bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduced dengue incidence following deployments of Wolbachia-infected Aedes aegypti in Yogyakarta, Indonesia: a quasi-experimental trial using controlled interrupted time series analysis
Authors: Indriani Citra , Tantowijoyo Warsito , Rancès Edwige , Andari Bekti , Prabowo Equatori , Yusdi Dedik , Ansari Muhammad Ridwan , Wardhana Dwi Satria , Supriyati Endah , Nurhayati Indah , Ernesia Inggrid , Setyawan Sigit , Fitriana Iva , Arguni Eggi , Amelia Yudiria , Ahmad Riris Andono , Jewell Nicholas P. , Dufault Suzanne M. , Ryan Peter A. , Green Benjamin R. , McAdam Thomas F. , O’Neill Scott L. , Tanamas Stephanie K. , Simmons Cameron P. , Anders Katherine L. , Utarini Adi
Published: March 2020

Background

Ae. aegypti mosquitoes stably transfected with the intracellular bacterium Wolbachia pipientis (wMel strain) have been deployed for the biocontrol of dengue and related arboviral diseases in multiple countries. Field releases in northern Australia have previously demonstrated near elimination of local dengue transmission from Wolbachia-treated communities, and pilot studies in Indonesia have demonstrated the feasibility and acceptability of the method. We conducted a quasi-experimental trial to evaluate the impact of scaled Wolbachia releases on dengue incidence in an endemic setting in Indonesia.

Methods and findings

In Yogyakarta City, Indonesia, following an extensive community engagement campaign, wMel Wolbachia-carrying mosquitoes were released every two weeks for 13–15 release rounds over seven months in 2016–17, in a contiguous 5 km2 area (population 65,000). A 3 km2 area (population 34,000) on the opposite side of the city was selected a priori as an untreated control area, on the basis of comparable socio-demographic characteristics and historical dengue incidence. Passive surveillance data on notified hospitalised dengue patients was used to evaluate the epidemiological impact of Wolbachia deployments, using controlled interrupted time series analysis. Rapid and sustained introgression of wMel Wolbachia into local Ae. aegypti populations was achieved. Thirty-four dengue cases were notified from the intervention area and 53 from the control area (incidence 26 vs 79 per 100,000 person-years) during the 24 months after Wolbachia was deployed. This corresponded in the regression model to a 73% reduction in dengue incidence (95% confidence interval 49%,86%) associated with the Wolbachia intervention. Exploratory analysis including an additional 6 months of post-intervention observations showed a small strengthening of this effect (30 vs 115 per 100,000 person-years; 76% reduction in incidence, 95%CI 60%,86%).

Conclusions

These findings demonstrate a significant reduction in dengue incidence following successful introgression of Wolbachia into local Ae. aegypti populations in an endemic setting in Indonesia. These results are consistent with previous field trials in northern Australia, and support the effectiveness of this novel approach for the control of dengue and other Aedes-borne diseases.
Association between Prolonged Intermittent Renal Replacement Therapy and All-Cause Mortality in COVID-19 Patients Undergoing Invasive Mechanical Ventilation: a Retrospective Cohort Study
Authors: Yang Yi , Shi Jia , Ge Shuwang , Guo Shuiming , Xing Xue , Wang Yanan , Cheng Anying , Liu Qingquan , Li Junhua , Ning Yong , He Fan , Xu Gang
Published: March 2020

Background

For the coronavirus disease 2019 (COVID-19), critically ill patients had a high mortality rate. We aimed to assess the association between prolonged intermittent renal replacement therapy (PIRRT) and mortality in patients with COVID-19 undergoing invasive mechanical ventilation.

Methods

In this retrospective cohort study, we included all patients with COVID-19 undergoing invasive mechanical ventilation from February 12nd to March 2nd, 2020. All patients were followed until death or March 28th, and all survivors were followed for at least 30 days.

Results

For 36 hospitalized COVID-19 patients with invasive mechanical ventilation, the mean age was 69.4 (± 10.8) years, and 30 patients (83.3%) were men. Twenty-two (61.1%) patients received PIRRT (PIRRT group) and 14 cases (38.9%) were managed with conventional strategy (non-PIRRT group). There were no differences in age, sex, comorbidities, complications, treatments and most of the laboratory findings. During median follow-up period of 9.5 (interquartile range 4.3-33.5) days, 13 of 22 (59.1%) patients in the PIRRT group and 11 of 14 (78.6%) patients in the non-PIRRT group died. Kaplan-Meier analysis demonstrated prolonged survival in patients in the PIRRT group compared with that in the non-PIRRT group (P = 0.042). The association between PIRRT and a reduced risk of mortality remained significant in three different models, with adjusted hazard ratios varying from 0.332 to 0.398. Higher levels of IL-2 receptor, TNF-α, procalcitonin, prothrombin time, and NT-proBNP were significantly associated with an increased risk of mortality in patients with PIRRT.

Conclusion

PIRRT may be beneficial for the treatment of COVID-19 patients with invasive mechanical ventilation. Further prospective multicenter studies with larger sample sizes are required.
Transmissibility of 2019 Novel Coronavirus: zoonotic vs. human to human transmission, China, 2019-2020
Authors: Mizumoto Kenji , Kagaya Katsushi , Chowell Gerardo
Published: March 2020

Objectives

The novel coronavirus (2019-nCoV) originating from Wuhan has rapidly spread throughout China. While the origin of the outbreak remains uncertain, accumulating evidence links a wet market in Wuhan for the early spread of 2019-nCoV. Similarly, the influence of the marketplace on the early transmission dynamics is yet to be investigated.

