bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between retinal pigment epithelium tear and anti-vascular endothelial growth factor therapy: A systematic review and meta-analysis
Authors: Shi Hekai , Guo Nuojin , Zhao Zeming , Duan Jialiang 
Published: October 2023

Abstract

Purpose:
To identify the prevalence of retinal pigment epithelium tear (RPET) after anti-vascular endothelial growth factor (VEGF) therapy and determine the efficacy of continued anti-VEGF therapy in patients with RPET.

Methods:
We screened all relevant clinical trials and observational studies in several online databases. The main outcomes were the incidence of RPET after anti-VEGF therapy and changes in visual acuity for patients with RPET treated with continued anti-VEGF. The time point for outcome assessment was the last follow-up time.

Results:
The pooled incidence of RPET after anti-VEGF therapy from twenty-four studies with 17,354 patients was 1.9% (95% CI: 1.3–2.7%). Most new RPET cases were concentrated in the first month at baseline or after the first injection during anti-VEGF therapy and gradually decreased by the subsequent month or injection. Thirteen studies with 157 patients reported that for patients who received anti-VEGF therapy after RPET, their pooled best-corrected visual acuity improved but did not reach a significant level (SMD 0.34; 95% CI: -0.03, 0.71).

Conclusion:
The incidence of RPET after anti-VEGF therapy is low. The intravitreal anti-VEGF injection might accelerate this process . For patients with RPET, maintenance of anti-VEGF therapy ensure visual acuity stability.
Fibrinogen Aα gene genotyping in patients with inherited afibrinogenemia deficiency; a novel mutation in Iranian afibrinogenemia patients
Authors: Moazzeni Ali , Naderi Majid , Dorgalaleh Akbar , Alizadeh Shaban 
Published: October 2023

Background
Congenital fibrinogen deficiencies (CFD) are a group of rare bleeding disorders (RBD). Afibrinogenemia as a subclass of these disorders would occurs as a result of mutations in fibrinogen gene. Here in, the sequences of Aα chain of fibrinogen (FGA) in patients with inherited afibrinogenemia disorder in south-eastern of Iran were analysed.

Methods
The FGA gene exons were amplified using PCR method and the DNA sequences were analysed to study the mutations in Aα chain of Fibrinogen.

Results
Results showed that there was no large deletion in FGA gene. Although a frame shift mutation: c.196_197insT p.Ser66PhefsX10 in a patient and a novel mutation of IVS2-1G>A in two other patients were detected which were different from those detected in European population.

Conclusion
Different mutations are responsible of afibrinogenemia deficiency which requires more relevant studies for confirmation. The type and distribution of mutations in fibrinogen gene in Iranian patients is significantly different with reported mutations in European patients.
Impact of continued alcohol use on liver-related outcomes of alcohol-associated cirrhosis: a retrospective study of 440 patients
Authors: Kalambokis Georgios N. , Chouliara Nikolleta , Tsiakas Ilias , Filippas-Ntekuan Sempastien , Christaki Maria , Despotis Grigorios , Milionis Haralampos 
Published: October 2023

Background and aim
The prevalence of alcohol-associated cirrhosis is increasing. In this respect, we investigated the long-term impact of non-abstinence on the clinical course of alcohol-associated cirrhosis.

Methods
We retrospectively evaluated 440 patients with alcohol-associated cirrhosis (compensated cirrhosis: n = 190; decompensated cirrhosis: n = 250) diagnosed between January 2000 and July 2017 who consumed alcohol until diagnosis of cirrhosis. We assessed liver-related outcomes including first and further decompensating events (ascites, variceal bleeding, and hepatic encephalopathy), and death in relation to continued alcohol use.

Results
Overall, 53.6% of patients remained abstinent (compensated cirrhosis: 57.9%; decompensated cirrhosis: 50.4%). Non-abstinent versus abstinent patients with compensated cirrhosis and decompensated cirrhosis showed significantly higher 5-year probability of first decompensation (80.2% vs. 36.8%; P < 0.001) and further decompensation (87.9% vs. 20.6%; P < 0.001), respectively. Five-year survival was substantially lower among non-abstinent patients with compensated cirrhosis (45.9% vs. 90.7%; P < 0.001) and decompensated cirrhosis (22.9% vs. 73.8%; P < 0.001) compared to abstinent. Non-abstinent versus abstinent patients of the total cohort showed an exceedingly lower 5-year survival (32.2% vs. 82.4%; P < 0.001). Prolonged abstinence (≥2 years) was required to influence outcomes. Non-abstinence independently predicted mortality in the total cohort (hazard ratio [HR] 3.371; confidence interval [CI]: 2.388–4.882; P < 0.001) along with the Child-Pugh class (HR: 4.453; CI: 2.907–6.823; P < 0.001) and higher age (HR: 1.023; CI: 1.007–1.039; P = 0.005).

