SAIBR: a simple, platform-independent method for spectral autofluorescence correction.

Biological systems are increasingly viewed through a quantitative lens that demands accurate measures of gene expression and local protein concentrations. CRISPR/Cas9 gene tagging has enabled increased use of fluorescence to monitor proteins at or near endogenous levels under native regulatory control. However, owing to typically lower expression levels, experiments using endogenously tagged genes run into limits imposed by autofluorescence (AF). AF is often a particular challenge in wavelengths occupied by commonly used fluorescent proteins (GFP, mNeonGreen). Stimulated by our work in C. elegans, we describe and validate Spectral Autofluorescence Image Correction By Regression (SAIBR), a simple platform-independent protocol and FIJI plug-in to correct for autofluorescence using standard filter sets and illumination conditions. Validated for use in C. elegans embryos, starfish oocytes and fission yeast, SAIBR is ideal for samples with a single dominant AF source; it achieves accurate quantitation of fluorophore signal, and enables reliable detection and quantification of even weakly expressed proteins. Thus, SAIBR provides a highly accessible low-barrier way to incorporate AF correction as standard for researchers working on a broad variety of cell and developmental systems.

Understanding formation processes of calcareous nephrolithiasis in renal interstitium and tubule lumen.

Kidney stone, one of the oldest known diseases, has plagued humans for centuries, consistently imposing a heavy burden on patients and healthcare systems worldwide due to their high incidence and recurrence rates. Advancements in endoscopy, imaging, genetics, molecular biology and bioinformatics have led to a deeper and more comprehensive understanding of the mechanism behind nephrolithiasis. Kidney stone formation is a complex, multi-step and long-term process involving the transformation of stone-forming salts from free ions into asymptomatic or symptomatic stones influenced by physical, chemical and biological factors. Among the various types of kidney stones observed in clinical practice, calcareous nephrolithiasis is currently the most common and exhibits the most intricate formation mechanism. Extensive research suggests that calcareous nephrolithiasis primarily originates from interstitial subepithelial calcified plaques and/or calcified blockages in the openings of collecting ducts. These calcified plaques and blockages eventually come into contact with urine in the renal pelvis, serving as a nidus for crystal formation and subsequent stone growth. Both pathways of stone formation share similar mechanisms, such as the drive of abnormal urine composition, involvement of oxidative stress and inflammation, and an imbalance of stone inhibitors and promoters. However, they also possess unique characteristics. Hence, this review aims to provide detailed description and present recent discoveries regarding the formation processes of calcareous nephrolithiasis from two distinct birthplaces: renal interstitium and tubule lumen.

StreamSAXS: a Python-based workflow platform for processing streaming SAXS/WAXS data.

StreamSAXS is a Python-based small- and wide-angle X-ray scattering (SAXS/WAXS) data analysis workflow platform with graphical user interface (GUI). It aims to provide an interactive and user-friendly tool for analysis of both batch data files and real-time data streams. Users can easily create customizable workflows through the GUI to meet their specific needs. One characteristic of StreamSAXS is its plug-in framework, which enables developers to extend the built-in workflow tasks. Another feature is the support for both already acquired and real-time data sources, allowing StreamSAXS to function as an offline analysis platform or be integrated into large-scale acquisition systems for end-to-end data management. This paper presents the core design of StreamSAXS and provides user cases demonstrating its utilization for SAXS/WAXS data analysis in offline and online scenarios.

In situ/operando plug-flow fixed-bed cell for synchrotron PXRD and XAFS investigations at high temperature, pressure, controlled gas atmosphere and ultra-fast heating.

A plug-flow fixed-bed cell for synchrotron powder X-ray diffraction (PXRD) and X-ray absorption fine structure (XAFS) idoneous for the study of heterogeneous catalysts at high temperature, pressure and under gas flow is designed, constructed and demonstrated. The operating conditions up to 1000°C and 50 bar are ensured by a set of mass flow controllers, pressure regulators and two infra-red lamps that constitute a robust and ultra-fast heating and cooling method. The performance of the system and cell for carbon dioxide hydrogenation reactions under specified temperatures, gas flows and pressures is demonstrated both for PXRD and XAFS at the P02.1 (PXRD) and the P64 (XAFS) beamlines of the Deutsches Elektronen-Synchrotron (DESY).