Methods

Using the daily series of 2019-nCov incidenceincluding contact history with the market, we have conducted quantitative modeling analyses to estimate the reproduction numbers (R) for the market-to-human and human-to-human transmission together with the reporting probability and the early effects of public health interventions.

Results

Our mean R estimates for China in 2019-2020 are estimated at 0.37 (95%CrI: 0.02-1.78) for market-to-human transmission, and 3.87 (95%CrI: 3.18-4.78) for human-to-human transmission, respectively. Moreover we estimated that the reporting rate cases stemming from market-to-human transmission was 3-31 fold higher than that for cases stemming from human-to-human transmission, suggesting that contact history with the wet market played a key role in identifying 2019-nCov cases.

Conclusions

Our findings suggest that the proportions of asymptomatic and subclinical patients constitute a substantial component of the epidemic’s magnitude. Findings suggest that the development of rapid diagnostic tests could help bring the epidemic more rapidly under control.
Emerging high-level ciprofloxacin-resistant Salmonella enterica serovar Typhi haplotype H58 in travelers returning from India to the Republic of Korea
Authors: Shin Eunkyung , Park Ae Kyung , Park Jungsun , Kim Soojin , Jeong Hyun Ju , Na Kyoungin , Lee Hyerim , Chun Jeong-hoon , Hwang Kyu Jam , Kim Chul-Joong , Kim Junyoung
Published: March 2020

In Korea, typhoid fever is a rare disease due to improved living standards. However, this disease remains a major burden in developing countries and regions, such as India and Southeast Asia, In this study, we isolated Salmonella Typhi (S. Typhi) from eight typhoid patients, travelers returning from India. Isolated strains characterized with antimicrobial susceptibility profile and whole genome sequencing (WGS) analysis.

All strains were resistant to nalidixic acid and azithromycin. Among them, four isolates were highly resistant to ciprofloxacin (MIC ≥32 μg/ml) and never confirmed in Korea PulseNet DB. On the basis of the WGS, we found that the ciprofloxacin-resistant strain belonged to global dominant multi-drug resistant (MDR) genotype, haplotype H58 (SNP glpA C1047T, SptP protein Q185* (premature stop codon)) not harbour MDR plasmid. They have H58-associated SNPs in membranes and metabolism genes, including yhdA, yajI, hyaE, tryE, rlpB and metH. Also, Phylogenetic analysis showed that H58 strains were assigned sublineage II, and the non-H58 strains were closely related to haplotype H50.

High-level ciprofloxacin-resistant S. Typhi haplotype H58 in Korea was first confirmed as influx from overseas by travelers. This study provides information about intercontinental drug-resistant transmission between countries and suggests that travelers need to be careful about personal hygiene.

Author summary

Typhoid fever is a systemic human disease including gastroenteritis, fever, and severe diarrhea, caused by Salmonella enterica serotype typhi (S. Typhi), and requires prompt antibiotic treatment. Due to improved living standards, it has become a rare disease but still prevalent in developing countries such as India and Southeast Asia. Most of the reported case were related with travelers or immigrants from these regions. There is global health problem that emergence of antimicrobial resistant strain associated with fluoroquinolones and third-generation cephalosporins because of leading to treatment failure, serious morbidity, and as well as economic loss. Of antimicrobial resistant S. Typhi, haplotype H58 is a dominant multi-drug resistant lineage and has reported in endemic region over past two decades. We identified fluoroquinolones resistance in S. Typhi infected after travel to India. Among them, some strains highly resistant to ciprofloxacin were confirmed to have characteristics of haplotype H58. In Korea, S. Typhi haplotype H58 from traveller has not been confirmed before. This study provides information about intercontinental drug-resistant transmission between countries and suggests that travelers need to be careful about personal hygiene.
Endemic hepatitis B virus (HBV) among hospital in-patients in Bangladesh, including evidence of occult infection
Authors: Chowdhury Fazle Rabbi , McNaughton Anna L , Amin Mohammad Robed , Barai Lovely , Saha Mili Rani , Rahman Tanjila , Das Bikash Chandra , Hasan M Rokibul , Shahidul Islam K M , Faiz M A , Al-Mahtab Mamun , Mokaya Jolynne , Kronsteiner Barbara , Jeffery Katie , Andersson Monique I , de Cesare Mariateresa , Ansari M Azim , Dunachie Susanna , Matthews Philippa C
Published: March 2020

Bangladesh is one of the world’s top ten burdened countries for viral hepatitis. We investigated an adult fever cohort (n=201) recruited in Dhaka, to determine the prevalence of hepatitis B virus (HBV) infection and to identify cases of occult hepatitis B infection (OBI). HBV exposure (anti-HBc) was documented in 72/201 (36%), and active HBV infection in 16/201 (8%), among whom 3 were defined as OBI (defined as detectable HBV DNA but negative HBsAg). Applying a target-enrichment sequencing pipeline to samples with HBV DNA >3.0log10 IU/ml, we obtained deep whole genome sequences for four cases, identifying genotypes A, C and D. Polymorphisms in the surface gene of the OBI case may account for the negative HBsAg status. We identified mutations associated with nucleos(t)ide analogue resistance, although the clinical significance in this cohort is not known. The high prevalence of HBV in this setting highlights the benefits of offering screening in hospital patients and the importance of HBV DNA testing of transfusion products to reduce the risk of transmission. In order to work towards international Sustainable Development Goal targets for HBV elimination, increased investment is required for diagnosis, treatment and prevention in Bangladesh.
COVID-19 Progression Timeline and Effectiveness of Response-to-Spread Interventions across the United States
Authors: Liu Pai , Beeler Payton , Chakrabarty Rajan K.
Published: March 2020

