bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of single or repeated short-term heat challenges mimicking summer heat waves on thermoregulatory responses and performances in finishing pigs
Authors: Renaudeau David
Published: October 2020

The objectives of this study were to determine the effects of single or repeated short heat stress (HS) challenges that mimicked summer heat waves on performance and thermoregulatory responses in finishing pigs. A total of 45 crossbred castrated males were tested in three consecutive replicates of 15 pigs. Within each replicate, pigs were assigned to one of five treatments. Pigs in treatment group TTT were maintained in thermoneutral conditions (22 °C) for the entire experiment (45 d). Pigs in treatment group HHH were subjected to an HS challenge (32 °C for 5 d) at 113, 127, and 141 d of age (in experimental periods P1, P2, and P3, respectively). Pigs in treatment groups HTT, THT, and TTH were subjected to the HS challenge at 113, 127, or 141 d of age, respectively. Each 5-d challenge was preceded by a 3-d prechallenge period and followed by a 7-d recovery period. Pigs were housed in individual pens and fed ad libitum. HS significantly reduced average daily feed intake (ADFI) and the average daily gain (ADG). Expressed as a percentage of the performance observed during the prechallenge period, ADFI decreased by 12%, 22%, and 26% and ADG decreased by 12%, 43%, and 72% in the HTT, THT, and TTH groups, respectively. Regardless of the experimental group, no compensatory performance was observed during the recovery period, suggesting that HS has a long-lasting effect on animal performance. Pigs subjected to HS had an immediate increase in core body temperature (Tcore), skin temperature, and respiratory rate, all of which gradually decreased during the HS challenge. Based on Tcore measurements, hypothermia was observed during the recovery period in each of the three experimental periods, especially for pigs in the HHH and the HTT groups but only during the first HS cycle. Repeated exposure to HS for the HHH group resulted in heat acclimation responses characterized by a lower increase in Tcore and lower decrease in ADFI during P2 and P3 than during P1.
Up-regulation of phenylpropanoid biosynthesis system in peach species by peach aphids produces anthocyanins that protect the aphids against UVB and UVC radiation
Authors: Zhou Wei , Jia Mingyue , Zhang Guangchen , Sun Jian , Li Qilong , Wang Xianling , Hua Juan , Luo Shihong
Published: October 2020

Conspicuous color is a common trait of foliar galls, but their relationship with gall-inducing insects is unknown. Red and green galls were taken from sunny or shady parts of peach species Prunus persica (L.) Batsch. f. rubro-plena Schneid with peach aphid Tuberocephalus momonis (Matsumura) infestation. We found that the loss of photosynthetic pigments was associated with the conspicuous coloration of green gall tissues. The concentrations of anthocyanins significantly increased following ultraviolet (UV) irradiation of green gall tissues, suggesting that accumulation of anthocyanins in red galls is related to ultraviolet B and C (UVB and UVC) radiation. The expression of structural genes related to the biosynthesis of chlorogenic acid and malic acid benzoate was increased in all gall tissues and negatively correlated with the expression profiles of certain genes associated with photosynthetic biosynthesis, indicating that the increased transcript levels of the phenylpropanoid pathway might cause loss of photosynthetic efficiency in the gall tissues. Transcriptome and quantitative reverse transcription PCR analyses revealed that MYB transcription factors that up-regulate the biosynthesis of anthocyanins in red gall tissues might be activated by both UVB and UVC exposure. Comet assays suggest that green and red gall tissues have similar DNA damage following UV irradiation. No obvious effect of the up-regulated compounds on the growth of the peach aphid was observed. Interestingly, peach aphids under leaves painted with anthocyanins had lower mortality following UV irradiation than those in controls. These results suggest that the anthocyanins in red gall tissues have a defensive function for the peach aphid, protecting it against UV radiation.
Integrative taxonomy of giant crestedEusirusin the Southern Ocean, including the description of a new species (Crustacea: Amphipoda: Eusiridae)
Authors: Verheye Marie L , D’Udekem D’Acoz Cédric
Published: October 2020

Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.
Video Laryngoscope Intubation With an Aerosol Barrier Device: A Randomized Sequential Crossover Pilot Study
Authors: Idei Masafumi , Nomura Takeshi , Jouvet Philippe , Aubin Carl Eric , Kawaguchi Atsushi , Nakagawa Masashi
Published: October 2020

Objectives:

To assess the impact of the use of aerosol barrier device, Splashguard-CG, on the endotracheal intubation with different types of laryngoscope.

Design:

A pilot randomized sequential crossover simulation study.

Setting:

A single academic center in Japan.

Subjects:

Physicians in a single academic university hospital in Japan.

Interventions:

Use of Splashguard-CG.

