cssi/SciSciGPT-SciSciNet huggingface dataset:
Synthesis of Substituted 2-Pyridones via the Pummerer Cyclization-Deprotonation-Cycloaddition Cascade of Imidosulfoxides.

1-Ethanesulfinylacetylpiperidin-2-one was prepared from δ-valerolactam in two steps by heating with ethylsulfenylacetyl chloride followed by sodium periodate oxidation. Slow addition of the imidosu...
Transcranial Alternating Current Stimulation (tACS) Mechanisms and Protocols

Perception, cognition and consciousness can be modulated as a function of oscillating neural activity, while ongoing neuronal dynamics are influenced by synaptic activity and membrane potential. Consequently, transcranial alternating current stimulation (tACS) may be used for neurological intervention. The advantageous features of tACS include the biphasic and sinusoidal tACS currents, the ability to entrain large neuronal populations, and subtle control over somatic effects. Through neuromodulation of phasic, neural activity, tACS is a powerful tool to investigate the neural correlates of cognition. The rapid development in this area requires clarity about best practices. Here we briefly introduce tACS and review the most compelling findings in the literature to provide a starting point for using tACS. We suggest that tACS protocols be based on functional brain mechanisms and appropriate control experiments, including active sham and condition blinding.
Synthesis of spirofuranopyrimidine–piperidines

A concise synthesis of spirofuranopyrimidines is described and relies on the addition of isopropyl 4-oxopiperidine-1-carboxylate to a pyrimidine dianion. The diol intermediate formed is subjected to cycloetherification conditions leading to an unprecedented heterocyclic template.
Trifluoromethanesulfonamide derivatives of azoles

Abstract Trifluoromethanesulfonamide-substituted azoles were synthesized by the reaction of 5-aminotetrazole, 3-amino-1,2,4-triazole and 3,5-diamine-1,2,4-triazole with trifluoromethanesulfonyl fluoride to prepare only monosubstituted compounds. All the compounds were fully characterized using ( 1 H, 19 F, 13 C) NMR spectroscopy, mass spectrometry (MS), and elemental analysis.
Chemo-, regio- and stereoselective addition of nitrile oxides to cobalt-coordinated 1,3-enynes

Abstract Unlike the frequently unselective reactions of 1,3-enynes with 1,3-dipoles, nitrile oxides add chemo-, regio- and stereoselectively to the free double bond of (1,3-enyne)Co2(CO)6 complexes to provide 5-alkynyl-2-oxazoline derivatives in moderate to excellent yield.
Geometries and electronic properties of the tungsten-doped germanium clusters: WGen (n = 1-17).

Geometries associated with relative stabilities, energy gaps, and polarities of W-doped germanium clusters have been investigated systematically by using density functional theory. The threshold size for the endohedral coordination and the critical size of W-encapsulated Gen structures emerge as, respectively, n = 8 and n = 12, while the fullerene-like W@Gen clusters appears at n = 14. The evaluated relative stabilities in term of the calculated fragmentation energies reveal that the fullerene-like W@Ge14 and W@Ge16 structures as well as the hexagonal prism WGe12 have enhanced stabilities over their neighboring clusters. Furthermore, the calculated polarities of the W@Gen reveal that the bicapped tetragonal antiprism WGe10 is a polar molecule while the hexagonal prism WGe12 is a nonpolar molecule. Moreover, the recorded natural populations show that the charges transfer from the germanium framework to the W atom. Additionally, the WGe12 cluster with large highest occupied molecular orbital−lowest unoccupi...
3-D Coordination Network Structures Constructed from [W6S8(CN)6]6- Anions

Octahedral molybdenum and tungsten clusters face-capped by chalcogens M6Q8 (M = Mo, W; Q = S, Se, Te) have drawn extensive attention because of the well-known molybdenum-based Chevrel phases. Water-soluble cyanide complexes of these clusters can be prepared by cluster excision from the solid-state compound Mo6Se8 or by ligand exchange from W6S8(4-tert-butylpyridine)6. The [W6S8(CN)6]6- cluster anion can, in turn, be used as a building block to construct 3-D extended coordination networks with transition metal cations M2+ (M = Mn, Fe, Co, Zn) as linking units. The novel 3-D structures were determined by X-ray crystallography to be two-fold interpenetrating distorted cubic networks of [M(II)(H2O)4]3[W6S8(CN)6]·xH2O (x ≈ 23; M = Mn, Fe, Co) or a rutile-like network of K2[Zn(H2O)2]2[W6S8(CN)6]·26H2O, both bridged through W−CN−M−NC−W linkages. The properties of the new network structures are investigated and factors relevant to the construction of network structures containing W6S8 clusters are discussed.
Primordial black holes in phantom cosmology

We investigate the effects of accretion of phantom energy onto primordial black holes. Since Hawking radiation and phantom energy accretion contribute to a decrease of the mass of the black hole, the primordial black hole that would be expected to decay now due to the Hawking process would decay earlier due to the inclusion of the phantom energy. Equivalently, to have the primordial black hole decay now it would have to be more massive initially. We find that the effect of the phantom energy is substantial and the black holes decaying now would be much more massive—over ten orders of magnitude! This effect will be relevant for determining the time of production and hence the number of evaporating black holes expected in a universe accelerating due to phantom energy.
Gas Phase Photoproduction of Diatomic Metal Nitrides During Metal Nitride Laser Chemical Vapor Deposition.