Motivated by the rapid upsurge of COVID-19 cases in the United States beginning March 2020, we forecast the disease spread and assess the effectiveness of containment strategies by using an estalished network-driven epidemic dynamic model. Our model is initialized using the daily counts of active and confirmed COVID-19 cases across the US. Based on our model predictions for the March 14-16 timeframe, the national epidemic peak could be expected to arrive by early June, corresponding to a daily active count of ≈ 7% of the US population, if no containment plans are implemented. Epidemic peaks are expected to arrive in the states of Washington and New York by May 21 and 25, respectively. With a modest 25% reduction in COVID-19 transmissibility via community-level interventions, the epidemic progression could be delayed by up to 34 days. Wholesale interstate traffic restriction is ineffective in delaying the epidemic outbreak, but it does desynchronize the arrival of state-wise epidemic peaks, which could potentially alleviate the burden on limited available medical resources. In addition to forecasting the arrival timeline of the state-wise epidemic peaks, we attempt at informing the optimal timing necessary to enforce community-level interventions. Our findings underscore the pressing need for preparedness and timely interventions in states with a large fraction of the vulnerable uninsured and liquid-asset-poverty populations.

Forecast website

https://sites.google.com/view/covid19forecast
Reverse transcription loop-mediated isothermal amplification combined with nanoparticles-based biosensor for diagnosis of COVID-19
Authors: Zhu Xiong , Wang Xiaoxia , Han Limei , Chen Ting , Wang Licheng , Li Huan , Li Sha , He Lvfen , Fu Xiaoying , Chen Shaojin , Xing Mei , Chen Hai , Wang Yi
Published: March 2020

Given the scale and rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, known as 2019-nCov) infection (COVID-19), the ongoing global SARS-CoV-2 outbreak has become a huge public health issue. Rapid and precise diagnostic methods are thus immediately needed for diagnosing COVID-19, providing timely treatment and facilitating infection control. A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) coupled with nanoparticles-based biosensor (NBS) assay (RT-LAMP-NBS) was successfully established for rapidly and accurately diagnosing COVID-19. A simple equipment (such as heating block) was required for maintaining a constant temperature (63°C) for only 40 min. Using two designed LAMP primer sets, F1ab (opening reading frame 1a/b) and np (nucleoprotein) genes of SARS-CoV-2 were simultaneously amplified and detected in a ‘one-step’ and ‘single-tube’ reaction, and the detection results were easily interpreted by NBS. The sensitivity of SARS-CoV-2 RT-LAMP-NBS was 12 copies (each of detection target) per reaction, and no cross-reactivity was generated from non-SARS-CoV-2 templates. Among clinically diagnosed COVID-19 patients, the analytical sensitivity of SARS-CoV-2 was 100% (33/33) in the oropharynx swab samples, and the assay’s specificity was also 100% (96/96) when analyzed the clinical samples collected from non-COVID-19 patients. The total diagnosis test from sample collection to result interpretation only takes approximately 1 h. In sum, the RT-LAMP-NBS is a promising tool for diagnosing the current SARS-CoV-2 infection in first line field, public health and clinical laboratories, especially for resource-challenged regions.
Prism adaptation treatment for upper-limb Complex Regional Pain Syndrome: a double-blind randomized controlled trial
Authors: Halicka Monika , Vittersø Axel D. , McCullough Hayley , Goebel Andreas , Heelas Leila , Proulx Michael J. , Bultitude Janet H.
Published: March 2020

Initial evidence suggested that people with Complex Regional Pain Syndrome (CRPS) have reduced attention to the affected side of their body and the surrounding space, which might be related to pain and other clinical symptoms. Three previous unblinded, uncontrolled studies showed pain relief following treatment with prism adaptation, an intervention that has been used to counter lateralised attention bias in brain-lesioned patients. To provide a robust test of its effectiveness for CRPS, we conducted a double-blind randomized controlled trial of prism adaptation for unilateral upper-limb CRPS-I. Forty-nine eligible adults with CRPS were randomized to undergo two-weeks of twice-daily home-based prism adaptation treatment (n = 23) or sham treatment (n = 26). Outcomes were assessed in person four weeks prior to and immediately before treatment, and immediately after and four weeks post-treatment. Long-term postal follow-ups were conducted three and six months after treatment. We examined the effects of prism adaptation versus sham treatment on current pain intensity and CRPS symptom severity score (primary outcomes); as well as sensory, motor, and autonomic functions, self-reported psychological functioning, and experimentally tested neuropsychological functions (secondary outcomes). We found no evidence that primary or secondary outcomes differed between the prism adaptation and sham treatment groups when tested at either time point following treatment. Overall, CRPS severity significantly decreased over time for both groups, but we found no benefits of prism adaptation beyond sham treatment. Our findings do not support the efficacy of prism adaptation treatment for relieving upper-limb CRPS-I. This trial was prospectively registered (ISRCTN46828292).
Comparison of the coronavirus pandemic dynamics in Europe, USA and South Korea
Authors: Nesteruk Igor
Published: March 2020

The pandemic cased by coronavirus COVID-19 is of great concern. A detailed scientific analysis of this phenomenon is still to come, but now it is urgently needed to evaluate the disease dynamics in order to organize the appropriate quarantine activities, to estimate the required number of places in hospitals, the level of individual protection, the rate of isolation of infected persons, etc. South Korea has achieved the stabilization of the number of cases at rather low level. The epidemic dynamics there can be compared with its development in other countries to make some preliminary, but very important conclusions. Here we provide a simple method of data comparison that can be useful for both governmental organizations and anyone.
A brief review of antiviral drugs evaluated in registered clinical trials for COVID-19
Authors: Belhadi Drifa , Peiffer-Smadja Nathan , Lescure François-Xavier , Yazdanpanah Yazdan , Mentré France , Laouénan Cédric
Published: March 2020

Background

Although a number of antiviral agents have been evaluated for coronaviruses there are no approved drugs available. To provide an overview of the landscape of therapeutic research for COVID-19, we conducted a review of registered clinical trials.

