bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic Evolution of the Marine Bacterium Phaeobacter inhibens during Biofilm Growth
Authors: Majzoub Marwan E. , McElroy Kerensa , Maczka Michael , Schulz Stefan , Thomas Torsten , Egan Suhelen
Published: July 2021

Biofilm formation and dispersal are important survival strategies for environmental bacteria. During biofilm dispersal, cells often display stable and heritable variants from the parental biofilm.
Phaeobacter inhibens
is an effective colonizer of marine surfaces, in which a subpopulation of its biofilm dispersal cells displays a noncompetitive phenotype.
Improving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction Systems
Authors: Lal Piyush Behari , Wells Fritz , Myers Kevin S. , Banerjee Rajdeep , Guss Adam M. , Kiley Patricia J.
Published: July 2021

Zymomonas mobilis
is equipped with a number of traits that make it a desirable platform organism for metabolic engineering to produce valuable bioproducts. Engineering strains equipped with synthetic pathways for biosynthesis of new molecules requires integration of foreign genes.
Functional Expression of Two Unusual Acidic Peroxygenases from
Candolleomyces aberdarensis
in Yeasts by Adopting Evolved Secretion Mutations
Authors: Gomez de Santos Patricia , Hoang Manh Dat , Kiebist Jan , Kellner Harald , Ullrich René , Scheibner Katrin , Hofrichter Martin , Liers Christiane , Alcalde Miguel
Published: July 2021

In this work, we incorporated several secretion mutations from an evolved fungal peroxygenase to enhance the production of active and stable forms of two unusual acidic peroxygenases. The tandem-yeast expression system based on
S. cerevisiae
for directed evolution and
P. pastoris
for overproduction on an ∼300-mg/liter scale is a versatile tool to generate UPO variants.
Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost
Authors: Sipes Katie , Almatari Abraham , Eddie Alexander , Williams Daniel , Spirina Elena , Rivkina Elizaveta , Liang Renxing , Onstott Tullis C. , Vishnivetskaya Tatiana A. , Lloyd Karen G.
Published: July 2021

Permafrost around the world is thawing rapidly. Many scientists from a variety of disciplines have shown the importance of understanding what will happen to our ecosystem, commerce, and climate when permafrost thaws.
Exploration of Social Spreading Reveals That This Behavior Is Prevalent amongPedobacterand Pseudomonas fluorescens Isolates and That There Are Variations in the Induction of the Phenotype
Authors: McCully Lucy M. , Graslie Jasmine , McGraw Alana R. , Bitzer Adam S. , Sigurbjörnsdóttir Auður M. , Vilhelmsson Oddur , Silby Mark W.
Published: July 2021

Interspecies social spreading (ISS) is an emergent behavior observed whenPseudomonas fluorescensPf0-1 andPedobactersp. V48 interact, during which both species move together across a surface.
Molecular Epidemiology of Human Sapovirus among Children with Acute Gastroenteritis in Western Canada
Authors: Zhuo Ran , Ding Xiaofeng , Freedman Stephen B. , Lee Bonita E. , Ali Samina , Luong Jasper , Xie Jianling , Chui Linda , Wu Ying , Pang Xiaoli
Published: July 2021

Sapovirus is increasingly recognized as an important cause of acute gastroenteritis (AGE) worldwide; however, studies of sapovirus prevalence, genetic diversity, and strain-specific clinical implications have been scarce. To fill this knowledge gap, we used reverse transcription–real-time PCR and sequencing of the partial major capsid protein VP1 gene to analyze stool specimens and rectal swabs obtained from 3,347 children with AGE and 1,355 asymptomatic controls (all <18 years old) collected between December 2014 and August 2018 in Alberta, Canada.
Targeted Long-Read Sequencing Reveals Comprehensive Architecture, Burden, and Transcriptional Signatures from Hepatitis B Virus-Associated Integrations and Translocations in Hepatocellular Carcinoma Cell Lines
Authors: Ramirez Ricardo , van Buuren Nicholas , Gamelin Lindsay , Soulette Cameron , May Lindsey , Han Dong , Yu Mei , Choy Regina , Cheng Guofeng , Bhardwaj Neeru , Chiu Joy , Muench Robert C. , Delaney William E. , Mo Hongmei , Feierbach Becket , Li Li
Published: July 2021

HCC-derived cell lines have served as practical models to study HBV biology for decades. These cell lines harbor multiple HBV integrations and express only HBV surface antigen (HBsAg).
RNA Helicase DDX17 Inhibits Hepatitis B Virus Replication by Blocking Viral Pregenomic RNA Encapsidation
Authors: Mao Richeng , Dong Minhui , Shen Zhongliang , Zhang Hu , Liu Yuanjie , Cai Dawei , Mitra Bidisha , Zhang Jiming , Guo Haitao
Published: July 2021

Hepatitis B virus (HBV) chronic infection, a long-studied but yet incurable disease, remains a major public health concern worldwide. Given that HBV replication cycle highly depends on host factors, deepening our understanding of the host-virus interaction is thus of great significance in the journey of finding a cure.
Structural Determinants of Virion Assembly and Release in the C Terminus of the Mason-Pfizer Monkey Virus Capsid Protein
Authors: Buckmaster Marlene V. , Zadrozny Kaneil K. , Ganser-Pornillos Barbie K. , Pornillos Owen , Goff Stephen P.
Published: July 2021

