bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproducibility of Retinal Nerve Fiber Layer and Macular Ganglion Cell Layer Thickness Measurements by Optical Coherence Tomography in Myopic Eyes
Authors: Park Sang Min , Lee Kwan Bok , Kim Kyoung Nam , Hwang Young Hoon
Published: July 2021

Precis:

In myopic eyes, reproducibility of circumpapillary retinal nerve fiber layer (RNFL) and macular ganglion cell-inner plexiform layer thickness measurement by optical coherence tomography (OCT) showed excellent reproducibility except for the temporal quadrant RNFL thickness measurement.

Purpose:

The aim of this study was to evaluate the long-term reproducibility of circumpapillary RNFL and macular ganglion cell-inner plexiform layer (GCIPL) thickness measurements using OCT in myopic eyes.

Methods:

Sixty-five eyes with moderate-to-high myopia (spherical equivalent <−3.0 D, myopia group) and 53 eyes with low-to-no myopia (spherical equivalent ≥−3.0 D, control group) without ocular disorders, such as glaucoma or retinal diseases, were included. Three serial OCT scans recorded at 1-year intervals were analyzed. Reproducibility was evaluated using within-subject SD (Sw), coefficient of variation (CVw), and intraclass correlation coefficient (ICC).

Results:

Mean±SD refractive error was −0.30±0.80 and −6.26±2.45 D for control and myopia groups, respectively. The myopia group had thinner superior, inferior, and nasal quadrant RNFL, thicker temporal quadrant RNFL, and thinner GCIPL than the control group (P<0.05), except for the minimum and superotemporal GCIPL thicknesses (P>0.05). The myopia group had lower reproducibility in temporal quadrant RNFL thickness (Sw, 2.57 μm; CVw 3.27%; ICC, 0.979) than the control group (Sw, 1.80 μm; CVw 2.59%; ICC, 0.989), whereas in other sectors of RNFL and all GCIPL parameters, comparable reproducibility was observed between the 2 groups.

Conclusions:

Long-term reproducibility of RNFL and GCIPL thickness measurements in moderate-to-high myopia was comparable to that of low-to-no myopia, except RNFL thickness in the temporal quadrant. These findings should be considered when detecting RNFL and GCIPL changes.
Ocular, Orbital, and Adnexal Toxicity With High-dose Volumetric Modulated Arc Radiation Therapy for Orbital Malignancies
Authors: Garcia Giancarlo A. , Charlson Emily S. , Kolseth Clinton , Kim Namju , Kossler Andrea L.
Published: July 2021

Purpose:

Conventional modalities of external-beam radiation therapy (EBRT) are associated with high incidences of severe vision-threatening ocular and orbital toxicities when used to treat orbital malignancies. We investigate toxicities associated with high-dose volumetric modulated arc therapy (VMAT), a commonly used contemporary treatment modality for these tumors.

Methods:

Retrospective analysis of malignant orbital tumors managed with adjuvant high-dose VMAT preceded by globe-salvaging surgical therapy (GST) or exenteration. Dosimetric quantitation of target volumes and critical structures was performed. Incidence and severity of ocular, orbital, and adnexal toxicities were evaluated and assessed with regard to conventional EBRT toxicities for orbital malignancies described in the literature.

Results:

Eighty-four subjects (mean age = 65.9 ± 9.7 years) were included (N = 48 and N = 36 in GST and exenteration subgroups, respectively). Mean dose was 64.8 ± 2.1 Gy to the planning target volume. Dosing to critical structures typically did not surpass known tissue tolerance limits. Median follow up was 18.3 months. Visual acuity in the GST subgroup was not significantly different after VMAT (0.25 ± 0.06) compared with baseline (0.23 ± 0.02; P = 0.302). Whereas severe toxicities reported by major systematic analyses in the literature with older EBRT modalities were relatively common—for example, retinopathy (16–40%), optic neuropathy (16%), and corneal perforation (13%)—toxicities with VMAT were typically mild and less common. The most common toxicities with VMAT were mild dry eye (81.3%; 39/48), cataract (21.1%; 8/38 phakic eyes), and periocular dermatitis (15.5%; 13/84). Vision-threatening toxicities, including severe corneal pathologies, retinopathy, or optic neuropathy, were rare. There were no contralateral ocular or adnexal toxicities.

Conclusions:

High-dose VMAT for orbital malignancies demonstrated low incidence and severity of eye-related toxicity, in contradistinction to adverse events reported from conventional forms of radiotherapy.
Metastatic Uterine Carcinosarcoma to the Orbit
Authors: Qureshi Sana , Patel Nimesh A. , Patel Nish , Ghassibi Mark P. , Tse David T. , Dubovy Sander R.
Published: July 2021

Metastases of solid tumors to the eye and ocular adnexa are rare. Herein, the authors describe the clinical, histologic, and immunohistochemical findings of a patient with a history of adenocarcinoma of the colon and a uterine carcinosarcoma (malignant mixed Müllerian tumor) who presented with proptosis and decreased vision. Positive staining with PAX-8, p16 and negative reaction for CK20 and CDX2 helped to establish the uterine origin of the metastasis. This rare case demonstrates the utility of immunohistochemical probes, especially in patients with a complex oncological history, where multiple primary sources of the metastasis are in the differential diagnosis.
Association Analysis of Candidate Gene Polymorphisms and Tinnitus in Young Musicians
Authors: Bhatt Ishan Sunilkumar , Dias Raquel , Torkamani Ali
Published: July 2021

Introduction:

Subjective tinnitus, a perception of phantom sound, is a common otological condition that affects almost 15% of the general population. It is known that noise-induced hearing loss (NIHL) and tinnitus exhibit a high level of comorbidity in individuals exposed to intense noise and music. However, the influence of genetic variants associated with NIHL on tinnitus remains elusive. We hypothesized that young musicians carrying genetic variants associated with NIHL would exhibit a higher prevalence of tinnitus than their counterparts.

