bluuebunny/crossref_metadata_2025 huggingface dataset:
Better Together: Unifying Datalog and Equality Saturation
Authors: Zhang Yihong , Wang Yisu Remy , Flatt Oliver , Cao David , Zucker Philip , Rosenthal Eli , Tatlock Zachary , Willsey Max
Published: June 2023

We present egglog, a fixpoint reasoning system that unifies Datalog and equality saturation (EqSat). Like Datalog, egglog supports efficient incremental execution, cooperating analyses, and lattice-based reasoning. Like EqSat, egglog supports term rewriting, efficient congruence closure, and extraction of optimized terms.

We identify two recent applications -- a unification-based pointer analysis in Datalog and an EqSat-based floating-point term rewriter -- that have been hampered by features missing from Datalog but found in EqSat or vice-versa. We evaluate our system by reimplementing those projects in egglog. The resulting systems in egglog are faster, simpler, and fix bugs found in the original systems.
Feature-Sensitive Coverage for Conformance Testing of Programming Language Implementations
Authors: Park Jihyeok , Youn Dongjun , Lee Kanguk , Ryu Sukyoung
Published: June 2023

The conformance testing of programming language implementations is crucial to support correct and consistent execution environments. Because manually maintaining conformance tests for real-world programming languages is cumbersome and labor-intensive, researchers have presented various ways to make conformance tests effective and efficient. One such approach is to use graph coverage, one of the most widely-used coverage criteria, to generate tests that reach different parts of a mechanized language specification. Since mechanized specifications use functions or inductive definitions to describe the semantics of language features, traditional graph coverage criteria for software work as they are. However, they may not produce high-quality conformance tests because language implementations often have specialized execution paths for different features, even when their semantics descriptions use the same functions. Traditional graph coverage may not distinguish test requirements of such language features, which degrades the quality of conformance testing. Similarly, it may not distinguish test requirements of different parts of the same language feature when their semantics descriptions use the same functions.

We present feature-sensitive (FS) coverage as a novel coverage criterion to generate high-quality conformance tests for language implementations. It is a general extension of graph coverage, refining conventional test requirements using the innermost enclosing language features. We also introduce feature-call-path-sensitive (FCPS) coverage, a variant of FS coverage, and extend both coverage criteria using the 𝑘-limiting approach. To evaluate the effectiveness of the new coverage criteria for language implementations, we apply them to a mechanized specification of JavaScript. We extend JEST, the state-of-the-art JavaScript conformance test synthesizer using coverage-guided mutational fuzzing, with various FS and FCPS coverage criteria. For the latest JavaScript language specification (ES13, 2022), our tool automatically synthesizes 237,981 conformance tests in 50 hours with five coverage criteria. We evaluated the conformance of eight mainstream JavaScript implementations (four engines and four transpilers) with the synthesized conformance tests and discovered bugs in all of them. The tool detected 143 distinct conformance bugs (42 in engines and 101 in transpilers), 85 of which were confirmed by the developers and 83 of which were newly discovered bugs.
Psym: Efficient Symbolic Exploration of Distributed Systems
Authors: Pick Lauren , Desai Ankush , Gupta Aarti
Published: June 2023

Verification of distributed systems using systematic exploration is daunting because of the many possible interleavings of messages and failures.
When faced with this scalability challenge, existing approaches have traditionally mitigated state space explosion by avoiding exploration of redundant states (e.g., via state hashing) and redundant interleavings of transitions (e.g., via partial-order reductions).
In this paper, we present an efficient symbolic exploration method that not only avoids redundancies in states and interleavings, but additionally
avoids redundant computations that are performed during updates to states on transitions.
Our symbolic explorer leverages a novel, fine-grained, canonical representation of distributed system configurations (states) to identify opportunities for avoiding such redundancies on-the-fly.
The explorer also includes an interface that is compatible with abstractions for state-space reduction and with partial-order and other reductions for avoiding redundant interleavings.
We implement our approach in the tool Psym and empirically demonstrate that it outperforms a state-of-the-art exploration tool, can successfully verify many common distributed protocols, and can scale to multiple real-world industrial case studies across
Abstract Interpretation of Fixpoint Iterators with Applications to Neural Networks
Authors: Müller Mark Niklas , Fischer Marc , Staab Robin , Vechev Martin
Published: June 2023

We present a new abstract interpretation framework for the precise over-approximation of numerical fixpoint iterators.
Our key observation is that unlike in standard abstract interpretation (AI), typically used to over-approximate all reachable program states, in this setting, one only needs to abstract the concrete fixpoints, i.e., the final program states. Our framework targets numerical fixpoint iterators with convergence and uniqueness guarantees in the concrete and is based on two major technical contributions: (i) theoretical insights which allow us to compute sound and precise fixpoint abstractions without using joins, and (ii) a new abstract domain, CH-Zonotope, which admits efficient propagation and inclusion checks while retaining high precision.

