Chromosome structure modeling tools and their evaluation in bacteria.

The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.

Strategies for Achieving Ultra-Long ORR Durability-Rh Activates Interatomic Interactions in Alloys.

The stability of platinum-based alloy catalysts is crucial for the future development of proton exchange membrane fuel cells, considering the potential dissolution of transition metals under complex operating conditions. Here, we report on a Rh-doped Pt3Co alloy that exhibits strong interatomic interactions, thereby enhancing the durability of fuel cells. The Rh-Pt3Co/C catalyst demonstrates exceptional catalytic activity for oxygen reduction reactions (ORR) (1.31 A mgPt -1 at 0.9 V vs. the reversible hydrogen electrode (RHE) and maintaining 92 % of its mass activity after 170,000 potential cycles). Long-term testing has shown direct inhibition of Co dissolution in Rh-Pt3Co/C. Furthermore, tests on proton exchange membrane fuel cells (PEMFC) have shown excellent performance and long-term durability with low Pt loading. After 50,000 cycles, there was no voltage loss at 0.8 A cm-2 for Rh-Pt3Co/C, while Pt3Co/C experienced a loss of 200 mV. Theoretical calculations suggest that introducing transition metal atoms through doping creates a stronger compressive strain, which in turn leads to increased catalytic activity. Additionally, Rh doping increases the energy barrier for Co diffusion in the bulk phase, while also raising the vacancy formation energy of the surface Pt. This ensures the long-term stability of the alloy over the course of the cycle.

Generalized Encapsulations of ZIF-Based Fe-N-C Catalysts with Controllable Nitrogen-Doped Carbon for Significantly-Improved Stability Toward Oxygen Reduction Reaction.

The vigorous development of efficient platinum group metal-free catalysts is considerably important to facilitate the universal application of proton exchange membrane fuel cells. Although nitrogen-coordinated atomic iron intercalated in carbon matrix (Fe-N-C) catalysts exhibit promising catalytic activity, the performance in fuel cells, especially the short lifetime, remains an obstacle. Herein, a highly-active Fe-N-C catalyst with a power density of >1 w cm-2 and prolonged discharge stability with a current density of 357 mA cm-2 after 40 h of constant voltage discharge at 0.7 V in H2 -O2 fuel cells using a controllable and efficient N-C coating strategy is developed. It is clarified that a thicker N-C coating may be more favorable to enhance the stability of Fe-N-C catalysts at the expense of their catalytic activity. The stability enhancement mechanism of the N-C coating strategy is proven to be the synergistic effect of reduced carbon corrosion and iron loss. It is believed that these findings can contribute to the development of Fe-N-C catalysts with high activity and long lifetimes.

Atomically Dispersed, Low-Coordinate Co-N Sites on Carbon Nanotubes as Inexpensive and Efficient Electrocatalysts for Hydrogen Evolution.

Hydrogen produced using renewable electricity is considered the key to achieving a low-carbon energy economy. However, the large-scale application of electrochemical water splitting for hydrogen evolution currently requires expensive platinum-based catalysts. Therefore, it is important to develop efficient and stable catalysts based on the rich reserves of transition metals as alternatives. In this study, the authors prepare a carbon-nanotube material enriched with atomically dispersed CoN sites having uniquely low coordination numbers via the simple mixing, pyrolysis, and leaching of inexpensive precursors. These atomically dispersed low-coordinate CoN sites provide an overpotential of only 82 mV at 10 mA cm-2 for the hydrogen evolution reaction (HER) under challenging acidic conditions and show excellent durability in accelerated stability tests. Theoretical simulations also confirm that these unique, low-coordinate CoN2 sites have lower energy barriers in catalyzing the HER than Fe/NiN2 sites and commonly reported CoN3 /N4 sites. Therefore, the method provides a new concept for the design of single-atom catalytic sites with low coordination numbers. It also serves to reduce the cost of hydrogen production in the future owing to the high catalytic activity, low cost, and scalable production process.

