bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems
Authors: Zhang Yi , Takaki Yoshihiro , Yoshida-Takashima Yukari , Hiraoka Satoshi , Kurosawa Kanako , Nunoura Takuro , Takai Ken 
Published: October 2023

ABSTRACT

With the advance of high-throughput sequencing, the molecular basis of coevolutionary interaction between viruses and host microorganisms is predominantly elucidated by
in silico
genomic analyses, which revealed potential communication of genetic materials related to microbial immune systems such as the restriction-modification (R-M) system. However, the sequence-dependent information is often insufficient to output a conclusive argument without biochemical characterizations, particularly for homologs of rare genes considered less accurately annotated. We proposed a 1-day and one-pot workflow covering
in vitro
protein synthesis and enzymatic assays to confirm the exact function of putative R-M genes only with manual pipetting operations of microliter-scale liquids. The proof-of-demonstration experiments mainly focused on a series of putative R-M enzymes from our recently found deep-sea temperate bacteriophage and its host bacterium. Two new restriction endonucleases and two new methyltransferases with respective unambiguous substrate specificities, superior catalytic performance, or unique sequence preferences were quickly identified. A frequent discrepancy between sequence similarity search and single-molecule methylation-sensitive sequencing toward the prediction of recognition motifs can get settled with the established direct biochemical characterization. The proposed approach under the cell-free one-pot concept allows for preliminary characterizations of diverse categories (e.g., Types I, II, and III) of putative R-M systems at most laboratories with minimum equipment and time costs.

IMPORTANCE
The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.
Self-Similar Flows with a Shock Wave Advancing toward the Center or Axis of Symmetry
Authors: Valiev Kh. F. , Kraiko A. N. 
Published: October 2023

Abstract
We study one-dimensional flows of an ideal (inviscid and non-heat-conducting) perfect gas with an adiabatic exponent γ behind a shock wave moving toward the center (ν = 3) or axis (ν = 2) of symmetry in a cold gas at rest. Flows with a reflected shock wave and flows terminating with simultaneous arrival of a shock wave and a piston, which has compressed the gas into a point or line, to the center of symmetry are admitted.
The Influence of the Masker on the Localization of the Moving Signal in the Horizontal Plane
Authors: Agaeva M. Yu. , Nikitin N. I. 
Published: October 2023

Abstract
The effect of the masker on the localization of the moving signal was investigated in the free field conditions. The experiments were carried out in an anechoic chamber. Sound signals were presented from loudspeakers located on a semicircular arc in the horizontal plane. Bandpass noise bursts (5–18 kHz) were used to create a signal and a masker. The signal and the mask were uncorrelated stimuli and were created from two independent noise bursts. The stationary masker was always on the right at an angle of 15°. The moving signals traveled to or from the masker along two paths located at two places (–86° to –52° and –52° to –18°). The signal and the masker of 1-s duration each were presented either simultaneously or with a delay of the signal onset relative to the masker onset. The delay varied from 1 to 40 ms and 1200 ms. The subjects evaluated the start and end points of the trajectory of the moving sounds. Localization data for a moving signal under masking conditions were compared with spatial estimates of the same signal when presented in isolation (without a masker). Localization of the start and end points of the signal in masking condition was compared with localization of the moving source alone. Results showed that the masker affected the start and end points of the signal trajectory. The shift depended on the direction of movement. The starting points were always shifted in the direction of motion of the signal. The end points were shifted in the opposite direction.
Individualisation, personalisation and person-centredness in mental healthcare: a scoping review of concepts and linguistic network visualisation
Authors: Mayer Gwendolyn , Zafar Ali , Hummel Svenja , Landau Felix , Schultz Jobst-Hendrik 
Published: October 2023