We implement our framework in a tool called CRAFT and evaluate it on a novel fixpoint-based neural network architecture (monDEQ) that is particularly challenging to verify. Our extensive evaluation demonstrates that CRAFT exceeds the state-of-the-art performance in terms of speed (two orders of magnitude), scalability (one order of magnitude), and precision (25% higher certified accuracies).
Automated Expected Value Analysis of Recursive Programs
Authors: Avanzini Martin , Moser Georg , Schaper Michael
Published: June 2023

In this work, we study the fully automated inference of expected result values of probabilistic programs in the presence of natural programming constructs such as procedures, local variables and recursion. While crucial, capturing these constructs becomes highly non-trivial. The key contribution is the definition of a term representation, denoted as infer[.], translating a pre-expectation semantics into first-order constraints, susceptible to automation via standard methods. A crucial step is the use of logical variables, inspired by previous work on Hoare logics for recursive programs. Noteworthy, our methodology is not restricted to tail-recursion, which could unarguably be replaced by iteration and wouldn't need additional insights. We have implemented this analysis in our prototype ev-imp. We provide ample experimental evidence of the prototype's algorithmic expressibility.
Interval Parsing Grammars for File Format Parsing
Authors: Zhang Jialun , Morrisett Greg , Tan Gang
Published: June 2023

File formats specify how data is encoded for persistent storage. They cannot be formalized as context-free grammars since their specifications include context-sensitive patterns such as the random access pattern and the type-length-value pattern. We propose a new grammar mechanism called Interval Parsing Grammars IPGs) for file format specifications. An IPG attaches to every nonterminal/terminal an interval, which specifies the range of input the nonterminal/terminal consumes. By connecting intervals and attributes, the context-sensitive patterns in file formats can be well handled. In this paper, we formalize IPGs' syntax as well as its semantics, and its semantics naturally leads to a parser generator that generates a recursive-descent parser from an IPG. In general, IPGs are declarative, modular, and enable termination checking. We have used IPGs to specify a number of file formats including ZIP, ELF, GIF, PE, and part of PDF; we have also evaluated the performance of the generated parsers.
Covering All the Bases: Type-Based Verification of Test Input Generators
Authors: Zhou Zhe , Mishra Ashish , Delaware Benjamin , Jagannathan Suresh
Published: June 2023

Test input generators are an important part of property-based testing (PBT) frameworks. Because PBT is intended to test deep semantic and structural properties of a program, the outputs produced by these generators can be complex data structures, constrained to satisfy properties the developer believes is most relevant to testing the function of interest. An important feature expected of these generators is that they be capable of producingallacceptable elements that satisfy the function’s input type and generator-provided constraints. However, it is not readily apparent how we might validate whether a particular generator’s output satisfies thiscoveragerequirement. Typically, developers must rely on manual inspection and post-mortem analysis of test runs to determine if the generator is providing sufficient coverage; these approaches are error-prone and difficult to scale as generators become more complex. To address this important concern, we present a new refinement type-based verification procedure for validating the coverage provided by input test generators, based on a novel interpretation of types that embeds “must-style” underapproximate reasoning principles as a fundamental part of the type system. The types associated with expressions now capture the set of valuesguaranteedto be produced by the expression, rather than the typical formulation that uses types to represent the set of values an expressionmayproduce. Beyond formalizing the notion ofcoverage typesin the context of a rich core language with higher-order procedures and inductive datatypes, we also present a detailed evaluation study to justify the utility of our ideas.
Reliable Actors with Retry Orchestration
Authors: Tardieu Olivier , Grove David , Bercea Gheorghe-Teodor , Castro Paul , Cwiklik Jaroslaw , Epstein Edward
Published: June 2023

Cloud developers have to build applications that are resilient to failures and
interruptions. We advocate for a fault-tolerant programming model for the cloud
based on actors, retry orchestration, and tail calls. This model builds upon
persistent data stores and message queues readily available on the cloud. Retry
orchestration not only guarantees that (1) failed actor invocations will be
retried but also that (2) completed invocations are never repeated and (3) it
preserves a strict happen-before relationship across failures within call
stacks. Tail calls can break complex tasks into simple steps to minimize
re-execution during recovery. We review key application patterns and failure
scenarios. We formalize a process calculus to precisely capture the mechanisms
of fault tolerance in this model. We briefly describe our implementation. Using
an application inspired by a typical enterprise scenario, we validate
the functional correctness of our implementation and assess the impact
of fault preparedness and recovery on performance.
CommCSL: Proving Information Flow Security for Concurrent Programs using Abstract Commutativity
Authors: Eilers Marco , Dardinier Thibault , Müller Peter
Published: June 2023

Information flow security ensures that the secret data manipulated by a program does not influence its observable output. Proving information flow security is especially challenging for concurrent programs, where operations on secret data may influence the execution time of a thread and, thereby, the interleaving between different threads. Such internal timing channels may affect the observable outcome of a program even if an attacker does not observe execution times. Existing verification techniques for information flow security in concurrent programs attempt to prove that secret data does not influence the relative timing of threads. However, these techniques are often restrictive (for instance because they disallow branching on secret data) and make strong assumptions about the execution platform (ignoring caching, processor instructions with data-dependent runtime, and other common features that affect execution time).

In this paper, we present a novel verification technique for secure information flow in concurrent programs that lifts these restrictions and does not make any assumptions about timing behavior. The key idea is to prove that all mutating operations performed on shared data commute, such that different thread interleavings do not influence its final value. Crucially, commutativity is required only for an abstraction of the shared data that contains the information that will be leaked to a public output. Abstract commutativity is satisfied by many more operations than standard commutativity, which makes our technique widely applicable.