Conclusion
Liver-related outcomes are worse among non-abstinent patients with alcohol- associated cirrhosis prompting urgent interventions ensuring abstinence.
Stress-only versus rest-stress SPECT MPI in the detection and diagnosis of myocardial ischemia and infarction by machine learning
Authors: Wang Fanghu , Yuan Hui , Lv Jieqin , Han Xu , Zhou Zidong , Lu Wantong , Lu Lijun , Jiang Lei 
Published: October 2023

Background
Rest-stress SPECT myocardial perfusion imaging (MPI) is widely used to evaluate coronary artery disease (CAD). We aim to evaluate stress-only versus rest-stress MPI in diagnosing CAD by machine learning (ML).

Methods
A total of 276 patients with suspected CAD were randomly divided into training (184 patients) and validation (92 patients) cohorts. Variables extracted from clinical, physiological, and rest-stress SPECT MPI were screened. Stress-only and rest-stress MPI using ML were established and compared using the training cohort. Then the diagnostic performance of two models in diagnosing myocardial ischemia and infarction was evaluated in the validation cohort.

Results
Six ML models based on stress-only MPI selected summed stress score, summed wall thickness score of stress%, and end-diastolic volume of stress as key variables and performed equally good as rest-stress MPI in detecting CAD [area under the curve (AUC): 0.863 versus 0.877, P = 0.519]. Furthermore, stress-only MPI showed a reasonable prediction of reversible deficit, as shown by rest-stress MPI (AUC: 0.861). Subsequently, nomogram models using the above-stated stress-only MPI variables showed a good prediction of CAD and reversible perfusion deficit in training and validation cohorts.

Conclusion
Stress-only MPI demonstrated similar diagnostic performance compared with rest-stress MPI using 6 ML algorithms. Stress-only MPI with ML models can diagnose CAD and predict ischemia from scar.
Chronic pelvic pain; more than just the bladder
Authors: Messelink Bert , Flink Ida , dos Santos Ana , Adamse Corine 
Published: October 2023

Purpose of review
Chronic pelvic pain is much of a burden to those who suffer from it. Additionally, in many patients medical doctors, such as urologists are unable to identify a cause or clear pathology that can explain the pain. Still numerous patients and doctors keep on searching for a cause, focussing particularly on the pelvic organs. Lots of diagnostics and treatment methods are used but often without success. In recent years, we have gained increased insight into the mechanisms of pain and adapted the terminology accordingly.

Recent findings
Two aspects of chronic pelvic pain have gained more attention. First, the myofascial aspects, especially the role of the pelvic floor muscles in maintaining the pain and as a therapeutic option. Second, the role of the brain and the psychological aspects intertwine with the pain and its consequences also open up for alternative management options. In terminology chronic pain is now included in the ICD-11, a historical change. Introducing chronic primary pain (no cause found) helps us to look away from the organ and deal with the patient as a whole human being.

Summary
The findings reported here are helpful for your daily practice. Looking from a broad perspective gives the patient the feeling of being seen and heard. Working together in a multidisciplinary team makes your work easier and gives more satisfaction.

Video abstract

http://links.lww.com/COU/A44
Candida krusei pneumonia in graft-versus-host disease after allogeneic hematopoietic stem cell transplant for paroxysmal nocturnal hemoglobinuria: a case report
Authors: Zoowa Ronit , Shah Ravi , Pradhan Dipana , Karmacharya Sammridhi , Bhandari Dipen 
Published: October 2023

Introduction and importance:
Paroxysmal nocturnal hemoglobinuria (PNH) is a rare disorder caused by a somatic mutation of PIGA (phosphatidylinositol glycan anchor biosynthesis, class A) gene that leads to the destruction of blood cells. Allogeneic haematopoietic stem cell transplant (HSCT) is a treatment option for PHN, but it can cause graft-versus-host disease (GVHD). Long-term immunosuppression as a treatment of GVHD increases the risk for invasive fungal infections such as Candida krusei pneumonia.