BackgroundTargeted mental health interventions are increasingly described as individualised, personalised or person-centred approaches. However, the definitions for these terms vary significantly. Their interchangeable use prevents operationalisations and measures.ObjectiveThis scoping review provides a synthesis of key concepts, definitions and the language used in the context of these terms in an effort to delineate their use for future research.Study selection and analysisOur search on PubMed, EBSCO and Cochrane provided 2835 relevant titles. A total of 176 titles were found eligible for extracting data. A thematic analysis was conducted to synthesise the underlying aspects of individualisation, personalisation and person-centredness. Network visualisations of co-occurring words in 2625 abstracts were performed using VOSViewer.FindingsOverall, 106 out of 176 (60.2%) articles provided concepts for individualisation, personalisation and person-centredness. Studies using person-centredness provided a conceptualisation more often than the others. A thematic analysis revealed medical, psychological, sociocultural, biological, behavioural, economic and environmental dimensions of the concepts. Practical frameworks were mostly found related to person-centredness, while theoretical frameworks emerged in studies on personalisation. Word co-occurrences showed common psychiatric words in all three network visualisations, but differences in further contexts.Conclusions and clinical implicationsThe use of individualisation, personalisation and person-centredness in mental healthcare is multifaceted. While individualisation was the most generic term, personalisation was often used in biomedical or technological studies. Person-centredness emerged as the most well-defined concept, with many frameworks often related to dementia care. We recommend that the use of these terms follows a clear definition within the context of their respective disorders, treatments or medical settings.Scoping review registrationOpen Science Framework: osf.io/uatsc.
Developing an exercise intervention to improve bone mineral density in traumatic amputees: protocol for a Delphi study
Authors: Behan Fearghal P , Bull Anthony M J , Bennett Alexander 
Published: October 2023

IntroductionLower limb amputation results in reduced bone mineral density (BMD) on the amputated side. Exercise interventions have proven effective in improving BMD. However, such interventions have not been attempted in an amputee population. Exercises designed for people with intact limbs may not be suitable for amputees, due to joint loss and the mechanical interface between the exercise equipment and the femoral neck being mediated through a socket. Therefore, prior to intervention implementation, it would be prudent to leverage biomechanical knowledge and clinical expertise, alongside scientific evidence in related fields, to assist in intervention development. The objective of this study is to elicit expert opinion and gain consensus to define specific exercise prescription parameters to minimise/recover BMD loss in amputees.Methods and analysisThe Delphi technique will be used to obtain consensus among international experts; this will be conducted remotely as an e-Delphi process. 10–15 experts from ≥2 continents and ≥5 countries will be identified through published research or clinical expertise. Round 1 will consist of participants being asked to rate their level of agreement with statements related to exercise prescription to improve amputee BMD using a 5-point Likert Scale. Agreement will be deemed as ≥3 on the Likert Scale. Open feedback will be allowed in round 1 and any statement which less than 50% of the experts agree with will be excluded. Round 2 will repeat the remaining statements with the addition of any input from round 1 feedback. Round 3 will allow participants to reflect on their round 2 responses considering statistical representation of group opinion and whether they wish to alter any of their responses accordingly. Statements reaching agreement rates of 70% or above among the experts will be deemed to reach a consensus and will be implemented in a future exercise interventional trial.Ethics and disseminationEthical approval was received from Imperial College Research Ethics Committee (reference: 6463766). Delphi participants will be asked to provide digital informed consent. The findings will be disseminated through peer-reviewed publications.
Development of CORE-CM core outcome domain sets for trials of Chinese medicine for lumbar spinal stenosis
Authors: Sun Ya-Nan , An Yi , Weng Zhi-Wen , Zhou Yan-Ji , Wang Xi-You , Yu Chang-He 
Published: October 2023

