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.

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.

Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine.

Isolation of newly transcribed RNA is an invaluable approach that can be used to study the dynamic life of RNA in cellulo. Traditional methods of whole-cell RNA extraction limit subsequent gene expression analyses to the steady-state levels of RNA abundance, which often masks changes in RNA synthesis and processing. This chapter describes a methodology with low cytotoxicity that permits the labeling and isolation of nascent pre-mRNA in cell culture. The resulting isolate is suitable for use in a series of downstream applications aimed at studying changes in RNA synthesis, processing, or stability.

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.

MED GATA factors promote robust development of the C. elegans endoderm.

The MED-1,2 GATA factors contribute to specification of E, the progenitor of the Caenorhabditis elegans endoderm, through the genes end-1 and end-3, and in parallel with the maternal factors SKN-1, POP-1 and PAL-1. END-1,3 activate elt-2 and elt-7 to initiate a program of intestinal development, which is maintained by positive autoregulation. Here, we advance the understanding of MED-1,2 in E specification. We find that expression of end-1 and end-3 is greatly reduced in med-1,2(-) embryos. We generated strains in which MED sites have been mutated in end-1 and end-3. Without MED input, gut specification relies primarily on POP-1 and PAL-1. 25% of embryos fail to make intestine, while those that do display abnormal numbers of gut cells due to a delayed and stochastic acquisition of intestine fate. Surviving adults exhibit phenotypes consistent with a primary defect in the intestine. Our results establish that MED-1,2 provide robustness to endoderm specification through end-1 and end-3, and reveal that gut differentiation may be more directly linked to specification than previously appreciated. The results argue against an "all-or-none" description of cell specification, and suggest that activation of tissue-specific master regulators, even when expression of these is maintained by positive autoregulation, does not guarantee proper function of differentiated cells.

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.

The endometrial receptivity array for diagnosis and personalized embryo transfer as a treatment for patients with repeated implantation failure.

OBJECTIVE: To demonstrate the clinical value of the endometrial receptivity array (ERA) in patients with repeated implantation failure (RIF), for guiding their personalized embryo transfer (pET) as a novel therapeutic strategy. DESIGN: Prospective interventional multicenter clinical trial. SETTING: University-affiliated infertility and private clinics. PATIENT(S): Eighty-five RIF patients and 25 comparison patients. INTERVENTION(S): Endometrial sampling and pET guided by ERA. MAIN OUTCOME MEASURE(S): A receptive (R) or nonreceptive (NR) endometrial status according to ERA. Pregnancy (PR) and implantation (IR) rates after pET. RESULT(S): The ERA test gave an R result of 74.1% in RIF patients versus 88% in control subjects. Clinical follow-up was possible in 29 RIF patients, in whom pET was performed, resulting in 51.7% PR and 33.9% IR. The IRs and PRs in the 6 months after the biopsy showed that pregnancy was not related to the local injury. Twenty-two RIF patients (25.9%) were NR, and in 15 of them a second ERA validated a displacement of the window of implantation (WOI). In eight of them, pET was performed on the day designated by the ERA, resulting in 50.0% PR and 38.5% IR. These results should be considered as preliminary. CONCLUSION(S): There is an increased percentage of WOI displacement in RIF patients compared with comparison group patients, leading to the concept of pET as a therapeutic strategy. Rescue of NR patients by pET in a displaced WOI results in similar PR and IR.

Biotic factor does not limit operational pH in packed-bed bioreactor for ferrous iron biooxidation.

Ferrous ion biooxidation is a process with many promising industrial applications: mainly regeneration of ferric ion as an oxidizing reagent in bioleaching processes and depuration of acid mine drainage. The flooded packed-bed bioreactor (FPB) is the design that leads to the highest biooxidation rate. In this bioreactor, biomass is immobilized in a biofilm that consists of an inorganic matrix, formed by precipitated ferric compounds, in the pores of which cells are attached. This biofilm covers the surface of particles (siliceous stone) that form the bed. The chemical stability of this inorganic matrix defines the widest possible pH range in FPBs. At pH below 1, ferric matrix is dissolved and cells are washed out. At pH higher than 2, ferric ion precipitates massively, greatly hindering mass transfer to cells. Thus, among other parameters, pH is recognised as a key factor for operational control in FPBs. This paper aims to explain the effect of pH on FPB operation, with an emphasis on microbial population behaviour. FPBs seeded with mixed inocula were assayed in the pH range from 2.3 to 0.8 and the microbial population was characterised. The microbial consortium in the bioreactor is modified by pH; at pH above 1.3 Acidithiobacillus ferrooxidans is the dominant microorganism, whereas at pH below 1.3 Leptospirillum ferrooxidans dominates. Inoculum can be adapted to acidity during continuous operation by progressively decreasing the pH of the inlet solution. Thus, in the pH range from 2.3 to 1, the biotic factor does not compromise the bioreactor performance.

Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition.

In many species, both morphological and molecular traits related to sex and reproduction evolve faster in males than in females. Ultimately, rapid male evolution relies on the acquisition of genetic variation associated with differential reproductive success. Many newly evolved genes are associated with novel functions that might enhance male fitness. However, functional evidence of the adaptive role of recently originated genes in males is still lacking. The Sperm dynein intermediate chain multigene family, which encodes a Sperm dynein intermediate chain presumably involved in sperm motility, originated from complex genetic rearrangements in the lineage that leads to Drosophila melanogaster within the last 5.4 million years since its split from Drosophila simulans. We deleted all the members of this multigene family resident on the X chromosome of D. melanogaster by chromosome engineering and found that, although the deletion does not result in a reduction of progeny number, it impairs the competence of the sperm in the presence of sperm from wild-type males. Therefore, the Sperm dynein intermediate chain multigene family contributes to the differential reproductive success among males and illustrates precisely how quickly a new gene function can be incorporated into the genetic network of a species.

Mexican American adolescents' academic achievement and aspirations: the role of perceived parental educational involvement, acculturation, and self-esteem.

As the number of Mexican American school-aged children continues to increase, researchers, practitioners, and policymakers are in critical need of information to better understand and serve them. This study used structural equation modeling to examine the relationship among perceived parental educational involvement (PPEI), acculturation, gender, and self-esteem on the academic achievement and aspirations of Mexican American high school students (N = 298). Results revealed direct effects of perceived parental educational involvement, students' level of acculturation, and students' self-esteem on students' achievement and aspirations. Acculturation and self-esteem also revealed indirect effects on aspirations and achievement through parental educational expectations. Implications of these findings are discussed.