bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Whole-Genome Sequences of Campylobacter Strains Isolated from Brushtail Possums in New Zealand
Authors: Wilkinson David A. , Rogers Lynn E. , Fayaz Ahmed , Akhter Rukhshana N. , Biggs Patrick J. , French Nigel P. , Midwinter Anne C.
Published: November 2019

Draft genomes of five
Campylobacter
isolates recovered from New Zealand brushtail possums are described. Genome sizes ranged from 1.591 Mbp to 1.594 Mbp, with G+C contents of 29.9% to 29.95%. Comparison to Australian
Campylobacter
16S rRNA gene sequences suggests that the species may be common to possums.
Complete Genome Sequence of Proteus mirabilis Phage Mydo
Authors: Jones Benjamin T. , Lessor Lauren , O’Leary Chandler , Gill Jason , Liu Mei
Published: November 2019

Proteus mirabilisis a pathogen that has been linked to nosocomial infections. Studies on phages infectingP. mirabilismay provide therapeutics for infections caused by antibiotic-resistant strains of this pathogen. Here, we announce the complete genome sequence of aP. mirabilismyophage, Mydo, which is distantly related toEscherichia coliphage rv5.
Complete Genome Sequence of Proteus mirabilis Phage Myduc
Authors: Tran Jennifer , Lessor Lauren , O’Leary Chandler , Gill Jason , Liu Mei
Published: November 2019

Proteus mirabilisas a nosocomial pathogen is often the cause of urinary tract infections. This announcement describes the complete genome sequence of aP. mirabilismyophage named Myduc. Phage Myduc is related toEnterobacteriaphage phiEcoM-GJ1, which belongs to a group of myophages with small genome sizes (52,000 to 56,000 bp) possessing a T7-like RNA polymerase.
​Challenge in managing abnormal uterine bleeding in a patient on novel oral anticoagulant therapy
Authors: Bilal Sophia
Published: November 2019

This is a case report of a 48-year-old woman who presented with heavy per vaginal bleeding to the emergency department after being commenced on direct oral anticoagulants (DOACs) for venous thromboembolism. She had significant bleeding which initially required resuscitation and stabilisation. Her symptoms were ultimately managed by changing her anticoagulation agent to therapeutic low molecular weight heparin with Clexane©the agent of choice. This case study highlights the complexity of managing these patients as well as highlighting the need for ongoing research into DOACs in this area.
Could there be a relation between Steven-Johnson syndrome and ST-segment elevation myocardial infarction?
Authors: Siddika Aida , Alassaf Omar , Rajani Ali Raza , Elberry Mohamed Aboalela
Published: November 2019

Steven-Johnson syndrome (SJS) is a rare but serious mucocutaneous reaction to medications. We present a rare case of SJS developing after antibiotic administration for a lower respiratory tract infection and whose inpatient course was complicated with an acute ST-segment elevation myocardial infarction (MI). The laboratory findings revealed thrombocytosis which was possibly reactive and explained the underlying pathophysiology of the thrombus formation seen in the coronary artery. Stenting and aspiration of thrombus was performed. This case illustrates a possibly rare association between SJS and MI.
Frontal sinus cholesteatoma: a masquerading diagnosis
Authors: Kurien Regi , Thomas Leah , Varghese Lalee , Nair Bijesh Ravindran
Published: November 2019

Cholesteatoma of the paranasal sinus is a very rare condition. As in the tympanomastoid region where cholesteatomas are a common entity, the paranasal sinus cholesteatomas also tend to erode the surrounding bony structures. Because of the extensive bony erosion, this condition often masquerades as a chronic granulomatous or a malignant lesion. Clinical presentation can be quite varied like facial deformities, visual and neurological deficits. Radiological findings are also non-specific making a preoperative diagnosis challenging. Histopathological examination is the only confirmatory investigation. We present a patient with frontal cholesteatoma who presented with forehead swelling of 1 month duration. Since the diagnosis could be obtained only intraoperatively, the patient required multiple surgeries. Frontal sinus cholesteatomas often require a combined endoscopic and external approach to ensure complete disease clearance. Periodic follow-up is essential to rule out recurrence.
Neurosarcoidosis presenting with a partial Claude syndrome
Authors: Yip Hao Meng , Vallabhaneni Kirtana , Williams David
Published: November 2019

Neurosarcoidosis when encountered by neurologists most commonly presents as cranial neuropathy, peripheral mononeuropathy,polyneuropathy, myopathy, meningitis or myelopathy. There are limited reports in the current literature on the cases of neurosarcoidosis patients presenting with ischaemic stroke. We discuss a 52-year-old patient with a known previous history of cutaneous sarcoidosis presenting with an acute third nerve palsy, facial weakness and ataxia. His magnetic resonance imaging (MRI) brain demonstrated focal signal changes in the midbrain consistent with an acute ischaemic event in the region of his third nucleus, suggesting a partial Claude syndrome presentation. Cerebrospinal fluid (CSF) examination demonstrated an elevated angiotensin-converting enzyme (ACE) level. We discuss the difficulties associated with confirming a diagnosis for his presentation and consider distinctions in stroke in neurosarcoid and its management in comparison to more common causes.
Positive reinforcement by general practitioners is associated with greater physical activity in adults with type 2 diabetes
Authors: Geerling Ralph , Browne Jessica L , Holmes-Truscott Elizabeth , Furler John , Speight Jane , Mosely Kylie
Published: November 2019

Objective

In a sample of adults with type 2 diabetes mellitus (T2DM), the aim of this study was to examine whether self-reported physical activity level is associated with recall of specific physical activity-related interactions used by general practitioners (GP).