Photolysis of M(NEt2)4 in the gas phase produces diatomic MN molecules (M = Ti, Zr, Hf). TiN and ZrN molecules were identified in the gas phase under CVD conditions by emission spectroscopy and time-of-flight mass spectroscopy. Nanostructured deposits of TiN were formed on quartz substrates by irradiating Ti(NEt2)4 gas at 355 nm. These studies demonstrate the gas phase formation of diatomic molecules having the same stoichiometry as that of the desired solid-phase deposit.
Ultrafast infrared studies of the role of spin states in organometallic reaction dynamics.

ConspectusThe importance of spin state changes in organometallic reactions is a topic of significant interest, as an increasing number of reaction mechanisms involving changes of spin state are consistently being uncovered. The potential influence of spin state changes on reaction rates can be difficult to predict, and thus this class of reactions remains among the least well understood in organometallic chemistry. Ultrafast time-resolved infrared (TRIR) spectroscopy provides a powerful tool for probing the dynamics of spin state changes in organometallic catalysis, as such processes often occur on the picosecond to nanosecond time scale and can readily be monitored in the infrared via the absorptions of carbonyl reporter ligands. In this Account, we summarize recent work from our group directed toward identifying trends in reactivity that can be used to offer predictive insight into the dynamics of coordinatively unsaturated organometallic reaction intermediates.In general, coordinatively unsaturated 16-...
An acid-catalyzed macrolactonization protocol.

An efficient macrolactonization protocol devoid of any base was developed derived from the use of vinyl esters in transesterification. Subjecting a hydroxy acid and ethoxyacetylene to 2 mol % [RuCl2(p-cymene)]2 in toluene followed by addition of camphorsulfonic acid or inverse addition provided macrolactones in good yields.
Photophysical investigations of rhenium(I)Cl(CO)3(phenanthroline) complexes

Abstract The electronic states of three complexes with the generic formula Re(I)Cl(CO)3(s-phen) [s-phen=4,7-dimethyl-1,10-phenanthroline, 5,6-dimethyl-1,10-phenanthroline, and 3,4,7,8-tetramethyl-1,10-phenanthroline] have been characterized by absorption and luminescence spectroscopy and the T-dependence of the decay times in rigid glasses in the range 4–77 K. Methyl substitution leads to composite phosphorescence bands that arise from 3MLCT and 3ππ* terms that are separated by Franck–Condon barriers. Evidence is also presented for the existence of FC barriers in singlet manifolds. Criteria are defined for the occurrence of FC barriers and slow rates of radiationless transitions between terms arising from disparate electronic configurations. The energy splittings and the decay constants of the individual sublevels of the 3MLCT manifolds have been determined.
Efficient proximal gradient algorithm for inference of differential gene networks

Gene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in gene networks is very important to understand molecular basis of various biological process. While existing algorithms can be used to infer two gene networks separately from gene expression data under two different conditions, and then to identify network changes, such an approach does not exploit the similarity between two gene networks, and it is thus suboptimal. A desirable approach would be clearly to infer two gene networks jointly, which can yield improved estimates of network changes. In this paper, we developed a proximal gradient algorithm for differential network (ProGAdNet) inference, that jointly infers two gene networks under different conditions and then identifies changes in the network structure. Computer simulations demonstrated that our ProGAdNet outperformed existing algorithms in terms of inference accuracy, and was much faster than a similar approach for joint inference of gene networks. Gene expression data of breast tumors and normal tissues in the TCGA database were analyzed with our ProGAdNet, and revealed that 268 genes were involved in the changed network edges. Gene set enrichment analysis identified a significant number of gene sets related to breast cancer or other types of cancer that are enriched in this set of 268 genes. Network analysis of the kidney cancer data in the TCGA database with ProGAdNet also identified a set of genes involved in network changes, and the majority of the top genes identified have been reported in the literature to be implicated in kidney cancer. These results corroborated that the gene sets identified by ProGAdNet were very informative about the cancer disease status. A software package implementing the ProGAdNet, computer simulations, and real data analysis is available as Additional file 1. With its superior performance over existing algorithms, ProGAdNet provides a valuable tool for finding changes in gene networks, which may aid the discovery of gene-gene interactions changed under different conditions.
Enantioselective Construction of Functionalized Cyclopentanes by a Relay Ring-Closing Metathesis and Chiral Amine (Thio)urea-Promoted Michael Addition

A relay strategy is described that permits ring-closing metathesis and bifunctional chiral amine (thio)urea-catalyzed Michael­ addition reactions to proceed in a one-pot fashion. The process offers an alternative approach to the synthesis of structurally diverse chiral cyclopentanes in good yields and good enantioselectivities.
An RNA-Binding Multimer Specifies Nematode Sperm Fate