Controlling Solution-State Aggregation and Solid-State Microstructures of Conjugated Polymers by Tuning Backbone Conformation.

Molecular ordering of conjugated polymers both in solution-state aggregates and in solid-state microstructures is a determining factor of the charge transport properties in optoelectronic devices. However, the effect of backbone conformation in conjugated polymers on assembly structures is still unclear. Herein, to understand such backbone conformation effect, three novel chlorinated benzodifurandionge-based oligo(p-phenylene vinylene) (BDOPV) polymers are systematically developed. These BDOPV-based polymers exhibit significantly twisted backbone conformation (near 90° interunit torsion angle) between conjugated units, which can prevent polymer chains from forming ordered assembly structures by increasing conformational energy penalty in closely packed chains. A higher rotational barrier of the torsion angle would further prevent polymer chains from assembling, finally resulting in nonaggregated chains in solution and highly disordered solid-state packing structures. This work will deepen the understanding of the relationship between polymer backbone conformation and assembly structures, contributing to the exploration of the structure-property relationship of polymers.

"One-stop shop": safety and efficacy of combining atrial septal defect occlusion and left atrial appendage closure for patients with atrial septal defect and atrial fibrillation.

BACKGROUND: One-stop occlusion, which is defined as the combination of atrial septal defect [ASD] or patent foramen ovale [PFO] occlusion and left atrial appendage [LAA] closure, in patients with ASD/PFO and atrial fibrillation (AF) has not yet been investigated systematically. This study aimed to evaluate the safety and efficacy of one-stop occlusion in the treatment of adult patients with ASD/PFO and AF. METHODS: Inpatients with AF and ASD/PFO were recruited between August 2014 and April 2019. Preoperatively, transthoracic echocardiography (TTE) and transesophageal echocardiography (TEE) were conducted to identify the ASD/PFO size and margin, presence of thrombus in the LAA, and LAA orifice width and depth at 0°, 45°, 90°, and 135°. After confirmation of the indications of LAA closure (LAAC) and ASD/PFO occlusion, the procedures were performed simultaneously under general anesthesia. Oral anticoagulants were administered for 45-60 days, followed with regular evaluation of TTE and TEE. RESULTS: Forty-nine patients (age, 65.6 ± 9.6 years) were recruited in this study, including 24 patients with ASD and 25 patients with PFO. They were treated with LAAC and ASD/PFO occlusion successfully. The mean ASD size and mean diameter of the ASD occluders were 14.2 ± 7.7 and 25.4 ± 8.5 mm, respectively. The mean PFO size was 3.5 ± 0.4 mm. The mean maximal LAA orifice width and depth were 20.5 ± 3.4 and 28.3 ± 3.6 mm, respectively. All patients were implanted with a Watchman device (diameter, 27.1 ± 2.9 mm). Postoperatively, all patients took anticoagulants orally for 45-60 days, and their mean postoperative follow-up duration was 29.0 ± 12.1 months. Postoperative TEE showed that all had normal positioning of the LAA and ASD/PFO occluders. At 45-60 days after operation, TEE showed that the LAA and ASD/PFO occluder were in the normal position; however, two patients who took warfarin and novel oral anticoagulants, respectively, have developed occluder thrombosis. After adjusted anticoagulant therapy, TEE showed that the thrombus disappeared at 6 months after operation. CONCLUSION: One-stop occlusion is safe and effective for the treatment of adult patients with ASD/PFO and AF. It is also feasible to administer warfarin or novel oral anticoagulants after operation.

EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm.

BACKGROUND: More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need. RESULTS: We have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs. CONCLUSIONS: EVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.

Endothelial progenitor cell mobilization by preoperative exercise: a bone marrow response associated with postoperative outcome.