ObjectivesMost Asian countries have employed Chinese medicine (CM) and Western medicine to treat lumbar spinal stenosis (LSS). Evidence synthesis and comparison of effectiveness are difficult since outcomes examined and presented through trials possess heterogeneity. This study aimed to solve the outcome problems for CM clinical trials in LSS by building a core outcome set (COS).MethodsTo achieve an agreement on a set of core outcome domains, a four-phase study was carried out. First, we identified candidate outcome domains by systematically reviewing trials. In addition, we identified outcome domains associated with patients by conducting semistructured interviews with patients. Next, outcome domains were processed through a national two-round Delphi survey, in which 18 patients and 21 experts were recruited. Finally, the above domains were converted as a core outcome domain set based on a consensus meeting, in which 24 stakeholders were recruited.ResultsSeventeen outcome subdomains were identified by the systematic review and interviews. The Delphi survey assigned a priority to four outcome domains in the first round and four outcomes additionally in the second round. The core outcome domains were determined through discussion and redefinition of outcomes in the consensus meeting: pain and discomfort, health-related quality of life, lumbar function, activities of daily living, measures of walking, patient global assessment, adverse events and CM-specific outcomes.ConclusionCOS-CM-LSS is likely to enhance the consistency of outcomes reported in clinical trials. In-depth research should be conducted for the exploration of the best methods to examine the above outcomes.
Unintentional injuries in children in the south of Iran, 2004–2019: a trend analysis of mortality rates
Authors: Azarbakhsh Habibollah , Rezaei Fatemeh , Hamedi Andishe , Hassanzadeh Jafar , Razeghi Ahmadreza , Mirahmadizadeh Alireza 
Published: October 2023

IntroductionInjury is one of the main causes of death and disability in the world. This study was designed to determine the trend of mortality rate and years of life lost (YLLs) due to unintentional injuries in children in southern Iran.MethodIn this cross-sectional study, we extracted all death reports due to unintentional injuries based on age, gender and the year of death based on International Classification of Diseases (ICD-10)from the Electronic Death Registration System. The YLL analysis due to premature death related to unintentional injuries was executed by the 2015 YLL template from the WHO using the Excel V.2016 software. To examine the trend of crude mortality rate and YLL rates for different years, joinpoint regression was used based on the log-linear model.ResultsDuring the 16-year study period (2004–2019), 6590 deaths due to unintentional injuries in children aged 0–19 years have occurred. The total YLLs due to unintentional injuries were 138 482 in males and 53 168 in females. The three main causes of YLLs in our study were transportation injuries (67.37%), drowning (7.19%) and burns (6.70%). According to the joinpoint regression analysis, the 16-year trend of YLL rate due to premature mortality was decreasing; the annual per cent change was −5.2% (95% CI −6.5% to −3.9%, p<0.001) for males and −4.3% (95% CI −5.7% to −3.0%, p<0.001) for females.ConclusionBased on the findings of this study, the trend of mortality and YLL rate has been decreasing. Road traffic injuries were the most frequent injuries and the most common cause of death. Mortality rates fell by half. To improve child survival, injuries must now be recognised as a major child health problem, and to prevent deaths from injuries in children, early and preventive measures should be taken into account.
Maternal psychiatric and somatic illness, and the risk of unintentional injuries in children: variation by type of maternal illness, type of injury and child age
Authors: Tanskanen Antti O , Metsä-Simola Niina , Volotinen Lotta , Danielsbacka Mirkka , Martikainen Pekka , Remes Hanna 
Published: October 2023

