Output List Research Articles

Microbiome modeling: a beginner's guide.

Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.

Traceable mixnets

We introduce the notion of traceable mixnets. In a traditional mixnet, multiple mix-servers jointly permute and decrypt a list of ciphertexts to produce a list of plaintexts, along with a proof of correctness, such that the association between individual ciphertexts and plaintexts remains completely hidden. However, in many applications, the privacy-utility tradeoff requires answering some specific queries about this association, without revealing any information beyond the query result. We consider queries of the following types: a) given a ciphertext in the mixnet input list, whether it encrypts one of a given subset of plaintexts in the output list, and b) given a plaintext in the mixnet output list, whether it is a decryption of one of a given subset of ciphertexts in the input list. Traceable mixnets allow the mix-servers to jointly prove answers to the above queries to a querier such that neither the querier nor a threshold number of mix-servers learn any information beyond the query result. Further, if the querier is not corrupted, the corrupted mix-servers do not even learn the query result. We first comprehensively formalise these security properties of traceable mixnets and then propose a construction of traceable mixnets using novel distributed zero-knowledge proofs (ZKPs) of set membership and of a statement we call reverse set membership. Although set membership has been studied in the single-prover setting, the main challenge in our distributed setting lies in making sure that none of the mix-servers learn the association between ciphertexts and plaintexts during the proof. We implement our distributed ZKPs and show that they are faster than state-of-the-art by at least one order of magnitude.

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.

As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity. Here we propose PathIntegrate, a method for integrating multi-omics datasets based on pathways, designed to exploit knowledge of biological systems and thus provide interpretable models for such studies. PathIntegrate employs single-sample pathway analysis to transform multi-omics datasets from the molecular to the pathway-level, and applies a predictive single-view or multi-view model to integrate the data. Model outputs include multi-omics pathways ranked by their contribution to the outcome prediction, the contribution of each omics layer, and the importance of each molecule in a pathway. Using semi-synthetic data we demonstrate the benefit of grouping molecules into pathways to detect signals in low signal-to-noise scenarios, as well as the ability of PathIntegrate to precisely identify important pathways at low effect sizes. Finally, using COPD and COVID-19 data we showcase how PathIntegrate enables convenient integration and interpretation of complex high-dimensional multi-omics datasets. PathIntegrate is available as an open-source Python package.

Determining and weighting effective outputs of humanities research to meet scientific and professional goals: A study of language and literature fields

Abstract Considering the specific nature of humanities and their fields and the need to design scientific outputs in proportion to these fields, the present study has sought to determine types of scientific outputs in the fields of language and literature and assess their significance and position for the evaluation of research. The study has been conducted in three stages: (1) extracting all the different types of scientific outputs in the fields of language and literature from published articles on the subject, (2) seeking opinions from experts in the fields of language and literature to modify and complete the list of outputs, and (3) Weighing scientific outputs according to the goals and approaches of research. According to the research findings, researchers in the fields of language and literature have generally preferred and prioritized three goals and approaches for their research activities: (1) production of science and promotion of knowledge foundations, (2) applicability and responsiveness to society’s problems, and (3) literary creation/creative literature. Based on the data obtained from the review of documents and interviews, scientific outputs can be divided into two categories of formats and activities. The formats adopted by language and literature researchers to share their results are journal article, book, research project, dissertation/thesis, and conference article. Besides, experts in the fields of language and literature have preferred to do their scientific activities in policy-making, social (media), social (scientific-promotional), and economic contexts. The journal article for the first goal and the book has more weight for the second and third goals. In all three goals, social (media) activities are prioritized.

ITaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.

The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.

SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models

BackgroundNext-generation sequencing technologies yield large numbers of genetic alterations, of which a subset are missense variants that alter an amino acid in the protein product. These variants can have a potentially destabilizing effect leading to an increased risk of misfolding and aggregation. Multiple software tools exist to predict the effect of single-nucleotide variants on proteins, however, a pipeline integrating these tools while starting from an NGS data output list of variants is lacking.ResultsThe previous version SNPeffect 4.0 (De Baets in Nucleic Acids Res 40(D1):D935–D939, 2011) provided an online database containing pre-calculated variant effects and low-throughput custom variant analysis. Here, we built an automated and parallelized pipeline that analyzes the impact of missense variants on the aggregation propensity and structural stability of proteins starting from the Variant Call Format as input. The pipeline incorporates the AlphaFold Protein Structure Database to achieve high coverage for structural stability analyses using the FoldX force field. The effect on aggregation-propensity is analyzed using the established predictors TANGO and WALTZ. The pipeline focuses solely on the human proteome and can be used to analyze proteome stability/damage in a given sample based on sequencing results.ConclusionWe provide a bioinformatics pipeline that allows structural phenotyping from sequencing data using established stability and aggregation predictors including FoldX, TANGO, and WALTZ; and structural proteome coverage provided by the AlphaFold database. The pipeline and installation guide are freely available for academic users on https://github.com/vibbits/snpeffect and requires a computer cluster.

Подходы к разработке информационного ресурса для управления потоками пациентов в медицинской организации в период глобального биовызова (на примере COVID‑19)

Patient flow management in medical organizations and rational use of human, material, medical and technical resources during the period of global biological challenge are the key to the effective functioning of the health care system. The formation of a set of indicators and criteria that allow the organization, planning and management of hospitalizations should be carried out with using of modern information aggregators integrated with medical information systems both at the level of a single hospital and in general across a network of medical organizations in the region that provide specialized medical care in hospitals. Purpose of the study is to develop an information system architecture that allows assessing the level of use of the resources of a medical organization during a global biological challenge (on the example of COVID-19) and distributing patient flows depending on its current capabilities. Materials and methods. Based on the data on the results of hospitalization of 7576 patients with COVID-19 in the Noginsk Central District Hospital, 6 consecutive stages of developing an information system were formed, including user stratification and determining roles and levels of access to information for them, classifying the resources of a medical organization, developing digital models of databases data, standardization and mapping of work processes in the structural divisions of the hospital, compiling a list of input (accounting) and output (reporting) indicators correlated with each other through the use of directories and registers, as well as on the basis of logical links. Results. Digital layouts of 4 registration cards were developed (data of medical workers; data of patients, medical services provided to them and the time for their implementation; use of medical equipment and time spent on research; registration of hospitalizations in hospital departments), 10 reporting forms (on the activities of medical workers and medical services rendered by them; on the structure of hospitalized and diagnostic tests carried out by them; on the use of medical equipment; on hospitalizations and the use of hospital beds) and templates of analytical reports for making management decisions based on the data of reporting forms for 6 categories of users (for medical workers of the relevant structural units of the hospital heads of structural subdivisions, deputy heads of a medical organization and head of a medical organization, a specialist of a public authority of a constituent entity of the Russian Federation in the field of health protection). Conclusion: The information resource proposed for development makes it possible to carry out a current assessment of the workload of medical workers and medical equipment, the employment of the bed fund, compliance with time parameters when performing standard operating procedures in the structural divisions of the hospital and ensure operational management of patient flows.

Contextual Isotope Ranking Criteria for Peak Identification in Gamma Spectroscopy Using a Large Database

Isotope identification is a recurrent problem in gamma spectroscopy with high purity germanium detectors. In this work, new strategies are introduced to facilitate this type of analysis. Five criteria are used to identify the parent isotopes making a query on a large database of gamma-lines from a multitude of isotopes producing an output list whose entries are sorted so that the gamma-lines with the highest chance of being present in a sample are placed at the top. A metric to evaluate the performance of the different criteria is introduced and used to compare them. Two of the criteria are found to be superior than the others: one based on fuzzy logic, and another that makes use of the gamma relative emission probabilities. A program called histoGe implements these criteria using a SQLite database containing the gamma-lines of isotopes which was parsed from WWW Table of Radioactive Isotopes. histoGe is Free Software and is provided along with the database so they can be used to analyze spectra obtained with generic gamma-ray detectors.