Measurements and Main Results:

All participants were asked to perform endotracheal intubation to a manikin simulator using three different devices (Macintosh laryngoscope; Airway Scope [Nihon Kohden, Tokyo, Japan]; and McGRATH MAC [Aircraft Medical, Edinburgh, United Kingdom]) with and without Splashguard-CG in place, which required a total of six attempts and measured the intubation time as the primary outcome. Thirty physicians (15 experienced physicians and 15 less-experienced physicians) were included. Intubation time using Macintosh laryngoscope was significantly longer in the group with Macintosh laryngoscope and Splashguard-CG compared with the group without Splashguard-CG by the median difference of 4.3 seconds (interquartile range, 2.6–7.4 s; p < 0.001). There was no significant increase in the intubation time with or without Splashguard-CG for the Airway Scope (0.6 s; interquartile range, –3.7 to 3.2 s; p = 0.97) and the McGRATH MAC (0.5 s; interquartile range, –1.4 to 4.6 s; p = 0.09). This trend was found in both the experienced and less-experienced groups. We observed significant increases of subjective difficulty of the endotracheal intubation evaluated by using a Visual Analog Scale in the Splashguard-CG groups for all three types of devices.

Conclusions:

The use of a video laryngoscope with an aerosol barrier device does not impact the time required endotracheal intubation in a simulation environment. This method can be considered as airway management for coronavirus disease 2019.
Early Prediction of Sepsis From Clinical Data Using Ratio and Power-Based Features
Authors: Nesaragi Naimahmed , Patidar Shivnarayan
Published: October 2020

Objectives:

Early prediction of sepsis is of utmost importance to provide optimal care at an early stage. This work aims to deploy soft-computing and machine learning techniques for early prediction of sepsis.

Design:

An algorithm for early identification of sepsis using ratio and power-based feature transformation of easily obtainable clinical data.

Setting:

PhysioNet Challenge 2019 provided ICU data from three separate hospital systems. Publicly shared data from two hospital systems are used for training and validation purposes, whereas sequestered data from all the three systems is used for testing.

Patients:

Over 60,000 ICU patients with up to 40 clinical variables are sourced for each hour of their ICU stay. The Sepsis-3 criterion is applied for annotation.

Interventions:

None.

Measurements and Main Results:

The clinical feature exploration for early prediction of sepsis is achieved using the proposed framework named genetic algorithm optimized ratio and power-based expert algorithm. An optimal feature set containing 46 ratio and power-based features is computed from the given patient covariates using genetic algorithm optimized ratio and power-based expert and grouped with identified 17 raw features and 55 statistical features to form a final feature set of 118 clinical features to predict the onset of sepsis in the proceeding 6 hours. The obtained features are fed to a hybrid Random Under-Sampling-Boosting algorithm, called RUSBoost for alleviating the involved class imbalance. The optimal RUSBoost model has achieved a normalized utility score of 0.318 on full test data.

Conclusions:

The proposed study supports the realization of a hospital-specific customized solution in the form of an early-warning system for sepsis. However, an extended analysis is necessary to apply this framework for hospital-independent diagnosis of sepsis in general. Nevertheless, the clinical utility of hospital-specific customized solutions based on the proposed method across a wide range of hospital systems needs to be studied.
Reconstruction of Orbital Exenteration Defect With Cheek or Combined Cheek and Forehead Advancement Flaps
Authors: Bilge Ayse Dolar , Yazici Bulent , Efe Ayse Cetin
Published: October 2020

Purpose:

To review the outcomes of orbital exenteration defect reconstruction using cheek or combined cheek-forehead advancement flap.

Methods:

Charts of 14 patients who underwent reconstruction of the exenterated orbit with cheek advancement flap were reviewed. In surgery, a cheek flap elevated via a nasofacial sulcus incision, and preperiosteal dissection was advanced over the defect. The upper orbital defect, if necessary, was covered with a forehead flap, which was dissected through an incision in the midline or temporal forehead and advanced inferiorly.

Results:

In all patients (7 women, 7 men; mean age, 65 years), total (n = 7) or extended (n = 7) exenteration was performed for a malignant tumor. In 12 patients (86%), the defect was primarily closed with cheek flap alone (n = 6) or cheek plus forehead (n = 6) advancement flaps. Eight patients received radiotherapy before and after surgery. Four patients (29%) had a total of 6 postoperative complications (skin graft infection, orbital cavitary abscess, osteomyelitis, chronic skin ulcer, and 2 sino-orbital fistulae). The mean follow-up duration was 43 months (range, 11–79 months).

Conclusions:

Cheek advancement flap can be used alone or together with a forehead advancement flap to cover the orbital defects after total or extended exenteration. This repair may be resistant to radiotherapy-related complications in some cases.
Long noncoding RNA HOTAIRM1 promotes myeloid-derived suppressor cell expansion and suppressive functions through up-regulating HOXA1 expression during latent HIV infection
Authors: Zhang Jinyu , Thakuri Bal Krishna Chand , Zhao Juan , Nguyen Lam N. , Nguyen Lam N.T. , Cao Dechao , Dang Xindi , Khanal Sushant , Schank Madison , Lu Zeyuan , Wu Xiao Y. , Morrison Zheng D. , Gazzar Mohamed El , Li Zhengke , Jiang Yong , Ning Shunbin , Wang Ling , Moorman Jonathan P. , Yao Zhi Q.
Published: October 2020

Objective:

Myeloid-derived suppressor cells (MDSCs) contribute to HIV progression by impairing antiviral immunity; however, the mechanisms responsible for MDSC development during HIV infection are incompletely understood. HOX antisense intergenic RNA myeloid 1 (HOTAIRM1) is a long noncoding RNA (lncRNA) that plays a pivotal role in regulating myeloid cell development via targeting HOXA1. The role of HOTAIRM1--HOXA1 in the differentiation and functions of MDSCs during HIV infection remains unclear.

