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Abstract Background Improvements in oxygenation and lung mechanics with prone position (PP) in patients with acute respiratory distress syndrome (ARDS) are inconstant. The objectives of the study were (i) to identify baseline variables, including the recruitment-to-inflation ratio (R/I), associated with a positive response to PP in terms of oxygenation (improvement of the ratio of arterial oxygen partial pressure over the inspired oxygen fraction (PaO2/FiO2) ≥ 20 mmHg) and lung mechanics; (ii) to evaluate whether the response to the previous PP session is associated with the response to the next session. Methods In this prospective, observational, single-center study in patients who underwent PP for ARDS due to COVID-19, respiratory variables were assessed just before PP and at the end of the session. Respiratory variables included mechanical ventilation settings and respiratory mechanics variables, including R/I, an estimate of the potential for lung recruitment compared to lung overinflation. Results In 50 patients, 201 PP sessions lasting 19 ± 3 h were evaluated. Neuromuscular blockades were used in 116 (58%) sessions. The PaO2/FiO2 ratio increased from 109 ± 31 mmHg to 165 ± 65 mmHg, with an increase ≥ 20 mmHg in 142 (71%) sessions. In a mixed effect logistic regression, only pre-PP PaO2/FiO2 (OR 1.12 (95% CI [1.01–1.24])/every decrease of 10 mmHg, p = 0.034) in a first model and improvement in oxygenation at the previous PP session (OR 3.69 (95% CI [1.27–10.72]), p = 0.017) in a second model were associated with an improvement in oxygenation with PP. The R/I ratio (n = 156 sessions) was 0.53 (0.30–0.76), separating lower- and higher-recruiters. Whereas PaO2/FiO2 improved to the same level in both subgroups, driving pressure and respiratory system compliance improved only in higher-recruiters (from 14 ± 4 to 12 ± 4 cmH2O, p = 0.027, and from 34 ± 11 to 38 ± 13 mL/cmH2O, respectively, p = 0.014). Conclusions A lower PaO2/FiO2 at baseline and a positive O2-response at the previous PP session are associated with a PP-induced improvement in oxygenation. In higher-recruiters, lung mechanics improved along with oxygenation. Benefits of PP could thus be greater in these patients.

Continuous venovenous hemofiltation (CVVH) with citrate anticoagulation has been shown to be associated with substantial losses of calcium and negative calcium balance in ICU patients, which may lead to excessive bone loss and osteoporosis. The aim of this study is to investigate whether plasma parathormone monitoring can identify patients with negative calcium balance during CVVH. This is a retrospective single-center study of all adult ICU patients treated with citrate CVVH from 2021 to 2023. PTH was measured routinely once per week. Calcium excretion in ultrafiltrate fluid and CVVH calcium balance were measured daily. In total, 274 PTH measurements were performed in 111 patients. In 61 measurements (22%), PTH was higher than the upper limit of normal (>8 pmol/L). If PTH was higher than normal, plasma ionized calcium was less than 1.16 mmol/L in 77% of cases and hypercalcemia was never present. In a subgroup of patients treated with CVVH for at least 36 h in the preceding 72 h, PTH values were similar for quartiles by cumulative calcium balance. Increased plasma concentrations of PTH are frequently found in ICU patients treated with citrate CVVH, but no association was found between PTH and the CVVH calcium balance over the last 72 h.

Abstract The primary aim of this study was to evaluate computed tomography (CT)-based bone density analysis at the level of thoracic vertebra 12 (Th12) as a screening method for decreased bone density in patients admitted to the intensive care unit (ICU). Interobserver variability was analyzed. Secondary aims were to assess the prevalence of CT-based low bone density upon ICU admission in a cohort of COVID-19 patients and to assess the potential effect of long-term ICU stay on bone density in these patients. Retrospective single-center cohort study. ICU of the Leiden University Medical Center (LUMC), the Netherlands. Patients admitted to the ICU of the LUMC between March 1st, 2020 and February 1st, 2022 with a diagnosis of COVID-19, and a length of ICU stay of ≥ 21 days. In the included patients both baseline chest CT scans (obtained upon ICU admission) and follow-up chest CT scans (obtained ≥ 21 days after ICU admission) were available for analysis. A total of 118 CT scans in 38 patients were analyzed. There was a good interobserver variability, with an overall mean absolute difference (between measurements of three observers) of 9.7 Hounsfield Units (HU) and an intraclass correlation coefficient (ICC) of 0.93 (95% CI 0.88–0.96). The effect of intravenous contrast administration on bone density measurements was small (+ 7.5 HU (95% CI 3.4–11.5 HU)) higher in contrast enhanced CT images compared to non contrast enhanced CT images). Thirty-seven percent of patients had a bone density

