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Tuberculous meningitis (TBM) is the most severe form of tuberculosis. Corticosteroids are currently recommended as an adjunctive therapy in HIV-negative adults with TBM. However, benefit from corticosteroids in TBM may depend upon host leukotriene A4 hydrolase (LTA4H) genotype and the corresponding inflammatory phenotypes. This article describes the planned analyses for the primary publication of the results of the LAST ACT clinical trial (NCT03100786): ‘Leukotriene A4 hydrolase Stratified Trial of Adjunctive Corticosteroids for HIV-negative adults with Tuberculous meningitis’. The primary hypothesis addressed by the trial is that LTA4H genotype, in particular CC or CT genotype, determines whether adjunctive dexamethasone benefits or harms adults with TBM. The trial was an LTA4H genotype stratified, parallel group, randomised, double blind, placebo-controlled multi-centre Phase III trial of dexamethasone given for 6–8 weeks in addition to standard anti-tuberculosis drugs. LTA4H genotype (CC, CT, TT) was determined in all participants prior to randomisation; only those with CC or CT genotype were randomised to dexamethasone or placebo. All TT genotype participants received dexamethasone because prior data indicated survival was increased by dexamethasone in this genotype. The primary endpoint was all-cause death or new neurological event over the first 12 months after randomisation. We took a hybrid trial-design approach which aims to prove non-inferiority of placebo first but also allows claiming superiority of placebo in case dexamethasone causes substantial harm. This statistical analysis plan expands upon and updates the analysis plan outlined in the published study protocol.

Background Awake prone positioning (APP) may be beneficial in patients with respiratory failure who are not receiving mechanical ventilation. Randomized controlled trials of APP have been performed during peak COVID-19 periods in unvaccinated populations, with limited data on compliance or patient acceptability. We aimed to evaluate the efficacy and acceptability of APP in a lower-middle income country in an open-label randomized controlled trial using a dedicated APP implementation team and wearable continuous-monitoring devices. Methods The trial was performed at a tertiary level hospital in Ho Chi Minh City, Vietnam, recruiting adults (≥18 years) hospitalized with moderate or severe COVID-19 and receiving supplemental oxygen therapy via nasal/facemask systems or high-flow nasal cannula (HFNC). Patients were allocated by a computer-generated random number sequence in a 1:1 ratio to standard care or APP, where a dedicated team provided bedside support. Wearable devices continuously recorded pulse oximetry and body position continuously. Our primary outcome was escalation of respiratory support within 28 days of randomization. Results Ninety-three patients were enrolled in this study between March 2022 and March 2023. Eighty (86%) patients had received ≥2 doses of SARS-CoV2 vaccine. The study was terminated early because of a reduction in the number of eligible patients. Data from 46 patients allocated to APP and 47 to standard care were available for analysis. At baseline, 19/47 (40%) patients allocated to the standard care group and 14/46 (30%) patients allocated to the APP group received HFNC. Continuous monitoring data were available for all patients monitored with wearable devices. Significantly greater mean daily APP times were achieved in those allocated to APP, however, most achieved less than the target 8 h/day. We did not detect clear differences in the primary outcome (relative risk,RR, 0.85, 95% CI 0.40-1.78, p=0.67) or secondary outcomes, including intubation rate and 28-day mortality. Patients reported prone positioning was comfortable, although almost all patients preferred supine positioning. No adverse events associated with the intervention were observed. Conclusions APP was not associated with benefit, but there was no sign of harm. Continuous monitoring with wearable devices is both feasible and acceptable for patients. In our population, achieving prolonged APP time was challenging despite a dedicated support team, and patients preferred supine positioning. Clinical Trials Registration NCT05083130.

Tuberculous meningitis (TBM) is the most severe form of tuberculosis. Corticosteroids are currently recommended as an adjunctive therapy in HIV-negative adults with TBM. However, benefit from corticosteroids in TBM may depend upon host leukotriene A4 hydrolase (LTA4H) genotype and the corresponding inflammatory phenotypes. This article describes the planned analyses for the primary publication of the results of the LAST ACT clinical trial (NCT03100786): ‘Leukotriene A4 hydrolase Stratified Trial of Adjunctive Corticosteroids for HIV-negative adults with Tuberculous meningitis’. The primary hypothesis addressed by the trial is that LTA4H genotype, in particular CC or CT genotype, determines whether adjunctive dexamethasone benefits or harms adults with TBM. The trial was an LTA4H genotype stratified, parallel group, randomised, double blind, placebo-controlled multi-centre Phase III trial of dexamethasone given for 6–8 weeks in addition to standard anti-tuberculosis drugs. LTA4H genotype (CC, CT, TT) was determined in all participants prior to randomisation; only those with CC or CT genotype were randomised to dexamethasone or placebo. All TT genotype participants received dexamethasone because prior data indicated survival was increased by dexamethasone in this genotype. The primary endpoint was all-cause death or new neurological event over the first 12 months after randomisation. We took a hybrid trial-design approach which aims to prove non-inferiority of placebo first but also allows claiming superiority of placebo in case dexamethasone causes substantial harm. This statistical analysis plan expands upon and updates the analysis plan outlined in the published study protocol.