Methods:

To test this hypothesis, we analyzed the database by Bhatt et al. (2020) (originally developed by Phillips et al., 2015) that investigated the genetic links to NIHL in young college-aged musicians. The present study identified 186 participants (average age = 20.3 yrs, range = 18–25 yrs) with normal tympanometry and otoscopic findings and with no missing data. We included 19 single nucleotide polymorphisms in 13 cochlear genes that were previously associated with NIHL. The candidate genes include: KCNE1, KCNQ1, CDH23, GJB2, GJB4, KCNJ10, CAT, HSP70, PCDH70, MYH14, GRM7, PON2, and ESRRB.

Results:

We find that individuals with at least one minor allele of rs163171 (C > T) in KCNQ1 exhibit significantly higher odds of reporting tinnitus compared to individuals carrying the major allele of rs163171. KCNE1 rs2070358 revealed a suggestive association (p = 0.049) with tinnitus, but the FDR corrected p-value did not achieve statistical significance (p < 0.05). A history of ear infection and sound level tolerance showed a statistically significant association with tinnitus. Music exposure showed a suggestive association trend with tinnitus. Biological sex revealed a statistically significant association with distortion product otoacoustic emissions SNR measures.

Conclusions:

We concluded that KCNQ1/KCNE1 voltage-gated potassium ion channel plays a critical role in the pathogenesis of NIHL and tinnitus. Further research is required to construct clinical tools for identifying genetically predisposed individuals well before they acquire NIHL and tinnitus.
Assessment of volumetric parameters derived from 68Ga-PSMA PET/CT in prostate cancer patients with biochemical recurrence: an institutional experience
Authors: Okudan Berna , Coşkun Nazim , Seven Bedri , Atalay Merve Ağcioğlu , Yildirim Aslihan , Görtan Fatma Arzu
Published: July 2021

Objective

The aim of this study was to evaluate the relationship between volumetric parameters calculated using semiautomatic quantification of lesions detected in 68Ga-labeled prostate-specific membrane antigen PET-computed tomography (68Ga-PSMA PET/CT) and clinical characteristics in prostate cancer (PCa) patients with biochemical recurrence.

Methods

A total of 85 consecutive PCa patients with biochemical recurrence who underwent 68Ga-PSMA PET/CT at our institution from January 2019 to March 2020 were retrospectively assessed. 68Ga-PSMA PET/CT-derived volumetric parameters, including whole-body PSMA tumor volume (wbPSMA-TV) and whole-body total lesion PSMA (wbTL-PSMA), as well as the established maximum and mean standardized uptake value (SUVmax and SUVmean), were calculated for each patient. All PET-derived parameters were analyzed for correlation with prostate-specific antigen (PSA) levels and for association with Gleason scores.

Results

Eighty-five patients with a mean age of 68.9 ± 7.8 years (range, 47–83 years) and a mean PSA level of 40.9 ± 92.1 ng/ml (range, 0.2–533.2 ng/ml) were analyzed. Volumetric parameters, that is, wbPSMA-TV and wbTL-PSMA, demonstrated a statistically significant correlation with PSA levels (r = 0.403 and r = 0.556, respectively, all at P < 0.001) and only the means of wbTL-PSMA were significantly different between the Gleason score groups (P < 0.05).

Conclusions

The results of our study indicate that 68Ga-PSMA PET/CT might be a valuable tool for the detection and follow-up of recurrence in PCa patients. 68Ga-PSMA PET/CT-derived quantitative volumetric parameters demonstrated a highly significant correlation with changes in PSA levels. Larger prospective studies are needed to help reveal the full potential of parameters such as PSMA-TV and TL-PSMA derived from PET imaging with 68Ga-PSMA.
Preoperative 18F-FDG SUVmax >6.3 or Size >2.3 cm of primary lesions predict lymph nodes metastasis with higher negative predictive value in peripheral cT1 non-small-cell lung cancer
Authors: Li Xiao-Feng , Shi Yun-Mei , Niu Rong , Yang Yan-Song , Shao Xiao-Nan , Wang Jian-Feng , Shao Xiao-Liang , Zhang Fei-Fei , Xue Xiu-Qing , Wang Yue-Tao
Published: July 2021

Background

Sublobar resection is suitable for peripheral cT1N0M0 non-small-cell lung cancer (NSCLC). The traditional PET-CT criterion (lymph node size ≥1.0 cm or SUVmax ≥2.5) for predicting lymph nodes metastasis (LNM) has unsatisfactory performance.

Objective

We explore the clinical role of preoperative SUVmax and the size of the primary lesions for predicting peripheral cT1 NSCLC LNM.

Methods

We retrospectively analyzed 174 peripheral cT1 NSCLC patients underwent preoperative 18F-FDG PET-CT and divided into the LNM and non-LNM group by pathology. We compared the differences of primary lesions’ baseline characteristics between the two groups. The risk factors of LNM were determined by univariate and multivariate analysis, and we assessed the diagnostic efficacy with the area under the receiver operating characteristic curve (AUC), sensitivity, specificity, positive predictive value and negative predictive value (NPV).