Methods:

In this study, we measured MDSC induction and suppressive functions by flow cytometry, RT-PCR, and co-culture experiments using CD33+ myeloid cells derived from people living with HIV (PLHIV) on antiretroviral therapy (ART). We also manipulated the HOTAIRM1--HOXA1 axis in myeloid cells using knockdown and overexpression approaches.

Results:

We demonstrate that HOTAIRM1 and HOXA1 expressions are reciprocally upregulated and are responsible for increased levels of immunosuppressive molecules, such as arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), signal transducer and activator of transcription 3 (STAT3), and reactive oxygen species (ROS), in CD33+ myeloid cells derived from PLHIV on ART. We found that overexpression of HOTAIRM1 or HOXA1 in CD33+ cells isolated from healthy individuals promoted the differentiation and suppressive functions of MDSCs, whereas silencing of HOTAIRM1 or HOXA1 expression in MDSCs derived from PLHIV significantly inhibited the frequency of MDSCs and expressions of the immunosuppressive molecules and reduced their immunosuppressive effects on T cells.

Conclusion:

These results indicate that the HOTAIRM1--HOXA1 axis enhances differentiation and suppressive functions of MDSCs and could be a potential therapeutic target for immunomodulation during latent HIV infection.
Differential effects of antiretroviral drug toxicity in male versus female children who are HIV-exposed but uninfected
Authors: Gilmore Julian C. , Serghides Lena , Bendayan Reina
Published: October 2020

In recent years, widespread use of antiretroviral therapy (ART) during pregnancy has been increasingly effective in reducing risk of vertical transmission of HIV, with over 80% of pregnant women living with HIV now accessing ART, and a 41% reduction in new infections in children between 2010 and 2018. Despite these strides, the developmental toxicity of widely administered antiretroviral drugs (ARVs) remains poorly described and existing literature often fails to account for fetal and infant sex as a variable. Recent reports have identified associations between in-utero exposure to commonly used antiretroviral regimens and alteration in neurodevelopment, growth, and metabolism amongst children who are HIV-exposed but uninfected, with findings of sex differences in the prevalence and severity of ARV toxicity. These differences are potentially explained by variable exposure to ARV drugs in utero or exacerbation of existing sex-linked risk factors. Fetal ARV exposure is mediated by placental and fetal drug transporters and metabolic enzymes, which may contribute to the manifestation of sex differences. Existing evidence of sex differences in ARV toxicity in fetal development is concerning, and demands further research to guide optimal treatment options for maternal health and prevention of vertical HIV transmission.
A systematic review of early adoption of implementation science for HIV prevention or treatment in the United States
Authors: Shangani Sylvia , Bhaskar Nidhi , Richmond Natasha , Operario Don , van den Berg Jacob J.
Published: October 2020

Objective:

To provide the first systematic review of the early adoption of implementation science for HIV prevention or treatment in the United States. We identified primary research studies that addressed implementation of HIV prevention or treatment in the United States and qualitatively assessed the reporting of implementation outcomes and intervention descriptions.

Methods:

We searched PubMed, PsycInfo, and CINAHL databases for evaluations of HIV prevention or treatment interventions that at least reported one implementation outcome and were published between 2014 and 2018. We used the 12-item Template for Intervention Description and Replication to assess study interventions.

Results:

A total of 2275 articles were identified. Thirty-nine studies met inclusion criteria. Of these, 84.6% used quantitative methods with 5% being hybrid effectiveness-implementation studies and 15% used qualitative methods. No studies cited a formal theoretical framework for implementation science. Acceptability and feasibility were the most frequently reported implementation outcomes. Eligible studies were diverse with regard to demographic categories. Most interventions focused on HIV prevention, particularly risk-reduction strategies. HIV treatment interventions targeted linkage to care and adherence to medications. Key implementation outcome findings indicated that these interventions are feasible and acceptable in the real world.

Conclusion:

HIV implementation science could support dissemination of HIV prevention or treatment in the United States, although HIV treatment interventions are limited. Theoretical frameworks and key implementation outcomes like fidelity, penetration, and appropriateness could promote the rigor of future HIV treatment implementation research, helping the field deliver the promise of HIV prevention or treatment efforts in the United States.
Incident type 2 diabetes mellitus after initiation of common HIV antiretroviral drugs
Authors: Hsu Ricky , Brunet Laurence , Fusco Jennifer S. , Mounzer Karam , Vannappagari Vani , Henegar Cassidy E. , Van Wyk Jean , Curtis Lloyd , Lo Janet , Fusco Gregory P.
Published: October 2020

Objectives:

To describe the prevalence and incidence of prediabetes and type 2 diabetes mellitus (T2DM) among people living with HIV (PLHIV) and evaluate the association between antiretroviral therapy (ART) initiation with dolutegravir (DTG), elvitegravir/cobicistat (EVG/c), raltegravir (RAL), or boosted darunavir (bDRV) and incident T2DM.

