Water chlorination increases the relative abundance of an antibiotic resistance marker in developing sourdough starters.

Multiple factors explain the proper development of sourdough starters. Although the role of raw ingredients and geography, among other things, have been widely studied recently, the possible effect of air quality and water chlorination on the overall bacterial communities associated with sourdough remains to be explored. Here, using 16S rRNA amplicon sequencing, we show that clean, filtered-air severely limited the presence of lactic acid bacteria in sourdough starters, suggesting that surrounding air is an important source of microorganisms necessary for the development of sourdough starters. We also show that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, using targeted sequencing, which offers a higher resolution, we found that the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic-resistance genes in spoilage and pathogenic bacteria, increased significantly with the level of water chlorination. Although our results suggest that water chlorination might not impact sourdough starters at a deep phylogenetic level, they indicate that it can favor the spread of genetic elements associated with spoilage bacteria. IMPORTANCE: Proper development of sourdough starters is critical for making tasty and healthy bread. Although many factors contributing to sourdough development have been studied, the effect of water chlorination on the bacterial communities in sourdough has been largely ignored. Researchers used sequencing techniques to investigate this effect and found that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, they discovered that water chlorination could increase the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic resistance genes in spoilage and pathogenic bacteria. This suggests that water chlorination could favor the growth of key spoilage bacteria and compromise the quality and safety of the bread. These findings emphasize the importance of considering water quality when developing sourdough starters for the best possible bread.

Single-molecule detection and super-resolution imaging with a portable and adaptable 3D-printed microscopy platform (Brick-MIC).

Over the past decades, single-molecule and super-resolution microscopy have advanced and represent essential tools for life science research. There is, however, a growing gap between the state of the art and what is accessible to biologists, biochemists, medical researchers, or labs with financial constraints. To bridge this gap, we introduce Brick-MIC, a versatile and affordable open-source 3D-printed microspectroscopy and imaging platform. Brick-MIC enables the integration of various fluorescence imaging techniques with single-molecule resolution within a single platform and exchange between different modalities within minutes. We here present variants of Brick-MIC that facilitate single-molecule fluorescence detection, fluorescence correlation spectroscopy, time-correlated single-photon counting and super-resolution imaging (STORM and PAINT). Detailed descriptions of the hardware and software components, as well as data analysis routines, are provided, to allow non-optics specialists to operate their own Brick-MIC with minimal effort and investments. We foresee that our affordable, flexible, and open-source Brick-MIC platform will be a valuable tool for many laboratories worldwide.

Cortical mechanisms of across-ear speech integration investigated using functional near-infrared spectroscopy (fNIRS).

This study aimed to investigate integration of alternating speech, a stimulus which classically produces a V-shaped speech intelligibility function with minimum at 2-6 Hz in typical-hearing (TH) listeners. We further studied how degraded speech impacts intelligibility across alternating rates (2, 4, 8, and 32 Hz) using vocoded speech, either in the right ear or bilaterally, to simulate single-sided deafness with a cochlear implant (SSD-CI) and bilateral CIs (BiCI), respectively. To assess potential cortical signatures of across-ear integration, we recorded activity in the bilateral auditory cortices (AC) and dorsolateral prefrontal cortices (DLPFC) during the task using functional near-infrared spectroscopy (fNIRS). For speech intelligibility, the V-shaped function was reproduced only in the BiCI condition; TH (with ceiling scores) and SSD-CI conditions had significantly higher scores across all alternating rates compared to the BiCI condition. For fNIRS, the AC and DLPFC exhibited significantly different activity across alternating rates in the TH condition, with altered activity patterns in both regions in the SSD-CI and BiCI conditions. Our results suggest that degraded speech inputs in one or both ears impact across-ear integration and that different listening strategies were employed for speech integration manifested as differences in cortical activity across conditions.

Assessing Mechanisms of Potential Local Adaptation Through a Seascape Genomic Approach in a Marine Gastropod, Littoraria flava.

