cssi/SciSciGPT-SciSciNet huggingface dataset:
Electrode Colonization by the Feammox Bacterium Acidimicrobiaceae sp. Strain A6.

ABSTRACT Acidimicrobiaceae sp. strain A6 (A6), from the Actinobacteria phylum, was recently identified as a microorganism that can carry out anaerobic ammonium (NH4+) oxidation coupled to iron reduction, a process also known as Feammox. Being an iron-reducing bacterium, A6 was studied as a potential electrode-reducing bacterium that may transfer electrons extracellularly onto electrodes while gaining energy from NH4+ oxidation. Actinobacteria species have been overlooked as electrogenic bacteria, and the importance of lithoautotrophic iron reducers as electrode-reducing bacteria at anodes has not been addressed. By installing electrodes in the soil of a forested riparian wetland where A6 thrives, in soil columns in the laboratory, and in A6-bioaugmented constructed wetland (CW) mesocosms and by operating microbial electrolysis cells (MECs) with pure A6 culture, the characteristics and performances of this organism as an electrode-reducing bacterium candidate were investigated. In this study, we show that Acidimicrobiaceae sp. strain A6, a lithoautotrophic bacterium, is capable of colonizing electrodes under controlled conditions. In addition, A6 appears to be an electrode-reducing bacterium, since current production was boosted shortly after the CWs were seeded with enrichment A6 culture and current production was detected in MECs operated with pure A6, with the anode as the sole electron acceptor and NH4+ as the sole electron donor. IMPORTANCE Most studies on electrogenic microorganisms have focused on the most abundant heterotrophs, while other microorganisms also commonly present in electrode microbial communities, such as Actinobacteria strains, have been overlooked. The novel Acidimicrobiaceae sp. strain A6 (Actinobacteria) is an iron-reducing bacterium that can colonize the surface of anodes in sediments and is linked to electrical current production, making it an electrode-reducing bacterium. Furthermore, A6 can carry out anaerobic ammonium oxidation coupled to iron reduction. Therefore, findings from this study open the possibility of using electrodes instead of iron as electron acceptors, as a means to promote A6 to treat NH4+-containing wastewater more efficiently. Altogether, this study expands our knowledge of electrogenic bacteria and opens the possibility of developing Feammox-based technologies coupled to bioelectric systems for the treatment of NH4+ and other contaminants in anoxic systems.
Mixed convection with uniform shear flow over horizontal and vertical walls

Abstract A study is made to determine similarity solutions for uniform shear flow along horizontal and vertical heated plates. Only for specified variations of the wall temperature along the plates are these solutions possible. For vertical walls the temperature must decrease as x − 1 ∕ 3 while for horizontal walls it must increase as x 1 ∕ 3 , where x is the streamwise coordinate along each semi-infinite plate.
Teacher self-efficacy in online education: a review of the literature

Although empirical validation of teacher self-efficacy in face-to-face environments continues, it remains a relatively new construct in online education. This literature review, which was conducted over academic databases and which examined work published in the past 15 years, explores three areas of research about teacher self-efficacy in online education: (1) ease of adopting online teaching, (2) online teaching self-efficacy in comparison to demographic and experience variables and (3) changes in teacher self-efficacy in professional development scenarios where self-efficacy was measured before and after treatment. Research studies demonstrate agreement (or no discernible disagreement) in the importance of system/curriculum quality in the implementation of online learning and the recognition that a measure of self-efficacy in online pedagogy has not yet been empirically derived. Researchers continue to examine the balance of technological and pedagogical knowledge that supports the development of teacher self-efficacy, the role of learner self-efficacy in teacher self-efficacy and whether teacher self-efficacy differs fundamentally in online education. In addition, it seems clear that empirical validation of the association of teacher self-efficacy and student success has yet to occur in online education with the rigour seen in face-to-face modes of delivery. Published: 17 October 2018 Citation: Research in Learning Technology 2018, 26 : 2047 - http://dx.doi.org/10.25304/rlt.v26.2047
Long-Run Growth of Financial Data Technology

"Big data" financial technology raises concerns about market inefficiency. A common concern is that the technology might induce traders to extract others' information, rather than to produce information themselves. We allow agents to choose how much they learn about future asset values or about others' demands, and we explore how improvements in data processing shape these information choices, trading strategies and market outcomes. Our main insight is that unbiased technological change can explain a market-wide shift in data collection and trading strategies. However, in the long run, as data processing technology becomes increasingly advanced, both types of data continue to be processed. Two competing forces keep the data economy in balance: data resolve investment risk, but future data create risk. The efficiency results that follow from these competing forces upend two pieces of common wisdom: our results offer a new take on what makes prices informative and whether trades typically deemed liquidity-providing actually make markets more resilient.
SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants.

Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function. In addition to understanding molecular mechanisms and interactions on the atomic scale, translational applications of those approaches include drug screening, development of novel molecular therapies, and targeted treatment planning. Supporting the continued development of these applications, we have developed the SNP2SIM workflow that generates reproducible molecular dynamics and molecular docking simulations for downstream functional variant analysis. The Python workflow utilizes molecular dynamics software (NAMD (Phillips et al., J Comput Chem 26(16):1781-802, 2005), VMD (Humphrey et al., J Mol Graph 14(1):33-8, 27-8, 1996)) to generate variant specific scaffolds for simulated small molecule docking (AutoDock Vina (Trott and Olson, J Comput Chem 31(2):455-61, 2010)). SNP2SIM is composed of three independent modules that can be used sequentially to generate the variant scaffolds of missense protein variants from the wildtype protein structure. The workflow first generates the mutant structure and configuration files required to execute molecular dynamics simulations of solvated protein variant structures. The resulting trajectories are clustered based on the structural diversity of residues involved in ligand binding to produce one or more variant scaffolds of the protein structure. Finally, these unique structural conformations are bound to small molecule ligand libraries to predict variant induced changes to drug binding relative to the wildtype protein structure. SNP2SIM provides a platform to apply molecular simulation based functional analysis of sequence variation in the protein targets of small molecule therapies. In addition to simplifying the simulation of variant specific drug interactions, the workflow enables large scale computational mutagenesis by controlling the parameterization of molecular simulations across multiple users or distributed computing infrastructures. This enables the parallelization of the computationally intensive molecular simulations to be aggregated for downstream functional analysis, and facilitates comparing various simulation options, such as the specific residues used to define structural variant clusters. The Python scripts that implement the SNP2SIM workflow are available (SNP2SIM Repository. https://github.com/mccoymd/SNP2SIM , Accessed 2019 February ), and individual SNP2SIM modules are available as apps on the Seven Bridges Cancer Genomics Cloud (Lau et al., Cancer Res 77(21):e3-e6, 2017; Cancer Genomics Cloud [ www.cancergenomicscloud.org ; Accessed 2018 November]).
Two-photon physics

It is reviewed how Compton scattering sum rules relate low-energy nucleon structure quantities to the nucleon excitation spectrum. In particular, the GDH sum rule and recently proposed extensions of it will be discussed. These extensions are sometimes more calculationally robust, which may be an advantage when estimating the chiral extrapolations of lattice QCD results, such as for anomalous magnetic moments. Subsequently, new developments in our description of the nucleon excitation spectrum will be discussed, in particular a recently developed chiral effective field theory framework for the Δ(1232)-resonance region. Within this framework, we discuss results on N and Δ masses, the γNΔ transition and the Δ magnetic dipole moment.
Effect some Factors on the Structural Properties of the CdS Thin Films Prepared by Chemical Bath Deposition

CdS thin films were prepared by chemical bath deposition technique(CBD) onto the glass substrates at different conditions of preparation. The obtained samples are studied by X-Ray diffraction (XRD). The XRD patterns of CdS samples revealed the formation with a hexagonal crystal structure P36mc, and the clear effect of the concentration of thiourea , cadmium sulfide ,NaOH ,time and temperature deposition, and annealing temperature ,on the structure of the prepared thin films . through the study , we found that the samples have preferred orientation along [002] , also the thickness of thin films decrease with deposition time after certain value , with the appearance of free cadmium . It has been found that the 200 ° C is the best temperature for annealing to improve the other structural and physical properties of films. Keywords :Structure properties, CdS Thin films ,Chemical Bath Deposition.
Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools.

We produced an extensive collection of deep re-sequencing datasets for the Venter/HuRef genome using the Illumina massively-parallel DNA sequencing platform. The original Venter genome sequence is a very-high quality phased assembly based on Sanger sequencing. Therefore, researchers developing novel computational tools for the analysis of human genome sequence variation for the dominant Illumina sequencing technology can test and hone their algorithms by making variant calls from these Venter/HuRef datasets and then immediately confirm the detected variants in the Sanger assembly, freeing them of the need for further experimental validation. This process also applies to implementing and benchmarking existing genome analysis pipelines. We prepared and sequenced 200 bp and 350 bp short-insert whole-genome sequencing libraries (sequenced to 100x and 40x genomic coverages respectively) as well as 2 kb, 5 kb, and 12 kb mate-pair libraries (49x, 122x, and 145x physical coverages respectively). Lastly, we produced a linked-read library (128x physical coverage) from which we also performed haplotype phasing. Machine-accessible metadata file describing the reported data (ISA-Tab format)
The Impact of Scholarship on Contemporary “Gnosticism(s)”: A Case Study on the Apostolic Johannite Church and Jeremy Puma

