Genomic Surveillance Reveals the Rapid Expansion of the XBB Lineage among Circulating SARS-CoV-2 Omicron Lineages in Southeastern Wisconsin, USA

SARS-CoV-2 caused a life-threatening COVID-19 pandemic outbreak worldwide. The Southeastern Region of Wisconsin, USA (SERW) includes large urban Milwaukee and six suburban counties, namely Kenosha, Ozaukee, Racine, Walworth, Washington and Waukesha. Due to the lack of detailed SARS-CoV-2 genomic surveillance in the suburban populations of the SERW, whole-genome sequencing was employed to investigate circulating SARS-CoV-2 lineages and characterize dominant XBB lineages among this SERW population from November 2021 to April 2023. For an unbiased data analysis, we combined our 6709 SARS-CoV-2 sequences with 1520 sequences from the same geographical region submitted by other laboratories. Our study shows that SARS-CoV-2 genomes were distributed into 357 lineages/sublineages belonging to 13 clades, of which 88.8% were from Omicron. We document dominant sublineages XBB.1.5 and surging XBB.1.16 and XBB.1.9.1 with a few additional functional mutations in Spike, which are known to contribute to higher viral reproduction, enhanced transmission and immune evasion. Mutational profile assessment of XBB.1.5 Spike identifies 38 defining mutations with high prevalence occurring in 49.8-99.6% of the sequences studied, of which 32 mutations were in three functional domains. Phylogenetic and genetic relatedness between XBB.1.5 sequences reveal potential virus transmission occurring within households and within and between Southeastern Wisconsin counties. A comprehensive phylogeny of XBB.1.5 with global sub-dataset sequences confirms the wide spread of genetically similar SARS-CoV-2 strains within the same geographical area. Altogether, this study identified proportions of circulating Omicron variants and genetic characterization of XBB.1.5 in the SERW population, which helped state and national public health agencies to make compelling mitigation efforts to reduce COVID-19 transmission in the communities and monitor emerging lineages for their impact on diagnostics, treatments and vaccines.

Effect of Sperm Selection by Magnetic-Activated Cell Sorting in D-IUI: A Randomized Control Trial

Clinical outcome in assisted reproduction techniques (ARTs) is mainly influenced by the quality of gametes used. It is known that a high percentage of sperm DNA fragmentation (DNAf) decreases the success of ART clinical results. Therefore, techniques such as magnetic-activated cell sorting (MACS) help to improve results in cases of patients with a high percentage of DNAf. Cryopreservation of sperm in donor intrauterine insemination (D-IUI) treatments increases sperm DNAf, so patients using these sperm samples can benefit from using this technique. This prospective randomized national multicenter study analyzed clinical outcomes of 181 D-IUI treatments. MACS was performed after density gradient centrifugation (DGC) in 90 thawed semen donor samples (MACSG), whereas only DGC was performed in 91 thawed semen donor samples (CG). To our knowledge, this is the first study analyzing the effect of MACS on D-IUI cycles. Our results show no significant differences in gestation, live birth, or miscarriage rates between the two groups. We believe that further studies with a larger sample size are needed to evaluate the application of MACS in combination with standard IUI donor sperm preparations in fertility clinics.

Splice site proximity influences alternative exon definition

Alternative splicing enables higher eukaryotes to expand mRNA diversity from a finite number of genes through highly combinatorial splice site selection mechanisms that are influenced by the sequence of competing splice sites, cis-regulatory elements binding trans-acting factors, the length of exons and introns harbouring alternative splice sites and RNA secondary structures at putative splice junctions. To test the hypothesis that the intron definition or exon definition modes of splice site recognition direct the selection of alternative splice patterns, we created a database of alternative splice site usage (ALTssDB). When alternative splice sites are embedded within short introns (intron definition), the 5' and 3' splice sites closest to each other across the intron preferentially pair, consistent with previous observations. However, when alternative splice sites are embedded within large flanking introns (exon definition), the 5' and 3' splice sites closest to each other across the exon are preferentially selected. Thus, alternative splicing decisions are influenced by the intron and exon definition modes of splice site recognition. The results demonstrate that the spliceosome pairs splice sites that are closest in proximity within the unit of initial splice site selection.

