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Humans have been driving a global erosion of species richness for millennia, but the consequences of past extinctions for other dimensions of biodiversity-functional and phylogenetic diversity-are poorly understood. In this work, we show that, since the Late Pleistocene, the extinction of 610 bird species has caused a disproportionate loss of the global avian functional space along with ~3 billion years of unique evolutionary history. For island endemics, proportional losses have been even greater. Projected future extinctions of more than 1000 species over the next two centuries will incur further substantial reductions in functional and phylogenetic diversity. These results highlight the severe consequences of the ongoing biodiversity crisis and the urgent need to identify the ecological functions being lost through extinction.

Tricho-rhino-phalangeal syndrome (TRPS) is a rare malformation syndrome characterized by distinctive facial, ectodermal, and skeletal features. TRPS is divided into TRPS type I/III caused by pathogenic variants in TRPS1 and TRPS type II caused by contiguous gene deletions also spanning EXT1 and RAD21. Due to its rarity, knowledge of the clinical course of TRPS remains limited. Therefore, we collected and characterized a case series of 15 TRPS type I patients (median age at diagnosis 15 [interquartile range: 10-18] years, 11 females [73%]) seen at Aarhus University Hospital, Denmark, with a median follow-up period of 10 years. We estimated a minimum point prevalence of 0.5 in 100,000 (95% CI: 0.3-0.8 per 100,000) persons. Common craniofacial features included fine and sparse hair with a high anterior hairline, eyebrows with lateral thinning and a thicker medial part, prominent ears, a bulbous nose tip with small nasal alae, a low-hanging, and often wide columella, and a long philtrum with a thin upper vermillion. Specific skeletal features included short stature and deviating and short fingers with cone-shaped epiphyses and shortened metacarpals on radiographs. The most significant morbidity of the cohort was joint complaints, which were reported by all patients, often already before the TRPS diagnosis was established. We identified ten different TRPS1 variants including both frameshift/nonsense, missense, and splice-site variants, including seven variants not previously reported in the literature. In accordance with previous literature, no genotype-phenotype correlation was identified. The clinical trajectories were heterogeneous involving pediatrics, dermatology, orthopedic surgery, clinical genetics, and/or odontology, emphasizing that close multidisciplinary collaboration is essential for early diagnosis of TRPS and to ensure proper and timely patient care and counseling., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to declare., (Copyright © 2024 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

Background: Men with obstructive azoospermia (OA) due to impaired development of the genital tract often carry at least one Cystic Fibrosis Transmembrane Conductance Regulator CFTR mutation., Objective: To determine the frequency of Congenital Bilateral Absence of Vas deferens (CBAVD) in men with azoospermia carrying CFTR gene mutations., Materials and Methods: Non-vasectomized men with azoospermia referred to our andrological center were consecutively included. All men underwent palpation of the scrotal parts of the Vasa deferentia, ultrasonography of the testicles and hormone profile, and genetic analyses. Testicular biopsy was usually performed. A panel of 32 of the most important CFTR mutations was examined from genomic DNA isolated from blood lymphocytes. Either multiplex PCR analysis or a next-generation sequencing technique was performed., Results: Among the 639 men with azoospermia, 69 (10.8%) had at least one CFTR mutation. Of the 43 patients with at least one of the two CFTR mutations, ΔF508 and R117H, 19 (44.2%) showed CBAVD, 2 (4.7%) Congenital Unilateral Absence of Vas deferens (CUAVD), and 22 (51.2%) presence of the scrotal parts of the Vasa deferentia. In contrast, only 1/21 men (4.8%) with an isolated IVS8-5T variant showed CBAVD. Among the further 20 men with an isolated IVS8-5T variant, 11 had a history of cryptorchidism. Among the 570 men without CFTR mutations, CBAVD was found in only two men and CUAVD in one. FSH level was higher and testicular volume lower in men with present Vasa deferentia compared to those without (P < .001; Student's t test). Thirty-one men with either ΔF508 or R117H mutations, or both, had a testicular biopsy. Motile spermatozoa were found in 100% of 16 cases with CBAVD but in only 6 out of 15 cases with present Vasa deferentia (P < .01; Fisher's exact test)., Discussion and Conclusions: CBAVD was found in ~ 44% of men with ΔF508/R117H mutations. The data may support that CFTR mutations might affect male fertility through other mechanisms than obstruction of the genital tract. For a practical, clinical purpose analysis for only ΔF508, R117H and IVS8-5T seems sufficient until further research shows anything else., (© 2020 The Authors. Andrology published by Wiley Periodicals LLC on behalf of American Society of Andrology and European Academy of Andrology.)