BackgroundMaternal mental illness appears to increase the risk of unintentional childhood injuries, which are a common cause of morbidity and mortality in early childhood. However, little is known about the variations in this association by type of injury and child’s age, and studies on the effects of maternal somatic illness on children’s injury risk are scarce.MethodsWe used Finnish total population register data from 2000 to 2017 to link 1 369 325 children to their biological mothers and followed them for maternal illness and childhood injuries until the children’s sixth birthday. Cox regression models were used to examine the associations between maternal illness and children’s injuries by type of illness (neurological, psychiatric and cancer), type of injury (transport injuries, falls, burns, drowning or suffocations, poisonings, exposure to inanimate and animate mechanical forces) and child’s age (<1 year-olds, 1–2 year-olds, 3–5 year-olds).ResultsAfter adjustment for family structure, maternal age at birth, maternal education, income, child’s gender, native language and region of residence, children of unwell mothers showed a higher risk of injuries (HR: 1.21, 95% CI: 1.19 to 1.23). This association was clear for maternal neurological (HR: 1.31, 95% CI: 1.26 to 1.36) and psychiatric illnesses (HR: 1.20, 95% CI: 1.18 to 1.23) but inconsistent for cancer. Maternal illness predicted an increased risk of injury across all age groups.ConclusionsMaternal mental and somatic illness may both increase children’s injury risk. Adequate social and parenting support for families with maternal illness may reduce childhood injury.
Safety and Efficacy of Flow Diverters for Treatment of Unruptured Anterior Communicating Artery Aneurysms: Retrospective Multicenter Study
Authors: Benalia Victor H C , Cortez Gustavo M , Mounayer Charbel , Saatci Isil , Cekirge H Saruhan , Kocer Naci , Islak Civan , Dabus Guilherme , Brinjikji Waleed , Baltacioglu Feyyaz , Pereira Vitor M , Nishi Hidehisa , Siddiqui Adnan H , Monteiro Andre , Lopes Demetrius K , Aghaebrahim Amin , Sauvageau Eric , Hanel Ricardo A 
Published: October 2023

BackgroundThe anterior communicating artery (AComm) region is the most common site of intracranial aneurysms, with increased rupture risk compared with other locations. Overall, flow diverters present as a safe and efficacious treatment for intracranial aneurysms, but there is paucity of data for their use in the treatment of unruptured AComm aneurysms. We present the largest multicentric analysis evaluating the outcomes of flow diverters in AComm aneurysm treatment.MethodsDatabases from 10 centers were retrospectively reviewed for unruptured AComm aneurysms treated with flow diverters. Demographics, clinical presentation, radiographic characteristics, procedural complications, and outcomes were assessed.ResultsA total of 144 patients harboring 147 AComm aneurysms were treated between January 2012 and December 2021. Seventy-four were women (51.4%) and median age was 60 (IQR 50–67) years. All were unruptured AComm aneurysms. Half of the cohort had similar anterior cerebral artery sizes (51.4%). The most common morphology was saccular (94.6%), with a branch involvement in 32.7% of cases. Median vessel diameter was 2.4 mm, and the Pipeline Flex was the most prevalent device (32.7%). Median follow-up time was 17 months, with complete occlusion in 86.4% at the last follow-up. Functional independence (modified Rankin Scale score 0–2) was reported in 95.1%. Intraprocedural complications occurred in 5.6%, and postoperative complications were noted in 9.7% of cases. Combined major complication and mortality rate was 2.1%.ConclusionsOur study suggests that flow diverters are a useful treatment for AComm aneurysms. Mid-term results indicated favorable aneurysm occlusion with a good safety profile. Additional prospective studies with longer follow-up periods and independent adjudication are warranted to better assess these results.
Equality Saturation Theory Exploration à la Carte
Authors: Pal Anjali , Saiki Brett , Tjoa Ryan , Richey Cynthia , Zhu Amy , Flatt Oliver , Willsey Max , Tatlock Zachary , Nandi Chandrakana 
Published: October 2023

