Intrinsic PARG inhibitor sensitivity is mimicked by TIMELESS haploinsufficiency and rescued by nucleoside supplementation.

A subset of cancer cells are intrinsically sensitive to inhibitors targeting PARG, the poly(ADP-ribose) glycohydrolase that degrades PAR chains. Sensitivity is accompanied by persistent DNA replication stress, and can be induced by inhibition of TIMELESS, a replisome accelerator. However, the nature of the vulnerability responsible for intrinsic sensitivity remains undetermined. To understand PARG activity dependency, we analysed Timeless model systems and intrinsically sensitive ovarian cancer cells. We show that nucleoside supplementation rescues all phenotypes associated with PARG inhibitor sensitivity, including replisome speed and fork stalling, S-phase completion and mitotic entry, proliferation dynamics and clonogenic potential. Importantly nucleoside supplementation restores PARG inhibitor resistance despite the continued presence of PAR chains, indicating that sensitivity does not correlate with PAR levels. In addition, we show that inhibition of thymidylate synthase, an enzyme required for dNTP homeostasis, induces PARG-dependency. Together, these observations suggest that PARG inhibitor sensitivity reflects an inability to control replisome speed and/or maintain helicase-polymerase coupling in response to nucleotide imbalances.

A Microtiter Plate Assay at Acidic pH to Identify Potentiators that Enhance Pyrazinamide Activity Against Mycobacterium tuberculosis.

Pyrazinamide (PZA) is a key component of chemotherapy for the treatment of drug-susceptible tuberculosis (TB) and is likely to continue to be included in new drug combinations. Potentiation of PZA could be used to reduce the emergence of resistance, shorten treatment times, and lead to a reduction in the quantity of PZA consumed by patients, thereby reducing the toxic effects. Acidified medium is required for the activity of PZA against Mycobacterium tuberculosis. In vitro assessments of pyrazinamide activity are often avoided because of the lack of standardization, which has led to a lack of effective in vitro tools for assessing and/or enhancing PZA activity.We have developed and optimized a novel, robust, and reproducible, microtiter plate assay, that centers around acidity levels that are low enough for PZA activity. The assay can be applied to the evaluation of novel compounds for the identification of potentiators that enhance PZA activity. In this assay, potentiation of PZA is demonstrated to be statistically significant with the addition of rifampicin (RIF), which can, therefore, be used as a positive control. Conversely, norfloxacin demonstrates no potentiating activity with PZA and can be used as a negative control. The method, and the associated considerations, described here, can be adapted in the search for potentiators of other antimicrobials.

Czech medical coding assistant based on transformer networks.

The International Classification of Diseases (ICD) hierarchical taxonomy is used for so-called clinical coding of medical reports, typically presented in unstructured text. In the Czech Republic, it is currently carried out manually by a so-called clinical coder. However, due to the human factor, this process is error-prone and expensive. The coder needs to be properly trained and spends significant effort on each report, leading to occasional mistakes. The main goal of this paper is to propose and implement a system that serves as an assistant to the coder and automatically predicts diagnosis codes. These predictions are then presented to the coder for approval or correction, aiming to enhance efficiency and accuracy. We consider two classification tasks: main (principal) diagnosis; and all diagnoses. Crucial requirements for the implementation include minimal memory consumption, generality, ease of portability, and sustainability. The main contribution lies in the proposal and evaluation of ICD classification models for the Czech language with relatively few training parameters, allowing swift utilisation on the prevalent computer systems within Czech hospitals and enabling easy retraining or fine-tuning with newly available data. First, we introduce a small transformer-based model for each task followed by the design of a transformer-based "Four-headed" model incorporating four distinct classification heads. This model achieves comparable, sometimes even better results, against four individual models. Moreover this novel model significantly economises memory usage and learning time. We also show that our models achieve comparable results against state-of-the-art English models on the Mimic IV dataset even though our models are significantly smaller.

Hydrogen bonding heterogeneity correlates with protein folding transition state passage time as revealed by data sonification.

Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated "rarity" measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with "Highway" versus "Meander" versus "Ambiguous" transitions and to design algorithms that can identify these same folding pathways and critical protein-water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein-water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape.

Influence of Patient Weight on Prehospital Advanced Airway Procedure Success Rates.