Transcatheter closure of a large coronary cameral fistula presenting as a calcified cystic right atrial mass.

A 51-year-old patient with progressive right heart dysfunction was found to have a large calcified right atrial mass on echocardiography. As part of the work up for an intracardiac mass he had a cardiac computed tomogram which detailed a large coronary cameral fistula from the circumflex coronary artery to the right atrium associated with a spherical calcific pseudo-aneurysmal sac. Transcatheter occlusion of the exit point into the atrium with a vascular plug was performed directly from a right atrial approach without the need for an arteriovenous wire loop. This case details a unique presentation of a coronary cameral fistula to an unusual position within the right atrium which facilitated the rare ability to occlude the fistula from a venous approach without creating an arteriovenous wire rail.

Transapical concomitant transseptal transcatheter closure of a giant mitral paravalvular leak under three-dimensional printing guidance.

A mitral paravalvular leak (PVL) is a significant complication of surgical valve replacement that has a profound impact on the health and survival of patients. Transcatheter closure of PVL has emerged as a promising treatment option. We present the case of a 65-year-old patient who experienced exertional dyspnea, chest tightness, and peripheral edema (New York Heart Association functional class Ⅵ) following surgical aortic and mitral valve replacement. Echocardiography and computed tomography performed on admission revealed a giant mitral PVL (1 bundle, volume 25.0 mL, area 13.0 cm²). Due to the patient's high surgical risk and complex anatomical characteristics, a patient-specific three-dimensional printed model was utilized to visualize anatomical structures and simulate the main procedures. After careful consideration, the surgical team opted to perform transcatheter closure of the giant mitral PVL via a transapical concomitant transseptal approach using two carefully selected devices of different sizes (14-mm and 16-mm Amplatzer Vascular Plug II). The procedure was carried out successfully. During the 1-month follow-up, the patient remained asymptomatic (New York Heart Association functional class Ⅰ). Transcatheter closure of a giant and complex mitral PVL utilizing three-dimensional printing guidance has proven to be a feasible approach.

A forced aeration system for microbial culture of multiple shaken vessels suppresses volatilization.

Shake-flask culture, an aerobic submerged culture, has been used in various applications involving cell cultivation. However, it is not designed for forced aeration. Hence, this study aimed to develop a small-scale submerged shaking culture system enabling forced aeration into the medium. A forced aeration control system for multiple vessels allows shaking, suppresses volatilization, and is attachable externally to existing shaking tables. Using a specially developed plug, medium volatilization was reduced to less than 10%, even after 45 h of continuous aeration (~ 60 mL/min of dry air) in a 50 mL working volume. Escherichia coli IFO3301 cultivation with aeration was completed within a shorter period than that without aeration, with a 35% reduction in the time-to-reach maximum bacterial concentration (26.5 g-dry cell/L) and a 1.25-fold increase in maximum concentration. The maximum bacterial concentration achieved with aeration was identical to that obtained using the Erlenmeyer flask, with a 65% reduction in the time required to reach it.

Are comparable studies really comparable? Suggestions from a problem-solving experiment on urban and rural great tits.

Performance in tests of various cognitive abilities has often been compared, both within and between species. In intraspecific comparisons, habitat effects on cognition has been a popular topic, frequently with an underlying assumption that urban animals should perform better than their rural conspecifics. In this study, we tested problem-solving ability in great tits Parus major, in a string-pulling and a plug-opening test. Our aim was to compare performance between urban and rural great tits, and to compare their performance with previously published problem solving studies. Our great tits perfomed better in string-pulling than their conspecifics in previous studies (solving success: 54%), and better than their close relative, the mountain chickadee Poecile gambeli, in the plug-opening test (solving success: 70%). Solving latency became shorter over four repeated sessions, indicating learning abilities, and showed among-individual correlation between the two tests. However, the solving ability did not differ between habitat types in either test. Somewhat unexpectedly, we found marked differences between study years even though we tried to keep conditions identical. These were probably due to small changes to the experimental protocol between years, for example the unavoidable changes of observers and changes in the size and material of test devices. This has an important implication: if small changes in an otherwise identical set-up can have strong effects, meaningful comparisons of cognitive performance between different labs must be extremely hard. In a wider perspective this highlights the replicability problem often present in animal behaviour studies.

