cssi/SciSciGPT-SciSciNet huggingface dataset:
Stereoselective Total Synthesis of the Pseudopterolide Kallolide A.

A total synthesis of the pseudopterolides, kallolide A (36) and kallolide A acetate (35), has been achieved. The racemic forms were prepared from the syn adduct 20 of furan 13 and stannane 17 (BF(3).OEt(2)-promoted addition) via the 15-membered propargylic allylic ether 25. [2,3]Wittig ring contraction led to the cis, anti, cis product 26. Alcohol 26 was transformed to butenolide 34 with net retention of configuration by Pd(PPh(3))(4)-catalyzed carbonylation of the mesylate 27 and ensuing AgNO(3)-catalyzed cyclization of the derived allenic acid 29. Solvolysis of the SEM ether (at C2) 34 in acetic acid or aqueous t-BuOH afforded racemic kallolide A acetate (35) and kallolide A (36), respectively, with inversion of stereochemistry by an S(N)1 process. Key elements of stereocontrol, including the steric outcome of the [2,3]Wittig ring contraction, the allenic ester isomerization, and the solvolysis reactions, were predicted from molecular mechanics calculations. The C8 and C2 epimers 45 and 46 of the cis, anti, cis kallolide A SEM ether precursor 34 were also prepared. The synthetic route originated from the anti adduct 19 of aldehyde 13 and the allylic chloride 16 and CuCl (cat), HSiCl(3), and i-Pr(2)NEt. Adduct 19 was subjected to the same sequence as the syn counterpart 20 to produce the trans, anti, cis [2,3]Wittig ring contraction product 42. The derived allenoate 44 afforded a 1:1 mixture of butenolides 45 and 46 upon sequential treatment with TBAF and AgNO(3). Finally, the natural enantiomer (+)-36 of kallolide A was synthesized from the enantioenriched syn adduct (+)-20, prepared by addition of allylic stannane 17 to aldehyde 13 promoted by a modified chiral acyloxyborane Lewis acid.
Convenient Synthesis of 2,7-Diamino-9,9- bis(4-aminophenyl)fluorene

Abstract For the synthesis of 2,7-diamino-9,9-bis(4-aminophenyl)fluorene 2 , first 2,7-dinitro-9,9-bis(4-aminophenyl)fluorene 1 was synthesized by the reaction of 2,7-dinitro-9-fluorenone with aniline and aniline hydrochloride. 2 was obtained by the reduction of 1 with hydrazine hydrate and 10% palladium on carbon.
Detecting sterile dark matter in space

Space-based instruments provide new and, in some cases, unique opportunities to search for dark matter. In particular, if dark matter comprises sterile neutrinos, the X-ray detection of their decay line is the most promising strategy for discovery. Sterile neutrinos with masses in the keV range could solve several long-standing astrophysical puzzles, from supernova asymmetries and the pulsar kicks to star formation, reionization, and baryogenesis. The best current limits on sterile neutrinos come from Chandra and XMM-Newton. Future advances can be achieved with a high-resolution X-ray spectrometry in space.
Flow-Tube Investigation of the High-Temperature Reaction between BCl3 and NH3

The reaction between BCl3 and NH3 to produce dichloroboramine (Cl2BNH2) and HCl was probed using a flow-tube reactor interfaced to a molecular-beam mass-sampling system. A composite method that cou...
Silyl triflate-accelerated additions of catalytically generated zinc acetylides to N -phenyl nitrones

Abstract Terminal alkynes readily form zinc acetylides in the presence of iPr2NEt and 20 mol % ZnBr2, then attack N-phenyl nitrones activated by trimethylsilyl trifluoromethanesulfonate. Deprotection with aqueous acid yields N-hydroxyl propargylamine. Yields are generally high for nitrones derived from aromatic aldehydes. Control experiments suggest that silyl triflate has a significant accelerating effect upon the reaction.
Predicting pathogenicity of missense variants with weakly supervised regression.

Quickly growing genetic variation data of unknown clinical significance demand computational methods that can reliably predict clinical phenotypes and deeply unravel molecular mechanisms. On the platform enabled by the Critical Assessment of Genome Interpretation (CAGI), we develop a novel "weakly supervised" regression (WSR) model that not only predicts precise clinical significance (probability of pathogenicity) from inexact training annotations (class of pathogenicity) but also infers underlying molecular mechanisms in a variant-specific manner. Compared to multiclass logistic regression, a representative multiclass classifier, our kernelized WSR improves the performance for the ENIGMA Challenge set from 0.72 to 0.97 in binary area under the receiver operating characteristic curve (AUC) and from 0.64 to 0.80 in ordinal multiclass AUC. WSR model interpretation and protein structural interpretation reach consensus in corroborating the most probable molecular mechanisms by which some pathogenic BRCA1 variants confer clinical significance, namely metal-binding disruption for p.C44F and p.C47Y, protein-binding disruption for p.M18T, and structure destabilization for p.S1715N.
A Persistence Detector for Metabolic Network Rewiring in an Animal.