This article examines the impact of academic discourses on Neo-Gnosticism. The identities and ritual practices of Neo-Gnostics are constructed with reference to Gnostic Studies. Analysis of two case studies (the Apostolic Johannite Church and Jeremy Puma) shows how academic discourse legitimizes, challenges, or reforms Gnostic identity in the twenty-first century.
The complex architecture and epigenomic impact of plant T-DNA insertions

The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion of a sequence of interest called Transfer-DNA (T-DNA) into any plant genome. Although these transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. Here we applied two single-molecule technologies and analyzed Arabidopsis thaliana lines from three widely used T-DNA insertion collections (SALK, SAIL and WISC). Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and the length of individual insertions from 27 to 236 kilobases. De novo nanopore sequencing-based assemblies for two segregating lines partially resolved T-DNA structures and revealed multiple translocations and exchange of chromosome arm ends. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. The unprecedented contiguous nucleotide-level resolution enabled an in-depth study of the epigenome at T-DNA insertion sites. SALK_059379 line T-DNA insertions were enriched for 24nt small interfering RNAs (siRNA) and dense cytosine DNA methylation, resulting in transgene silencing via the RNA-directed DNA methylation pathway. In contrast, SAIL_232 line T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. Additionally, we profiled the H3K4me3, H3K27me3 and H2A.Z chromatin environments around T-DNA insertions using ChIP-seq in SALK_059379, SAIL_232 and five additional T-DNA lines. We discovered various effect s ranging from complete loss of chromatin marks to the de novo incorporation of H2A.Z and trimethylation of H3K4 and H3K27 around the T-DNA integration sites. This study provides new insights into the structural impact of inserting foreign fragments into plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes.
Gradient-Based Aeroservoelastic Optimization with Static Output Feedback

Static output feedback considers an optimal low-order feedback matrix which directly connects the sensors to the control inputs. This work demonstrates the numerical techniques needed to compute the analytical gradient of the optimal feedback matrix with respect to design variables, which may then be used for gradient-based optimization. The derivatives are demonstrated for aeroservoelastic optimization under a series of closed- loop gust load alleviation constraints, considering a continuous stochastic gust load applied to a transport vehicle configuration, among other design constraints such as utter and maneuver loads. The optimal trade-o s between passive load alleviation and active load alleviation for static output feedback are compared with those from full-state feedback, which may be considered an upper-bound for effective sensor-based control.
Cause Marketing: Product Pricing, Design, and Distribution

Problem definition: In a cause marketing (CM) campaign, a firm donates part of its sales revenue to a charity for a social cause when customers purchase the cause-linked product. We study a firm’s ...
From Language to Goals: Inverse Reinforcement Learning for Vision-Based Instruction Following

Reinforcement learning is a promising framework for solving control problems, but its use in practical situations is hampered by the fact that reward functions are often difficult to engineer. Specifying goals and tasks for autonomous machines, such as robots, is a significant challenge: conventionally, reward functions and goal states have been used to communicate objectives. But people can communicate objectives to each other simply by describing or demonstrating them. How can we build learning algorithms that will allow us to tell machines what we want them to do? In this work, we investigate the problem of grounding language commands as reward functions using inverse reinforcement learning, and argue that language-conditioned rewards are more transferable than language-conditioned policies to new environments. We propose language-conditioned reward learning (LC-RL), which grounds language commands as a reward function represented by a deep neural network. We demonstrate that our model learns rewards that transfer to novel tasks and environments on realistic, high-dimensional visual environments with natural language commands, whereas directly learning a language-conditioned policy leads to poor performance.
Perioperative Risk Factors for Postoperative Delirium in Patients Undergoing Esophagectomy.

Background Postoperative delirium affects up to 50% of patients undergoing esophagectomy and is associated with negative outcomes. The perioperative risk factors for delirium in this population are not well understood. We conducted this study to assess perioperative risk factors for postoperative delirium among esophagectomy patients. Methods We performed a secondary data analysis of patients enrolled in a randomized controlled trial evaluating the efficacy of haloperidol prophylaxis postoperatively in reducing delirium among esophagectomy patients. Postoperative delirium was assessed twice daily using the Confusion Assessment Method for the ICU. Univariate and logistic regression analyses were performed to examine the association between perioperative variables and development of postoperative delirium. Results Of 84 consecutive esophagectomy patients, postoperative delirium developed in 27 (32%). These patients had higher Acute Physiology and Chronic Health Evaluation II scores (22.1 [SD, 6.5] vs 17.4 [SD, 6.8]; p = 0.003), longer mechanical ventilation days (1.7 [SD, 1.4] days vs 1.0 [SD, 1.1] days; p = 0.001), and longer intensive care unit (ICU) days (5.1 [SD, 2.6] days vs 2.6 [SD, 1.6] days; p Conclusions ICU length of stay was significantly associated with postoperative delirium. Other perioperative factors, including duration of procedure, blood loss, and hemoglobin levels, were not significantly associated with postoperative delirium.
Offloading Deadline-Constrained Cellular Traffic