Summary FOG-3 is a master regulator of sperm fate in Caenorhabditis elegans and homologous to Tob/BTG proteins, which in mammals are monomeric adaptors that recruit enzymes to RNA binding proteins. Here, we determine the FOG-3 crystal structure and in vitro demonstrate that FOG-3 forms dimers that can multimerize. The FOG-3 multimeric structure has a basic surface potential, suggestive of binding nucleic acid. Consistent with that prediction, FOG-3 binds directly to nearly 1,000 RNAs in nematode spermatogenic germ cells. Most binding is to the 3′ UTR, and most targets (94%) are oogenic mRNAs, even though assayed in spermatogenic cells. When tethered to a reporter mRNA, FOG-3 represses its expression. Together these findings elucidate the molecular mechanism of sperm fate specification and reveal the evolution of a protein from monomeric to multimeric form with acquisition of a distinct mode of mRNA repression.
DILUTED MAGNETIC SEMICONDUCTORS IN HIGH MAGNETIC FIELDS

Magnetization studies of diluted magnetic semiconductors in high fields are reviewed. Magnetization steps due to pairs were originally used to measure the near neighbor exchange constant J1. They are now also used to determine: (1) the smaller exchange constants J2 and J3 , (2) the difference between J1 's for inequivalent near neighbors in wurtzite diluted magnetic semiconductors, and (3) the Dzyaloshinski-Moriya interaction. A different type of magnetization step, due to isolated ions, is used to determine the un iaxial anisotropy of Co ++ ions in wurtzite diluted magnetic semiconductors. In Fe-based diluted magnetic semiconductors the high-field magnetization exhibits two effects: (1) strong dependence on field direction in cubic diluted magnetic semiconductors, and (2) reversal of the un iaxial magnetization-anisotropy in wurtzite diluted magnetic semiconductors. In (100) EuTe/PbTe superlattices the antiferromagnetic transition, both at zero and finite H, is depressed when the EuTe 1ayer becomes only a few monolayers thick. The easy directions are in the (100) plane of the layer, which is explained by the dipole-dipole anisotropy.
Concise Synthesis of cis- and trans-Theaspirones via Oxonium Ion-Initiated Pinacol Ring Expansion

The odoriferous principle of black tea has been produced from 2,2-dimethylcyclopentanone. The reaction sequence begins with 1,2-addition of 5-lithio-2-methyl-2,3-dihydrofuran to this ketone and immediate acid-catalyzed ring expansion of the resulting carbinols to a separable pair of spiro ethers. Individual conversion of these diastereomers to α,β-unsaturated ketones is followed by tandem condensation with the methyllithium−lithium bromide complex and oxidation with pyridinium chlorochromate.
Diisopropylethylamine mono(hydrogen fluoride) for nucleophilic fluorination of sensitive substrates: synthesis of sevoflurane

Abstract Diisopropylethylamine mono(hydrogen fluoride) ( 8 ), which can be prepared by addition of two equivalents of diisopropylethylamine to the complex diisopropylethylamine tris(hydrogen fluoride) ( 7 ), is shown to be an effective and selective nucleophilic fluorinating reagent when applied to halogen-exchange reactions of chloromethyl ethers, in particular the conversion of 1,1,1,3,3,3-hexafluoroisopropyl chloromethyl ether ( 3 ) to the volatile anesthetic sevoflurane (1,1,1,3,3,3-hexafluoroisopropyl fluoromethyl ether). The amine portion of the reagent does not react with the starting material to give a troublesome quaternary ammonium salt, as is the case for the species formed by addition of two equivalents of triethylamine to triethylamine tris(hydrogen fluoride). These particular chloromethyl ether substrates require a 1:1 stoichiometry of diisopropylethylamine to hydrogen fluoride to give useful rates of reaction and yields when solventless conditions are desired. Two other complexes, diisopropylethylamine bis(hydrogen fluoride) and 7 , are ineffective for conversion of 3 to sevoflurane.
One-step deprotonation route to zinc amide and ester enolates for use in aldol reactions and Negishi couplings

Abstract Simple amides and esters are conveniently deprotonated by Zn(tmp) 2 (tmp = 2,2,6,6-tetramethylpiperidinyl anion) to generate Zn enolates. Enolates formed by this method are suitable for use in aldol reactions that tolerate base-sensitive functional groups. Additionally, the Zn enolates are readily coupled with aryl bromides using typical Pd-catalyzed coupling methods.
Intramolecular cyclization reactions of aziridines with π-nucleophiles

We have found that aziridines will react with a variety of π-nucleophiles in intramolecular cyclization reactions to produce nitrogen containing core structures found in a variety of bioactive molecules. These cyclizations are more general and facile than corresponding intermolecular reactions. We have examined the effects of ring size, π-nucleophile identity and substitution on this reaction.
Sagittal subtalar and talocrural joint assessment between barefoot and shod walking: A fluoroscopic study.

