Data recovery methods for DNA storage based on fountain codes.

Today's digital data storage systems typically offer advanced data recovery solutions to address the problem of catastrophic data loss, such as software-based disk sector analysis or physical-level data retrieval methods for conventional hard disk drives. However, DNA-based data storage currently relies solely on the inherent error correction properties of the methods used to encode digital data into strands of DNA. Any error that cannot be corrected utilizing the redundancy added by DNA encoding methods results in permanent data loss. To provide data recovery for DNA storage systems, we present a method to automatically reconstruct corrupted or missing data stored in DNA using fountain codes. Our method exploits the relationships between packets encoded with fountain codes to identify and rectify corrupted or lost data. Furthermore, we present file type-specific and content-based data recovery methods for three file types, illustrating how a fusion of fountain encoding-specific redundancy and knowledge about the data can effectively recover information in a corrupted DNA storage system, both in an automatic and in a guided manual manner. To demonstrate our approach, we introduce DR4DNA, a software toolkit that contains all methods presented. We evaluate DR4DNA using both in-silico and in-vitro experiments.

Diphtheria in a Swiss Asylum Seeker Reception Centre: Outbreak Investigation and Evaluation of Testing and Vaccination Strategies.

Objectives: To describe a suspected diphtheria outbreak in a Swiss asylum seeker reception centre, and to analyse its management response regarding testing and vaccination. Methods: We retrospectively analysed clinical, microbiology, and case management data of all asylum seekers tested for C. diphtheriae between 28th August and 31st December 2022 while residing at the centre. Results are reported descriptively. Results: Among 265 individuals tested, ten cases of cutaneous diphtheria, one simultaneous respiratory and cutaneous case, and nine respiratory carriers were identified. Mass throat screening, targeted throat testing and targeted wound testing yielded 4.8%, 4.3%, and 17.4% positive results, respectively. No respiratory carrier was identified among cutaneous cases undergoing a throat swab, and no symptomatic case was identified among individuals with unspecific throat symptoms. Rates of vaccination implementation of newly arriving asylum seekers before and after the outbreak were low (17.5% and 15.5%, respectively), as were rates of targeted vaccination among cases and close contacts. Conclusion: We provide evidence for transmission both prior to arrival and within the setting, suboptimal practices and timeliness of testing, and implementation gaps in vaccination.

Medicine Non-Adherence: A New Viewpoint on Adherence Arising from Research Focused on Sub-Saharan Africa.

Adherence is vital for medicine to have an effect, yet adherence is considered to be low, with approximately half of the patients not fully adherent. However, research into adherence tends to focus on quantitative analysis of performance, which fails to perceive how people are adherent in their many different environments. As a contribution to gaining a deeper understanding, interviews were held with thirty individuals in the UK, Egypt, Kazakhstan, and six countries in sub-Saharan Africa to understand their perceptions on adherence to a range of drugs, and these were compared with an existing well-regarded list. New or undocumented reasons for non-adherence were discovered. Reasons for non-adherence were consistent across both developing and developed worlds. A new viewpoint on adherence is suggested, which considers adherence to be a single act and therefore as an individual opportunity to be adherent, permitting greater focus on the enablers and inhibitors of adherence at any given point in time.

Establishment of a Novel Short Tandem Repeat Typing Method for Exophiala dermatitidis.

The opportunistic black yeast-like fungus Exophiala dermatitidis frequently colonizes the respiratory tract of cystic fibroses (CF) patients. Additionally, it can cause superficial, systemic, and cerebral forms of phaeohyphomycoses. The objective of this study was to develop and apply a microsatellite or short tandem repeat (STR) genotyping scheme for E. dermatitidis. In total, 82 E. dermatitidis isolates from various geographic origins (environmental = 9, CF = 63, invasive isolates = 9, melanin-deficient mutant = 1) were included in this study. After next-generation sequencing of a reference strain and sequence filtering for microsatellites, six STR markers were selected and amplified in two multiplex PCR reactions. The included isolates were discriminated in a genetic cluster analysis using the Pearson algorithm to reveal the relatedness of the isolates. The E. dermatitidis isolates clustered on basis of both, their source and their origin. The invasive isolates from Asia were unrelated to isolates from CF. Nearly all environmental isolates were grouped separately from patients' isolates. The Simpson index was 0.94. In conclusion, we were able to establish a STR genotyping scheme for investigating population genomics of E. dermatitidis.