We formalize our technique in CommCSL, a relational concurrent separation logic with support for commutativity-based reasoning, and prove its soundness in Isabelle/HOL. We implemented CommCSL in HyperViper, an automated verifier based on the Viper verification infrastructure, and demonstrate its ability to verify challenging examples.
On the Zeros of Exponential Polynomials
Authors: Chonev Ventsislav , Ouaknine Joel , Worrell James
Published: June 2023

We consider the problem of deciding the existence of real roots of real-valued exponential polynomials with algebraic coefficients. Such functions arise as solutions of linear differential equations with real algebraic coefficients. We focus on two problems: theZero Problem, which asks whether an exponential polynomial has a real root, and theInfinite Zeros Problem, which asks whether such a function has infinitely many real roots. Our main result is that for differential equations of order at most 8 the Zero Problem is decidable, subject to Schanuel’s Conjecture, while the Infinite Zeros Problem is decidable unconditionally. We show moreover that a decision procedure for the Infinite Zeros Problem at order 9 would yield an algorithm for computing the Lagrange constant of any given real algebraic number to arbitrary precision, indicating that it will be very difficult to extend our decidability results to higher orders.
Adversarial Multi-task Learning for Efficient Chinese Named Entity Recognition
Authors: Yan Yibo , Zhu Peng , Cheng Dawei , Yang Fangzhou , Luo Yifeng
Published: June 2023

Named entity recognition (NER) is a fundamental task for information extraction applications. NER is challenging because of semantic ambiguities in academic literature, especially for non-Latin languages. Besides word semantic information, recognizing Chinese named entities needs to consider word boundary information, as words contained in Chinese texts are not separated with spaces. Leveraging word boundary information could help to determine entity boundaries and thus improve entity recognition performance. In this article, we propose to combine word boundary information and semantic information for named entity recognition based on multi-task adversarial learning. Specifically, we learn commonly shared boundary information of entities from multiple kinds of tasks, including Chinese word segmentation (CWS), part-of-speech (POS) tagging, and entity recognition, with adversarial learning. We learn task-specific semantic information of words from these tasks and combine the learned boundary information with the semantic information to improve entity recognition with multi-task learning. We then propose a compression method based on improved clustering to accelerate the proposed model. We conduct extensive experiments on four public benchmark datasets and two private datasets, compared with state-of-the-art baseline models, and the experimental results demonstrate that our model achieves considerable performance improvements on various evaluation datasets.
Welfare of Decapod Crustaceans with Special Emphasis on Stress Physiology
Authors: Wuertz Sven , Bierbach David , Bögner Mirko
Published: June 2023

Despite the growing concern on animal welfare in crustacean farming, both from legislative bodies as well as the common public, studies on welfare are limited and transfer to routine farming is missing. While biocertification schemes such as the Aquaculture Stewardship Council (ASC) involve a welfare dimension, these dimensions cannot be communicated to the consumer in a scientifically sound manner. Animal welfare is recognized as integral part of sustainability due to the losses associated with bad animal welfare standards and is considered highly relevant by consumers around the world. On the other hand, increasing animal welfare is also required for the optimisation of aquaculture technology. Behaviour of the animals suggests that decapod crustaceans experience nociception and there are several indications of pain perception as well. Also, distress has rarely been evaluated under routine aquaculture conditions and markers for chronic stress detection need to be identified. Indeed, most work on welfare of crustaceans focuses on cellular, oxidative stress only. Here, a comprehensive assessment of chronic stress should be carried out to optimize rearing technology in nurseries, during ongrowing, harvesting, anesthesia, transportation, and humane slaughter in terms of a good aquaculture practise.
Substituting Fish Meal with Tubiechong (Eupolyphaga sinensis) By-Product in the Diets of Largemouth Bass (Micropterus salmoides): Effects on Growth, Meat Quality, and Liver Health
Authors: Yue Yuhua , Tong Binbin , Chen Mingshi , Bao Xiaoxue , Qiu Yanming , Yang Ying , Yu Hui , Yu Yingying
Published: June 2023

A feeding trial was conducted to evaluate the effect of replacing 0% (control), 10% (T10), 20% (T20), 30% (T30), and 40% (T40) fish meal with a Tubiechong (Eupolyphaga sinensis) by-product in largemouth bass (Micropterus salmoides). Triplicate groups of 30 fish (

5.36
±
0.01
 
g

) were fed two times daily to apparent satiation for 60 days. The experimental results showed that the Tubiechong by-product could improve the growth performance of largemouth bass by increasing the FBW, WGR, and SGR until the replacement ratio was 40%. The quadratic regression analysis showed that the proportion of the Tubiechong by-product was 20.79% and 20.91%, respectively, when WGR and SGR were the best. Concurrently, the meat quality in the replacement groups was higher, specifically, the lightness and white values were higher, and the water loss rates were lower (

P
<
0.05

) than that in the control group. Moreover, the changes of the activities of CAT and GSH in the liver and T-AOC and GSH in serum could reveal the antioxidant capacity improvement of fish by the Tubiechong by-product. In the study, the replacement groups had lower T-CHO and HDL-C in serum (