Methods

A review of currently registered clinical trials was performed on registries, including the Chinese (chictr.org.cn) and US (clinicaltrials.gov) databases to identify relevant studies up to March, 7th 2020. The search was conducted using the search terms “2019-nCoV”, “COVID-19”, “SARS-CoV-2”, “Hcov-19”, “new coronavirus”, “novel coronavirus”. We included interventional clinical trials focusing on patients with COVID-19 and assessing antiviral drugs or agents.

Findings

Out of the 353 studies identified, 115 clinical trials were selected for data extraction. Phase IV trials were the most commonly reported study type (n=27, 23%). However, 62 trials (54%) did not describe the phase of the study. Eighty percent (n=92) of the trials were randomized with parallel assignment and the median number of planned inclusions was 63 (IQR, 36-120). Open-label studies were the most frequent (46%) followed by double-blind (13%) and single blind studies (10%). The most frequently assessed therapies were: stem cells therapy (n=23 trials), lopinavir/ritonavir (n=15), chloroquine (n=11), umifenovir (n=9), hydroxychloroquine (n=7), plasma treatment (n=7), favipiravir (n=7), methylprednisolone (n=5), and remdesivir (n=5). Remdesivir was tested in 5 trials with a median of 400 (IQR, 394-453) planned inclusions per trial, while stem cells therapy was tested in 23 trials, but had a median of 40 (IQR, 23-60) planned inclusions per trial. Lopinavir/ritonavir was associated with the highest total number of planned inclusions (2606) followed by remdesivir (2155). Only 52% of the clinical trials reported the treatment dose (n=60) and only 34% (n=39) the duration. The primary outcome was clinical in 76 studies (66%), virological in 27 (23%); radiological in 9 (8%) or immunological in three studies (3%).

Interpretation

Numerous clinical trials have been registered since the beginning of the COVID-19 outbreak, however, a number of information regarding drugs or trial design were lacking.

Funding

None
Extended SIR prediction of the epidemics trend of COVID-19 in Italy and compared with Hunan, China
Authors: Wangping Jia , Ke Han , Yang Song , Wenzhe Cao , Shengshu Wang , Shanshan Yang , Jianwei Wang , Fuyin Kou , Penggang Tai , Jing Li , Miao Liu , Yao He
Published: March 2020

Background

Coronavirus Disease 2019 (COVID-19) is currently a global public health threat. Outside of China, Italy is one of the most suffering countries with the COVID-19 epidemic. It is important to predict the epidemics trend of COVID-19 epidemic in Italy to help develop public health strategies.

Methods

We used time-series data of COVID-19 from Jan 22,2020 to Mar 16,2020. An infectious disease dynamic extended susceptible-infected-removed (eSIR) model, which covers the effects of different intervention measures in dissimilar periods, was applied to estimate the epidemic trend in Italy. The basic reproductive number was estimated using Markov Chain Monte Carlo methods and presented using the resulting posterior mean and 95% credible interval (CI). Hunan, with similar total number of populations in Italy, was used as a comparative item.

Results

In the eSIR model, we estimated that the basic reproductive number for COVID-19 was respectively 4.10 (95% CI: 2.15–6.77) in Italy and 3.15(95% CI: 1.71–5.21) in Hunan. There would be totally 30 086 infected cases (95%CI:7920-81 869) under the current country blockade and the endpoint would be Apr 25 (95%CI: Mar 30 to Aug 07) in Italy. If the country blockade is imposed 5 day later, the total number of infected cases would expand the infection scale 1.50 times.

Conclusion

Italy’s current strict measures can efficaciously prevent the further spread of COVID-19 and should be maintained. Necessary strict public health measures be implemented as soon as possible in other European countries with a high number of COVID-19 cases. The most effective strategy needs to be confirmed in further studies.
Selective antibiofilm properties and biocompatibility of nano-ZnO and nano-ZnO/Ag coated surfaces
Authors: Rosenberg M. , Visnapuu M. , Vija H. , Kisand V. , Kasemets K. , Kahru A. , Ivask A.
Published: March 2020

Spread of pathogenic microbes and antibiotic-resistant bacteria in health-care settings and public spaces is a serious public health challenge. Materials that prevent solid surface colonization or impede touch-transfer of viable microbes could provide means to decrease pathogen transfer from high-touch surfaces in critical applications. ZnO and Ag nanoparticles have shown great potential in antimicrobial applications. Less is known about nano-enabled surfaces. Here we demonstrate that surfaces coated with nano-ZnO or nano-ZnO/Ag composites are not cytotoxic to human keratinocytes and possess species-selective medium-dependent antibiofilm activity againstEscherichia coli, Staphylococcus aureusandCandida albicans. Colonization of nano-ZnO and nano-ZnO/Ag surfaces byE. coliandS. aureuswas decreased in static oligotrophic conditions (no planktonic growth). Moderate to no effect was observed for bacterial biofilms in growth medium (supporting exponential growth). Inversely, nano-ZnO surfaces enhanced biofilm formation byC. albicansin oligotrophic conditions. However, enhancedC. albicansbiofilm formation on nano-ZnO surfaces was effectively counteracted by the addition of Ag. Possible selective enhancement of biofilm formation by the yeastC. albicanson Zn-enabled surfaces should be taken into account in antimicrobial surface development. Our results also indicated the importance of the use of application-appropriate test conditions and exposure medium in antimicrobial surface testing.
Dynamin-related Irgm proteins modulate LPS-induced caspase-4 activation and septic shock
Authors: Finethy Ryan , Dockterman Jacob , Kutsch Miriam , Orench-Rivera Nichole , Wallace Graham , Piro Anthony S. , Luoma Sarah , Haldar Arun K. , Hwang Seungmin , Martinez Jennifer , Kuehn Meta J. , Taylor Gregory A. , Coers Jörn
Published: March 2020