Algebraic Soft Decoding of Elliptic Codes

This paper proposes the algebraic soft decoding (ASD) for one-point elliptic codes, where the interpolation problem is solved from the perspective of module basis reduction. In ASD, the interpolation polynomial <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mathcal {Q}(x, y, z)$ </tex-math></inline-formula> is the minimum candidate of a Gröbner basis. Based on a multiplicity matrix, an interpolation ideal can be defined. With the decoding output list size, an equivalent interpolation module can be led to. By further defining the set of interpolation points, a sequence of modules from the elliptic curve coordinate ring can be obtained. Based on the Lagrange interpolation functions over elliptic function field, a basis of the interpolation module can be constructed. The desired Gröbner basis that contains <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mathcal {Q}$ </tex-math></inline-formula> can be determined by reducing the module basis. Re-encoding transform (ReT) is further introduced to reduce the basis reduction complexity. It is also shown that the interpolation can be facilitated by assessing the degree of the Lagrange interpolation polynomials. The decoding complexity is analyzed, which is verified by numerical results. That shows the advantage of this interpolation technique over the conventional Kötter’s interpolation. The ASD performance of elliptic codes is also presented.

Optimal Rate List Decoding over Bounded Alphabets Using Algebraic-geometric Codes

We give new constructions of two classes of algebraic code families that are efficiently list decodable with small output list size from a fraction 1-R-ε of adversarial errors, where R is the rate of the code, for any desired positive constant ε. The alphabet size depends only ε and is nearly optimal. The first class of codes are obtained by folding algebraic-geometric codes using automorphisms of the underlying function field. The second class of codes are obtained by restricting evaluation points of an algebraic-geometric code to rational points from a subfield . In both cases, we develop a linear-algebraic approach to perform list decoding, which pins down the candidate messages to a subspace with a nice “periodic” structure. To prune this subspace and obtain a good bound on the list size, we pick subcodes of these codes by pre-coding into certain subspace-evasive sets that are guaranteed to have small intersection with the sort of periodic subspaces that arise in our list decoding. We develop two approaches for constructing such subspace-evasive sets. The first is a Monte Carlo construction of hierearchical subspace-evasive (h.s.e.) sets that leads to excellent list size but is not explicit. The second approach exploits a further ultra-periodicity of our subspaces and uses a novel construct called subspace designs , which were subsequently constructed explicitly and also found further applications in pseudorandomness. To get a family of codes over a fixed alphabet size, we instantiate our approach with algebraic-geometric codes based on the Garcia–Stichtenoth tower of function fields. Combining this with pruning via h.s.e. sets yields codes list-decodable up to a 1-R-ε error fraction with list size bounded by O (1/ε), matching the existential bound for random codes up to constant factors. Further, the alphabet size can be made exp ( Õ (1/ε 2 )), which is not much worse than the lower bound of exp (Ω (1/ε)). The parameters we achieve are thus quite close to the existential bounds in all three aspects (error-correction radius, alphabet size, and list size) simultaneously. This construction is, however, Monte Carlo and the claimed list-decoding property only holds with high probability. Once the code is (efficiently) sampled, the encoding/decoding algorithms are deterministic with a running time O _ε ( N c ) for an absolute constant c , where N is the code’s block length. Using subspace designs instead for the pruning, our approach yields the first deterministic construction of an algebraic code family of rate R with efficient list decoding from 1-R-ε fraction of errors over an alphabet of constant size exp (Õ(1/ε 2 )). The list-size bound is upper bounded by a very slowly growing function of the block length N ; in particular, it is at most O(log ( r ) N ) (the r th iterated logarithm) for any fixed integer r . The explicit construction avoids the shortcoming of the Monte Carlo sampling at the expense of a slightly worse list size.