BACKGROUND: Preoperative anaemia is associated with increased morbidity in patients undergoing major surgery. Whether erythrocytes are the only bone-marrow-derived cell lineage that associates with increased surgical complications is unknown. This prospective observational trial studied the mobilization of endothelial progenitor cells (EPCs) in response to exercise in association with postoperative complications. METHODS: After IRB approval, 60 subjects undergoing major thoracic surgery were exercised to exhaustion (peak V̇(O2)). Peripheral blood collected before and after peak exercise was quantified for EPC lineages by fluorescence-activated cell sorter analysis. Complication analysis was based on the Clavien-Dindo classification. RESULTS: Exhaustive exercise increased EPC [CD45-133+34+ cells=150 (0.00-5230) to 220 (0.00-1270) cells µl(-1); median change (range)=20 (-4,180-860) cells µl(-1); P=0.03] but not mature endothelial cell (EC) subpopulations. Pre-exercise levels [odds ratio (OR)=0.86, 95% confidence interval (CI): 0.37-2.00, P=0.72), change after exercise as a continuous variable (OR=0.95, 95% CI: 0.41-2.22, P=0.91) and a positive response after exercise (change >0 cells µl(-1); OR=0.41, 95% CI: 0.13-1.28, P=0.12) were not statistically significantly associated with the incidence of postoperative complications. Post-hoc receiver operating characteristic curve analyses revealed that subjects with a CD45-133+34+ increase ≥60 cells µl(-1) in response to exercise suffered fewer postoperative complications [86% sensitivity, 48% specificity and AUC=0.67 (95% CI: 0.52-0.81)]. CONCLUSIONS: Preoperative exercise induces EPC into the peripheral circulation. Subjects with a poor EPC response had a pre-existing propensity for postoperative complications. This warrants further research into the role of bone marrow function as a critical component to endothelial repair mechanisms. CLINICAL TRIAL REGISTRATION: IRB 2003-0434 (University of Texas M.D. Anderson Cancer Center, Houston, TX, USA).

Non-invasive brain stimulation improves pain in patients with central post-stroke pain: a systematic review and meta-analysis.

BACKGROUND: Central post-stroke pain (CPSP) significantly interferes with the quality of life and psychological well-being of stroke patients. Non-invasive brain stimulation (NIBS) has attracted significant attention as an emerging method for treating patients with CPSP. OBJECTIVE: To compare the clinical efficacy of noninvasive brain stimulation on pain, and psychological status of patients with central post-stroke pain using meta-analysis. METHODS: A computerized search of multiple databases was performed for identification of randomized controlled trials involving NIBS-led treatment of CPSP patients. Two researchers worked independently on literature screening, data extraction, and quality assessment. Research was conducted from inception of the database until October 2023. RevMan 5.0 and Stata 15.0 software were used to conduct statistical analysis. RESULTS: Sixteen papers with 807 patients were finally included. The results showed that NIBS reduced patients' pain intensity [SMD = -0.39, 95% CI (-0.54, -0.24), p < 0.01] and was more effective in short-term CPSP patients. However, the included studies did not show a significant impact on psychological status, particularly depression. Subgroup analysis suggested that the M1 stimulation point was more effective than other stimulation points [SMD = -0.45, 95% CI (-0.65, -0.25), p < 0.001]. Other stimulation modalities also demonstrated favorable outcomes when compared to rTMS [SMD = -0.67, 95% CI (-1.09, -0.25), p < 0.01]. CONCLUSION: NIBS has a positive impact on pain relief in patients with CPSP, but does not enhance patients' psychological well-being in terms of anxiety or depression. Furthermore, large-sample, high-quality, and multi-center RCTs are needed to explore the benefits of different stimulation durations and parameters in patients with CPSP. The current study has been registered with Prospero under the registration number CRD42023468419.

Design of Linear-Polymer-Coated Graphene Nanosheets with π-Conjugated Structure and Multi-Active-Center for Long-Lifespan and High-Rate Li-Storage Performance.

