bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of chronic kidney disease defined by decreased estimated glomerular filtration rate in individuals with different prediabetic phenotypes: results from a prospective cohort study in China
Authors: Li Wei , Wang Anping , Jiang Jiajia , Liu Guangxu , Wang Meiping , Li Dongxue , Wen Jing , Mu Yiming , Du Xiaoyan , Gaisano Herbert , Dou Jingtao , He Yan 
Published: April 2020

ObjectiveWe aimed to investigate the effects of prediabetes and its phenotypes of impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and elevated glycated hemoglobin A1c (EHbA1c) on chronic kidney disease (CKD) occurrence, and define the cut-off point of each glycemic index that significantly increases the risk of CKD.Research design and methodsIn this prospective cohort study, 6446 non-diabetic subjects aged 40 years and over were followed over a period of 3 years to track the new onset of CKD. Cox regression was used to assess the association of prediabetes and its phenotypes with CKD. Receiver operating characteristic curves were used to define the cut-off point of each glycemic index that significantly increases the occurrence of CKD. Population attributable risk percent was calculated to estimate the contribution of prediabetes to CKD.ResultsCompared to subjects with normal glucose tolerance, patients with prediabetes significantly increased the risk of development of CKD (HR=2.33 (1.19–4.55)). Specifically, this increased risk of CKD development was observed in patients with IFG, IGT and EHbA1c. The cut-off points shown to significantly increase the risk of CKD are fasting plasma glucose of 5.63 mmol/L, 2-hour plasma glucose of 6.80 mmol/L and HbA1cof 5.6%. The contribution of prediabetes to CKD occurrence in the study population was 60.6%.ConclusionsThis result suggests that the stricter criteria might be needed to define normal plasma glucose level in China that would not be predisposed to diabetic complications, particularly CKD.
Estimating the incidence of abortion: a comparison of five approaches in Ghana
Authors: Keogh Sarah C , Otupiri Easmon , Chiu Doris W , Polis Chelsea B , Hussain Rubina , Bell Suzanne O , Nakua Emmanuel K , Larsen-Reindorf Roderick 
Published: April 2020

IntroductionInduced abortion estimates are critical for reproductive health programming. In countries like Ghana where abortion is somewhat legally restricted and highly stigmatised, official records are incomplete and different approaches are needed to measure abortion incidence. We conducted a study in Ghana to test five methodologies for estimating incidence: direct reporting, the list experiment, the confidante method, the Abortion Incidence Complications Method (AICM) and a modified AICM.MethodsThe direct reporting, list experiment and confidante method were implemented through a nationally representative community-based survey (CBS) of 4722 women. The AICM used data from a nationally representative health facilities survey (HFS) and a knowledgeable informant survey. The modified AICM combined CBS and HFS data. For each approach, we calculated abortion incidence nationally and for Ghana’s three ecological zones and conducted checks to determine the most internally valid approaches.ResultsNational incidence estimates ranged from 27 per 1000 (AICM) to 61 (confidante method). The Northern zone displayed lower rates than the other two zones for all approaches. Validity and reliability checks found that the list experiment was invalid. The approaches that stood up to the internal validity checks and were most reliable were the direct reporting, confidante method and modified AICM. These approaches provide lower and upper bound estimates for the abortion rate, and the mean of the estimates from the three approaches yields a final abortion rate of 44 per 1000 and an unintended pregnancy rate of 103 per 1000.ConclusionsComparing five approaches to estimating abortion enabled cross-validation of findings and highlighted strengths, pitfalls and requirements of each approach that can inform abortion estimation in other settings.
Retrospective chart review of minor tibial fractures in preschoolers: immobilisation and complications
Authors: Ferrier Charlotte A , Schembri Rachel , Hopper Sandy M 
Published: April 2020