The C-terminal domain of the capsid protein of many retroviruses has been shown to be critical for virion assembly and maturation, but the functions of this region of M-PMV are uncertain. We show that a short “clasp” motif in the capsid domain of the M-PMV Gag protein plays a key role in M-PMV virion assembly, genome packaging, and infectivity.
EGR1 Suppresses Porcine Epidemic Diarrhea Virus Replication by Regulating IRAV To Degrade Viral Nucleocapsid Protein
Authors: Wang Hua , Kong Ning , Jiao Yajuan , Dong Sujie , Sun Dage , Chen Xiaoyong , Zheng Hao , Tong Wu , Yu Hai , Yu Lingxue , Zhang Wen , Tong Guangzhi , Shan Tongling
Published: July 2021

PEDV is a highly contagious enteric coronavirus that has rapidly emerged worldwide and has caused severe economic losses. No currently available drugs or vaccines can effectively control PEDV.
Suppression of CD80 Expression by ICP22 Affects Herpes Simplex Virus Type 1 Replication and CD8+IFN-γ+Infiltrates in the Eyes of Infected Mice but Not Latency Reactivation
Authors: Matundan Harry H. , Wang Shaohui , Jaggi Ujjaldeep , Yu Jack , Ghiasi Homayon
Published: July 2021

Direct binding of HSV-1 ICP22 to the CD80 promoter downregulates the expression of the costimulatory molecule CD80 but not CD86. In this study, we fine mapped the region of ICP22 required for binding to the CD80 promoter and constructed a recombinant virus containing a deletion in ICP22 that failed to bind to the CD80 promoter.
Novel
Gloeobacterales
spp. from Diverse Environments across the Globe
Authors: Grettenberger Christen L.
Published: July 2021

Early branching photosynthetic
Cyanobacteria
such as the
Gloeobacterales
may provide clues into the evolutionary history of oxygenic photosynthesis, but there are few genomes or cultured taxa from this order. Five new metagenome-assembled genomes suggest that members of the
Gloeobacterales
all contain reduced photosystems and lack genes associated with thylakoids and circadian rhythms.
Anaerobic Growth of
Listeria monocytogenes
on Rhamnose Is Stimulated by Vitamin B
12
and Bacterial Microcompartment-Dependent 1,2-Propanediol Utilization
Authors: Zeng Zhe , Li Siming , Boeren Sjef , Smid Eddy J. , Notebaart Richard A. , Abee Tjakko
Published: July 2021

Listeria monocytogenes
is a foodborne pathogen causing severe illness and, as such, it is crucial to understand the molecular mechanisms contributing to its survival strategy and pathogenicity. Rhamnose is a deoxyhexose sugar abundant in a range of environments, including the human intestine, and can be degraded in anaerobic conditions into 1,2-propanediol.
Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution
Authors: Fiedoruk Krzysztof , Drewnowska Justyna M. , Mahillon Jacques , Zambrzycka Monika , Swiecicka Izabela
Published: July 2021

This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically,
Bacillus mycoides
, a psychrotrophic member of the
Bacillus cereus
group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the
B. mycoides
pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history.
Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity
Authors: Scott William T. , van Mastrigt Oscar , Block David E. , Notebaart Richard A. , Smid Eddy J.
Published: July 2021

Saccharomyces cerevisiaeis widely used in grape juice fermentation to produce wines. Along with the genetic background, the nitrogen in the environment in whichS. cerevisiaegrows impacts its regulation of metabolism.
Geospatial analysis of pediatric surgical need and geographical access to care in Somaliland: a cross-sectional study
Authors: Cotache-Condor Cesia F , Moody Katelyn , Concepcion Tessa , Mohamed Mubarak , Dahir Shukri , Adan Ismail Edna , Cook Jonathan , Will John , Rice Henry E , Smith Emily R
Published: July 2021

Background

The global burden of disease in children is large and disproportionally affects low-income and middle-income countries (LMICs). Geospatial analysis offers powerful tools to quantify and visualise disparities in surgical care in LMICs. Our study aims to analyse the geographical distribution of paediatric surgical conditions and to evaluate the geographical access to surgical care in Somaliland.

Methods

Using the Surgeons OverSeas Assessment of Surgical Need survey and a combined survey from the WHO’s (WHO) Surgical Assessment Tool—Hospital Walkthrough and the Global Initiative for Children’s Surgery Global Assessment in Paediatric Surgery, we collected data on surgical burden and access from 1503 children and 15 hospitals across Somaliland. We used several geospatial tools, including hotspot analysis, service area analysis, Voronoi diagrams, and Inverse Distance Weighted interpolation to estimate the geographical distribution of paediatric surgical conditions and access to care across Somaliland.

Results

Our analysis suggests less than 10% of children have timely access to care across Somaliland. Patients could travel up to 12 hours by public transportation and more than 2 days by foot to reach surgical care. There are wide geographical disparities in the prevalence of paediatric surgical conditions and access to surgical care across regions. Disparities are greater among children travelling by foot and living in rural areas, where the delay to receive surgery often exceeds 3 years. Overall, Sahil and Sool were the regions that combined the highest need and the poorest surgical care coverage.