Targeted PCR of Mucorales in pediatric bronchoalveolar lavage samples indicates low prevalence of airway colonization and sample contamination.

Mucorales are a large order of ubiquitous saprophytic zygomycete fungi and act as opportunistic pathogens in humans. In pediatric patients, little is known about the role of Mucorales in airway colonization and infection or their role as contaminants of respiratory samples. Currently, polymerase chain reaction (PCR) is the most sensitive mode of detection Mucorales in clinical specimen. In this study, we aimed to determine the prevalence of Mucorales in bronchoalveolar lavage samples (BAL) from a large, diverse group of pediatric patients. We performed commercial Mucorales PCR (MucorGenius®, Pathonostics, Maastricht, NL, USA) on 102 thawed BAL samples of 100 patients. Mucorales PCR was negative in all samples. Our data suggest that Mucorales spp. have a low prevalence in paediatric airways and do not frequently contaminate pediatric BAL samples.

Effect of Hyperthermic Intraperitoneal Chemotherapy on Cytoreductive Surgery in Gastric Cancer With Synchronous Peritoneal Metastases: The Phase III GASTRIPEC-I Trial.

PURPOSE: In patients with peritoneal metastasis (PM) from gastric cancer (GC), chemotherapy is the treatment of choice. Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) are still being debated. This randomized, controlled, open-label, multicenter phase III trial (EudraCT 2006-006088-22; ClinicalTrials.gov identifier: NCT02158988) explored the impact on overall survival (OS) of HIPEC after CRS. PATIENTS AND METHODS: Adult patients with GC and histologically proven PM were randomly assigned (1:1) to perioperative chemotherapy and CRS alone (CRS-A) or CRS plus HIPEC (CRS + H). HIPEC comprised mitomycin C 15 mg/m2 and cisplatin 75 mg/m2 in 5 L of saline perfused for 60 minutes at 42°C. The primary end point was OS; secondary endpoints included progression-free survival (PFS), other distant metastasis-free survival (MFS), and safety. Analyses followed the intention-to-treat principle. RESULTS: Between March 2014 and June 2018, 105 patients were randomly assigned (53 patients to CRS-A and 52 patients to CRS + H). The trial stopped prematurely because of slow recruitment. In 55 patients, treatment stopped before CRS mainly due to disease progression/death. Median OS was the same for both groups (CRS + H, 14.9 [97.2% CI, 8.7 to 17.7] months v CRS-A, 14.9 [97.2% CI, 7.0 to 19.4] months; P = .1647). The PFS was 3.5 months (95% CI, 3.0 to 7.0) in the CRS-A group and 7.1 months (95% CI, 3.7 to 10.5; P = .047) in the CRS + H group. The CRS + H group showed better MFS (10.2 months [95% CI, 7.7 to 14.7] v CRS-A, 9.2 months [95% CI, 6.8 to 11.5]; P = .0286). The incidence of grade ≥3 adverse events (AEs) was similar between groups (CRS-A, 38.1% v CRS + H, 43.6%; P = .79). CONCLUSION: This study showed no OS difference between CRS + H and CRS-A. PFS and MFS were significantly better in the CRS + H group, which needs further exploration. HIPEC did not increase AEs.

Auxetic piezoelectric effect in heterostructures.