The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience.

Hit finding, scaffold hopping, and structure–activity relationship studies are important tasks in rational drug discovery. Implementation of these tasks strongly depends on the availability of compounds similar to a known bioactive molecule. SwissSimilarity is a web tool for low-to-high-throughput virtual screening of multiple chemical libraries to find molecules similar to a compound of interest. According to the similarity principle, the output list of molecules generated by SwissSimilarity is expected to be enriched in compounds that are likely to share common protein targets with the query molecule and that can, therefore, be acquired and tested experimentally in priority. Compound libraries available for screening using SwissSimilarity include approved drugs, clinical candidates, known bioactive molecules, commercially available and synthetically accessible compounds. The first version of SwissSimilarity launched in 2015 made use of various 2D and 3D molecular descriptors, including path-based FP2 fingerprints and ElectroShape vectors. However, during the last few years, new fingerprinting methods for molecular description have been developed or have become popular. Here we would like to announce the launch of the new version of the SwissSimilarity web tool, which features additional 2D and 3D methods for estimation of molecular similarity: extended-connectivity, MinHash, 2D pharmacophore, extended reduced graph, and extended 3D fingerprints. Moreover, it is now possible to screen for molecular structures having the same scaffold as the query compound. Additionally, all compound libraries available for screening in SwissSimilarity have been updated, and several new ones have been added to the list. Finally, the interface of the website has been comprehensively rebuilt to provide a better user experience. The new version of SwissSimilarity is freely available starting from December 2021.

Design of High-Speed Multiway Merge Sorting Networks Using Fast Single-Stage N-Sorters and N-Filters

In hardware such as FPGAs, Kenneth Batcher&#x2019;s Odd-Even Merge Sort and Bitonic Merge Sort are the state-of-the-art methodologies used to quickly sort a list of more than 16 input values. Both sorting networks feature merges of 2 sorted input lists into a single sorted output list. For both, a full sort of 64 and 512 input values requires 21 and 45 serial stages, respectively. Multiway merge sorting networks described here require significantly fewer serial stages. For example, 8-way merge networks fully sort 64 and 512 input values in 9 and 20 serial stages, less than half the number of the respective 2-way networks. When the multiway merge sorting networks utilize the single-stage <i>N</i>-sorters recently defined by the authors, they are considerably faster than Batcher&#x2019;s networks. In the AMD-Xilinx Ultrascale+ xcvu9p FPGA, the two 8-way merge networks have speedups of 1.85 and 1.74 versus the comparable 2-way networks. A fully pipelined 3-way merge network in this FPGA is capable of fully sorting 500 million lists of 729 unsorted 32-bit values in one second. In software, multiway merge methods are used to find the median of certain pixel rectangles in images, since the median can be determined in fewer stages than are required to fully sort the rectangle. However, the software still requires a series of many 2-sorter operations to find a median. These multiway merge median methods are dramatically sped up in hardware, where the authors&#x2019; new single-stage <i>N</i>-sorters and <i>N</i>-filters operate in parallel in each stage of the merge process.

GALExtin: an alternative online tool to determine the interstellar extinction in the Milky Way

ABSTRACT Estimates of interstellar extinction are essential in a broad range of astronomical research. In the last decades, several maps and models of the large-scale interstellar extinction in the Galaxy have been published. However, these maps and models have been developed in different programming languages, with different user interfaces and input/output formats, which makes using and comparing results from these maps and models difficult. To address this issue, we have developed a tool called GALExtin (http://www.galextin.org), which estimates interstellar extinction based on both available 3D models/maps and 2D maps. The user only needs to provide a list with coordinates (and distance) and to choose a model/map. GALExtin will then provide an output list with extinction estimates. It can be implemented in any other portal or model that requires interstellar extinction estimates. Here, a general overview of GALExtin is presented, along with its capabilities, validation, performance and some results.