Summary Biological systems must possess mechanisms that prevent inappropriate responses to spurious environmental inputs. Caenorhabditis elegans has two breakdown pathways for the short-chain fatty acid propionate: a canonical, vitamin B12-dependent pathway and a propionate shunt that is used when vitamin B12 levels are low. The shunt pathway is kept off when there is sufficient flux through the canonical pathway, likely to avoid generating shunt-specific toxic intermediates. Here, we discovered a transcriptional regulatory circuit that activates shunt gene expression upon propionate buildup. Nuclear hormone receptor 10 (NHR-10) and NHR-68 function together as a “persistence detector” in a type 1, coherent feed-forward loop with an AND-logic gate to delay shunt activation upon propionate accumulation and to avoid spurious shunt activation in response to a non-sustained pulse of propionate. Together, our findings identify a persistence detector in an animal, which transcriptionally rewires propionate metabolism to maintain homeostasis.
Mass spectral evidence of alkali metal insertion into C60-cyclooctatetraene complexes: M+@C60-C8H8.3-

C60 can be reduced to its trianion anion radical in hexamethylphosphoramide with potassium or cesium metal. The addition of water to these solutions, followed by toluene extraction, yields material...
Enantioselective Synthesis of Ceralure B1, Ethyl cis-5-Iodo-trans-2-methylcyclohexane-1-carboxylate

Abstract Ethyl (1R, 2R, 5R)-5-iodo-2-methylcyclohexane-1-carboxylate is a potent attractant for the Mediterranean fruit fly. This compound was stereoselectively synthesized on a multigram scale in nine steps in 15% yield. Key steps of the synthesis involved an asymmetric Diels–Alder reaction, iodolactonization, stereoselective reduction of the carbonyl, and inversion of configuration with iodide.
ORGANOSULFUR TRANSFER WITH DISULFIDES IN THE PRESENCE OF CCl4

Abstract Thiols and protic nucleophiles undergo sulfur-element bond formation in the presence of CCl4/base. Sulfenylation of CH-acidic compounds with thiols occur via disulfides, formed in a preliminary step. Uses and advantages of this organosulfur transfer are described.
Timing of ESCRT-III protein recruitment and membrane scission during HIV-1 assembly

Viruses need to be able to enter and leave the cells of their hosts to multiply and spread infections. Once inside the cell, many viruses, including the HIV virus, hijack the cell’s genetic material to produce more HIV particles and release them back into the surroundings. As the new viruses leave the cell, they wrap themselves in the membrane of their host cell. The shell of HIV consists of thousands of copies of a protein called Gag, which helps to release the viruses. Gag aggregates inside of the host cell membrane, which then begins to bulge outwards forming a spherical bud that subsequently pinches off. These released virus particles are now able to infect other cells. Both assembling and budding of the virus particles requires the help of specific cell proteins called ESCRTs. Cells usually use ESCRTs to cut membrane-bound compartments during cell division. HIV can control ESCRTs to separate the bud from the cell, but where and how they are involved is still not fully understood. Some models propose that the ESCRTs bend the membrane, while others suggest that the ESCRTs are required during the split, providing the force for the cutting process. Now, Johnson et al. used fluorescent light to follow how individual viruses in human cells grown in the laboratory assemble, and polarized light to detect how the orientation of Gag changed as the membrane bends into a sphere. The experiments revealed that the virus particles started to form a sphere at the same time Gag began to gather at the cell membrane, before any ESCRTs were present. Once enough Gag proteins had accumulated, the ESCRTs were recruited to the spot and removed within tens of seconds, just before the virus was cut off from the host cell. This suggest that the ESCRTs may help prepare the membrane to split, but are not involved in the actual cutting process. The findings of Johnson et al. will help us to better understand the behavior of HIV viruses. Knowing how they assemble and leave the host cell may help to create new strategies for disrupting these processes in particular, so stopping the virus from spreading. Moreover, ESCRTs are involved in numerous activities of a cell, such as cell division or repair of the cell surface after rupture, but little is known about how they work. For the first time, it has been shown that ESCRTs are neither the driving force for bending the membrane nor are they present when the cutting of a virus happens. This may also apply to other processes in the cell that involve membrane-splitting by ESCRT proteins, and researchers may be compelled to reevaluate their proposed role in other systems.
Successful application of Marcus Theory to catalysis by labile metal ions

The successful applications of Marcus theory to catalysis by labile metal ions in the base-catalyzed enolization and decarboxylation of oxalacetate and in the ketonization and condensation of enolpyruvate are described. Illustrations are presented describing the prediction of rate constants and the use of the theory in original and expanded versions to gain insight into possible features of a reaction mechanism.
BISMUTH NITRATE-MEDIATED DEPROTECTION OF OXIMES

ABSTRACT Bismuth nitrate in wet silica gel was found to be an excellent reagent for the regeneration of ketones from oximes.
Identification of circadian rhythms in Nannochloropsis species using bioluminescence reporter lines.