Conclusion

Our study demonstrated wide disparities in the distribution of surgical disease and access to surgical care for children across Somaliland. Geospatial analysis offers powerful tools to identify critical areas and strategically allocate resources and interventions to efficiently scale-up surgical care for children in Somaliland.
The PROGRAM study: awake mapping versus asleep mapping versus no mapping for high-grade glioma resections: study protocol for an international multicenter prospective three-arm cohort study
Authors: Gerritsen Jasper Kees Wim , Satoer Djaina D , Dirven Clemens Maria Franciscus , De Vleeschouwer Steven , Seidel Kathleen , Schucht Philippe , Jungk Christine , Krieg Sandro M , Nahed Brian Vala , Berger Mitchel Stuart , Broekman Marike Lianne Daphne , Vincent Arnaud Jean Pierre Edouard
Published: July 2021

Introduction

The main surgical dilemma during glioma resections is the surgeon’s inability to accurately identify eloquent areas when the patient is under general anaesthesia without mapping techniques. Intraoperative stimulation mapping (ISM) techniques can be used to maximise extent of resection in eloquent areas yet simultaneously minimise the risk of postoperative neurological deficits. ISM has been widely implemented for low-grade glioma resections backed with ample scientific evidence, but this is not yet the case for high-grade glioma (HGG) resections. Therefore, ISM could thus be of important value in HGG surgery to improve both surgical and clinical outcomes.

Methods and analysis

This study is an international, multicenter, prospective three-arm cohort study of observational nature. Consecutive HGG patients will be operated with awake mapping, asleep mapping or no mapping with a 1:1:1 ratio. Primary endpoints are: (1) proportion of patients with National Institute of Health Stroke Scale deterioration at 6 weeks, 3 months and 6 months after surgery and (2) residual tumour volume of the contrast-enhancing and non-contrast-enhancing part as assessed by a neuroradiologist on postoperative contrast MRI scans. Secondary endpoints are: (1) overall survival and (2) progression-free survival at 12 months after surgery; (3) oncofunctional outcome and (4) frequency and severity of serious adverse events in each arm. Total duration of the study is 5 years. Patient inclusion is 4 years, follow-up is 1 year.

Ethics and dissemination

The study has been approved by the Medical Ethics Committee (METC Zuid-West Holland/Erasmus Medical Center; MEC-2020–0812). The results will be published in peer-reviewed academic journals and disseminated to patient organisations and media.

Trial registration number

ClinicalTrials.gov ID numberNCT04708171(PROGRAM-study),NCT03861299(SAFE-trial)
Cohort profile: an observational longitudinal data collection of health aspects in a cohort of female cancer survivors with a history of pelvic radiotherapy—a population-based cohort in the western region of Sweden
Authors: Åkeflo Linda , Dunberger Gail , Elmerstig Eva , Skokic Viktor , Steineck Gunnar , Bergmark Karin
Published: July 2021

Purpose

The study ‘Health among women after pelvic radiotherapy’ was conducted in response to the need for more advanced and longitudinal data concerning long-term radiotherapy-induced late effects and chronic states among female cancer survivors. The objective of this paper is to detail the cohort profile and the study procedure in order to provide a sound basis for future analyses of the study cohort.

Participants

Since 2011, and still currently ongoing, participants have been recruited from a population-based study cohort including all female patients with cancer, over 18 years of age, treated with pelvic radiotherapy with curative intent at Sahlgrenska University Hospital in Gothenburg, in the western region of Sweden, which covers 1.7 million of the Swedish population. The dataset presented here consists of baseline data provided by 605 female cancer survivors and 3-month follow-up data from 260 individuals with gynaecological, rectal or anal cancer, collected over a 6-year period.

Findings to date

Data have been collected from 2011 onwards. To date, three studies have been published using the dataset reporting long-term radiation-induced intestinal syndromes and late adverse effects affecting sexuality, the urinary tract, the lymphatic system and physical activity. These projects include the evaluation of interventions developed by and provided in a nurse-led clinic.

Future plans

This large prospective cohort offers the possibility to study health outcomes in female pelvic cancer survivors undergoing a rehabilitation intervention in a nurse-led clinic, and to study associations between demographics, clinical aspects and long-term late effects. Analysis focusing on the effect of the interventions on sexual health aspects, preinterventions and postinterventions, is currently ongoing. The cohort will be expanded to comprise the entire data collection from 2011 to 2020, including baseline data and data from 3-month and 1-year follow-ups after interventions. The data will be used to study conditions and treatment-induced late effects preintervention and postintervention.
Experimental study of fixed-ended RC deep beams under cyclic and monotonic loading
Authors: Arabzadeh Abolfazl , Yang T.Y. , Hizaji Rouhollah , Amani Dashlejeh Asghar
Published: July 2021