Case presentation:
We present the case of a 22-year-old male with C. krusei pneumonia in a known case of chronic GVHD following HSCT for PNH undergoing long-term immunosuppressive therapy. The patient presented with progressive shortness of breath, productive cough, palpitations, and difficulty swallowing. On examination, he had skin rashes and oral lesions, along with signs of severe malnutrition. Diagnosis was made on the basis of radiological imaging and fungal culture.

Discussion:
The combination of PNH, GVHD, and HSCT created an immunocompromised state, making the patient susceptible to opportunistic infections, including fungal pneumonia. Early recognition of this condition is challenging due to its non-specific symptoms and potential overlap with other post-transplant complications. Timely diagnosis and appropriate treatment, including antifungal therapy and immunosuppression management, are crucial for optimising patient outcomes.

Conclusion:
This case highlights the importance of early recognition and timely treatment of fungal infections in patients with severe conditions such as GVHD following HSCT for PNH. Timely treatment with appropriate antifungals is necessary for optimal outcomes. Additionally, more research with long-term follow-up and monitoring is necessary to address the necessary knowledge gaps in this field.
The use of Titanium Meshes in Surgical Closure of the Oroantral Fistula. A Randomized Clinical Trial Study
Authors: Tabrizi Reza , Akhlaghi Fahimeh , Javaheri Pouria , Malekigorji Mohsen 
Published: October 2023

The closure of oroantral communications (OACs) is challenging. The study aimed to assess the effect of titanium meshes in the outcome of OAC closure by local flaps.
This is a prospective randomized, nonblinded clinical trial. Patients with a delay and large (≥7 mm2) OAC were studied. Patients were randomly divided into 2 groups: in group 1, patients underwent OAC closure through a modified Rehrmann buccal advancement flap with a titanium mesh, and in group 2, the modified Rehrmann buccal advancement flap. The primary predictive factor was the use of titanium mesh. Dehiscence (the breakdown of the edge of flaps without the complete reopening of the defect) was a primary outcome. The defect’s reopening was considered a secondary outcome.
Nineteen patients in group 1 and 20 in group 2 were studied. In 2 months after treatments, the prevalence of dehiscence in group 1 was 3, and 10 patients in group 2 (P=0.041). In group 1, patients did not show OAC exposure. However, OAC exposure was observed in 2 patients in group 2.
This study demonstrates that using titanium mesh in combination with a modified Rehman flap decreases the prevalence of dehiscence compared with a flap alone.
PCLAF-DREAM Drives Alveolar Cell Plasticity for Lung Regeneration
Authors: Kim Bongjun , Huang Yuanjian , Ko Kyung-Pil , Zhang Shengzhe , Zou Gengyi , Zhang Jie , Kim Moon Jong , Little Danielle , Ellis Lisandra Vila , Paschini Margherita , Jun Sohee , Park Kwon-Sik , Chen Jichao , Kim Carla , Park Jae-Il 
Published: October 2023

AbstractSpatiotemporal control of stem and progenitor cells is essential for lung regeneration, the failure of which leads to lung disease. However, the mechanism of alveolar cell plasticity during regeneration remains elusive. We previously found that PCLAF remodels the DREAM complex for cell cycle re-entry. PCLAF expression is specifically enriched in proliferating lung progenitor cells, along with the DREAM target genes by lung damage. Genetic ablation ofPclafinhibited alveolar type I (AT1) cell regeneration from alveolar type II (AT2) cells, inducing lung fibrosis. Mechanistically, the PCLAF-DREAM complex directly transactivatesCLIC4, promoting TGF-β signaling that regulates the balance between AT1 and AT2 cells. Furthermore, a drug candidate that mimics the PCLAF-DREAM transcriptional signatures for lung regeneration was identified and validated in organoids and mice. Our study unveils an unexpected role of the PCLAF-DREAM axis in controlling alveolar cell plasticity for lung regeneration and proposes a viable option for lung fibrosis prevention.One Sentence SummaryPCLAF-DREAM-driven alveolar cell plasticity is crucial for lung regeneration and can be pharmacologically targeted as a therapeutic strategy for lung fibrosis.
OxPhos in adipose tissue macrophages regulated by BTK enhances their M2-like phenotype and confers a systemic immunometabolic benefit in obesity
Authors: Purvis Gareth S. D. , Collino Massimo , van Dam Andrea D. , Einaudi Giacomo , Ng Yujung , Shanmuganathan Mayooran ,   Oxford Acute Myocardial Infarction (OxAMI) Study, Patel Smita Y. , Thiemermann Christoph , Channon Keith M. , Greaves David R. 
Published: October 2023