Understanding the combined effects of environmental heterogeneity and evolutionary processes on marine populations is a primary goal of seascape genomic approaches. Here, we utilized genomic approaches to identify local adaptation signatures in Littoraria flava, a widely distributed marine gastropod in the tropical West Atlantic population. We also performed molecular evolution analyses to investigate potential selective signals across the genome. After obtaining 6,298 and 16,137 single nucleotide polymorphisms derived from genotyping-by-sequencing and RNA sequencing, respectively, 69 from genotyping-by-sequencing (85 specimens) and four from RNA sequencing (40 specimens) candidate single nucleotide polymorphisms were selected and further evaluated. The correlation analyses support different evolutionary pressures over transcribed and non-transcribed regions. Thus, single nucleotide polymorphisms within transcribed regions could account for the genotypic and possibly phenotypic divergences in periwinkles. Our molecular evolution tests based on synonymous and non-synonymous ratio (kN/kS) showed that genotype divergences containing putative adaptive single nucleotide polymorphisms arose mainly from synonymous and/or UTR substitutions rather than polymorphic proteins. The distribution of genotypes across different localities seems to be influenced by marine currents, pH, and temperature variations, suggesting that these factors may impact the species dispersion. The combination of RNA sequencing and genotyping-by-sequencing derived datasets provides a deeper understanding of the molecular mechanisms underlying selective forces responses on distinct genomic regions and could guide further investigations on seascape genomics for non-model species.

Permeability partitioning through the brittle-to-ductile transition and its implications for supercritical geothermal reservoirs.

Geothermal projects utilizing supercritical water (≥400 °C) could boost power output tenfold compared to conventional plants. However, these reservoirs commonly occur in crustal areas where rocks are semi-ductile or ductile, impeding large-scale fractures and cracking, and where hydraulic properties are largely unknown. Here, we explore the complex permeability of rocks under supercritical conditions using mechanical data from a gas-based triaxial apparatus, high-resolution synchrotron post-mortem 3D imagery, and finite element modeling. We report a first order control of strain partitioning on permeability. In the brittle regime, strain localizes on permeable faults without necessarily increasing sample apparent permeability. In the semi-ductile regime, distributed strain increases permeability both in deformation bands and the bulk, leading to a more than tenfold permeability increase. This study challenges the belief that the brittle-ductile transition (BDT) marks a cutoff for fluid circulation in the crust, demonstrating that permeability can develop in deforming semi-ductile rocks.

Development and Optimization of a Bladder Cancer Algorithm Using SEER-Medicare Claims Data.

PURPOSE: Categorizing patients with cancer by their disease stage can be an important tool when conducting administrative claims-based studies. As claims databases frequently do not capture this information, algorithms are increasingly used to define disease stage. To our knowledge, to date, no study has used an algorithm to categorize patients with bladder cancer (BC) by disease stage (non-muscle-invasive BC [NMIBC], muscle-invasive BC [MIBC], or locally advanced/metastatic urothelial carcinoma [la/mUC]) in a US-based health care claims database. METHODS: A claims-based algorithm was developed to categorize patients by disease stage on the basis of the administrative claims portion of the SEER-Medicare linked data. The algorithm was validated against a reference SEER registry, and the algorithm's parameters were iteratively modified to improve its performance. Patients were included if they had an initial diagnosis of BC between January 2016 and December 2017 recorded in SEER registry data. Medicare claims data were available for these patients until December 31, 2019. The algorithm was evaluated by assessing percentage agreement, Cohen's kappa (κ), specificity, positive predictive value (PPV), and negative predictive value (NPV) against the SEER categorization. RESULTS: A total of 15,484 patients with SEER-confirmed BC were included: 10,991 (71.0%) with NMIBC, 3,645 (23.5%) with MIBC, and 848 (5.5%) with la/mUC. After multiple rounds of algorithm optimization, the final algorithm had an agreement of 82.5% with SEER, with a κ of 0.58, a PPV of 87.0% for NMIBC, and 76.8% for MIBC and a high NPV for la/mUC of 98.0%. CONCLUSION: This claims-based algorithm could be a useful approach for researchers conducting claims-based studies categorizing patients with BC at diagnosis.

Patterns of occurrence, phenology, and phylogeny of Phloeosinus punctatus LeConte (Coleoptera: Curculionidae, Scolytinae) in giant sequoia.