Design:

Longitudinal study based on electronic health records of 29 674 PLHIV from the Observational Pharmaco-Epidemiology Research and Analysis (OPERA) cohort.

Methods:

Calculate prevalence of prediabetes and T2DM at regimen initiation. Among PLHIV without prevalent disease, estimate prediabetes and T2DM incidence (Poisson regression) and association between regimen and incident T2DM (multivariate Cox proportional hazards regression). Analyses stratified by ART experience.

Results:

Among ART-naive and ART-experienced/suppressed PLHIV, the estimated prevalence of prediabetes was 8 and 11%; that of T2DM was 4 and 10%, respectively. The T2DM incidence rate was 9 per 1000 person-years [95% confidence interval (CI): 8–11] among ART-naive and 13 per 1000 person-years (95% CI: 12–15) among ART-experienced/suppressed PLHIV, with no statistically significant differences between regimens. Compared with DTG, no statistically significant association between T2DM risk and regimen was observed among ART-naive on EVG/c [adjusted hazard ratios: 0.70 (95% CI: 0.47–1.05)] or bDRV [0.53 (0.26–1.04)] and ART-experienced/suppressed on EVG/c [0.96 (0.70–1.33)], RAL [1.17 (0.70–1.96)] or bDRV [0.90 (0.57–1.42)].

Conclusion:

No increased risk of T2DM was observed with EVG/c, RAL or bDRV compared with DTG in ART-naive and experienced PLHIV. However, despite a large cohort, there was a small number of events and differential risk cannot be excluded.
Prognostic significance of preinjury anticoagulation in patients with traumatic brain injury: A systematic review and meta-analysis
Authors: Lim Xin Tian , Ang Eshen , Lee Zong Xuan , Hajibandeh Shahin , Hajibandeh Shahab
Published: October 2020

BACKGROUND

Traumatic brain injury (TBI) is a leading cause of injury-related deaths and neurological disability globally. Considering the widespread anticoagulant use among the aging population, we aimed to perform a systematic review and meta-analysis to evaluate the prognostic significance of preinjury anticoagulation in TBI patients.

METHODS

This systematic review was conducted according to a predefined protocol (International Prospective Register of Systematic Reviews CRD42020192323). In compliance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Meta-Analysis of Observational Studies in Epidemiology standards, a structured electronic database search was undertaken to identify all observational studies comparing preinjury anticoagulation with no preinjury anticoagulation in TBI patients. The primary outcome measure was overall mortality. The secondary outcome measures comprised in-hospital mortality, length of hospital stay, length of intensive care unit stay, need for neurosurgical procedure, and number of patients discharged home. All outcome data were analyzed using random effects modeling.

RESULTS

Twelve comparative studies enrolling a total of 4,417 patients were included. Preinjury anticoagulation was associated with higher risk of overall mortality (odds ratio [OR], 2.39; 95% confidence interval [CI], 1.63–3.50, p < 0.00001), in-hospital mortality (OR, 2.47; 95% CI, 1.56–3.93, p = 0.0001), and longer length of intensive care unit stay (mean difference, 1.06; 95% CI, 0.54–1.57; p < 0.0001) compared with no preinjury anticoagulation. No statistical difference was observed in length of hospital stay (mean difference, −2.15; 95% CI, −5.36 to 1.05, p = 0.19), need for neurosurgical procedure (OR, 1.30; 95% CI, 0.70–2.44; p = 0.41), and discharged home (OR, 0.76; 95% CI, 0.55–1.04; p = 0.09) between the two groups.

CONCLUSION

Preinjury anticoagulation is a powerful prognosticator of mortality in TBI patients. This highlights the need for dedicated triage and trauma team activation protocols considering earlier intervention and more aggressive imaging in all anticoagulated patients. Future studies should focus on strategies that can potentially reduce the risk of mortality in this population. The prognostic significance of direct oral anticoagulants versus warfarin remains unanswered.

LEVEL OF EVIDENCE

Systematic review and meta-analysis of observational studies, level III.
Ethinyl estradiol sulfate acts without fluid resuscitation through estrogen receptors to rapidly protect the cardiovascular system from severe hemorrhage
Authors: Hubbard William J. , Yang Shaolong , Chaudry Irshad H.
Published: October 2020

BACKGROUND

Our in vivo rodent and pig model evidenced that estrogen and its derivative, ethinyl estradiol sulfate (EES), promote survival following hemorrhagic shock. To determine its mechanism, we first confirmed EES binding to estrogen receptor (ER) and improving/restoring cellular signaling, countering the assumption that EES, an ethinyl estradiol metabolite, is inactive. In addition, we examined if EES acts rapidly, consistent with nongenomic signaling. We selected the biomarkers of cardiovascular performance, reduction of apoptosis and proinflammatory responses, and elaboration of nitric oxide (NO) to validate efficacy.