Research design and methods

Adults with T2DM completed an online survey reporting physical activity behaviors and recall of 14 GP–patient interactions about physical activity, mapped onto discrete behavior change techniques (BCT). Stepped logistical regression examined associations between recommended physical activity (≥600 MET-min/week) and GP–patient interactions, controlling for body mass index, diabetes-related comorbidities, depressive symptoms and self-efficacy.

Results

In total, 381 respondents (55% men, mean±SD age: 62±10 years and T2DM duration 8±8 years) provided complete data. Most (73%) reported receiving ‘general advice’, while interactions related to goal setting, monitoring, and relapse prevention were least commonly reported (all <20%). Self-reported achievement of the recommended physical activity level was significantly associated with recall of GP interactions involving praise for ‘efforts to be active’ (OR 2.1; 95% CI 1.24 to 3.53), ‘lost weight’ (OR 1.81; 95% CI 1.05 to 3.12) or lowering ‘glucose levels as a result of being active’ (OR 1.75; 95% CI 1.03 to 2.96).

Conclusions

Findings suggest GPs can be somewhat effective in promoting physical activity with simple, positive, reinforcing messages/interactions. Future research to develop and evaluate very brief primary care BCT-based physical activity interventions is needed.
Characteristics and short-term outcomes of young women with acute myocardial infarction in Malaysia: a retrospective analysis from the Malaysian National Cardiovascular Database registry
Authors: Venkatason Padmaa , Zubairi Yong Z , Zaharan Nur Lisa , Wan Ahmad Wan Azman , Hafidz Muhammad Imran , Ismail Muhammad Dzafir , Hadi Mohd Firdaus , Md Sari Norashikin , Zuhdi Ahmad Syadi Mahmood
Published: November 2019

Objective

Young women form a minority but an important group of patients with acute myocardial infarction (MI) as it can potentially cause devastating physical and socioeconomic impact. This study was aimed to investigate the characteristics and outcomes of young women with MI in Malaysia.

Design

This is a retrospective analysis of women with ST-elevation MI (STEMI) and non-STEMI (NSTEMI) from 18 hospitals across Malaysia using the Malaysian National Cardiovascular Database registry–acute coronary syndrome (NCVD-ACS).

Participants

Women patients diagnosed with acute MI from year 2006 to 2013 were identified and divided into young (age ≤ 45, n=292) and older women (age >45, n=5580).

Primary outcome measure

Comparison of demographics, clinical characteristics and in-hospital management was performed between young and older women. In-hospital and 30-day all-cause mortality were examined.

Results

Young women (mean age 39±4.68) made up 5% of women with MI and were predominantly of Malay ethnicities (53.8%). They have a higher tendency to present as STEMI compared with older women. Young women have significantly higher rates of family history of premature coronary artery disease (CAD) (20.5% vs 7.8% p<0.0001). The prevalence of risk factors, such as hypertension, diabetes and dyslipidaemia was high in both groups. The primary reperfusion strategy was thrombolysis with no significant differences observed in the choice of intervention for both groups. Other than aspirin, rates of prescriptions for evidence-based medications were similar with >80% prescribed statins and aspirin. The all-cause mortality rates of young women were lower for both in-hospital and 30 days, especially in those with STEMI with adjusted mortality ratio to the older group, was 1:9.84.

Conclusion

Young women with MI were over-represented by Malays and those with a family history of premature CAD. Preventive measures are needed to reduce cardiovascular risks in young women. Although in-hospital management was similar, short-term mortality outcomes favoured young compared with older women.
Systematic review and meta-analysis of the incidence and prevalence and 30-year trend of inflammatory bowel diseases in Asia: a study protocol
Authors: Safarpour Ali Reza , Mehrabi Manoosh , Keshtkar Abbasali , Edjtehadi Fardad , Bagheri Lankarani Kamran
Published: November 2019

Introduction

Inflammatory bowel diseases, including ulcerative colitis (UC), Crohn’s disease (CD) and inflammatory bowel disease type unclassified (IBDU), are debilitating conditions that are rapidly growing in developing countries. Given the absence of a comprehensive systematic review and meta-analysis containing a rigorous pooled estimate of incidence and prevalence of UC, CD and IBDU, this study was conducted to determine the incidence and prevalence of these conditions in Asia and their 30-year trend.