Results

Of the enrolled cases, the incidence of LNM was 24.7%. The preoperative SUVmax >6.3 or size >2.3 cm of the primary lesions were independent risk factors of peripheral cT1 NSCLC LNM (ORs, 95% CIs were 6.18 (2.40–15.92) and 3.03 (1.35–6.81). The sensitivity, NPV of SUVmax >6.3 or size >2.3 cm of the primary lesions were higher than the traditional PET-CT criterion for predicting LNM (100.0 vs. 86.0%, 100.0 vs. 89.7%). A Hosmer–Lemeshow test showed a goodness-of-fit (P = 0.479).

Conclusions

The excellent sensitivity and NPV of preoperative of the SUVmax >6.3 or size >2.3 cm of the primary lesions based on 18F-FDG PET-CT might identify the patients at low-risk LNM in peripheral cT1 NSCLC.
Through Their Eyes
Authors: Moore Riley , Hayward Alexandra , Necaise Kellee
Published: July 2021

Background:

Personal protective equipment (PPE) plays a critical role in protecting health care workers (HCWs). During the coronavirus disease-2019 (COVID-19) pandemic, shortages of PPE supplies drastically changed the way PPE was obtained and used by HCWs.

Purpose:

The objective was to investigate the impact of the COVID-19 pandemic and patient isolation type on PPE compliance.

Methods:

This investigation was a survey of HCWs at a level 1 trauma teaching hospital regarding PPE compliance patterns prior to and during the COVID-19 pandemic.

Results:

HCWs reported an increase in PPE compliance during the COVID-19 pandemic. Nearly half (48.6%) of respondents reported that isolation type impacted the decision to wear PPE, of which most were likely to forgo PPE with contact precautions.

Conclusions:

HCWs identified multiple barriers to compliance. The underutilization of PPE with contact precautions suggests that the risk of exposure is interpreted as low, and this could be a future target of education.
Parental Perspectives on Children's Functional Experiences After Limb Fracture
Authors: Golden-Plotnik Stevi , Ali Samina , Moir Mackenzie , Drendel Amy L. , Poonai Naveen , van Manen Michael
Published: July 2021

Background

Fractures are a common childhood injury. Although the pain associated with fractures is well described, the related functional impact is less understood. When a child's function is impaired, his or her ability to participate in day-to-day life is restricted. Eighty percent of children with fractures experience compromise in daily function. An in-depth understanding of function can guide emergency department (ED) providers' discharge instructions.

Objectives

Our aim was to report caregivers' perspectives of the functional impact of limb fractures on their children's day-to-day life activities.

Methods

We performed a qualitative study using interviews of caregivers of children (aged 5 to 11 years) who received care for acute, nonoperative long bone fractures in a pediatric ED. Audio-recorded, semistructured telephone interviews were completed 7 to 14 days after the ED visit. Interviews were primarily open ended, including questions targeting areas of function from existing pediatric fracture literature. Qualitative analysis was completed using content analysis.

Results

Twenty-five interviews were included in the final analysis. Most of the children were diagnosed with upper extremity fractures, and most participants were mothers. All parents reported a change in their child's function. The most commonly affected areas were sleep, activities of daily living, and play. Play was either self-limited by the child or restricted by the parent. Pain was worse in the first days after discharge. Many children struggled emotionally with functional limitations. All children required help from their parents to perform daily tasks; this required adaptive strategies such as planning, changes to household routine, and missed work. Key concerns from parents included regression in the child's independence and fracture healing and complications.

Conclusions

Function is universally impaired in young children with fractures, significantly affecting family life after discharge. Discharge conversations with families should include pain management, changes to activities of daily living, family routines and play, and expectations for fracture healing.
Clinicopathologic and Prognostic Significance of CD47 Expression and Tumor-associated Macrophages in Endometrial Carcinoma
Authors: Sercan Çiğdem , Haberal Reyhan Asuman N. , Özen Özlem , Ayhan Ali
Published: July 2021

Tumor-associated macrophages (TAMs) influence cancer progression. CD47 is an antiphagocytic molecule aiding tumor resistance against host immune surveillance. The relationship between CD47 expression and TAM-related microenvironment in endometrial carcinoma (EC) is poorly understood. The expression and prognostic significance of CD47 and CD163-labeled TAMs in 165 EC cases was assessed with CD47 and CD163 immunohistochemical studies. CD47 expression was found in 156/165 (94.6%) cases. CD47 expression was significantly higher in nonendometrioid carcinomas. CD47 overexpression was associated with histologic grade. High epithelial and stromal TAMs counts were also associated with high tumoral CD47 expression. High epithelial, stromal, and margin TAMs counts were associated with higher histologic grade and lymphovascular invasion. Epithelial TAMs counts were higher in patients with nonendometrioid carcinomas (P=0.0001) and cases with recurrence (P=0.018). High stromal TAMs counts were associated with deeper myometrial invasion (P=0.017) and the presence of distant metastasis (P=0.024). The counts of margin TAMs was significantly correlated with the depth of myometrial invasion, lymphovascular invasion, FIGO stage, lymph node metastases, distant metastasis, and recurrence (P=0.0001, 0.0001, 0.004, 0.005, 0.014, and 0.04, respectively). CD47 expression was not associated with overall survival (OS) and progression-free survival. However, high epithelial and stromal TAM counts were associated with shorter OS. Besides, high epithelial and margin TAM counts were associated with shorter progression-free survival. Furthermore, increased stromal and margin TAM counts were determined to be an independent prognostic marker of reduced OS. TAM count is, therefore, a significant prognostic factor in EC and the CD47 assessment has potential benefit for future clinical use.
SARS-CoV-2 screening: effectiveness and risk of increasing transmission
Authors: Skittrall Jordan P.
Published: July 2021

