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Designed enzymes are of fundamental and technological interest. Experimental directed evolution still has significant limitations, and computational approaches are a complementary route. A designed enzyme should satisfy multiple criteria: stability, substrate binding, transition state binding. Such multi-objective design is computationally challenging. Two recent studies used adaptive importance sampling Monte Carlo to redesign proteins for ligand binding. By first flattening the energy landscape of the apo protein, they obtained positive design for the bound state and negative design for the unbound. We have now extended the method to design an enzyme for specific transition state binding, i.e., for its catalytic power. We considered methionyl-tRNA synthetase (MetRS), which attaches methionine (Met) to its cognate tRNA, establishing codon identity. Previously, MetRS and other synthetases have been redesigned by experimental directed evolution to accept noncanonical amino acids as substrates, leading to genetic code expansion. Here, we have redesigned MetRS computationally to bind several ligands: the Met analog azidonorleucine, methionyl-adenylate (MetAMP), and the activated ligands that form the transition state for MetAMP production. Enzyme mutants known to have azidonorleucine activity were recovered by the design calculations, and 17 mutants predicted to bind MetAMP were characterized experimentally and all found to be active. Mutants predicted to have low activation free energies for MetAMP production were found to be active and the predicted reaction rates agreed well with the experimental values. We suggest the present method should become the paradigm for computational enzyme design.

The archaeal ribosome is of the eukaryotic type. TACK and Asgard superphyla, the closest relatives of eukaryotes, have ribosomes containing eukaryotic ribosomal proteins not found in other archaea, eS25, eS26 and eS30. Here, we investigate the case of Saccharolobus solfataricus , a TACK crenarchaeon, using mainly leaderless mRNAs. We characterize the small ribosomal subunit of S. solfataricus bound to SD-leadered or leaderless mRNAs. Cryo-EM structures show eS25, eS26 and eS30 bound to the small subunit. We identify two ribosomal proteins, aS33 and aS34, and an additional domain of eS6. Leaderless mRNAs are bound to the small subunit with contribution of their 5’-triphosphate group. Archaeal eS26 binds to the mRNA exit channel wrapped around the 3’ end of rRNA, as in eukaryotes. Its position is not compatible with an SD:antiSD duplex. Our results suggest a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation. Here, structures of archaeal ribosome show details of ribosomal proteins and leaderless mRNAs binding to the small subunit, suggesting a positive role of eS26 in leaderless mRNAs translation and possible evolutionary routes from archaeal to eukaryotic translation.

Barbiturates are proposed as a second/third line treatment for intracranial hypertension in traumatic brain injury (TBI) patients, but the literature remains uncertain regarding their benefit/risk balance. We aimed to evaluate the impact of barbiturates therapy in TBI patients with early intracranial hypertension on the intensive care unit (ICU) survival, the occurrence of ventilator-associated pneumonia (VAP), and the patient’s functional status at three months. We used the French AtlanREA prospective cohort of trauma patients. Using a propensity score-based methodology (inverse probability of treatment weighting), we compared patients having received barbiturates within the first 24 hours of admission (barbiturates group) and those who did not (control group). We used cause-specific Cox models for ICU survival and risk of VAP, and logistic regression for the 3-month Glasgow Outcome Scale (GOS) evaluation. Among the 1396 patients with severe trauma, 383 had intracranial hypertension on admission and were analyzed. Among them, 96 (25.1%) received barbiturates. The early use of barbiturates was significantly associated with increased ICU mortality (HR = 1.85, 95%CI 1.03–3.33). However, barbiturates treatment was not significantly associated with VAP (HR = 1.02, 95%CI 0.75–1.41) or 3-month GOS (OR = 1.67, 95%CI 0.84–3.33). Regarding the absence of relevant clinical trials, our results suggest that each early prescription of barbiturates requires a careful assessment of the benefit/risk ratio.