METHODS

A rat trauma-hemorrhage model, consisting of a midline laparotomy and controlled bleeding (60% blood loss) without fluid resuscitation, was used. At 30 minutes after hemorrhage, heart performance was monitored, and Western blots were used to quantify biochemical analytes. The specificity of EES for ER was profiled with ER antagonists. Binding studies by Sekisui XenoTech (Kansas City, KS) determined an LD50 value for EES binding the rat ER.

RESULTS

The EES IC50 value was 1.52 × 10−8 Mol/L, consistent with pharmacologic efficacy. Ethinyl estradiol sulfate raised mean arterial pressure and ±derivative of pressure over time (dP/dT) significantly (but did not fully restore) within a 30-minute window. Levels of apoptosis and activation of NF-κB were dramatically reduced, as was elaboration of nitric oxide (NO) by inducible nitric oxide synthase. Phospho-endothelial nitric oxide synthase (eNOS) was restored to physiological levels. The restoration of cellular signaling occurs before restoration of cardiac contractility.

CONCLUSION

Ethinyl estradiol sulfate is a potent drug for improving heart performance, which also dramatically reduces damage by apoptosis, proinflammatory activity, and NO production, validating that EES can blunt multiple harmful outcomes arising from hypoxia and hypovolemia. The actions are dependent on receptor engagement, where specificity is confirmed by ER antagonists. The constraint of a 30-minute sampling window affirms that the responses are nongenomic and very likely restricted to cell-surface receptor engagement. The rapidity of these responses makes EES promising for intervention in the “golden hour.”
Swimming kinematics and hydrodynamics of barnacle larvae throughout development
Authors: Wong J. Y. , Chan Benny K. K. , Chan K. Y. Karen
Published: October 2020

Changes in size strongly influence organisms' ecological performances. For aquatic organisms, they can transition from viscosity- to inertia-dominated fluid regimes as they grow. Such transitions are often associated with changes in morphology, swimming speed and kinematics. Barnacles do not fit into this norm as they have two morphologically distinct planktonic larval phases that swim differently but are of comparable sizes and operate in the same fluid regime (Reynolds number 100–101). We quantified the hydrodynamics of the rocky intertidal stalked barnacleCapitulum mitellafrom the nauplius II to cyprid stage and examined how kinematics and size increases affect its swimming performance. Cyprids beat their appendages in a metachronal wave to swim faster, more smoothly, and with less backwards slip per beat cycle than did all naupliar stages. Micro-particle image velocimetry showed that cyprids generated trailing viscous vortex rings that pushed water backwards for propulsion, contrary to the nauplii's forward suction current for particle capture. Our observations highlight that zooplankton swimming performance can shift via morphological and kinematic modifications without a significant size increase. The divergence in ecological functions through ontogeny in barnacles and the removal of feeding requirement likely contributed to the evolution of the specialized, taxonomically unique cyprid phase.
The ammonite septum is not an adaptation to deep water: re-evaluating a centuries-old idea
Authors: Lemanis Robert
Published: October 2020

The shells of ammonoid cephalopods are among the most recognizable fossils, whose fractally folded, internal walls (septa) have inspired many hypotheses on their adaptive value. The enduring explanation for their iterative evolution is that they strengthen the shell against pressure at increasing water depths. The fossil record does not definitively support this idea and much of the theoretical mechanical work behind it has suffered from inaccurate testing geometries and conflicting results. By using a different set of mathematical methods compared with previous studies, I generate a system of finite-element models that explore how different parameters affect the shell's response to water pressure. Increasing the number of initial folds of the septa ultimately has little to no effect on the resulting stress in the shell wall or the septum itself. The introduction of higher-order folds does reduce the tensile stress in the shell wall; however, this is coupled with a higher rate of increase of tensile stress in the septum itself. These results reveal that the increase in complexity should not be expected to have a significant effect on the shell's strength and suggests that the evolution of ammonitic septa does not reflect a persistent trend towards deeper-water habitats.
Staphylococcus borealis sp. nov., isolated from human skin and blood
Authors: Pain Maria , Wolden Runa , Jaén-Luchoro Daniel , Salvà-Serra Francisco , Iglesias Beatriz Piñeiro , Karlsson Roger , Klingenberg Claus , Cavanagh Jorunn Pauline
Published: October 2020

When analysing a large cohort of

Staphylococcus haemolyticus

, using whole-genome sequencing, five human isolates (four from the skin and one from a blood culture) with aberrant phenotypic and genotypic traits were identified. They were phenotypically similar with yellow colonies, nearly identical 16S rRNA gene sequences and initially speciated as

S. haemolyticus

based on 16S rRNA gene sequence and MALDI-TOF MS. However, compared to

S. haemolyticus

, these five strains demonstrate: (i) considerable phylogenetic distance with an average nucleotide identity <95 % and inferred DNA–DNA hybridization <70  %; (ii) a pigmented phenotype; (iii) urease production; and (iv) different fatty acid composition. Based on the phenotypic and genotypic results, we conclude that these strains represent a novel species, for which the name Staphylococcus borealis sp. nov. is proposed. The novel species belong to the genus