OBJECTIVE: Previous investigations of the relationship between obesity and difficult airway management have provided mixed results. Almost universally, these studies were conducted in the hospital setting, and the influence of patient body weight on successful prehospital airway management remains unclear. Because patient weight could be one readily identifiable risk factor for problematic airway interventions, we sought to evaluate this relationship. METHODS: We conducted a retrospective analysis using the 2020 ESO Data Collaborative dataset. The inclusion criteria consisted of adult patients weighing >30kg with an attempted orotracheal intubation (OTI) and/or blind insertion airway device (BIAD) placement. Separate logistic regression models were developed to determine the influence of weight (dichotomized at 100 kg) on cumulative procedure success for OTI and BIAD, and linear regression models were used to identify trends for each across weight strata. RESULTS: A total of 45,344 patients met inclusionary criteria, among which 40,668(89.7%) suffered from a medical emergency, followed by 3,130(6.9%) with traumatic injuries, and 1,546(3.4%) attributable to a combined medical-trauma etiology. Cardiac arrest occurred either prior to EMS arrival or at some point during EMS care in 38,210(84.3%) patients. OTI was attempted in 18,153(40.0%) patients, while 21,597(47.6%) had a BIAD attempt and 5,594(12.3%) had both airway types attempted. The overall cumulative insertion success rates for OTI and BIAD were 79.5% and 92.7%, respectively. Altogether, 2,711(6.0%) had no advanced airway of any type successfully placed, which represents the overall failed advanced airway rate. After controlling for patient age, sex, minority status, and call type (medical vs. trauma), weight >100kg was associated with decreased likelihood of cumulative OTI success (OR = 0.64, p < 0.001), but higher likelihood of cumulative BIAD success (OR = 1.31, p < 0.001). Cumulative OTI success was associated with a negative 0.6% linear trend per 5 kg of body weight (p < 0.001) while cumulative BIAD success had a 0.2% positive trend (p < 0.001). CONCLUSION: This retrospective analysis of a national EMS database revealed that increasing patient weight was negatively associated with intubation success. A positive, but smaller, linear trend was observed for BIAD placement. Patient weight may be an easily identifiable predictor of difficult oral intubation and may be a consideration when selecting an airway management strategy.

Interlaboratory comparison of a multiplex immunoassay that measures human serum IgG antibodies against six-group B streptococcus polysaccharides.

Measurement of IgG antibodies against group B streptococcus (GBS) capsular polysaccharide (CPS) by use of a standardized and internationally accepted multiplex immunoassay is important for the evaluation of candidate maternal GBS vaccines in order to compare results across studies. A standardized assay is also required if serocorrelates of protection against invasive GBS disease are to be established in infant sera for the six predominant GBS serotypes since it would permit the comparison of results across the six serotypes. We undertook an interlaboratory study across five laboratories that used standardized assay reagents and protocols with a panel of 44 human sera to measure IgG antibodies against GBS CPS serotypes Ia, Ib, II, III, IV, and V. The within-laboratory intermediate precision, which included factors like the lot of coated beads, laboratory analyst, and day, was generally below 20% relative standard deviation (RSD) for all six serotypes, across all five laboratories. The cross-laboratory reproducibility was < 25% RSD for all six serotypes, which demonstrated the consistency of results across the different laboratories. Additionally, anti-CPS IgG concentrations for the 44-member human serum panel were established. The results of this study showed assay robustness and that the resultant anti-CPS IgG concentrations were reproducible across laboratories for the six GBS CPS serotypes when the standardized assay was used.

An externally validated guide to anatomical interpretation using a direct-vision ('IRIS') feeding tube.