Methods and analysis

Based on predefined criteria, electronic databases, including PubMed/MEDLINE, Scopus, WoS (Clarivate Analytics), Embase and Google Scholar, and some databases pertaining to Asian countries will be searched for population-based cross-sectional studies and the baseline data and final reports of population-based cohort studies involving paediatric and adult patients, with no language restrictions, from 1 January 1988 to 30 December 2018. Any disagreement in the stages of screening, selecting, quality assessment and data extraction between the two independent reviewers will be resolved by consensus, and if the disagreement is not resolved, a third expert opinion will be sought. The combination method will be used based on methodological similarities in the included studies by the Fixed Effect Model or the Random Effect Model. Forest plots will be plotted for all the studies to show the separated and pooled incidence and prevalence and their corresponding 95% CIs. The Q-statistic test and I2statistic will be used to assess statistical heterogeneity. Funnel plots will be used to assess potential reporting bias and nonsignificant study effect. Begg’s and Egger’s tests will also be performed, and significant results (p>0.1) shall suggest a publication bias, in which case the ‘trim and fill’ method will be used. The time trends for UC, CD and IBDU will be calculated using a cumulative meta-analysis.

Ethics and dissemination

Since this review will use previously published studies, it will not require the consent of an Ethics Committee. The results will be prepared and disseminated through a peer-reviewed journal and will be presented in relevant conferences.

PROSPERO registration number

CRD42019131477.
Visualising the body: health professionals’ perceptions of their clinical drawing practices
Authors: Lyon Philippa Morag , Turland Martha
Published: November 2019

Health professionals routinely draw for patients, carers and colleagues as part of clinical communication to describe, explain and record. The drawings that result are either discarded, kept by patients or become part of a patient’s records. Some health professionals also draw when engaged in teaching and training in clinical contexts. Very little literature has acknowledged that such drawing regularly takes place and there does not appear to have been formal research into the reasons, benefits or disadvantages of these drawing practices. This study examined the perceptions of seven UK health professionals, from different specialties, who draw as part of their daily professional practice. In this qualitative study, the researchers carried out in-depth individual interviews, during which they invited participants to make exemplar drawings. The findings included that for nearly all, drawing was a flexible, sensitive and spontaneous method of visualising information. In making explanatory drawings for patients, health professionals were taking care to provide information in a way that was accessible and personally relevant. While one participant indicated that ‘live’ drawing had been superseded by professionally illustrated material and video in their profession, the other participants believed that drawing remained the more practical, effective and emotionally appropriate method of visualising explanations. Health professionals convey and clarify knowledge for one another through drawing, yet it does not appear to be included in their training. Drawing was also described as useful and often pleasurable for the professionals themselves. Further research is now needed to explore patients’ perspectives on such drawing practices.
Timing of secondhand smoke, pet, dampness or mould exposure and lung function in adolescence
Authors: Milanzi Edith B , Koppelman Gerard H , Smit Henriette A , Wijga Alet H , Vonk Judith M , Brunekreef Bert , Gehring Ulrike
Published: November 2019

Background

The relevance of timing of exposure in the associations of secondhand tobacco smoke (SHS), pets, and dampness or mould exposure with lung function is unclear. We investigated the relevance of timing of these exposures for lung function in adolescence.

Methods

We used data from participants of the Dutch Prevention and Incidence of Asthma and Mite Allergy (PIAMA) cohort with spirometric measurements at ages 12 and 16 years (n=552). Data on residential exposure to SHS, pets, and dampness or mould were obtained by repeated parental questionnaires. We characterised timing of exposure through longitudinal patterns using latent class growth modelling and assessed associations of these patterns with FEV1 and FVC at ages 12 and 16 and FEV1 and FVC growth between ages 12 and 16 using linear regression models.

Results

Childhood SHS exposure was associated with reduced FEV1 growth/year (95% CI) (−0.34% (−0.64% to −0.04%)). Late childhood and early life pet exposure was associated with increased FEV1 growth (0.41% (0.14% to 0.67%)) and reduced FVC growth (−0.28% (−0.53% to −0.03%)), respectively, compared with very low exposure. Early life dampness or mould exposure was associated with reduced lung function growth. All time windows of SHS exposure tended to be associated with lower attained lung function and pet exposure tended to be associated with higher FEV1.

Conclusion

SHS exposure during childhood could lead to reduced lung function growth and lower attained lung function in adolescence. While pet exposure in late childhood may not adversely affect lung function, early childhood pet exposure may slow down FVC growth in adolescence.
Histological evidence of reproductive senescence in Atlantic herring (Clupea harengus)
Authors: Benoît Hugues P. , Benhalima Kadra , McDermid Jenni L.
Published: November 2019

Senescence is the age-specific decline in fitness of adult organisms principally associated with a decline in survival rate (actuarial senescence) and fecundity (reproductive senescence). Although common in natural populations of many taxa, there are few examples in fishes. A recent study found age-specific increases in the relative frequency of macroscopically non-reproductive Atlantic herring (Clupea harengus Linnaeus, 1758), consistent with reproductive senescence in a number of Canadian populations. However, a non-adaptive explanation for these patterns, unrelated to senescence, could not be definitively ruled out. Here, we present the results of histological examination of herring gonads undertaken to examine this and another hypothesis. The sample size of macroscopically senescent gonads was small (n = 4 females), a function of the low abundance of large, older, purportedly senescent, herring in these populations subjected to high mortality rates, and constraints on obtaining fresh samples. The results indicate that these fish were senescent and not merely skip spawning, providing further evidence of senescence and the occurrence of a post-reproductive period in herring in Atlantic Canada. Based on existing theory for the evolution of senescence, observations of actuarial senescence in Norwegian spring-spawning herring suggest that this population may also experience reproductive senescence and that the phenomenon may occur broadly in the species.
A new angle on an old problem: helicity approach to neutron beta decay in the Standard Model
Authors: Groote Stefan , Körner Jürgen G. , Melić Blaženka
Published: November 2019