ObjectiveTo compare the treatment practices (immobilisation vs non-immobilisation) of toddler fractures and other minor tibial fractures (both proven and suspected) in preschoolers, aged 9 months–4 years, and examine rates of ED re-presentations and complications.MethodsRetrospective chart review of presentations of minor tibial fractures, both proven (radiologically confirmed) or suspected (negative X-ray but clinical evidence of bony injury), in children aged 9 months–4 years presenting to a single tertiary level paediatric ED from May 2016 to April 2018. Data collected included treatment practices, subsequent unscheduled re-presentations (including reasons) and complications (defined as problems relating to the injury that required further active care).ResultsA search of medical records yielded 240 cases: 102 had proven fractures (spiral, buckle or Salter-Harris II) and 138 were diagnosed with a suspected fracture. 73.5% of proven fractures were immobilised, predominantly with backslabs. 79% of suspected fractures were treated with expectant observation without immobilisation. Patients treated with immobilisation were more likely to re-present to ED compared with non-immobilised patients (18/104, 17.3% vs 9/136, 6.6% RR 2.62, 95% CI 1.23 to 5.58). 21 complications were seen in 19/104 (18.3%) immobilised patients. There were eight skin complications (complication rate of 7.7%) and 11 cast issues (complication rate of 10.6%). Two (1.5%) of the 136 patients had complications related to pain or limp. Pain was uncommonly found, although follow-up was not universal.ConclusionIn our centre, proven minor tibial fractures were more likely to receive a backslab, whereas for suspected fractures, expectant observation without immobilisation was performed. Although there is potential bias in the identification of complications with immobilisation, the study suggests that non-immobilisation approach should be investigated.
Johne's disease in dairy herds 2. Effective control using the National Johne's Management Plan
Authors: Orpin Pete , Sibley Dick , Bond Karen 
Published: April 2020

BackgroundThe major focus of the National Johne's Management Plan is to secure engagement, enthusiasm and compliance with robust Johne's disease control. The primary method of control depends largely on husbandry to block direct and indirect transmission from infectious animals to animals and environments where susceptible youngstock are reared.Aim of the articleThis article, the second in a two‐part series, describes how to control Johne's disease (JD) effectively using the National Johne's Management Plan (NJMP). The first article in this series, which was published in the January/February issue of In Practice (Orpin and others 2020), provided information on JD and the NJMP, giving an understanding of the disease in terms of the importance and economics of its control in dairy herds, and its transmission routes.
Ultrastructural mechanisms of macrophage-induced demyelination in Guillain-Barré syndrome
Authors: Koike Haruki , Fukami Yuki , Nishi Ryoji , Kawagashira Yuichi , Iijima Masahiro , Katsuno Masahisa , Sobue Gen 
Published: April 2020

ObjectiveTo describe the pathological features of Guillain-Barré syndrome focusing on macrophage-associated myelin lesions.MethodsLongitudinal sections of sural nerve biopsy specimens from 11 patients with acute inflammatory demyelinating polyneuropathy (AIDP) exhibiting macrophage-associated demyelinating lesions were examined using electron microscopy. A total of 1205 nodes of Ranvier were examined to determine the relationship of the macrophage-associated demyelinating lesions with the nodal regions. Additionally, immunohistochemical and immunofluorescent studies were performed to elucidate the sites of complement deposition.ResultsOverall, 252 macrophage-associated myelin lesions were identified in longitudinal sections. Of these, 40 lesions exhibited complete demyelination with no association with the lamellar structures of myelin. In 183 lesions, macrophage cytoplasm was located at internodes without association with the nodes of Ranvier or paranodes. In particular, these internodal lesions were more frequent in one patient (152 lesions). In the remaining 29 lesions, the involvement of nodal regions was obvious. Lesions involving nodal regions were more frequently observed than those involving internodes in four patients. Invasion of the macrophage cytoplasmic processes into the space between the paranodal myelin terminal loops and the axolemma from the nodes of Ranvier was observed in three of these patients. Immunostaining suggested complement deposition corresponding to putative initial macrophage-associated demyelinating lesions.ConclusionsThe initial macrophage-associated demyelinating lesions appeared to be located at internodes and at nodal regions. The sites at which the macrophages initiated phagocytosis of myelin might be associated with the location of complement deposition in certain patients with AIDP.
Genetic diversity of HIV in seminal plasma remains higher than in blood after short-term antiretroviral therapy
Authors: López Zúñiga Miguel Ángel , Chueca Natalia , de Salazar Adolfo , Fernández Caballero José Angel , Gutierrez Valencia Alicia , Vinuesa García David , Omar Mohamed Balgahata Mohamed , Hidalgo Tenorio Carmen , Lopez-Ruz Miguel Angel , Garcia Federico 
Published: April 2020