Circadian clocks allow organisms to predict environmental changes caused by the rotation of the Earth. Although circadian rhythms are widespread among different taxa, the core components of circadian oscillators are not conserved and differ between bacteria, plants, animals and fungi. Stramenopiles are a large group of organisms in which circadian rhythms have been only poorly characterized and no clock components have been identified. We have investigated cell division and molecular rhythms in Nannochloropsis species. In the four strains tested, cell division occurred principally during the night period under diel conditions; however, these rhythms damped within 2-3 days after transfer to constant light. We developed firefly luciferase reporters for the long-term monitoring of in vivo transcriptional rhythms in two Nannochlropsis species, Nannochloropsis oceanica CCMP1779 and Nannochloropsis salina CCMP537. The reporter lines express anticipatory behavior under light/dark cycles and free-running bioluminescence rhythms with periods of ~21-31 h that damped within ~3-4 days under constant light. Using different entrainment regimes, we demonstrate that these rhythms are modulated by a circadian-type oscillator. In addition, the phase of free-running luminescence rhythms can be modulated pharmacologically using a CK1 e/δ inhibitor, suggesting a role of this kinase in the Nannochloropsis clock. Together with the molecular and genomic tools available for Nannochloropsis species, these reporter lines represent an excellent system for future studies on the molecular mechanisms of stramenopile circadian oscillators.
Microwave-Assisted Alkylations of Activated Methylene Groups

Abstract Alkylations under ‘dry conditions’ of nitrophenylacetates, of an indole, and of methyl benzylidene glycinate induced by microwaves have been studied, leading to a very simple synthesis of arenes linked by a long hydrocarbon chain. N-Alkylation of the indole occurs, and monoalkylated methyl benzylideneglycinate is obtained, but in poor yield.
Synthesis of benzo[c]selenophene and derivatives via new routes.

Benzo[c]selenophene has been generated via facile bromination−dehydrobromination as well as oxidation of the 1,3-dihydrobenzo[c]selenophene. Benzo[c]selenophene thus generated has been lithiated in situ and treated with ClCOOEt to give the first functionalized derivative subject to X-ray crystallographic analysis.
Catalytic transformations of vinylthiiranes by tungsten carbonyl complexes. A new route to 3,6-dihydro-1,2-dithiins

W(CO){sub 5}(NCMe) has been found to transform vinylthiirane and a series of methyl-substituted vinylthiiranes into a series of 3,6-dihydro-1,2-dithiin compounds. Two equivalents of the vinylthiirane are required, and 1 equiv of a butadiene is formed by the transfer of its sulfur atom to the second vinylthiirane, which is then transformed into the dihydrodithiin. The formation of 3,6-dihydro-1,2-dithiin proceeds at 15 turnovers/h at 25 C using vinylthiirane as the catalyst. The catalyst is long-lived (up to 2,000 turnovers have been obtained without loss of activity) and relatively insensitive to air. Methyl substituents on the vinyl group increase the rate of reaction while methyl substituents on the thiirane ring slow it considerably. The introduction of phosphine ligands to the catalyst also leads to significant increases in the rate of reaction. The dithiin complex W(CO){sub 5}({ovr SSCH{sub 2}CH{double_bond}CHC}H{sub 2}) was isolated from the catalytic reactions and was structurally characterized. The dihydrodithiin is coordinated to the tungsten atom through one of its two sulfur atoms. This product was shown to be a species in the catalytic cycle. A mechanism involving a vinylthiirane intermediate that undergoes spontaneous ring opening, followed by addition of a second vinylthiirane to the terminal carbon of the chain, elimination ofmore » 1 equiv of butadiene, and formation of a sulfur-sulfur bond leading to the compound above is proposed. The vinylthiirane intermediate is regenerated by ligand substitution which releases the dihydrodithiin product. 3,6-dihydro1,2-dithiin readily polymerizes when its pure form is exposed to visible light. If the polymerization is interrupted at an early stage, 1,2,7,8-tetrathiacyclododeca-4,10-diene, a dimer, can be isolated. The dimer was obtained in 5.6% yield and was structurally characterized crystallographically.« less
Antimalarial cyclic peroxy ketals.

Over 20 new, cyclic, peroxy ketals have been prepared via a two-step protocol starting with readily available aryl methyl ketones. Structure−activity correlations using in vitro antimalarial data as a guide for optimization of potency have led to the design and synthesis of seven new peroxides that have IC50 values of 31−85 nM (artemisinin IC50 = 8.4 nM). Some SAR generalizations are discussed.
A stereoselective, multiple-component approach to α–β-substituted-β-amino carbonyl derivatives ☆

Abstract A new stereoselective multiple-component condensation is presented. This three-component condensation combines an aldehyde, aniline, and chlorotitanium enolates, to afford α–β-substituted-β-amino carbonyl compounds as its core structure.
Glycomimetics: A Versatile de Novo Synthesis of β-1-C-Aryl-deoxymannojirimycin Analogues

The synthesis of 11 β-1-C-aryl-deoxymannojirimycin analogues using a versatile de novo strategy is described. The origins of this report are derived from several recent developments in the area of C1-substituted glycomimetic polyhydroxylated piperidines. This study is designed as a structure−activity comparison to explore the effects of aryl substitution on the ability of the title compounds to inhibit glycosidase enzymes. The polyhydroxylated piperidine ring was constructed using vinyl bromide 10, which was synthesized in six steps from the bromobenzene microbial oxidation metabolite bromo diol 9. A palladium-catalyzed Suzuki cross-coupling of vinyl bromide 10 and the corresponding arylboronic acid served as the key pseudoanomeric carbon−carbon bond-forming step. Ozonolysis and selective reduction of the resultant carbonyl functions followed by reductive amination served to produce the azasugar ring. The complete NMR analysis of the resultant piperidine ring stereochemistry is also discussed. Fully depro...
Regioselectivity in the Cu(I)-Catalyzed [4 + 2]-Cycloaddition of 2-Nitrosopyridine with Unsymmetrical Dienes