Rewrite rules are critical in equality saturation, an increasingly popular technique
in optimizing compilers, synthesizers, and verifiers. Unfortunately,
developing high-quality rulesets is difficult and error-prone. Recent
work on automatically inferring rewrite rules does not scale to large
terms or grammars, and existing rule inference tools are monolithic and
opaque. Equality saturation users therefore struggle to guide inference and
incrementally construct rulesets. As a result, most users still
manually develop and maintain rulesets.
This paper proposes Enumo, a new domain-specific language for
programmable theory exploration. Enumo provides a small set of core
operators that enable users to strategically guide rule inference and
incrementally build rulesets. Short Enumo programs easily replicate
results from state-of-the-art tools, but Enumo programs can also scale
to infer deeper rules from larger grammars than prior approaches. Its
composable operators even facilitate developing new strategies for
ruleset inference. We introduce a new fast-forwarding strategy that does not require
evaluating terms in the target language, and can thus support domains
that were out of scope for prior work.
We evaluate Enumo and fast-forwarding across a variety of domains. Compared to
state-of-the-art techniques, enumo can synthesize better rulesets over a
diverse set of domains, in some cases matching the effects of
manually-developed rulesets in systems driven by equality saturation.
Structural Subtyping as Parametric Polymorphism
Authors: Tang Wenhao , Hillerström Daniel , McKinna James , Steuwer Michel , Dardha Ornela , Fu Rongxiao , Lindley Sam 
Published: October 2023

Structural subtyping and parametric polymorphism provide similar flexibility and reusability to programmers. For example, both features enable the programmer to provide a wider record as an argument to a function that expects a narrower one. However, the means by which they do so differs substantially, and the precise details of the relationship between them exists, at best, as folklore in literature.
In this paper, we systematically study the relative expressive power of structural subtyping and parametric polymorphism. We focus our investigation on establishing the extent to which parametric polymorphism, in the form of row and presence polymorphism, can encode structural subtyping for variant and record types. We base our study on various Church-style λ-calculi extended with records and variants, different forms of structural subtyping, and row and presence polymorphism.
We characterise expressiveness by exhibiting compositional translations between calculi. For each translation we prove a type preservation and operational correspondence result. We also prove a number of non-existence results. By imposing restrictions on both source and target types, we reveal further subtleties in the expressiveness landscape, the restrictions enabling otherwise impossible translations to be defined. More specifically, we prove that full subtyping cannot be encoded via polymorphism, but we show that several restricted forms of subtyping can be encoded via particular forms of polymorphism.
Rapid: Region-Based Pointer Disambiguation
Authors: Chitre Khushboo , Kedia Piyus , Purandare Rahul 
Published: October 2023

Interprocedural alias analyses often sacrifice precision for scalability. Thus, modern compilers such as GCC and LLVM implement more scalable but less precise intraprocedural alias analyses. This compromise makes the compilers miss out on potential optimization opportunities, affecting the performance of the application. Modern compilers implement loop-versioning with dynamic checks for pointer disambiguation to enable the missed optimizations. Polyhedral access range analysis and symbolic range analysis enable 𝑂 (1) range checks for non-overlapping of memory accesses inside loops. However, these approaches work only for the loops in which the loop bounds are loop invariants. To address this limitation, researchers proposed a technique that requires 𝑂 (𝑙𝑜𝑔 𝑛) memory accesses for pointer disambiguation. Others improved the performance of dynamic checks to single memory access by constraining the object size and alignment. However, the former approach incurs noticeable overhead due to its dynamic checks, whereas the latter has a noticeable allocator overhead. Thus, scalability remains a challenge.
In this work, we present a tool, Rapid, that further reduces the overheads of the allocator and dynamic checks proposed in the existing approaches. The key idea is to identify objects that need disambiguation checks using a profiler and allocate them in different regions, which are disjoint memory areas. The disambiguation checks simply compare the regions corresponding to the objects. The regions are aligned such that the top 32 bits in the addresses of any two objects allocated in different regions are always different. As a consequence, the dynamic checks do not require any memory access to ensure that the objects belong to different regions, making them efficient.
Rapid achieved a maximum performance benefit of around 52.94% for Polybench and 1.88% for CPU SPEC 2017 benchmarks. The maximum CPU overhead of our allocator is 0.57% with a geometric mean of -0.2% for CPU SPEC 2017 benchmarks. Due to the low overhead of the allocator and dynamic checks, Rapid could improve the performance of 12 out of 16 CPU SPEC 2017 benchmarks. In contrast, a state-of-the-art approach used in the comparison could improve only five CPU SPEC 2017 benchmarks.