Abstract Background While wearing shoes is common in daily activities, most foot kinematic models report results on barefoot conditions. It is difficult to describe foot position inside shoes. This study used fluoroscopic images to determine talocrural and subtalar motion. Research Question What are the differences in sagittal talocrual and subtalar kinematics between walking barefoot and while wearing athletic walking shoes? Methods Thirteen male subjects (mean age 22.9 ± 2.9 years, mean weight 77.2 ± 6.9 kg, mean height 178.2 ± 3.7 cm) screened for normal gait were tested. A fluoroscopy unit was used to collect images during stance. Sagittal motion of the talocrural and subtalar joints of the right foot were analyzed barefoot and in an athletic walking shoe. Results Shod talocrural position at heel strike was 6.0° of dorsiflexion and shod peak talocrural plantarflexion was 4.2°. Barefoot talocrural plantarflexion at heel strike was 4.2° and barefoot peak talocrural plantarflexion was 10.9°. Shod subtalar position at heel strike was 2.6° of plantarflexion and peak subtalar dorsiflexion was 1.5°. The barefoot subtalar joint at heel strike was in 0.4° dorsiflexion and barefoot peak subtalar dorsiflexion was 3.5°. As the result of wearing shoes, average walking speed and stride length increased and average cadence decreased. Comparing barefoot to shod walking there was a statistical significance in talocrural dorsiflexion and at heel strike and peak talocrural dorsiflexion, subtalar plantarflexion at heel strike and peak subtalar dorsiflexion, walking speed, stride length, and cadence. Significance This work demonstrates the ability to directly measure talocrural and subtalar kinematics of shod walking using fluoroscopy. Future work using this methodology can be used to increase understanding of hindfoot kinematics during a variety of non-barefoot activities.
Single cell observations show persister cells wake based on ribosome content

Since persister cells survive antibiotic treatments through dormancy and resuscitate to reconstitute infections, it is imperative to determine the rate at which these cells revive. Using two sets of Escherichia coli persister cells, those arising after antibiotic treatment at low levels and those generated at high levels by ceasing transcription via rifampicin pretreatment (shown to be bona fide persisters through eight sets of experiments), we used microscopy of single cells to determine that the resuscitation of dormant persisters is heterogeneous and includes cells that grow immediately. In all, five phenotypes were found during the observation of persister cells when fresh nutrients were added: (i) immediate division, (ii) immediate elongation followed by division, (iii) immediate elongation but no division, (iv) delayed elongation/division and (v) no growth. In addition, once cell division begins, the growth rate is that of exponential cells. Critically, the greater the ribosome content, the faster the persister cells resuscitate.
Isolating mitotic and meiotic germ cells from male mice by developmental synchronization, staging, and sorting

Abstract Isolating discrete populations of germ cells from the mouse testis is challenging, because the adult testis contains germ cells at every step of spermatogenesis, in addition to somatic cells. We present a novel method for isolating precise, high-purity populations of male germ cells. We first synchronize germ cell development in vivo by manipulating retinoic acid metabolism, and perform histological staging to verify synchronization. We use fluorescence-activated cell sorting to separate the synchronized differentiating germ cells from contaminating somatic cells and undifferentiated spermatogonia. We achieve ~90% purity at each step of development from undifferentiated spermatogonia through late meiotic prophase. Utilizing this “3 S” method (synchronize, stage, and sort), we can separate germ cell types that were previously challenging or impossible to distinguish, with sufficient yield for epigenetic and biochemical studies. 3 S expands the toolkit of germ cell sorting methods, and should facilitate detailed characterization of molecular and biochemical changes that occur during the mitotic and meiotic phases of spermatogenesis.
Structural and Magnetic Properties of a New Type of Ordered Oxygen-Deficient Perovskite, KMnVO4

A new ternary vanadate KMnVO4 was prepared by a solid-state reaction and was shown to be a new type of ordered oxygen-deficient perovskite ABO3 - δ with δ = 1/3. Its formula can be rewritten as (K2,Mn)[Mn,V2]O8□1. An ordered distribution of potassium and manganese atoms in the A site and of vanadium and manganese atoms in the B site is observed. The manganese atoms are in distorted octahedral and tetrahedral sites, whereas all of the vanadium atoms form VO43- tetrahedra. This oxide contains four different types of high-spin Mn2+ ions in equal number. Magnetic susceptibility and specific heat measurements as well as spin dimer analysis show that substantial antiferromagnetic spin-exchange interactions occur primarily among three of the four different types of Mn2+ ions, and the fourth Mn2+ ion remains paramagnetic down to 2 K.
Stereoselective Synthetic Approaches to Highly Substituted Cyclopentanes via Electrophilic Additions to Mono-, Di-, and Trisubstituted Cyclopentenes

Electrophilic additions to allylically substituted alkenes are of broad synthetic utility. The control of stereoselectivity in such reactions has attracted considerable interest. However, the effect of allylic and homoallylic substituents in cyclopentenyl systems has not been investigated systematically. Studies on a series of mono, di-, and trisubstituted cyclopentenes are reported in which trans-vicinal-additions favor a syn-selective approach of electrophiles to the cyclopentene system. The formal addition of HOBr, HOCl, CH3SCl, and dimethyl(methylthio)sulfonium tetrafluoroborate (DMTSF)/NaN3 with a variety of cyclopentene substrates has been carried out, and the effects of various allylic substituents on these selectivities have been examined. Additions of HOBr, HOCl, and DMTSF to highly functionalized substrates proceed predictably with syn selectivity, giving predominantly or exclusively one product. Methanesulfenyl chloride additions are less predictable, but can be tuned by suitable alteration of ...
High-throughput Discovery of Topologically Non-trivial Materials using Spin-orbit Spillage.