The thermal (uncatalyzed) and Cu(I)-catalyzed reactions of 2-nitrosopyridine (PyrNO) with the dienes 1,3-pentadiene, E,E-2,4-hexadienol, and 1-phenylbutadiene are investigated experimentally and computationally. The uncatalyzed reactions of the first two dienes occur with low regioselectivity, while the latter proceeds with complete proximal selectivity. Using the M06/6-311+G(d,p)–SDD method, various concerted transition states for the reactions of 2-nitrosopyridine with (E)-1,3-pentadiene and 1-phenylbutadiene were computed. In quantitative agreement with the experimental findings, (a) no energy difference (0.0 kcal/mol) is found between the most stable transition states, endo-prox-anti and endo-dist-anti, in the pentadiene/PyrNO reaction, leading to nearly equal amounts of prox and dist cycloadducts, and (b) the proximal transition state is strongly favored (by 3.7 kcal/mol) over the distal for the highly selective phenylbutadiene/PyrNO reaction. The regioselectivity of the pentadiene/PyrNO reaction is ...
RNA AND THE SMALL MOLECULE WORLD

A key role in essential cellular processes is played by RNA molecules, and these are attractive targets for drug design. The functional diversity of RNA can be attributed to the sophisticated three-dimensional structures it assumes. These intricate folds create potential binding pockets for ions, low molecular weight ligands, and proteins. Recent experiments have demonstrated that small molecules such as tobramycin (1) can regulate gene expression in living cells through specific interactions with a messenger RNA (mRNA).
Adaptive Identification of Cortical and Subcortical Imaging Markers of Early Life Stress and Posttraumatic Stress Disorder

Background and purpose Posttraumatic stress disorder (PTSD) is a heterogeneous condition associated with a range of brain imaging abnormalities. Early life stress (ELS) contributes to this heterogeneity, but we do not know how a history of ELS influences traditionally defined brain signatures of PTSD. Here, we used a novel machine learning method - evolving partitions to improve classification (EPIC) - to identify shared and unique structural neuroimaging markers of ELS and PTSD in 97 combat-exposed military veterans. Methods We used EPIC with repeated cross-validation (CV) to determine how combinations of cortical thickness, surface area, and subcortical brain volumes could contribute to classification of PTSD (n = 40) versus controls (n = 57), and classification of ELS within the PTSD (ELS+ n = 16; ELS- n = 24) and control groups (ELS+ n = 16; ELS- n = 41). Additional inputs included intracranial volume, age, sex, adult trauma, and depression. Results On average, EPIC classified PTSD with 69% accuracy (SD = 5%), and ELS with 64% accuracy in the PTSD group (SD = 10%), and 62% accuracy in controls (SD = 6%). EPIC selected unique sets of individual features that classified each group with 75-85% accuracy in post hoc analyses; combinations of regions marginally improved classification from the individual atlas-defined brain regions. Across analyses, surface area in the right posterior cingulate was the only variable that was repeatedly selected as an important feature for classification of PTSD and ELS. Conclusions EPIC revealed unique patterns of features that distinguished PTSD and ELS in this sample of combat-exposed military veterans, which may represent distinct biotypes of stress-related neuropathology.
Reduced cognitive deficits after FLASH irradiation of whole mouse brain are associated with less hippocampal dendritic spine loss and neuroinflammation.

Abstract Aim To evaluate the impact of ultra-rapid FLASH mouse whole brain irradiation on hippocampal dendritic spines and neuroinflammation, factors associated with cognitive impairment after brain irradiation. Methods We administered 30 Gy whole brain irradiation to C57BL6/J mice in sub-second (FLASH) vs. 240 s conventional delivery time keeping all other parameters constant, using a custom configured clinical linac. Ten weeks post-irradiation, we evaluated spatial and non-spatial object recognition using novel object location and object recognition testing. We measured dendritic spine density by tracing Golgi-stained hippocampal neurons and evaluated neuroinflammation by CD68 immunostaining, a marker of activated microglia, and expression of 10 pro-inflammatory cytokines using a multiplex immunoassay. Results At ten weeks post-irradiation, compared to unirradiated controls, conventional delivery time irradiation significantly impaired novel object location and recognition tasks whereas the same dose given in FLASH delivery did not. Conventional delivery time, but not FLASH, was associated with significant loss of dendritic spine density in hippocampal apical dendrites, with a similar non-significant trend in basal dendrites. Conventional delivery time was associated with significantly increased CD68-positive microglia compared to controls whereas FLASH was not. Conventional delivery time was associated with significant increases in 5 of 10 pro-inflammatory cytokines in the hippocampus (and non-significant increases in another 3), whereas FLASH was associated with smaller increases in only 3. Conclusion Reduced cognitive impairment and associated neurodegeneration were observed with FLASH compared to conventional delivery time irradiation, potentially through decreased induction of neuroinflammation, suggesting a promising approach to increasing therapeutic index in radiation therapy of brain tumors.
A dimension‐invariant cascade model for VIX futures

