bluuebunny/crossref_metadata_2025 huggingface dataset:
Expiratory variability index (EVI) is associated with the severity of acute bronchial obstruction in small children: A proof‐of‐concept study
Authors: Seppä Ville‐Pekka , Turkalj Mirjana , Hult Anton , Maloča Vuljanko Ivana , Plavec Davor ,   Collaborators, Erceg Damir , Petković Giorgie
Published: April 2020

Background

Lung function testing in small children is cumbersome. However, reduced variability of tidal breathing recorded using impedance pneumography (IP) during sleep was recently found to be a potential objective marker of wheeze in children aged 1‐5 years. We aimed to investigate how an acute bronchial obstruction (BO) and its severity, and recovery thereof reflect in expiratory variability index (EVI).

Methods

EVI was measured using a wearable IP system (Ventica®) during sleep in 40 healthy controls (aged 1.5‐5.9 years) and 30 patients hospitalized due to acute BO (aged 1.3‐5.3 years). In healthy controls, EVI was measured for 1‐3 nights at their homes. Patients were measured for several nights during hospitalization, as practically feasible, and at home 2 and 4 weeks post‐discharge.

Results

We received 79 EVI results from 39 controls and 139 from 30 patients. 90% had previous BO episodes, 30% used asthma controller medication before and 100% after hospitalization. Compared to controls, EVI was significantly lower during hospitalization (P < .0001) having significant correlation with number of days to discharge (r = −.38, P = .004). At 2 or 4 weeks post‐discharge, EVI was not significantly different from the controls (P = .14, P = .49, respectively). EVI was significantly associated with chest auscultation findings (P = .0001) being 17.5 (4.9) (median, IQR) with normal auscultation, 15.6 (7.4) in those with prolonged expiration and 11.4 (6.8) in those with wheeze and/or rales and crackles.

Conclusions

EVI was found to be a sensitive, objective marker of acute BO, showing strong association with changes in clinical status in wheezy children aged 1‐5 years.
Rediscovering Li Zehou: From the perspective of philosophy of language
Authors: Yang Xiaobo
Published: April 2020

This article seeks to shed new light on Li Zehou's thought by examining the long‐neglected dimension of the philosophy of language in his philosophical system. In addition, an effort is made to analyze how this dimension is generated by Li's creative combination of Marxism and Chinese philosophy. Insisting on the priority of life and practice to language, Li attacks the ‘linguistic turn’ so as to lead the focus of philosophy from language back to life. Li's treatment of language consistently seeks to keep pace with the development of his thinking, incorporating an evolutionary continuum from practice to life. One of the primary approaches adopted by Li in the construction of his philosophy is to deconstruct the language‐centered ontology that resulted from the ‘linguistic turn’ in the West. Notwithstanding this, his deconstruction still performs the same task as the philosophy of language typically does, that is, addressing philosophical problems through clarifying the nature of language. What is distinctive, however, is that he goes beyond this to expose the limitations of language.
Recent work on the proof paradox
Authors: Ross Lewis D.
Published: April 2020

Recent years have seen fresh impetus brought to debates about the proper role of statistical evidence in the law. Recent work largely centers on a set of puzzles known as the “proof paradox.” While these puzzles may initially seem academic, they have important ramifications for the law: raising key conceptual questions about legal proof, and practical questions about DNA evidence. This article introduces the proof paradox, why we should care about it, and new work attempting to resolve it.
Is corticosteroid use truly not associated with improved outcomes in AE‐IPF? – Reply
Authors: Farrand Erica , Collard Harold R.
Published: April 2020

See Letter
Is corticosteroid use truly not associated with improved outcomes in AE‐IPF?
Authors: Arai Toru , Inoue Yoshikazu
Published: April 2020

See Reply
Characterizing the resting metabolic rate ratio in ovulatory exercising women over 12 months
Authors: Strock Nicole C. A. , Koltun Kristen J. , Mallinson Rebecca J. , Williams Nancy I. , De Souza Mary Jane
Published: April 2020

Purpose

A reduced resting metabolic rate (RMR) ratio and suppressed total triiodothyronine (TT3) have been demonstrated to reflect metabolic compensation to chronic energy deficiency. However, it is unknown whether the relationship between RMR ratio and TT3 remains constant over time.

Objective

To examine the relationship between RMR ratio and TT3 in free‐living exercising, ovulatory, weight‐stable women (n = 14) for a 12‐month observational period.

Methods

Dual‐energy X‐ray absorptiometry (DXA) and indirect calorimetry provided data on anthropometrics and energy expenditure. Harris‐Benedict, DXA, and Cunningham (1980 and 1991) equations estimated RMR and RMR ratio (measured RMR/predicted RMR). Repeated measures analysis assessed changes over time (ANOVA and Friedman). Generalized linear modeling tested whether RMR ratio threshold predicted TT3 > 73.2 ng/dL or TT3 > 80 ng/dL over 12‐months.