Inflammation associated with gram-negative bacterial infections is often instigated by the bacterial cell wall component lipopolysaccharide (LPS). LPS-induced inflammation and resulting life-threatening sepsis are mediated by the two distinct LPS receptors TLR4 and caspase-4. Whereas the regulation of TLR4 activation by extracellular and phago-endosomal LPS has been studied in great detail, auxiliary host factors that specifically modulate recognition of cytosolic LPS by caspase-4 are largely unknown. This study identifies dynamin-related membrane remodeling proteins belonging to the family of Immunity related GTPases M clade (IRGM) as negative regulators of caspase-4 activation in macrophages. Phagocytes lacking expression of mouse isoform Irgm2 aberrantly activate caspase-4-dependent inflammatory responses when exposed to extracellular LPS, bacterial outer membrane vesicles or gram-negative bacteria. Consequently, Irgm2-deficient mice display increased susceptibility to caspase-4-mediated septic shockin vivo.ThisIrgm2phenotype is partly reversed by the simultaneous genetic deletion of the two additionalIrgmparalogsIrgm1andIrgm3,indicating that dysregulated Irgm isoform expression disrupts intracellular LPS processing pathways that limit LPS availability for caspase-4 activation.
Identification of an antiretroviral small molecule that appears to be a host-targeting inhibitor of HIV-1 assembly
Authors: Reed Jonathan C. , Solas Dennis , Kitaygorodskyy Anatoliy , Freeman Beverly , Ressler Dylan T. B. , Phuong Daryl J. , Swain J. Victor , Matlack Kent , Hurt Clarence R. , Lingappa Vishwanath R. , Lingappa Jaisri R.
Published: March 2020

Given the projected increase in multidrug resistant HIV-1, there is an urgent need for development of antiretrovirals that act on virus life-cycle stages that are not targeted by antiretrovirals currently in use. Host-targeting drugs are of particular interest because they can offer a high barrier to resistance. Here we report identification of two related small molecules that inhibit HIV-1 late events, a stage of the HIV-1 life cycle for which potent and specific inhibitors are lacking. This chemotype was discovered using cell-free protein synthesis and assembly systems that recapitulate intracellular host-catalyzed viral capsid assembly pathways. These compounds inhibit replication of HIV-1 in human T cell lines and PBMCs and are effective against a primary isolate. They reduce virus production, likely by inhibiting a post-translational step in HIV-1 Gag assembly. Notably, the compound colocalizes with HIV-1 Gagin situ; however, unexpectedly, selection experiments failed to identify compound-specific resistance mutations ingagorpol, even though known resistance mutations developed in a parallel nelfinavir selection. Thus, we hypothesized that instead of binding to Gag directly, these compounds might localize to assembly intermediates, the intracellular multiprotein complexes containing Gag and host factors that are formed during immature HIV-1 capsid assembly. Indeed, imaging of infected cells showed colocalization of the compound with two host enzymes found in assembly intermediates, ABCE1 and DDX6. While the exact target and mechanism of action of this chemotype remain to be determined, these findings suggest that these compounds represent first-in-class, host-targeting inhibitors of intracellular events in HIV-1 assembly.

IMPORTANCE

The success of antiretroviral treatment for HIV-1 is at risk of being undermined by the growing problem of drug resistance. Thus, there is a need to identify antiretrovirals that act on viral life cycle stages not targeted by drugs in use, such as the events of HIV-1 Gag assembly. To address this gap, we developed a compound screen that recapitulates the intracellular events of HIV-1 assembly, including viral-host interactions that promote assembly. This effort led to identification of a new chemotype that inhibits HIV-1 replication at nanomolar concentrations by inhibiting virus production. This compound colocalized with Gag and two host enzymes that facilitate capsid assembly but resistance selection did not result in compound-specific mutations ingag,suggesting that the chemotype does not directly target Gag. We hypothesize that this chemotype may represent a first-in-class inhibitor of virus production that acts by targeting a viral-host complex important for HIV-1 Gag assembly.
Mixed method estimation of population level HIV viral suppression rate in the Western Cape, South Africa
Authors: Mukonda Elton , Hsiao Nei-Yuan , Vojnov Lara , Myer Landon , Lesosky Maia
Published: March 2020

Introduction

There are few population-wide data on viral suppression (VS) that can be used to monitor programmatic targets in sub-Saharan Africa. We describe how routinely collected viral load (VL) data from ART programmes can be extrapolated to estimate population VS and validate this using a combination of empiric and model-based estimates.

Methods

VL test results from were matched using a record linkage algorithm to obtain linked results for individuals. Test- and individual-level VS rates were based on test VL values <1000 cps/ml, and individual VL <1000 cps/mL in a calendar year, respectively. We calculated population VS among people living with HIV (PLWH) in the province by combining census-derived mid-year population estimates, HIV prevalence estimates and individual level VS estimates from routine VL data.