Reinforced concrete (RC) deep beams are commonly used in structural design to transfer vertical loads when there is a vertical discontinuity in the load path. Much experimental research has been conducted on simply supported deep beams, but little research has been carried out using monotonic loads. In our study, an experimental investigation was conducted to study fixed-ended reinforced concrete deep beams under cyclic and monotonic loads. Five specimens were experimentally tested. The specimens had similar geometry but different reinforcement details. Four specimens were tested under cyclic loads and one specimen under a monotonic load to observe the deflection of the mid-span where the load was applied, as well as the crack patterns, failure modes, and shear strengths. The results show that web reinforcements are more effective than longitudinal bars at increasing shear capacity in fixed-ended RC deep beams.
Domain-specific risk assessment using integrated simulation: a case study of an onshore wind project
Authors: Mohamed Emad , Seresht Nima Gerami , Hague Stephen , Chehouri Adam , AbouRizk Simaan
Published: July 2021

Although many quantitative risk assessment models have been proposed in literature, their use in construction practice remain limited due to a lack of domain-specific models, tools, and application examples. This is especially true in wind farm construction, where the state-of-the-art integrated Monte Carlo simulation and critical path method (MCS–CPM) risk assessment approach has yet to be demonstrated. The present case study is the first reported application of the MCS–CPM method for risk assessment in wind farm construction and is the first case study to consider correlations between cost and schedule impacts of risk factors using copulas. MCS–CPM provided reasonable risk assessment results for a wind farm project, and its use in practice is recommended. To facilitate the practical application of quantitative risk assessment methods, this case study provides a much-needed analytical generalization of MCS–CPM, offering application examples, discussion of expected results, and recommendations to wind farm construction practitioners.
Geophysical reassessment of the role of ancient lineaments on the development of the western Laurentian margin and its sediment-hosted Zn–Pb deposits, Yukon and Northwest Territories, Canada
Authors: Hayward Nathan , Paradis Suzanne
Published: July 2021

A new three-dimensional (3D) inversion strategy is applied to new compilations of gravity and magnetic data to reassess the role of crustal lineaments in the development of the western Laurentian margin, Selwyn Basin, and associated sediment-hosted zinc–lead (Zn–Pb) deposits. The region’s history is obscured by multiple tectonic overprints, including terrane accretion, plutonism, and thrust faulting. Regionally continuous, broadly northeast-trending crustal lineaments, including the Liard line, Fort Norman structure, and Leith Ridge fault, were interpreted as having had long-standing influence on craton, margin, and sedimentary basin development. An east–northeast-trending lineament, Mackenzie River, traced from the Misty Creek Embayment to Great Bear Lake, is interpreted as the southern edge of a cratonic promontory. The location of the Liard line, associated with a transfer fault that bounds the Macdonald Platform promontory, is refined. New geophysical results support the continuity of the Fort Norman structure below the Selwyn Basin, but limited evidence exists for the Leith Ridge fault in this area. A northwest-trending lineament that bounds the craton is interpreted as a crustal manifestation of lithospheric thinning of the Laurentian margin, as echoed by a change in the depth of the lithosphere–asthenosphere boundary. The structure delimits the eastern extent of mid- to Late Cretaceous granitic intrusions and is straddled by Mississippi Valley-type Zn–Pb occurrences, following their palinspastic restoration. Clastic-dominated Zn–Pb occurrences are aligned along another northwest-trending lineament interpreted to be associated with a shallowing of lower crustal rocks.
Optical sensors to predict sugarbeet yield, quality, and fertilizer nitrogen application rate
Authors: Van Eerd Laura L. , MacFarlane J. Mitchell , Chahal Inderjot
Published: July 2021

Nitrogen (N) management is critical for sugarbeet (Beta vulgaris L.) because N inversely influences root yield and recoverable white sucrose per tonne (RWST). In Ontario, from 2015 to 2017, the use of optical sensors (e.g., a soil plant analysis development (SPAD) chlorophyll meter, GreenSeeker handheld crop sensor) was evaluated as a method to guide N application and harvest date (late-September, late-October) selection by predicting root yield RWST and partial profit margins. In a commercial field, 4 to 5 fertilizer N rates, and 8 to 12 cultivars were tested in a split block design experiment with three replications and two harvest dates. In all years, few cultivars (≤2) had a root yield response to applied N, which was attributed to high inherent soil fertility, and limited our evaluation of optical sensors to adjust in-season N applications. The optimal N rate to maximize RWST and profits was 0 to 45 kg N·ha−1 and confirmed their negative relationship to applied N. Optical sensor readings correlated negatively with RWST across the majority (>60%) of cultivars tested in mid-August and September. Across all cultivars, the regression model of optical sensors to predict RWST at early harvest was strongest (R2 = 0.48 for SPAD; 0.24 for GreenSeeker) when readings were taken in early September. Although future research to refine this relationship is needed, we recommend the use of optical sensors, particularly the SPAD meter, in early September to guide harvest selection to maximize RWST.
CONDENSATION PHASE CHANGE BEHAVIORS ON A ROUGH SURFACE CHARACTERIZED BY FRACTAL CANTOR
Authors: WANG HE , DENG ZILONG , YAO FENG , ZHANG CHENGBIN
Published: July 2021