In this work we study the problem of hard-deadline constrained data offloading in cellular networks. A single-Base-Station (BS) single-frequency-channel down-link system is studied where users request the same packet from the BS at the beginning of each time slot. Packets have a hard deadline of one time slot. The slot is divided into two phases. Out of those users having high channel gain allowing them to decode the packet in the first phase, one is chosen to rebroadcast it to the remaining users in the second phase. This gives the remaining users a second opportunity to potentially decode this packet before the deadline passes. By this, the BS has offloaded the packet to a “local network of users” which eliminates unnecessary BS retransmissions. The problem is modeled as a rate-adaptation and scheduling optimization problem to maximize the duration of this second phase such that each user receives a certain percentage of the packets. We show that the proposed algorithm has a polynomial complexity in the number of users with optimal performance.
Protecting effect of mass transport during electrochemical reduction of oxygenated carbon dioxide feedstocks

Electrochemical CO2 reduction is a promising path toward mitigating carbon emissions while also monetizing waste gas through chemicals production and storage of surplus renewable energy. However, deploying such a technology for use on industrial CO2 sources requires an understanding of the effects that gas feed impurities have upon CO2 reduction reaction (CO2RR). In this work, we elucidate the impact of molecular oxygen on the network of reactions occurring in a CO2 reduction system. Our findings indicate that for a planar, polycrystalline Au electrode in an aqueous environment, oxygen reduction current is limited by the transport characteristics specific to the cell geometry and solvent; as a result, mass transport confers a protective effect by mitigating the otherwise thermodynamically and kinetically favorable reduction of oxygen. The presence of oxygen does not appear to have a significant impact on either CO2RR or hydrogen evolution partial currents, indicating that the mechanisms of reduction reactions involving oxygen are independent of CO2RR and hydrogen evolution. Further, an electrokinetic mechanistic analysis indicates many feasible candidates for the rate-determining step of CO2RR; there is no indication that the CO2RR mechanism at PCO2 = 0.5 atm is altered by the presence of oxygen, as the Tafel slopes (59 mV dec−1) and reaction orders with respect to bicarbonate (0), CO2 (∼1.5), and protons (0 from lack of KIE) are consistent between systems with PO2 = 0 atm and those with PO2 = 0.5 atm. While this is promising for the robustness of CO2RR to oxygen impurities in gas feeds, the ultimate design tradeoff when utilizing CO2 sources containing oxygen is between the cost of separation processes and the corresponding cost of power inefficiency as a result of electrons lost to oxygen reduction. This represents a first step in understanding kinetic and transport considerations in the design of gas-impurity-tolerant CO2 reduction systems.
A full characterization of best-response functions in the lottery Colonel Blotto game

Abstract We fully characterize best-response functions in Colonel Blotto games with lottery contest success functions.
A Review and Extension of Merger and Acquisition Research Between REITs and General Corporations

Abstract We review the key differences between the finance and real estate literature on mergers and acquisitions (M&As) from 1980 to 2016. We summarize the differences in M&As between REITs and ge...
The Czar and the Slaves: Two Puzzles in the History of International Arbitration

In 1822, the Russian czar resolved a dispute over compensation for slaves fleeing to British lines during the War of 1812. American observers have long asserted that this canonical decision favored the United States. But new debate has recently arisen among historians. Uncovering evidence from diplomatic archives, this Article concludes that the czar did indeed side with the United States. Moreover, the case demonstrates how nineteenth-century American statesmen pressed international law into service in support of slavery.
Organizing to Organize: The Case of a Successful Long-Haul Campaign for Collective Bargaining Rights

After nearly four decades of campaigning, faculty and academic staff union members across the University of Wisconsin system won the right to bargain collectively in June 2009 when the governor signed legislation that modified state labor law. In this article, the author presents historical and interdisciplinary analyses of the organizational structures that were critical to the campaign’s success. While the case study should be interesting for academics across disciplines, the Wisconsin experience carries generalizable lessons for union organizing in any sector of the economy. In addition to cataloguing the tens of legislative attempts that faculty and academic staff unionists undertook to win collective bargaining rights in Wisconsin, the article juxtaposes the legislative goals with environmental variables, such as which political party controlled state government and how many faculty and academic staff were committed to the campaign at any given time as regular dues-paying members. It is clear in this...
One-step three-component reaction among organoboronic acids, amines and salicylaldehydes

Abstract Alkenyl, aryl and heteroaryl boronic acids react with amines and salicylaldehydes in a single step to give novel aminophenol derivatives.
Serum-Mediated Cleavage of Bacillus anthracis Protective Antigen Is a Two-Step Process That Involves a Serum Carboxypeptidase