Results

Women were 25.9 ± 5.4 years, weighed 59.6 ± 5.2 kg with BMI 22.3 ± 1.4 kg/m2 at baseline, which remained constant throughout the study (weight: P = .523; BMI: P = .511). There was no significant effect of time for RMR (P = .886), TT3 (P = .890), energy availability (P = .212), and RMR ratio (Harris‐Benedict: P = .852; DXA: P = .607; Cunningham1980: P = .754; Cunningham1991: P = .739). When TT3 > 73.2 ng/dL, each RMR ratio threshold (Harris‐Benedict: P = .021; DXA: P = .019; Cunningham1980: P = .019; Cunningham1991: P = .016) significantly predicted participants as energy replete; however, when using a more lenient clinical TT3 threshold of >80 ng/dL, only the DXA ratio threshold yielded a significant prediction of TT3 (P < .001).

Conclusions

The relationship between RMR ratio and TT3 remains significant and consistent over time in free‐living exercising women, validating the use of RMR ratio for the longitudinal characterization of energetic status in this population (ie, prospective serial monitoring).
From industrial restructuring to the financial crisis: Mainstream nationalism and minimum income in the Basque Country
Authors: Sanzo González Luis
Published: April 2020

The uneven development of minimum incomes in Spain is one of the factors that explain the significant differences in the poverty indicators that characterize the Spanish regions, generally in favour of the territories most committed to these policies (Basque Country, Navarra and Asturias). However, there are other aspects that deserve some consideration when interpreting the specific method of developing minimum incomes in southern Europe. One aspect has to do with the differing dynamics of countries, such as Spain and Italy, which have opted for a decentralized regional model. In this regard, the regional autonomous initiative of the Basque Country played a decisive role in promoting minimum income programs in the late 1980s. Without its leadership in the launch of the regional minimum income policy, Spanish trade unions would probably not have opted for this method as a mechanism for combating poverty in the 1990s. No Italian region went on to play this driving role at that time. This article analyses the ideological foundations of the Basque minimum income policy introduced in the late 1980s and which grew significantly before and during the crisis that started in 2007‐2008. It examines the dominant political narrative on this issue by analysing the discourse of some of the key nationalist leaders involved in the birth and development of the minimum income scheme. The approach shows that the experience of social decline linked to industrial restructuring processes was instrumental in the construction of the nationalist narrative.
An Overview of Saharon Shelah's Contributions to Mathematical Logic, in Particular to Model Theory
Authors: Väänänen Jouko
Published: April 2020

I will give a brief overview of Saharon Shelah's work in mathematical logic. I will focus on three transformative contributions Shelah has made: stability theory, proper forcing and PCF theory. The first is in model theory and the other two are in set theory.
The process of implementing child mortality reviews in low‐ and middle‐income countries: a narrative systematic review
Authors: Young Andrew , Duke Trevor
Published: April 2020

Objectives

This review aims to describe the processes that have been used to implement child mortality reviews in LMICs and to identify the facilitators and barriers to their implementation and impact. This will help to inform healthcare professionals and managers planning to implement a child mortality review in their setting.

Methods

MEDLINE and Embase databases were searched for papers published between January 1996 and April 2019. Studies reporting the implementation of a child mortality review process in LMICs were considered eligible. A narrative approach was used to describe the stages in the audit process outlined in the WHO ‘Operational guide for facility‐based audit and review of paediatric mortality’ which were completed, and to synthesise the barriers and facilitators to implementation and impact of the child mortality review process.

Results

From 776 potentially relevant articles, seven studies were included. In six studies, problems contributing to child deaths and possible solutions were identified, in four, these solutions were implemented, and in one, this implementation was monitored. Key factors influencing implementation and impact were attendance at meetings, use of a blame‐free approach, allocating adequate human and financial resources to make changes, and level of engagement from leadership.

Conclusions

Despite the common use of mortality reviews in paediatric departments, there are few studies published on this topic. The transition from identifying problems and solutions to implementing and monitoring action plans appears to be the most difficult aspect of the process, which requires commitment of adequate resources and strong leadership.
Stoichiometry of two plant glycine decarboxylase complexes and comparison with a cyanobacterial glycine cleavage system
Authors: Wittmiß Maria , Mikkat Stefan , Hagemann Martin , Bauwe Hermann
Published: April 2020

The multienzyme glycine cleavage system (GCS) converts glycine and tetrahydrofolate to the one‐carbon compound 5,10‐methylenetetrahydrofolate, which is of vital importance for most if not all organisms. Photorespiring plant mitochondria contain very high levels of GCS proteins organised as a fragile glycine decarboxylase complex (GDC). The aim of this study is to provide mass spectrometry‐based stoichiometric data for the plant leaf GDC and examine whether complex formation could be a general property of the GCS in photosynthesizing organisms. The molar ratios of the leaf GDC component proteins are 1L2‐4P2‐8T‐26H and 1L2‐4P2‐8T‐20H for pea and Arabidopsis, respectively, as determined by mass spectrometry. The minimum mass of the plant leaf GDC ranges from 1550 to 1650 kDa, which is larger than previously assumed. The Arabidopsis GDC contains four times more of the isoforms GCS‐P1 and GCS‐L1 in comparison with GCS‐P2 and GCS‐L2, respectively, whereas the H‐isoproteins GCS‐H1 and GCS‐H3 are fully redundant as indicated by their about equal amounts. Isoform GCS‐H2 is not present in leaf mitochondria. In the cyanobacterium Synechocystis sp. PCC 6803, GCS proteins concentrations are low but above the complex formation threshold reported for pea leaf GDC. Indeed, formation of a cyanobacterial GDC from the individual recombinant GCS proteins in vitro could be demonstrated. Presence and metabolic significance of a Synechocystis GDC in vivo remain to be examined but could involve multimers of the GCS H‐protein that dynamically crosslink the three GCS enzyme proteins, facilitating glycine metabolism by the formation of multienzyme metabolic complexes. Data are available via ProteomeXchange with identifier PXD018211.
Efficacy of three disinfectant formulations and a hydrogen peroxide/silver fogging system on surfaces experimentally inoculated with meticillin‐resistant Staphylococcus pseudintermedius
Authors: Soohoo Julie , Daniels Joshua B. , Brault Stephanie A. , Rosychuk Rod A.W. , Schissler Jennifer R.
Published: April 2020