Wire guided localization is widely used as the standard method of pre-operative localization of breast lesions. The aim was to assess outcomes following the introduction of a novel non-wire guided, magnetic surgical marker navigation system. A prospective study between May 2022 and June 2023 established a data base of the first 200 procedures performed using the Sirius Pintuition GPS Detect magnetic marker. The primary outcome measures were the successful excision of the target lesion and retrieval of the magnetic marker. The primary lesion was excised and the magnetic marker was retrieved in all 200 procedures. In 17 procedures (8.5% of the total sample), the magnetic marker was dislodged during surgery; however, the primary lesion was still effectively excised with clear margins without the need for an additional procedure or radiologic assistance. The re-excision rate to achieve margin clearance was 9%. Insertion of the marker was classified as “easy” and “in contact with the target” by the radiologist in all cases (100%). This study has shown that surgical marker navigation reliably localizes lesions and is associated with low re-excision rates. We also perceived improvement in theater planning.

Background Neoadjuvant chemotherapy has several advantages, including reducing the number of mastectomies. Breast conserving surgeries avoid certain complications and sequelae, reduces hospital stays and improves patients’ quality of life and aesthetics. The objective was to investigate factors associated with breast conserving surgery after neoadjuvant chemotherapy for breast cancer. Methods A single-center, retrospective, observational cohort study was conducted. For all women diagnosed with breast cancer between 2012 and 2022 who had received neoadjuvant chemotherapy prior to surgery, sociodemographic, clinical, anatomopathological and radiological data before and after neoadjuvant chemotherapy were recorded. Patients were divided into two groups: “breast conserving” surgery and “total mastectomy” surgery. Descriptive statistics were used to summarize the data. Factors associated with breast conserving surgery were studied using univariate and multivariate (logistic regression model) analyses. Results A total of 361 patients were included: 212 (58.7%) with breast conserving surgery and 149 (41.3%) with total mastectomy surgery. In multivariate analysis, unifocal disease (OR = 3.4; 95% CI [1.5; 7.6]; p  = 0.004), clinical complete response (OR = 4.4; 95% CI [2.1; 9.1]; p  < 0.0001) and clinical tumor less than 5 cm (stages T0, T1 or T2) (OR = 3.4; 95% CI [1.6; 6.9]; p  = 0.001) were independently associated with breast conserving surgery. There was no difference in Scarff Bloom and Richardson grade, Ki67 proliferation index, molecular subtype or metastatic status. Conclusion Several factors were independently associated with breast conserving surgery, including: unifocality, clinical complete response (cCR) and clinical tumor less than 5 cm.

The aim of this study was to develop a new diagnostic tool to predict lymph node metastasis (LNM) in patients with advanced epithelial ovarian cancer undergoing primary cytoreductive surgery. The FRANCOGYN group's multicenter retrospective ovarian cancer cohort furnished the patient population on which we developed a logistic regression model. The prediction model equation enabled us to create LNM risk groups with simple lymphadenectomy decision rules associated with a user-friendly free interactive web application called shinyLNM. 277 patients from the FRANCOGYN cohort were included; 115 with no LNM and 162 with LNM. Three variables were independently and significantly (p<0.05) associated with LNM in multivariate analysis: pelvic and/or para-aortic LNM on CT and/or PET/CT (p<0.00), initial PCI [greater than or equal to] 10 and/or diaphragmatic carcinosis (p = 0.02), and initial CA125 [greater than or equal to] 500 (p = 0.02). The ROC-AUC of this prediction model after leave-one-out cross-validation was 0.72. There was no difference between the predicted and the observed probabilities of LNM (p = 0.09). Specificity for the group at high risk of LNM was 83.5%, the LR+ was 2.73, and the observed probability of LNM was 79.3%; sensitivity for the group at low-risk of LNM was 92.0%, the LR- was 0.24, and the observed probability of LNM was 25.0%. This new tool may prove useful for improving surgical planning and provide useful information for patients.