Staphylococcus

and is coagulase- and oxidase-negative and catalase-positive. The type strain, 51-48T, is deposited in the Culture Collection University of Gothenburg (CCUG 73747T) and in the Spanish Type Culture Collection (CECT 30011T).
The glycan alphabet is not universal: a hypothesis
Authors: Srivastava Jaya , Sunthar P. , Balaji Petety V.
Published: October 2020

Several monosaccharides constitute naturally occurring glycans, but it is uncertain whether they constitute a universal set like the alphabets of proteins and DNA. Based on the available experimental observations, it is hypothesized herein that the glycan alphabet is not universal. Data on the presence/absence of pathways for the biosynthesis of 55 monosaccharides in 12 939 completely sequenced archaeal and bacterial genomes are presented in support of this hypothesis. Pathways were identified by searching for homologues of biosynthesis pathway enzymes. Substantial variations were observed in the set of monosaccharides used by organisms belonging to the same phylum, genera and even species. Monosaccharides were grouped as common, less common and rare based on their prevalence in Archaea and Bacteria. It was observed that fewer enzymes are sufficient to biosynthesize monosaccharides in the common group. It appears that the common group originated before the formation of the three domains of life. In contrast, the rare group is confined to a few species in a few phyla, suggesting that these monosaccharides evolved much later. Fold conservation, as observed in aminotransferases and SDR (short-chain dehydrogenase reductase) superfamily members involved in monosaccharide biosynthesis, suggests neo- and sub-functionalization of genes led to the formation of the rare group monosaccharides. The non-universality of the glycan alphabet begets questions about the role of different monosaccharides in determining an organism’s fitness.
Characteristics and clinical features of SARS-CoV-2 infections among ambulatory and hospitalized children and adolescents in an integrated health care system in Tennessee
Authors: Howard Leigh M. , Garguilo Kathryn , Gillon Jessica , Seegmiller Adam C. , Schmitz Jonathan E. , Webber Steven A. , Halasa Natasha B. , Banerjee Ritu
Published: October 2020

Background

Little is known regarding the full spectrum of illness among children with SARS-CoV-2 infection across ambulatory and inpatient settings.

Methods

Active surveillance was performed for SARS-CoV-2 by polymerase chain reaction among asymptomatic and symptomatic individuals in a quaternary care academic hospital laboratory in Tennessee from March 12-July 17, 2020. For symptomatic patients ≤18 years of age, we performed phone follow-up and medical record review to obtain sociodemographic and clinical data on days 2, 7, and 30 after diagnosis and on day 30 for asymptomatic patients ≤18 years. Daily and 7-day average test positivity frequencies were calculated for children and adults beginning April 26, 2020.

Results

SARS-CoV-2 was detected in 531/10327 (5.1%) specimens from patients ≤18 years, including 46/5752 (0.8%) asymptomatic and 485/4575 (10.6%) specimens from 459 unique symptomatic children. Cough (51%), fever (42%), and headache (41%) were the most common symptoms associated with SARS-CoV-2 infection. SARS-CoV-2-related hospitalization was uncommon (18/459 children; 4%); no children with SARS-CoV-2 infection during the study period required intensive care unit admission. Symptom resolution occurred by follow-up day 2 in 192/459 (42%), by day 7 in 332/459 (72%), and by day 30 in 373/396 (94%). The number of cases and percent positivity rose in late June and July in all ages.

Conclusions

In an integrated healthcare network, most pediatric SARS-CoV-2 infections were mild, brief, and rarely required hospital admission, despite increasing cases as community response measures were relaxed.

Key points

In an integrated healthcare network in the Southeastern United States, symptomatic SARS-CoV-2 infection in children was generally mild, resolved rapidly, and rarely required hospitalization. Cases increased in children and adults as community mitigation measures became less restrictive.
What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis
Authors: Roshandel M. Reza , Nateqi Masoud , Lak Ramin , Aavani Pooya , Motlagh Reza Sari , Badr Tannaz Aghaei , Sfakianos John , Kaplan Steven A. , Shariat Shahrokh F. , Tewari Ashutosh K.
Published: October 2020

Objective

Investigating the infectivity of body fluid can be useful for preventative measures in the community and ensuring safety in the operating rooms and on the laboratory practices.

Methods

We performed a literature search of clinical trials, cohorts, and case series using PubMed/MEDLINE, Google Scholar, and Cochrane library, and downloadable database of CDC. We excluded case reports and searched all-language articles for review and repeated until the final drafting. The search protocol was registered in the PROSPERO database.

Results

Thirty studies with urinary sampling for viral shedding were included. A total number of 1,271 patients were enrolled initially, among which 569 patients had undergone urinary testing. Nine studies observed urinary viral shedding in urine from 41 patients. The total incidence of urinary SARS-CoV-2 shedding was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively. The summarized risk ratio (RR) estimates for urine positive rates compared to the pharyngeal rate was 0.08. The pertaining RR urine compared to blood and stool positive rates were 0.20 and 0.33 respectively.