Understanding the fundamental mechanisms of vapor condensation on rough surfaces is crucial to a wide range of industrial applications. A hybrid thermal lattice Boltzmann model of the condensation heat transfer process on downward-facing rough surfaces characterized by the Cantor fractal is developed and numerically analyzed to investigate the condensation phase change behaviors on rough hydrophobic and hydrophilic surfaces. The dynamic behaviors of vapor condensation, including the evolutions of vapor–liquid interface, heat flux, condensate mass, and temperature distribution, on the hydrophilic and hydrophobic rough surfaces are presented and compared with corresponding smooth surfaces. The results indicate that the rough surface preferred a filmwise condensation under hydrophilic conditions but a hybrid dropwise–filmwise condensation under hydrophobic conditions. On the rough hydrophobic surface, the liquid film can rapidly adsorb droplets, maintaining a high-efficiency dropwise condensation. The absorption of droplets accelerates the liquid film growth and detachment process on the rough hydrophobic surface, which reduces the time-averaged thermal resistance of the filmwise region. These two behaviors together enhance condensation heat transfer on the downward-facing rough hydrophobic surface. Besides, stable dropwise condensation could also be formed on smooth hydrophilic surfaces and has better heat transfer performance than corresponding hydrophobic surfaces under the same heat transfer condition.
EFFECTS OF A CAVITY’S FRACTAL BOUNDARY ON THE FREE FRONT INTERFACE OF THE POLYMER FILLING STAGE
Authors: LI XUEJUAN , WANG DAN
Published: July 2021

The unsmooth boundary of a cavity for the stage of filling glass fiber-reinforced polymer melt affects the flow property and the shape of the free interface’s shape, as a result, it will affect greatly the process, the degree and the location of the front interface, and the weld lines’ property and product quality as well. Here, the two-scale fractal theory is adopted to figure out the basic property of the unsmooth boundary, and governing equations are established in a fractal space. The numerical results can provide insight into the filling process and reveal the main factors affecting the shape of the free interface. The fractal interface is illustrated by the least-square method in different fractal spaces based on numerical simulation results. The fractal cavity sheds a new light on controlling the interface.
NEW HERMITE–HADAMARD–FEJÉR TYPE INEQUALITIES VIA RIEMANN–LIOUVILLE FRACTIONAL INTEGRALS FOR CONVEX FUNCTIONS
Authors: QI YONGFANG , LI GUOPING
Published: July 2021

In this paper, we present new Hermite–Hadamard–Fejér type inequalities via Riemann–Liouville fractional integrals for the function [Formula: see text], where [Formula: see text] is convex function and [Formula: see text] is symmetric with respect to [Formula: see text]. Our results in some special cases yield the well-known classic Hermite–Hadamard–Fejér type inequalities. At the end of the paper, the applications of our results are given.
A NEW FRACTAL APPARENT PERMEABILITY MODEL FOR LIQUID FLOW IN TORTUOUS NANOPORES FROM LATTICE BOLTZMANN SIMULATIONS TO THE THEORETICAL MODEL
Authors: WANG HAN , SU YULIANG , WANG WENDONG , MENG YANG , XIE XIUHENG , XU JILONG , ZHANG QI
Published: July 2021

Tortuous pores are ubiquitous in natural porous media; however, the linear effects of tortuosity on the liquid flow behaviors are usually considered through capillary bundle models, which lead to inaccurate permeability prediction. Additionally, in the nanopores, due to the existence of heterogeneous viscosity and boundary slip, the effects of tortuosity on nanoconfined liquid flow behaviors are more complicated. In this paper, we comprehensively use the theoretical models and a nanoscale multi-relaxation-time lattice Boltzmann method (MRT-LBM) to characterize water flow behaviors in the tortuous nanopores, where heterogeneous viscosity and boundary slip are considered. The results show that the increase of tortuosity causes more negative effects, which results in a decreasing apparent permeability. The conventional model of the influence of tortuosity on the apparent permeability is linear[Formula: see text], which greatly underestimates the effect of tortuosity on apparent permeability. Then, a new fractal apparent permeability model [Formula: see text] based on modified tortuous effects is obtained by fitting the results from the MRT-LBM simulations. Based on the new fractal apparent permeability models, the results show that with an increasing fractal tortuosity dimension, the apparent permeability decreases rapidly first and then this trend becomes moderate. Our works can provide a more accurate basic model for studying liquid flow in porous media based on the capillary bundle model or pore network model.
ANALOG IMPLEMENTATION OF FRACTIONAL-ORDER ELECTRIC ELEMENTS USING CAPUTO–FABRIZIO AND ATANGANA–BALEANU DEFINITIONS
Authors: LIAO XIAOZHONG , LIN DA , DONG LEI , RAN MANJIE , YU DONGHUI
Published: July 2021

This study employs the Caputo–Fabrizio and Atangana–Baleanu fractional derivatives to determine the impedance and admittance model of fractional capacitor and inductor. The analog implementation circuits are proposed aiming at fractional-order electric elements based on these two derivatives, which can be widely used in a variety of electrical systems using new fractional operators. Constant phase capacitor and inductor are approximated by the Oustaloup algorithm and the recursive net-grid-type analog circuit, respectively. Based on that, approximation circuits of fractional electric components under Caputo–Fabrizio and Atangana–Baleanu definitions are given. For the purpose of judging whether the implementation topology of fractional-order capacitor and inductor is accurate, taking fractional RC and RL circuit defined by Caputo, Caputo–Fabrizio and Atangana–Baleanu derivatives as examples, the comparison of numerical and circuit simulations is carried out. The correctness of the analog implementation circuits using the Caputo–Fabrizio and Atangana–Baleanu definitions is verified. Fractional-order RC charging circuit experiments based on Caputo, Caputo–Fabrizio and Atangana–Baleanu derivatives are taken as examples. Several experiments with different fractional-order and circuit parameters are carried out. The validity of the implementation methods is ulteriorly proved with experiment data.
PERFORMANCE IMPROVEMENT EVALUATION OF A LATENT HEAT STORAGE UNIT ENHANCED BY VICSEK FRACTAL FINS
Authors: HUANG YONGPING , DENG ZILONG , GAO WEI
Published: July 2021