Inherent symmetry breaking at the interface has been fundamental to a myriad of physical effects and functionalities, such as efficient spin-charge interconversion, exotic magnetic structures and an emergent bulk photovoltaic effect. It has recently been demonstrated that interface asymmetry can induce sizable piezoelectric effects in heterostructures, even those consisting of centrosymmetric semiconductors, which provides flexibility to develop and optimize electromechanical coupling phenomena. Here, by targeted engineering of the interface symmetry, we achieve piezoelectric phenomena behaving as the electrical analogue of the negative Poisson's ratio. This effect, termed the auxetic piezoelectric effect, exhibits the same sign for the longitudinal (d33) and transverse (d31, d32) piezoelectric coefficients, enabling a simultaneous contraction or expansion in all directions under an external electrical stimulus. The signs of the transverse coefficients can be further tuned via in-plane symmetry anisotropy. The effects exist in a wide range of material systems and exhibit substantial coefficients, indicating potential implications for all-semiconductor actuator, sensor and filter applications.

Diagnostic Accuracy of Multiplex Polymerase Chain Reaction in Early Onset Neonatal Sepsis.

Early onset neonatal sepsis is a significant contributor to neonatal morbidity and mortality. Although blood cultures remain the diagnostic gold standard, they detect pathogens in only a minority of suspected cases. This study compared the accuracy of blood cultures with a rapid multiplex PCR test. Newborns at risk of neonatal sepsis were prospectively screened as recommended per national guidelines. Evaluations included laboratory parameters (CrP, IL6, differential blood count), blood culture, and a molecular multiplex PCR test (ROCHE LightCycler SeptiFast®) identifying 20 common microbial agents. Blood samples were taken simultaneously from umbilical cord or venous sources on the first day of life. Of 229 infants included, 69% were born preterm. Blood culture and multiplex PCR sensitivity were 7.4% and 14.8%, respectively. Specificity, negative and positive predictive values between methods showed no significant variance, although multiplex PCR had more false positives due to contamination. The limited sensitivity of blood cultures for early onset neonatal sepsis is concerning. Despite quicker results, multiplex PCR does not enhance diagnostic accuracy or antibiotic therapy guidance, thus it cannot be recommended for this indication.

Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss.

Male-pattern hair loss (MPHL) is common and highly heritable. While genome-wide association studies (GWAS) have generated insights into the contribution of common variants to MPHL etiology, the relevance of rare variants remains unclear. To determine the contribution of rare variants to MPHL etiology, we perform gene-based and single-variant analyses in exome-sequencing data from 72,469 male UK Biobank participants. While our population-level risk prediction suggests that rare variants make only a minor contribution to general MPHL risk, our rare variant collapsing tests identified a total of five significant gene associations. These findings provide additional evidence for previously implicated genes (EDA2R, WNT10A) and highlight novel risk genes at and beyond GWAS loci (HEPH, CEPT1, EIF3F). Furthermore, MPHL-associated genes are enriched for genes considered causal for monogenic trichoses. Together, our findings broaden the MPHL-associated allelic spectrum and provide insights into MPHL pathobiology and a shared basis with monogenic hair loss disorders.

Depression and associated factors among Brazilian adults: the 2019 national healthcare population-based study.

BACKGROUND: Mental disorders represent a major public health challenge worldwide, affecting 80% of people living in low- and middle-income countries. Depression, a mental disorder, is a chronic disease of long duration that causes changes in the brain, resulting from a combination of genetic, physiologic, environmental, and behavioral factors. The aim of this study was to investigate possible factors associated with depression in Brazilian adults. METHODS: A population-based, cross-sectional study was carried out using the public domain database of the 2019 National Health Survey, conducted in Brazil. Depression was considered the dependent variable, and through hierarchical analysis, predictor variables were investigated such as, at the distal level-socioeconomic variables, at the intermediate level-variables related to lifestyle behavior, health condition, and history, and at the proximal level-demographic variables. Logistic regression analysis was used to obtain the adjusted Odds Ratio and the respective 95% confidence interval to identify possible factors associated with depression. RESULTS: The study included 88,531 participant records with 10.27% diagnosed with depression. The adjusted association measurements, after selecting the independent variables in the hierarchical analysis, showed the following factors associated with depression with differing magnitudes: age, brown and white race/skin color, female sex, poor, very poor, or regular self-reported health condition, diagnosis of cardiovascular disease, work-related musculoskeletal disorder, history of smoking habit, and macroeconomic region. CONCLUSIONS: An effective strategy for preventing and managing depression in Brazilian adults must include the control of health status and lifestyle behavior factors, with actions and programs to reduce people's exposure to these factors, understanding that socioeconomic-demographic differences of each population can potentially reduce the disease burden.