We elaborate on the dichotomy between the description of the semileptonic decays of heavy hadrons on the one hand and the semileptonic decays of light hadrons such as neutron $$\beta $$β decays on the other hand. For example, almost without exception the semileptonic decays of heavy baryons are described in cascade fashion as a sequence of two two-body decays $$B_1 \rightarrow B_2 + W_\mathrm{off-shell}$$B1→B2+Woff-shell and $$W_{\mathrm{off-shell}} \rightarrow \ell + \nu _\ell $$Woff-shell→ℓ+νℓ whereas neutron $$\beta $$β decays are analyzed as true three-body decays $$n \rightarrow p + e^- +{\bar{\nu }}_e$$n→p+e-+ν¯e. Within the cascade approach it is possible to define a set of seven angular observables for polarized neutron $$\beta $$β decays as well as the longitudinal, transverse and normal polarization of the decay electron. We determine the dependence of the observables on the usual vector and axial vector form factors. In order to be able to assess the importance of recoil corrections we expand the rate and the $$q^2$$q2 averages of the observables up to NLO and NNLO in the recoil parameter $$\delta =(M_n-M_p)/(M_n+M_p)= 0.689\cdot 10^{-3}$$δ=(Mn-Mp)/(Mn+Mp)=0.689·10-3. Remarkably, we find that the rate and three of the four parity conserving polarization observables that we analyze are protected from NLO recoil corrections when the second class current contributions are set to zero.
Acceleration in Friedmann cosmology with torsion
Authors: Pereira S. H. , Lima R. de C. , Jesus J. F. , Holanda R. F. L.
Published: November 2019

A Friedmann like cosmological model in Einstein–Cartan framework is studied when the torsion function is assumed to be proportional to a single $$\phi (t)$$ϕ(t) function coming just from the spin vector contribution of ordinary matter. By analysing four different types of torsion function written in terms of one, two and three free parameters, we found that a model with $$\phi (t)=- \alpha H(t) \big ({\rho _{m}(t)}/{\rho _{0c}}\big )^n$$ϕ(t)=-αH(t)(ρm(t)/ρ0c)n is totally compatible with recent cosmological data, where $$\alpha $$α and n are free parameters to be constrained from observations, $$\rho _m$$ρm is the matter energy density and $$\rho _{0c}$$ρ0c the critical density. The recent accelerated phase of expansion of the universe is correctly reproduced by the contribution coming from torsion function, with a deceleration parameter indicating a transition redshift of about 0.65.
Synchronization of cerebral and peripheral blood flow at the latent stage of stroke
Authors: Pavlova Olga N. , Abdurashitov Arkady S. , Terskov Andrey V. , Semyachkina-Glushkovskaya Oxana V. , Pavlov Alexey N.
Published: November 2019

Synchronization between cerebral and peripheral circulation at the pre-stroke stage is discussed in newborn rats using a model of stress-induced hemorrhagic stroke. It is considered how the degree of coherence between the rhythmic components of the blood flow velocity is varied under normal and pathological conditions. It is shown that the degree of entrainment changes significantly after severe stress, provoking the transformation of normal vascular dynamics into pathological ones. Strong increase in the coherence measure is revealed, characterizing the entrainment in the dynamics of blood flow in the microvascular network surrounding the sagittal sinus and in the vein of the neck. Such changes can be considered as a precursor of the latent stage of stroke development in risk groups.
Stochastic resonance in a periodic potential system driven by cross-correlated noises and periodic signal
Authors: Guo Yongfeng , Lou Xiaojuan , Dong Qiang , Wang Linjie
Published: November 2019

In this paper, the stochastic resonance (SR) in a periodic potential system driven by cross-correlated noises and periodic signal is investigated. The signal-to-noise ratio (SNR) is used to characterize the SR. Using the algorithm of fourth-order Runge–Kutta, we obtain the curves of SNR for different parameters. The effects of some system parameters, additive Gaussian white noise and multiplicative Gaussian colored noise intensity on SR are characterized by analyzing SNR curves. When increasing system parameter and noise cross-correlation strength in SNR-D, the SR of the system can be enhanced. However, the SR will be weakened by increasing other parameters. Otherwise, the phenomena in SNR-Q are opposite to in SNR-D when increasing signal amplitude and correlation time.
Inferences on Non-Identical Stress and Generalized Augmented Strength Reliability Parameters Under Informative Priors
Authors: Chandra N. , Rathaur V. K.
Published: November 2019