Dipicolinic acid (DPA) is a major constituent of spores and reportedly provides protection against inactivation by various thermal processes; however, the relationship between DPA and resistance towards pressure-assisted thermal processing is not well understood. Thermal and pressure-assisted thermal inactivation studies of Clostridium botulinum nonproteolytic strains QC-B and 610-F, proteolytic strain Giorgio-A, and thermal surrogate Clostridium sporogenes PA3679 spores suspended in ACES buffer (0.05 M, pH 7.0) were performed to determine if a relationship exists between DPA release and log reduction of spores. Thermal inactivation at 80, 83, and 87 °C for nonproteolytic strains and 101, 105, and 108 °C for the proteolytic strain and thermal surrogate were conducted. Pressure-assisted thermal inactivation for nonproteolytic strains at 83 °C/600 MPa and for the proteolytic strain and thermal surrogate at 105 °C/600 MPa were performed. Surviving spores were enumerated by 5-tube MPN method for log reductions and analyzed for released DPA by liquid chromatography-tandem mass spectrometry. The correlation between MPN log reductions, released DPA, and D-values were calculated. A positive correlation between released DPA and log reduction of spores was observed for QC-B and 610-F at 80 and 83 °C (r = 0.6073 − 0.7755; P 0.05). A strong, positive correlation (r = 0.8359 − 0.9284; P 0.05) was found for PA3679 after pressure-assisted thermal treatment. These results suggest a correlation exists between DPA release and heat resistance; however, the level of correlation varied between strains and temperatures. The findings from this research may aid in the development of spore inactivation strategies targeting the thermal resistance profiles of various strains of C. botulinum spores.

Mortality and morbidity from tuberculous meningitis (TBM) are common, primarily due to inflammatory response to Mycobacterium tuberculosis infection, yet the underlying mechanisms remain poorly understood. We aimed to uncover genes and pathways associated with TBM pathogenesis and mortality, and determine the best predictors of death, utilizing whole-blood RNA sequencing from 281 Vietnamese adults with TBM, 295 pulmonary tuberculosis (PTB), and 30 healthy controls. Through weighted gene co-expression network analysis, we identified hub genes and pathways linked to TBM severity and mortality, with a consensus analysis revealing distinct patterns between HIV-positive and HIV-negative individuals. We employed multivariate elastic-net Cox regression to select candidate predictors of death, then logistic regression and internal bootstrap validation to choose best predictors. Increased neutrophil activation and decreased T and B cell activation pathways were associated with TBM mortality. Among HIV-positive individuals, mortality associated with increased angiogenesis, while HIV-negative individuals exhibited elevated TNF signaling and impaired extracellular matrix organization. Four hub genes—MCEMP1, NELL2, ZNF354C, and CD4—were strong TBM mortality predictors. These findings indicate that TBM induces a systemic inflammatory response similar to PTB, highlighting critical genes and pathways related to death, offering insights for potential therapeutic targets alongside a novel four-gene biomarker for predicting outcomes.

Tuberculosis (TB) causes more deaths worldwide than any other infectious disease. Progress in reducing the global burden of TB stalled during the COVID-19 pandemic; an estimated 10.6 million persons became [...]

Code obfuscation has become an essential practice in modern software development, designed to make source or machine code challenging for both humans and computers to comprehend. It plays a crucial role in cybersecurity by protecting intellectual property, safeguarding trade secrets, and preventing unauthorized access or reverse engineering. However, the lack of transparency in obfuscated code raises significant ethical concerns, including the potential for harmful or unethical uses such as hidden data collection, malicious features, back doors, and concealed vulnerabilities. These issues highlight the need for a balanced approach that ensures the protection of developers’ intellectual property while addressing ethical responsibilities related to user privacy, transparency, and societal impact. This paper investigates various code obfuscation techniques, their benefits, challenges, and practical applications, underscoring their relevance in contemporary software development. This study examines obfuscation methods and tools, evaluates machine learning models—including Random Forest, Gradient Boosting, and Support Vector Machine—and presents experimental results aimed at classifying obfuscated versus non-obfuscated files. Our findings demonstrate that these models achieve high accuracy in identifying obfuscation methods employed by tools such as Jlaive, Oxyry, PyObfuscate, Pyarmor, and py-obfuscator. This research also addresses emerging ethical concerns and proposes guidelines for a balanced, responsible approach to code obfuscation.