Background

Effective environmental disinfection is necessary to prevent nosocomial infections from meticillin‐resistant Staphylococcus pseudintermedius (MRSP). However, there are currently no commercial disinfectant sprays or fogging systems with label claims against MRSP.

Hypothesis/objectives

To evaluate the efficacy of a quaternary ammonium product (QAC), an accelerated hydrogen peroxide product (AHP), a hydrogen peroxide and silver product (HAL), and a hydrogen peroxide and silver fogging system (FOG) against MRSP.

Methods and materials

Sterile plastic surfaces inoculated with MRSP were treated with 200 µL of QAC, AHP or HAL for the recommended contact times. For FOG, inoculated samples were placed in eight positions within a sealed room before fogging for the recommended contact time. Post‐treatment bacterial counts were compared to untreated positive controls. Sterile uninoculated surfaces served as negative controls.

Results

Least‐squares mean reduction (log10) in colony forming units (cfu) was 3.55 log10 for QAC (P < 0.0001), 3.60 log10 for AHP (P < 0.0001), 1.66 log10 for HAL (P < 0.0001) and 0.32 log10 for FOG (P = 0.004). QAC, AHP and HAL reduced MRSP cfu by 99.97%, 99.98% and 97.81%, respectively. FOG reduced cfu by 52.14%.

Conclusions and clinical importance

QAC and AHP effectively disinfected surfaces inoculated with MRSP. Although HAL provided lower MRSP reduction, it may be considered clinically acceptable. FOG as a sole means of MRSP disinfection was not supported yet may have utility as an adjunctive disinfectant in clinical areas with bacterial densities lower than our experimental inoculum.
Inactivation of severe acute respiratory syndrome coronavirus 2 in plasma and platelet products using a riboflavin and ultraviolet light‐based photochemical treatment
Authors: Keil Shawn D. , Ragan Izabela , Yonemura Susan , Hartson Lindsay , Dart Nicole K. , Bowen Richard
Published: April 2020

Background and Objective

Severe acute respiratory distress syndrome coronavirus‐2 (SARS‐CoV‐2), the causative agent of coronavirus disease 2019 (COVID‐19), is a member of the coronavirus family. Coronavirus infections in humans are typically associated with respiratory illnesses; however, viral RNA has been isolated in serum from infected patients. Coronaviruses have been identified as a potential low‐risk threat to blood safety. The Mirasol Pathogen Reduction Technology (PRT) System utilizes riboflavin and ultraviolet (UV) light to render blood‐borne pathogens noninfectious, while maintaining blood product quality. Here, we report on the efficacy of riboflavin and UV light against the pandemic virus SARS‐CoV‐2 when tested in both plasma and platelets units.

Materials and Methods

Stock SARS‐CoV‐2 was grown in Vero cells and inoculated into either plasma or platelet units. Those units were then treated with riboflavin and UV light. The infectious titres of SARS‐CoV‐2 were determined by plaque assay using Vero cells. A total of five (n = 5) plasma and three (n = 3) platelet products were evaluated in this study.

Results

In both experiments, the measured titre of SARS‐CoV‐2 was below the limit of detection following treatment with riboflavin and UV light. The mean log reductions in the viral titres were ≥3·40 and ≥4·53 for the plasma units and platelet units, respectively.

Conclusion

Riboflavin and UV light effectively reduced the titre of SARS‐CoV‐2 in both plasma and platelet products to below the limit of detection in tissue culture. The data suggest that the process would be effective in reducing the theoretical risk of transfusion transmitted SARS‐CoV‐2.
How many species of angulate tortoises occur in Southern Africa? (Testudines: Testudinidae: Chersina)
Authors: Spitzweg Cäcilia , Vamberger Melita , Ihlow Flora , Fritz Uwe , Hofmeyr Margaretha D.
Published: April 2020

Using range‐wide sampling and 1,143 bp of mtDNA (cytochrome b gene) and 14 microsatellite loci, we examined genetic differentiation in the widely distributed Southern African angulate tortoise (Chersina angulata). We found evidence for two genealogical lineages that differ in both genetic marker systems and their preferred habitat conditions. According to a fossil‐calibrated molecular clock for all African tortoise lineages using 1,870 bp mitochondrial and 1,416 bp nuclear DNA, the two lineages of C. angulata diverged in the Pliocene (approx. 3.8 million years ago). Species distribution models reveal that the ranges of the two lineages shifted little since the Last Glacial Maximum, which is in agreement with the demographic population descriptors suggestive of stationary populations that did not experience expansion. One lineage occurs in the west, and the other in the south of the extant distribution range. In the geographic contact zone, the two lineages hybridize extensively, providing evidence for their conspecificity under the biological species concept. Each lineage could be recognized as a distinct subspecies, but the ill‐defined geographic origins of the type material of the available names prevent their identification with any taxon. With respect to the nuclear genomic markers, the western lineage shows further north‐south substructuring. A few genetically mismatched tortoises are interpreted as human translocations. Our study underlines that confiscated or captive angulate tortoises of unknown geographic provenance should not be released without prior genetic screening to avoid genetic pollution of wild populations.
Multiple two-step oscillation regimes produced by the alto saxophone
Authors: Colinot Tom , Guillemain Philippe , Vergez Christophe , Doc Jean-Baptiste , Sanchez Patrick
Published: April 2020