Testing asymptomatic people for SARS-CoV-2 aims to reduce COVID-19 transmission. Screening programmes’ effectiveness depends upon testing strategy, sample handling logistics, test sensitivity and individual behaviour, in addition to dynamics of viral transmission. The interaction between these factors is not fully characterized. We investigated the interaction between these factors to determine how to optimize reduction of transmission. We estimate that under idealistic assumptions 70% of transmission may be averted, but under realistic assumptions only 7% may be averted. We show that programmes that overwhelm laboratory capacity or reduce isolation of those with minor symptoms have increased transmission compared with those that do not: programmes need to be designed to avoid these issues, or they will be ineffective or even counter-productive. Our model allows optimal selection of whom to test, quantifies the balance between accuracy and timeliness, and quantifies potential impacts of behavioural interventions. We anticipate our model can be used to understand optimal screening strategies for other infectious diseases with substantially different dynamics.
A new sensitive and robust next-generation sequencing platform for HIV-1 drug resistance mutations testing
Authors: Yu Bin , Jin Changzhong , Ma Zixuan , Cai Ziwei , Li Tingsen , Wang Dan , Xiao Wenwen , Zheng Yanghao , Yin Wanpeng , Wu Nanping , Jiang Miao
Published: July 2021

Next-generation sequencing (NGS) is a trending new platform which allows cheap, quantitative, high-throughput, parallel sequencing for minority variants with frequencies less than 20% of the HIV-1 quasi-species. In clinical setting, these advantages are crucial for choosing antiretroviral drugs with low genetic barriers and will potentially benefit treatment outcomes.

In this investigation, we implemented the Boxin HIV-1 NGS platform for genotyping the drug-resistance-associated variants in PR/RT regions. Plasmids with known mutations were used to analyze the accuracy, reproducibility, and reliability of the Boxin NGS assay. Variant frequencies reported by Boxin NGS and the theoretical value were highly concordant. The Bland-Altman plot and the coefficient of variation (7%) suggested that the method has excellent reproducibility and reliability. Sanger sequencing confirmed the existence of these known variants with frequencies equal or above 20%.

78 blood samples were obtained from AIDS patients and underwent PR/RT region genotyping by Sanger sequencing and Boxin NGS. 33 additional drug resistance mutations were identified by Boxin NGS, 23/33 mutations were minority variants with frequencies below 20%.

15 blood samples obtained from AIDS patients underwent PR/RT region genotyping by Sanger sequencing, Boxin NGS, and Vela NGS. The Bland-Altman plot suggested that the variant frequencies detected by Boxin and Vela were highly concordant. Moreover, Boxin NGS assay detected five more minority variants with frequencies ranged from 1% to 20%. In a series of samples collected from 2016 to 2017, Boxin NGS reported a M184V mutation with a frequency of 4.92%, 3 months earlier than this mutation was firstly detected by Vela NGS and Sanger sequencing.

In conclusion, Boxin NGS had good accuracy, reproducibility, and reliability. Boxin NGS was highly concordant with Sanger sequencing and Vela NGS. In terms of genotyping HIV-1 variants in PR/RT regions, Boxin NGS was more cost-efficient and appeared to have increased sensitivity without compromising sequence accuracy.
Association between the COVID-19 pandemic and pertussis in France using multiple nationwide data sources
Authors: Matczak Soraya , Levy Corinne , Fortas Camille , Cohen Jérémie F. , Béchet Stéphane , El Belghiti Fatima Aït , Guillot Sophie , Trombert-Paolantoni Sabine , Jacomo Véronique , Savitch Yann , Paireau Juliette , Brisse Sylvain , Guiso Nicole , Lévy-Bruhl Daniel , Cohen Robert , Toubiana Julie
Published: July 2021

Background

Interventions to mitigate coronavirus disease 19 (COVID-19) pandemic may impact other respiratory diseases such as pertussis. We aimed to study the course of pertussis in France over an 8-year period and its association with COVID-19 mitigation strategies, using multiple nationwide data sources.

Methods

We analyzed the number of French pertussis cases between 2013 and 2020, using the PCR test results from nationwide outpatient laboratories (Source 1) and the pediatric network of 41 hospitals (Source 2), and using the reports of an office-based pediatric national network (Source 3). We conducted a quasi-experimental interrupted time-series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles, and secular trend, and included a binary variable for the first national lockdown (ordered on March 16, 2021).

Results

We identified 19,039 cases of pertussis from the three data sources during the study period. There was a significant decrease of pertussis cases following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.102 (95% CI 0.040-0.256) and 0.216 (95% CI 0.071-0.656) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 (median of 1 [IQR 0-2] vs. 0 [IQR 0-0] pertussis cases per month before and after lockdown, respectively, p=0.0048).

Conclusion

The drastic reduction of outpatient and hospitalized cases of pertussis strongly suggests an impact of COVID-19 mitigation measures and their consequences on pertussis epidemiology. Pertussis vaccination recommendations should be carefully followed, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.

