Validation of open-path dual-comb spectroscopy against an O2 background: erratum.

This erratum corrects errors that appear in Opt. Express31, 5042 (2023).10.1364/OE.480301.

Pulse interaction induced systematic errors in dual comb spectroscopy.

Systematic errors are observed in dual comb spectroscopy when pulses from the two sources travel in a common fiber before interrogating the sample of interest. When sounding a molecular gas, these errors distort both the line shapes and retrieved concentrations. Simulations of dual comb interferograms based on a generalized nonlinear Schrodinger equation highlight two processes for these systematic errors. Self-phase modulation changes the spectral content of the field interrogating the molecular response but affects the recorded spectral baseline and absorption features differently, leading to line intensity errors. Cross-phase modulation modifies the relative inter-pulse delay, thus introducing interferogram sampling errors and creating a characteristic asymmetric distortion on spectral lines. Simulations capture the shape and amplitude of experimental errors which are around 0.1% on spectral transmittance residuals for 10 mW of total average power in 10 meters of common fiber, scaling up to above 0.6% for 20 mW and 60 m.

Evolution of rhodopsin in flatfishes (Pleuronectiformes) is associated with depth and migratory behavior.

Visual signals are involved in many fitness-related tasks and are therefore essential for survival in many species. Aquatic organisms are ideal systems to study visual evolution, as the high diversity of spectral properties in aquatic environments generates great potential for adaptation to different light conditions. Flatfishes are an economically important group, with over 800 described species distributed globally, including halibut, flounder, sole, and turbot. The diversity of flatfish species and wide array of environments they occupy provides an excellent opportunity to understand how this variation translates to molecular adaptation of vision genes. Using models of molecular evolution, we investigated how the light environments inhabited by different flatfish lineages have shaped evolution in the rhodopsin gene, which is responsible for mediating dim-light visual transduction. We found strong evidence for positive selection in rhodopsin, and this was correlated with both migratory behavior and several fundamental aspects of habitat, including depth and freshwater/marine evolutionary transitions. We also identified several mutations that likely affect the wavelength of peak absorbance of rhodopsin, and outline how these shifts in absorbance correlate with the response to the light spectrum present in different habitats. This is the first study of rhodopsin evolution in flatfishes that considers their extensive diversity, and our results highlight how ecologically-driven molecular adaptation has occurred across this group in response to transitions to novel light environments.

Sacropelvic Fixation with Porous Fusion/Fixation Screws: A Technical Note and Retrospective Review.

OBJECTIVE: The goal of this study was to analyze our initial experience using a novel porous fusion/fixation screw (PFFS) for pelvic fixation, and to determine our rate of screw malposition requiring intraoperative repositioning. METHODS: We reviewed 83 consecutive patients who underwent sacropelvic fixation with PFFS at our institution from 6/1/2022-6/30/2023 using intraoperative CT-based computer-assisted navigation (CAN) via an open posterior approach. Following PFFS insertion, intraoperative CT scans were obtained to assess screw positioning. Demographic data was collected, and operative reports and patient images were reviewed to determine what implants were used and if any PFFS required repositioning. RESULTS: 74 patients (26M:48F) were included, and 57 (77.0%) had a prior sacroiliac joint or lumbar spine surgery. A stacked screw configuration was used in 62/74 cases (83.8%). A total of 235 PFFS were used and six (2.6%) were malpositioned. Of 88 cephalic screws placed in stacked configuration, 4 were malpositioned (4.5%); and 1/123 caudal screws were malpositioned (0.8%). One of 24 SAI screws placed in a stand-alone configuration was malpositioned (4.2%). Malpositions included four medial, one lateral, and one inferior; and all were revised intraoperatively without major sequela. CONCLUSIONS: Although PFFS are larger than traditional sacropelvic fixation screws, stacked SAI instrumentation can be done safely with CAN. We found a low malposition rate in our initial series of patients, the majority being the cephalad screw in a stacked configuration. This isn't surprising, as these are placed after the caudal screws which reduces the available corridor size and increases the placement difficulty.

Filling the gaps on root hair development under salt stress and phosphate starvation using current evidence coupled with a meta-analysis approach.