A saxophone mouthpiece fitted with sensors is used to observe the oscillation of a saxophone reed, as well as the internal acoustic pressure, allowing to identify qualitatively different oscillating regimes. In addition to the standard two-step regime, where the reed channel successively opens and closes once during an oscillation cycle, the experimental results show regimes featuring two closures of the reed channel per cycle, as well as inverted regimes, where the reed closure episode is longer than the open episode. These regimes are well-known on bowed string instruments and some were already described on the Uilleann pipes. A simple saxophone model using measured input impedance is studied with the harmonic balance method, and is shown to reproduce the same two-step regimes. The experiment shows qualitative agreement with the simulation: in both cases, the various regimes appear in the same order as the blowing pressure is increased. Similar results are obtained with other values of the reed opening control parameter, as well as another fingering.
Safety and Tolerability of More than Six Days of Tedizolid Treatment
Authors: Mensa Vendrell Mireia , Tasias Pitarch Maria , Salavert Lletí Miguel , Calabuig Muñoz Eva , Morata Ruiz Laura , Castells Lao Genís , López Suñé Ester , Mensa Pueyo Jose , Oltra Sempere Maria Rosa , Pedro-Botet Montoya Maria-Luisa , Isernia Valentina , Reynaga Sosa Esteban Alberto , Moreno Nuñez Leonor , Pasquau Liaño Juan , Sequera Arquelladas Sergio , Yuste Ara José Ramón , Soriano Viladomiu Alex
Published: April 2020

Tedizolid has demonstrated its efficacy and safety in clinical trials; however, data concerning its tolerability in long-term treatments are scarce. The aim of the study was to assess the indications and to describe the long-term safety profile of tedizolid. A multicentric retrospective study of patients who received tedizolid for more than 6 days was conducted. Adverse events (AEs) were identified from patients’ medical records and laboratory data. The World Health Organization causality categories were used to discern AEs that were probably associated with tedizolid.
The Emerging Role of β-Lactams in the Treatment of Methicillin-Resistant Staphylococcus aureus Bloodstream Infections
Authors: Molina Kyle C. , Morrisette Taylor , Miller Matthew A. , Huang Vanthida , Fish Douglas N.
Published: April 2020

Methicillin-resistant
Staphylococcus aureus
(MRSA) bloodstream infections (BSI) are associated with substantial morbidity and mortality. Monotherapy with first-line antimicrobials such as vancomycin (VAN; glycopeptide) and daptomycin (DAP; lipopeptide) are inadequate in some cases due to reduced antibiotic susceptibilities or therapeutic failure. In recent years, β-lactam antibiotics have emerged as a potential option for combination therapy with VAN and DAP that may meet an unmet therapeutic need for MRSA BSI.
Species Distribution and Comparison between EUCAST and Gradient Concentration Strips Methods for Antifungal Susceptibility Testing of 112
Aspergillus
Section
Nigri
Isolates
Authors: Carrara B. , Richards R. , Imbert S. , Morio F. , Sasso M. , Zahr N. , Normand A. C. , Le Pape P. , Lachaud L. , Ranque S. , Maubon D. , Piarroux R. , Fekkar A.
Published: April 2020

Aspergillus niger
, the third species responsible for invasive aspergillosis, has been considered as a homogeneous species until DNA-based identification uncovered many cryptic species. These species have been recently reclassified into the
Aspergillus
section
Nigri
. However, little is yet known among the section
Nigri
about the species distribution and the antifungal susceptibility pattern of each cryptic species. A total of 112 clinical isolates collected from 5 teaching hospitals in France and phenotypically identified as
A. niger
were analyzed.
The Andes Orthohantavirus NSs Protein Antagonizes the Type I Interferon Response by Inhibiting MAVS Signaling
Authors: Vera-Otarola Jorge , Solis Loretto , Lowy Fernando , Olguín Valeria , Angulo Jenniffer , Pino Karla , Tischler Nicole D. , Otth Carola , Padula Paula , López-Lastra Marcelo
Published: April 2020

Andes orthohantavirus
(ANDV) is endemic in Argentina and Chile and is the primary etiological agent of hantavirus cardiopulmonary syndrome (HCPS) in South America. ANDV is distinguished from other hantaviruses by its unique ability to spread from person to person. In a previous report, we identified a novel ANDV protein, ANDV-NSs. Until now, ANDV-NSs had no known function. In this new study, we established that ANDV-NSs acts as an antagonist of cellular innate immunity, the first line of defense against invading pathogens, hindering the cellular antiviral response during infection. This study provides novel insights into the mechanisms used by ANDV to establish its infection.
A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies
Authors: Culviner Peter H. , Guegler Chantal K. , Laub Michael T.
Published: April 2020