Here, we describe patterns of reproduction and flight phenology of putative Phloeosinus punctatus in giant sequoia groves and compare morphology and genotypes of beetles from sympatric giant sequoia (Sequoiadendron giganteum) and California incense-cedar (Calocedrus decurrens). Surveys conducted in 2022 revealed that numerous branches fall from giant sequoia crowns (on average ~30 branches/tree), with 20%-50% of trees per site shedding branches, depositing breeding material for beetles on the forest floor that subsequently becomes colonized. When noninfested branches cut from mature giant sequoias were placed at the ground surface, they were colonized by P. punctatus and produced an average of 28 beetles/kg branch. Climbing and examination of sequoia crowns in 2023 showed that 75% of mature trees across 11 groves showed evidence of adult beetle entrance holes in their crowns. In 2021, tests with sticky traps showed that beetles alighted on fallen branches from 20th May to 20th August (peak landing: 2nd July); a logistic model developed from emergence data in 2021 and 2022 predicts the emergence of F1 offspring from branches between 10th July and 1st September (peak emergence: 8th August). Beetles emerging from giant sequoia preferred to settle on giant sequoia, did not reproduce in incense-cedar, and diverged morphologically from beetles emerging from incense-cedar. However, phylogenetic analysis of three genes (28S, CAD, and COI) revealed no clear pattern of sequence divergence, suggesting a single species (P. punctatus) that colonizes both hosts, though cryptic speciation may not be detectable with standard barcoding genes. Ecological and potential management implications are discussed.

Hematological and biochemical profiles, infection and habitat quality in an urban rat population.

Host condition is key in understanding disease dynamics. In an urban population of Rattus norvegicus, we aimed to assess whether infection of Leptospira interrogans and helminths was associated with patterns of host hematological and hormone-biochemical stress-related conditions. Rat kidney imprints and urine were used to identify and quantify L. interrogans, and feces samples for helminth eggs and corticosterone metabolites. Blood samples were taken for complete blood counts and specific biochemicals in rats' sera. Principal Component Analyses were performed to check whether rats would be grouped according to health profiles. We obtained hematological and hormone-biochemical data from 95 and 61 rats, respectively. Hematological PCA revealed distinct rat groups: typical (T), eosinophil deficient (Eos-D), eosinophil- and monocyte- deficient (EM-D) and monocyte deficient with high immature neutrophils (Mon-D). No association between L. interrogans or helminths and rat health profiles was observed, except with Trichiuridae, which mean intensity was significantly higher when all deficient groups were pooled together compared to the T-group. The poorest condition group was found in areas with fewer rat burrows than the T-group, indicating EM-D had a reduced ability to occupy "good" quality habitats. In natural populations, hematological profiles may reflect host's overall condition, instead of responses to specific infections.

MNK-driven eIF4E phosphorylation regulates the fibrogenic transformation of mesenchymal cells and chronic lung allograft dysfunction.

Tissue fibrosis remains unamenable to meaningful therapeutic interventions and is the primary cause of chronic graft failure after organ transplantation. Eukaryotic translation initiation factor (eIF4E), a key translational regulator, serves as convergent target of multiple upstream profibrotic signaling pathways that contribute to mesenchymal cell (MC) activation. Here, we investigate the role of MAP kinase-interacting serine/threonine kinase-induced (MNK-induced) direct phosphorylation of eIF4E at serine 209 (Ser209) in maintaining fibrotic transformation of MCs and determine the contribution of the MNK/eIF4E pathway to the pathogenesis of chronic lung allograft dysfunction (CLAD). MCs from patients with CLAD demonstrated constitutively higher eIF4E phosphorylation at Ser209, and eIF4E phospho-Ser209 was found to be critical in regulating key fibrogenic protein autotaxin, leading to sustained ß-catenin activation and profibrotic functions of CLAD MCs. MNK1 signaling was upregulated in CLAD MCs, and genetic or pharmacologic targeting of MNK1 activity inhibited eIF4E phospho-Ser209 and profibrotic functions of CLAD MCs in vitro. Treatment with an MNK1/2 inhibitor (eFT-508) abrogated allograft fibrosis in an orthotopic murine lung-transplant model. Together these studies identify what we believe is a previously unrecognized MNK/eIF4E/ATX/ß-catenin signaling pathway of fibrotic transformation of MCs and present the first evidence, to our knowledge, for the utility of MNK inhibitors in fibrosis.