We propose a new stochastic volatility model by allowing for a cascading structure of volatility components. The model, under a minor assumption, allows us to add as many components as desired with no additional parameters, effectively defeating the curse of dimensionality often encountered in traditional models. We derive a semi‐closed‐form solution to the VIX futures price, and find that our six‐factor model with only six parameters can closely fit spot VIX and VIX futures prices from 2004 to 2015 and produce out‐of‐sample pricing errors of magnitudes similar to those of in‐sample errors.
Communication-Aware Scheduling of Serial Tasks for Dispersed Computing

There is a growing interest in the development of in-network dispersed computing paradigms that leverage the computing capabilities of heterogeneous resources dispersed across the network for processing a massive amount of data collected at the edge of the network. We consider the problem of task scheduling for such networks, in a dynamic setting in which arriving computation jobs are modeled as chains, with nodes representing tasks, and edges representing precedence constraints among tasks. In our proposed model, motivated by significant communication costs in dispersed computing environments, the communication times are taken into account. More specifically, we consider a network where servers can serve all task types, and sending the outputs of processed tasks from one server to another server results in some communication delay. We first characterize the capacity region of the network, then propose a novel virtual queueing network encoding the state of the network. Finally, we propose a Max-Weight type scheduling policy, and considering the stochastic network in the fluid limit, we use a Lyapunov argument to show that the policy is throughput-optimal. Beyond the model of chains, we extend the scheduling problem to the model of the directed acyclic graph (DAG) which imposes a new challenge, namely logic dependency difficulty, requiring the data of processed parents tasks to be sent to the same server for processing the child task. We propose a virtual queueing network for DAG scheduling over broadcast networks, where servers always broadcast the data of processed tasks to other servers, and prove that Max-Weight policy is throughput-optimal.
Decay rate of triaxially deformed proton emitters

The decay rate of a triaxially deformed proton emitter is calculated in a particle-rotor model, which is based on a deformed Woods-Saxon potential and includes a deformed spin-orbit interaction. The wave function of the $I=7∕{2}^{\ensuremath{-}}$ ground state of the deformed proton emitter $^{141}\mathrm{Ho}$ is obtained in the adiabatic limit, and a Green's function technique is used to calculate the decay rate and branching ratio to the first excited ${2}^{+}$ state of the daughter nucleus. Only for values of the triaxial angle $\ensuremath{\gamma}l5\ifmmode^\circ\else\textdegree\fi{}$ is good agreement obtained for both the total decay rate and the ${2}^{+}$ branching ratio.
Coresets Meet EDCS: algorithms for matching and vertex cover on massive graphs

There is a rapidly growing need for scalable algorithms that solve classical graph problems, such as maximum matching and minimum vertex cover, on massive graphs. For massive inputs, several different computational models have been introduced, including the streaming model, the distributed communication model, and the massively parallel computation (MPC) model that is a common abstraction of MapReduce-style computation. In each model, algorithms are analyzed in terms of resources such as space used or rounds of communication needed, in addition to the more traditional approximation ratio.In this paper, we give a single unified approach that yields better approximation algorithms for matching and vertex cover in all these models. The highlights include:• The first one pass, significantly-better-than-2-approximation for matching in random arrival streams that uses subquadratic space, namely a (1.5 + e-approximation streaming algorithm that uses O(n1.5) space for constant e > 0.• The first 2-round, better-than-2-approximation for matching in the MPC model that uses sub-quadratic space per machine, namely a (1.5 + e)-approximation algorithm with [MATH HERE] memory per machine for constant e > 0.By building on our unified approach, we further develop parallel algorithms in the MPC model that give a (1+e)-approximation to matching and an 0(1)-approximation to vertex cover in only 0(log log n) MPC rounds and 0(n/polylog(n)) memory per machine. These results settle multiple open questions posed by Czumaj et al. [STOC 2018].We obtain our results by a novel combination of two previously disjoint set of techniques, namely randomized composable coresets and edge degree constrained subgraphs (EDCS). We significantly extend the power of these techniques and prove several new structural results. For example, we show that an EDCS is a sparse certificate for large matchings and small vertex covers that is quite robust to sampling and composition.
The Hilbert transform does not map $L^1(Mw)$ to $L^{1,\infty}(w)$

We prove that the analogue for the Hilbert transform of a classical weighted inequality by Fefferman and Stein for the Hardy Littlewood maximal operator does not hold. This is a sequel to paper arXiv:1008.3943 by the first author, which shows the same for the general Haar multiplier operator.
Structural Basis of the Differential Binding of Engineered Knottins to Integrins αVβ3 and α5β1.