Examination Surveillance TOTAL Database System.(Dept.E)

This paper introduces a database System for the examination committe surveillances. The system is implemented in TOTAL database management System. The end user interacts easily with the menu-driven TOTAL surveillance system through an application program. The application program acts as a simple query language since TOTAL does not support built-in query language. This query language allows the user to insert. modify and delete data in the database. It also allows the user to check data about examination and staff data sets and outputs surveillance tables for a faculty member, a grade or a date. An evaluation model has been built to evaluate the implemented system performance. search and retrieval times for output lists are measured and contrasted against modeled times under different loads.

Social value measurement in basketball clubs: is it possible?

In recent decades, sport has become one of the most important social activities in the&nbsp;Western world, showing an important capacity to attract people from different backgrounds. In&nbsp;this sense, basketball clubs do not pursue economic profit maximization, but instead they need to&nbsp;be analyzed according to their capacity of creating both social and economic value. In this regard,&nbsp;social accounting, as a tool that measures social effects, is also applicable to a basketball club. For that end, in this paper we have applied part of a social accounting methodology, the SPOLY&nbsp;Methodology (Retolaza, San-Jose, &amp; Ru&iacute;z-Roque&ntilde;i, 2015), to two elite basketball clubs of the ACB&nbsp;League (Spanish First Division), in order to make further steps towards the future monetization of&nbsp;social value. For that purpose, in this paper we will identify different outputs and proxy-s corresponding&nbsp;to a range of specific social value variables established in the interviews with the different&nbsp;stakeholders that were identified in a standard stakeholder map for elite basketball clubs (Mendizabal et al., 2020). Subsequently, 13 sports management experts, both lecturers and practitioners, have validated&nbsp;the list of specific social value outputs and proxy-s identified. The findings support the application&nbsp;of the SPOLY Methodology in basketball clubs, and the process of adaptation and validation carried&nbsp;out throughout the paper. The results also open a way towards the application of SPOLY Methodology&nbsp;in other top-flight sport organizations.

Inflect: Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis.

The CETSA and Thermal Proteome Profiling (TPP) analytical methods are invaluable for the study of protein–ligand interactions and protein stability in a cellular context. These tools have increasingly been leveraged in work ranging from understanding signaling paradigms to drug discovery. Consequently, there is an important need to optimize the data analysis pipeline that is used to calculate protein melt temperatures (Tm) and relative melt shifts from proteomics abundance data. Here, we report a user-friendly analysis of the melt shift calculation workflow where we describe the impact of each individual calculation step on the final output list of stabilized and destabilized proteins. This report also includes a description of how key steps in the analysis workflow quantitatively impact the list of stabilized/destabilized proteins from an experiment. We applied our findings to develop a more optimized analysis workflow that illustrates the dramatic sensitivity of chosen calculation steps on the final list of reported proteins of interest in a study and have made the R based program Inflect available for research community use through the CRAN repository [McCracken, N. Inflect: Melt Curve Fitting and Melt Shift Analysis. R package version 1.0.3, 2021]. The Inflect outputs include melt curves for each protein which passes filtering criteria in addition to a data matrix which is directly compatible with downstream packages such as UpsetR for replicate comparisons and identification of biologically relevant changes. Overall, this work provides an essential resource for scientists as they analyze data from TPP and CETSA experiments and implement their own analysis pipelines geared toward specific applications.