In this paper, an attempt has been made to estimate the augmented strength reliability of a system for the generalized case of Augmentation Strategy Plan (ASP) by assuming that the strength [Formula: see text] and common stress [Formula: see text] are independently but not identically distributed as gamma distribution with parameters [Formula: see text] and [Formula: see text], respectively. ASP deals with two important challenges (i) early failures in a newly manufactured system while first and subsequent use and (ii) frequent failures of used system. ASP has a significant role in enhancing the strength of a weaker (or poor) system for failure-free journey to achieve its mission life. The maximum likelihood (ML) and Bayes estimation of augmented strength reliability are considered. In Bayesian context, the informative types of priors (Gamma and Inverted gamma) are chosen under symmetric and asymmetric loss functions for better comprehension purpose. A comparison between the ML and Bayes estimators of the augmented strength reliability is carried out on the basis of their mean square errors (mse’s) and absolute biases by simulating Monte-Carlo samples from posterior distribution through Metropolis–Hasting approximation. Real life data sets are also considered for illustration purpose.
Detection of Large-Scale Noisy Multi-Periodic Patterns with Discrete Double Fourier Transform
Authors: Chechetkin V. R. , Lobzin V. V.
Published: November 2019

In many processes, the variations in underlying characteristics can be approximated by noisy multi-periodic patterns. If large-scale patterns are superimposed by a noise with long-range correlations, the detection of multi-periodic patterns becomes especially challenging. To solve this problem, we developed a discrete double Fourier transform (DDFT). DDFT is based on the equidistance property of harmonics generated by multi-periodic patterns in the discrete Fourier transform (DFT) spectra. As the large-scale patterns generate long enough equidistant series, they can be detected by the iteration of the primary DFT. DDFT is defined as Fourier transform of intensity spectral harmonics or of their functions. It comprises widely used cepstrum transform as a particular case. We present also the relevant analytical criteria for the assessment of the statistical significance of peak harmonics in DDFT spectra in the presence of noise. DDFT technique was tested by extensive numerical simulations. The practical applications of the DDFT technique are illustrated by the analysis of variations in solar wind speed related to solar rotation and by the study of large-scale multi-periodic patterns in DNA sequences. The latter application can be considered as a generic example for the general spectral analysis of symbolic sequences. The results are compared with those obtained by the cepstrum transform. The mutual combination of DFT and DDFT provides an efficient technique to search for noisy large-scale multi-periodic patterns.
On extremal bipartite graphs with given number of cut edges
Authors: Chen Hanlin , Wu Renfang
Published: November 2019

Let [Formula: see text] be a topological index of a graph. If [Formula: see text] (or [Formula: see text], respectively) for each edge [Formula: see text], then [Formula: see text] is monotonically decreasing (or increasing, respectively) with the addition of edges. In this paper, by a unified approach, we determine the extremal values of some monotonic topological indices, including the Wiener index, the hyper-Wiener index, the Harary index, the connective eccentricity index, the eccentricity distance sum, among all connected bipartite graphs with a given number of cut edges, and characterize the corresponding extremal graphs, respectively.
Clustering stream data by exploring the evolution of density mountain
Authors: Gong Shufeng , Zhang Yanfeng , Yu Ge
Published: November 2019

Stream clustering is a fundamental problem in many streaming data analysis applications. Comparing to classical batch-mode clustering, there are two key challenges in stream clustering: (i) Given that input data are changing continuously, how to incrementally update their clustering results efficiently? (ii) Given that clusters continuously evolve with the evolution of data, how to capture the cluster evolution activities? Unfortunately, most of existing stream clustering algorithms can neither update the cluster result in real-time nor track the evolution of clusters.

In this paper, we propose a stream clustering algorithm
EDMStream
by exploring the Evolution of Density Mountain. The
density mountain
is used to abstract the data distribution, the changes of which indicate data distribution evolution. We track the evolution of clusters by monitoring the changes of density mountains. We further provide efficient data structures and filtering schemes to ensure that the update of density mountains is in real-time, which makes online clustering possible. The experimental results on synthetic and real datasets show that, comparing to the state-of-the-art stream clustering algorithms, e.g., D-Stream, DenStream, DBSTREAM and MR-Stream, our algorithm is able to response to a cluster update much faster (say 7-15x faster than the best of the competitors) and at the same time achieve comparable cluster quality. Furthermore,
EDMStream
successfully captures the cluster evolution activities.
Froid
Authors: Ramachandra Karthik , Park Kwanghyun , Emani K. Venkatesh , Halverson Alan , Galindo-Legaria César , Cunningham Conor
Published: November 2019

For decades, RDBMSs have supported declarative SQL as well as imperative functions and procedures as ways for users to express data processing tasks. While the evaluation of declarative SQL has received a lot of attention resulting in highly sophisticated techniques, the evaluation of imperative programs has remained naïve and highly inefficient. Imperative programs offer several benefits over SQL and hence are often preferred and widely used. But unfortunately, their abysmal performance discourages, and even prohibits their use in many situations. We address this important problem that has hitherto received little attention.