ObjectiveTo provide insight on viral kinetics and genetic diversity of HIV in seminal plasma at baseline and 1 month after initiating antiretroviral therapy (ART).Patients and methodsBlood and seminal samples from patients with newly diagnosed HIV were obtained before ART initiation (T0) and 1 month after ART initiation (T1). HIVenvgenetic diversity was studied using deep sequencing Nextera and V3 chemistry in a MiSeq Illumina platform. The number of viral quasispecies (5% cut-off) and Shannon Index were used to analyse diversity.ResultsForty-seven ART-naive patients were recruited between September 2016 and November 2018. At enrolment, the number of quasispecies in blood (median 4 (IQR 2–5)) was lower than in the seminal compartment (median 6, (IQR 4–8)) (p<0.01); the Shannon Index was also higher (p<0.001) in the seminal compartment than in blood (1.77 vs 0.64). At T1, for the 13 patients with detectable HIV in both blood/seminal plasma, viral diversity remained higher (p=0.139) in seminal plasma (median 2 (IQR 1–4.5)) than in blood (median 1 (IQR 1–1.5)) Integrase inhibitors (INI)-based regimens achieved higher levels of undetectability and led more frequently to lower variability (p<0.001) than protease inhibitors (PI) or non-nucleoside reverse transcriptase inhibitors (NNRTI).ConclusionWe provide here further evidence of a larger genetic diversity in seminal plasma, both at diagnosis and short term after ART initiation. Our results strengthen previous findings on HIV diversity in seminal plasma. In addition, INIs decrease variability more rapidly than PI and NNRTI in both blood and seminal plasma.
Study of the interactions of the axion with mesons and photons using a chiral effective Lagrangian model
Authors: Landini Giacomo , Meggiolaro Enrico 
Published: April 2020

AbstractWe investigate the most interesting decay processes involving axions, photons and the lightest pseudoscalar mesons, making use of a chiral effective Lagrangian model with $$L=3$$L=3 light quark flavors, which also includes the flavor-singlet pseudoscalar meson and implements the U(1) axial anomaly of the fundamental theory. In particular, we compute the electromagnetic coupling of the axion to photons and we compare our result with the prediction of the Chiral Effective Lagrangian with $$L=2$$L=2 light quark flavors. Moreover, we study the decay channels $$\eta /\eta '\rightarrow \pi \pi a$$η/η′→ππa and we estimate the corresponding decay widths, using the existing bounds on the $$U(1)_{PQ}$$U(1)PQ breaking scale.
Multi-stage replay with crosscut
Authors: Chow Jim , Lucchetti Dominic , Garfinkel Tal , Lefebvre Geoffrey , Gardner Ryan , Mason Joshua , Small Sam , Chen Peter M. 
Published: April 2020