Results

Approximately 1.9 million VL test results between 2008 – 2018 were analysed. Among individuals in care, VS increased from 85.5% in 2008 to 90% in 2018. Population VS among all PLWH in the province increased from 12.2% in 2008 to 51.0% in 2017. The estimates derived from this method are comparable to those from other published studies. Sensitivity analyses showed that the results are robust to variations in linkage method, but sensitive to the extreme combinations of assumed ART coverage and population HIV prevalence.

Conclusion

While validation of this method in other settings is required, this approach provides a simple, robust method for estimating population VS using routine data from ART services that can be employed by national programmes in high-burden settings.
Simulating Emergency Department Boarding Using a Difference Equation
Authors: Brown Edward G. , Howard Patricia K. , Moore Daniel
Published: March 2020

Background

This paper aims to provide a model that can be used to simulate the effect of patient presentation counts on ED boarder counts and investigate strategies that might be used for managing ED boarding levels.

Methods

A boarding simulation model is constructed using a random variable and two regressions that are linked together in a difference equation. The simulation is run under varying constraints, including time interval, presentation counts, and boarder count threshold. Bootstrapping is used to run the simulation a large number of times so that mean and medians can be calculated along with confidence intervals.

Results

The method outlined in this paper can be used to simulate the effect of presentation levels on ED boarder counts. Using these methods one can derive quantifiable estimates of time that an emergency department might meet or exceed a particular boarder count threshold.

Conclusions

These simulation methods can help an emergency department understand the dynamics of the system in the status quo of normal operations and quantify the relationship of presentation counts and throughput to the hospital. We are hopeful that others may use these methods, adapting, developing, and testing for their own institutions.
Complement active human and porcine serum induces natural competence for genetic transformation in the emerging zoonotic pathogenStreptococcus suis
Authors: Ferrando Maria Laura , Gussak Alex , Mentink Saskia , van Baarlen Peter , Wells Jerry Mark
Published: March 2020

The acquisition of novel genetic traits by natural competence is a strategy used by bacteria in microbe-rich environments including animal or human hosts where microbial competition, antibiotics and host immune defences threaten their survival. We show here that several virulent strains ofStreptococcus suis, an important porcine pathogen and zoonotic agent, become naturally competent for genetic transformation with plasmid or genomic DNA when cultured in active porcine and human serum, but not when it is pre-heated for 30 minutes at 56°C to inactivate complement. Competence is also not induced in active fetal bovine serum, which contains less complement factors and immunoglobulins than adult serum. Late competence genes, encoding the uptake machinery for environmental DNA, were highly upregulated in active serum. Competence development was independent of the early competence regulatory switch suggesting the presence of an alternative stress-induced pathway for regulation of the transformasome, a type 4-like pilus DNA binding and transport apparatus.
An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 and multiple endemic, epidemic and bat coronavirus
Authors: Sheahan Timothy P. , Sims Amy C. , Zhou Shuntai , Graham Rachel L. , Hill Collin S. , Leist Sarah R. , Schäfer Alexandra , Dinnon Kenneth H. , Montgomery Stephanie A. , Agostini Maria L. , Pruijssers Andrea J. , Chapell James D. , Brown Ariane J. , Bluemling Gregory R. , Natchus Michael G. , Saindane Manohar , Kolykhalov Alexander A. , Painter George , Harcourt Jennifer , Tamin Azaibi , Thornburg Natalie J. , Swanstrom Ronald , Denison Mark R. , Baric Ralph S.
Published: March 2020

Coronaviruses (CoVs) traffic frequently between species resulting in novel disease outbreaks, most recently exemplified by the newly emerged SARS-CoV-2. Herein, we show that the ribonucleoside analog β-D-N4-hydroxycytidine (NHC, EIDD-1931) has broad spectrum antiviral activity against SARS-CoV 2, MERS-CoV, SARS-CoV, and related zoonotic group 2b or 2c Bat-CoVs, as well as increased potency against a coronavirus bearing resistance mutations to another nucleoside analog inhibitor. In mice infected with SARS-CoV or MERS-CoV, both prophylactic and therapeutic administration of EIDD-2801, an orally bioavailable NHC-prodrug (b-D-N4-hydroxycytidine-5’-isopropyl ester), improved pulmonary function, and reduced virus titer and body weight loss. Decreased MERS-CoV yieldsin vitroandin vivowere associated with increased transition mutation frequency in viral but not host cell RNA, supporting a mechanism of lethal mutagenesis. The potency of NHC/EIDD-2801 against multiple coronaviruses, its therapeutic efficacy, and oral bioavailabilityin vivo, all highlight its potential utility as an effective antiviral against SARS-CoV-2 and other future zoonotic coronaviruses.
Size aftereffect is non-local
Authors: Altan Ecem , Boyaci Huseyin
Published: March 2020

It is well known that prolonged exposure to a certain size stimulus alters the perceived size of a subsequently presented stimulus at the same location. How the rest of the visual space is affected by this size adaptation, however, has not been systematically studied before. Here, to fill this gap in literature, we tested size adaptation at the adapter location as well as the rest of the visual space. We used peripherally presented solid discs (Experiment 1) and rings (Experiment 2) as adapter and target (test) stimuli. Observers adapted to a mid-sized stimulus and judged the size of the subsequently presented smaller or larger target stimuli. Results showed that the perceived sizes of target stimuli were repelled away from the adapter size, not only at the adapter location but also at distant locations. These findings demonstrate that size adaptation causes widespread distortion of the visual space and alters perceived size. We discuss possible computational models that may underpin the perceptual effect.
Sparse long-range connections in visual cortex for cost-efficient small-world networks
Authors: Baek Seungdae , Park Youngjin , Paik Se-Bum
Published: March 2020