Organic material holds immense potential for Li-ion batteries (LIBs) due to their eco-friendly nature, high structural designability, abundant sources, and high theoretical capacity. However, the limited redox-active sites, low electronic conductivity, sluggish ionic diffusion, and high solubility hinder their practical application. Here, we reported the use of a linear polymer called poly(naphthalenetetracarboxylic dianhydride-pyrene-4,5,9,10-tetraone)-coated graphene nanosheets (NPT/rGO) as a cathode material for LIBs. The NPT polymer has a rotation angle of approximately 63° between each plane, which helps in exposing the active sites and preventing structural pulverization during cycling. The highly conjugated skeleton of the polymer, along with graphene, forms a synergistic effect through a π-π interaction. This combination enhances the conductivity and restricts solubility. Additionally, the linear structure of NPT and the two-dimensional rGO substrates work together to enhance charge transfer and ion diffusion rates, resulting in faster reaction kinetics. Consequently, NPT/rGO exhibits excellent electrochemical performance in terms of high capacity, superior cyclic stability, and good rate capability for LIBs. Moreover, through the combination of experimental investigations and theoretical simulations, a multiple electron reaction mechanism, an efficient Li-ion storage behavior, and a reversible dynamic evolution have been revealed. This study introduces a rational molecular design approach to enhance the electrochemical performance of polyimide derivatives, thereby contributing to the advancement of cutting-edge organic electrode materials for LIBs.

Primary diffuse large B-cell lymphoma of adrenal gland: A case report.

INTRODUCTION: Most adrenal tumors are benign and primary adrenal malignancies are relatively rare. Primary adrenal lymphoma (PAL) is a very rare and highly aggressive malignant tumor with unknown etiology, atypical clinical symptoms, nonspecific imaging manifestations, difficult disease diagnosis and poor prognosis. CASE REPORT: This case report details a 42-year-old woman who was admitted to the hospital with a 1-year-old bilateral adrenal mass and 1-month-old left upper abdominal pain. Enhanced CT of the abdomen showed a right adrenal nodule and a large occupying lesion in the left adrenal region, with a high probability of pheochromocytoma. Intraoperatively, a huge tumor measuring about 12*12*10 cm was found in the left adrenal region, infiltrating the left kidney, spleen and pancreatic tail. Postoperative pathology: lymphocytes were found in the renal capsule and subcapsule, lymphocytes were found in the pancreas; lymphocytes were found in the spleen. Consider a tumor of the lymphohematopoietic system, possibly lymphoma. CONCLUSION: This case demonstrates that primary adrenal diffuse large B-cell lymphoma (PADLBCL) is highly aggressive, has a poor prognosis, is prone to recurrence, has poor therapeutic outcomes, and is difficult to diagnose. Clinicians should consider the possibility of PADLBCL when encountering huge adrenal-occupying lesions and consider chemotherapy before surgery. Reducing the tumor size before surgery is a more favorable therapeutic approach, thus prolonging the patient life and improving the quality of survival.

Progress and opportunities for metal-organic framework composites in electrochemical sensors.

Metal-organic framework composites have the advantages of large surface area, high porosity, strong catalytic efficiency and good stability, which provide a great possibility of finding excellent electrode materials for electrochemical sensors. However, MOF composites still face various challenges and difficulties, which limit their development and application. This paper reviews the application of MOF composites in electrochemical sensors, including MOF/carbon composites, MOF/metal nanoparticle composites, MOF/metal oxide composites and MOF/enzyme composites. In addition, the application challenges of MOF composites in electrochemical sensors are summarized. Finally, the application prospect for MOF composites is considered to promote the synthesis of more MOF composites with excellent properties.

Porous Organic Polymer with Hierarchical Structure and Limited Volume Expansion for Ultrafast and Highly Durable Sodium Storage.