Population expansion is a global issue, especially for food production. Meanwhile, global climate change is damaging our soils, making it difficult for crops to thrive and lowering both production and quality. Poor nutrition and salinity stress affect plant growth and development. Although the impact of individual plant stresses has been studied for decades, the real stress scenario is more complex due to the exposure to multiple stresses at the same time. Here we investigate using existing evidence and a meta-analysis approach to determine molecular linkages between two contemporaneous abiotic stimuli, phosphate (Pi) deficiency and salinity, on a single plant cell model, the root hairs (RHs), which is the first plant cell exposed to them. Understanding how these two stresses work molecularly in RHs may help us build super-adaptable crops and sustainable agriculture in the face of global climate change.

Combination Targeted Therapy with Lenvatinib and Pembrolizumab in Progressive, Radioiodine-Refractory Differentiated Thyroid Cancers.

PURPOSE: Lenvatinib, a potent multi-kinase inhibitor, improves progression-free survival (PFS) in patients with radioiodine (RAI)-refractory differentiated thyroid cancer (DTC); however, most patients experience disease progression, warranting further therapy. We evaluated the efficacy and safety of combination lenvatinib plus pembrolizumab (LP) in these patients. PATIENTS AND METHODS: We enrolled patients with progressive, RAI-refractory DTC that were either naïve to multi-kinase inhibitors (cohort 1) or who had progressed on lenvatinib (cohort 2). Patients received oral lenvatinib daily (cohort 1, 20 mg; cohort 2, dose at progression ) and intravenous pembrolizumab (200 mg) every 21 days. RESULTS: 30 and 27 patients were enrolled in cohort 1 and 2, respectively. Adverse events were consistent with those observed in other cancers. In cohort 1, the confirmed overall response rate (ORR) was 65.5%. There were no complete responses (CR, primary endpoint). The 12 and 18-month PFS were 72.0% and 58.0%, respectively, and median PFS was 26.8 months. In cohort 2, the confirmed ORR was 16% (primary endpoint), and median PFS was 10.0 months (95% CI; 7.0-17.9 months). Tumor histology, driver mutations, and immune-related biomarkers, including PD-L1 expression, thyroid-specific antibody levels, and CD8+ T cell tumor infiltrate, did not correlate with response to therapy. Increased baseline peripheral blood monocytes and neutrophil to lymphocyte ratio were associated with a worse PFS in cohort 1. CONCLUSIONS: Combination lenvatinib plus pembrolizumab may enhance the durability of lenvatinib monotherapy in lenvatinib-naïve patients. Furthermore, the addition of pembrolizumab may be a viable salvage therapy for patients who have progressed on lenvatinib.

Boron-Silicon Alloy Nanoparticles as a Promising New Material in Lithium-Ion Battery Anodes.

Silicon's potential as a lithium-ion battery (LIB) anode is hindered by the reactivity of the lithium silicide (Li x Si) interface. This study introduces an innovative approach by alloying silicon with boron, creating boron/silicon (BSi) nanoparticles synthesized via plasma-enhanced chemical vapor deposition. These nanoparticles exhibit altered electronic structures as evidenced by optical, structural, and chemical analysis. Integrated into LIB anodes, BSi demonstrates outstanding cycle stability, surpassing 1000 lithiation and delithiation cycles with minimal capacity fade or impedance growth. Detailed electrochemical and microscopic characterization reveal very little SEI growth through 1000 cycles, which suggests that electrolyte degradation is virtually nonexistent. This unconventional strategy offers a promising avenue for high-performance LIB anodes with the potential for rapid scale-up, marking a significant advancement in silicon anode technology.

Brain structure and connectivity mediate the association between lifestyle and cognition: The Maastricht Study.