Flow Behavior of Entangled Polymer Nanoparticle Composites in a Nanotube: Insights into Jamming State.

Using molecular dynamics simulations, this study investigates the equilibrium properties and flow behaviors of entangled polymer nanoparticle composites (PNCs) within a nanotube. The results show that the density distribution of nanoparticles (NPs), displacement of polymer chains and NPs, and the moduli of PNCs remain relatively unaffected when NP volume fractions (ΦN) ≤0.10. However, the flow behavior of entangled PNCs deviates from the ideal parabolic profile seen in unentangled PNCs, displaying plug-like flow characteristics with a significant platform region, indicating the presence of shear bands. Interestingly, entangled PNCs at intermediate ΦN values undergo a significant alteration in NP distribution under steady flow, resulting in notable NP aggregation. At ΦN = 0.30, a distinct change in the static structure of PNCs occurs, reducing the equilibrium distance between neighboring NPs. Consequently, the motion of both polymer chains and NPs becomes restricted, leading to an increase in the moduli of PNCs resembling solid-like behavior. Additionally, the entangled PNCs experience a complete absence of flow, indicating the entry into a jamming state. This study contributes to the understanding of PNCs flow behavior and provides insights into fundamental aspects and practical implications of PNCs.

Rapidly progressive mucus plugs in allergic bronchopulmonary mycosis.

INTRODUCTION: Allergic bronchopulmonary mycosis (ABPM) is a chronic airway disease characterized by the presence of fungi that trigger allergic reactions and airway obstruction. Here, we present a unique case of ABPM in which a patient experienced sudden respiratory failure due to mucus plug-induced airway obstruction. The patient's life was saved by venovenous extracorporeal membrane oxygenation (VV-ECMO) and bronchoscopic removal of the plug. This case emphasizes the clinical significance of mucus plug-induced airway obstruction in the differential diagnosis of respiratory failure in patients with ABPM. CASE STUDY: A 52-year-old female clerical worker with no smoking history, presented with dyspnea. CT scan revealed mucus plugs in both lungs. Despite treatment, the dyspnea progressed rapidly to respiratory failure, leading to VV-ECMO placement. RESULTS: CT revealed bronchial wall thickening, obstruction, and extensive atelectasis. Bronchoscopy revealed extensive mucus plugs that were successfully removed within two days. The patient's respiratory status significantly improved. Follow-up CT revealed no recurrence. Fungal cultures identified Schizophyllum commune, confirming ABPM. Histological examination of the mucus plugs revealed aggregated eosinophils, eosinophil granules, and Charcot-Leyden crystals. Galectin-10 and major basic protein (MBP) staining supported these findings. Eosinophil extracellular traps (EETs) and eosinophil cell death (ETosis), which contribute to mucus plug formation, were identified by citrullinated histone H3 staining. CONCLUSION: Differentiating between asthma exacerbation and mucus plug-induced airway obstruction in patients with ABPM and those with acute respiratory failure is challenging. Prompt evaluation of mucous plugs and atelectasis using CT and timely decision to introduce ECMO and bronchoscopic mucous plug removal are required.

High attenuation mucus in bronchi with allergic bronchopulmonary mycosis.