BACKGROUND & AIMS: Most of the 11.5 million feeding tubes placed annually in Europe and the USA are placed 'blind'. This carries a 1.6% risk that these tubes will enter the lung and 0.5% cause pneumothorax or pneumonia regardless of whether misplacement is identified prior to feeding. Tube placement by direct vision may reduce the risk of respiratory or oesophageal misplacement. This study externally validated whether an 'operator guide' would enable novice operators to differentiate the respiratory and alimentary tracts. METHODS: One IRIS tube was placed in each of 40 patients. Novice operators interpreted anatomical position using the built-in tube camera. Interpretation was checked from recorded images by consultant gastroenterologists and end-of-procedure checks using pH or X-ray checked by Radiologists and a consultant intensivist. RESULTS: The 40 patients were a median of 68y (IQR: 56-75), 70% male, mostly medical (65%), conscious (67.5%) and 70% had no artificial airway. Three tubes were removed due to failed placement. In the remaining 37 placements, novice operators identified the airway in 17 (45.9%) and airway + respiratory tract in 19 (51.4%), but redirected all these tubes into the oesophagus. By using direct vision to reduce the proportion of tubes near the airway or in respiratory tract from 0.514 to 0, operator discrimination between the respiratory and alimentary tracts was highly significant (0.514 vs 0: p < 0.0001, power >99.9% when significance = 0.05). In addition, organ boundaries (respiratory tract vs oesophagus, oesophagus vs stomach, stomach vs intestine) were identified in 100%. CONCLUSIONS: Novice operators, trained using the guide, identified all respiratory misplacements and accurately interpreted IRIS tube position. Guide-based training could enable widespread use of direct vision as a means to prevent tube-related complications.

Mapping the distance between fire hazard and disaster for communities in Canadian forests.

Communities interspersed throughout the Canadian wildland are threatened by fires that have become bigger and more frequent in some parts of the country in recent decades. Identifying the fireshed (source area) and pathways from which wildland fire may ignite and spread from the landscape to a community is crucial for risk-reduction strategy and planning. We used outputs from a fire simulation model, including fire polygons and rate of spread, to map firesheds, fire pathways and corridors and spread distances for 1980 communities in the forested areas of Canada. We found fireshed sizes are larger in the north, where the mean distances between ecumene and fireshed perimeters were greater than 10 km. The Rayleigh Z test indicated that simulated fires around a large proportion of communities show significant directional trends, and these trends are stronger in the Boreal Plains and Shields than in the Rocky Mountain area. The average distance from which fire, when spreading at the maximum simulated rate, could reach the community perimeter was approximately 5, 12 and 18 km in 1, 2 and 3 days, respectively. The average daily spread distances increased latitudinally, from south to north. Spread distances were the shortest in the Pacific Maritime, Atlantic Maritime and Boreal Plains Ecozones, implying lower rates of spread compared to the rest of the country. The fire corridors generated from random ignitions and from ignitions predicted from local fire history differ, indicating that factors other than fuel (e.g. fire weather, ignition pattern) play a significant role in determining the direction that fires burn into a community.

Towards a core outcome set for dysarthria after stroke: What should we measure?

OBJECTIVE: To identify and agree on what outcome domains should be measured in research and clinical practice when working with stroke survivors who have dysarthria. DESIGN: Delphi process, two rounds of an online survey followed by two online consensus meetings. SETTING: UK and Australia. PARTICIPANTS: Stroke survivors with experience of dysarthria, speech and language therapists/pathologists working in stroke and communication researchers. METHODS: Initial list of outcome domains generated from existing literature and with our patient and public involvement group to develop the survey. Participants completed two rounds of this survey to rate importance. Outcomes were identified as 'in', 'unclear' or 'out' from the second survey. All participants were invited to two consensus meetings to discuss these results followed by voting to identify critically important outcome domains for a future Core Outcome Set. All outcomes were voted on in the consensus meetings and included if 70% of meeting participants voted 'yes' for critically important. RESULTS: In total, 148 surveys were fully completed, and 28 participants attended the consensus meetings. A core outcome set for dysarthria after stroke should include four outcome domains: (a) intelligibility of speech, (b) ability to participate in conversations, (c) living well with dysarthria, (d) skills and knowledge of communication partners (where relevant). CONCLUSIONS: We describe the consensus of 'what' speech outcomes after stroke are valued by all stakeholders including those with lived experience. We share these findings to encourage the measurement of these domains in clinical practice and research and for future research to identify 'how' best to measure these outcomes.

Efficient Large-Scale, Targeted Gravitational-Wave Probes of Supermassive Black-Hole Binaries.

Binary systems of supermassive black holes are promising sources of low-frequency gravitational waves (GWs) and bright electromagnetic emission. Pulsar timing array GW searches for individual binaries have been limited to only a few candidate systems due to computational demands, which get worse as more pulsars are added. By modeling the GW signal using only components from when the GW passes Earth (rather than also each pulsar), we find constraints on the binary's total mass and GW frequency that are similar to a full signal analysis, yet ∼70 times more efficient.

Specialized replication mechanisms maintain genome stability at human centromeres.