The ability to examine global patterns of gene expression in microbes through RNA sequencing has fundamentally transformed microbiology. However, RNA-seq depends critically on the removal of rRNA from total RNA samples. Otherwise, rRNA would comprise upward of 90% of the reads in a typical RNA-seq experiment, limiting the reads coming from mRNA or requiring high total read depth. A commonly used kit for rRNA subtraction from Illumina was recently unavailable for an extended period of time, disrupting routine rRNA depletion. Here, we report the development of a “do-it-yourself” kit for rapid, cost-effective, and robust depletion of rRNA from total RNA. We present an algorithm for designing biotinylated oligonucleotides that will hybridize to the rRNAs from a target set of species. We then demonstrate that the designed oligonucleotides enable sufficient rRNA depletion to produce RNA-seq data with 75 to 80% of reads coming from mRNA. The methodology presented should enable RNA-seq studies on any species or metagenomic sample of interest.
Ehrlichia chaffeensis Uses an Invasin To Suppress Reactive Oxygen Species Generation by Macrophages via CD147-Dependent Inhibition of Vav1 To Block Rac1 Activation
Authors: Teymournejad Omid , Rikihisa Yasuko
Published: April 2020

Ehrlichia chaffeensis
is an obligatory intracellular bacterium with the capability of causing an emerging infectious disease called human monocytic ehrlichiosis.
E. chaffeensis
preferentially infects monocytes and macrophages, professional phagocytes, equipped with an arsenal of antimicrobial mechanisms, including rapid reactive oxygen species (ROS) generation upon encountering bacteria. As
Ehrlichia
isolated from host cells are readily killed upon exposure to ROS,
Ehrlichia
must have evolved a unique mechanism to safely enter phagocytes. We discovered that binding of the
Ehrlichia
surface invasin to the host cell surface receptor not only triggers
Ehrlichia
entry but also blocks ROS generation by the host cells by mobilizing a novel intracellular signaling pathway. Knowledge of the mechanisms by which ROS production is inhibited may lead to the development of therapeutics for ehrlichiosis as well as other ROS-related pathologies.
Human Serum Albumin Facilitates Heme-Iron Utilization by Fungi
Authors: Pinsky Mariel , Roy Udita , Moshe Shilat , Weissman Ziva , Kornitzer Daniel
Published: April 2020

Heme constitutes a major iron source for microorganisms and particularly for pathogenic microbes; to overcome the iron scarcity in the animal host, many pathogenic bacteria and fungi have developed systems to extract and take up heme from host proteins such as hemoglobin. Microbial heme uptake mechanisms are usually studied using growth media containing free heme or hemoglobin as a sole iron source. However, the animal host contains heme-scavenging proteins that could prevent this uptake. In the human host in particular, the most abundant serum heme-binding protein is albumin. Surprisingly, however, we found that in the case of fungi of the
Candida
species family, albumin promoted rather than prevented heme utilization. Albumin thus constitutes a human-specific factor that can affect heme-iron utilization and could serve as target for preventing heme-iron utilization by fungal pathogens. As a proof of principle, we identify two drugs that can inhibit albumin-stimulated heme utilization.
Coping with COVID: How a Research Team Learned To Stay Engaged in This Time of Physical Distancing
Authors: Sutherland Danica M. , Taylor Gwen M. , Dermody Terence S.
Published: April 2020

Physical distancing imposed by the COVID-19 pandemic has led to alterations in routines and new responsibilities for much of the research community. We provide some tips for how research teams can cope with physical distancing, some of which require a change in how we define productivity. Importantly, we need to maintain and strengthen social connections in this time when we can’t be physically together.
X-Linked RNA-Binding Motif Protein Modulates HIV-1 Infection of CD4
+
T Cells by Maintaining the Trimethylation of Histone H3 Lysine 9 at the Downstream Region of the 5′ Long Terminal Repeat of HIV Proviral DNA
Authors: Ma Li , Jiang Qing-An , Sun Li , Yang Xianguang , Huang Hai , Jin Xia , Zhang Chiyu , Wang Jian-Hua
Published: April 2020

HIV-1 latency featuring silence of transcription from HIV-1 proviral DNA represents a major obstacle for HIV-1 eradication. Reversible repression of HIV-1 5′-LTR-mediated transcription represents the main mechanism for HIV-1 to maintain latency. The 5′-LTR-driven HIV gene transcription can be modulated by multiple host factors and mechanisms. The hnRNPs are known to regulate gene expression. A member of the hnRNP family, RBMX, has been identified in this study as a novel HIV-1 restriction factor that modulates HIV-1 5′-LTR-driven transcription of viral genome in CD4
+
T cells and maintains viral latency. These findings provide a new understanding of how host factors modulate HIV-1 infection and latency and suggest a potential new target for the development of HIV-1 therapies.
Validating women’s reports of antenatal and postnatal care received in Bangladesh, Cambodia and Kenya
Authors: McCarthy Katharine J , Blanc Ann K , Warren Charlotte , Bajracharya Ashish , Bellows Benjamin
Published: April 2020

Background

Global indicators for monitoring progress in maternal and newborn health have tended to rely on contact coverage indicators rather than the content of services received. As part of the effort to improve measurement of progress in maternal and newborn health, this study examines how accurately women can report on information and health interventions received during an antenatal or postnatal health consultation at health facilities in Bangladesh, Cambodia and Kenya.