Chemical composition and antimycobacterial, anti-Malassezia furfur and cytotoxic activities of essential oils from Callistemon viminalis (Sol. ex Gaertn.) G. Don leaves and flowers.

Callistemon viminalis has been widely known due to its therapeutic properties. Tuberculosis is a deadly infectious disease caused predominantly by Mycobacterium tuberculosis. Other respiratory diseases may also be caused by nontuberculous mycobacteria. Malassezia furfur causes dermal inflammation and tissue damage. This study aimed to evaluate in vitro inhibitory effects of essential oils (EOs) from C. viminalis leaves (EO-CL) and flowers (EO-CF) against M. tuberculosis, Mycobacterium kansasii, Mycobacterium avium and M. furfur strains. Their cytotoxic activity was evaluated by the brine shrimp assay. Resulting MIC values of all EOs under study were promising since they ranged from 50 to 100 µg/mL. Both EO-CL and EO-CF showed nontoxicity against Artemia salina by the brine shrimp assay (LC50 > 1000 µg/mL). GC-FID and GC-MS analyses showed that 1,8-cineole was the major component of both EOs. These results revealed the promising potential of EO-CL and EO-CF to develop new antibacterial and antifungal drugs.

Medical school students' perspectives on virtual anatomy education in a developing country.

Understanding the fundamental role anatomy education plays in medical training and taking into consideration the nascence of online education in Nigeria, this study evaluated the perceptions of medical and allied-health students toward online anatomy education both during the COVID-19 lockdown in Nigeria and for the future. For this study, Google Form questionnaires were distributed via different social and academic platforms to medical and allied-health students in Nigeria between September 28 and December 17, 2020. A total of 954 students participated in the study and 947 valid responses were recorded. The results showed that 77.6% of the students had reported computer/IT skills and 12.1% admitted that they had never attended an online class. Interestingly, 60% of the respondents disapproved of online learning approaches as effective tools for instructions in the anatomical sciences. Majority of the students (84%) agreed that their performance in anatomy would have been better if the classes were face-to-face, while 55% found the online anatomy classes uninteresting. Furthermore, 91.5% agreed that anatomy educators needed advanced skills for online education, while 94.2% agreed that anatomy online teaching needs more advanced technology to be implemented in Nigeria. This study revealed an overall negative perception about the suitability and effectiveness of online anatomy education in Nigerian medical/health training. This study recommends further investigations into the challenges that were presented during online anatomy education at the peak of the pandemic. This will help direct the development and implementation of a workable and sustainable online education model for anatomical sciences in Nigeria.

Association of meeting the 24-h movement guidelines with high blood pressure in adolescents: a cross-sectional study.

The 24-h movement guidelines for children and adolescents comprise recommendations for adequate sleep, moderate to vigorous physical activity (MVPA) and sedentary behaviour (SB). However, whether adolescents who meet these 24-h movement guidelines may be less likely to have high blood pressure (HBP) has not been established. The present study assessed the association between meeting 24-h movement guidelines and HBP in a school-based sample of 996 adolescents between 10-17 years (13.2 ± 2.4 years, 55.4% of girls). Blood pressure was measured using a digital oscillometric device, while sleep, MVPA and SB were measured using the Baecke questionnaire. The association between the 24-h movement guidelines and HBP was performed using binary logistic regression adjusted for sex, age, socioeconomic status, and body mass index. It was observed that less than 1% of the sample meet the three 24-h movement guidelines. The prevalence of HBP was lower in adolescents who meet all three movement 24-h guidelines (11.1%) compared to those who did not meet any guidelines (27.2%). Individual 24-h movement guidelines analysis showed that adolescents with adequate sleep were 35% less likely to have HBP (OR = 0.65; 95% CI 0.46-0.91). Meeting sleep guidelines combined with meeting MVPA (OR = 0.69; 95% CI 0.50-0.95) or SB (OR = 0.67; 95% CI 0.48-0.94) was inversely associated with HBP. Adolescents who meet two or three 24-h movement guidelines were respectively 47% (OR = 0.53; 95% CI 0.29-0.98) and 34% (OR = 0.66; 95% CI 0.48-0.91) less likely to have HBP. In adolescents, meeting sleep and 24-h movement guidelines were inversely associated with HBP.