The mature and scale utilization of renewable energy is restricted by the deficient efficiency of latent heat storage (LHS) technology. To address this, an innovative Vicsek fractal fin is first proposed herein for the heat charging/discharging rate enhancement. The phase transition behavior and thermal characteristics of the innovative LHS unit are solved numerically and compared to the traditional one, employing the enthalpy–porosity algorithm and a two-dimensional transient model. The results indicate that Vicsek fractal fins remarkably promote the thermal efficiency of LHS units. Compared to the traditional LHS units, innovative LHS units with Vicsek fractal fins, respectively, reduce the melting/solidification duration by 16.1% and 28.7%. The melting process is divided into early thermal conduction, subsequent convective thermal transport, and later thermal conduction, while solidification processes are dominated by the initial natural convection and the subsequent continuous heat conduction. Moreover, the impact of free convection is higher on melting processes than on solidification processes. Importantly, the efficient heat transfer path of Vicsek fractal fins allows the inherent natural convection suppression to be much weaker than the improvement level of heat transfer efficiency, facilitating the interstitial thermal transport between the phase change material (PCM) and fins and improving the overall temperature uniformity of LHS units.
China–US Rapidly Changing Dynamics and Small States: A View from Singapore
Authors: LYE Liang Fook
Published: July 2021

As a small state, Singapore is particularly acute to the state of US–China relations that defines the strategic landscape. Since independence, Singapore has carefully managed its ties with the big powers—an increasingly challenging task amid rising US–China tensions and growing pressure to take a certain position. Safeguarding its national interest will continue to be the imperative and reliable approach for Singapore to grow its ties with major powers.
TRIPDECODER: Study Travel Time Attributes and Route Preferences of Metro Systems from Smart Card Data
Authors: Tian Xiancai , Zheng Baihua , Wang Yazhe , Huang Hsiao-Ting , Hung Chih-Chieh
Published: July 2021

In this article, we target at recovering the exact routes taken by commuters inside a metro system that are not captured by an Automated Fare Collection (AFC) system and hence remain unknown. We strategically propose two inference tasks to handle the recovering, one to infer the travel time of each travel link that contributes to the total duration of any trip inside a metro network and the other to infer the route preferences based on historical trip records and the travel time of each travel link inferred in the previous inference task. As these two inference tasks have interrelationship, most of existing works perform these two tasks simultaneously. However, our solution
TripDecoder
adopts a totally different approach.
TripDecoder
fully utilizes the fact that there are some trips inside a metro system with only one practical route available. It strategically decouples these two inference tasks by only taking those trip records with only one practical route as the input for the first inference task of travel time and feeding the inferred travel time to the second inference task as an additional input, which not only improves the accuracy but also effectively reduces the complexity of both inference tasks. Two case studies have been performed based on the city-scale real trip records captured by the AFC systems in Singapore and Taipei to compare the accuracy and efficiency of
TripDecoder
and its competitors. As expected,
TripDecoder
has achieved the best accuracy in both datasets, and it also demonstrates its superior efficiency and scalability.
Research On Pre-Training Method and Generalization Ability of Big Data Recognition Model of the Internet of Things
Authors: Tan Junyang , Xia Dan , Dong Shiyun , Zhu Honghao , Xu Binshi
Published: July 2021

The Internet of Things and big data are currently hot concepts and research fields. The mining, classification, and recognition of big data in the Internet of Things system are the key links that are widely of concern at present. The artificial neural network is beneficial for multi-dimensional data classification and recognition because of its strong feature extraction and self-learning ability. Pre-training is an effective method to address the gradient diffusion problem in deep neural networks and could result in better generalization. This article focuses on the performance of supervised pre-training that uses labelled data. In particular, this pre-training procedure is a simulation that shows the changes in judgment patterns as they progress from primary to mature within the human brain. In this article, the state-of-the-art of neural network pre-training is reviewed. Then, the principles of the auto-encoder and supervised pre-training are introduced in detail. Furthermore, an extended structure of supervised pre-training is proposed. A set of experiments are carried out to compare the performances of different pre-training methods. These experiments include a comparison between the original and pre-trained networks as well as a comparison between the networks with two types of sub-network structures. In addition, a homemade database is established to analyze the influence of pre-training on the generalization ability of neural networks. Finally, an ordinary convolutional neural network is used to verify the applicability of supervised pre-training.
Deep Neural Network Based Noised Asian Speech Enhancement and Its Implementation on a Hearing Aid App
Authors: Fan Xiaoqian , Yang Bowen , Chen Wenzhi , Fan Quanfang
Published: July 2021