The performance of different polarization propagator methods, such as RPA, RPA(D), HRPA, HRPA(D), and SOPPA, have been tested against CC3 values for both static and dynamic polarizabilities. The test set consists of 14 (hetero-)aromatic medium-sized organic molecules, mostly with a high degree of symmetry. The benchmark of the methods remarkably reveals that RPA and HRPA(D) yield results comparable with the CC3 values and that they outperform SOPPA for these molecules. For a subset of the molecules, a comparison could be made to experimental values. The comparison for static polarizabilities proves that RPA and HRPA(D) as well as RPA(D) reproduce experimental values to a satisfying precision, whereas the SOPPA method compared to these three methods appears to perform only adequately. An investigation of the performance of Sadlej's polarized triple zeta basis set against Dunning's aug-cc-pVTZ basis set was also carried out. It is found that in contrast to other methods, Sadlej's basis set did not perform sufficiently compared to the larger aug-cc-pVTZ basis set for the RPA based methods.

A benchmark study of several correlated second-order methods for frequency-dependent polarizabilities has been carried out. For the benchmark, a set of 14 (hetero)aromatic medium-sized molecules has been chosen. For the first time, CC3 polarizabilities are reported for these molecules using Sadlej's polarized triple-ζ basis set, and for a subset of these molecules the polarizabilities were obtained at the CC3 level also with the larger aug-cc-pVTZ basis set. These CC3 values are used as the reference values for benchmarking the second-order methods: SOPPA, SOPPA(CC2), SOPPA(CCSD), CC2, as well as CCSD. The influence of different basis sets, aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ, d-aug-cc-pVTZ, and Sadlej's polarized triple-ζ basis set, on static and frequency-dependent polarizabilities was investigated for the full set of molecules at the SOPPA level. It was found that the choice of basis set had a somewhat greater influence on the frequency-dependent polarizabilities than on the static polarizabilities, but all effects were small. The aug-cc-pVTZ basis set performed adequately for both static and frequency-dependent polarizabilities, having an insignificant offset from the values obtained with the larger d-aug-cc-pVTZ and aug-cc-pVQZ basis sets. Comparing the second-order methods, SOPPA, SOPPA(CC2), SOPPA(CCSD), CC2, as well as CCSD, to the CC3 reference values, it was found that the best performing method was CCSD, as expected. The SOPPA method, on the contrary, outperformed the CC2 method, suggesting the use of SOPPA rather than CC2 for polarizabilities, at least for these kinds of molecules. The SOPPA results were found to improve further when the Møller-Plesset correlation coefficients in the wave function were replaced by coupled-cluster amplitudes in the SOPPA(CC2) and SOPPA(CCSD) methods. Finally, a comparison was made for a small subset of the molecules between experimental data and calculated polarizabilities. It shows that, for this set of molecules, the trend in the performance of the different second-order methods does not depend on whether the reference values are calculated CC3 values or experimental values.

Hydatidiform moles (HMs) are abnormal human pregnancies with vesicular chorionic villi, imposing two clinical challenges; miscarriage and a risk of gestational trophoblastic neoplasia (GTN). The parental type of most HMs are either diandric diploid (PP) or diandric triploid (PPM). We consecutively collected 154 triploid or near-triploid samples from conceptuses with vesicular chorionic villi. We used analysis of DNA markers and/or methylation sensitive-MLPA and collected data from registries and patients records. We performed whole genome SNP analysis of one case of twinning (PP+PM).In all 154 triploids or near-triploids we found two different paternal contributions to the genome (P1P2M). The ratios between the sex chromosomal constitutions XXX, XXY, and XYY were 5.7: 6.9: 1.0. No cases of GTN were observed. Our results corroborate that all triploid human conceptuses with vesicular chorionic villi have the parental type P1P2M. The sex chromosomal ratios suggest approximately equal frequencies of meiosis I and meiosis II errors with selection against the XYY conceptuses or a combination of dispermy, non-disjunction in meiosis I and meiosis II and selection against XYY conceptuses. Although single cases of GTN after a triploid HM have been reported, the results of this study combined with data from previous prospective studies estimate the risk of GTN after a triploid mole to 0% (95% CI: 0-1,4%).

The aim of this study was to examine the value of testing for a 22q11 microdeletion in fetuses with nuchal translucency (NT) above the 99th percentile (>3.5 mm). A 22q11 microdeletion results in the development of 22q11 deletion syndrome, a spectrum of disorders also known as DiGeorge/Velocardiofacial syndrome. A total of 146 pregnancies met the inclusion criteria of NT >3.5 mm between 11+2 and 13+6 weeks' gestation, no structural malformation and normal karyotype. Chorionic villi samples were tested with either multiplex ligation-dependent probe amplification (MLPA) or fluorescent in situ hybridization (FISH) analysis for 22q11 microdeletion. None were diagnosed with the microdeletion. The estimated prevalence of 22q11 microdeletion in these otherwise normal fetuses with increased NT is below 2.7%.