P
<
0.05

), indicating that the Tubiechong by-product had an active role in improving blood lipid and regulating lipid metabolism. Simultaneously, the replacement groups had a normal structure with central hepatocytes’ nuclei and deviated from the center partly, while most of the hepatocytes were swollen in the control group with nuclear degeneration. The results showed that the Tubiechong by-product had a positive effect on the liver health of fish. Conclusively, the present study indicated that the partial dietary replacement of fish meal using the Tubiechong by-product (for up to 40% replacement level) in the diet of largemouth bass not only caused no adverse effects on fish health but also improved the growth performance, meat quality, antioxidant capacity, and hepatic health and is conducive to supplying nutritious, high-quality, and healthy aquatic products.
Field Temperature Data Analysis of the Water Resistance Performance of Freeze-Sealing Pipe Roof Used in Tunnel through Water-Rich Strata
Authors: Wu Yuanhao , Hong Zequn , Li Jinfei , Li Xinyi
Published: June 2023

A new presupporting technology named freeze-sealing pipe roof (FSPR) method was adopted in the construction of Gongbei tunnel (Zhuhai, P.R. China), which was a critical part of Hong Kong-Zhuhai-Macau Bridge (HZMB). The method combined the pipe-roofing with artificial ground freezing (AGF). The water resistance performance of FSPR surrounded by water-rich soils was studied based on the field temperature data. The time-dependent temperature changes of the frozen soil between two adjacent pipes were presented, and the thicknesses of the frozen soil in different freeze period were calculated. Besides, the remote temperature monitoring system used in this field research was presented systematically. The thermal effects of the Hurricane Nicole on the frozen soil wall were also observed. The results showed that the closure of frozen soil wall can be classified into two different modes. The frozen soil between the pipes before excavation had met the design requirements before excavation, and the FSPR maintained satisfied water resistance performance.
Nonpolynomial Spline Method for Singularly Perturbed Time‐Dependent Parabolic Problem with Two Small Parameters
Authors: Mekonnen Tariku Birabasa , Duressa Gemechis File
Published: June 2023

This study deals with the numerical solution of parabolic convection‐diffusion problems involving two small positive parameters and arising in modeling of hydrodynamics. To approximate the solution, the backward Euler method for time stepping and fitted trigonometric‐spline scheme for spatial discretization are considered on uniform meshes. The resulting scheme is shown to be uniformly convergent and its rate of convergence is one in the time variable and two in the space variable. The accuracy and rate of convergence are enhanced by using the Richardson extrapolation. To support the theoretically shown convergence analysis, we have taken some numerical examples and compared the absolute maximum error of the current method with some methods existing in the literature.
Effectiveness of Virtual Reality on the Caregiving Competence and Empathy of Caregivers for Elderly with Chronic Diseases: A Systematic Review and Meta-Analysis
Authors: Wang Jinyao , Li Qian , Cui Jun , Tu Shuangyan , Deng Zhiqiang , Yang Rong , Wang Ying
Published: June 2023

Aims. To synthesize evidence on the effectiveness of virtual reality-based training of caregivers for the elderly with chronic diseases. Background. With a growing number of elderly suffering from chronic diseases, caregivers who lack the necessary caregiving skills and competence need practical training. Nowadays, virtual reality in training is a promising approach due to technological advancements. Evaluation. We did a comprehensive search in the following six electronic databases (Web of Science, EMBASE, PubMed, SCOPUS, MEDLINE, and CINAHL) from their inception to April 2022 for original studies. We searched clinical trial registries of Clinical Trials.gov, International Standard Randomized Controlled Trial Number (ISRCTN) Registry, and the International Clinical Trials Registry Platform (ICTRP), for clinical trials. Key Issues. 7610 searched records were yielded, of which nine studies (four randomized controlled trials and five nonrandomized controlled trials) met the eligibility criteria and were included with 1090 caregivers. There was a small but significant overall effect of virtual reality-based interventions on caregivers’ caregiving competence (effect size = 0.362, 95% CI 0.181–0.543,

p
<
0.001

, I2 = 25.636). The subgroup analysis results showed significant improvement in caregiving competence in caregivers trained by the Dementia LiveTM program (effect size = 0.322, 95% CI 0.046–0.597,

p
=
0.022

). Regarding empathy, we did not find a statistically significant overall effect. The subgroup analysis results indicated that caregivers showed improvement in empathy after exposure to the Into D’mentia program (effect size = 0.265, 95% CI 0.015–0.515,

p
=
0.037

). Conclusions. Findings of our meta-analysis demonstrated that virtual reality could have merits for improving the caregiving competence of caregivers taking care of the elderly with chronic diseases. Implications for Nursing Management. Virtual reality may be a training alternative for caregivers to improve their caregiving competence. However, empowering the embodiment of virtual reality programs remains a technological challenge that needs to be addressed in the future.
Evaluation of the Antibacterial and Antibiofilm Effects of Ethyl Acetate Root Extracts from Vernonia adoensis (Asteraceae) against Pseudomonas aeruginosa
Authors: Masuku Mercy , Mozirandi Winnie , Mukanganyama Stanley
Published: June 2023