This article studies noised Asian speech enhancement based on the deep neural network (DNN) and its implementation on an app. We use the THCHS-30 speech dataset and the common noise dataset in daily life as training and testing data of the DNN. To stack the frequency data of multiple audio frames to improve the effect of speech enhancement, the system compares the best number of stacked frames during training and testing. At the same time, the influence of training rounds on the PESQ is compared, and the best number of rounds is obtained. On this basis, the best model is implemented on the hearing aid app, and the real-time performance of the device is tested. The experiment shows that based on the DNN, using an appropriate number of rounds for training and using an appropriate number of audio frames stacking to improve the speech enhancement effect, and transplanting this speech enhancement model to the hearing aid app, can effectively improve speech clarity and intelligibility within a reasonable time delay range.
Humanized Recommender Systems: State-of-the-art and Research Issues
Authors: Tran Thi Ngoc Trang , Felfernig Alexander , Tintarev Nava
Published: July 2021

Psychological factors such aspersonality, emotions, social connections, anddecision biasescan significantly affect the outcome of a decision process. These factors are also prevalent in the existing literature related to the inclusion of psychological aspects in recommender system development.Personalityandemotionsof users have strong connections with their interests and decision-making behavior. Hence, integrating these factors into recommender systems can help to better predict users’ item preferences and increase the satisfaction with recommended items. In scenarios where decisions are made by groups (e.g., selecting a tourism destination to visit with friends),group compositionandsocial connectionsamong group members can affect the outcome of a group decision.Decision biasesoften occur in a recommendation process, since users usually apply heuristics when making a decision. These biases can result in low-quality decisions. In this article, we provide a rigorous review of existing research on the influence of the mentioned psychological factors on recommender systems. These factors are not only considered in single-user recommendation scenarios but, importantly, also in group recommendation ones, where groups of users are involved in a decision-making process. We include working examples to provide a deeper understanding of how to take into account these factors in recommendation processes. The provided examples go beyond single-user recommendation scenarios by also considering specific aspects of group recommendation settings.
On-Shelf Utility Mining of Sequence Data
Authors: Zhang Chunkai , Du Zilin , Yang Yuting , Gan Wensheng , Yu Philip S.
Published: July 2021

Utility mining has emerged as an important and interesting topic owing to its wide application and considerable popularity. However, conventional utility mining methods have a bias toward items that have longer on-shelf time as they have a greater chance to generate a high utility. To eliminate the bias, the problem of on-shelf utility mining (OSUM) is introduced. In this article, we focus on the task of OSUM of sequence data, where the sequential database is divided into several partitions according to time periods and items are associated with utilities and several on-shelf time periods. To address the problem, we propose two methods, OSUM of sequence data (OSUMS) and OSUMS
+
, to extract on-shelf high-utility sequential patterns. For further efficiency, we also design several strategies to reduce the search space and avoid redundant calculation with two upper bounds time prefix extension utility (
TPEU
) and time reduced sequence utility (
TRSU
). In addition, two novel data structures are developed for facilitating the calculation of upper bounds and utilities. Substantial experimental results on certain real and synthetic datasets show that the two methods outperform the state-of-the-art algorithm. In conclusion, OSUMS may consume a large amount of memory and is unsuitable for cases with limited memory, while OSUMS
+
has wider real-life applications owing to its high efficiency.
Community Detection in Partially Observable Social Networks
Authors: Tran Cong , Shin Won-Yong , Spitz Andreas
Published: July 2021

The discovery of community structures in social networks has gained significant attention since it is a fundamental problem in understanding the networks’ topology and functions. However, most social network data are collected from partially observable networks with
both missing nodes and edges
. In this article, we address a new problem of detecting
overlapping
community structures in the context of such an
incomplete
network, where communities in the network are allowed to overlap since nodes belong to multiple communities at once. To solve this problem, we introduce
KroMFac
, a new framework that conducts community detection via regularized
nonnegative matrix factorization (NMF)
based on the
Kronecker graph
model. Specifically, from an inferred Kronecker generative parameter matrix, we first estimate the missing part of the network. As our major contribution to the proposed framework, to improve community detection accuracy, we then characterize and select
influential
nodes (which tend to have high degrees) by ranking, and add them to the existing graph. Finally, we uncover the community structures by solving the regularized NMF-aided optimization problem in terms of maximizing the likelihood of the underlying graph. Furthermore, adopting normalized mutual information (NMI), we empirically show superiority of our
KroMFac
approach over two baseline schemes by using both synthetic and real-world networks.
Dynamically Adjusting Diversity in Ensembles for the Classification of Data Streams with Concept Drift
Authors: Hidalgo Juan I. G. , Santos Silas G. T. C. , Barros Roberto S. M.
Published: July 2021