Funding

There was no specific funding for the study.
High frequency, high throughput quantification of SARS-CoV-2 RNA in wastewater settled solids at eight publicly owned treatment works in Northern California shows strong association with COVID-19 incidence
Authors: Wolfe Marlene K. , Topol Aaron , Knudson Alisha , Simpson Adrian , White Bradley , Vugia Duc J. , Yu Alexander T. , Li Linlin , Balliet Michael , Stoddard Pamela , Han George S. , Wigginton Krista R. , Boehm Alexandria B.
Published: July 2021

A number of recent retrospective studies have demonstrated that SARS-CoV-2 RNA concentrations in wastewater are associated with COVID-19 cases in the corresponding sewersheds. Implementing high-resolution, prospective efforts across multiple plants depends on sensitive measurements that are representative of COVID-19 cases, scalable for high throughput analysis, and comparable across laboratories. We conducted a prospective study across eight publicly owned treatment works (POTWs). A focus on SARS-CoV-2 RNA in solids enabled us to scale-up our measurements with a commercial lab partner. Samples were collected daily and results were posted to a website within 24-hours. SARS-CoV-2 RNA in daily samples correlated to incidence COVID-19 cases in the sewersheds; a 1 log10 increase in SARS-CoV-2 RNA in settled solids corresponds to a 0.58 log10 (4X) increase in sewershed incidence rate. SARS-CoV-2 RNA signals measured with the commercial laboratory partner were comparable across plants and to measurements conducted in a university laboratory when normalized by pepper mild mottle virus PMMoV RNA. Results suggest that SARS-CoV-2 RNA should be detectable in settled solids for COVID-19 incidence rates > 1/100,000 (range 0.8 - 2.3 cases per 100,000). These sensitive, representative, scalable, and comparable methods will be valuable for future efforts to scale-up wastewater-based epidemiology.

Importance

Access to reliable, rapid monitoring data is critical to guide response to an infectious disease outbreak. For pathogens that are shed in feces or urine, monitoring wastewater can provide a cost-effective snapshot of transmission in an entire community via a single sample. In order for a method to be useful for ongoing COVID-19 monitoring, it should be sensitive for detection of low concentrations of SARS-CoV-2, representative of incidence rates in the community, scalable to generate data quickly, and comparable across laboratories. This paper presents a method utilizing wastewater solids to meet these goals, producing measurements of SARS-CoV-2 RNA strongly associated with COVID-19 cases in the sewershed of a publicly owned treatment work. Results, provided within 24 hrs, can be used to detect incidence rates as low as approximately 1/100,000 cases and can be normalized for comparison across locations generating data using different methods.
One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects nonhuman primates from SARS-CoV-2
Authors: Tioni Mariana F. , Jordan Robert , Pena Angie Silva , Garg Aditya , Wu Danlu , Phan Shannon I. , Cheng Xing , Greenhouse Jack , Orekov Tatyana , Valentin Daniel , Kar Swagata , Pessaint Laurent , Andersen Hanne , Stobart Christopher C. , Bloodworth Melissa H. , Peebles R. Stokes , Liu Yang , Xie Xuping , Shi Pei-Yong , Moore Martin L. , Tang Roderick S.
Published: July 2021

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 is an enveloped RNA virus that relies on its trimeric surface glycoprotein, spike, for entry into host cells. Here we describe the COVID-19 vaccine candidate MV-014-212, a live attenuated, recombinant human respiratory syncytial virus (RSV) expressing a chimeric SARS-CoV-2 spike as the only viral envelope protein. MV-014-212 was attenuated and immunogenic in African green monkeys (AGMs). One mucosal administration of MV-014-212 in AGMs protected against SARS-CoV-2 challenge, reducing by more than 200- fold the peak shedding of SARS-CoV-2 in the nose. MV-014-212 elicited mucosal immunity in the nose and neutralizing antibodies in serum that exhibited cross-neutralization against two virus variants of concern. Intranasally delivered, live attenuated vaccines such as MV-014-212 entail low-cost manufacturing suitable for global deployment. MV-014-212 is currently in phase 1 clinical trials as a single-dose intranasal COVID-19 vaccine.
Key substitutions in the spike protein of SARS-CoV-2 variants can predict resistance to monoclonal antibodies, but other substitutions can modify the effects
Authors: Lusvarghi Sabrina , Wang Wei , Herrup Rachel , Neerukonda Sabari Nath , Vassell Russell , Bentley Lisa , Eakin Ann E. , Erlandson Karl J. , Weiss Carol D.
Published: July 2021

Mutations in the spike protein of SARS-CoV-2 variants can compromise the effectiveness of therapeutic antibodies. Most clinical-stage therapeutic antibodies target the spike receptor binding domain (RBD), but variants often have multiple mutations in several spike regions. To help predict antibody potency against emerging variants, we evaluated 25 clinical-stage therapeutic antibodies for neutralization activity against 60 pseudoviruses bearing spikes with single or multiple substitutions in several spike domains, including the full set of substitutions in B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.429 (Epsilon), B.1.526 (Iota), A.23.1 and R.1 variants. We found that 14 of 15 single antibodies were vulnerable to at least one RBD substitution, but most combination and polyclonal therapeutic antibodies remained potent. Key substitutions in variants with multiple spike substitutions predicted resistance, but the degree of resistance could be modified in unpredictable ways by other spike substitutions that may reside outside of the RBD. These findings highlight the importance of assessing antibody potency in the context of all substitutions in a variant and show that epistatic interactions in spike can modify virus susceptibility to therapeutic antibodies.