Sustainable organic electrode materials, as promising alternatives to conventional inorganic electrode materials for sodium-ion batteries (SIBs), are still challenging to realize long-lifetime and high-rate batteries because of their poor conductivity, limited electroactivity, and severe dissolution. It is also urgent to deeply reveal their electrochemical mechanism and evolution processes. A porous organic polymer (POP) with a conjugated and hierarchical structure is designed and synthesized here. The unique molecule and structure endow the POP with electron delocalization, high ionic diffusivity, plentiful active sites, exceptional structure stability, and limited solubility in electrolytes. When evaluated as an anode for SIBs, the POP exhibits appealing electrochemical properties regarding reversible capacity, rate behaviors, and long-duration life. Importantly, using judiciously combined experiments and theoretical computation, including in situ transmission electron microscopy (TEM), and ex situ spectroscopy, we reveal the Na-storage mechanism and dynamic evolution processes of the POP, including 12-electron reaction process with Na, low volume expansion (125-106% vs the initial 100%), and stable composition and structure evolution during repeating sodiation/de-sodiation processes. This quantitative design for ultrafast and highly durable sodium storage in the POP could be of immediate benefit for the rational design of organic electrode materials with ideal electrochemical properties.

The Spatial Organization of Bacterial Transcriptional Regulatory Networks.

The transcriptional regulatory network (TRN) is the central pivot of a prokaryotic organism to receive, process and respond to internal and external environmental information. However, little is known about its spatial organization so far. In recent years, chromatin interaction data of bacteria such as Escherichia coli and Bacillus subtilis have been published, making it possible to study the spatial organization of bacterial transcriptional regulatory networks. By combining TRNs and chromatin interaction data of E. coli and B. subtilis, we explored the spatial organization characteristics of bacterial TRNs in many aspects such as regulation directions (positive and negative), central nodes (hubs, bottlenecks), hierarchical levels (top, middle, bottom) and network motifs (feed-forward loops and single input modules) of the TRNs and found that the bacterial TRNs have a variety of stable spatial organization features under different physiological conditions that may be closely related with biological functions. Our findings provided new insights into the connection between transcriptional regulation and the spatial organization of chromosome in bacteria and might serve as a factual foundation for trying spatial-distance-based gene circuit design in synthetic biology.

Aged Mouse Hippocampus Exhibits Signs of Chronic Hypoxia and an Impaired HIF-Controlled Response to Acute Hypoxic Exposures.

Altered hypoxia-inducible factor-alpha (HIF-α) activity may have significant consequences in the hippocampus, which mediates declarative memory, has limited vascularization, and is vulnerable to hypoxic insults. Previous studies have reported that neurovascular coupling is reduced in aged brains and that diseases which cause hypoxia increase with age, which may render the hippocampus susceptible to acute hypoxia. Most studies have investigated the actions of HIF-α in aging cortical structures, but few have focused on the role of HIF-α within aged hippocampus. This study tests the hypothesis that aging is associated with impaired hippocampal HIF-α activity. Dorsal hippocampal sections from mice aged 3, 9, 18, and 24 months were probed for the presence of HIF-α isoforms or their associated gene products using immunohistochemistry and fluorescent in situ hybridization (fISH). A subset of each age was exposed to acute hypoxia (8% oxygen) for 3 h to investigate changes in the responsiveness of HIF-α to hypoxia. Basal mean intensity of fluorescently labeled HIF-1α protein increases with age in the hippocampus, whereas HIF-2α intensity only increases in the 24-month group. Acute hypoxic elevation of HIF-1α is lost with aging and is reversed in the 24-month group. fISH reveals that glycolytic genes induced by HIF-1α (lactose dehydrogenase-a, phosphoglycerate kinase 1, and pyruvate dehydrogenase kinase 1) are lower in aged hippocampus than in 3-month hippocampus, and mRNA for monocarboxylate transporter 1, a lactose transporter, increases. These results indicate that lactate, used in neurotransmission, may be limited in aged hippocampus, concurrent with impaired HIF-α response to hypoxic events. Therefore, impaired HIF-α may contribute to age-associated cognitive decline during hypoxic events.

Bladder malacoplakia: A case report.