There is an increase in mortality and morbidity in the health facilities due to nosocomial infections caused by multidrug-resistant nosocomial bacteria; hence, there is a need for new antibacterial agents. Vernonia adoensis has been found to possess medicinal value. Plant phytochemicals may have antimicrobial activity against some resistant pathogens. The antibacterial efficacy of root extracts against Staphylococcus aureus and Pseudomonas aeruginosa was investigated using the microbroth dilution method. All extracts from the roots had an inhibitory effect on the growth of both bacteria, with the most susceptible being P. aeruginosa. The most potent extract was the ethyl acetate extract which caused a percentage inhibition of 86% against P. aeruginosa. The toxicity of the extract was determined on sheep erythrocytes, and its effect on membrane integrity was determined by quantifying the amount of protein and nucleic acid leakage from the bacteria. The lowest concentration of extract used, which was 100 µg/ml, did not cause haemolysis of the erythrocytes, while at 1 mg/ml of the extract, 21% haemolysis was observed. The ethyl acetate extract caused membrane impairment of P. aeruginosa, leading to protein leakage. The effect of the extract on the biofilms of P. aeruginosa was determined in 96-microwell plates using crystal violet. In the concentration range of 0–100 µg/ml, the extract inhibited the formation of biofilms and decreased the attachment efficiency. The phytochemical constituents of the extract were determined using gas chromatography-mass spectrometry. Results of analysis showed the presence of 3-methylene-15-methoxy pentadecanol, 2-acetyl-6-(t-butyl)-4-methylphenol, 2-(2,2,3,3-tetrafluoropropanoyl) cyclohexane-1,4-dione, E,E,Z-1,3,12-nonadecatriene-5,14-diol, and stigmasta-5,22-dien-3-ol. Fractionation and purification will elucidate the potential antimicrobial compounds which are present in the roots of V. adoensis.
Promising Modulatory Effects of Cenicriviroc on the Progression of Mouse Colorectal Cancer through Inhibition of CCR2_CCL2 Signaling Pathway
Authors: Eslami Mina , Azizi Jalilian Farid , Najafi Rezvan , Mahdavinezhad Ali , Amini Razieh
Published: June 2023

The study was designed to assay the efficacy of cenicriviroc (CVC) on the progression of mouse colorectal cancer by downregulation of CCR2_CCL2. In this study, CVC was used to inhibit the CCR2 receptor. Next, an MTT assay was performed to evaluate the cytotoxic effects of CVC on the CT26 cell line. CT26 cells were implanted subcutaneously in BALB/c mice. After tumor implantation, one group of animals received 20 mg/kg of CVC several times. The mRNA levels of CCR2, CCL2, VEGF, NF‐κB, c‐Myc, vimentin, and IL33 were determined in the CT26 cell line and then tumor tissues (after 21 days), by qRT‐PCR. Protein levels of the above‐mentioned targets were determined by western blot and ELISA. Flow cytometry was performed to assess the changes in apoptosis. Tumor growth inhibition was measured on the 1st, 7th, and 21st days after the first treatment. In both cell line and tumor cells treated with CVC, expression levels of the markers of our interest in mRNA and protein levels were significantly reduced compared to controls. A significantly higher apoptotic index was observed in CVC‐treated groups. The rates of tumor growth were significantly decreased on the 7th and 21st days after the first injection. To our knowledge, this was the first time that we demonstrated the promising effect of CVC on the development of CRC through inhibition of the CCR2_CCL2 signaling and its downstream biomarkers.
Positive Selection in Zinc Finger Protein Reveals Genetic Signatures of Adaptive Evolution in Undifferentiated Stem Cells during Evolution in Mammals
Authors: Ali Mahboob , Khan Palwasha , Mahmood Mahreen , Han Jilong , Afzal Gulnaz , Qadeer Iram , Azmal Syed Ali , El-Mouhty Nadia R. A. , Mahmoud Samy F. , Jafri Ibrahim , Ali Muhammad , Hashmi Nighat
Published: June 2023

Positive selection refers to the process by which certain genetic variations are more likely to be passed on to future generations because they confer some advantage in terms of survival or reproduction. Zinc finger proteins are a type of transcription factor that plays a role in regulating gene expression, particularly in undifferentiated stem cells. Suppose it has been found that certain zinc finger proteins show genetic signatures of positive selection in mammals. In that case, it suggests that these proteins may have played a role in adaptive evolution in undifferentiated stem cells. This could mean that the specific genetic changes in these zinc finger proteins gave an advantage to the organisms that possessed them, helping them survive and reproduce more effectively. These genetic changes may have allowed the organisms to adapt to changing environments or to develop new abilities, such as increased resistance to disease or faster growth. Undifferentiated stem cells that underwent adaptive evolution during the evolution of mammals can be identified genetically by the outcomes of positive selection on zinc finger proteins. Because of selection pressures like environmental shifts or the introduction of novel pathogens, it is plausible that some zinc finger proteins have experienced fast evolution. The emergence of novel activities or higher expression levels of these proteins as a result of this quick evolution may have given the creatures that possessed them a survival edge. Another possible outcome of positive selection in zinc finger proteins is the emergence of new genetic variations that allow for increased diversity and plasticity in stem cells. This increased diversity and plasticity could have allowed for more efficient adaptation to changing environments and could have played a role in the evolution of new organisms or new characteristics in existing organisms. Overall, the results of positive selection in zinc finger proteins can provide insight into how adaptive evolution occurred in undifferentiated stem cells during the evolution of mammals and how this evolution may have contributed to the development of new organisms and new characteristics and adaptations to changing environments.
Metasurface-Based Solar Absorption Prediction System Using Artificial Intelligence
Authors: Alam Md. Mottahir , Haque Ahteshamul , Khan Asif Irshad , Kasim Samir , Ali Pasha Amjad , Zafar Aasim , Irshad Kashif , Chaudhary Anis Ahmad , Samsuzzaman Md. , Azim Rezaul
Published: June 2023