Importance

Therapeutic antibodies are effective in preventing severe disease from SARS-CoV-2 infection (COVID-19), but their effectiveness may be reduced by virus variants with mutations affecting the spike protein. To help predict resistance to therapeutic antibodies in emerging variants, we profiled resistance patterns of 25 antibody products in late stages of clinical development against a large panel of variants that include single and multiple substitutions found in the spike protein. We found that the presence of a key substitution in variants with multiple spike substitutions can predict resistance against a variant, but that other substitutions can affect the degree of resistance in unpredictable ways. These finding highlight complex interactions among substitutions in the spike protein affecting virus neutralization and potentially virus entry into cells.
Pathotyping of Newcastle disease virus: A novel single BsaHI digestion method of detection and differentiation of avirulent strains (lentogenic and mesogenic vaccine strains) from virulent virus
Authors: Desingu Perumal Arumugam , Singh Shambhu Dayal , Dhama Kuldeep , Vinodhkumar Obli Rajendran , Nagarajan K. , Singh Rajendra , Malik Yashpal Singh , Singh Raj Kumar
Published: July 2021

We provide a novel single restriction enzyme (RE) (BsaHI) digestion approach for detecting distinct pathotypes of the Newcastle disease virus (NDV). After scanning 4000 F gene nucleotide sequences in the NCBI database, a single RE (BsaHI) digesting site was discovered in the cleavage site. APMV-I “F gene” Class II specific primer-based reverse transcriptase PCR (RT-PCR) was utilized to amplify a 535 bp fragment, which was then digested with a single RE (BsaHI) for pathotyping avian NDV field isolates and pigeon paramyxovirus-1 isolates. The avirulent (lentogenic and mesogenic strains) produce 189 and 346 bp fragments, respectively, but the result in velogenic strains remains undigested with 535 bp fragments. In addition, 45 field NDV isolates and 8 vaccine strains were used to confirm the approach. The sequence-based analysis also agrees with the data obtained utilizing the single RE (BsaHI) digestion approach. The proposed technique had the potential to distinguish between avirulent and virulent strains in a short space of time, making it valuable in NDV surveillance and monitoring research.
Integrated Genomic Analyses Identify High-Risk Factors and Actionable Targets in T-Cell Acute Lymphoblastic Leukemia
Authors: Zhu Haichuan , Dong Bingjie , Zhang Yingchi , Wang Mei , Rao Jianan , Cui Bowen , Liu Yu , Jiang Qian , Wang Weitao , Yang Lu , Yu Anqi , Li Zongru , Liu Chao , Zhang Leping , Huang Xiaojun , Zhu Xiaofan , Wu Hong
Published: July 2021

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy often associated with poor outcomes. To identify high-risk factors and potential actionable targets for T-ALL, we perform integrated genomic and transcriptomic analyses on samples from 165 Chinese pediatric and adult T-ALL patients, of whom 85% have outcome information. The genomic mutation landscape of this Chinese cohort is very similar to the Western cohort published previously, except that the rate of NOTCH1 mutations is significant lower in the Chinese T-ALL patients. Among 47 recurrently mutated genes in 7 functional categories, we identify RAS pathway and PTEN mutations as poor survival factors for non-TAL and TAL subtypes, respectively. Mutations in the PI3K pathway are mutually exclusive with mutations in the RAS and NOTCH1 pathways as well as transcription factors. Further analysis demonstrates that approximately 43% of the high-risk patients harbor at least one potential actionable alteration identified in this study, and T-ALLs with RAS pathway mutations are hypersensitive to MEKi in vitro and in vivo. Thus, our integrated genomic analyses not only systematically identify high-risk factors but suggest that these high-risk factors are promising targets for T-ALL therapies.
Intrabody induced cell death by targeting theT. bruceicytoskeletal proteinTbBILBO1
Authors: Broster Reix Christine E. , Ramanantsalama Miharisoa Rijatiana , Primo Carmelo Di , Minder Laëtitia , Bonhivers Mélanie , Dacheux Denis , Robinson Derrick R.
Published: July 2021

Trypanosoma bruceibelongs to a genus of protists that cause life-threatening and economically important diseases of human and animal populations in Sub-Saharan Africa. T. bruceicells are covered in surface glycoproteins some of which are used to escape the host immune system. Exo-/endocytotic trafficking of these and other molecules occursviaa single copy organelle called the flagellar pocket (FP). The FP is maintained and enclosed around the flagellum by the flagellar pocket collar (FPC). To date, the most important cytoskeletal component of the FPC is an essential, calcium-binding, polymer-forming protein calledTbBILBO1. In searching for novel immune-tools to study this protein, we raised nanobodies againstTbBILBO1. Nanobodies (Nb) that were selected according to their binding properties toTbBILBO1, were tested as immunofluorescence tools, and expressed as intrabodies (INb). One of them, Nb48, proved to be the most robust nanobody and intrabody. We further demonstrate that inducible, cytoplasmic expression of INb48 was lethal to these parasites, producing abnormal phenotypes resembling those ofTbBILBO1 RNAi knockdown. Our results validate the feasibility of generating functional single-domain antibody derived intrabodies to target trypanosome cytoskeleton proteins.
Low-coverage sequencing in a deep intercross of the Virginia body weight lines provides insight to the polygenic genetic architecture of growth: novel loci revealed by increased power and improved genome-coverage
Authors: Rönneburg T. , Zan Y. , Honaker C.F. , Siegel P.B. , Carlborg Ö.
Published: July 2021