We present Froid, an extensible framework for optimizing imperative programs in relational databases. Froid's novel approach automatically transforms entire User Defined Functions (UDFs) into relational algebraic expressions, and embeds them into the calling SQL query. This form is now amenable to cost-based optimization and results in efficient, set-oriented, parallel plans as opposed to inefficient, iterative, serial execution of UDFs. Froid's approach additionally brings the benefits of many compiler optimizations to UDFs with no additional implementation effort. We describe the design of Froid and present our experimental evaluation that demonstrates performance improvements of up to multiple orders of magnitude on real workloads.
An experimental study on hub labeling based shortest path algorithms
Authors: Li Ye , U Leong Hou , Yiu Man Lung , Kou Ngai Meng
Published: November 2019

Shortest path distance retrieval is a core component in many important applications. For a decade, hub labeling (HL) techniques have been considered as a practical solution with fast query response time (e.g., 1--3 orders of magnitude faster), competitive indexing time, and slightly larger storage overhead (e.g., several times larger). These techniques enhance query throughput up to hundred thousands queries per second, which is particularly helpful in large user environment. Despite the importance of HL techniques, we are not aware of any comprehensive experimental study on HL techniques. Thus it is difficult for a practitioner to adopt HL techniques for her applications.

To address the above issues, we provide a comprehensive experimental study on the state-of-the-art HL technique with analysis of their efficiency, effectiveness and applicability. From insightful summary of different HL techniques, we further develop a simple yet effective HL techniques called Significant path based Hub Pushing (SHP) which greatly improves indexing time of previous techniques while retains good query performance. We also complement extensive comparisons between HL techniques and other shortest path solutions to demonstrate robustness and efficiency of HL techniques.
Concurrent log-structured memory for many-core key-value stores
Authors: Merritt Alexander , Gavrilovska Ada , Chen Yuan , Milojicic Dejan
Published: November 2019

Key-value stores are an important tool in managing and accessing large in-memory data sets. As many applications benefit from having as much of their working state fit into main memory, an important design of the memory management of modern key-value stores is the use of log-structured approaches, enabling efficient use of the memory capacity, by compacting objects to avoid fragmented states.

However, with the emergence of thousand-core and peta-byte memory platforms (DRAM or future storage-class memories) log-structured designs struggle to scale, preventing parallel applications from exploiting the full capabilities of the hardware: careful coordination is required for background activities (compacting and organizing memory) to remain asynchronous with respect to the use of the interface, and for insertion operations to avoid contending for centralized resources such as the log head and memory pools.

In this work, we present the design of a log-structured key-value store called Nibble that incorporates a
multi-head log
for supporting concurrent writes, a novel
distributed epoch
mechanism for scalable memory reclamation, and an optimistic concurrency index. We implement Nibble in the Rust language in ca. 4000 lines of code, and evaluate it across a variety of data-serving workloads on a 240-core cache-coherent server. Our measurements show Nibble scales linearly in uniform YCSB workloads, matching competitive non-log-structured key-value stores for write- dominated traces at 50 million operations per second on 1 TiB-sized working sets. Our memory analysis shows Nibble is efficient, requiring less than 10% additional capacity, whereas memory use by non-log-structured key-value store designs may be as high as 2x.
Cardinality estimation
Authors: Harmouch Hazar , Naumann Felix
Published: November 2019

Data preparation and data profiling comprise many both basic and complex tasks to analyze a dataset at hand and extract metadata, such as data distributions, key candidates, and functional dependencies. Among the most important types of metadata is the number of distinct values in a column, also known as the zeroth-frequency moment. Cardinality estimation itself has been an active research topic in the past decades due to its many applications. The aim of this paper is to review the literature of cardinality estimation and to present a detailed experimental study of twelve algorithms, scaling far beyond the original experiments.

First, we outline and classify approaches to solve the problem of cardinality estimation - we describe their main idea, error-guarantees, advantages, and disadvantages. Our experimental survey then compares the performance all twelve cardinality estimation algorithms. We evaluate the algorithms' accuracy, runtime, and memory consumption using synthetic and real-world datasets. Our results show that different algorithms excel in different in categories, and we highlight their trade-offs.
SQL statement logging for making SQLite truly lite
Authors: Park Jong-Hyeok , Oh Gihwan , Lee Sang-Won
Published: November 2019

The lightweight codebase of SQLite was helpful in making it become the de-facto standard database in most mobile devices, but, at the same time, forced it to take less-complicated transactional schemes, such as physical page logging, journaling, and force commit, which in turn cause excessive write amplification. Thus, the write IO cost in SQLite is not lightweight at all.

In this paper, to make SQLite truly lite in terms of IO efficiency for the transactional support, we propose
SQLite/SSL
, a
per-transaction SQL statement logging
scheme: when a transaction commits,
SQLite/SSL
ensures its durability by storing only SQL statements of small size, thus writing less and performing faster at no compromise of transactional solidity. Our main contribution is to show that, based on the observation that mobile transactions tend to be
short
and exhibit
strong update locality
, logical logging can, though long discarded, become an elegant and perfect fit for SQLite-based mobile applications. Further, we leverage the WAL journal mode in vanilla SQLite as a
transaction-consistent checkpoint
mechanism which is indispensable in any logical logging scheme. In addition, we show for the first time that byte-addressable NVM (non-volatile memory) in host-side can realize the full potential of logical logging because it allows to store fine-grained logs quickly.

