0.455) via its effects on the positions and flux ratios of the quadruply-imaged background quasar (z_s=1.689). We start with a smooth mass model, add individual, truncated isothermal clumps near the lensed images, and use the Bayesian evidence to compare the quality of different models. Compared with smooth models, models with at least one clump near image A are strongly favored. The mass of this clump within its Einstein radius is log(Mein/Msun) = 7.65 +0.87/-0.84. The Bayesian evidence provides weaker support for a second clump near image B, with log(Mein/Msun) = 6.55 +1.01/-1.51. We also examine models with a full population of substructure, and find the mass fraction in substructure at the Einstein radius to be f_sub > 0.00077, assuming the total clump masses follow a mass function dN/dM proportional to M^(-1.9) over the range M = 10^7-10^10 Msun. Few-clump and population models produce similar Bayesian evidence values, so neither type of model is objectively favored.
Selective Pneumocystis carinii dihydrofolate reductase inhibitors: design, synthesis, and biological evaluation of new 2,4-diamino-5-substituted-furo[2,3-d]pyrimidines.

Nonclassical antifolates, 2,4-diamino-5-substituted-furo[2,3-d]pyrimidines 3−12 with bridge region variations of C8−S9, C8−N9, and C8−O9 and 1-naphthyl, 2-naphthyl, 2-phenoxyphenyl, 4-phenoxyphenyl, and 2-biphenyl side chains were synthesized as phenyl ring appended analogues of previously reported 2,4-diamino-5-(anilinomethyl)furo[2,3-d]pyrimidines. The phenyl ring appended analogues were designed to specifically interact with Phe69 of dihydrofolate reductase (DHFR) from Pneumocystis carinii (pc) to afford selective inhibitors of pcDHFR. Additional substituted phenyl side chains which include 2,5-dichloro, 3,4-dichloro, 3,4,5-trichloro, 3-methoxy, and 2,5-dimethoxy analogues 13−17 were also synthesized. The compounds were prepared by nucleophilic displacement of 2,4-diamino-5-(chloromethyl)furo[2,3-d]pyrimidine(2) with the appropriate thiol, amine, or naphthol. Compound 2 was obtained from 2,4-diamino-6-hydroxypyrimidine and 1,3-dichloroacetone. The compounds were evaluated as inhibitors against DHFR fro...
Hydrogen-bond directed palladium-catalyzed allylic substitution of cyclic substrates

The regioselectivity of the Pd-catalyzed allylic substitution of cyclic substrates possessing an adjacent amide functional group was investigated. With imide-like nucleophiles, six-membered ring substrates were found to proceed with a high level of regiodirection whereas hydrogen-bond directed addition was not a significant factor in the five-membered ring substrates.
Regioselective ring-closing metathesis on terpenoid acrylates and acrylamides

Abstract A series of acrylate esters was prepared by treatment of representative terpenoid aldehydes with allyl or vinyl magnesium bromide followed by reaction with acryloyl chloride. In all cases, ring-closing metathesis (RCM) resulted in regioselective formation of unsaturated lactones through metathesis of the acrylate and terminal olefins. After condensation of farnesal with a primary amine, a parallel series of reactions led to formation of the corresponding lactam.
Novel Multinuclear Catalysts for the Electroreduction of Dioxygen Directly to Water