Time of sample collection is critical for the replicability of microbiome analyses.

As the microbiome field moves from descriptive and associative research to mechanistic and interventional studies, being able to account for all confounding variables in the experimental design, which includes the maternal effect1, cage effect2, facility differences3, as well as laboratory and sample handling protocols4, is critical for interpretability of results. Despite significant procedural and bioinformatic improvements, unexplained variability and lack of replicability still occur. One underexplored factor is that the microbiome is dynamic and exhibits diurnal oscillations that can change microbiome composition5-7. In this retrospective analysis of 16S amplicon sequencing studies in male mice, we show that sample collection time affects the conclusions drawn from microbiome studies and its effect size is larger than those of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups is unique to each experiment. Sample collection times as short as only 4 hours apart can lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. The impact of diurnal rhythms on the outcomes and study design of other fields is unknown but likely significant.

Assessing a Suitable Radiotherapy Utilisation Benchmark for Older Patients With Head and Neck Cancer.

AIMS: To (i) determine the actual radiotherapy utilization (RTU) stratified by age, (ii) develop an age- and co-morbidity adjusted optimal RTU model and (iii) examine the tolerance and toxicity of treatment of older patients with head and neck cancer. MATERIALS AND METHODS: A retrospective cohort study based on New South Wales Cancer Registry records (2010-2014) linked to radiotherapy data (2010-2015) and admitted patient data (2008-2015) for patients diagnosed with head and neck cancer. We calculated the actual RTU, defined as the proportion of patients who received at least one course of radiotherapy within a year of diagnosis, by age group, including patients aged 80+ years. We also calculated the age and comorbidity-adjusted optimal RTU. For treatment tolerance, the radiotherapy dose for each age group and the completion rate for a seven week 70 Gray (Gy) course of curative intent radiotherapy were computed. The number of emergency department (ED) presentations were used as a surrogate measure of acute treatment toxicity for patients receiving 70 Gy. RESULTS: Of the 5966 patients diagnosed with head and neck cancer, 814 (13.6%) were aged 80+ years. For all age groups, the actual RTU was less than the optimal RTU. The age- and comorbidity-adjusted optimal RTU for patients aged 80+ was 52% (95% CI: 51%-53%), and the actual RTU was 40% (95% CI: 37%-44%). Only 4.4% of patients aged 80+ received 70 Gy, and the completion rate for a 70 Gy course of radiotherapy for these patients was 92%. The ED presentation rate was similar for all age groups. CONCLUSION: The actual RTU was less in the 80+ years patients and across all age groups. Fewer patients in the 80+ group received curative intent schedules compared to the actual RTU rate for younger age groups, despite similar rates of completion of curative intent radiotherapy and acute toxicity.

Molecular Biomarkers Detected Using Fluorescence in situ Hybridization in a Filipino with Retinoblastoma.

Background and Objective: Retinoblastoma is one of the most common intraocular cancers among children usually caused by the loss of retinoblastoma protein function. Despite being a highly heritable disease, conventional diagnostic and prognostic methods depend on clinical examination, with limited consideration of cancer genetics in the standard of care. CD133, KRT19, and MUC1 are commonly explored genes for their utility in liquid biopsies of cancer including lung adenocarcinoma. To date, there are few extensive molecular studies on retinoblastoma in Filipino patients. To this end, the study aimed to describe the copy number of CD133, KRT19, and MUC1 in retinoblastoma samples from a Filipino patient and quantitate the respective expression level of these genes. Methods: Hematoxylin & Eosin (H&E) staining was utilized to characterize the retinoblastoma tissue while fluorescence in situ hybridization (FISH) using probes specific to CD133, KRT19, and MUC1 was performed to determine the copy number of genes in retinoblastoma samples from a Filipino patient (n = 1). The gene expression of CD133, MUC1, and KRT19 was quantitated using RT-qPCR. Results: The H&E staining in the retinoblastoma tissue shows poorly differentiated cells with prominent basophilic nuclei. CD133 was approximately 1.5-fold overexpressed in the retinoblastoma tissue with respect to the normal tissue, while MUC1 and KRT19 are only slightly expressed. Multiple intense signals of each probe were localized in the same nuclear areas throughout the retinoblastoma tissue, with high background noise. Conclusion: These findings suggest that CD133 is a potential biomarker for the staging and diagnosis of retinoblastoma in Filipino cancer patients. However, further optimization of the hybridization procedures is recommended.