Summary Targeting both integrins αVβ3 and α5β1 simultaneously appears to be more effective in cancer therapy than targeting each one alone. The structural requirements for bispecific binding of ligand to integrins have not been fully elucidated. RGD-containing knottin 2.5F binds selectively to αVβ3 and α5β1, whereas knottin 2.5D is αVβ3 specific. To elucidate the structural basis of this selectivity, we determined the structures of 2.5F and 2.5D as apo proteins and in complex with αVβ3, and compared their interactions with integrins using molecular dynamics simulations. These studies show that 2.5D engages αVβ3 by an induced fit, but conformational selection of a flexible RGD loop accounts for high-affinity selective binding of 2.5F to both integrins. The contrasting binding of the highly flexible low-affinity linear RGD peptides to multiple integrins suggests that a "Goldilocks zone" of conformational flexibility of the RGD loop in 2.5F underlies its selective binding promiscuity to integrins.
The graph structure of graph groups that are subgroups of Thompson’s group V

We determine exactly which graph products, also known as Right Angled Artin Groups, embed into Richard Thompson’s group V. It was shown by Bleak and Salazar-Diaz that ℤ2 ∗ ℤ was an obstruction. We show that this is the only obstruction. This is shown by proving a graph theory result giving an alternate description of simple graphs without an appropriate induced subgraph.
Computing points of small height for cubic polynomials

Let f in Q[z] be a polynomial of degree d at least two. The associated canonical height \hat{h}_f is a certain real-valued function on Q that returns zero precisely at preperiodic rational points of f. Morton and Silverman conjectured in 1994 that the number of such points is bounded above by a constant depending only on d. A related conjecture claims that at non-preperiodic rational points, \hat{h}_f is bounded below by a positive constant (depending only on d) times some kind of height of f itself. In this paper, we provide support for these conjectures in the case d=3 by computing the set of small height points for several billion cubic polynomials.
Can Neural Generators for Dialogue Learn Sentence Planning and Discourse Structuring

Responses in task-oriented dialogue systems often realize multiple propositions whose ultimate form depends on the use of sentence planning and discourse structuring operations. For example a recommendation may consist of an explicitly evaluative utterance e.g. Chanpen Thai is the best option, along with content related by the justification discourse relation, e.g. It has great food and service, that combines multiple propositions into a single phrase. While neural generation methods integrate sentence planning and surface realization in one end-to-end learning framework, previous work has not shown that neural generators can: (1) perform common sentence planning and discourse structuring operations; (2) make decisions as to whether to realize content in a single sentence or over multiple sentences; (3) generalize sentence planning and discourse relation operations beyond what was seen in training. We systematically create large training corpora that exhibit particular sentence planning operations and then test neural models to see what they learn. We compare models without explicit latent variables for sentence planning with ones that provide explicit supervision during training. We show that only the models with additional supervision can reproduce sentence planning and discourse operations and generalize to situations unseen in training.
Hidden parameter markov decision processes: a semiparametric regression approach for discovering latent task parametrizations

Control applications often feature tasks with similar, but not identical, dynamics. We introduce the Hidden Parameter Markov Decision Process (HiP-MDP), a framework that parametrizes a family of related dynamical systems with a low-dimensional set of latent factors, and introduce a semiparametric regression approach for learning its structure from data. We show that a learned HiP-MDP rapidly identifies the dynamics of new task instances in several settings, flexibly adapting to task variation.
Large Scale Scene Text Verification with Guided Attention.

Many tasks are related to determining if a particular text string exists in an image. In this work, we propose a new framework that learns this task in an end-to-end way. The framework takes an image and a text string as input and then outputs the probability of the text string being present in the image. This is the first end-to-end framework that learns such relationships between text and images in scene text area. The framework does not require explicit scene text detection or recognition and thus no bounding box annotations are needed. It is also the first work in scene text area that tackles such a weakly labeled problem. Based on this framework, we developed a model called Guided Attention. Our designed model achieves better results than several state-of-the-art scene text reading based solutions for a challenging Street View Business Matching task. The task tries to find correct business names for storefront images and the dataset we collected for it is substantially larger, and more challenging than existing scene text dataset. This new real-world task provides a new perspective for studying scene text related problems.
Phase-Coupled Oscillators with Plastic Coupling: Synchronization and Stability

In this article we study synchronization of systems of homogeneous phase-coupled oscillators with plastic coupling strengths and arbitrary underlying topology. The dynamics of the coupling strength between two oscillators is governed by the phase difference between these oscillators. We show that, under mild assumptions, such systems are gradient systems, and always achieve frequency synchronization. Furthermore, we provide sufficient stability and instability conditions that are based on results from algebraic graph theory. For a special case when underlying topology is a tree, we formulate a criterion (necessary and sufficient condition) of stability of equilibria. For both, tree and arbitrary topologies, we provide sufficient conditions for phase-locking, i.e., convergence to a stable equilibrium almost surely. We additionally find conditions when the system possesses a unique stable equilibrium, and thus, almost global stability follows. Several examples are used to demonstrate variety of equilibria the system has, their dependence on system's parameters, and to illustrate differences in behavior of systems with constant and plastic coupling strengths.
A Monetary Mechanism for Stabilizing Cooperative Data Exchange with Selfish Users