We present a novel methodology to identify topologically non-trivial materials based on band inversion induced by spin-orbit coupling (SOC) effect. Specifically, we compare the density functional theory (DFT) based wavefunctions with and without spin-orbit coupling and compute the ‘spin-orbit-spillage’ as a measure of band-inversion. Due to its ease of calculation, without any need for symmetry analysis or dense k-point interpolation, the spillage is an excellent tool for identifying topologically non-trivial materials. Out of 30000 materials available in the JARVIS-DFT database, we applied this methodology to more than 4835 non-magnetic materials consisting of heavy atoms and low bandgaps. We found 1868 candidate materials with high-spillage (using 0.5 as a threshold). We validated our methodology by carrying out conventional Wannier-interpolation calculations for 289 candidate materials. We demonstrate that in addition to Z2 topological insulators, this screening method successfully identified many semimetals and topological crystalline insulators. Importantly, our approach is applicable to the investigation of disordered or distorted as well as magnetic materials, because it is not based on symmetry considerations. We discuss some individual example materials, as well as trends throughout our dataset, which is available at the websites: https://www.ctcms.nist.gov/~knc6/JVASP.html and https://jarvis.nist.gov/ .
A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this paper, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision. In contrast to prior methods, we develop a mathematical framework that defines the types of mapping targets we uncover, establish probabilistic estimates of p-value and sensitivity, and demonstrate tolerance for alignment error rates up to 20%. With this framework, our algorithm automatically adapts to different minimum length and identity requirements and provides both positional and identity estimates for each mapping reported. For mapping human PacBio reads to the hg38 reference, our method is 290x faster than BWA-MEM with a lower memory footprint and recall rate of 96%. We further demonstrate the scalability of our method by mapping noisy PacBio reads (each \(\ge 5\) kbp in length) to the complete NCBI RefSeq database containing 838 Gbp of sequence and \(> 60,000\) genomes.
Essential Roles of the sppRA Fructose-Phosphate Phosphohydrolase Operon in Carbohydrate Metabolism and Virulence Expression by Streptococcus mutans.

ABSTRACT The dental caries pathogen Streptococcus mutans can ferment a variety of sugars to produce organic acids. Exposure of S. mutans to certain nonmetabolizable carbohydrates, such as xylitol, impairs growth and can cause cell death. Recently, the presence of a sugar-phosphate stress in S. mutans was demonstrated using a mutant lacking 1-phosphofructokinase (FruK) that accumulates fructose-1-phosphate (F-1-P). Here, we studied an operon in S. mutans, sppRA, which was highly expressed in the fruK mutant. Biochemical characterization of a recombinant SppA protein indicated that it possessed hexose-phosphate phosphohydrolase activity, with preferences for F-1-P and, to a lesser degree, fructose-6-phosphate (F-6-P). SppA activity was stimulated by Mg2+ and Mn2+ but inhibited by NaF. SppR, a DeoR family regulator, repressed the expression of the sppRA operon to minimum levels in the absence of the fructose-derived metabolite F-1-P and likely also F-6-P. The accumulation of F-1-P, as a result of growth on fructose, not only induced sppA expression, but it significantly altered biofilm maturation through increased cell lysis and enhanced extracellular DNA release. Constitutive expression of sppA, via a plasmid or by deleting sppR, greatly alleviated fructose-induced stress in a fruK mutant, enhanced resistance to xylitol, and reversed the effects of fructose on biofilm formation. Finally, by identifying three additional putative phosphatases that are capable of promoting sugar-phosphate tolerance, we show that S. mutans is capable of mounting a sugar-phosphate stress response by modulating the levels of certain glycolytic intermediates, functions that are interconnected with the ability of the organism to manifest key virulence behaviors. IMPORTANCEStreptococcus mutans is a major etiologic agent for dental caries, primarily due to its ability to form biofilms on the tooth surface and to convert carbohydrates into organic acids. We have discovered a two-gene operon in S. mutans that regulates fructose metabolism by controlling the levels of fructose-1-phosphate, a potential signaling compound that affects bacterial behaviors. With fructose becoming increasingly common and abundant in the human diet, we reveal the ways that fructose may alter bacterial development, stress tolerance, and microbial ecology in the oral cavity to promote oral diseases.
An asymmetric Kharasch reaction mediated by D-xylose: long range diastereocontrol

Abstract An asymmetric Kharasch-type atom transfer reaction was studied under 13 different sets of reaction conditions in order to obtain the highest levels of diastereoselection. The highest ratio of 12.5:1 (71%) was observed at low temperatures (−78°C) using the Lewis acid Eu(OTf) 3 . Because the new asymmetric center is so distant from the d -xylose, we propose a transition state involving two sugars. The conversion of the major product to a naturally occurring chiral γ-butyrolactone, under basic conditions, is described which also confirmed the diastereoselectivity and absolute stereochemistry of the Kharasch reaction.
Diels−Alder Reactions of Cyclic Isoimidium Salts

Diels−Alder reactions of cyclic isoimidium salts are described. The corresponding cycloadducts are obtained with high regio- and stereoselectivity. The use of homochiral cyclic isoimidium salts delivers cycloadducts with excellent diastereoselectivity (>99:1) that can be efficiently converted to enantiomerically pure lactones.
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity.