Deterministic record-replay has many useful applications, ranging from fault tolerance and forensics to reproducing and diagnosing bugs. When choosing a record-replay solution, the system administrator must choose a priori how comprehensively to record the execution and at what abstraction level to record it. Unfortunately, these choices may not match well with how the recording is eventually used. A recording may contain too little information to support the end use of replay, or it may contain more sensitive information than is allowed to be shown to the end user of replay. Similarly, fixing the abstraction level at the time of recording often leads to a semantic mismatch with the end use of replay.
This paper describes how to remedy these problems by adding customizable replay stages to create special-purpose logs for the end users of replay. Our system, called Crosscut, allows replay logs to be "sliced" along time and abstraction boundaries. Using this approach, users can create slices that include only the processes, applications, or components of interest, excluding parts that handle sensitive data. Users can also retarget the abstraction level of the replay log to higher-level platforms, such as Perl or Valgrind. Execution can then be augmented with additional analysis code at replay time, without disturbing the replayed components in the slice. Crosscut thus uses replay itself to transform logs into a more efficient, secure, and usable form for replay-based applications.
Our current Crosscut prototype builds on VMware Workstation's record-replay capabilities, and supports a variety of different replay environments. We show how Crosscut can create slices of only the parts of the computation of interest and thereby avoid leaking sensitive information, and we show how to retarget the abstraction level of the log to enable more convenient use during replay debugging.
AASH
Authors: Kazempour Vahid , Kamali Ali , Fedorova Alexandra 
Published: April 2020

Asymmetric multicore processors (AMP) consist of cores exposing the same instruction-set architecture (ISA) but varying in size, frequency, power consumption and performance. AMPs were shown to be more power efficient than conventional symmetric multicore processors, and it is therefore likely that future multicore systems will include cores of different types. AMPs derive their efficiency from core specialization: instruction streams can be assigned to run on the cores best suited to their demands for architectural resources. System efficiency is improved as a result. To perform effective matching of threads to cores, the thread scheduler must be asymmetry-aware; and while asymmetry-aware schedulers for operating systems are a well studied topic, asymmetry-awareness in hypervisors has not been addressed. A hypervisor must be asymmetry-aware to enable proper functioning of asymmetry-aware guest operating systems; otherwise they will be ineffective in virtual environments. Furthermore, a hypervisor must ensure that asymmetric cores are shared among multiple guests in a fair fashion or in accordance with their priorities.
This work for the first time implements simple changes to the hypervisor scheduler, required to make it asymmetry-aware, and evaluates the benefits and overheads of these asymmetry-aware mechanisms. Our evaluation was performed using an open source hypervisor Xen on a real multicore system where asymmetry was emulated via CPU frequency scaling. We compared the asymmetry-aware hypervisor to default Xen. Our results indicate that asymmetry support can be implemented with low overheads, and resulting performance improvements can be significant, reaching up to 36% in our experiments. Most performance improvements are derived from the fact that an asymmetry-aware hypervisor ensures that the fast cores do not go idle before slow cores and from the fact that it maps virtual cores to physical cores for asymmetry-aware guests according to the guest's expectations. Other benefits from asymmetry awareness are fairer sharing of computing resources among VMs and more stable execution times.
DBT path selection for holistic memory efficiency and performance
Authors: Guha Apala , hazelwood Kim , Soffa Mary Lou 
Published: April 2020

Dynamic binary translators(DBTs) provide powerful platforms for building dynamic program monitoring and adaptation tools. DBTs, however, have high memory demands because they cache translated code and auxiliary code to a software code cache and must also maintain data structures to support the code cache. The high memory demands make it difficult for memory-constrained embedded systems to take advantage of DBT-based tools. Previous research on DBT memory management focused on the translated code and auxiliary code only. However, we found that data structures are comparable to the code cache in size. We show that the translated code size, auxiliary code size and the data structure size interact in a complex manner, depending on the path selection (trace selection and link formation) strategy. Therefore, holistic memory efficiency (comprising translated code, auxiliary code and data structures) cannot be improved by focusing on the code cache only. In this paper, we use path selection for improving holistic memory efficiency which in turn impacts performance in memory-constrained environments. Although there has been previous research on path selection, such research only considered performance in memory-unconstrained environments.
The challenge for holistic memory efficiency is that the path selection strategy results in complex interactions between the memory demand components. Also, individual aspects of path selection and the holistic memory efficiency may impact performance in complex ways. We explore these interactions to motivate path selection targeting holistic memory demand. We enumerate all the aspects involved in a path selection design and evaluate a comprehensive set of approaches for each aspect. Finally, we propose a path selection strategy that reduces memory demands by 20% and at the same time improves performance by 5-20% compared to an industrial-strength DBT.
Less is more
Authors: Arnoldus B. J. , van den Brand M. G.J. , Serebrenik A. 
Published: April 2020