The electroreduction of O_2 to H_2O in aqueous acid at potentials close to the thermodynamically permitted value remains a daunting challenge for designers of superior fuel cells and batteries that utilize dioxygen as the reducible reactant. The four-electron reduction of O_2, which involves the rupture of the O-O bond and the formation of four O-H bonds, requires the use of catalysts to obtain useful rates at cathode potentials of interest in practical applications. The standard potential of the O_2/H_2O couple in solutions containing 1 M H^+ and saturated with O_2 at 1 atm is ca. 1.0 V (vs the saturated calomel electrode, SCE), but the highest cathode potentials achievable with currently available catalysts are closer to 0.55 V. (Molecules, functional groups, or metallic deposits that accelerate the rates of electrode reactions when they are confined to the surfaces of electrodes are often called electrocatalysts, a terminology that will be adopted in this Account.) Finely divided platinum supported on high area carbon is the electrocatalyst employed most frequently to achieve the electroreduction of O_2 to H_2O in presently available fuel cells. However, this type of electrocatalyst suffers from the disadvantages of high cost and gradual loss in catalytic activity as the surface area of the active platinum particles decreases because of sintering, dissolution, physical dislodgment, and/or adsorption of impurities. Searches for superior electrocatalysts for the reduction of O2 have often focused on cobalt porphyrins which are well-known to exhibit electrocatalytic activity toward the reduction of O_2, although H_2O_2 instead of H_2O is the usual product. However, it was discovered in recent years that a variety of molecular catalysts consisting of dimeric cofacial cobalt porphyrins adsorbed on the surface of graphite electrodes are able to catalyze the direct four-electron electroreduction of O_2 without passing through H_2O_2 as an intermediate. Both dimeric and monomeric iridium por phyrins have also been found to accomplish the electroreduction of O_2 to H_2O at unusually positive potentials. The mechanisms through which dimeric electrocatalysts are believed to operate involve the simultaneous interaction of both metal centers with the two oxygen atoms of the O_2 molecule as the O-O bond is severed. The ideas and strategies that underlay the development of these electrocatalysts have been described.
The prevalence of repeating fast radio bursts

Fast radio bursts are extragalactic, sub-millisecond radio impulses of unknown origin1,2. Their dispersion measures, which quantify the observed frequency-dependent dispersive delays in terms of free-electron column densities, greatly exceed predictions from models3 of the Milky Way interstellar medium. The excess dispersions are probably accrued as fast radio bursts propagate through their host galaxies, gaseous galactic halos and the intergalactic medium4,5. Despite extensive follow-up observations of the published sample of 72 burst sources6, only two have been observed to repeat7,8, and it is unknown whether the remainder are truly one-off events. Here I show that the volumetric occurrence rate of the fast radio bursts that have not been observed to repeat thus far probably exceeds the rates of candidate cataclysmic progenitor events, and also probably exceeds the birth rates of candidate compact-object sources. This analysis is based on the high detection rate of bursts with low dispersion measures by the Canadian Hydrogen Intensity Mapping Experiment (CHIME)9. Within the existing suite of astrophysical scenarios for fast radio burst progenitors, I conclude that most observed cases must originate from sources that emit several bursts over their lifetimes. Of the 72 known fast radio burst (FRB) sources only two have been observed to emit repeat bursts. By calculating the volumetric occurrence rate of non-repeating FRBs, Vikram Ravi shows that there are not enough candidate cataclysmic progenitor events for most FRBs to be one-off phenomena, and therefore most FRBs must repeat.
Building large updatable colored de Bruijn graphs via merging.

MOTIVATION There exist several large genomic and metagenomic data collection efforts, including GenomeTrakr and MetaSub, which are routinely updated with new data. To analyze such datasets, memory-efficient methods to construct and store the colored de Bruijn graph were developed. Yet, a problem that has not been considered is constructing the colored de Bruijn graph in a scalable manner that allows new data to be added without reconstruction. This problem is important for large public datasets as scalability is needed but also the ability to update the construction is also needed. RESULTS We create a method for constructing the colored de Bruijn graph for large datasets that is based on partitioning the data into smaller datasets, building the colored de Bruijn graph using a FM-index based representation, and succinctly merging these representations to build a single graph. The last step, merging succinctly, is the algorithmic challenge which we solve in this article. We refer to the resulting method as VariMerge. This construction method also allows the graph to be updated with new data. We validate our approach and show it produces a three-fold reduction in working space when constructing a colored de Bruijn graph for 8000 strains. Lastly, we compare VariMerge to other competing methods-including Vari, Rainbowfish, Mantis, Bloom Filter Trie, the method of Almodaresi et al. and Multi-BRWT-and illustrate that VariMerge is the only method that is capable of building the colored de Bruijn graph for 16 000 strains in a manner that allows it to be updated. Competing methods either did not scale to this large of a dataset or do not allow for additions without reconstruction. AVAILABILITY AND IMPLEMENTATION VariMerge is available at https://github.com/cosmo-team/cosmo/tree/VARI-merge under GPLv3 license. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Inflation in Low-Income Countries