We have prototyped
SQLite/SSL
by augmenting vanilla SQLite with a transaction-consistent checkpoint mechanism and a redo-only recovery logic, and have evaluated its performance using a set of synthetic and real workloads. When a real NVM board is used as its log device,
SQLite/SSL
can outperform vanilla SQLite's WAL mode by up to 300x and also outperform the state-of-the-arts SQLite/PPL scheme by several folds in terms of IO time.
Regulation and Effects of FGF23 in Chronic Kidney Disease
Authors: Musgrove John , Wolf Myles
Published: November 2019

Chronic kidney disease (CKD) is a global health epidemic that accelerates cardiovascular disease, increases risk of infection, and causes anemia and bone disease, among other complications that collectively increase risk of premature death. Alterations in calcium and phosphate homeostasis have long been considered nontraditional risk factors for many of the most morbid outcomes of CKD. The discovery of fibroblast growth factor 23 (FGF23), which revolutionized the diagnosis and treatment of rare hereditary disorders of FGF23 excess that cause hypophosphatemic rickets, has also driven major paradigm shifts in our understanding of the pathophysiology and downstream end-organ complications of disordered mineral metabolism in CKD. As research of FGF23 in CKD has rapidly advanced, major new questions about its regulation and effects continuously emerge. These are promoting exciting innovations in laboratory, patient-oriented, and epidemiological research and stimulating clinical trials of new therapies and repurposing of existing ones to target FGF23.
TRIM27 promotes IL-6-induced proliferation and inflammation factor production by activating STAT3 signaling in HaCaT cells
Authors: Miao Xiao , Xiang Yanwei , Mao Weiwei , Chen Yiran , Li Qi , Fan Bin
Published: November 2019

The IL-6/STAT3 signaling pathway is required for the development of psoriatic lesions, and tripartite motif-containing 27 (TRIM27) is a protein inhibitor of activated STAT3 (PIAS3)-interacting protein that could modulate IL-6-induced STAT3 activation. However, whether TRIM27 is associated with the IL-6/STAT3 signaling pathway in psoriasis remains enigmatic. TRIM27 expression and gene set enrichment analysis in patients with psoriasis were determined using bioinformatics. Human keratinocyte HaCaT cells treated with recombinant protein IL-6 (rh-IL-6) were transduced with lentivirus silencing TRIM27 and/or PIAS3 or, otherwise, transduced with lentivirus expressing TRIM27 and/or lentivirus silencing STAT3, or MG132, a proteasome-specific protease inhibitor. Cell proliferation and inflammation factor production were measured using Cell Counting Kit-8 and ELISA, respectively. TRIM27, proliferation marker protein Ki-67 (Ki67), phospho-STAT3 (p-STAT3), STAT3, and PIAS3 expressions were determined using real-time quantitative PCR, immunofluorescence staining, or Western blot analysis. Coimmunoprecipitation combined with ubiquitination analysis was performed to explore the interaction between TRIM27 and PIAS3. In the present study, TRIM27 expression was increased in psoriatic lesions, associated with the IL-6 signaling pathway, and induced by rh-IL-6 in a time-dependent manner. The increased cell proliferation, inflammation factor production, and expression of Ki67 and of p-STAT3 relative to STAT3 induced by rh-IL-6 and TRIM27 overexpression were significantly inhibited by TRIM27 silencing and STAT3 silencing, respectively. More importantly, TRIM27 interacted with PIAS3, and its overexpression promoted PIAS3 ubiquitination in HaCaT cells. PIAS3 silencing also significantly promoted TRIM27-dependent and IL6-induced STAT3 activation, cell proliferation, and inflammation factor production. In conclusion, our results highlight that TRIM27 expression is significantly increased by IL-6 and suggest a TRIM27/STAT3-dependent mechanism for regulation of inflammation and proliferation-associated development of psoriasis.
Gamma oscillations in the pedunculopontine nucleus are regulated by F-actin: neuroepigenetic implications
Authors: Urbano Francisco J. , Bisagno Veronica , Garcia-Rill Edgar
Published: November 2019

The pedunculopontine nucleus (PPN) is part of the reticular activating system (RAS) in charge of arousal and rapid eye movement sleep. The presence of high-frequency membrane oscillations in the gamma-band range in the PPN has been extensively demonstrated both in vivo and in vitro. Our group previously described histone deacetylation (HDAC) inhibition in vitro induced protein changes in F-actin cytoskeleton and intracellular Ca2+ concentration regulation proteins in the PPN. Here, we present evidence that supports the presence of a fine balance between HDAC function and calcium calmodulin kinase II-F-actin interactions in the PPN. We modified F-actin polymerization in vitro by using jasplakinolide (1 μM, a promoter of F-actin stabilization), or latrunculin-B (1 μM, an inhibitor of actin polymerization). Our results showed that shifting the balance in either direction significantly reduced PPN gamma oscillation as well as voltage-dependent calcium currents.
Lung eosinophils increase vagus nerve-mediated airway reflex bronchoconstriction in mice
Authors: Nie Zhenying , Maung Jessica N. , Jacoby David B. , Fryer Allison D.
Published: November 2019