Life-course exposure to risk and protective factors impacts brain macro- and micro-structure, which in turn affects cognition. The concept of brain-age gap assesses brain health by comparing an individual's neuroimaging-based predicted age with their calendar age. A higher BAG implies accelerated brain ageing and is expected to be associated with worse cognition. In this study, we comprehensively modelled mutual associations between brain health and lifestyle factors, brain age and cognition in a large, middle-aged population. For this study, cognitive test scores, lifestyle and 3T MRI data for n = 4881 participants [mean age (± SD) = 59.2 (±8.6), 50.1% male] were available from The Maastricht Study, a population-based cohort study with extensive phenotyping. Whole-brain volumes (grey matter, cerebrospinal fluid and white matter hyperintensity), cerebral microbleeds and structural white matter connectivity were calculated. Lifestyle factors were combined into an adapted LIfestyle for BRAin health weighted sum score, with higher score indicating greater dementia risk. Cognition was calculated by averaging z-scores across three cognitive domains (memory, information processing speed and executive function and attention). Brain-age gap was calculated by comparing calendar age to predictions from a neuroimaging-based multivariable regression model. Paths between LIfestyle for BRAin health tertiles, brain-age gap and cognitive function were tested using linear regression and structural equation modelling, adjusting for sociodemographic and clinical confounders. The results show that cerebrospinal fluid, grey matter, white matter hyperintensity and cerebral microbleeds best predicted brain-age gap (R 2 = 0.455, root mean squared error = 6.44). In regression analysis, higher LIfestyle for BRAin health scores (greater dementia risk) were associated with higher brain-age gap (standardized regression coefficient ß = 0.126, P < 0.001) and worse cognition (ß = -0.046, P = 0.013), while higher brain-age gap was associated with worse cognition (ß=-0.163, P < 0.001). In mediation analysis, 24.7% of the total difference in cognition between the highest and lowest LIfestyle for BRAin health tertile was mediated by brain-age gap (ß indirect = -0.049, P < 0.001; ß total = -0.198, P < 0.001) and an additional 3.8% was mediated via connectivity (ß indirect = -0.006, P < 0.001; ß total = -0.150, P < 0.001). Findings suggest that associations between health- and lifestyle-based risk/protective factors (LIfestyle for BRAin health) and cognition can be partially explained by structural brain health markers (brain-age gap) and white matter connectivity markers. Lifestyle interventions targeted at high-risk individuals in mid-to-late life may be effective in promoting and preserving cognitive function in the general public.

Rapid synthesis of hydrogen bond templated handcuff rotaxanes.

The rapid synthesis of hydrogen bond templated handcuff rotaxanes is described. The isolated rotaxanes were characterized by NMR and IR spectroscopies and high resolution mass spectrometry. This report represents a rare demonstration of preparing (2)handcuff [2]rotaxanes by covalently linking separate axles threaded through the rings of a bis-macrocycle by use of the copper catalyzed azide-alkyne cycloaddition (CuAAC) reaction.

Crop use structures resource selection strategies for African elephants in a human-dominated landscape.

To conserve wide-ranging species in degraded landscapes, it is essential to understand how the behavior of animals changes in relation to the degree and composition of modification. Evidence suggests that large inter-individual variation exists in the propensity for use of degraded areas and may be driven by both behavioral and landscape factors. The use of cultivated lands by wildlife is of particular interest, given the importance of reducing human-wildlife conflicts and understanding how such areas can function as biodiversity buffers. African elephant space use can be highly influenced by human activity and the degree to which individuals crop-raid. We analyzed GPS data from 56 free-ranging elephants in the Serengeti-Mara Ecosystem using resource selection functions (RSFs) to assess how crop use may drive patterns of resource selection and space use within a population. We quantified drivers of similarity in resource selection across individuals using proximity analysis of individual RSF coefficients derived from random forest models. We found wide variation in RSF coefficient values between individuals indicating strongly differentiated resource selection strategies. Proximity assessment indicated the degree of crop use in the dry season, individual repeatability, and time spent in unprotected areas drove similarity in resource selection patterns. Crop selection was also spatially structured in relation to agricultural fragmentation. In areas with low fragmentation, elephants spent less time in crops and selected most strongly for crops further from protected area boundaries, but in areas of high fragmentation, elephants spent twice as much time in crops and selected most strongly for crops closer to the protected area boundary. Our results highlight how individual differences and landscape structure can shape use of agricultural landscapes. We discuss our findings in respect to the conservation challenges of human-elephant conflict and incorporating behavioral variation into human-wildlife coexistence efforts.

miRNA signatures underlie chemoresistance in the gemcitabine-resistant pancreatic ductal adenocarcinoma cell line MIA PaCa-2 GR.