Methods

We conducted secondary analysis of matched observation and client interview data to compare women’s reports of care received at exit interview with observation by a trained third-party observer. We assessed indicator accuracy by calculating sensitivity, specificity, area under the receiver operating characteristic curve (AUC) and inflation factor (IF). Indicators considered to have both high individual accuracy (an AUC value of 0.70 or greater) and low population-level bias (0.75<IF<1.25) were considered to have acceptable validity. In addition, we considered the number of countries where both validation criteria were met.

Results

For indicators of antenatal care, we found 16 of 18 indicators in Bangladesh, 3 of 6 in Cambodia and 3 of 8 in Kenya met both validation criteria. For postnatal care, we found evidence of acceptable validity for 6 of 8 indicators in Bangladesh, 5 of 14 in Cambodia and 3 of 16 in Kenya. In general, we documented higher validity for indicators related to concrete, observable actions, as opposed to information or advice given. Women were more likely to recall care received for themselves, rather than for their newborn.

Conclusions

Women reported accurately on multiple aspects of antenatal and postnatal care. While we describe broad patterns in the types of indicators likely to be recalled with accuracy, differences by setting warrant further investigation. Findings inform efforts to better monitor the coverage and quality of maternal and newborn health interventions.
Extending an open-source tool to measure data quality: case report on Observational Health Data Science and Informatics (OHDSI)
Authors: Dixon Brian E , Wen Chen , French Tony , Williams Jennifer L , Duke Jon D , Grannis Shaun J
Published: April 2020

Introduction

As the health system seeks to leverage large-scale data to inform population outcomes, the informatics community is developing tools for analysing these data. To support data quality assessment within such a tool, we extended the open-source software Observational Health Data Sciences and Informatics (OHDSI) to incorporate new functions useful for population health.

Methods

We developed and tested methods to measure the completeness, timeliness and entropy of information. The new data quality methods were applied to over 100 million clinical messages received from emergency department information systems for use in public health syndromic surveillance systems.

Discussion

While completeness and entropy methods were implemented by the OHDSI community, timeliness was not adopted as its context did not fit with the existing OHDSI domains. The case report examines the process and reasons for acceptance and rejection of ideas proposed to an open-source community like OHDSI.
Cytology in the time of coronavirus disease (COVID-19): an Italian perspective
Authors: Vigliar Elena , Iaccarino Antonino , Bruzzese Dario , Malapelle Umberto , Bellevicine Claudio , Troncone Giancarlo
Published: April 2020

Introduction

The coronavirus disease 2019 (COVID-19) is changing the way we practice pathology, including fine needle aspiration (FNA) diagnostics. Although recommendations have been issued to prioritise patients at high oncological risk, postponing those with unsuspicious presentations, real world data have not been reported yet.

Methods

The percentages of the cytological sample types processed at the University of Naples Federico II, during the first 3 weeks of Italian national lockdown were compared with those of the same period in 2019.

Results

During the emergency, the percentage of cytology samples reported as malignant increased (p<0.001), reflecting higher percentages of breast (p=0.002) and lymph nodes FNAs (p=0.008), effusions (p<0.001) and urine (p=0.005). Conversely, thyroid FNAs (p<0.001) and Pap smears (p=0.003) were reduced.

Conclusions

Even in times of COVID-19 outbreak, cytological examination may be safely carried out in patients at high oncological risk, without the need to be postponed.
Frost heave and thaw consolidation modelling. Part 2: One-dimensional thermohydromechanical (THM) framework
Authors: Yu Fan , Guo Peijun , Lai Yuanming , Stolle Dieter
Published: April 2020

This paper presents a thermohydromechanical framework to model frost heave and (thaw) consolidation simultaneously, in which effective and total stresses are taken as the stress variables for unfrozen and frozen soils, respectively. “Effective (total) stresses – void ratio – permeability” relations are proposed to interpret the frost heave behavior of soil in different cooling modes, (thaw) consolidation processes, and changes in key parameters induced by freeze–thaw cycles. The water flux function proposed by Yu et al. in a companion paper is used to calculate frost heave in the frozen zone and to determine the moving boundary of the unfrozen zone during thaw consolidation. Compared with conventional methods, two other modifications are made to characterize the effect of residual stress and the influence of freeze–thaw cycling on permeability in the thaw consolidation analysis. After the governing equations developed in Lagrangian coordinates are implemented in a finite-element system, the framework is firstly verified by a comparison with both small- and large-strain thaw consolidation theories, in terms of simulating a semi-infinite thaw consolidation case, and is then examined with a focus on the three modifications one-by-one. Following that, the framework is assessed by two numerical examples that reasonably reproduce the freeze–thaw cycling processes in both seasonal frost and permafrost regions.
SNP analyses highlight a unique, imperiled southern walleye (Sander vitreus) in the Mobile River Basin
Authors: Zhao Honggang , Silliman Katherine , Lewis Matthew , Johnson Sarah , Kratina Garret , Rider Steve J. , Stepien Carol A. , Hallerman Eric M. , Beck Benjamin , Fuller Adam , Peatman Eric
Published: April 2020