Genetic dissection of highly polygenic traits is a challenge, in part due to the power necessary to confidently identify loci with minor effects. Experimental crosses are valuable resources for mapping such traits. Traditionally, genome-wide analyses of experimental crosses have targeted major loci using data from a single generation, often the F2, with additional, later generation individuals being generated for replication and fine-mapping. Here, we aim to confidently identify minor-effect loci contributing to the highly polygenic basis of the long-term, divergent bi-directional selection responses for 56-day body weight in the Virginia chicken lines. To achieve this, a powerful strategy was developed to make use of data from all generations (F2-F18) of an advanced intercross line, developed by crossing the low and high selected lines after 40 generations of selection. A cost-efficient low-coverage sequencing based approach was used to obtain high-confidence genotypes in 1Mb bins across 99.3% of the chicken genome for >3,300 intercross individuals. In total, 12 genome-wide significant and 10 additional suggestive QTL for 56-day body weight were mapped, with only two of these QTL reaching genome-wide, and one suggestive, significance in analyses of the F2 generation. Five of the significant, and four of the suggestive, QTL were among the 20 loci reaching a 20% FDR-threshold in previous analyses of data from generation F15. The novel, minor-effect QTL mapped here were generally mapped due to an overall increase in power by integrating data across generations, with minor contributions from increased genome-coverage and improved marker information content. Significant and suggestive QTL now explain >60% of the difference between the parental lines, three times more than the previously reported significant QTL. Making integrated use of all available samples from multiple generations in experimental crosses is now economically feasible using the low-cost, sequencing-based genotyping strategies outlined here. Our empirical results illustrate the value of this strategy for mapping novel minor-effect loci contributing to complex traits to provide a more confident, comprehensive view of the individual loci that form the genetic basis of the highly polygenic, long-term selection responses for 56-day body weight in the Virginia chicken lines.
The amplitude of fNIRS hemodynamic response in the visual cortex unmasks autistic traits in typically developing children
Authors: Mazziotti Raffaele , Scaffei Elena , Conti Eugenia , Marchi Viviana , Rizzi Riccardo , Cioni Giovanni , Battini Roberta , Baroncelli Laura
Published: July 2021

Autistic traits represent a continuum dimension across the population, with autism spectrum disorder (ASD) being the extreme end of the distribution. Accumulating evidence shows that neuroanatomical and neurofunctional profiles described in relatives of ASD individuals reflect an intermediate neurobiological pattern between the clinical population and healthy controls. This suggests that quantitative measures detecting autistic traits in the general population represent potential candidates for the development of biomarkers identifying early pathophysiological processes associated with ASD. Functional near-infrared spectroscopy (fNIRS) has been extensively employed to investigate neural development and function. In contrast, the potential of fNIRS to define reliable biomarkers of brain activity has been barely explored. Features of non-invasiveness, portability, ease of administration and low-operating costs make fNIRS a suitable instrument to assess brain function for differential diagnosis, follow-up, analysis of treatment outcomes and personalized medicine in several neurological conditions. Here, we introduce a novel standardized procedure with high entertaining value to measure hemodynamic responses (HDR) in the occipital cortex of adult subjects and children. We found that the variability of evoked HDR correlates with the autistic traits of children, assessed by the Autism-Spectrum Quotient. Interestingly, HDR amplitude was especially linked to social and communication features, representing the core symptoms of ASD. These findings establish a quick and easy strategy for measuring visually-evoked cortical activity with fNIRS that optimize the compliance of young subjects, setting the background for testing the diagnostic value of fNIRS visual measurements in the ASD clinical population.
Prenatal androgen treatment does not alter the firing activity of hypothalamic arcuate kisspeptin neurons in female mice
Authors: Gibson Amanda G. , Jaime Jennifer , Burger Laura L. , Moenter Suzanne M.
Published: July 2021

Neuroendocrine control of reproduction is disrupted in many individuals with polycystic ovary syndrome, who present with increased luteinizing hormone (LH), and presumably gonadotropin-releasing hormone (GnRH), release frequency, and high androgen levels. Prenatal androgenization (PNA) recapitulates these phenotypes in primates and rodents. Female offspring of mice injected with dihydrotestosterone (DHT) on gestational D16-18 exhibit disrupted estrous cyclicity, increased LH and testosterone, and increased GnRH neuron firing rate as adults. PNA also alters the developmental trajectory of GnRH neuron firing rates, markedly blunting the prepubertal peak in firing that occurs in 3wk-old controls. GnRH neurons do not express detectable androgen receptors and are thus probably not the direct target of DHT. Rather, PNA likely alters GnRH neuronal activity by modulating upstream neurons, such as hypothalamic arcuate neurons co-expressing kisspeptin, neurokinin B (gene Tac2), and dynorphin, aka KNDy neurons. We hypothesized PNA treatment changes firing rates of KNDy neurons in a similar age-dependent manner as GnRH neurons. We conducted targeted extracellular recordings (0.5-2h) of Tac2-identified KNDy neurons from control and PNA mice at 3wks of age and in adulthood. About half of neurons were quiescent (<0.005Hz). Long-term firing rates of active cells varied, suggestive of episodic activity, but were not different among groups. Short-term burst firing was also similar. We thus reject the hypothesis that PNA alters the firing rate of KNDy neurons. This does not preclude altered neurosecretory output of KNDy neurons, involvement of other neuronal populations, or in-vivo networks as critical drivers of altered GnRH firing rates in PNA mice.