Introduction: Chemotherapy resistance remains a significant challenge in the treatment of pancreatic adenocarcinoma (PDAC), particularly in relation to gemcitabine (Gem), a commonly used chemotherapeutic agent. MicroRNAs (miRNAs) are known to influence cancer progression and chemoresistance. This study investigates the association between miRNA expression profiles and gemcitabine resistance in PDAC. Methods: The miRNA expression profiles of a gemcitabine-sensitive (GS) PDAC cell line, MIA PaCa-2, and its gemcitabine-resistant (GR) progeny, MIA PaCa-2 GR, were analyzed. miRNA sequencing (miRNA-seq) was employed to identify miRNAs expressed in these cell lines. Differential expression analysis was performed, and Ingenuity Pathway Analysis (IPA) was utilized to elucidate the biological functions of the differentially expressed miRNAs. Results: A total of 1867 miRNAs were detected across both cell lines. Among these, 97 (5.2%) miRNAs showed significant differential expression between the GR and GS cell lines, with 65 (3.5%) miRNAs upregulated and 32 (1.7%) miRNAs downregulated in the GR line. The most notably altered miRNAs were implicated in key biological processes such as cell proliferation, migration, invasion, chemosensitization, alternative splicing, apoptosis, and angiogenesis. A subset of these miRNAs was further analyzed in patient samples to identify potential markers for recurrent tumors. Discussion: The differential miRNA expression profiles identified in this study highlight the complex regulatory roles of miRNAs in gemcitabine resistance in PDAC. These findings suggest potential targets for improving prognosis and tailoring treatment strategies in PDAC patients, particularly those showing resistance to gemcitabine. Future research should focus on validating these miRNAs as biomarkers for resistance and exploring their therapeutic potential in overcoming chemoresistance.

Correction to "Intra- and Inter-Molecular Charge Transfer Dynamics of Carbene-Metal-Amide Photosensitizers".

[This corrects the article DOI: 10.1021/acs.jpcc.4c01994.].

CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.

Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.

Childhood Air Pollution Exposure Associated with Self-Reported Bronchitic Symptoms in Adulthood.

RATIONALE: Few studies have examined the effects of long-term childhood air pollution exposure on adult respiratory health, including whether childhood respiratory effects underlie this relation. OBJECTIVES: To evaluate associations between childhood air pollution exposure and self-reported adult bronchitic symptoms, while considering child respiratory health, in the Southern California Children's Health Study. METHODS: Nitrogen dioxide (NO2), ozone, particulate matter<2.5µm (PM2.5) and <10µm (PM10) exposures assessed using inverse-distance-squared spatial interpolation based on childhood (birth-17 years) residential histories. Bronchitic symptoms (bronchitis, cough, or phlegm in last 12 months) were ascertained via questionnaire in adulthood. Associations between mean air pollution exposure across childhood and self-reported adult bronchitic symptoms were estimated using logistic regression. We further adjusted for childhood bronchitic symptoms and asthma to understand whether associations operated beyond childhood respiratory health impacts. Effect modification was assessed for family history of asthma, childhood asthma, and adult allergies. MEASUREMENTS AND MAIN RESULTS: 1308 participants were included (mostly non-Hispanic White [56%] or Hispanic [32%]). At adult assessment (age mean=32.0 years, standard deviation [SD]=4.7) 25% reported bronchitic symptoms. Adult bronchitic symptoms were associated with NO2 and PM10 childhood exposures. Odds ratios per SD increase: 1.69 (95%CI:1.14,2.49) for NO2 (SD=11.1ppb); 1.51 (95%CI:1.00,2.27) for PM10 (SD=14.2µg/m3). Adjusting for childhood bronchitic symptoms or asthma produced similar results. NO2 and PM10 associations were modified by childhood asthma, with larger associations among asthmatics. CONCLUSION: Childhood NO2 and PM10 exposures were associated with adult bronchitic symptoms. Associations were not explained by childhood respiratory health impacts; however, participants with childhood asthma had stronger associations.

Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters.

The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ∼200-250 bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased Pol2 pausing at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, as well as proteins that interact with the N-terminal transactivation domain (which included histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (which included TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.

Lumbar Drain Use during Middle Fossa Approaches for Nonneoplastic Pathology of the Skull Base.