Summary CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web application to help biologists design crRNAs with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model organisms and can be easily extended to cover other species. CRISPR-RT will empower researchers in RNA editing. Availability and implementation Freely available at http://bioinfolab.miamioh.edu/CRISPR-RT. Contact liangc@miamioh.edu. Supplementary information Supplementary data are available at Bioinformatics online.
ARBoR: an identity and security solution for clinical reporting.

Motivation Clinical genome sequencing laboratories return reports containing clinical testing results, signed by a board-certified clinical geneticist, to the ordering physician. This report is often a PDF, but can also be a paper copy or a structured data file. The reports are frequently modified and reissued due to changes in variant interpretation or clinical attributes. Materials and methods To precisely track report authenticity, we developed ARBoR (Authenticated Resources in a Hashed Block Registry), an application for tracking the authenticity and lineage of versioned clinical reports even when they are distributed as PDF or paper copies. ARBoR tracks clinical reports as cryptographically signed hash blocks in an electronic ledger file, which is then exactly replicated to many clients. Results ARBoR was implemented for clinical reporting in the Human Genome Sequencing Center Clinical Laboratory, initially as part of the National Institute of Health's Electronic Medical Record and Genomics (eMERGE) project. Conclusions To date, we have issued 15 205 versioned clinical reports tracked by ARBoR. This system has provided us with a simple and tamper-proof mechanism for tracking clinical reports with a complicated update history.
MeshAdv: Adversarial Meshes for Visual Recognition

Highly expressive models such as deep neural networks (DNNs) have been widely applied to various applications. However, recent studies show that DNNs are vulnerable to adversarial examples, which are carefully crafted inputs aiming to mislead the predictions. Currently, the majority of these studies have focused on perturbation added to image pixels, while such manipulation is not physically realistic. Some works have tried to overcome this limitation by attaching printable 2D patches or painting patterns onto surfaces, but can be potentially defended because 3D shape features are intact. In this paper, we propose meshAdv to generate "adversarial 3D meshes" from objects that have rich shape features but minimal textural variation. To manipulate the shape or texture of the objects, we make use of a differentiable renderer to compute accurate shading on the shape and propagate the gradient. Extensive experiments show that the generated 3D meshes are effective in attacking both classifiers and object detectors. We evaluate the attack under different viewpoints. In addition, we design a pipeline to perform black-box attack on a photorealistic renderer with unknown rendering parameters.
Benchmarking collateral of triple-a rated securities

ABSTRACTThis paper presents a simple method to estimate the collateral associated with a Aaa tranche. The method is similar to historical simulation in the sense that there are no specific distribu...
Associations between HPV vaccination among women and their 11-14-year-old children.

The human papillomavirus (HPV) vaccine has been available in the United States for over a decade. We sought to examine the associations between self-reported receipt of HPV vaccination among women ...
Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure

MOTIVATION High-throughput conformation capture experiments, such as Hi-C provide genome-wide maps of chromatin interactions, enabling life scientists to investigate the role of the three-dimensional structure of genomes in gene regulation and other essential cellular functions. A fundamental problem in the analysis of Hi-C data is how to compare two contact maps derived from Hi-C experiments. Detecting similarities and differences between contact maps are critical in evaluating the reproducibility of replicate experiments and for identifying differential genomic regions with biological significance. Due to the complexity of chromatin conformations and the presence of technology-driven and sequence-specific biases, the comparative analysis of Hi-C data is analytically and computationally challenging. RESULTS We present a novel method called Selfish for the comparative analysis of Hi-C data that takes advantage of the structural self-similarity in contact maps. We define a novel self-similarity measure to design algorithms for (i) measuring reproducibility for Hi-C replicate experiments and (ii) finding differential chromatin interactions between two contact maps. Extensive experimental results on simulated and real data show that Selfish is more accurate and robust than state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION https://github.com/ucrbioinfo/Selfish.
Privacy preserving distributed optimization using homomorphic encryption

Abstract This paper studies how a system operator and a set of agents securely execute a distributed projected gradient-based algorithm. In particular, each participant holds a set of problem coefficients and/or states whose values are private to the data owner. The concerned problem raises two questions: how to securely compute given functions; and which functions should be computed in the first place. For the first question, by using the techniques of homomorphic encryption, we propose novel algorithms which can achieve secure multiparty computation with perfect correctness. For the second question, we identify a class of functions which can be securely computed. The correctness and computational efficiency of the proposed algorithms are verified by two case studies of power systems, one on a demand response problem and the other on an optimal power flow problem.
A Two-Phase Free Boundary Problem for Harmonic Measure