Abstract Background Scaffolding is a bioinformatics problem aimed at completing the contig assembly process by determining the relative position and orientation of these contigs. It can be seen as a paths and cycles cover problem of a particular graph called the “scaffold graph”. Results We provide some NP-hardness and inapproximability results on this problem. We also adapt a greedy approximation algorithm on complete graphs so that it works on a special class aiming to be close to real instances. The described algorithm is the first polynomial-time approximation algorithm designed for this problem on non-complete graphs. Conclusion Tests on a set of simulated instances show that our algorithm provides better results than the version on complete graphs.

Abstract Background International guidelines recommend to offer supportive care during a next pregnancy to couples affected by recurrent pregnancy loss (RPL). In previous research, several options for supportive care have been identified and women’s preferences have been quantified. Although it is known that RPL impacts the mental health of both partners, male preferences for supportive care have hardly been explored. Methods A cross-sectional study was conducted in couples who visited a specialized RPL clinic in the Netherlands between November 2018 and December 2019. Both members of the couples received a questionnaire that quantified their preferences for supportive care in a next pregnancy and they were asked to complete this independently from each other. Preferences for each supportive care option were analysed on a group level (by gender) and on a couple level, by comparing preferences of both partners. Results Ninety-two questionnaires (completed by 46 couples) were analysed. The overall need for supportive care indicated on a scale from 1 to 10 was 6.8 for men and 7.9 for women (P = 0.002). Both genders preferred to regularly see the same doctor with knowledge of their obstetric history, to make a plan for the first trimester and to have frequent ultrasound examinations. A lower proportion of men preferred a doctor that shows understanding (80% of men vs. 100% of women, P = 0.004) and a doctor that informs on wellbeing (72% vs. 100%, P = ≤0.000). Fewer men preferred support from friends (48% vs. 74%, P = 0.017). Thirty-seven percent of men requested more involvement of the male partner at the outpatient clinic, compared to 70% of women (P = 0.007). In 28% of couples, partners had opposing preferences regarding peer support. Conclusions While both women and men affected by RPL are in need of supportive care, their preferences may differ. Current supportive care services may not entirely address the needs of men. Health care professionals should focus on both partners and development of novel supportive care programs with specific attention for men should be considered.

The Fifth Haverford excavation season at Tel Beth-Shemesh (Ain Shams) in 1933 revealed a fractured tablet bearing a cuneiform inscription dating to the Late Bronze Age. Considered to be the earliest alphabetic cuneiform text uncovered in the Canaanite arena outside of Ugarit, this tablet quickly became the focus of many studies. Later readings suggested that this was the earliest example of a South Semitic Alphabetical sequence. Through petrographic material analysis, the present study examines the possible location of production of the tablet and discusses the implications with regard to the object's function and cultural context. [ABSTRACT FROM AUTHOR]