Introduction The middle fossa craniotomy (MFCs) is commonly utilized for spontaneous cerebrospinal fluid (CSF) leaks, encephaloceles, and superior semicircular canal dehiscence (SSCD). This study compares postoperative outcomes of MFCs with and without LD use. Methods A retrospective cohort study of adults over the age of 18 years presenting for the repair of nonneoplastic CSF leak, encephalocele, or SSCD via MFC from 2009 to 2021 was conducted. The main exposure of interest was the placement of an LD. The primary outcome was the presence of postoperative complications (acute/delayed neurologic deficit, meningitis, intracranial hemorrhage, and stroke). Secondary outcomes included operating room (OR) time, length of stay, recurrence, and need for reoperation. Results In total, 172 patients were included, 96 of whom received an LD and 76 who did not. Patients not receiving an LD were more likely to receive intraoperative mannitol ( n = 24, 31.6% vs. n = 16, 16.7%, p = 0.02). On univariate logistic regression, LD placement did not influence overall postoperative complications (OR: 0.38, 95% confidence interval [CI]: 0.05-2.02, p = 0.28), CSF leak recurrence (OR: 0.75, 95% CI: 0.25-2.29, p = 0.61), or need for reoperation (OR: 1.47, 95% CI: 0.48-4.96, p = 0.51). While OR time was shorter for patients not receiving LD (349 ± 71 vs. 372 ± 85 minutes), this difference was not statistically significant ( p = 0.07). Conclusion No difference in postoperative outcomes was observed in patients who had an intraoperative LD placed compared to those without LD. Operative times were increased in the LD cohort, but this difference was not statistically significant. Given the similar outcomes, we conclude that LD is not necessary to facilitate safe MCF for nonneoplastic skull base pathologies.

Increasing Use of Rapid Magnetic Resonance Imaging for Children with Blunt Head Injury.

OBJECTIVE: To increase the percentage of patients who undergo rapid magnetic resonance imaging (rMRI) rather than computed tomography (CT) for evaluation of mild traumatic brain injury (TBI) from 45% in 2020 to 80% by December 2021. STUDY DESIGN: This was a quality improvement initiative targeted to patients presenting to the pediatric emergency department presenting with mild TBI, with baseline data collected from January 2020 to December 2020. From January 2021 to August 2021, we implemented a series of improvement interventions and tracked the percentage of patients undergoing neuroimaging who received rMRI as their initial study. Balancing measures included proportion of all patients with mild TBI who underwent neuroimaging of any kind, proportion of patients requiring sedation, emergency department length of stay, and percentage with clinically important TBI. RESULTS: The utilization of rMRI increased from a baseline of 45% to a mean of 92% in the intervention period. Overall neuroimaging rates did not change significantly after the intervention (19.8 vs 23.2%, P = .24). There was no difference in need for anxiolysis (12 vs 7%, P = .30) though emergency department length of stay was marginally increased (1.4 vs 1.7 hours, P = < 0.01). CONCLUSION: In this quality improvement initiative, transition to rMRI as the primary imaging modality for the evaluation of minor TBI was achieved at a level 1 pediatric trauma center with no significant increase in overall use of neuroimaging.

Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery.

While genome sequencing has transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.

Clinical and immunophenotype correlating with response to immunotherapy in paediatric patients with primary liver carcinoma. A case series.

BACKGROUND: Paediatric hepatocellular carcinomas (HCC) traditionally arise in the context of a normal structural and functional liver and carry a dismal prognosis. While chemotherapy is the frontline standard, there is emerging interest in the study of immunotherapies for paediatric patients with relapsed/refractory disease. There is limited data to support whether immunotherapies will be of utility in this patient population. METHODS: Six paediatric patients (median age:16 years, range: 12-17 at the time of treatment) with advanced hepatocellular neosplams, either conventional hepatocellular or fibrolamellar carcinoma, were treated with immunotherapy. Patients were consented to institutional genomic profiling and biobanking protocols. Baseline samples and serial tissue samples, when available, were evaluated for somatic mutation rate, actionable gene mutations, and pan-immune bulk RNA expression profiling. Results were correlated with clinical course. FINDINGS: Three patients responded to checkpoint inhibition: one achieved a complete, durable response and the other two, prolonged stable disease. Three additional patients progressed. Diagnostic tissue from the complete responder demonstrated a higher relative mutational burden and robust immune infiltrate. Pre-treatment samples from the three responders demonstrated decreased expression of genes associated with T-cell dysfunction. INTERPRETATION: A subset of patients with primary paediatric hepatocellular tumours will respond to immunotherapy. Immunotherapies are currently under prospective study for relapsed/refractory liver tumours in paediatric patients. Results from this report support the prospective collection of serial serum and tissue samples which may further identify genomic and immunophenotypic patterns predictive of response. FUNDING: This work was supported by Philanthropic funds (Pan Mass Challenge, Team Angus and Team Perspective).