We study a 2-phase free boundary problem for harmonic measure first considered by Kenig and Toro and prove a sharp H\"older regularity result. The central difficulty is that there is no a priori non-degeneracy in the free boundary condition. Thus we must establish non-degeneracy by means of monotonicity formulae.
Distributed Charging Control of Electric Vehicles Using Online Learning

We propose an algorithm for distributed charging control of electric vehicles (EVs) using online learning and online convex optimization. Many distributed charging control algorithms in the literature implicitly assume fast two-way communication between the distribution company and EV customers. This assumption is impractical at present and also raises security and privacy concerns. Our algorithm does not use this assumption; however, at the expense of slower convergence to the optimal solution and by relaxing the sense of optimality. The proposed algorithm requires one-way communication, which is implemented through the distribution company publishing the pricing profiles for the previous days. We provide convergence results for the algorithm and illustrate the results through numerical examples.
Cube-like incidence complexes and their groups

The article studies power complexes and generalized power complexes, and investigates the algebraic structure of their automorphism groups. The combinatorial incidence structures involved are cube-like, in the sense that they have many structural properties in common with higher dimensional cubes and cubical tessellations on manifolds. Power complexes have repeatedly appeared in applications.
Community detection in political Twitter networks using nonnegative matrix factorization methods

Community detection is a fundamental task in social network analysis. In this paper, first we develop an endorsement filtered user connectivity network by utilizing Heider's structural balance theory and certain Twitter triad patterns. Next, we develop three Nonnegative Matrix Factorization frameworks to investigate the contributions of different types of user connectivity and content information in community detection. We show that user content and endorsement filtered connectivity information are complementary to each other in clustering politically motivated users into pure political communities. Word usage is the strongest indicator of users' political orientation among all content categories. Incorporating user-word matrix and word similarity regularizer provides the missing link in connectivity-only methods which suffer from detection of artificially large number of clusters for Twitter networks.
An Approximate Bayesian Long Short- Term Memory Algorithm for Outlier Detection

Long Short-Term Memory networks trained with gradient descent and back-propagation have received great success in various applications. However, point estimation of the weights of the networks is prone to over-fitting problems and lacks important uncertainty information associated with the estimation. However, exact Bayesian neural network methods are intractable and non-applicable for real-world applications. In this study, we propose an approximate estimation of the weights uncertainty using Ensemble Kalman Filter, which is easily scalable to a large number of weights. Furthermore, we optimize the covariance of the noise distribution in the ensemble update step using maximum likelihood estimation. To assess the proposed algorithm, we apply it to outlier detection in five realworld events retrieved from the Twitter platform.
On enforcing maximum principles and achieving element-wise species balance for advection-diffusion-reaction equations under the finite element method

These figures show the fate of the product in a transient transport-controlled bimolecular reaction under vortex-stirred mixing. The left figure is obtained using a popular numerical formulation, which violates the non-negative constraint. The right figure is based on the proposed computational framework. These figures clearly illustrate the main contribution of this paper: The proposed computational framework produces physically meaningful results for advective-diffusive-reactive systems, which is not the case with many popular formulations. We present a robust computational framework for advective-diffusive-reactive systems that satisfies maximum principles, the non-negative constraint, and element-wise species balance property. The proposed methodology is valid on general computational grids, can handle heterogeneous anisotropic media, and provides accurate numerical solutions even for very high Peclet numbers. The significant contribution of this paper is to incorporate advection (which makes the spatial part of the differential operator non-self-adjoint) into the non-negative computational framework, and overcome numerical challenges associated with advection. We employ low-order mixed finite element formulations based on least-squares formalism, and enforce explicit constraints on the discrete problem to meet the desired properties. The resulting constrained discrete problem belongs to convex quadratic programming for which a unique solution exists. Maximum principles and the non-negative constraint give rise to bound constraints while element-wise species balance gives rise to equality constraints. The resulting convex quadratic programming problems are solved using an interior-point algorithm. Several numerical results pertaining to advection-dominated problems are presented to illustrate the robustness, convergence, and the overall performance of the proposed computational framework.
The Classification of Reversible Bit Operations

We present a complete classification of all possible sets of classical reversible gates acting on bits, in terms of which reversible transformations they generate, assuming swaps and ancilla bits are available for free. Our classification can be seen as the reversible-computing analogue of Post's lattice, a central result in mathematical logic from the 1940s. It is a step toward the ambitious goal of classifying all possible quantum gate sets acting on qubits. Our theorem implies a linear-time algorithm (which we have implemented), that takes as input the truth tables of reversible gates G and H, and that decides whether G generates H. Previously, this problem was not even known to be decidable (though with effort, one can derive from abstract considerations an algorithm that takes triply-exponential time). The theorem also implies that any n-bit reversible circuit can be "compressed" to an equivalent circuit, over the same gates, that uses at most 2^{n}poly(n) gates and O(1) ancilla bits; these are the first upper bounds on these quantities known, and are close to optimal. Finally, the theorem implies that every non-degenerate reversible gate can implement either every reversible transformation, or every affine transformation, when restricted to an "encoded subspace." Briefly, the theorem says that every set of reversible gates generates either all reversible transformations on n-bit strings (as the Toffoli gate does); no transformations; all transformations that preserve Hamming weight (as the Fredkin gate does); all transformations that preserve Hamming weight mod k for some k; all affine transformations (as the Controlled-NOT gate does); all affine transformations that preserve Hamming weight mod 2 or mod 4, inner products mod 2, or a combination thereof; or a previous class augmented by a NOT or NOTNOT gate. Prior to this work, it was not even known that every class was finitely generated. Ruling out the possibility of additional classes, not in the list, requires involved arguments about polynomials, lattices, and Diophantine equations.
Service Rate Region of Content Access from Erasure Coded Storage