BACKGROUND: Bladder malacoplakia is a rare chronic granulomatous disease. The most common site of the malacoplakia is the urinary system. The etiology of bladder malacoplakia is complex, with its clinical misdiagnosis rate is high. Therefore, exposure to more clinical cases is necessary to improve the diagnosis and treatment of this condition. CASE SUMMARY: A 65-year-old woman was admitted to our hospital because of dysuria. She presented with dysuria, frequent urination, urgency, pain, and absence of hematuria and pyuria. After the examination, bladder tumor electrocision was performed under combined intravenous and inhalation anesthesia on September 6, 2021. During the operation, electrotomy and electrocoagulation were performed. The operation was then followed by anti-infection treatment, and the patient recovered well. The postoperative pathology was diagnosed as bladder malacoplakia by light and electron microscopic analyses. On a follow-up after 4 mo, no significant difference between electrotomy and electrocoagulation was found, with both achieving a curative effect. CONCLUSION: Diagnosing bladder malacoplakia depends on histopathological examination. Antibiotic treatment with bladder tumor resection or electrocoagulation provides better therapeutic effect.

Coating Porous TiO2 Films on Carbon Nanotubes to Enhance the Durability of Ultrafine PtCo/CNT Nanocatalysts for the Oxygen Reduction Reaction.

The development of excellent activity and durability catalysts for the oxygen reduction reaction (ORR) is essential for the commercialization of proton exchange membrane fuel cells (PEMFCs). Reducing the size of catalyst particles can provide more reaction sites to mitigate the performance degradation caused by reduced platinum loading. However, at the same time, it makes the particles more prone to agglomeration and exfoliation, leading to a rapid reduction in catalyst activity. Here, we present the design of a composite support (TiO2/CNT) with a porous TiO2 film that immobilizes PtCo nanoparticles (NPs) loaded on the support while protecting the carbon nanotubes inside. The particle size of PtCo NPs was only 1.99 nm (determined by transmission electron microscopy), but the nanocatalyst (PtCo/TiO2/CNT) maintained high catalytic performance and stability on account of the strong metal support interaction (SMSI). PtCo/TiO2/CNT exhibited a high mass activity (MA, 0.476 A mgPt-1) and was found to have MA retention rates of 91.7 and 88.8% in durability tests performed at 0.6-1.0 V and 1.0-1.5 V, respectively.

Bladder triangle amyloidosis: A case report and literature review.

RATIONALE: Amyloidosis is a group of benign lesions characterized by extracellular deposition of amyloid proteins. Amyloidosis lesions can occur in various organs of the body, but rarely in the urinary system. Amyloidosis in the bladder trigone is extremely rare. PATIENT CONCERNS: An 80-year-old female patient presented with painless whole-course gross hematuria with reddish urine and no blood clots, accompanied by right lumbar discomfort. DIAGNOSIS: Based on the patient's medical history and cystoscopy findings, the relevant literature was reviewed and a preoperative diagnosis of bladder tumor was made, although bladder amyloidosis was not excluded. Postoperative pathology ultimately revealed bladder amyloidosis. INTERVENTIONS: The patient underwent resection of bladder tumor and ureteral stent implantation. Postoperatively, the patient was maintained on antibiotics and oral colchicine treatment. OUTCOMES: Two months after surgery the patient reported that the gross hematuria had disappeared, and that the right lumbar discomfort was significantly relieved.Cystoscopy showed no obvious recurrence in the operative area, but magnetic resonance imaging (MRI) suggested recurrence. The patient refused partial cystectomy, and the ureteral stent was removed. LESSON: The clinical manifestations of bladder amyloidosis are nonspecific, and under cystoscopy can be easily confused with bladder tumors. Accurate diagnosis of bladder amyloidosis relies on histopathology. Transurethral resection of bladder tumors or partial cystectomy is an option for surgical treatment; the latter should be performed if the ureteral opening is involved.

Planar refractive index patterning through microcontact photo-thermal annealing of a printable organic/inorganic hybrid material.

We demonstrate proof-of-concept refractive-index structures with large refractive-index-gradient profiles, using a micro-contact photothermal annealing (µCPA) process to pattern organic/inorganic hybrid materials comprising titanium oxide hydrate within a poly(vinyl alcohol) binder. A significant refractive index modulation of up to Δn ≈ +0.05 can be achieved with µCPA within less than a second of pulsed lamp exposure, which promises the potential for a high throughput fabrication process of photonic structures with a polymer-based system.