Eosinophils mediate airway hyperresponsiveness by increasing vagally mediated reflex bronchoconstriction. Here, we tested whether circulating or airway eosinophils change nerve function. Airway resistance in response to aerosolized 5-hydroxytryptamine (5-HT, 10–300 mM) was measured in wild-type mice or transgenic mice that overexpress IL5 in T cells (+IL5T), overexpress IL5 in airway epithelium (+IL5AE), or overexpress IL5 but are devoid of eosinophils (+IL5AE/−Eos). Inflammatory cells in bronchoalveolar lavage (BAL), blood, and bone marrow were quantified. Blood eosinophils were increased in +IL5Tand +IL5AEmice compared with wild-type mice. +IL5Tmice had increased eosinophils in bone marrow while +IL5AEmice had increased eosinophils in BAL. Eosinophils surrounding large airways were significantly increased only in +IL5AEmice. With intact vagal innervation, aerosolized 5-HT significantly increased airway resistance in +IL5AEmice. 5-HT-induced bronchoconstriction was blocked by vagotomy or atropine, demonstrating that it was mediated via a vagal reflex. Airway resistance was not increased in +IL5AE/−Eos mice, demonstrating that it required lung eosinophils, but was not affected by increased bone marrow or blood eosinophils or by increased IL5 in the absence of eosinophils. Eosinophils did not change M3 function on airway smooth muscle, since airway responses to methacholine in vagotomized mice were not different among strains. Eosinophils surrounding large airways were sufficient, even in the absence of increased IL5 or external insult, to increase vagally mediated reflex bronchoconstriction. Specifically blocking or reducing eosinophils surrounding large airways may effectively inhibit reflex hyperresponsiveness mediated by vagus nerves in eosinophilic asthma.
Inhibition of the stem cell factor 248 isoform attenuates the development of pulmonary remodeling disease
Authors: Rasky Andrew , Habiel David M. , Morris Susan , Schaller Matthew , Moore Bethany B. , Phan Sem , Kunkel Steven L. , Phillips Martin , Hogaboam Cory , Lukacs Nicholas W.
Published: November 2019

Stem cell factor (SCF) and its receptor c-kit have been implicated in inflammation, tissue remodeling, and fibrosis. Ingenuity Integrated Pathway Analysis of gene expression array data sets showed an upregulation of SCF transcripts in idiopathic pulmonary fibrosis (IPF) lung biopsies compared with tissue from nonfibrotic lungs that are further increased in rapid progressive disease. SCF248, a cleavable isoform of SCF, was abundantly and preferentially expressed in human lung fibroblasts and fibrotic mouse lungs relative to the SCF220 isoform. In fibroblast-mast cell coculture studies, blockade of SCF248 using a novel isoform-specific anti-SCF248 monoclonal antibody (anti-SCF248), attenuated the expression of COL1A1, COL3A1, and FN1 transcripts in cocultured IPF but not normal lung fibroblasts. Administration of anti-SCF248 on days 8 and 12 after bleomycin instillation in mice significantly reduced fibrotic lung remodeling and col1al, fn1, acta2, tgfb, and ccl2 transcript expression. In addition, bleomycin increased numbers of c-kit+ mast cells, eosinophils, and ILC2 in lungs of mice, whereas they were not significantly increased in anti-SCF248-treated animals. Finally, mesenchymal cell-specific deletion of SCF significantly attenuated bleomycin-mediated lung fibrosis and associated fibrotic gene expression. Collectively, these data demonstrate that SCF is upregulated in diseased IPF lungs and blocking SCF248 isoform significantly ameliorates fibrotic lung remodeling in vivo suggesting that it may be a therapeutic target for fibrotic lung diseases.
Osmoregulatory role of the intestine in the sea lamprey (Petromyzon marinus)
Authors: Barany A. , Shaughnessy C. A. , Fuentes J. , Mancera J. M. , McCormick S. D.
Published: November 2019

Lampreys are the most basal vertebrates with an osmoregulatory strategy. Previous research has established that the salinity tolerance of sea lamprey increases dramatically during metamorphosis, but underlying changes in the gut have not been examined. In the present work, we examined changes in intestinal function during metamorphosis and seawater exposure of sea lamprey ( Petromyzon marinus). Fully metamorphosed juvenile sea lamprey had 100% survival after direct exposure to 35 parts per thousand seawater (SW) and only slight elevations in plasma chloride (Cl−) levels. Drinking rates of sea lamprey juveniles in seawater were 26-fold higher than juveniles in freshwater (FW). Na+-K+-ATPase (NKA) activity in the anterior and posterior intestine increased 12- and 3-fold, respectively, during metamorphosis, whereas esophageal NKA activity was lower than in the intestine and did not change with development. Acclimation to SW significantly enhanced NKA activity in the posterior intestine but did not significantly change NKA activity in the anterior intestine, which remained higher than that in the posterior intestine. Intestinal Cl−and water uptake, which were observed in ex vivo preparations of anterior and posterior intestine under both symmetric and asymmetric conditions, were higher in juveniles than in larvae and were similar in magnitude of those of teleost fish. Inhibition of NKA by ouabain in ex vivo preparations inhibited intestinal water absorption by 64%. Our results indicate drinking and intestinal ion and water absorption are important to osmoregulation in SW and that preparatory increases in intestinal NKA activity are important to the development of salinity tolerance that occurs during sea lamprey metamorphosis.