Therapeutic strategies for epithelial ovarian cancers are evolving with the advent of immunotherapy, such as PD-L1 inhibitors, with encouraging results. However, little data are available on PDL-1 expression in ovarian cancers. Thus, we set out to determine the PD-L1 expression according to histological subtype. We evaluated the expression of two PD-L1 clones – QR1 and E1L3N – with two scores, one based on the percentage of labeled tumor cells (tumor proportion score, TPS) and the other on labeled immune cells (combined proportion score, CPS) in a consecutive retrospective series of 232 ovarian cancers. PD-L1 expression was more frequent in high grade serous carcinoma (27.5% with E1L3N clone and 41.5% with QR1 clone), grade 3 endometrioid carcinoma (25% with E1L3N clone and 50% with QR1 clone), and clear-cell carcinomas (27.3% with E1L3N clone and 29.6% with QR1 clone) than other histological subtypes with CPS score. Using the CPS score, 17% of cases were labeled with E1L3N vs 28% with QR1. Using the TPS score, 14% of cases were positive to E1L3N vs 17% for QR1. For TPS and CPS, respectively, 77% and 78% of the QR1 cases were concordant with E1L3N for the thresholds of 1%. Overall and progression-free survival between PD-L1 positive and PD-L1 negative patients were not different across all histological types, and each subtype in particular for serous carcinomas expressing PD-L1. Expression of PD-L1 is relatively uncommon in epithelium ovarian tumors. When positive, usually <10% of tumor cells are labeled. QR1 clone and CPS appear the best tools to evaluate PD-L1 expression.

Introduction/BackgroundLow-grade serous ovarian cancer (LGSOC) is a recent histologic diagnosis. The surgical approach of this disease has been little investigated and modeled on the management of high-grade serous ovarian carcinoma. The prognostic impact of the largest dimension of residual disease after primary surgery is still debated. This study evaluates the impact of size of residuals after primary debulking surgery (PDS) on progression-free (PFS) and overall survival (OS) in patient with advanced LGSOC.MethodologyA comprehensive search of PubMed and Cochrane Library databases was conducted to obtain all the studies from 1/2005 to 1/2023 evaluating progression-free and overall survival in patients with no residual disease (CC0 - CC1) as compared to patients with residual disease (CC2) after PDS for LGSOC. Meta-analysis was performed, and survival outcomes were calculated.ResultsA total of 12 relevant studies (2030 patients) were identified for analysis. The proportion of PDS was 87%. The median proportion of patients in each cohort undergoing suboptimal cytoreductive surgery (CC2) was 27%. The median follow-up for all cohorts was 22 months (16.7–56.8) in PFS and 72 months (48.3–130.7) in OS. The presence of residual disease (CC2) after primary debulking surgery had a significant negative impact on PFS (HR = 2.50, 95% CI = 1.95–3.21, p<0.01), and on OS (HR = 2.27, 95% CI = 1.50–3.43, p<0.01).ConclusionFor advanced LGSOC, primary debulking surgery with macroscopic residual disease is associated with poor survival in PFS and OS. Primary debulking surgery with no gross residual peritoneal disease should be preferred when it is possible.DisclosuresAll the authors have no potential conflict of interest to report.

PurposeShortening the duration of antibiotic therapy (ABT) is a key measure in antimicrobial stewardship. The optimal duration of ABT for treatment of postoperative intra-abdominal infections (PIAI) in critically ill patients is unknown.MethodsA multicentre prospective randomised trial conducted in 21 French intensive care units (ICU) between May 2011 and February 2015 compared the efficacy and safety of 8-day versus 15-day antibiotic therapy in critically ill patients with PIAI. Among 410 eligible patients (adequate source control and ABT on day 0), 249 patients were randomly assigned on day 8 to either stop ABT immediately (n = 126) or to continue ABT until day 15 (n = 123). The primary endpoint was the number of antibiotic-free days between randomisation (day 8) and day 28. Secondary outcomes were death, ICU and hospital length of stay, emergence of multidrug-resistant (MDR) bacteria and reoperation rate, with 45-day follow-up.ResultsPatients treated for 8 days had a higher median number of antibiotic-free days than those treated for 15 days (15 [6–20] vs 12 [6–13] days, respectively; P < 0.0001) (Wilcoxon rank difference 4.99 days [95% CI 2.99–6.00; P < 0.0001). Equivalence was established in terms of 45-day mortality (rate difference 0.038, 95% CI − 0.013 to 0.061). Treatments did not differ in terms of ICU and hospital length of stay, emergence of MDR bacteria or reoperation rate, while subsequent drainages between day 8 and day 45 were observed following short-course ABT (P = 0.041).ConclusionShort-course antibiotic therapy in critically ill ICU patients with PIAI reduces antibiotic exposure. Continuation of treatment until day 15 is not associated with any clinical benefit.Clinicaltrials.gov identifierNCT01311765.