Diagnostic Accuracy Study Comparing Hysterosalpingo-Foam Sonography and Hysterosalpingography for Fallopian Tube Patency Assessment

Introduction: Simplified ultrasound-based infertility protocols that appear to provide enough information to plan effective management have been described. Thus, the objective of this study is to compare the diagnostic accuracy of the hysterosalpingo-foam sonography (HyFoSy) in tubal patency testing with the traditional hysterosalpngography (HSG) for establishing a new diagnostic strategy in infertility. Material and Methods: Prospective observational diagnostic accuracy was performed in a private fertility clinic in which 106 women undergoing a preconceptionally visit were recruited. All of them had low risk for tubal disease, had performed an HSG and were negative for Chlamydia trachomatis antibody. Main outcome measures were tubal patency and pain grade. Results: Evaluation of tubal patency by HyFoSy showed a total concordance with the results of the previous HSG in 72.6% (n = 77), and a total discordance for 4.7% (n = 6), with the inter-test agreement Kappa equal to 0.57, which means moderate concordance. Among the patients, 59.1% did not report pain during the procedure, while the remaining 48.1% indicated pain in different degrees; patients usually report less pain and only 6.6% described more pain with HyFoSy than with HSG (OR 6.57 (CI 95% 3.11–13.89)). Clinical outcomes after performing HyFoSy were not affected. Conclusions: HyFoSy is in concordance with HSG regarding tubal patency results and it is a less painful technique than HSG. HyFoSy is more economical and can be performed in an exam room only equipped with an ultrasound scanner. Based on these results, HyFoSy could be the first-choice diagnostic option to assess tubal patency in patients with low risk of tubal disease.

Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study

Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3-7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3' ends, with 3-5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.

Preliminary results of a network meta-analysis on the efficacy of long-acting injectable antipsychotics in schizophrenia

Introduction

Long-acting injectable antipsychotics (LAIs) are currently the most effective alternative for patients with schizophrenia who exhibit poor adherence. Although a recent meta-analysis reported similar efficacy between first and second-generation LAIs, these results were only based on 3 studies due to the limited number of head-to-head comparisons.

Objectives

Present the preliminary results of a network meta-analysis on the comparative efficacy of LAIs in schizophrenia.

Methods

Studies were obtained from a previous study, where we carried out a systematic search from until May 2019 in various databases. Included trials of adults with schizophrenia compared the efficacy of LAI vs LAI or placebo through the Positive and Negative Syndrome Scale (PANSS). Efficacy was evaluated through the mean differences (MD) from baseline to endpoint in the PANSS total scores. Network meta-analysis was performed in MetaInsight through direct and indirect comparisons using a Bayesian approach.

Results

from 12 studies are presented in Figures 1 and 2. All LAIs except zuclopenthixol were more effective than placebo. There were no significant differences between LAIs except for aripiprazole and risperidone, which were more efficacious than zuclopenthixol. The largest change occurred with aripiprazole LAI, but was not significantly higher than haloperidol.

Figure 1. Comparison of treatment pairs. Effect sizes are presented as MD and 95% confidence intervals (*p<0.05).

Figure 1. Overall change in symptoms

Conclusions

Preliminary results from a network meta-analysis also suggest that in the long-term haloperidol decanoate is equally effective in overall symptom changes compared to other LAIs. Further analyses are needed to obtain a better perspective on these drugs.

Disclosure

No significant relationships.

Recovery of zinc and copper from copper smelter flue dust. Optimisation of sulphuric acid leaching

Copper smelter flue dust is a residue, rich in zinc, originating from the pyrometallurgical process of copper, and constitutes a potential raw material for zinc production. In order to valorise this waste by hydrometallurgical processes, its leaching with sulphuric acid at constant pH is studied. Experimental conditions (temperature, pH, and pulp density) are optimised by design of experiments in order to maximise Zn and Cu extractions while minimising the leaching of Fe. The experimental results are fitted to a full-quadratic second-order equation model by applying multiple regression analysis for extractions of Zn, Cu, and Fe. In order to determine the optimum conditions, the response surfaces are overlaid and the intersection of the plot of the three responses identifies conditions of pH and pulp density that satisfy recoveries of Zn higher than 95%, recoveries of Cu around 70%, and Fe extractions lower than 35%. Under the best conditions, that is, pH = 2, 10% of pulp density, and at 25°C, a liquor rich in zinc and copper, and a lead concentrate are obtained.