Microbiological Non-Culture-Based Methods for Diagnosing Invasive Pulmonary Aspergillosis in ICU Patients.

The diagnosis of invasive pulmonary aspergillosis (IPA) in intensive care unit (ICU) patients is crucial since most clinical signs are not specific to invasive fungal infections. To detect an IPA, different criteria should be considered. Next to host factors and radiological signs, microbiological criteria should be fulfilled. For microbiological diagnostics, different methods are available. Next to the conventional culture-based approaches like staining and culture, non-culture-based methods can increase sensitivity and improve time-to-result. Besides fungal biomarkers, like galactomannan and (1→3)-ß-D-glucan as nonspecific tools, molecular-based methods can also offer detection of resistance determinants. The detection of novel biomarkers or targets is promising. In this review, we evaluate and discuss the value of non-culture-based microbiological methods (galactomannan, (1→3)-ß-D-glucan, Aspergillus PCR, new biomarker/targets) for diagnosing IPA in ICU patients.

The Impact of Heavy Smoking on Male Infertility and Its Correlation with the Expression Levels of the PTPRN2 and PGAM5 Genes.

Smoking has been linked to male infertility by affecting the sperm epigenome and genome. In this study, we aimed to determine possible changes in the transcript levels of PGAM5 (the phosphoglycerate mutase family member 5), PTPRN2 (protein tyrosine phosphatase, N2-type receptor), and TYRO3 (tyrosine protein kinase receptor) in heavy smokers compared to non-smokers, and to investigate their association with the fundamental sperm parameters. In total, 118 sperm samples (63 heavy-smokers (G1) and 55 non-smokers (G2)) were included in this study. A semen analysis was performed according to the WHO guidelines. After a total RNA extraction, RT-PCR was used to quantify the transcript levels of the studied genes. In G1, a significant decrease in the standard semen parameters in comparison to the non-smokers was shown (p < 0.05). Moreover, PGAM5 and PTPRN2 were differentially expressed (p ≤ 0.03 and p ≤ 0.01, respectively) and downregulated in the spermatozoa of G1 compared to G2. In contrast, no difference was observed for TYRO3 (p ≤ 0.3). In G1, the mRNA expression level of the studied genes was correlated negatively with motility, sperm count, normal form, vitality, and sperm membrane integrity (p < 0.05). Therefore, smoking may affect gene expression and male fertility by altering the DNA methylation patterns in the genes associated with fertility and sperm quality, including PGAM5, PTPRN2, and TYRO3.

Determinants of quality of life in adults with epilepsy: a multicenter, cross-sectional study from Germany.