AbstractBruton’s tyrosine kinase (BTK) is a non-receptor bound kinase involved in pro-inflammatory signalling in activated macrophages, however, its role within adipose tissue macrophages remains unclear. We have demonstrated that BTK signalling regulates macrophage M2-like polarisation state by up-regulating subunits of mitochondrially encoded electron transport chain Complex I (ND4andNDL4) and Complex IV (mt-CO1,mt-CO2andmt-CO3) resulting in an enhanced rate of oxidative phosphorylation (OxPhos) in an NF-κB independent manner. Critically, BTK expression is elevated in adipose tissue macrophages from obese individuals with diabetes, while key mitochondrial genes (mtC01, mtC02 and mtC03) are decreased in inflammatory myeloid cells from obese individuals. Inhibition of BTK signalling either globally (Xid mice) or in myeloid cells (LysMCreBTK), or therapeutically (Acalabrutinib) protects HFD-fed mice from developing glycaemic dysregulation by improving signalling through the IRS1/Akt/GSK3b pathway. The beneficial effects of acalabrutinib treatment are lost in macrophage ablated mice. Inhibition of BTK signalling in myeloid cells but not B-cells, induced a phenotypic switch in adipose tissue macrophages from a pro-inflammatory M1-state to a pro-resolution M2-like phenotype, by shifting macrophage metabolism towards OxPhos. This reduces both local and systemic inflammation and protects mice from the immunometabolic consequences of obesity. Therefore, in BTK we have identified a macrophage specific, druggable target that can regulate adipose tissue polarisation and cellular metabolism that can confer systematic benefit in metabolic syndrome.Article high lightsObesity and diabetes are associated with inflammation, particularly within the adipose tissue. We have found a new druggable target called Bruton’s tyrosine kinase (BTK) that is highly expressed in adipose tissue macrophages. When BTK is inhibited in macrophages, it allows these cells to undergo a phenotypic switch towards an M2-like pro-resolution macrophage. This achieved by increasing expression of key mitochondrially encoded components of the electron transport chain allowing for enhanced OxPhos. Inhibition of BTK signalling in myeloid cells but not B-cells protects HFD-fed mice from developing glycaemic dysregulation.
First record of Zaprionus tuberculatus (Diptera: Drosophilidae) in mainland France
Authors: Georges Romain , Yassin Amir , Colinet Hervé 
Published: October 2023

AbstractBACKGROUNDAs most drosophilid species are not considered as primary pest, studies of the whole drosophilid communities, including other genera thanDrosophila, with standardized surveys are relatively sparse. However, the spotted wing drosophilaDrosophila suzukii(Matsumura, 1931) and its rapid expansion through the world led to the implementation of many monitoring programs in various countries. As part of a research project onD. suzukii, we set up in 2022 an annual fly monitoring in 16 fruits farms to understand populations dynamics ofD. suzukiiand to survey drosophilid communities.RESULTSWe report here the first observation ofZaprionus tuberculatusMalloch, 1932 (Diptera: Drosophilidae) in mainland France. Over the whole monitoring, we trapped a total of 111 specimens in a fig orchard located in southern France (Salses-le-Château), both in fig trees and nearby hedgerows. The first detection ofZ. tuberculatusoccurred in July 2022 in the hedgerow and captures continued until January 2023 with an interruption in November and December. In addition, in this orchard we collected overripe figs in September 2023 from which over 15Z. tuberculatushave emerged in the following two weeks.CONCLUSIONThe pest status ofZ. tuberculatusand its potential risk for agriculture is not clear, but the pest behavior of the close-relative speciesZaprionus indianus, especially on figs, should be a warning point for the entry ofZ. tuberculatusinto the EU and France, as they may have similar nutritional ecology. The pest status, the establishment and the future spread ofZ. tuberculatusshould thus be monitored to assess possible damages to fruits productions.
AP-LASR: Automated Protein Libraries from Ancestral Sequence Reconstruction
Authors: VanAntwerp James , Mardikoraem Mehrsa , Pascual Nathaniel , Woldring Daniel 
Published: October 2023