The high incidence of whole-arm chromosome aneuploidy and translocations in tumors suggests instability of centromeres, unique loci built on repetitive sequences and essential for chromosome separation. The causes behind this fragility and the mechanisms preserving centromere integrity remain elusive. We show that replication stress, hallmark of pre-cancerous lesions, promotes centromeric breakage in mitosis, due to spindle forces and endonuclease activities. Mechanistically, we unveil unique dynamics of the centromeric replisome distinct from the rest of the genome. Locus-specific proteomics identifies specialized DNA replication and repair proteins at centromeres, highlighting them as difficult-to-replicate regions. The translesion synthesis pathway, along with other factors, acts to sustain centromere replication and integrity. Prolonged stress causes centromeric alterations like ruptures and translocations, as observed in ovarian cancer models experiencing replication stress. This study provides unprecedented insights into centromere replication and integrity, proposing mechanistic insights into the origins of centromere alterations leading to abnormal cancerous karyotypes.

Factor Structure of the Teacher Strengths and Difficulties Questionnaire in a Large Community-Based Sample: An Investigation of Alternative Measurement Models.

The Strengths and Difficulties Questionnaire (SDQ) is a screening measure commonly used to assess behavioral and emotional symptoms and strengths among children and adolescents. However, despite its frequent use, its underlying factor structure remains an important area of inquiry. Whereas the original five-factor structure has often been supported through exploratory factor analysis, results from confirmatory analyses continue to yield mixed results. We analyzed data from youth in Grades K through 12 from a large epidemiologic study in the Southeastern United States. Teacher-report SDQ data were used to test three confirmatory factor models by school level (i.e., elementary [Grades K-5] and secondary [Grades 6-12]): The original five-factor model, a three-factor model, and a bifactor model. Model fit indices and reliability measures supported the original five-factor model as the preferred model when using the teacher-reported SDQ with both elementary and secondary school children. Implications for using the SDQ in applied research and predictive modeling are discussed.

Reproducible image-based profiling with Pycytominer.

Technological advances in high-throughput microscopy have facilitated the acquisition of cell images at a rapid pace, and data pipelines can now extract and process thousands of image-based features from microscopy images. These features represent valuable single-cell phenotypes that contain information about cell state and biological processes. The use of these features for biological discovery is known as image-based or morphological profiling. However, these raw features need processing before use and image-based profiling lacks scalable and reproducible open-source software. Inconsistent processing across studies makes it difficult to compare datasets and processing steps, further delaying the development of optimal pipelines, methods, and analyses. To address these issues, we present Pycytominer, an open-source software package with a vibrant community that establishes an image-based profiling standard. Pycytominer has a simple, user-friendly Application Programming Interface (API) that implements image-based profiling functions for processing high-dimensional morphological features extracted from microscopy images of cells. Establishing Pycytominer as a standard image-based profiling toolkit ensures consistent data processing pipelines with data provenance, therefore minimizing potential inconsistencies and enabling researchers to confidently derive accurate conclusions and discover novel insights from their data, thus driving progress in our field.

Traditional Uses, Pharmacological Activities, and Phytochemical Analysis of Diospyros mespiliformis Hochst. ex. A. DC (Ebenaceae): A Review.

Diospyros mespiliformis Hochst. ex. A. DC is widely distributed throughout Africa and around the world. It is utilized ethnobotanically to treat fevers, wounds, malaria, diabetes mellitus, and other diseases. This review aims to provide an exhaustive overview of the traditional uses, pharmacology, and phytochemical analysis of D. mespiliformis, with the objective of identifying its therapeutic potential for further research. Scientific resources, including Google Scholar, Science Direct, Web of Science, Pub Med, and Scopus, were used to find pertinent data on D. mespiliformis. Secondary metabolites tentatively identified from this species were primarily terpenoids, naphthoquinones, phenolics, and coumarins. D. mespiliformis has been reported to demonstrate pharmacological activities, including antimicrobial, antiproliferative, antiparasitic, antioxidant, anti-inflammatory, antiviral, anti-hypersensitivity, and antidiabetic properties. The phytochemicals and extracts from D. mespiliformis have been reported to have some pharmacological effects in in vivo studies and were not toxic to the animal models that were utilized. The D. mespiliformis information reported in this review provides researchers with a comprehensive summary of the current research status of this medicinal plant and a guide for further investigation.

Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs.