ABSTRACT Much of our understanding of the activity of anthrax toxin is based on in vitro systems, which delineate the interaction between Bacillus anthracis toxins and the cell surface. However, these systems fail to account for the intimate association of B. anthracis with the circulatory system, including the contribution of serum proteins to the host response and processing of anthrax toxins. Using a variety of immunological techniques to inhibit serum processing of B. anthracis protective antigen (PA) along with mass spectrometry analysis, we demonstrate that serum digests PA via 2 distinct reactions. In the first reaction, serum cleaves PA83 into 2 fragments to produce PA63 and PA20 fragments, similarly to that observed following furin digestion. This is followed by carboxypeptidase-mediated removal of the carboxy-terminal arginine and lysines from PA20. IMPORTANCE Our findings identify a serum-mediated modification of PA20 that has not been previously described. These observations further imply that the processing of PA is more complex than currently thought. Additional study is needed to define the contribution of serum processing of PA to the host response and individual susceptibility to anthrax.
Palladium-phosphinous acid-catalyzed cross-coupling of aliphatic and aromatic acyl chlorides with boronic acids

Abstract The cross-coupling of aromatic and aliphatic acyl chlorides with arylboronic acids in the presence of 2.5 mol % of (t-Bu2POH)2PdCl2 (POPd) provides rapid access to ketones that are obtained in up to 93% yield. This palladium-phosphinous acid-catalyzed reaction is completed within 10 min when microwave irradiation is used, and it overcomes typical drawbacks of Friedel–Crafts acylation procedures such as harsh reaction conditions, untunable regiocontrol, and low substrate scope.
Recent Advances in s-Block Metal Carboxylate Networks

The use of s-block metal centers to construct coordination networks (CNs) is comparatively rare. The predominance of ionic forces and the absence of well-defined secondary building units make the rational construction of porous s-block CNs a challenging task. However, the nontoxic subset of these metals (Li, Na, K, Mg, Ca) based CNs, potentially useful for gas storage, separation, drug delivery, catalysis, and electrochemical applications, makes exploratory synthesis a worthwhile endeavor. In this review, we discuss the recent advances in the synthesis of s-block-CNs, produced using common carboxylic acid based linkers.
Attacking NTP's Authenticated Broadcast Mode.

We identify two attacks on the Network Time Protocol (NTP)’s cryptographically-authenticated broadcast mode. First, we present a replay attack that allows an on-path attacker to indefinitely stick a broadcast client to a specific time. Second, we present a denial-of-service (DoS) attack that allows an off-path attacker to prevent a broadcast client from ever updating its system clock; to do this, the attacker sends the client a single malformed broadcast packet per query interval. Our DoS attack also applies to all other NTP modes that are ‘ephemeral’ or ‘preemptable’ (including manycast, pool, etc). We then use network measurements to give evidence that NTP’s broadcast and other ephemeral/preemptable modes are being used in the wild. We conclude by discussing why NTP’s current implementation of symmetric-key cryptographic authentication does not provide security in broadcast mode, and make some recommendations to improve the current state of affairs.
Asymmetric synthesis and absolute stereochemistry of 4,4-bis-(trifluoromethyl)imidazoline based ACAT inhibitors

Abstract An asymmetric synthesis of 1, a potent orally active ACAT inhibitor, is reported. The absolute configuration of 1 has been determined by exciton CD spectra and X-ray crystal structure analysis.
Synthesis of conformationally tailored pentaazacyclopentadecanes. Preorganizing peptide cyclizations

Abstract A general method for the preparation of rigidified pentaazamacrocycles using trans-(1R,2R)-diaminocyclohexane as the conformational controller element. High macrocyclization yields have been obtained by strategic placement of the diaminocyclohexane group within the pseudopeptide backbone.
Effect of Fluorine Substitution on the Carbon Acidity of Methane, Methyl Isocyanide, Acetonitrile, Acetaldehyde, and Nitromethane

The effect of fluorine substitution on the acidity of the title compounds has been examined via ab initio molecular orbital theory. Multiple fluorine substitution has a synergetic effect on the acidity of methane. In the case of substituted methanes, the acidity of methyl isocyanide increases linearly with the fluorine substitution while a smaller effect is observed with acetonitrile, and little effect is found with acetaldehyde and nitromethane. The acetaldehydes are unique in that the anion of difluoroacetaldehyde remains planar, whereas all of the other difluoroanions become markedly pyramidal with large inversion barriers. The ionization process was examined in terms of the changes in atomic charges and bond orders. Fluorine has a larger effect on the acidity of compounds with pyramidal anions than those with planar ones. The stabilization appears to be a consequence of the competition for p character by the fluorine atoms which tends to place the anionic charge into an orbital with high s character.
Continuous-state HMMs for modeling time-series single-cell RNA-Seq data.