List-Decoding with Double Samplers

We strengthen the notion of double samplers, first introduced by Dinur and Kaufman [``High dimensional expanders imply agreement expanders,” in Proc. 58th IEEE Symp. on Foundations of Comp. Science, IEEE, 2017, pp. 974--985], which are samplers with additional combinatorial properties, and whose existence we prove using high-dimensional expanders. The ABNNR code construction [N. Alon et al., IEEE Trans. Inform. Theory, 38 (1992), pp. 509--516] achieves large distance by starting with a base code $C$ with moderate distance, and then amplifying the distance using a sampler. We show that if the sampler is part of a larger double sampler, then the construction has an efficient list-decoding algorithm. Our algorithm works even if the ABNNR construction is not applied to a base code $C$ but rather to any string. In this case the resulting code is approximate-list-decodable, i.e., the output list contains an approximation to the original input. Our list-decoding algorithm works as follows: It uses a local voting scheme from which it constructs a unique games constraint graph. The constraint graph is an expander, so we can solve unique games efficiently. These solutions are the output of the list-decoder. This is a novel use of a unique games algorithm as a subroutine in a decoding procedure, as opposed to the more common situation in which unique games are used for demonstrating hardness results. Double samplers and high-dimensional expanders are akin to pseudorandom objects in their utility, but they greatly exceed random objects in their combinatorial properties. We believe that these objects hold significant potential for coding theoretic constructions and view this work as demonstrating the power of double samplers in this context.

Howard Jacobson by Howard Jacobson

Reviewed by: Howard Jacobson by Howard Jacobson Joshua Lander (bio) David Brauner. Howard Jacobson. Manchester University Press, 2020. 248 pp. $110.50, hardback, $104.97, ebook. Howard Jacobson has been repeatedly called the “English Philip Roth,” a comparison that has at times irked and irritated the British-Jewish writer. The comparison is not without merit, however, as Jacobson’s oeuvre oozes with the same (icky) corporeal masculinist gumption that emanates from Roth’s prose. David Brauner’s Howard Jacobson (2020) is the first monograph devoted to Jacobson and sets out to illuminate the “rich complexity and nuance of [Jacobson’s] work, rather than to pin its author down” (2). Brauner triumphantly brings into focus the importance, relevance, and aesthetic complexities of Jacobson’s writings. Ironically, Brauner’s criticism shines most brightly when he elucidates the Rothian intertextualisms dotted throughout Jacobson’s work. The book is structured thematically and is split into three chapters: “Being Funny” (Chapter 1), “Being Men” (Chapter 2), and “Being Jewish” (Chapter 3). Brauner’s task is tricky in that Jacobson has written extensively, having chalked up sixteen novels and five nonfiction texts. To compound matters, Jacobson’s literary outputs have been rather uneven in terms of quality, meaning Brauner has the unenviable task of analyzing (though not necessarily defending) some of Jacobson’s lesser fictions. To his credit, Brauner generously connects these works by stressing how Jacobson’s ideas develop from his weaker fictions and emerge more strongly in his better (and more successful) novels. Helpfully, for those unfamiliar with Jacobson, Brauner in his Afterword identifies five of Jacobson’s most “exceptional” (203) novels: The Very Model of a Man (1992), The Mighty Walzer (1999), Kalooki Nights (2006), J (2014), and Live a Little (2019) (he also gives an honorary mention to Peeping Tom [1984], Who’s Sorry Now? [2002], The Act of Love [2008], and The Finkler Question [2010]). The fact that this monograph only has three sections to discuss Jacobson’s long list of literary outputs means each of Brauner’s chapters is quite lengthy. Thankfully, however, Brauner’s writing, especially in Chapter 3, is engaging, nuanced, and insightful, even when the source material itself is laborious and plodding. [End Page 115] Jacobson, as Brauner discusses in his Introduction, is a divisive writer with divisive opinions. His (formerly held) views on student-lecturer relationships are dubious and he, like Roth, has been accused of misogyny. His books, like Roth’s, are (for the most part) heavily focused on Jewish masculinity, and his representation of women is problematic (to put it mildly). Brauner provides us with a detailed overview of Jacobson’s public persona(s) and reviews his contentious personal politics but thankfully resists in the book’s main body any impulse to locate the author within his characters. Instead, Brauner offers a robust and critically considerate overview of Jacobson’s literature. In Chapter 1, Brauner examines Jacobson’s deployment of the comedic, ranging from “light-hearted sexual farce to acerbic political satire” to an “anti-pastoral sensibility and a preoccupation with literary politics” (42). Brauner deftly outlines the anti-pastoralism of Jacobson’s two novels Coming from Behind (1983) and Peeping Tom but seems to shift away from this topic in his discussion of Redback (1986), an academic satire set in Australia. Nevertheless, Brauner is adroit in ensuring his book creates links between each of the texts he discusses. Chapter 2, “Being Men: Masculinity, Mortality and Sexual Politics,” provides a detailed and lengthy analysis of masculinism in Jacobson’s fiction. Brauner refutes any suggestion that Jacobson’s novels conform to ideals of heteronormative masculinity, instead arguing Jacobson’s fiction perennially reconstructs ideas of what it means to be a man. The chapter’s analysis of Live a Little stands out, as does its discussion of The Very Model of a Man. Both sections elucidate the vivacity and complexity of Jacobson’s writings and his nuanced depiction of masculinity. The third chapter, “Being Jewish: Philip Roth, Antisemitism and the Holocaust,” is the strongest of the three, and for readers of Philip Roth Studies, I suspect the most eye-catching. The chapter’s strength stems from Brauner’s theoretical approach and the texts he examines. He...