Walleye (Sander vitreus) is a popular sportfish threatened by overexploitation, habitat destruction, and loss of genetic integrity due to non-native walleye stocking. Previous studies have identified a genetically distinct lineage of walleye in the Mobile River Basin, but further work is needed to assess population structure and introgression among this southern lineage and northern populations. Here we generated 2782 genome-wide single nucleotide polymorphisms (SNPs) to characterize the genetic uniqueness of southern walleye. We also found strong evidence for a historical declining population trend with reduced genetic diversity and effective population size in a southern walleye population of conservation importance. A 68-SNP panel was developed for rapid identification of genetic integrity and hybrid classification among northern and southern walleye, enabling us to identify an anthropogenic hybrid zone resulting from the previous introduction of northern walleye into the Black Warrior River drainage, Alabama. Our results highlight the need for conservation management of southern walleye in the Mobile River Basin, with our 68-SNP assay already being implemented in ongoing stream survey and captive breeding programs.
Hydrothermal Synthesis and Photocatalytic Property of Sn-doped β-Ga2O3 Nanostructure
Authors: Ryou Heejoong , Yoo Tae Hee , Yoon Youngbin , Lee In Gyu , Shin Myunghun , Cho Junsang , Cho Byung Jin , Hwang Wan Sik
Published: April 2020

Tin (Sn)-doped beta phase gallium oxide (β-Ga2O3) nanostructures at different Sn concentrations (0 to 7.3 at%) are synthesized using a facile hydrothermal method. The Sn-doped β-Ga2O3 nanostructures are characterized using scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, and absorbance spectroscopy. In addition, their photocatalytic activity is evaluated by observing methylene blue degradation under ultraviolet light (254 nm) irradiation. The photocatalytic activity of the Sn-doped (0.7 at%) β-Ga2O3 nanostructures is significantly enhanced compared to that of intrinsic β-Ga2O3 nanostructures due to the elevated charge separation. Excessive Sn concentrations (exceeding 2.2 at%) above the solid solubility limit of the Sn in β-Ga2O3 nanostructures lead to SnO2 and SnO precipitation. The presence of SnO2 and SnO degrades the photocatalytic efficiency in the β-Ga2O3 nanostructures. The results suggest new opportunities for the synthesis of highly effective β-Ga2O3-based photocatalysts for applications in environmental remediation, disinfection, and selective organic transformations.
Stimulation of the pelvic nerve increases bladder capacity in the PGE2 cat model of overactive bladder
Authors: Langdale Christopher L. , Hokanson James A. , Milliken Philip H. , Sridhar Arun , Grill Warren M.
Published: April 2020

Selective electrical stimulation of the pudendal nerve exhibits promise as a potential therapy for treating overactive bladder (OAB) across species (rats, cats, and humans). More recently, pelvic nerve (PelN) stimulation was demonstrated to improve cystometric bladder capacity in a PGE2 rat model of OAB. However, PelN stimulation in humans or in an animal model that is more closely related to humans has not been explored. Therefore, our objective was to quantify the effects of PGE2 and PelN stimulation in the cat. Acute cystometry experiments were conducted in 14 α-chloralose-anesthetized adult, neurologically intact female cats. Intravesical PGE2 decreased bladder capacity, residual volume, threshold contraction pressure, and mean contraction pressure. PelN stimulation reversed the PGE2-induced decrease in bladder capacity and increased evoked external urethral sphincter electromyographic activity without influencing voiding efficiency. The increases in bladder capacity generated by PelN stimulation were similar in the rat and cat, but the stimulation parameters to achieve this effect differed (threshold amplitude at 10 Hz in the rat vs. twice threshold amplitude at 1 Hz in the cat). These results highlight the potential of PGE2 as a model of OAB and provide further evidence that PelN stimulation is a promising approach for the treatment of OAB symptoms.
Image Quality and Dose Comparison of Single-Energy CT (SECT) and Dual-Energy CT (DECT)
Authors: Ghasemi Shayan Ramin , Oladghaffari Maryam , Sajjadian Fakhrosadat , Fazel Ghaziyani Mona
Published: April 2020

CT and its comprehensive usage have become one of the most indispensable components in medical field especially in the diagnosis of several diseases. SECT and DECT have developed CT diagnostic potentials in several means. In this review article we have discussed the basic principles of single-energy and dual-energy computed tomography and their important physical differences which can cause better diagnostic evaluation. Moreover, different organs diagnostic evaluations through single-energy and dual-energy computed tomography have been discussed. Conventional or single-energy CT (SECT) uses a single polychromatic X-ray beam (ranging from 70 to 140 kVp with a standard of 120 kVp) emitted from a single source and received by a single detector. The concept of dual-energy computed tomography (DECT) is almost as old as the CT technology itself; DECT initially required substantially higher radiation doses (nearly two times higher than those employed in single-energy CT) and presented problems associated with spatial misregistration of the two different kV image datasets between the two separate acquisitions. The basic principles of single-energy and dual-energy computed tomography and their important physical differences can cause better diagnostic evaluation. Moreover, different organs diagnostic evaluations through single-energy and dual-energy computed tomography have been discussed. According to diverse data and statistics it is controversial to definitely indicate the accurate comparison of image quality and dose amount.
Characterization of Nonstationary Phase Noise Using the Wigner–Ville Distribution
Authors: Levy Chagai , Pinchas Monika , Pinhasi Yosef
Published: April 2020