Solar energy is a significant, environment-friendly source of renewable energy. The solar absorber transforms solar radiation into heat energy as an effective green energy source. Therefore, increasing its absorbing capacity can improve a solar absorber’s effectiveness. This paper proposes a tungsten tantalum alloy with silicon dioxide (WTa-SiO2) ceramic layer-based solar absorber system with two different metasurfaces to enhance absorptivity and boost the solar absorber efficacy. The absorbance is also improved by adjusting the resonator thickness and material thickness, and the maximum visible light absorption is achieved by the suggested solar filter design. Moreover, Golden Eagle Optimization (GE)-based deep AlexNet algorithm is proposed for predicting the parameter variation and their effect on absorbance. The optimization technique is used to increase the effectiveness of the solar absorber by optimizing the design parameters. The features from the WTa-SiO2 design are extracted by the proposed Principal Component-Autoencoder (PC-AE) method. Experimental results show that the proposed system can effectively predict absorptivity with a reduced computational time. The proposed method demonstrates superior prediction performance with an absorption prediction efficiency of 99.8% compared to the existing methods. Thus, the proposed WTa-SiO2 metasurface-based solar absorber can be used for photovoltaic applications.
Table S3 from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirström Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: June 2023

Supplementary Table 3. Table. Sample list with TP53 status. All 20 WT cases and their corresponding samples are listed. ‘Sample position’ refers to the individual sample and its position in a certain paraffin block (see Figure 1 for details.) IR= intermediate risk, BT= blastemal type, DA= diffuse anaplasia. Headings marked in grey show TP53 sequencing results; wt=wild type, mut=mutation, NA= not annotated (i.e. not sequenced), aa= amino acid, REF= reference nucleotide, ALT= alternative nucleotide, TP53 ref= number of wild type TP53 alleles, TP53 mut=number of TP53 mutated alleles. Genomic positions according to hg19. In all columns with grey headings (except column ‘TP53’), semicolons (;) denote when more than one unique TP53 mutation is present in the same tumor sample.
Table S2 from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirström Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: June 2023

Supplementary Table 2. Representativeness of study participants. Details on how the patients with Wilms tumor in the present study compare to the general population of patients diagnosed with with Wilms tumor.
Fig S3 from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirström Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: June 2023

Supplementary Figure 3. Relationship between anaplasia, copy number aberrations, regression and mitotic rate.
Fig S2 from Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirström Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: June 2023

Supplementary Figure 2. Complexity of phylogenetic tree, comparing WT DA to IR and BT WT.
Data from Dual PI3K/mTOR Inhibition in Colorectal Cancers with APC and PIK3CA Mutations
Authors: Foley Tyler M , Payne Susan N. , Pasch Cheri A. , Yueh Alex E. , Van De Hey Dana R , Korkos Demetra P , Clipson Linda , Maher Molly E , Matkowskyj Kristina A. , Newton Michael A. , Deming Dustin A.
Published: June 2023

Therapeutic targeting of the phosphoinositide 3-kinase (PI3K) pathway is an active area of research in multiple cancer types, including breast and endometrial cancers. This pathway is commonly altered in cancer and plays an integral role in numerous vital cellular functions. Mutations in the PIK3CA gene, resulting in a constitutively active form of PI3K, often occur in colorectal cancer (CRC), though the population of patients who would benefit from targeting this pathway has yet to be identified. In human CRCs, PIK3CA mutations most commonly occur concomitantly with loss of Adenomatous Polyposis Coli (APC). Here treatment strategies are investigated that target the PI3K pathway in colon cancers with mutations in APC and PIK3CA. CRC spheroids with Apc and Pik3ca mutations were generated and characterized confirming that these cultures represent the tumors from which they were derived. Pan and alpha isomer-specific PI3K inhibitors did not induce a significant treatment response, whereas the dual PI3K/mTOR inhibitors BEZ235 and LY3023414 induced a dramatic treatment response through decreased cellular proliferation and increased differentiation. The significant treatment responses were confirmed in mice with Apc and Pik3ca mutant colon cancers as measured using endoscopy with a reduction in median lumen occlusion of 53% with BEZ235 and a 24% reduction with reduction with LY3023414 compared to an increase of 53% in controls (p<0.001 and p=0.03, respectively). This response was also confirmed with 18F-FDG microPET/CT imaging. Implications: Spheroid models and transgenic mice suggest that dual PI3K/mTOR inhibition is a potential treatment strategy for APC and PIK3CA mutant colorectal cancers. Thus, further clinical studies of dual PI3K/mTOR inhibitors are warranted in colorectal cancers with these mutations.
Table S1 from Deconstructing Olfactory Epithelium Developmental Pathways in Olfactory Neuroblastoma
Authors: Finlay John B. , Abi Hachem Ralph , Jang David W. , Osazuwa-Peters Nosayaba , Goldstein Bradley J.
Published: June 2023

Tumor demographics separated by Hyams grade, Dulguerov T stage, and gene expression groups (low versus high) used for survival analysis in Figure 5 and Figure S4. Average Ki-67 mRNA expression obtained from bulk RNA-Seq outputs. Average Ki-67 index obtained from histology data reported by Classe et al., 2018. +/- in the last two columns is standard error of the mean (SEM).
Figure S4 from Deconstructing Olfactory Epithelium Developmental Pathways in Olfactory Neuroblastoma
Authors: Finlay John B. , Abi Hachem Ralph , Jang David W. , Osazuwa-Peters Nosayaba , Goldstein Bradley J.
Published: June 2023