Conclusions

Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight percent of patients but also its incidence may have associations with the severity of the systemic disease, ICU admission, and fatality rates. Moreover, the findings in our review suggest that a larger population size may reveal more positive urinary cases possibly by minimizing biases. However, it is important to notice that it is the naso-pharyngeal specimens, stool, and serum that show more possibilities to became positive, respectively.

Take-home bullet points

❖

The urinary shedding incidence was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively.

❖

Urinary shedding may have associations with the severity of the systemic disease, ICU admission, and fatality rates.

❖

Repeat urinary testing is warranted throughout the disease phases, especially in clinically suspected cases with an initially negative results.

❖

Technical errors in handling samples, as well as different rRT-PCR methods can be responsible for diversity found in results, in part.
Prevalence and Determinants of Premarital Sexual Practice Among Youths in Ethiopia: Further analysis of the Ethiopian Demographic and Health Survey
Authors: Getie Kegnie Shitu , Kassie Ayenew , Woldie Maereg
Published: October 2020

Introduction

Premarital sexual practice becomes a common phenomenon among youths in Ethiopia. It is usually associated with an unwanted pregnancy, abortion, and sexually transmitted diseases including HIV/AIDS.

Objective

This study aimed to assess the prevalence and determinants of premarital sexual practice among Ethiopian youths.

Methods and Materials

A Community-based cross-sectional study was conducted in all regions of Ethiopia from January 18 to June 27, 2016. All participants from the age of 15-24 (7, 389) were included for the analysis of the present study. Bivariable and multivariable binary logistic regression analytical models were fitted to identify factors associated with the premarital sexual practice. A 95% CI and p-value < 0.05 were used to declare statistical significance.

Result

The prevalence of premarital sexual practice was 10.8% (95% CI, 10 % – 11.5%). Being in the age group of 20 - 24 (AOR = 3.6, 95% CI (2.8, 4.6)), male sex (AOR = 1.7, 95% CI (1.3, 2.2)), employed (AOR = 1.4, 95% CI (1.03, 1.8)), from pastorals region (AOR= 1.4, 95% CI (1.3,2.4)), having mobile phone (AOR=1.7, 95% CI, (1.3, 2.3)), ever use of internet (AOR = 1.8, 95% CI (1.3, 2.5)), ever drinking alcohol AOR = 2.4, 95% CI (1.7, 2.5)), ever chewed khat (AOR = 2.4, 95% CI (1.6, 3.5), and ever tested for HIV (AOR = 1.3, 95% CI (1.1,1.6)) were a statistically significant factors associated with premarital sexual practice at p value less than 0.05.

Conclusion

For every 10 youths at least one of them had sexual intercourse before they got married. Being in the age group of 20 - 24, male sex, employed, from a pastoral region, having a mobile phone, ever use of the internet, alcohol drinking, khat chewing, and ever tested for HIV were significant factors associated with the premarital sexual practice. Thus, national sexual education and reproductive health behavior change interventions should give due attention for those groups. Indeed, adequate education should be given about premarital sexual intercourse when youths come for HIV test.
Explaining the Effective Reproduction Number of COVID-19 through Mobility and Enterprise Statistics: Evidence from the First Wave in Japan
Authors: Kajitani Yoshio , Hatayama Michinori
Published: October 2020

This study uses mobility statistics combined with business census data for the eight Japanese prefectures with the highest COVID-19 infection rates to study the effect of mobility reductions on the effective reproduction number (i.e., the average number of secondary cases caused by one infected person). Mobility statistics are a relatively new data source created by compiling smartphone location data. Based on data for the first wave of infections in Japan, we found that reductions targeting the hospitality industry were more effective than restrictions on general business activities. Specifically, we found that to hold back the pandemic (that is, to reduce the effective reproduction number to one or less for all days), a 20-35% reduction in weekly mobility is required, depending on the region. A lesser goal, 80% of days with one or less observed transmission, can be achieved with a 6-30% reduction in weekly mobility. These are the results if other potential causes of spread are ignored; more careful observations and expanded data sets are needed.
A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades
Authors: Islam Md. Tanvir , Alam A. S. M. Rubayet Ul , Sakib Najmuj , Hasan Md. Shazid , Chakrovarty Tanay , Tawyabur Md. , Islam Ovinu Kibria , Al-Emran Hassan M. , Jahid Iqbal Kabir , Hossain M. Anwar
Published: October 2020