Motivation Methods for reconstructing developmental trajectories from time-series single-cell RNA-Seq (scRNA-Seq) data can be largely divided into two categories. The first, often referred to as pseudotime ordering methods are deterministic and rely on dimensionality reduction followed by an ordering step. The second learns a probabilistic branching model to represent the developmental process. While both types have been successful, each suffers from shortcomings that can impact their accuracy. Results We developed a new method based on continuous-state HMMs (CSHMMs) for representing and modeling time-series scRNA-Seq data. We define the CSHMM model and provide efficient learning and inference algorithms which allow the method to determine both the structure of the branching process and the assignment of cells to these branches. Analyzing several developmental single-cell datasets, we show that the CSHMM method accurately infers branching topology and correctly and continuously assign cells to paths, improving upon prior methods proposed for this task. Analysis of genes based on the continuous cell assignment identifies known and novel markers for different cell types. Availability and implementation Software and Supporting website: www.andrew.cmu.edu/user/chiehl1/CSHMM/. Supplementary information Supplementary data are available at Bioinformatics online.
Synthesis of Proteasome Inhibitor Omuralide Featuring Stereocontrolled Ugi Reaction and Novel Convertible Isocyanide

Stereocontrolled formal total synthesis of proteasome inhibitor omuralide is described. This is featured by the application of Ugi 4–center 3–component condensation reaction to prepare a highly functionalized pyroglutamic acid. To this end, a novel convertible isocyanide was developed, which is readily available by preparative synthesis from nitrotoluene. The hydrolysis of the sterically hindered C–terminal amide derived from the isocyanide was facilitated by the conversion to N–acylindole. By careful design of the γ–ketoacid precursor, a substrate–controlled diastereoselective Ugi reaction was successfully accomplished. Also, several highly functionalized pyroglutamic acid amides were prepared with high diastereoselectivity.
Time-resolved fluorescence intensity and anisotropy decays of 2,5-diphenyloxazole by two-photon excitation and frequency-domain fluorometry

We report the first time-resolved fluorescence measurements of the intensity and anisotropy decays resulting from two-photon excitation. A 10-GHz frequency-domain fluorometer (Rev. Sci. Instrum 1990, 61, 2331), equipped with two focal lenses and an emission monochromator, was used for steady-state and time-resolved measurements of PPO fluorescence. The emission spectra and the intensity decays observed with single- and two-photon excitation were essentially identical
One-step conversion of esters to acyl azides using diethylaluminum azide

Abstract Diethylaluminum azide, prepared from either sodium azide and diethylaluminum chloride or hydrazoic acid and triethylaluminum, reacts with esters to yield acyl azides in one step.
Organic synthesis in deep eutectic solvents: Paal–Knorr reactions

Abstract Deep eutectic solvents (the combination of either urea or glycerol with choline chloride) are effective solvents/catalysts for Paal–Knorr reactions to form pyrroles of furans. The reaction conditions are quite mild and do not require the addition of an additional Bronsted or Lewis acid catalyst. Given the inexpensive, non-toxic, and recyclable nature of the DES, these reaction conditions are simple and highly environmentally friendly.
Multidisciplinary Management of Patients with Unresectable Hepatocellular Carcinoma: A Critical Appraisal of Current Evidence

Hepatocellular carcinoma (HCC) is a leading cause of new cancer diagnoses in the United States, with an incidence that is expected to rise. The etiology of HCC is varied and can lead to differences between patients in terms of presentation and natural history. Subsequently, physicians treating these patients need to consider a variety of disease and patient characteristics when they select from the many different treatment options that are available for these patients. At the same time, the treatment landscape for patients with HCC, particularly those with unresectable HCC, has been rapidly evolving as new, evidence-based options become available. The treatment plan for patients with HCC can include surgery, transplant, ablation, transarterial chemoembolization, transarterial radioembolization, radiation therapy, and/or systemic therapies. Implementing these different modalities, where the optimal sequence and/or combination has not been defined, requires coordination between physicians with different specialties, including interventional radiologists, hepatologists, and surgical and medical oncologists. As such, the implementation of a multidisciplinary team is necessary to develop a comprehensive care plan for patients, especially those with unresectable HCC.
Alpha-band oscillations track the retrieval of precise spatial representations from long-term memory

Previous EEG work has shown that category-level information observed during encoding is recapitulated during memory retrieval, but studies with this time-resolved method have not demonstrated the r...
Equilibrium Geometry, Stability, and Magnetic Properties of Small MnO Clusters

The equilibrium geometries, binding energies, electronic structure, and magnetic properties of small stoichiometric MnO clusters are presented for the first time. The results are based on first-principles self-consistent calculations performed within the framework of density functional theory and the generalized gradient approximation. The nature of bonding between manganese and oxygen atoms is partly ionic. The charge transfer between Mn and O atoms, as well as the average Mn−O bond distance, remains insensitive to cluster size. However, the magnetic properties of these clusters exhibit very unusual characteristics. In contrast to their bulk behavior, the small clusters of MnO are ferromagnetic with magnetic moments per MnO molecule varying between 4 and 5 μB. Almost all of these moments are localized at the Mn site. The (MnO)8 cluster exhibits magnetic bistability, with ferromagnetic and antiferromagnetic configurations being nearly degenerate. The structural growth of these clusters also differs substa...
Internal Lewis Acid Assisted Benzoic Acid Catalysis