BACKGROUND: Assessment of quality of life (QoL) has become an important indicator for chronic neurological diseases. While these conditions often limit personal independence and autonomy, they are also associated with treatment-related problems and reduced life expectancy. Epilepsy has a tremendous impact on the QoL of patients and their families, which is often underestimated by practitioners. The aim of this work was to identify relevant factors affecting QoL in adults with epilepsy. METHODS: This cross-sectional, multicenter study was conducted at four specialized epilepsy centers in Germany. Patients diagnosed with epilepsy completed a standardized questionnaire focusing on QoL and aspects of healthcare in epilepsy. Univariate regression analyses and pairwise comparisons were performed to identify variables of decreased QoL represented by the overall Quality of Life in Epilepsy Inventory (QOLIE-31) score. The variables were then considered in a multivariate regression analysis after multicollinearity analysis. RESULTS: Complete datasets for the QOLIE-31 were available for 476 patients (279 [58.6%] female, 197 [41.4%] male, mean age 40.3 years [range 18-83 years]). Multivariate regression analysis revealed significant associations between low QoL and a high score on the Liverpool Adverse Events Profile (LAEP; beta=-0.28, p < 0.001), Hospital Anxiety and Depression Scale - depression subscale (HADS-D; beta=-0.27, p < 0.001), Neurological Disorders Depression Inventory in Epilepsy (NDDI-E; beta=-0.19, p < 0.001), revised Epilepsy Stigma Scale (beta=-0.09, p = 0.027), or Seizure Worry Scale (beta=-0.18, p < 0.001) and high seizure frequency (beta = 0.14, p < 0.001). CONCLUSION: Epilepsy patients had reduced QoL, with a variety of associated factors. In addition to disease severity, as measured by seizure frequency, the patient's tolerability of anti-seizure medications and the presence of depression, stigma, and worry about new seizures were strongly associated with poor QoL. Diagnosed comorbid depression was underrepresented in the cohort; therefore, therapeutic decisions should always consider individual psychobehavioral and disease-specific aspects. Signs of drug-related adverse events, depression, fear, or stigmatization should be actively sought to ensure that patients receive personalized and optimized treatment. TRIAL REGISTRATION: German Clinical Trials Register (DRKS00022024; Universal Trial Number: U1111-1252-5331).

The Sperm DNA Fragmentation Assay with SDF Level Less Than 15% Provides a Useful Prediction for Clinical Pregnancy and Live Birth for Women Aged under 40 Years.

This retrospective cohort study was conducted on 1148 males who presented along with their partners for infertility management at the PIVET Medical Centre between 2013 and 2022 and had a sperm DNA fragmentation (SDF) assay performed by Halosperm, thereafter participating in 1600 assisted reproductive technology (ART) cycles utilising one of three modalities, namely, IVF-Only, ICSI-Only or IVF-ICSI Split cycles. The outcomes from the ART cycles were then analysed as two groups based on SDF levels <15% and ≥15%. The study showed the unadjusted fertilization rates were not different between the groups, neither across the four female age ranges. However, when the fertilization rates were adjusted for the mature oocytes (metaphase-II oocytes), there was a highly significant difference in fertilization rates in favour of the group with SDF levels < 15% where the women were in the younger age grouping of <35 years (78.4% vs. 73.0%; p < 0.0001). Overall, there was no difference in the rates of blastocyst development nor clinical pregnancy rates between the two SDF groups, but there was a significantly higher pregnancy rate for the younger women (<35 years) with the group of SDF level < 15% (44.1% vs. 37.4%; p = 0.04). Similarly, there was no difference in the miscarriage rates overall with respect to SDF groups, and no clear picture could be deciphered among the women's age groups. With respect to cumulative live births, this reflected the pregnancy rates with no overall difference between the two SDF groups, but there was a significantly higher cumulative live birth rate for women <35 years where the SDF level was <15% (38.6% vs. 28.6%; p < 0.01). Among the three modalities, the highest cumulative live birth rate occurred within the group with SDF level < 15%, being highest with the IVF mode, particularly for women aged <40 years (43.0% vs. 37.7% for IVF-ICSI Split and 27.9% for ICSI; p = 0.0002), noting that the IVF case numbers were disproportionately low.

Periodontitis in individuals with few remaining teeth and a high gingival bleeding index increases the probability of dyslipidemia.