We consider storage systems in which $K$ files are stored over $N$ nodes. A node may be systematic for a particular file in the sense that access to it gives access to the file. Alternatively, a node may be coded, meaning that it gives access to a particular file only when combined with other nodes (which may be coded or systematic). Requests for file $f_{k}$ arrive at rate $\lambda _{k}$, and we are interested in the rate that can be served by a particular system. In this paper, we determine the set of request arrival rates for the a 3-file coded storage system. We also provide an algorithm to maximize the rate of requests served for file $K$ given $\lambda _{1}$,..., $\lambda _{K-1}$ in a general K-file case.
Robust logitboost and adaptive base class (ABC) logitboost

Logitboost is an influential boosting algorithm for classification. In this paper, we develop robust logitboost to provide an explicit formulation of tree-split criterion for building weak learners (regression trees) for logitboost. This formulation leads to a numerically stable implementation of logitboost. We then propose abc-logitboost for multi-class classification, by combining robust logitboost with the prior work of abc-boost. Previously, abc-boost was implemented as abc-mart using the mart algorithm. Our extensive experiments on multi-class classification compare four algorithms: mart, abc-mart, (robust) logitboost, and abc-logitboost, and demonstrate the superiority of abc-logitboost. Comparisons with other learning methods including SVM and deep learning are also available through prior publications.
A Coalition Formation Approach to Coordinated Task Allocation in Heterogeneous UAV Networks

The problem of adversary target detection and the subsequent task completion using a heterogeneous network of resource-constrained UAVs is considered. No prior knowledge about locations and required resources to identify these targets is available to the UAVs. In the proposed leader-follower coalition formation model, the UAV that first locates a target serves as the coalition leader and selects a group of follower UAVs to complete the task associated with the identified target. The goal of the coalition formation is to complete the designated tasks with minimal resource utilization. Another role of coalition members is to make the ground station aware of the detected adversary target by forwarding its signal to the station via a distributed cooperative relaying scheme. We also propose a reputation-based mechanism for coalition formation to monitor the cooperative behavior of the UAVs over the course of time and exclude potentially untrustworthy UAVs. Simulation results show the efficiency of the proposed method in forming optimal coalitions compared to alternative methods.
Leveraging mmWave Imaging and Communications for Simultaneous Localization and Mapping

In this work, we propose a novel approach for high accuracy user localization by merging tools from both millimeter wave (mmWave) imaging and communications. The key idea of the proposed solution is to leverage mmWave imaging to construct a high-resolution 3D image of the line-of-sight (LOS) and non-line-of-sight (NLOS) objects in the environment at one antenna array. Then, uplink pilot signaling with the user is used to estimate the angle-of-arrival and time-of-arrival of the dominant channel paths. By projecting the AoA and ToA information on the 3D mmWave images of the environment, the proposed solution can locate the user with a sub-centimeter accuracy. This approach has several gains. First, it allows accurate simultaneous localization and mapping (SLAM) from a single standpoint, i.e., using only one antenna array. Second, it does not require any prior knowledge of the surrounding environment. Third, it can locate NLOS users, even if their signals experience more than one reflection and without requiring an antenna array at the user. The approach is evaluated using a hardware setup and its ability to provide sub-centimeter localization accuracy is shown.
Surjective homomorphisms between surface braid groups

Let PBn(Sg,p) be the pure braid group of a genus g > 1 surface with p punctures. In this paper we prove that any surjective homomorphism PBn(Sg,p) → PBm(Sg,p) factors through one of the forgetful homomorphisms. We then compute the automorphism group of PBm(Sg,p), which gives a simpler proof of Irmak–Ivanov–McCarthy [IIM03, Theorem 1]. Surprisingly, in contrast to the n = 1 case, any automorphism of PBn(Sg,p) for n > 1 is geometric.
Preferred and Non-Preferred Creditors

International financial institutions (IFIs) generally enjoy preferred creditors treatment (PCT). Although PCT rarely appears in legal contracts, when sovereigns restructure bilateral or commercial debts they normally pay IFIs in full. This paper presents a model where a creditor, such as an IFI, that can commit to lend limited amounts at the risk-free rate and can refrain from lending into arrears is always repaid and adds value. The analysis suggests that IFIs should not mimic commercial lenders, but exploit their complementarity, even if banning commercial borrowing can sometimes be optimal. IFIs should also focus on countries with limited market access and should not be forced into debt restructurings.