Single cell spatial interrogation of the immune-structural interactions in COVID -19 lungs is challenging, mainly because of the marked cellular infiltrate and architecturally distorted microstructure. To address this, we develop a suite of mathematical tools to search for statistically significant co-locations amongst immune and structural cells identified using 37-plex imaging mass cytometry. This unbiased method reveals a cellular map interleaved with an inflammatory network of immature neutrophils, cytotoxic CD8 T cells, megakaryocytes and monocytes co-located with regenerating alveolar progenitors and endothelium. Of note, a highly active cluster of immature neutrophils and CD8 T cells, is found spatially linked with alveolar progenitor cells, and temporally with the diffuse alveolar damage stage. These findings offer further insights into how immune cells interact in the lungs of severe COVID-19 disease. We provide our pipeline [Spatial Omics Oxford Pipeline (SpOOx)] and visual-analytical tool, Multi-Dimensional Viewer (MDV) software, as a resource for spatial analysis.

Development of A Standardized Opsonophagocytosis Killing Assay for Group B Streptococcus and Assessment in an Interlaboratory Study.

The placental transfer of antibodies that mediate bacterial clearance via phagocytes is likely important for protection against invasive group B Streptococcus (GBS) disease. A robust functional assay is essential to determine the immune correlates of protection and assist vaccine development. Using standard reagents, we developed and optimized an opsonophagocytic killing assay (OPKA) where dilutions of test sera were incubated with bacteria, baby rabbit complement (BRC) and differentiated HL60 cells (dHL60) for 30 min. Following overnight incubation, the surviving bacteria were enumerated and the % bacterial survival was calculated relative to serum-negative controls. A reciprocal 50% killing titer was then assigned. The minimal concentrations of anti-capsular polysaccharide (CPS) IgG required for 50% killing were 1.65-3.70 ng/mL (depending on serotype). Inhibition of killing was observed using sera absorbed with homologous CPS but not heterologous CPS, indicating specificity for anti-CPS IgG. The assay performance was examined in an interlaboratory study using residual sera from CPS-conjugate vaccine trials with international partners in the Group B Streptococcus Assay STandardisatiON (GASTON) Consortium. Strong correlations of reported titers between laboratories were observed: ST-Ia r = 0.88, ST-Ib r = 0.91, ST-II r = 0.91, ST-III r = 0.90 and ST-V r = 0.94. The OPKA is an easily transferable assay with accessible standard reagents and will be a valuable tool to assess GBS-specific antibodies in natural immunity and vaccine studies.

Advanced Female Primary Urethral Carcinoma with Nodal Extension Managed with Exclusive Use of Chemoradiotherapy: Report of a Case and Review of the Relevant Current Literature.

Primary urethral carcinoma (PUC) is a rare disease with frequent nodal metastasis at the time of diagnosis. Few risk factors have been established and overall prognosis remains poor. As of now, no clear therapeutic guidelines are established and management of advanced PUC often involves surgery which can have negative functional and psychological outcomes for the patient. Few authors have already reported the use of chemoradiotherapy alone to avoid surgery with some good short-term results. We report the case of a 48-year-old woman with advanced high-grade urothelial carcinoma of distal urethra associated to bilateral inguinal nodal metastasis. She was similarly and successfully treated using chemoradiotherapy exclusively without significant adverse effects. This experience reinforces benefits of a surgery-sparing management, when possible, as recommended in current guidelines.

Refinement of an ovine-based immunoglobulin therapy against SARS-CoV-2, with comparison of whole IgG versus F(ab')2 fragments.

The development of new therapies against SARS-CoV-2 is required to extend the toolkit of intervention strategies to combat the global pandemic. In this study, hyperimmune plasma from sheep immunised with whole spike SARS-CoV-2 recombinant protein has been used to generate candidate products. In addition to purified IgG, we have refined candidate therapies by removing non-specific IgG via affinity binding along with fragmentation to eliminate the Fc region to create F(ab')2 fragments. These preparations were evaluated for in vitro activity and demonstrated to be strongly neutralising against a range of SARS-CoV-2 strains, including Omicron B2.2. In addition, their protection against disease manifestations and viral loads were assessed using a hamster SARS-CoV-2 infection model. Results demonstrated protective effects of both IgG and F(ab')2, with the latter requiring sequential dosing to maintain in vivo activity due to rapid clearance from the circulation.