BACKGROUND: High-attenuation mucus (HAM) is a specific manifestation of allergic bronchopulmonary mycosis (ABPM) on chest computed tomography (CT). OBJECTIVES: To compare the diagnostic accuracy of the two definitions of HAM and to clarify the clinical and radiographic characteristics of HAM-positive and HAM-negative ABPM. METHODS: CT images at the diagnosis of ABPM using Asano's criteria were retrospectively analysed. In Study #1, radiographic data obtained using the same CT apparatus in a single institute were analysed to determine the agreement between the two definitions of HAM: a mucus plug that is visually denser than the paraspinal muscles or that with a radiodensity ≥70 Hounsfield units. In Study #2, HAM was diagnosed by comparison with the paraspinal muscles in patients with ABPM reporting to 14 medical institutes in Japan. RESULTS: In Study #1, 93 mucus plugs from 26 patients were analysed. A substantial agreement for HAM diagnosis was observed between the two methods, with a κ coefficient of 0.72. In Study #2, 60 cases of ABPM were analysed; mucus plugs were present in all cases and HAM was diagnosed in 45 (75%) cases. The median A. fumigatus-specific IgE titre was significantly lower in HAM-positive patients than in HAM-negative patients (2.5 vs. 24.3 UA /mL, p = .004). Nodular shadows were observed more frequently in the airways distal to HAM than in those distal to non-HAM mucus plugs (59% vs. 32%, p < .001). CONCLUSION: In conclusion, agreement between the two methods to diagnose HAM was substantial. HAM was associated with some immunological and radiographic characteristics, including lower levels of sensitization to A. fumigatus and the presence of distal airway lesions.

Progress in Ocular Drug Delivery: Challenges and Constraints.

The eye has several dynamic and static barriers in place to limit the entry of foreign substances including therapeutics. As such, efficient drug delivery, especially to posterior segment tissues, has been challenging. This chapter describes the anatomical and physiological challenges associated with ocular drug delivery before discussing constraints with regard to formulation parameters. Finally, it gives an overview of advanced drug delivery technologies with a specific focus on recently marketed and late-stage clinical trial products.

Treatment of late paravalvular regurgitation after transcatheter aortic valve implantation: prognostic implications.

AIMS: Paravalvular regurgitation (PVR) after transcatheter aortic valve implantation (TAVI) is associated with increased morbidity and mortality. The effect of transcatheter interventions to treat PVR after the index TAVI was investigated. METHODS AND RESULTS: A registry of consecutive patients who underwent transcatheter intervention for ≥ moderate PVR after the index TAVI at 22 centers. The principal outcomes were residual aortic regurgitation (AR) and mortality at 1 year after PVR treatment. A total of 201 patients were identified: 87 (43%) underwent redo-TAVI, 79 (39%) plug closure, and 35 (18%) balloon valvuloplasty. Median TAVI-to-re-intervention time was 207 (35; 765) days. The failed valve was self-expanding in 129 (63.9%) patients. The most frequent devices utilized were a Sapien 3 valve for redo-TAVI (55, 64%), an AVP II as plug (33, 42%), and a True balloon for valvuloplasty (20, 56%). At 30 days, AR ≥ moderate persisted in 33 (17.4%) patients: 8 (9.9%) after redo-TAVI, 18 (25.9%) after plug, and 7 (21.9%) after valvuloplasty (P = 0.036). Overall mortality was 10 (5.0%) at 30 days and 29 (14.4%) at 1 year: 0, 8 (10.1%), and 2 (5.7%) at 30 days (P = 0.010) and 11 (12.6%), 14 (17.7%), and 4 (11.4%) at 1 year (P = 0.418), after redo-TAVI, plug, and valvuloplasty, respectively. Regardless of treatment strategy, patients in whom AR was reduced to ≤ mild had lower mortality at 1 year compared with those with AR persisting ≥ moderate [11 (8.0%) vs. 6 (21.4%); P = 0.007]. CONCLUSION: This study describes the efficacy of transcatheter treatments for PVR after TAVI. Patients in whom PVR was successfully reduced had better prognosis. The selection of patients and the optimal PVR treatment modality require further investigation.

Amplatzer Vascular Plug closure of an iatrogenic interatrial tunnel-type communication.

A 50-year-old woman who had atrial septal defect surgery at 11 months old underwent ascending aortic aneurysm resection and two attempts at closure of a residual atrial septal defect. Post-operatively, she had severe cyanosis. She was referred to our centre where a transesophageal echocardiogram and cardiac catheterisation showed an iatrogenic interatrial tunnel-type communication that was closed with an Amplatzer Vascular Plug.