The brain performs visual object recognition using much shallower hierarchical stages than artificial deep neural networks employ. However, the mechanism underlying this cost-efficient function is elusive. Here, we show that cortical long-range connectivity(LRC) may enable this parsimonious organization of circuits for balancing cost and performance. Using model network simulations based on data in tree shrews, we found that sparse LRCs, when added to local connections, organize a small-world network that dramatically enhances object recognition of shallow feedforward networks. We found that optimization of the ratio between LRCs and local connections maximizes the small-worldness and task performance of the network, by minimizing the total length of wiring needed for integration of the global information. We also found that the effect of LRCs varies by network size, which explains the existence of species-specific LRCs in mammalian visual cortex of various sizes. Our results demonstrate a biological strategy to achieve cost-efficient brain circuits.

Highlights

Long-range connections (LRCs) enhance the object recognition of shallow networks

Sparse LRCs added to dense local connections organize a small-world type network

Small-worldness of networks modulates the balance between performance and wiring cost

Distinct LRCs in various species are due to the size-dependent effect of LRCs

Significance statement

The hierarchical depth of the visual pathway in the brain is constrained by biological factors, whereas artificial deep neural networks consist of super-deep structures (i.e., as deep as computational power allows). Here, we show that long-range horizontal connections (LRCs) observed in mammalian visual cortex may enable shallow biological networks to perform cognitive tasks that require deeper artificial structures, by implementing cost-efficient organization of circuitry. Using model simulations based on anatomical data, we found that sparse LRCs, when added to dense local circuits, organize “small-world” type networks and that this dramatically enhances image classification performance by integrating both local and global components of visual stimulus. Our findings show a biological strategy of brain circuitry to balance sensory performance and wiring cost in the networks.

One sentence summary

Cortical long-range connections organize a small-world type network to achieve cost-efficient functional circuits under biological constraints
PacBio SMRT-based full-length transcriptome data ofAscosphaera apismycelium and spore
Authors: Du Yu , Wang Jie , Chen Huazhi , Fan Xiaoxue , Zhu Zhiwei , Fan Yuanchan , Jiang Haibin , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui
Published: March 2020

Ascosphaera apisis an entomopathogenic fungus that exclusively infects honeybee larvae, resulting in chalkbrood disease, a widespread fungal disease damaging the beekeeping industry all over the world. In this article, purified mycelia (Aam) and spores (Aas) ofA. apispure culture under lab condition were sequenced using PacBio Sequel platform. In total, 13,302,489 and 9,911,345 subreads were yielded from Aam and Aas, respectively; 394,142 and 274,928 circular consensus sequence (CCS) reads were identified as being full-length non-chimeric (FLNC) reads, with a mean length of 2820 bp and 2602 bp, respectively. Furthermore, 174,095 and 103,845 corrected isoforms were identified, with a N50 length of 3543 bp and 3262 bp, respectively. The reported full-length transcriptome data ofA. apismycelium and spore will provide a valuable resource for improvement of genome and transcriptome annotations as well as better understanding of transcript structure such as alternative splicing and polyadenylation.

Value of the data

Current dataset offers a set of high-quality full-length transcripts ofA. apis.

The data can facilitate the improvement ofA. apisgenome and transcriptome annotations.

This dataset benefits further exploration of alternative splicing and polyadenylation ofA. apismRNAs.
The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice
Authors: Shchuka Virlana M. , Abatti Luis E. , Hou Huayun , Dorogin Anna , Wilson Michael D. , Shynlova Oksana , Mitchell Jennifer A.
Published: March 2020

During gestation, uterine smooth muscle cells transition from a state of quiescence to one of contractility, but the molecular mechanisms underlying this transition at a genomic level are not well-known. To better understand these events, we evaluated the epigenetic landscape of the mouse myometrium during pregnancy, labor and post-partum. We established gestational timepoint-specific enrichment profiles involving histone H3K27 acetylation (H3K27ac), H3K4 tri-methylation (H3K4me3), and RNA polymerase II (RNAPII) occupancy by chromatin immunoprecipitation sequencing (ChIP-seq), as well as gene expression profiles by total RNA-sequencing (RNA-seq). Our findings reveal that 533 genes, including known contractility-driving genes (Gja1, Fos, Oxtr, Ptgs2), are upregulated during active labor due to an increase in transcription at gene bodies. Their promoters and putative intergenic enhancers, however, are epigenetically activated by H3K27ac as early as day 15, four days prior to the onset of active labor on day 19. In fact, we find that the majority of genome-wide H3K27ac or H3K4me3 peaks identified during active labor are present in the myometrium on day 15. Despite the early presence of H3K27ac at labor-associated genes, both an increase in non-coding enhancer RNA (eRNA) production, and in recruitment of RNAPII to corresponding genes occur during active labor, at labor upregulated gene loci. Our findings indicate that epigenetic activation of the myometrial genome precedes active labor by at least four days in the mouse model, suggesting the myometrium is poised for rapid activation of contraction-associated genes in order to exit the state of quiescence.
A Sec14-like Phosphatidylinositol Transfer Protein Paralog Defines a Novel Class of Heme-binding Proteins With An Unusual Heme Coordination Mechanism
Authors: Khan Danish , Lee Dongju , Gulten Gulcin , Aggarwal Anup , Wofford Joshua , Krieger Inna , Tripathi Ashutosh , Patrick John W. , Eckert Debra M. , Laganowsky Arthur , Sacchettini James , Lindahl Paul , Bankaitis Vytas A.
Published: March 2020