An encoder–decoder LSTM-based EMPC framework applied to a building HVAC system

Numerous studies have demonstrated the benefit of economic model predictive control (EMPC) applied to building heating, ventilation, and air conditioning (HVAC) systems. However, the construction and training of predictive models for building HVAC systems are widely recognized as a key technological barrier preventing large-scale adoption of EMPC for buildings. In this work, an encoder–decoder long short-term memory-based EMPC framework is developed. The key advantage of the approach is that a model may be automatically generated from a list of inputs and outputs. From the definition of inputs and outputs, the constructed model may be trained and automatically embedded into the EMPC framework for real-time estimation and control. The overall end-to-end EMPC framework from model training to on-line estimation and control are described. To this end, the encoder–decoder model provides a natural framework for state estimation (encoder), which is required to provide an initial condition for the predictive model of EMPC (decoder). Closed-loop simulations using EnergyPlus are performed to demonstrate the approach. The simulated closed-loop system consists of a building zone from a multi-zone building, which is served by an air handling unit-variable air volume HVAC system. For the HVAC example considered, the trained encoder–decoder model can predict the indoor air temperature and HVAC sensible cooling rate of a building zone over a two-day horizon with high accuracy. Considering a time-of-use electric rate structure, the EMPC, which manipulates the zone temperature setpoint, can reduce the HVAC power consumption cost relative to keeping the zone temperature setpoint at its maximum value (i.e., minimum energy approach).

A probabilistic framework for improving reverse geocoding output

AbstractReverse geocoding, which transforms machine‐readable GPS coordinates into human‐readable location information, is widely used in a variety of location‐based services and analysis. The output quality of reverse geocoding is critical because it can greatly impact these services provided to end‐users. We argue that the output of reverse geocoding should be spatially close to and topologically correct with respect to the input coordinates, contain multiple suggestions ranked by a uniform standard, and incorporate GPS uncertainties. However, existing reverse geocoding systems often fail to fulfill these aims. To further improve the reverse geocoding process, we propose a probabilistic framework that includes: (1) a new workflow that can adapt all existing address models and unitizes distance and topology relations among retrieved reference data for candidate selections; (2) an advanced scoring mechanism that quantifies characteristics of the entire workflow and orders candidates according to their likelihood of being the best candidate; and (3) a novel algorithm that derives statistical surfaces for input GPS uncertainties and propagates such uncertainties into final output lists. The efficiency of the proposed approaches is demonstrated through comparisons to the four commercial reverse geocoding systems and through human judgments. We envision that more advanced reverse geocoding output ranking algorithms specific to different application scenarios can be built upon this work.