Background Awake prone positioning (APP) may be beneficial in patients with respiratory failure who are not receiving mechanical ventilation. Randomized controlled trials of APP have been performed during peak COVID-19 periods in unvaccinated populations, with limited data on compliance or patient acceptability. We aimed to evaluate the efficacy and acceptability of APP in a lower-middle income country in an open-label randomized controlled trial using a dedicated APP implementation team and wearable continuous-monitoring devices. Methods The trial was performed at a tertiary level hospital in Ho Chi Minh City, Vietnam, recruiting adults (≥18 years) hospitalized with moderate or severe COVID-19 and receiving supplemental oxygen therapy via nasal/facemask systems or high-flow nasal cannula (HFNC). Patients were allocated by a computer-generated random number sequence in a 1:1 ratio to standard care or APP, where a dedicated team provided bedside support. Wearable devices continuously recorded pulse oximetry and body position continuously. Our primary outcome was escalation of respiratory support within 28 days of randomization. Results Ninety-three patients were enrolled in this study between March 2022 and March 2023. Eighty (86%) patients had received ≥2 doses of SARS-CoV2 vaccine. The study was terminated early because of a reduction in the number of eligible patients. Data from 46 patients allocated to APP and 47 to standard care were available for analysis. At baseline, 19/47 (40%) patients allocated to the standard care group and 14/46 (30%) patients allocated to the APP group received HFNC. Continuous monitoring data were available for all patients monitored with wearable devices. Significantly greater mean daily APP times were achieved in those allocated to APP, however, most achieved less than the target 8 h/day. We did not detect clear differences in the primary outcome (relative risk,RR, 0.85, 95% CI 0.40-1.78, p=0.67) or secondary outcomes, including intubation rate and 28-day mortality. Patients reported prone positioning was comfortable, although almost all patients preferred supine positioning. No adverse events associated with the intervention were observed. Conclusions APP was not associated with benefit, but there was no sign of harm. Continuous monitoring with wearable devices is both feasible and acceptable for patients. In our population, achieving prolonged APP time was challenging despite a dedicated support team, and patients preferred supine positioning. Clinical Trials Registration NCT05083130.

Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15–60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.

A fundamental aspect of decision making is the speed-accuracy tradeoff (SAT): slower decisions tend to be more accurate, but because time is a scarce resource people prefer to conclude decisions more quickly. The current research adds to the SAT literature by documenting two previously unrecognized influences on the SAT: perception shifts and goal activation. Decision makers' perceptions of what constitutes a "fast" or a "slow" decision, and what constitutes an "accurate" or "inaccurate" decision, are based on prior experience, and these perceptions influence decision speed. Similarly, previous experience in a decision context associates the context with a particular decision goal. Thus, in later decisions the decision context will activate this goal, and influence decision speed. Both of these mechanisms contribute to a specific decision bias: decision speeds are biased toward original decision speeds in a decision context. Four experiments provide evidence for the bias and the two contributing mechanisms.

Abstract Salmonella enterica serotype 1,4,[5],12:i:- (Typhimurium monophasic variant) of sequence type (ST) 34 has emerged as the predominant pandemic genotype in recent decades. Despite increasing reports of resistance to antimicrobials in Southeast Asia, Salmonella ST34 population structure and evolution remained understudied in the region. Here we performed detailed genomic investigations on 454 ST34 genomes collected from Vietnam and diverse geographical sources to elucidate the pathogen’s epidemiology, evolution and antimicrobial resistance. We showed that ST34 has been introduced into Vietnam in at least nine occasions since 2000, forming five co-circulating major clones responsible for paediatric diarrhoea and bloodstream infection. Most expansion events were associated with acquisitions of large multidrug resistance plasmids of IncHI2 or IncA/C2. Particularly, the self-conjugative IncA/C2 pST34VN2 (co-transferring bla CTX-M-55, mcr-3.1, and qnrS1) underlies local expansion and intercontinental spread in two separate ST34 clones. At the global scale, Southeast Asia was identified as a potential hub for the emergence and dissemination of multidrug resistant Salmonella ST34, and mutation analysis suggests of selection in antimicrobial responses and key virulence factors.