Yeast Sfh5 is an unusual member of the Sec14-like phosphatidylinositol transfer protein (PITP) family. Whereas PITPs are defined by their abilities to transfer phosphatidylinositol between membranes in vitro, and to stimulate phosphoinositide signaling in vivo, Sfh5 does not exhibit these activities. Rather, Sfh5 is a redox-active penta-coordinate high spin FeIIIheme-binding protein with an unusual heme-binding arrangement that involves a co-axial tyrosine/histidine coordination strategy and a complex electronic structure connecting the open shell irond-orbitals with three aromatic ring systems. That Sfh5 is not a PITP is supported by demonstrations that heme is not a readily exchangeable ligand, and that phosphatidylinositol-exchange activity is resuscitated in heme binding-deficient Sfh5 mutants. The collective data identify Sfh5 as the prototype of a new class of fungal hemoproteins, and emphasize the versatility of the Sec14-fold as scaffold for translating the binding of chemically distinct ligands to the control of diverse sets of cellular activities.
Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD
Authors: Zhang G. , Pomplun S. , Loftis A. R. , Tan X. , Loas A. , Pentelute B. L.
Published: March 2020

Coronavirus disease 19 (COVID-19) is an emerging global health crisis. With over 7 million confirmed cases to date, this pandemic continues to expand, spurring research to discover vaccines and therapies. SARS-CoV-2 is the novel coronavirus responsible for this disease. It initiates entry into human cells by binding to angiotensin-converting enzyme 2 (ACE2) via the receptor binding domain (RBD) of its spike protein (S). Disrupting the SARS-CoV-2-RBD binding to ACE2 with designer drugs has the potential to inhibit the virus from entering human cells, presenting a new modality for therapeutic intervention. Peptide-based binders are an attractive solution to inhibit the RBD-ACE2 interaction by adequately covering the extended protein contact interface. Using molecular dynamics simulations based on the recently solved cryo-EM structure of ACE2 in complex with SARS-CoV-2-RBD, we observed that the ACE2 peptidase domain (PD) α1 helix is important for binding SARS-CoV-2-RBD. Using automated fast-flow peptide synthesis, we chemically synthesized a 23-mer peptide fragment of the ACE2 PD α1 helix (SBP1) composed entirely of proteinogenic amino acids. Chemical synthesis of SBP1 was complete in 1.5 hours, and after work up and isolation >20 milligrams of pure material was obtained. Bio-layer interferometry (BLI) revealed that SBP1 associates with micromolar affinity to insect-derived SARS-CoV-2-RBD protein obtained from Sino Biological. Association of SBP1 was not observed to an appreciable extent to HEK cell-expressed SARS-CoV-2-RBD proteins and insect-derived variants acquired from other vendors. Moreover, competitive BLI assays showed SBP1 does not outcompete ACE2 binding to Sino Biological insect-derived SARS-CoV-2-RBD. Further investigations are ongoing to gain insight into the molecular and structural determinants of the variable binding behavior to different SARS-CoV-2-RBD protein variants.
Ammonia-based enrichment and long-term propagation of zone I hepatocyte-like cells
Authors: Tsuneishi Ruri , Saku Noriaki , Miyata Shoko , Javaregowda Palaksha Kanive , Ite Kenta , Toyoda Masashi , Kimura Tohru , Kuroda Masahiko , Nakazawa Atsuko , Kasahara Mureo , Nonaka Hidenori , Kamiya Akihide , Kiyono Tohru , Yamauchi Junji , Umezawa Akihiro
Published: March 2020

Zone I and zone III hepatocytes metabolize ammonia through urea cycle and drug by cytochrome P450, respectively. Ammonia has a cytotoxic effect, and can therefore be used as a selection agent for enrichment of hepatocytes. Besides, isolated hepatocytes from livers can be propagated ex vivo under appropriate condition. However, it has not been investigated so far whether ammonia-treated hepatocyte-like cells are able to proliferate in vitro. In this study, we employed the ammonia selection strategy to purify hepatocyte-like cells that were differentiated from human pluripotent stem cells (PSCs) that are embryonic stem cells (ESCs) and induced pluripotent stem cells. Hepatocyte-like cells after exposure to ammonia highly expressed the CPS1 gene that metabolizes ammonia to carbamoyl phosphate. The resistance to cytotoxicity or cell death by ammonia is probably attributed to the metabolic activity of ammonia in the cells. In addition to the ammonia metabolism-related genes, ammonia-selected PSC-derived hepatocytes increased expression of the CYP3A4 gene, one of the cytochrome P450 genes, that is mainly expressed in zone III hepatocytes. Ammonia-selected hepatocyte-like cells derived from both ESCs and iPSCs can be propagated in vitro up to 30 population doublings for more than 190 days without affecting expression of the liver-associated genes, implying that the ammonia-selected cells have immortality or equivalent life span on the appropriate feeder cells like ESCs and iPSCs. The long-term cultivation of ammonia-selected hepatocyte-like cells resulted in the increased expression of hepatocyte-associated genes such as the CPS1 and CYP3A4 genes. The ammonia selection method to enrich a hepatocyte population was also applicable to immortalized cells from the liver. Ammonia treatment in combination with in vitro propagation will be used to obtain large amounts of hepatocytes or hepatocyte-like cells for pharmacology, toxicology and regenerative medicine.