AbstractBackgroundAncestral sequence reconstruction (ASR) provides an informative roadmap of evolutionary protein sequence space that benefits protein design and engineering in pursuitof high stability and diverse functionality. Using statistical and biological knowledge, ASR can determine the most probable ancestor among potential alternative amino acid states. However, the inherent uncertainty of ASR can be further leveraged to determine viable “nearby” ancestors with wide-ranging functionalities by sampling alternative amino acid states.ResultsHere we introduce AP-LASR which i) automates ASR and ii) leverages uncertainty in ASR to generate diverse protein sequence libraries that consist of ancestral sequences and near-ancestor sequences. In addition to automating pre-processing tasks (e.g., data cleaning, multiple sequence alignment, and software dependency management), AP-LASR offers several user-definable hyperparameters (e.g., input data size, ancestral probability cut-off, and sequence supplementation) to control the properties of the generated library. AP-LASR features an improved eLnP score (a metric for quantifying reconstructed ancestral sequence confidence) compared to FireProtASR, a well-established ASR workflow, for all four functionally diverse protein families studied. Furthermore, the rigorous statistical analysis undertaken in this study elucidates the influence of hyperparameters on ASR, enabling researchers to refine AP-LASR to their specific research.ConclusionAP-LASR offers an automated ASR experience that surpasses existing software by including a novel library design feature, powering curated protein libraries for wet-lab evaluation. We demonstrate how computational parameters impact the quality of ASR results, library composition, and the tradeoffs therein. AP-LASR offers a powerful tool for protein engineers to efficiently navigate the vast protein sequence landscape.Software available at:https://github.com/WoldringLabMSU/AP-LASR
New realm of precision multiplexing enabled by massively-parallel single molecule UltraPCR
Authors: Lai Janice H. , Keum Jung won , Lee Haeun G. , Molaei Mehdi , Blair Emily J. , Li Sixing , Soliman Jesse W. , Raol Vedant K. , Barker Camille L. , Fodor Stephen P.A. , Fan H. Christina , Shum Eleen Y. 
Published: October 2023

ABSTRACTPCR has been a reliable and inexpensive method for nucleic acid detection in the past several decades. In particular, multiplex PCR is a powerful tool to analyze many biomarkers in the same reaction, thus maximizing detection sensitivity and reducing sample usage. However, balancing the amplification kinetics between amplicons and distinguishing them can be challenging, diminishing the broad adoption of high order multiplex PCR panels. Here, we present a new paradigm in PCR amplification and multiplexed detection using UltraPCR. UltraPCR utilizes a simple centrifugation workflow to split a PCR reaction into ∼34 million partitions, forming an optically clear pellet of spatially separated reaction compartments in a PCR tube. Afterin situthermocycling, light sheet scanning is used to produce a 3D reconstruction of the fluorescent positive compartments within the pellet. At typical sample DNA concentrations, the magnitude of partitions offered by UltraPCR dictate that the vast majority of target molecules occupy a compartment uniquely. This single molecule realm allows for isolated amplification events, thereby eliminating competition between different targets and generating unambiguous optical signals for detection. Using a 4-color optical setup, we demonstrate that we can incorporate 10 different fluorescent dyes in the same UltraPCR reaction. We further push multiplexing to an unprecedented level by combinatorial labeling with fluorescent dyes — referred to as “comboplex” technology. Using the same 4-color optical setup, we developed a 22-target comboplex panel that can detect all targets simultaneously at high precision. Collectively, UltraPCR has the potential to push PCR applications beyond what is currently available, enabling a new class of precision genomics assays.
Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum
Authors: Gonçalves Osiel S. , Fernandes Alexia S. , Tupy Sumaya M. , Ferreira Tauanne G. , Almeida Luciano N. , Creevey Christopher J. , Santana Mateus F. 
Published: October 2023

AbstractThe prevalence and abundance of Acidobacteriota raise concerns about their ecological function and metabolic activity in the environment. Studies have reported the potential of some members of Acidobacteriota to interact with plants and play a significant role in biogeochemical cycles. However, their role in this context has not been extensively studied. Here, we performed a comprehensive genomic analysis of 758 metagenome-assembled genomes (MAGs) and 121 RefSeq genomes of Acidobacteriota. Our analysis revealed a high frequency of plant growth-promoting traits (PGPTs) genes in theAcidobacteriaceae, Bryobacteraceae, Koribacteraceae, andPyrinomonadaceaefamilies. These PGPTs include genes involved in nitrogen fixation, phosphorus solubilization, exopolysaccharide production, siderophore production, and plant growth hormone production. Expression of such genes was found to be transcriptionally active in different environments. In addition, we identified numerous carbohydrate-active enzymes and peptidases involved in plant polymer degradation. By applying an in-depth insight into the diversity of the phylum, we expanded previous role in carbon, nitrogen, sulfur, and trace metal cycling. This study underscores the distinct potential ecological roles of each of these taxonomic groups, providing valuable insights for future research.