A code generator is a program translating an input model into code. In this paper we focus on template-based code generators in the context of the model view controller architecture (MVC).
The language in which the code generator is written is known as a metalanguage in the code generation parlance. The metalanguage should be, on the one side, expressive enough to be of practical value, and, on the other side, restricted enough to enforce the separation between the view and the model, according to the MVC.

In this paper we advocate the notion of
unparser-complete metalanguages
as providing the right level of expressivity. An unparser-complete metalanguage is capable of expressing an unparser, a code generator that translates any legal abstract syntax tree into an equivalent sentence of the corresponding context-free language. A metalanguage not able to express an unparser will fail to produce all sentences belonging to the corresponding context-free language. A metalanguage able to express more than an unparser will also be able to implement code violating the model/view separation.

We further show that a metalanguage with the power of a linear deterministic tree-to-string transducer is unparser-complete. Moreover, this metalanguage has been successfully applied in a non-trivial case study where an existing code generator is refactored using templates.
Synthesizing iterators from abstraction functions
Authors: Rayside Derek , Montaghami Vajihollah , Leung Francesca , Yuen Albert , Xu Kevin , Jackson Daniel 
Published: April 2020

A technique for synthesizing iterators from declarative abstraction functions written in a relational logic specification language is described. The logic includes a transitive closure operator that makes it convenient for expressing reachability queries on linked data structures. Some optimizations, including tuple elimination, iterator flattening, and traversal state reduction, are used to improve performance of the generated iterators.
A case study demonstrates that most of the iterators in the widely used JDK Collections classes can be replaced with code synthesized from declarative abstraction functions. These synthesized iterators perform competitively with the hand-written originals.
In a user study the synthesized iterators always passed more test cases than the hand-written ones, were almost always as efficient, usually took less programmer effort, and were the qualitative preference of all participants who provided free-form comments.
Local Reasoning for Global Invariants, Part II
Authors: Banerjee Anindya , Naumann David A. 
Published: April 2020

Dedicated to the memory of John C. Reynolds (1935--2013).
The hiding of internal invariants creates a mismatch between procedure specifications in an interface and proof obligations on the implementations of those procedures. The mismatch is sound if the invariants depend only on encapsulated state, but encapsulation is problematic in contemporary software due to the many uses of shared mutable objects. The mismatch is formalized here in a proof rule that achieves flexibility via explicit restrictions on client effects, expressed using ghost state and ordinary first order assertions. The restrictions amount to a stateful frame condition that must be satisfied by any client; this dynamic encapsulation boundary complements conventional scope-based encapsulation. The technical development is based on a companion article, Part I, that presents Region Logic---a programming logic with stateful frame conditions for commands.
Local Reasoning for Global Invariants, Part I
Authors: Banerjee Anindya , Naumann David A. , Rosenberg Stan 
Published: April 2020

Dedicated to the memory of Stephen L. Bloom (1940--2010).
Shared mutable objects pose grave challenges in reasoning, especially for information hiding and modularity. This article presents a novel technique for reasoning about error-avoiding partial correctness of programs featuring shared mutable objects, and investigates the technique by formalizing a logic. Using a first-order assertion language, the logic provides heap-local reasoning about mutation and separation, via ghost fields and variables of type “region” (finite sets of object references). A new form of frame condition specifies write, read, and allocation effects using region expressions; this supports a frame rule that allows a command to read state on which the framed predicate depends. Soundness is proved using a standard program semantics. The logic facilitates heap-local reasoning about object invariants, as shown here by examples. Part II of this article extends the logic with second-order framing which formalizes the hiding of data invariants.