Investigating the neurobiology of maternal opioid use disorder and prenatal opioid exposure using brain organoid technology.

Over the past two decades, Opioid Use Disorder (OUD) among pregnant women has become a major global public health concern. OUD has been characterized as a problematic pattern of opioid use despite adverse physical, psychological, behavioral, and or social consequences. Due to the relapsing-remitting nature of this disorder, pregnant mothers are chronically exposed to exogenous opioids, resulting in adverse neurological and neuropsychiatric outcomes. Collateral fetal exposure to opioids also precipitates severe neurodevelopmental and neurocognitive sequelae. At present, much of what is known regarding the neurobiological consequences of OUD and prenatal opioid exposure (POE) has been derived from preclinical studies in animal models and postnatal or postmortem investigations in humans. However, species-specific differences in brain development, variations in subject age/health/background, and disparities in sample collection or storage have complicated the interpretation of findings produced by these explorations. The ethical or logistical inaccessibility of human fetal brain tissue has also limited direct examinations of prenatal drug effects. To circumvent these confounding factors, recent groups have begun employing induced pluripotent stem cell (iPSC)-derived brain organoid technology, which provides access to key aspects of cellular and molecular brain development, structure, and function in vitro. In this review, we endeavor to encapsulate the advancements in brain organoid culture that have enabled scientists to model and dissect the neural underpinnings and effects of OUD and POE. We hope not only to emphasize the utility of brain organoids for investigating these conditions, but also to highlight opportunities for further technical and conceptual progress. Although the application of brain organoids to this critical field of research is still in its nascent stages, understanding the neurobiology of OUD and POE via this modality will provide critical insights for improving maternal and fetal outcomes.

Observation of the Fermionic Joule-Thomson Effect.

We report the first observation of the quantum Joule-Thomson (JT) effect in ideal and unitary Fermi gases. We study the temperature dynamics of these systems while they undergo an energy-per-particle conserving rarefaction. For scale-invariant systems, whose equations of state satisfy the relation U∝PV, this rarefaction conserves the specific enthalpy, which makes it thermodynamically equivalent to a JT throttling process. We observe JT heating in an ideal Fermi gas, a direct consequence of Pauli blocking. In a unitary Fermi gas, we observe that the JT heating is marginal in the temperature range 0.2≲T/T_{F}≲0.8 as the repulsive quantum-statistical effect is lessened by the attractive interparticle interactions.

Tgfbr1 controls developmental plasticity between the hindlimb and external genitalia by remodeling their regulatory landscape.

The hindlimb and external genitalia of present-day tetrapods are thought to derive from an ancestral common primordium that evolved to generate a wide diversity of structures adapted for efficient locomotion and mating in the ecological niche occupied by the species. We show that despite long evolutionary distance from the ancestral condition, the early primordium of the mouse external genitalia preserved the capacity to take hindlimb fates. In the absence of Tgfbr1, the pericloacal mesoderm generates an extra pair of hindlimbs at the expense of the external genitalia. It has been shown that the hindlimb and the genital primordia share many of their key regulatory factors. Tgfbr1 controls the response to those factors by modulating the accessibility status of regulatory elements that control the gene regulatory networks leading to the formation of genital or hindlimb structures. Our work uncovers a remarkable tissue plasticity with potential implications in the evolution of the hindlimb/genital area of tetrapods, and identifies an additional mechanism for Tgfbr1 activity that might also contribute to the control of other physiological or pathological processes.