Significance statement

Prenatal androgenization (PNA) recapitulates key aspects of the common reproductive disorder polycystic ovary syndrome. It is postulated that disruptions in the episodic pattern of gonadotropin-releasing hormone (GnRH) secretion in part underly this disorder, yet GnRH neurons do not express androgen receptor to respond directly to elevated androgens. A population of kisspeptin, neurokinin B, and dynorphin-expressing (KNDy) neurons in the hypothalamic arcuate nucleus are thought to regulate pulsatile GnRH release and some express androgen receptor. We did not find evidence, however, that PNA altered spontaneous activity of KNDy neurons before puberty at 3wks of age or in adulthood. This suggests that PNA likely acts through other components of the broader hypothalamic network to change the patterns of GnRH release.
The joint evolution of animal movement and competition strategies
Authors: Gupte Pratik R. , Netz Christoph F. G. , Weissing Franz J.
Published: July 2021

Competition typically takes place in a spatial context, but eco-evolutionary models rarely address the joint evolution of movement and competition strategies. Here we investigate a spatially explicit producer-scrounger model where consumers can either forage on a heterogeneous resource landscape or steal resource items from conspecifics (kleptoparasitism). We consider three scenarios: (1) a population of foragers in the absence of kleptoparasites; (2) a population of consumers that are either specialized on foraging or on kleptoparasitism; and (3) a population of individuals that can fine-tune their behavior by switching between foraging and kleptoparasitism depending on local conditions. By means of individual-based simulations, we study the joint evolution of movement and competition strategies, and we investigate the implications on the resource landscape and the distribution of consumers over this landscape. In all scenarios and for all parameters considered, movement and competition strategies evolved rapidly and consistently across replicate simulations. The evolved movement and resource exploitation patterns differ considerably across the three scenarios. For example, foragers are attracted by conspecifics in scenario (1), while they are repelled by conspecifics in scenario (2). Generally the movement strategies of kleptoparasites differ markedly from those of foragers, but even within each class of consumers polymorphisms emerge, corresponding to pronounced differences in movement patterns. In all scenarios, the distribution of consumers over resources differs substantially from ‘ideal free’ predictions. We show that this is related to the intrinsic difficulty of moving effectively on a depleted landscape with few reliable cues for movement. Our study emphasises the advantages of a mechanistic approach when studying competition in a spatial context, and suggests how evolutionary modelling can be integrated with current work in animal movement ecology.
Host species identity shapes the diversity and structure of insect microbiota
Authors: Malacrinò Antonino
Published: July 2021

As for most of the life that inhabits our planet, microorganisms play an essential role in the fitness of insects, including nutrition, reproduction, defence, and many other functions. More recently, we assisted in an exponential growth of studies describing the taxonomical composition of bacterial communities across insects’ phylogeny. However, there is still an outstanding question that needs to be answered: which factors contribute most to shape insects’ microbiomes? This study tries to find an answer to this question by taking advantage of publicly available sequencing data and reanalysing over 4,000 samples of insect-associated bacterial communities under a common framework. Results suggest that insect taxonomy has a wider impact on the structure and diversity of their associated microbial communities than the other factors considered (diet, sex, life stage, sample origin, and treatment). However, when specifically testing for signatures of co-diversification of insect species and their microbiota, analyses found weak support for this, suggesting that while insect species strongly drive the structure and diversity of insect microbiota, the diversification of those microbial communities did not follow their host’s phylogeny. Furthermore, a parallel survey of the literature highlights several methodological limitations that need to be considered in future research endeavours.
A regulatory circuit motif dictates whether protein turnover fluxes are more predictive as biomarkers than protein abundances
Authors: Loriaux Paul M , Tang Ying , Hoffmann Alexander
Published: July 2021

The identification of prognostic biomarkers fuels personalized medicine. Here we tested two underlying, but often overlooked assumptions: 1) measurements at the steady state are sufficient for predicting the response to drug action, and 2) specifically, measurements of molecule abundances are sufficient. It is not clear that these are justified, as 1) the response results from non-linear molecular relationships, and 2) the steady state is defined by both abundance and orthogonal flux information. An experimentally validated mathematical model of the cellular response to the anti-cancer agent TRAIL was our test case. We developed a mathematical representation in which abundances and fluxes (static and kinetic network features) are largely independent, and simulated heterogeneous drug responses. Machine learning revealed predictive power, but that kinetic, not static network features were most informative. Analytical treatment of the underlying network motif identified kinetic buffering as the relevant circuit design principle. Our work suggests that network topology considerations ought to guide biomarker discovery efforts.

Graphic abstract

Highlights

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Biomarkers are usually molecule abundances but underlying networks are dynamic

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Our method allows separate consideration of heterogeneous abundances and fluxes

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For the TRAIL cell death network machine learning reveals fluxes as more predictive

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Network motif analyses could render biomarker discovery efforts more productive

eTOC blurb

Precision medicine relies on discovering which measurements of the steady state predict therapeutic outcome. Loriaux et al show – using a new analytical approach – that depending on the underlying molecular network, synthesis and degradation fluxes of regulatory molecules may be more predictive than their abundances. This finding reveals a flaw in an implicit but hitherto untested assumption of biomarker discovery efforts and suggests that dynamical systems modeling is useful for directing future clinical studies in precision medicine.