Different Endometrial Receptivity in Each Hemiuterus of a Woman with Uterus Didelphys and Previous Failed Embryo Transfers

The aim of this report is to describe the clinical case of a 31-year-old patient with uterus didelphys (double uterus) and primary infertility, who had been through several embryo transfers in the context of an in vitro fertilization (IVF) treatment with no success. In the case described, the patient is subjected to a new IVF treatment after an endometrial receptivity array (ERA) test performed in both hemiuteri, to assess endometrial receptivity. As a result, the test showed that the right-sided hemiuterus was receptive in 5 days since the beginning of progesterone administration while the left-sided hemiuterus was not receptive in that day. The IVF treatment is performed with vitrified oocytes and a single embryo in day-3 stage is transferred to the right hemiuterus. We concluded that the ERA analysis is a useful tool for IVF patients with uterus didelphys to choose the most appropriate hemiuterus and day to perform embryo transfer.

Recovery of Zn from acid mine water and electric arc furnace dust in an integrated process

In this paper, the purification of acid mine water and the treatment of electric arc furnace dust (EAFD) are integrated into one process with the aim of recovering the Zn content of both effluent and waste. Zinc recovery can reduce the cost of their environmental management: purified acid mine water is discharged after removing all metals; EAFD ceases to be hazardous waste; and Zn is valorised. The process consists of the recovery of Zn as zinc oxide and its purification into commercial products. First, EAFD is leached with acid water and the dissolved metals are selectively precipitated as hydroxides. After EADF leaching, ferrous iron is bio-oxidized and Fe and Al are then precipitated; in the following stage, Cu, Ni, Co and Cd are cemented and finally Zn is precipitated as ZnO. In order to purify water that finally is discharged to a river, lime is used as the neutralizing agent, which results in a precipitate of mainly gypsum, MnO, and ZnO. From the impure zinc oxide produced, various alternatives for the attainment of commercial products, such as basic zinc carbonate and electrolytic zinc, are studied in this work.

Influence of follicle rupture and uterine contractions on intrauterine insemination outcome: a new predictive model

OBJECTIVE

To correlate the detection of follicle rupture and the number of uterine contractions per minute with the outcome of IUI and to build a predictive model for the outcome of IUI including these parameters.

DESIGN

Retrospective cohort study.

SETTING

Fertility clinic.

PATIENT(S)

We analyzed data from 610 women who underwent homologous or donor double IUI from 2005 to 2010 and whose data of uterine contractions or follicle rupture were recorded.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Live-birth rate.

RESULT(S)

Nine hundred seventy-nine IUI cycles were included. The detection of follicle rupture (odds ratio [OR], 1.98; 95% confidence interval [CI], 1.30-3.01) and the number of uterine contractions per minute (OR, 1.67; 95% CI, 1.02-2.74) assessed after the second insemination procedure of a double IUI were positively correlated with the live-birth rate. A multiple logistic regression model showed that sperm origin, maternal age, follicle count at hCG administration day, follicle rupture, and the number of uterine contractions observed after the second insemination procedure were significantly associated with the live-birth rate.

CONCLUSION(S)

Follicle rupture and uterine contractions are associated with the success of an IUI cycle. This may open new possibilities to improve the methodology of IUI.

Esthetic restoration of primary incisors

A simple and esthetic technique for restoring cariously involved primary maxillary incisors is described. The technique includes mini-pins, a preformed celluloid crown and resin-based composite.

Prevalence of marginal alveolar bone loss in children

Previous studies have indicated that the prevalence of marginal alveolar bone loss (MABL) in several populations, but not yet in the Mexican children. Therefore, the present study examined the prevalence of MABL in a group of Mexican children. The characteristics of the proximal surfaces and the status of the adjacent alveolar bone, were recorded at 1307 sites from 209 diagnostic bite-wing radiographs, from 115 children. MABL was found in the radiographs of 7.8% of the children or 1.5% of the sites. The present prevalence finding is relatively low when compared to previous studies on children attending dental clinics. MABL was found already in 4-year-old children, confirming previous studies, which indicate the possibility of early onset of periodontitis in children.

Surgical reconstruction of the interdental papilla

The traditional goal of disease elimination in the anterior region opens the interproximal spaces, causing flattening or cratering of the interdental papilla. Today's patients increasingly demand esthetic results in addition to periodontal treatment, and recent advances in periodontal plastic surgery have enhanced the periodontist's ability to address these concerns. Three case reports demonstrate a proposed surgical technique for the reconstruction of collapsed interdental papillae using a connective tissue graft under the buccal and palatal flaps.