Additional Kaplan-Meier survival curves based on Hyams Grade, Dulguerov T-stage, and MKI67 gene expression. Log-rank test used to determine statistical significance.
FIGURE 5 from Deconstructing Olfactory Epithelium Developmental Pathways in Olfactory Neuroblastoma
Authors: Finlay John B. , Abi Hachem Ralph , Jang David W. , Osazuwa-Peters Nosayaba , Goldstein Bradley J.
Published: June 2023

Glandular and olfactory ensheathing cell markers are present in low-grade ONB and are associated with increased survival. A, UMAP visualization of non-tumor olfactory mucosa scRNA-seq data depicts the cell type–specific expression of selected transcripts. PLP1 and S100B are expressed in olfactory ensheathing cells (OEC, red arrow); SOX9 is highly expressed in Bowman's glands (black arrow) and the TRPM5+ subset of microvillar cells (blue arrow). Scale bar shows normalized counts. B, Kaplan–Meier survival curves showing significant survival advantage in ONB tumors with higher expression of Bowman's gland and OEC markers. Statistical significance determined by log-rank test. C, SOX9+ cells are rarely Ki-67+ and do not colocalize with SOX2. In contrast, some SOX2+ cells show evidence of proliferation based on Ki-67 staining (arrowheads). D, The presence of S100B+ cells in a grade I ONB. Ki-67 costaining confirms the presence of the occasional proliferative S100B+ cell (arrowhead). In A, resp = respiratory; RBC = red blood cell; sus = sustentacular; in C and D, scale bar = 50 μm.
FIGURE 4 from Deconstructing Olfactory Epithelium Developmental Pathways in Olfactory Neuroblastoma
Authors: Finlay John B. , Abi Hachem Ralph , Jang David W. , Osazuwa-Peters Nosayaba , Goldstein Bradley J.
Published: June 2023

PRC2 complex expression in ONB. A, PRC2 transcripts in the core complex are mostly upregulated in high-grade ONB. B, EPOP expression is significantly increased in high-grade ONB compared with low grade, with no differences between low and high grade in proteins that form the PRC2.2 complex. For A and B, statistical significance assessed by Kruskal–Wallis test with post hoc Dunn test for multiple comparisons (*, P < 0.05; **, P < 0.01). C, EZH2 is present in basal cells and immature neurons (TUJ1+) but not in mature neurons (OMP+) in the normal human OE. D, Immunohistochemically, Ki-67+ cells are nearly uniformly positive for EZH2 and EED in a grade I ONB. Scale bars in C and D are 50 μm.
FIGURE 3 from Deconstructing Olfactory Epithelium Developmental Pathways in Olfactory Neuroblastoma
Authors: Finlay John B. , Abi Hachem Ralph , Jang David W. , Osazuwa-Peters Nosayaba , Goldstein Bradley J.
Published: June 2023

Patterns of gene expression in the normal differentiating OE. A, Trajectory UMAP depicting differentiation states across pseudotime, in seven normal olfactory mucosa biopsies scRNA-seq from Durante and colleagues, 2020 and Oliva and colleagues, 2021 (13, 24). B, Heat map showing canonical cell type–specific markers for selected OE cell stages. C, Schematic showing that the core PRC2 protein complex can combine with either EPOP+MTF2 to form PRC2.1 or with JARID2+AEBP2 to form PRC2.2. D, Heat map showing PRC2 gene expression (and IDH2). (HBC: horizontal basal cell; GBC: globose basal cell; INP: immediate neuronal precursor; iOSN: immature olfactory sensory neuron; mOSN: mature olfactory sensory neuron; PRC2: Polycomb repressive complex 2).
Supplementary Table 3 from A Mendelian Randomization Analysis of 55 Genetically Predicted Metabolic Traits with Breast Cancer Survival Outcomes in the Pathways Study
Authors: Fiorica Peter N. , Sheng Haiyang , Zhu Qianqian , Roh Janise M , Laurent Cecile A. , Ergas Isaac J , Delmerico Jennifer , Kwan Marilyn L , Kushi Lawrence H , Ambrosone Christine B , Yao Song
Published: June 2023

Time-varying covariates for Cox proportional hazard model
Supplementary Figure 2 from A Mendelian Randomization Analysis of 55 Genetically Predicted Metabolic Traits with Breast Cancer Survival Outcomes in the Pathways Study
Authors: Fiorica Peter N. , Sheng Haiyang , Zhu Qianqian , Roh Janise M , Laurent Cecile A. , Ergas Isaac J , Delmerico Jennifer , Kwan Marilyn L , Kushi Lawrence H , Ambrosone Christine B , Yao Song
Published: June 2023

Dot plot of statistically-significant findings stratified by tumor estrogen receptor (ER) status in whole analytic population, with 3,260 ER+ and 640 ER- individuals
Adaptação, tradução: o que há em um nome?
Authors: Hattnher Alvaro Luiz
Published: June 2023