This paper considers the problem of cooperative data exchange with selfish users. In this setting, each user has a subset of packets in the ground set $X$ , and wants all other packets in $X$ . The users can exchange coded combinations of their packets over a lossless broadcast channel, and monetary transactions are allowed between any pair of users. We define the utility of each user as the sum of two functions: (i) the difference between the total payment received by the user and the total transmission rate of the user, and (ii) the difference between the total number of required packets by the user and the total payment made by the user. A rate-vector and payment-matrix pair $(r,p)$ is said to stabilize the grand coalition (i.e., the set of all users) if $(r,p)$ is Pareto optimal over all minor coalitions (i.e., all proper subsets of users who collectively know all packets in $X$ ). Our goal is to design a stabilizing rate-payment pair with minimum sum-rate and minimum sum-payment for any given problem instance. In this work, we show that such a solution always exists, and we propose two algorithms to find such a solution. Moreover, we show that both algorithms maximize the sum utility of all users, while one also maximizes the minimum utility among all users.
Unconditional long-time stability of a velocity---vorticity method for the 2D Navier---Stokes equations

We prove unconditional long-time stability for a particular velocity---vorticity discretization of the 2D Navier---Stokes equations. The scheme begins with a formulation that uses the Lamb vector to couple the usual velocity---pressure system to the vorticity dynamics equation, and then discretizes with the finite element method in space and implicit---explicit BDF2 in time, with the vorticity equation decoupling at each time step. We prove the method's vorticity and velocity are both long-time stable in the $$L^2$$L2 and $$H^1$$H1 norms, without any timestep restriction. Moreover, our analysis avoids the use of Gronwall-type estimates, which leads us to stability bounds with only polynomial (instead of exponential) dependence on the Reynolds number. Numerical experiments are given that demonstrate the effectiveness of the method.
Supercharacters and the discrete Fourier, cosine, and sine transforms

Using supercharacter theory, we identify the matrices that are diagonalized by the discrete cosine and discrete sine transforms, respectively. Our method affords a combinatorial interpretation for ...
Idempotents in Tangle Categories Split

In this paper, we use 3-manifold techniques to illuminate the structure of the category of tangles. In particular, we show that every idempotent morphism A in such a category naturally splits as A ...
Performance Based Cost Functions for End-to-End Speech Separation

Recent neural network strategies for source separation attempt to model audio signals by processing their waveforms directly. Mean squared error (MSE) that measures the Euclidean distance between waveforms of denoised speech and the ground-truth speech, has been a natural cost-function for these approaches. However, MSE is not a perceptually motivated measure and may result in large perceptual discrepancies. In this paper, we propose and experiment with new loss functions for end-to-end source separation. These loss functions are motivated by BSS_Eval and perceptual metrics like source to distortion ratio (SDR), source to interference ratio (SIR), source to artifact ratio (SAR) and short-time objective intelligibility ratio (STOI). This enables the flexibility to mix and match these loss functions depending upon the requirements of the task. Subjective listening tests reveal that combinations of the proposed cost functions help achieve superior separation performance as compared to stand-alone MSE and SDR costs.
Time-dependent photon statistics in variable media

We find explicit solutions of the Heisenberg equations of motion for a quadratic Hamiltonian, describing a generic model of variable media, in the case of multi-parameter squeezed input photon configuration. The corresponding probability amplitudes and photon statistics are also derived in the Schroedinger picture in an abstract operator setting of the quantum electrodynamics (QED). Their time evolution is given in terms of solutions of certain Ermakov-type system. The unitary transformation and an extension of the squeeze/evolution operator are introduced formally.
Toward understanding the impact of user participation in autonomous ridesharing systems

Autonomous ridesharing systems (ARS) promise many societal and environmental benefits, including decreased accident rates, reduced energy consumption and pollutant emissions, and diminished land use for parking. To unleash ARS' potential, stakeholders must understand how the degree of passenger participation influences the ridesharing systems' efficiency. To date, however, a careful study that quantifies the impact of user participation on ARS' performance is missing. Here, we present the first simulation analysis to investigate how and to what extent user participation affects the efficiency of ARS. We demonstrate how specific configurations (e.g., fleet size, vehicle capacity, and the maximum waiting time) of a system can be identified to counter the performance loss due to users' uncoordinated behavior on ridesharing participation. Our results indicate that stakeholders of ARS should base decisions regarding system configurations on insights from data-driven simulations and make tradeoffs between system efficiency and price of anarchy for desired outcomes.
Coded caching for networks with the resolvability property

Coded caching is a recently proposed technique for dealing with large scale content distribution over the Internet. As in conventional caching, it leverages the presence of local caches at the end users. However, it considers coding in the caches and/or coded transmission from the central server and demonstrates that huge savings in transmission rate are possible when the server and the end users are connected via a single shared link. In this work, we consider a more general topology where there is a layer of relay nodes between the server and the users, e.g., combination networks studied in network coding are an instance of these networks. We propose novel schemes for a class of such networks that satisfy a so-called resolvability property and demonstrate that the performance of our scheme is strictly better than previously proposed schemes.
When the Cauchy Inequality Becomes a Formula

In this note, we revisit the classical geometric–arithmetic mean inequality and find a formula for the difference of the arithmetic and the geometric means of n given nonnegative numbers . The form...
PROXIMAL NEWTON-TYPE METHODS FOR MINIMIZING COMPOSITE FUNCTIONS