Oscillators and atomic clocks, as well as lasers and masers, are affected by physical mechanisms causing amplitude fluctuations, phase noise, and frequency instabilities. The physical properties of the elements composing the oscillator as well as external environmental conditions play a role in the coherence of the oscillatory signal produced by the device. Such instabilities demonstrate frequency drifts, modulation, and spectrum broadening and are observed to be nonstationary processes in nature. Most of the tools which are being used to measure and characterize oscillator stability are based on signal processing techniques, assuming time invariance within a temporal window, during which the signal is assumed to be stationary. This letter proposes a new time-frequency approach for the characterization of frequency sources. Our technique is based on the Wigner–Ville time-frequency distribution, which extends the spectral measures to include the temporal nonstationary behavior of the processes affecting the coherence of the oscillator and the accuracy of the clock. We demonstrate the use of the technique in the characterization of nonstationary phase noise in oscillators.
Identification of Potential Biomarkers Associated with Basal Cell Carcinoma
Authors: Liu Yong , Liu Hui , Bian Queqiao
Published: April 2020

Purpose. This work is aimed at identifying several molecular markers correlated with the diagnosis and development of basal cell carcinoma (BCC). Methods. The available microarray datasets for BCC were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were identified between BCC and healthy controls. Afterward, the functional enrichment analysis and protein‐protein interaction (PPI) network analysis of these screened DEGs were performed. An external validation for the DEG expression level was also carried out, and receiver operating characteristic curve analysis was used to evaluate the diagnostic values of DEGs. Result. In total, five microarray datasets for BCC were downloaded and 804 DEGs (414 upregulated and 390 downregulated genes) were identified. Functional enrichment analysis showed that these genes including CYFIP2, HOXB5, EGFR, FOXN3, PTPN3, CDC20, MARCKSL1, FAS, and PTCH1 were closely correlated with the cell process and PTCH1 played central roles in the BCC signaling pathway. Moreover, EGFR was a hub gene in the PPI network. The expression changes of six genes (CYFIP2, HOXB5, FOXN3, PTPN3, MARCKSL1, and FAS) were validated by an external GSE74858 dataset analysis. Finally, ROC analysis revealed that CYFIP2, HOXB5, PTPN3, MARCKSL1, PTCH1, and CDC20 could distinguish BCC and healthy individuals. Conclusion. Nine gene signatures (CYFIP2, HOXB5, EGFR, FOXN3, PTPN3, CDC20, MARCKSL1, FAS, and PTCH1) may serve as promising targets for BCC detection and development.
Theoretical Investigation of Nonlinear Time-Dependent Behavior of Two-Way High-Strength Concrete Walls
Authors: Huang Yue , Rao Rui , Huang Yonghui , Zhong Zilin
Published: April 2020

High-strength concrete (HSC) walls have been increasingly used in the past decades. However, the time-dependent behavior of HSC wall panels in two-way action was not investigated, and the time effect of creep is not included in the design codes in most countries. For this purpose, the nonlinear long-term behavior of two-way HSC wall is investigated in this paper. A theoretical model is developed using time-stepping analysis considering geometric nonlinearity and creep of concrete. A rheological material model that is based on the generalized Maxwell chain is adopted to model the concrete creep. Von Karman plate theory is used to derive the incremental governing equations. The equations are solved numerically at each time step based on a Fourier series expansion of the deformations and loads and numerical multiple shooting method. It shows that the model can effectively predict the time-dependent behavior of two-way HSC panels, where the out-of-plane deflection and internal bending moments increase with time due to the combined effects of creep and geometric nonlinearity, which may ultimately lead to creep buckling failures. A parametric study shows that the long-term behavior of the panel is very sensitive to the in-plane load level and eccentricity, slenderness ratio, aspect ratio, and edge support conditions.
Combat Mobile Evasive Malware via Skip-Gram-Based Malware Detection
Authors: Egitmen Alper , Bulut Irfan , Aygun R. Can , Gunduz A. Bilge , Seyrekbasan Omer , Yavuz A. Gokhan
Published: April 2020

Android malware detection is an important research topic in the security area. There are a variety of existing malware detection models based on static and dynamic malware analysis. However, most of these models are not very successful when it comes to evasive malware detection. In this study, we aimed to create a malware detection model based on a natural language model called skip-gram to detect evasive malware with the highest accuracy rate possible. In order to train and test our proposed model, we used an up-to-date malware dataset called Argus Android Malware Dataset (AMD) since the AMD contains various evasive malware families and detailed information about them. Meanwhile, for the benign samples, we used Comodo Android Benign Dataset. Our proposed model starts with extracting skip-gram-based features from instruction sequences of Android applications. Then it applies several machine learning algorithms to classify samples as benign or malware. We tested our proposed model with two different scenarios. In the first scenario, the random forest-based classifier performed with 95.64% detection accuracy on the entire dataset and 95% detection accuracy against evasive only samples. In the second scenario, we created a test dataset that contained zero-day malware samples only. For the training set, we did not use any sample that belongs to the malware families in the test set. The random forest-based model performed with 37.36% accuracy rate against zero-day malware. In addition, we compared our proposed model’s malware detection performance against several commercial antimalware applications using VirusTotal API. Our model outperformed 7 out of 10 antimalware applications and tied with one of them on the same test scenario.