BackgroundCanonical α/β T-cell receptors (TCRs) bind to human leukocyte antigen (HLA) displaying antigenic peptides to elicit T cell-mediated cytotoxicity. TCR-engineered T-cell immunotherapies targeting cancer-specific peptide-HLA complexes (pHLA) are generating exciting clinical responses, but owing to HLA restriction they are only able to target a subset of antigen-positive patients. More recently, evidence has been published indicating that naturally occurring α/β TCRs can target cell surface proteins other than pHLA, which would address the challenges of HLA restriction. In this proof-of-concept study, we sought to identify and engineer so-called HLA-independent TCRs (HiTs) against the tumor-associated antigen mesothelin.MethodsUsing phage display, we identified a HiT that bound well to mesothelin, which when expressed in primary T cells, caused activation and cytotoxicity. We subsequently engineered this HiT to modulate the T-cell response to varying levels of mesothelin on the cell surface.ResultsThe isolated HiT shows cytotoxic activity and demonstrates killing of both mesothelin-expressing cell lines and patient-derived xenograft models. Additionally, we demonstrated that HiT-transduced T cells do not require CD4 or CD8 co-receptors and, unlike a TCR fusion construct, are not inhibited by soluble mesothelin. Finally, we showed that HiT-transduced T cells are highly efficacious in vivo, completely eradicating xenografted human solid tumors.ConclusionHiTs can be isolated from fully human TCR-displaying phage libraries against cell surface-expressed antigens. HiTs are able to fully activate primary T cells both in vivo and in vitro. HiTs may enable the efficacy seen with pHLA-targeting TCRs in solid tumors to be translated to cell surface antigens.

[This corrects the article DOI: 10.1371/journal.pgph.0001788.].

ABSTRACTThe mammalian gut microbiota is a critical human health determinant with therapeutic potential for remediation of many diseases. The host diet is a key factor governing the gut microbiota composition by altering nutrient availability and supporting the expansion of distinct microbial populations. Diets rich in simple sugars modify the abundance of microbial subsets, enriching for microbiotas that elicit pathogenic outcomes. We previously demonstrated that diets rich in fructose and glucose can reduce the fitness and abundance of a human gut symbiont, Bacteroides thetaiotaomicron, by silencing the production of a critical intestinal colonization protein, called Roc, via its mRNA leader through an unknown mechanism. We have now determined that dietary sugars silence Roc by reducing the activity of BT4338, a master regulator of carbohydrate utilization. Here, we demonstrate that BT4338 is required for Roc synthesis, and that BT4338 activity is silenced by glucose or fructose. We show that the consequences of glucose and fructose on orthologous transcription factors are conserved across human intestinal Bacteroides species. This work identifies a molecular pathway by which a common dietary additive alters microbial gene expression in the gut that could be harnessed to modulate targeted microbial populations for future therapeutic interventions.

Abstract Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.

Code obfuscation has become an essential practice in modern software development, designed to make source or machine code challenging for both humans and computers to comprehend. It plays a crucial role in cybersecurity by protecting intellectual property, safeguarding trade secrets, and preventing unauthorized access or reverse engineering. However, the lack of transparency in obfuscated code raises significant ethical concerns, including the potential for harmful or unethical uses such as hidden data collection, malicious features, back doors, and concealed vulnerabilities. These issues highlight the need for a balanced approach that ensures the protection of developers' intellectual property while addressing ethical responsibilities related to user privacy, transparency, and societal impact. This paper investigates various code obfuscation techniques, their benefits, challenges, and practical applications, underscoring their relevance in contemporary software development. This study examines obfuscation methods and tools, evaluates machine learning models—including Random Forest, Gradient Boosting, and Support Vector Machine—and presents experimental results aimed at classifying obfuscated versus non-obfuscated files. Our findings demonstrate that these models achieve high accuracy in identifying obfuscation methods employed by tools such as Jlaive, Oxyry, PyObfuscate, Pyarmor, and py-obfuscator. This research also addresses emerging ethical concerns and proposes guidelines for a balanced, responsible approach to code obfuscation. [ABSTRACT FROM AUTHOR]