We generalize Newton-type methods for minimizing smooth functions to handle a sum of two convex functions: a smooth function and a nonsmooth function with a simple proximal mapping. We show that the resulting proximal Newton-type methods inherit the desirable convergence behavior of Newton-type methods for minimizing smooth functions, even when search directions are computed inexactly. Many popular methods tailored to problems arising in bioinformatics, signal processing, and statistical learning are special cases of proximal Newton-type methods, and our analysis yields new convergence results for some of these methods.
Stable auto-equivalences for local symmetric algebras

Abstract We construct nontrivial auto-equivalences of stable module categories for elementary, local symmetric algebras over a field k. These auto-equivalences are modeled after the spherical twists of Seidel and Thomas and the P n -twists of Huybrechts and Thomas, which yield auto-equivalences of the derived category of coherent sheaves on a variety. For group algebras of p-groups in characteristic p we recover many of the auto-equivalences corresponding to endo-trivial modules. We also obtain analogous auto-equivalences for local algebras of dihedral and semi-dihedral type, which are not group algebras.
Categorical matrix completion

We consider the problem of completing a matrix with categorical-valued entries from partial observations. This is achieved by extending the formulation and theory of one-bit matrix completion [1]. We recover a low-rank matrix M by maximizing the likelihood ratio with a constraint on the nuclear norm of M, and the observations are mapped from entries of M through multiple link functions. We establish theoretical upper and lower bounds on the recovery error, which meet up to a constant factor O(K3/2) where K is the fixed number of categories. The upper bound in our case depends on the number of categories implicitly through a maximization of terms that involve the smoothness of the link functions. In contrast to one-bit matrix completion, our bounds for categorical matrix completion are optimal up to a factor on the order of the square root of the number of categories, which is consistent with an intuition that the problem becomes harder when the number of categories increases. By comparing the performance of our method with the conventional matrix completion method on the MovieLens dataset, we demonstrate the advantage of our method.
Human-Planned Robotic Grasp Ranges: Capture and Validation.

Leveraging human grasping skills to teach a robot to perform a manipulation task is appealing, but there are several limitations to this approach: time-inefficient data capture procedures, limited generalization of the data to other grasps and objects, and inability to use that data to learn more about how humans perform and evaluate grasps. This paper presents a data capture protocol that partially addresses these deficiencies by asking participants to specify ranges over which a grasp is valid. The protocol is verified both qualitatively through online survey questions (where 95.38% of within-range grasps are identified correctly with the nearest extreme grasp) and quantitatively by showing that there is small variation in grasps ranges from different participants as measured by joint angles, contact points, and position. We demonstrate that these grasp ranges are valid through testing on a physical robot (93.75% of grasps interpolated from grasp ranges are successful).
A Characterization of Approximation Resistance.

A predicate f : {−1, 1} → {0, 1} with ρ(f) = |f −1(1)| 2k is called approximation resistant if given a near-satisfiable instance of CSP(f), it is computationally hard to find an assignment that satisfies at least ρ(f) + Ω(1) fraction of the constraints. We present a complete characterization of approximation resistant predicates under the Unique Games Conjecture. We also present characterizations in the mixed linear and semidefinite programming hierarchy and the Sherali-Adams linear programming hierarchy. In the former case, the characterization coincides with the one based on UGC. Each of the two characterizations is in terms of existence of a probability measure with certain symmetry properties on a natural convex polytope associated with the predicate. ∗NYU. khot@cims.nyu.edu Research partly supported by NSF Expeditions grant CCF-0832795, NSF Waterman Award and BSF grant 2008059. Part of the research carried out while the author was at U.Chicago. †Toyota Technological Institute at Chicago. madhurt@ttic.edu. Research supported by NSF Career Award CCF-1254044. ‡NYU. pworah@cims.nyu.edu Research partly supported by Subhash Khot’s NSF Waterman Award. Part of the research carried out while the author was at U.Chicago.
Asymptotic Behavior of Conjunctive Boolean Networks Over Weakly Connected Digraphs

A conjunctive Boolean network (CBN) is a finite state dynamical system, whose variables take values from a binary set, and the value update rule for each variable is a Boolean function consisting only of logic and operations. We investigate the asymptotic behavior of CBNs by computing their periodic orbits. When the underlying digraph is strongly connected, the periodic orbits of the associated CBN have been completely understood, one-to-one corresponding to binary necklaces of a certain length given by the loop number of the graph. We characterize in the paper the periodic orbits of CBNs over arbitrary weakly connected digraphs. We establish, among other things, a new method to investigate their asymptotic behavior. Specifically, we introduce a graphical approach, termed system reduction , which turns the underlying digraph into a special weakly connected digraph, whose strongly connected components are all cycles. We show that the reduced system uniquely determines the asymptotic behavior of the original system. Moreover, we provide a constructive method for computing the periodic orbit of the reduced system, which the system will enter for a given, but arbitrary initial condition.
Simple Helices on Fano Threefolds

Building on the work of Nogin, we prove that the braid group acts transitively on full exceptional collections of vector bundles on Fano threefolds with and . Equivalently, this group acts transitively on the set of simple helices (considered up to a shift in the derived category) on such a Fano threefold. We also prove that on threefolds with and very ample anticanonical class, every exceptional coherent sheaf is locally free.