Use of a modified microvascular plug to modify fenestration flow in a rapidly failing Fontan.

We report a case of an alternative transcatheter use of the modified Medtronic microvascular plug to modify fenestration stent flow in a patient with a rapidly deteriorating clinical condition. This four-year-old boy developed severe cyanosis following fenestration stent insertion, initially placed due to prolonged drainage post-Fontan with extra-cardiac conduit. In April 2023, he underwent urgent cardiac catheterisation and had partial occlusion of fenestration stent with a modified 9Q microvascular plug. His oxygen saturations improved from 50 to 89% in room air with no re-emergence of raised cavopulmonary pressures.

Preliminary experience with transcatheter closure of wind-sock-like perimembranous ventricular septal defects using Amplatzer Vascular Plug IV devices.

Amplatzer Vascular Plug IV (Abbott, USA) is usually used for the occlusion of abnormal tortuous vessels and has not been tried for the transcatheter closure of perimembranous ventricular septal defects with wind-sock morphology. Here, we report on three successful cases of perimembranous ventricular septal defect transcatheter closure using Amplatzer Vascular Plug IV. We did not observe residual shunting or new onset of complications during follow up. These preliminary positive results advocate the application and suitability of Amplatzer Vascular Plug IV for closing wind-sock-like perimembranous ventricular septal defects.

Investigations, management and outcome of neonates presenting with distal intestinal obstruction: challenging the need for contrast enemas.

PURPOSE: To characterise the investigations, management and ultimate diagnosis of neonates with distal intestinal obstruction. METHODS: Retrospective review of term (> 37 weeks) neonates with admission diagnosis of distal intestinal obstruction over 10 years (2012-2022). Patient pathways were identified and associations between presentations, response to treatments and outcome investigated. RESULTS: A total of 124 neonates were identified and all included. Initial management was colonic irrigation in 108, contrast enema in 4, and laparotomy in 12. Of those responding to irrigations none underwent contrast enema. Ultimately, 22 neonates proceeded to laparotomy. Overall, 106 had a suction rectal biopsy and 41 had genetic testing for cystic fibrosis. Final diagnosis was Hirschsprung disease (HD) in 67, meconium ileus with cystic fibrosis (CF) in 9, meconium plug syndrome in 19 (including 3 with CF), intestinal atresia in 10 and no formal diagnosis in 17. Median length of neonatal unit stay was 11 days (7-19). CONCLUSIONS: Initial management of neonates with distal bowel obstruction should be colonic irrigation since this is therapeutic in the majority and significantly reduces the need for contrast enema. These infants should all have suction rectal biopsy to investigate for HD unless another diagnosis is evident. If a meconium plug is passed, testing for CF is recommended. Evaluation and therapy are multimodal and time consuming, placing burden on resources and families.

Is salvage Plug-Assisted Retrograde Transvenous Obliteration (PARTO) safe and effective for bleeding gastric varices ?- A preliminary single-center experience.

BACKGROUND: Vascular plug-assisted retrograde transvenous obliteration (PARTO) obliterates the gastric varices and portosystemic shunt, thus resulting in a lower rebleeding rate than endoscopic glue/sclerotherapy. AIMS: To evaluate the safety and efficacy of PARTO as salvage therapy in liver cirrhosis with gastric variceal bleed (GVB) after failed endotherapy. We assessed the clinical success rate and changes in liver function at 6- months. MATERIALS AND METHODS: Patients who underwent salvage PARTO after failed endotherapy for GVB (between December 2021 and November 2022) were searched and analyzed from the hospital database. Clinical success rate and rebleed rate were obtained at six months. Child-Pugh score (CTP) and Model for end-stage liver disease (MELD) score were calculated and compared between baseline and 6-month follow-up. RESULTS: Fourteen patients (n = 14, Child-Pugh class A/B) underwent salvage PARTO. Nine had GOV-2, and five had IGV-1 varices. The mean shunt diameter was 11.6 ± 1.6 mm. The clinical success rate of PARTO was 100% (no recurrent gastric variceal hemorrhage within six months). No significant deterioration in CTP (6.79 ± 0.98 vs. 6.21 ± 1.52; p = 0.12) and MELD scores (11.5 ± 4.05 vs. 10.21 ± 3.19; p = 0.36) was noted at 6 months. All patients were alive at 6 months. One patient (n = 1, 7.1%) bled from esophageal varices after three days of PARTO and was managed with variceal banding. 21.4% (3/14) patients had progression of esophageal varices at 6 months requiring prophylactic band ligation. Three patients (21.4%) had new onset or worsening ascites and responded to low-dose diuretics therapy. CONCLUSIONS: PARTO is a safe and effective procedure for bleeding gastric varices without any deterioration in liver function even after six months. Patient selection is critical to prevent complications. Further prospective studies with larger sample size are required to validate our findings.