Self-reports are used ubiquitously to probe people's thoughts, feelings, and behaviors and inform medical decisions, enterprise operations, and government policy and legislation. Despite their pervasive use, self-report measures such as Likert scales have a profound problem: Standard analytic approaches do not control for the confounding effects of idiosyncratic response biases. Here, we present a model-based solution to this problem. Our model disentangles response bias from latent constructs of interest to obtain less biased scores of the latent states of respondents. Inspired by Thurstonian approaches in the psychophysics literature, the model requires nothing further than standard Likert scale design assumptions. The model uses a data-driven approach to control for response biases, without the need to prespecify bias types or response strategies. We demonstrate the model's ability to uncover more precise estimates of latent state associations, outperforming bias-affected standard scoring techniques, and garner insights into previously undetected codependencies between certain latent states and particular forms of response bias. The model is thus a tool which outperforms standard scoring methods and generates insights into, and controls for, the potentially confounding effects of response bias on self-report Likert scale data. [ABSTRACT FROM AUTHOR]

The early years are critical for physical literacy (PL) and physical activity (PA). With increasing numbers of children attending early childhood education and care (ECEC), educators play a significant role in childhood development and may influence young children's PL journey. Educators receive minimal training in PL and PA, but receive increasing direction to integrate these concepts into ECEC learning. The purpose of this study was to assess educators' PL, then determine which components of their PL were associated with self-reported intentions and behaviours to promote PL and PA. Educator PL was moderate, while self-reported intentions and behaviours to provide PL and PA opportunities were high. Only one component of PL was associated with intentions and behaviours. The PL of educators may not inform their intentions and behaviours to provide PL and PA within ECEC frameworks.

Children and youth with impairments in social skills and/or cognition face many barriers to community participation specifically physical activity (PA) (e.g., limited staff training). Inclusive PA settings may provide opportunities for children and youth with and without impairments to engage together and promote physical and social skill development. The purpose of this scoping review was to critically evaluate the literature on out-of-school PA programs (i.e., non-curriculum programming) that included children and/or youth with impairments in social skills and/or cognition. A keyword search of seven databases followed by eligibility screening led to ten articles for this scoping review. For each included study, two research team members independently extracted and synthesized the data, and appraised the study reporting quality using the published quality assessment tool (QATSDD). Experts' evaluation of the research literature was obtained. Ten studies, which varied from low to high reporting quality, collectively addressed the following outcomes, with all showing mixed impacts: anthropometrics and fitness; motor and sport skills; psychological well-being; and socialization. Experts suggested routes forward for research and practice including longitudinal designs and programming variety to meet individual needs. Out-of-school PA programs that include children and/or youth with impairments in social skills and/or cognition provide an opportunity to improve multiple areas of health and wellness. However, limited high-quality research has been conducted to-date. Further evaluation of program effectiveness is warranted.

Abstract Background Prostate cancer survivors (PCS) experience long-term side effects beyond treatment such as fatigue, depression and anxiety. Quality and engaging supportive care programs are needed to reduce these chronic and debilitating effects. Independent of physical activity (PA), high volumes of sedentary behavior (SB) are associated with chronic disease-related risk factors and poorer cancer-specific quality of life (QoL). Simultaneously increasing PA and decreasing SB may be an effective health promotion strategy. Given that PCS may face several barriers to engaging in supervised programs, there is a need to develop and assess the efficacy of interventions that employ distance-based approaches for behavior change. The primary aim of this study is to determine the effects of a 12-week intervention (Fitbit + behavioral counselling) vs. Fitbit-only control group in reducing SB among PCS. Secondary outcomes include light-intensity PA, QoL, motivational outcomes, and patient satisfaction. Methods This two-armed, randomized controlled trial will recruit inactive PCS (stage I-IV) across Canada who self-report engaging in >8 hours/day of SB. Participants will be randomized to the intervention (n=60; Fitbit and behavioral support) or active control group (n=60; Fitbit-only). The intervention consists of the use of a Fitbit and a series of six behavioral support sessions (two group, four individual) to aid PCS in gradually replacing SB with light-intensity PA by increasing their daily step counts to 3,000 steps above their baseline values. The Fitbit-only control condition will receive a Fitbit and public health PA resources. The primary outcome is change in SB measured objectively using activPAL inclinometers. All secondary outcomes will be measured via self-report, except for PA which will be measuring using Fitbits. Data will be collected at baseline, post-intervention, and at 6-month post-intervention. Discussion Reducing SB and increasing light-intensity PA plays an important, yet often undervalued role in the health and well-being of PCS. This study will create a unique distance-based platform that can be used by clinical and community-based organizations as a low-cost, supportive care tool to improve health outcomes for PCS. Trial Registration ClinicalTrials.gov Identifier NCT05214937 . Registered January 28, 2022 Protocol version: v.1