Abstract Background Diaphragm dysfunction is highly prevalent in mechanically ventilated patients. Recent work showed that changes in diaphragm shear modulus (ΔSMdi) assessed using ultrasound shear wave elastography (SWE) are strongly related to changes in Pdi (ΔPdi) in healthy subjects. The aims of this study were to investigate the relationship between ΔSMdi and ΔPdi in mechanically ventilated patients, and whether ΔSMdi is responsive to change in respiratory load when varying the ventilator settings. Methods A prospective, monocentric study was conducted in a 15-bed ICU. Patients were included if they met the readiness-to-wean criteria. Pdi was continuously monitored using a double-balloon feeding catheter orally introduced. The zone of apposition of the right hemidiaphragm was imaged using a linear transducer (SL10-2, Aixplorer, Supersonic Imagine, France). Ultrasound recordings were performed under various pressure support settings and during a spontaneous breathing trial (SBT). A breath-by-breath analysis was performed, allowing the direct comparison between ΔPdi and ΔSMdi. Pearson’s correlation coefficients (r) were used to investigate within-individual relationships between variables, and repeated measure correlations (R) were used for determining overall relationships between variables. Linear mixed models were used to compare breathing indices across the conditions of ventilation. Results Thirty patients were included and 930 respiratory cycles were analyzed. Twenty-five were considered for the analysis. A significant correlation was found between ΔPdi and ΔSMdi (R = 0.45, 95% CIs [0.35 0.54], p 0.06). Changing the condition of ventilation similarly affected ΔPdi and ΔSMdi. Patients in which ΔPdi–ΔSMdi correlation was non-significant had a faster respiratory rate as compared to that of patient with a significant ΔPdi–ΔSMdi relationship (median (Q1–Q3), 25 (18–33) vs. 21 (15–26) breaths.min−1, respectively). Conclusions We demonstrate that ultrasound SWE may be a promising surrogate to Pdi in mechanically ventilated patients. Respiratory rate appears to negatively impact SMdi measurement. Technological developments are needed to generalize this method in tachypneic patients. Trial registration NCT03832231 .

Retroviruses package two copies of their genomic RNA (gRNA) as non-covalently linked dimers. Many studies suggest that the retroviral nucleocapsid protein (NC) plays an important role in gRNA dimerization. The upper part of the L3 RNA stem-loop in the 5′ leader of the avian leukosis virus (ALV) is converted to the extended dimer by ALV NC. The L3 hairpin contains three stems and two internal loops. To investigate the roles of internal loops and stems in the NC-mediated extended dimer formation, we performed site-directed mutagenesis, gel electrophoresis, and analysis of thermostability of dimeric RNAs. We showed that the internal loops are necessary for efficient extended dimer formation. Destabilization of the lower stem of L3 is necessary for RNA dimerization, although it is not involved in the linkage structure of the extended dimer. We found that NCs from ALV, human immunodeficiency virus type 1 (HIV-1), and Moloney murine leukemia virus (M-MuLV) cannot promote the formation of the extended dimer when the apical stem contains ten consecutive base pairs. Five base pairs correspond to the maximum length for efficient L3 dimerization induced by the three NCs. L3 dimerization was less efficient with M-MuLV NC than with ALV NC and HIV-1 NC.

Abstract Mesenchymal stromal cells (MSC) secrete factors that contribute to organ homeostasis and repair in a tissue specific manner. For instance, kidney perivascular mesenchymal stromal cells (kPSCs) can facilitate renal epithelial repair through secretion of hepatocyte growth factor (HGF) while the secretome of bone marrow MSCs gives rise to immunosuppression. Stromal cells function in a complex 3-dimensional (3D) connective tissue architecture that induces conformational adaptation. Here we tested the hypothesis that surface topography and associated cell adaptations dictate stromal cell function through tuning of the cytokines released. To this end, we cultured human bone marrow and kidney perivascular stromal cells in the TopoWell plate, a custom-fabricated multi-well plate containing 76 unique bioactive surface topographies. Using fluorescent imaging, we observed profound changes in cell shape, accompanied by major quantitative changes in the secretory capacity of the MSCs. The cytokine secretion profile was closely related to cell morphology and was stromal cell type specific. Our data demonstrate that stromal cell function is determined by microenvironment structure and can be manipulated in an engineered setting. Our data also have implications for the clinical manufacturing of mesenchymal stromal cell therapy, where surface topography during bioreactor expansion should be taken into account to preserve therapeutic properties.

Historical urban warehouses are remarkable structures. Today, however, and despite their robust architecture, they have become vulnerable urban heritage threatened with demolition. Current research being carried out at the Vrije Universiteit Brussel focuses on the development of knowledge about the architecture, operation and construction of warehouses in Antwerp, Brussels and Ghent and their integration in the urban fabric, to support their preservation and respectful adaptive reuse. This paper contains the results of in-depth archival and first on-site investigations of nineteenth and twentieth-century warehouses in the historic city centre of Brussels, covering the first industrial zone around the river Senne and the docks. Eighty demolished and still existing urban warehouses are analysed by focusing first on the storage of some well-represented goods: hay, timber, beer and textile. The analysis shows that the four goods correspond to four types of warehouses that differ in their architecture, organisation, construction and integration in the urban fabric.