BACKGROUND: Dyslipidemia, a silent multifactorial condition, is characterized by changes in blood lipid levels, affecting all socioeconomic strata, increasing the risk for atherosclerotic diseases. This study investigated whether there is an association between dyslipidemia and the combined exposure of periodontitis plus the number of remaining teeth, gingival bleeding, or caries. METHODS: A two-center cross-sectional study was conducted involving 1270 individuals, with a minimum age of 18 years. Socioeconomic and demographic data, health conditions, lifestyle parameters, and anthropometric, biochemical, and oral clinical examinations were performed. The exposures considered were the presence of periodontitis, dental caries, number of remaining teeth, and gingival bleeding. The outcome was dyslipidemia as defined by the Brazilian Guidelines on Dyslipidemia and Prevention of Atherosclerosis. The combined associations between periodontitis plus other oral health conditions and dyslipidemia were estimated using confounder-adjusted prevalence ratios (PRsingle , PRmultiple , for single and multiple covariable adjustments) with 95% confidence intervals (95% CIs), in a Poisson regression model with robust variance. RESULTS: The occurrence of dyslipidemia was 70.1% and periodontitis was 84.1%. A positive association between periodontitis and dyslipidemia existed: PRsingle  = 1.13; 95% CI: 1.01-1.26. Combined exposure of periodontitis plus <11 remaining teeth (PRmultiple  = 1.23; 95% CI: 1.05-1.43), as well as combined exposure of periodontitis plus ≥10% gingival bleeding and <11 remaining teeth (PRmultiple  = 1.22; 95% CI: 1.03-1.44), represented greater probabilities of 23% and 22% of individuals having a diagnosis of dyslipidemia. CONCLUSION: Periodontitis combined with fewer than 11 teeth doubled the likelihood of being diagnosed with dyslipidemia.

Targeting the Granulocytic Defense against A. fumigatus in Healthy Volunteers and Septic Patients.

Neutrophil granulocytes (NGs) are among the key players in the defense against Aspergillus fumigatus (A. fumigatus). To better elucidate a pathophysiological understanding of their role and functions, we applied a human cell model using NGs from healthy participants and septic patients to evaluate their inhibitory effects on the growth of A. fumigatus ex vivo. Conidia of A. fumigatus (ATCC® 204305) were co-incubated with NGs from healthy volunteers or septic patients for 16 h. A. fumigatus growth was measured by XTT assays with a plate reader. The inhibitory effect of NGs on 18 healthy volunteers revealed great heterogeneity. Additionally, growth inhibition was significantly stronger in the afternoon than the morning, due to potentially different cortisol levels. It is particularly interesting that the inhibitory effect of NGs was reduced in patients with sepsis compared to healthy controls. In addition, the magnitude of the NG-driven defense against A. fumigatus was highly variable among healthy volunteers. Moreover, daytime and corresponding cortisol levels also seem to have a strong influence. Most interestingly, preliminary experiments with NGs from septic patients point to a strongly diminished granulocytic defense against Aspergillus spp.

Male Clinical Parameters (Age, Stature, Weight, Body Mass Index, Smoking History, Alcohol Consumption) Bear Minimal Relationship to the Level of Sperm DNA Fragmentation.

This retrospective cohort study reports on 1291 males who were the partners of women presenting with infertility requiring assisted reproduction and who had sperm DNA fragmentation (SDF) levels measured by the Halosperm test. These men provided clinical and biometric details which included their age, stature, weight, and body mass index (BMI). Of these men, 562 (43.5%) provided detailed historical records of their smoking and alcohol histories. The aim of this study was to determine whether any clinical and biometric parameters, or main lifestyle factors, had any influence on SDF. We found that the only clinical parameter with a direct correlation was that of advancing age (r = 0.064, p = 0.02), but none of the biometric parameters of stature, weight, or BMI showed any significant correlation. In respect to lifestyle, there were significant correlations with smoking history, but not in the way we expected. Our data showed significantly elevated SDF levels among non-smokers (p = 0.03) compared with smokers. We also found that, among the non-smokers, ex-smokers had higher SDF levels (p = 0.03). With respect to alcohol, consumers did not show any significant differences in SDF levels. These lifestyle findings did not show any significant relevance with respect to an SDF level of <15% or ≥15%. Furthermore, logistic regression analysis excluded age as a confounder in these lifestyle findings. It is therefore concluded that, apart from age, both clinical and lifestyle aspects have minimal relevance to SDF.