Tracing the globally circulating SARS-CoV-2 mutants is essential for the outbreak alerts and far-reaching epidemiological surveillance. The available technique to identify the phylogenetic clades through high-throughput sequencing is costly, time-consuming, and labor-intensive that hinders the viral genotyping in low-income countries. Here, we propose a rapid, simple and cost-effective amplification-refractory mutation system (ARMS)-based multiplex reverse-transcriptase PCR assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. This approach is applied on 24 COVID-19 positive samples as confirmed by CDC approved real-time PCR assay for SARS-CoV-2. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized in the primer concentration (0.2-0.6 µM) and annealing temperature (56-60°C) of PCR using 3-5 ng/µl cDNA template synthesized upon random- and oligo(dT)-primer based reverse transcription. The different primer concentration for the triplex and quadruplex adjusted to different strengths ensured an even amplification with a maximum resolution of all targeted amplicons. The targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with another set of our designed primers. This multiplex ARMS-PCR assay is sample, cost-effective, and convenient that can successfully discriminate the circulating phylogenetic clades of SARS-CoV-2.
Value CMR: Towards a Comprehensive, Rapid, Cost-Effective Cardiovascular Magnetic Resonance Imaging
Authors: Ibrahim El-Sayed H. , Frank Luba , Baruah Dhiraj , Rubenstein Jason C. , Arpinar V. Emre , Nencka Andrew S. , Koch Kevin M. , Muftuler L Tugan , Unal Orhan , Stojanovska Jadranka , Charlson John , Gore Elizabeth M. , Bergom Carmen
Published: October 2020

CMR is considered the gold standard for measuring heart function, including cardiac volumes and mass. Further, in a single CMR exam, information about cardiac function, structure, tissue composition, and blood flow could be obtained. Nevertheless, CMR is underutilized due to long scanning times, the need for multiple breath-holds, use of a contrast agent, and relatively higher cost compared to echocardiography.

In this study, we propose a rapid CMR exam based on recent developments in imaging sequences. The proposed exam is both rapid and provides comprehensive cardiovascular information without the need for a contrast agent or multiple breath-holds. The developed exam includes advanced sequences for evaluating global and regional cardiac functions, myocardial tissue characterization, and flow hemodynamics in the heart, valves, and large vessels. Time-consuming conventional sequences have been replaced by advanced sequences, which resulted in reducing scan time from > 1 hour with conventional CMR exam to <20 minutes with the proposed rapid CMR exam. Specifically, conventional two-dimensional (2D) cine and phase-contrast (PC) sequences have been replaced by optimized three-dimensional (3D)-cine and four-dimensional (4D)-flow sequences, respectively. Compared to 2D cine imaging that requires 12-16 separate breath-holds, the implemented 3D-cine sequence allows for whole heart coverage in 1-2 breath-holds; thus, reducing scan time by 80-90%. Similarly, compared to 2D PC flow imaging that requires multiple breath-holds and the presence of an experienced cardiac operator for precise prescription of the imaging planes, the implemented 4D-flow sequence allows for whole-chest coverage in ∼10-minute, free-breathing acquisition without the need for a navigator echo, which makes scan time independent of the patient’s breathing pattern. Furthermore, conventional myocardial tagging has been replaced by the fast strain-encoding (SENC) sequence, which reduces scan time from one slice per breath-hold to only one slice per heartbeat (∼1 second). Finally, T1 and T2 mapping sequences are included in this proposed exam, which allow for myocardial tissue characterization without the need for contrast. The proposed rapid exam has been tested on volunteers and measurements showed good agreement with those from conventional sequences despite the significant reduction in scan time.

In conclusion, we propose a rapid, contrast-free, and comprehensive cardiovascular exam that does not require repeated breath-holds or a cardiac experienced operator to run the exam, which would result in improving cost effectiveness of CMR and increasing its adoption in clinical practice.
Discovering early imaging biomarkers of osteoradionecrosis in oropharyngeal cancer by characterization of temporal changes in computed tomography mandibular radiomic features
Authors: Barua Souptik , Elhalawani Hesham , Volpe Stefania , Feghali Karine Al , Yang Pei , Ng Sweet Ping , Elgohari Baher , Granberry Robin C. , Mackin Dennis S. , Gunn G. Brandon , Hutcheson Katherine A. , Chambers Mark S. , Court Laurence E. , Mohamed Abdallah , Fuller Clifton D. , Lai Stephen Y. , Rao Arvind
Published: October 2020

Osteoradionecrosis (ORN) is a major side-effect of radiation therapy in oropharyngeal cancer (OPC) patients. In this study, we demonstrate that early prediction of ORN is possible by analyzing the temporal evolution of mandibular subvolumes receiving radiation. For our analysis, we use computed tomography (CT) scans from 21 OPC patients treated with Intensity Modulated Radiation Therapy (IMRT) with subsequent radiographically-proven ≥ grade II ORN, at three different time points: pre-IMRT, 2-months, and 6-months post-IMRT. For each patient, radiomic features were extracted from a mandibular subvolume that developed ORN and a control subvolume that received the same dose but did not develop ORN. We used a Multivariate Functional Principal Component Analysis (MFPCA) approach to characterize the temporal trajectories of these features. The proposed MFPCA model performs the best at classifying ORN vs Control subvolumes with an area under curve (AUC) = 0.74 (95% confidence interval (C.I.): 0.61-0.90), significantly outperforming existing approaches such as a pre-IMRT features model or a delta model based on changes at intermediate time points, i.e. at 2- and 6-month follow-up. This suggests that temporal trajectories of radiomics features derived from sequential pre- and post-RT CT scans can provide markers that are correlates of RT-induced mandibular injury, and consequently aid in earlier management of ORN.