Internal Lewis acid assisted benzoic acid derivatives are introduced as new low-molecular-weight single-hydrogen-bond donor catalysts for the activation of nitroalkenes. Selected 2-borylbenzoic acid derivatives gave good yields of products in the addition of indoles to nitroalkenes. Control experiments suggest that both the internal Lewis acid coordination and the carboxylic acid functionalities are critical to the optimal performance of these catalysts.
Transition-Metal-Catalyzed Functionalization of Propargylic Alcohols and Their Derivatives

Propargylic alcohols are valuable starting materials in organic synthesis; they are easily accessible and can be functionalized further, either through the triple bond or the alcohol functionality. Certain transition metals such as ruthenium or gold have an affinity for propargylic alcohols or alkyne units, which allows for catalytic activation of these substance classes. This review article provides a survey of various transition-metal-catalyzed functionalizations of propargylic alcohols with an emphasis on the latest literature. Examples of nucleophilic propargylic substitution reactions, allene formation, addition and coupling reactions, cyclization reactions, Meyer–Schuster, Rupe and redox–isomerization reactions are given in the article, along with the scope and limitations of the corresponding transformations and mechanistic considerations. 1 Introduction 2 Nucleophilic Propargylic Substitution Reactions 2.1 Nucleophilic Propargylic Substitution Reactions with Propargylic Alcohols 2.2 Nucleophilic Substitution Reactions Employing Propargylic Esters 2.3 Propargylic Amination Reactions 2.4 Mechanisms 3 Allene Formation 4 Addition and Coupling Reactions Involving the Alkyne Unit 5 Cyclization Reactions 5.1 Intramolecular Cycloisomerization or Substitution Reactions 5.2 Intramolecular Cyclization Reactions Preceded by a Propargylic Substitution or Addition Reaction 6 Isomerization Reactions 6.1 Meyer–Schuster Rearrangements 6.2 The Rupe Rearrangement 6.3 Redox Isomerizations 7 Conclusion and Outlook
Synthesis and Structural Analysis of BaCrS2

A new ternary chromium sulfide, BaCrS2, was synthesized. This solid state compound crystallizes in the orthorhombic, centrosymmetric space group Pmmn (No. 59) with a = 4.2606(6) A, b = 4.7944(7) A, c = 9.443(1) A, V = 192.89(5) A3, and Z = 2. The solid is similar to a previously known structure BaNiS2 in which the Ni atom is coordinated to five sulfur atoms in a square pyramidal fashion. In BaCrS2, the square pyramid distorts such that the two S(basal)−Cr−S(basal) angles are no longer equal. Thus the BaCrS2 solid is orthorhombic whereas BaNiS2 is tetragonal. The distortion from the square pyramidal coordination in the title compound is traced to the broken degeneracy of the dxy and dxz set by a computational analysis.
Science Fiction: Fictitious Experiments in Patents

Although it may surprise scientists, one can receive a patent in many jurisdictions without implementing an invention in practice and demonstrating that it works as expected. Instead, inventors applying for patents are allowed to include predicted experimental methods and results, known as prophetic examples, as long as the examples are not written in the past tense. Allowing untested inventions to be patented may encourage earlier disclosures about new ideas and provide earlier certainty regarding legal rights — which may help small firms acquire financing to bring their ideas to market. Yet granting patents too early may also discourage researchers from doing the work to bring ideas to fruition. Even if allowing untested inventions to be patented is desirable, we think prophetic examples deserve closer scrutiny, and clearer labeling, because of the likelihood that they are unnecessarily confusing — particularly to scientists, many of whom read patents but are unlikely to appreciate that not all the claims are based on actual data.
DeepHoops: Evaluating Micro-Actions in Basketball Using Deep Feature Representations of Spatio-Temporal Data

Basketball is one of a number of sports which, within the past decade, have seen an explosion in quantitative metrics and methods for evaluating players and teams. However, it is still challenging to evaluate individual off-ball events (e.g., screens, cuts away from the ball etc.) in terms of how they contribute to the success of a possession. In this study, we develop a deep learning framework DeepHoops to process a unique dataset composed of spatio-temporal tracking data from NBA games in order to generate a running stream of predictions on the expected points to be scored as a possession progresses. We frame the problem as a multi-class sequence classification problem in which our model estimates probabilities of terminal actions taken by players (e.g. take field goal, turnover, foul etc.) at each moment of a possession based on a sequence of ball and player court locations preceding the said moment. Each of these terminal actions is associated with an expected point value, which is used to estimate the expected points to be scored. One of the challenges associated with this problem is the high imbalance in the action classes. To solve this problem, we parameterize a downsampling scheme for the training phase. We demonstrate that DeepHoops is well-calibrated, estimating accurately the probabilities of each terminal action and we further showcase the model's capability to evaluate individual actions (potentially off-ball) within a possession that are not captured by boxscore statistics.
To increase trust, change the social design behind aggregated biodiversity data

Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors 'at the source.' We show that this strategy falls systematically short of a full diagnosis of the underlying causes of distrust. In particular, trust in an aggregator is not just a feature of the data signal quality provided by the sources to the aggregator, but also a consequence of the social design of the aggregation process and the resulting power balance between individual data contributors and aggregators. The latter have created an accountability gap by downplaying the authorship and significance of the taxonomic hierarchies-frequently called 'backbones'-they generate, and which are in effect novel classification theories that operate at the core of data-structuring process. The Darwin Core standard for sharing occurrence records plays an under-appreciated role in maintaining the accountability gap, because this standard lacks the syntactic structure needed to preserve the taxonomic coherence of data packages submitted for aggregation, potentially leading to inferences that no individual source would support. Since high-quality data packages can mirror competing and conflicting classifications, i.e. unsettled systematic research, this plurality must be accommodated in the design of biodiversity data integration. Looking forward, a key directive is to develop new technical pathways and social incentives for experts to contribute directly to the validation of taxonomically coherent data packages as part of a greater, trustworthy aggregation process.
Transvaginal Cystolithotomy: A Novel Approach.

Abstract Objective To describe a novel surgical option for cystolithiasis management in female patients with no urethral access and prior abdominal surgeries. We present a 51-year-old female with a history of traumatic spinal cord injury with pelvic fractures and resultant neurogenic bladder. She underwent transabdominal bladder neck closure and bladder augmentation with continent diversion 2 years prior. CT abdomen/pelvis demonstrated a 3 cm stone and significant amount of bowel anterior to the bladder. Methods Pouchoscopy was performed via ureteroscope through the catheterizable stoma to assess stone location and mobility. A 14F-Foley was inserted for intraoperative decompression. An inverted-U incision was made on the anterior vaginal wall overlying the bladder base. Sharp and blunt dissection was performed in an avascular plane to dissect the vagina off of the bladder. Electrocautery was utilized to open perivesical tissue and the detrusor layer transversely. Further sharp dissection of perivesical tissue was achieved using Metzenbaum scissors. The bladder was filled via stoma Foley to improve visualization of bladder mucosa. Cystotomy was made and the 3 cm stone was removed, intact, using a Babcock. The bladder was closed in 2 layers with absorbable suture in running fashion. The bladder was refilled and the closure was watertight. The outer detrusor layer was closed with running locking 2-0 Polysorb, and a separate layer of perivesical tissue was closed over our 2-layer bladder closure using simple interrupted stitches. The vaginal flap was closed with running-locking 2-0 Polysorb. Results Operative time was 55 minutes. Estimated blood loss was 25 cc. The patient was discharged on postoperative-day 0 with a 14F-Foley in the catheterizable channel. The Foley was removed at the 3-week postoperative visit and patient resumed self-catheterization. No postoperative imaging was required. No complications were reported within 1 year. Conclusion We demonstrate the feasibility of transvaginal cystolithotomy in females with bowel overlying bladder and no urethral access.
An additive approximate Gaussian process model for large spatio‐temporal data

Motivated by a large ground‐level ozone data set, we propose a new computationally efficient additive approximate Gaussian process. The proposed method incorporates a computational‐complexity‐reduction method and a separable covariance function, which can flexibly capture various spatio‐temporal dependence structures. The first component is able to capture nonseparable spatio‐temporal variability, whereas the second component captures the separable variation. Based on a hierarchical formulation of the model, we are able to utilize the computational advantages of both components and perform efficient Bayesian inference. To demonstrate the inferential and computational benefits of the proposed method, we carry out extensive simulation studies assuming various scenarios of an underlying spatio‐temporal covariance structure. The proposed method is also applied to analyze large spatio‐temporal measurements of ground‐level ozone in the Eastern United States.
Bringing Plants & Soils to Life through a Simple Role-Playing Activity

Interactions are at the core of many ecological and evolutionary forces in nature. Plant–soil interactions provide a rich example of the interconnectedness of living systems, but they are hidden from everyday view and overshadowed in the classroom by more popular teaching examples involving animals, reptiles, or invertebrates. To highlight the importance and relevance of plant–soil relationships, we devised a simple role-playing activity suitable for college students. Specifically, the activity simulates how feedbacks between plants and soil environments influence plant species abundance and community richness. With this activity, students will gain a better understanding of these prolific, but overlooked, forms of biological interactions that impact the diversity and functioning of ecosystems.