This paper studies the effects of global and domestic inflation shocks on core price inflation in 105 countries between 1970 and 2016, by using a heterogeneous panel vector-autoregressive model. The methodology allows accounting for differences across groups of countries (advanced economies, emerging markets and developing economies, and low-income countries) and across groups with different country characteristics (such as foreign exchange and monetary policy regimes). The empirical results indicate that most of the variation in inflation among low-income countries over the past decades is accounted for by external shocks. More than half of the variation in core inflation rates among low-income countries is due to global core price shocks, compared with one-eighth in advanced economies. Global food and energy price shocks account for another 13 percent of core inflation variation in low-income countries -- half more than in advanced economies and one-fifth more than in emerging markets and developing economies. This points to challenges in anchoring domestic inflation expectations, which have been most evident among low -- income countries with floating exchange rates, especially in cases where central bank independence has been weak.
Combinatorial Optimization Algorithms via Polymorphisms

An elegant characterization of the complexity of constraint satisfaction problems has emerged in the form of the the algebraic dichotomy conjecture of [BKJ00]. Roughly speaking, the characterization asserts that a CSP Λ is tractable if and only if there exist certain non-trivial operations known as polymorphisms to combine solutions to Λ to create new ones. In an entirely separate line of work, the unique games conjecture yields a characterization of approximability of MaxCSPs. Surprisingly, this characterization for Max-CSPs can also be reformulated in the language of polymorphisms. In this work, we study whether existence of non-trivial polymorphisms implies tractability beyond the realm of constraint satisfaction problems, namely in the value-oracle model. Specifically, given a function f in the value-oracle model along with an appropriate operation that never increases the value of f , we design algorithms to minimize f . In particular, we design a randomized algorithm to minimize a function f : [q]n → R that admits a fractional polymorphism which is measure preserving and has a transitive symmetry. We also reinterpret known results on MaxCSPs and thereby reformulate the unique games conjecture as a characterization of approximability of max-CSPs in terms of their approximate polymorphisms. Supported by NSF Career Award and Alfred. P. Sloan Fellowship ISSN 1433-8092 Electronic Colloquium on Computational Complexity, Report No. 7 (2015)
Capacity of Single-Server Single-Message Private Information Retrieval with Coded Side Information

This paper considers the problem of single-server single-message private information retrieval with coded side information (PIR-CSI). In this problem, there is a server storing a database, and a user which knows a linear combination of a subset of messages in the database as a side information. The number of messages contributing to the side information is known to the server, but the indices and the coefficients of these messages are unknown to the server. The user wishes to download a message from the server privately, i.e., without revealing which message it is requesting, while minimizing the download cost. In this work, we consider two different settings for the PIR-CSI problem depending on the demanded message being or not being one of the messages contributing to the side information. For each setting, we prove an upper bound on the maximum download rate as a function of the size of the database and the size of the side information, and propose a protocol that achieves the rate upper-bound.
Spectral analysis of virus spreading in random geometric networks

In this paper, we study the dynamics of a viral spreading process in random geometric graphs (RGG). The spreading of the viral process we consider in this paper is closely related with the eigenvalues of the adjacency matrix of the graph. We deduce new explicit expressions for all the moments of the eigenvalue distribution of the adjacency matrix as a function of the spatial density of nodes and the radius of connection. We apply these expressions to study the behavior of the viral infection in an RGG. Based on our results, we deduce an analytical condition that can be used to design RGG's in order to tame an initial viral infection. Numerical simulations are in accordance with our analytical predictions.
Quantization for low-rank matrix recovery

We study Sigma-Delta quantization methods coupled with appropriate reconstruction algorithms for digitizing randomly sampled low-rank matrices. We show that the reconstruction error associated with our methods decays polynomially with the oversampling factor, and we leverage our results to obtain root-exponential accuracy by optimizing over the choice of quantization scheme. Additionally, we show that a random encoding scheme, applied to the quantized measurements, yields a near-optimal exponential bit-rate. As an added benefit, our schemes are robust both to noise and to deviations from the low-rank assumption. In short, we provide a full generalization of analogous results, obtained in the classical setup of bandlimited function acquisition, and more recently, in the finite frame and compressed sensing setups to the case of low-rank matrices sampled with sub-Gaussian linear operators. Finally, we believe our techniques for generalizing results from the compressed sensing setup to the analogous low-rank matrix setup is applicable to other quantization schemes.