Historical urban warehouses are remarkable structures. Today, however, and despite their robust architecture, they have become vulnerable urban heritage threatened with demolition. Current research being carried out at the Vrije Universiteit Brussel focuses on the development of knowledge about the architecture, operation and construction of warehouses in Antwerp, Brussels and Ghent and their integration in the urban fabric, to support their preservation and respectful adaptive reuse. This paper contains the results of in-depth archival and first on-site investigations of nineteenth and twentieth-century warehouses in the historic city centre of Brussels, covering the first industrial zone around the river Senne and the docks. Eighty demolished and still existing urban warehouses are analysed by focusing first on the storage of some well-represented goods: hay, timber, beer and textile. The analysis shows that the four goods correspond to four types of warehouses that differ in their architecture, organisation, construction and integration in the urban fabric.

Historical urban warehouses are remarkable structures. Today, however, and despite their robust architecture, they have become vulnerable urban heritage threatened with demolition. Current research being carried out at the Vrije Universiteit Brussel focuses on the development of knowledge about the architecture, operation and construction of warehouses in Antwerp, Brussels and Ghent and their integration in the urban fabric, to support their preservation and respectful adaptive reuse. This paper contains the results of in-depth archival and first on-site investigations of nineteenth and twentieth-century warehouses in the historic city centre of Brussels, covering the first industrial zone around the river Senne and the docks. Eighty demolished and still existing urban warehouses are analysed by focusing first on the storage of some well-represented goods: hay, timber, beer and textile. The analysis shows that the four goods correspond to four types of warehouses that differ in their architecture, organisation, construction and integration in the urban fabric.

The HIV-1 nucleocapsid protein (NC) is a small basic protein containing two zinc fingers (ZF) separated by a short linker. It is involved in several steps of the replication cycle and acts as a nucleic acid chaperone protein in facilitating nucleic acid strand transfers occurring during reverse transcription. Recent analysis of three-dimensional structures of NC-nucleic acids complexes established a new property: the unpaired guanines targeted by NC are more often inserted in the C-terminal zinc finger (ZF2) than in the N-terminal zinc finger (ZF1). Although previous NMR dynamic studies were performed with NC, the dynamic behavior of the linker residues connecting the two ZF domains remains unclear. This prompted us to investigate the dynamic behavior of the linker residues. Here, we collected 15N NMR relaxation data and used for the first time data at several fields to probe the protein dynamics. The analysis at two fields allows us to detect a slow motion occurring between the two domains around a hinge located in the linker at the G35 position. However, the amplitude of motion appears limited in our conditions. In addition, we showed that the neighboring linker residues R29, A30, P31, R32, K33 displayed restricted motion and numerous contacts with residues of ZF1. Our results are fully consistent with a model in which the ZF1-linker contacts prevent the ZF1 domain to interact with unpaired guanines, whereas the ZF2 domain is more accessible and competent to interact with unpaired guanines. In contrast, ZF1 with its large hydrophobic plateau is able to destabilize the double-stranded regions adjacent to the guanines bound by ZF2. The linker residues and the internal dynamics of NC regulate therefore the different functions of the two zinc fingers that are required for an optimal chaperone activity.

HIV-1 nucleocapsid protein (NC) is involved in the rearrangement of nucleic acids occurring in key steps of reverse transcription. The protein, through its two zinc fingers, interacts preferentially with unpaired guanines in single-stranded sequences. In mini-cTAR stem-loop, which corresponds to the top half of the cDNA copy of the transactivation response element of the HIV-1 genome, NC was found to exhibit a clear preference for the TGG sequence at the bottom of mini-cTAR stem. To further understand how this site was selected among several potential binding sites containing unpaired guanines, we probed the intrinsic dynamics of mini-cTAR using (13)C relaxation measurements. Results of spin relaxation time measurements have been analyzed using the model-free formalism and completed by dispersion relaxation measurements. Our data indicate that the preferentially recognized guanine in the lower part of the stem is exempt of conformational exchange and highly mobile. In contrast, the unrecognized unpaired guanines of mini-cTAR are involved in conformational exchange, probably related to transient base-pairs. These findings support the notion that NC preferentially recognizes unpaired guanines exhibiting a high degree of mobility. The ability of NC to discriminate between close sequences through their dynamic properties contributes to understanding how NC recognizes specific sites within the HIV genome.