A data stream can be defined as a system that continually generates a lot of data over time. Today, processing data streams requires new demands and challenging tasks in the data mining and machine learning areas.
Concept Drift
is a problem commonly characterized as changes in the distribution of the data within a data stream. The implementation of new methods for dealing with data streams where concept drifts occur requires algorithms that can adapt to several scenarios to improve its performance in the different experimental situations where they are tested. This research proposes a strategy for dynamic parameter adjustment in the presence of concept drifts. Parameter Estimation Procedure (PEP) is a general method proposed for dynamically adjusting parameters which is applied to the diversity parameter (λ) of several classification ensembles commonly used in the area. To this end, the proposed estimation method (PEP) was used to create Boosting-like Online Learning Ensemble with Parameter Estimation (BOLE-PE), Online AdaBoost-based M1 with Parameter Estimation (OABM1-PE), and Oza and Russell’s Online Bagging with Parameter Estimation (OzaBag-PE), based on the existing ensembles BOLE, OABM1, and OzaBag, respectively. To validate them, experiments were performed with artificial and real-world datasets using Hoeffding Tree (HT) as base classifier. The accuracy results were statistically evaluated using a variation of the Friedman test and the Nemenyi post-hoc test. The experimental results showed that the application of the dynamic estimation in the diversity parameter (λ) produced good results in most scenarios, i.e., the modified methods have improved accuracy in the experiments with both artificial and real-world datasets.
Passages
Authors: Groce Alex
Published: July 2021

Douglas Hofstadter's "Metamagical Themas: Questing for the Essence of Mind and Pattern" is not the Hofstadter book people probably expected to eventually turn up in a Passages column, to be honest. And I do not want to disparage his most famous work; I read Godel, Escher, Bach: an Eternal Golden Braid (GEB) one Christmas vacation, I believe when I was in the eighth grade, and it was a revelatory and enchanting experience, with a profound impact on the course of my future life. But everyone knows about that book, and has an opinion on it; I think it's a literary masterpiece and even when it gets something wrong, it does so in an interesting way.
Pains and Gains of Peer-Reviewing in Software Engineering (5)
Authors: Soldani Jacopo
Published: July 2021

ACM SIGSOFT SEN's column on "Pains and Gains of Peer-Reviewing in Software Engineering" aims at fostering an open, constructive, and lively discussion on the peer-reviewing currently adopted by SE venues, e.g., how to further enhance them and make them sustainable on the long run. This fifth editorial introduces a new contribution to the column, which provides a journal-centric perspective on the topic.
An Interview with Laurie Williams - ACM Fellow 2020
Authors: Pfahl Dietmar
Published: July 2021

Laurie Williams is one of the five ACM Fellows of the 2020 cohort who are also active SIGSOFT members. To celebrate her award, we invited her to a question/answer session.
Reflections on
Authors: Posnett Daryl , Hindle Abram , Devanbu Premkumar
Published: July 2021

At UC Davis, in late 2010, we noticed that developers frequently debated the topic of code readability and style. Practitioners often expressed strong, off-the-cuff judgments regarding the read- ability of code, but mostly disagreed on the precise attributes of readability. While developers clearly cared about the factors they believed related to readability, the concept was not well defined.
Finding Polluter Tests Using Java PathFinder
Authors: Yi Pu , Wei Anjiang , Lam Wing , Xie Tao , Marinov Darko
Published: July 2021

Tests that modify (i.e., "pollute") the state shared among tests in a test suite are called \polluter tests". Finding these tests is im- portant because they could result in di erent test outcomes based on the order of the tests in the test suite. Prior work has proposed the PolDet technique for nding polluter tests in runs of JUnit tests on a regular Java Virtual Machine (JVM). Given that Java PathFinder (JPF) provides desirable infrastructure support, such as systematically exploring thread schedules, it is a worthwhile attempt to re-implement techniques such as PolDet in JPF. We present a new implementation of PolDet for nding polluter tests in runs of JUnit tests in JPF. We customize the existing state comparison in JPF to support the so-called \common-root iso- morphism" required by PolDet. We find that our implementation is simple, requiring only -200 lines of code, demonstrating that JPF is a sophisticated infrastructure for rapid exploration of re-search ideas on software testing. We evaluate our implementation on 187 test classes from 13 Java projects and nd 26 polluter tests. Our results show that the runtime overhead of PolDet@JPF com- pared to base JPF is relatively low, on average 1.43x. However, our experiments also show some potential challenges with JPF.
When Curation Becomes Creation
Authors: Leqi Liu , Hadfield-Menell Dylan , Lipton Zachary C.
Published: July 2021

Media platforms today benefit from: (1) discretion to organize content, (2) algorithms for curating user-posted content, and (3) absolution from liability. This favorable regulatory environment results from the current legal framework, which distinguishes between intermediaries and content providers. This distinction is ill-adapted to the modern social media landscape, where platforms deploy powerful data-driven algorithms to play an increasingly active role in shaping what people see, and where users supply disconnected bits of raw content as fodder. Today's platforms have license to monetize whatever content they like, moderate if and when it aligns with their corporate objectives, and curate their content however they wish.
Use of human tissue stem cell-derived organoid cultures to model enterohepatic circulation
Authors: Blutt Sarah E. , Crawford Sue E. , Bomidi Carolyn , Zeng Xi-Lei , Broughman James R. , Robertson Matthew , Coarfa Cristian , Tessier Mary Elizabeth M. , Savidge Tor , Hollinger F. Blaine , Curley Steven A. , Donowitz Mark , Estes Mary K.
Published: July 2021

Interorgan signaling is a critical feature of human biology and physiology, yet has remained difficult to study due to the lack of in vitro models. Here, we demonstrate that physical coupling of ex vivo human intestine and liver epithelial organoid cultures recapitulates in vivo interorgan bile acid signaling. These results suggest that coupling of multiple organoid systems provides new models to investigate interorgan communication and advances our knowledge of human physiological and pathophysiological processes.