Já faz algum tempo que os campos dos Estudos de Adaptação e dos Estudos de Tradução têm acenado mutuamente a certa distância um do outro, em um contato marcado muitas vezes por um possível temor de descaracterização ou perda de identidade de cada uma dessas áreas de investigação. Na verdade, as teorias de adaptação têm usado amplamente o termo ‘tradução’ para representar o processo de transformação que pode ocorrer entre arquiteturas textuais diferentes. Por sua vez, os estudiosos e, em especial, os profissionais da tradução usam o termo ‘adaptação’ para descrever procedimentos que, na verdade, representam o ato tradutório em si. Esse uso de ‘adaptação’ parece criar uma zona de conforto especial que pudesse abrigar tudo o que fosse um desvio dos posicionamentos de idolatria ao ‘texto original’. Examinar as formas como tais termos são empregados, em especial no Brasil, pode nos ajudar a repensar suas definições e limites.
“The Horse Dealer’s Daughter” e a Crítica ao Racionalismo, de D. H. Lawrence, na Tela: Uma Análise do Social e do Individual
Authors: Lopes Ana Caroline , Silva Carlos Augusto Viana da
Published: June 2023

O conto de “The Horse Dealer’s Daughter” (1918), de D. H. Lawrence, não segue a perspectiva dos projetos narrativos mais experimentais em termos de estrutura narrativa do período de sua publicação. Neste trabalho, investigaremos como o diretor/tradutor Robert Burgos, do filme The Horse Dealer’s Daughter (1983), lidou com esse texto na tela e quais as principais estratégias de tradução utilizadas para representar temas polêmicos desse universo literário particular no cinema, principalmente no que tange à temática do individual e do social. Como fundamentação teórica, utilizaremos a ideia de tradução como um tipo de reescritura (Lefevere 2007); o princípio da adaptação fílmica como tradução (Cattrysse (2014); e questões sobre representação (Shohat e Stam 2006).
Multimodalidade em duas traduções para Libras em vídeo do poema "Moça linda bem tratada" de Mário de Andrade
Authors: Vital Dafny Saldanha Hespanhol
Published: June 2023

O presente trabalho tem por objetivo comparar duas traduções para Libras do poema Moça linda bem tratada, de Mário de Andrade, realizadas na Universidade Federal do Rio de Janeiro (UFRJ), sendo a última no projeto Videoteca Acadêmica em Libras (ViaLibras), considerando-as como produtos multimodais (Diniz e Carneiro 2021; Baptista 2015). Para esta análise, consideraremos o conceito de multimodalidade e seus componentes design, produção e distribuição (Kress e Van Leeuwen 2001; Baptista 2015). Apresentaremos algumas escolhas tradutórias que diferem em cada tradução, relacionando com a ideia de recriação na tradução de textos criativos (Campos 1967 [1962]) e de recursos de rima e ritmo em línguas de sinais (Klamt 2014). Observou-se que a versão 2 apresentava multimodalidade mais rica que a versão 1, e que os leitores de ambas as traduções precisarão acionar competências previamente construídas no momento da leitura (Souza 2021). Espera-se que o trabalho possa trazer reflexões importantes a tradutores de Libras sobre a aplicabilidade dos aspectos relacionados à multimodalidade.
“Die Helige Bahn”: caminhos filosóficos e sendas poéticas em um poema de Friedrich Hölderlin
Authors: Faria Carolina Meire de
Published: June 2023

O poeta alemão Friedrich Hölderlin escreve, entre 1788 e 1793, uma série de poemas, hinos e elegias. Dentre esses textos se encontra o “Die heilige Bahn”, poema incompleto, concebido em 1787, quando o poeta estudava no monastério da cidade de Maulbronn. Este trabalho não se encontra nas coletâneas disponíveis que abrangem o período da fase de Tübingen, até este momento, no Brasil. Portanto, nossa proposta de tradução tem o objetivo de divulgar um texto inédito em português, colaborando para o conhecimento de um poema que consideramos ser de grande potência reflexiva. Além disso, propomos que no “Die heilige Bahn” já se expressam os gérmens do projeto filosófico do poeta cuja análise se faz necessária. Outro objetivo se refere ao interesse em contribuir para os estudos de textos de juventude de Hölderlin.
A primavera de Yosano Akiko: uma análise das flores e das cores em Midaregami
Authors: Buss Michelle Conterato , Martins Nathália da Silveira
Published: June 2023

O presente artigo tem por objetivo analisar poemas tanka da coletânea Midaregami (1901), da poeta japonesa Yosano Akiko (1878-1942), dentro da temática das flores e das cores em sua poesia. Buscamos empreender uma análise sobre as imagens e suas simbologias dentro do contexto cultural, histórico e literário japonês. Para tanto, a metodologia desse estudo e baseada em pesquisa bibliografica, mapeamento e análise de trechos em que flores e cores se destacam, focando em como elas são construídas como veículo condutor para revelar imagens que dialogam com a formação de Yosano como poeta e com outras obras da tradição literaria japonesa, chinesa e europeia. Utilizaremos o trabalho de Haruo Shirane (2012) como principal base teórica. A poética de Yosano, marcada por metáforas complexas e temáticas de amor e juventude, tem como traços marcantes em sua obra o individualismo, o sensual, o desejo e a mulher moderna. Após a definição inicial do corpus acima citado, selecionamos primeiramente 10 poemas traduzidos nos quais mapeamos as flores e as cores visando mapear a simbologia presente em suas metáforas. Dos 10 poemas, elegemos 7 e, a partir destes, examinamos a presença das flores e das cores a partir do repertorio cultural japonês.