Effects of Access Cavity Design and Placement Techniques on Mineral Trioxide Aggregate Obturation Quality in Simulated Immature Teeth: A Micro-Computed Tomography Study.

Background and Objectives: In teeth with open apices, performing single session apexification is a challenging treatment due to the difficulty in handling mineral trioxide aggregate (MTA). Minimally invasive approaches in dentistry have also influenced the cavity designs in endodontics. Until now, different techniques have not been investigated in addition to manual condensation during the process of placing MTA in traditional (TradACs) or conservative (ConsACs) endodontic access cavities. The aim of this in vitro study was to compare and evaluate the obturation quality of MTA apical plugs placed with different techniques in TradACs or ConsACs. Materials and Methods: Sixty upper central teeth were divided into two main groups based on cavity design, and then each main group was further divided into three subgroups according to MTA placement techniques (n = 10): TradAC-manual, TradAC-manual + indirect ultrasonic activation, TradAC-manual + XP-endo Shaper (XPS), ConsAC-manual, ConsAC-manual + indirect ultrasonic activation, and ConsAC-manual + XPS. Subsequently, the porosity percentages in the MTA apical plug were analyzed using micro-computed tomography. The statistical analysis was performed using the Kruskal-Wallis H test and Mann-Whitney U test. Statistical significance was set at p < 0.05. Results: There were differences in volume of porosity percentages (%) according to cavity designs and MTA application techniques (p < 0.05). Except for the XPS group, more porosity was observed in ConsACs compared to TradACs. In TradACs, the significantly lowest open and total porosity was observed in the manual, ultrasonic, and XPS techniques, respectively. In ConsACs, the significantly lowest porosity was observed in the manual, XPS, and ultrasonic techniques, respectively (p < 0.05). Conclusions: In MTA obturation, cavity designs and application techniques had an impact on the MTA porosity. Creating an apical plug in ConsACs may result in more porosity compared to TradACs, especially when manual or indirect ultrasonic activation is preferred. Opting for the manual technique alone may be considered sufficient for controlling porosity for both TradACs and ConsACs.

FliL and its paralog MotF have distinct roles in the stator activity of the Sinorhizobium meliloti flagellar motor.

The bacterial flagellum is a complex macromolecular machine that drives bacteria through diverse fluid environments. Although many components of the flagellar motor are conserved across species, the roles of FliL are numerous and species-specific. Here, we have characterized an additional player required for flagellar motor function in Sinorhizobium meliloti, MotF, which we have identified as a FliL paralog. We performed a comparative analysis of MotF and FliL, identified interaction partners through bacterial two-hybrid and pull-down assays, and investigated their roles in motility and motor rotation. Both proteins form homooligomers, and interact with each other, and with the stator proteins MotA and MotB. The ∆motF mutant exhibits normal flagellation but its swimming behavior and flagellar motor activity are severely impaired and erratic. In contrast, the ∆fliL mutant is mostly aflagellate and nonmotile. Amino acid substitutions in cytoplasmic regions of MotA or disruption of the proton channel plug of MotB partially restored motor activity to the ∆motF but not the ∆fliL mutant. Altogether, our findings indicate that both, MotF and FliL, are essential for flagellar motor torque generation in S. meliloti. FliL may serve as a scaffold for stator integration into the motor, and MotF is required for proton channel modulation.