bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a bacteriophage-derived recombinase system in Bacillus licheniformis for gene deletion
Authors: Xue Fang , Ma Xufan , Luo Cheng , Li Dongliang , Shi Guiyang , Li Youran 
Published: August 2023

AbstractBacillus licheniformis and its related strains have found extensive applications in diverse industries, agriculture, and medicine. However, the current breeding methods for this strain primarily rely on natural screening and traditional mutagenesis. The limited availability of efficient genetic engineering tools, particularly recombination techniques, has hindered further advancements in its applications. In this study, we conducted a comprehensive investigation to identify and characterize a recombinase, RecT, derived from a Bacillus phage. Remarkably, the recombinase exhibited a 105-fold enhancement in the recombination efficiency of the strain. To facilitate genome editing, we developed a system based on the conditional expression of RecT using a rhamnose-inducible promoter (Prha). The efficacy of this system was evaluated by deleting the amyL gene, which encodes an α-amylase. Our findings revealed that the induction time and concentration of rhamnose, along with the generation time of the strain, significantly influenced the editing efficiency. Optimal conditions for genome editing were determined as follows: the wild-type strain was initially transformed with the genome editing plasmid, followed by cultivation and induction with 1.5% rhamnose for 8 h. Subsequently, the strain was further cultured for an additional 24 h, equivalent to approximately three generations. Consequently, the recombination efficiency reached an impressive 16.67%. This study represents a significant advancement in enhancing the recombination efficiency of B. licheniformis through the utilization of a RecT-based recombination system. Moreover, it provides a highly effective genome editing tool for genetic engineering applications in this strain.
Decreased physical performance despite objective and subjective maximal exhaustion in post-COVID-19 individuals with fatigue
Authors: Vollrath Shirin , Matits Lynn , Schellenberg Jana , Kirsten Johannes , Steinacker Jürgen M. , Bizjak Daniel A. 
Published: August 2023

Abstract
Introduction
Fatigue is a common symptom in post-COVID-19 patients. Individuals with fatigue often perform less well compared to healthy peers or without fatigue. It is not yet clear to what extent fatigue is related to the inability to reach maximum exhaustion during physical exercise.

Methods
A symptom-based questionnaire based on the Carruthers guidelines (2003) was used for reporting the presence of fatigue and further symptoms related to COVID-19 from 85 participants (60.0% male, 33.5 ± 11.9 years). Cardiopulmonary exercise testing (CPET) and lactate measurement at the end of the test were conducted. Objective and subjective exhaustion criteria according to Wasserman of physically active individuals with fatigue (FS) were compared to those without fatigue (NFS).

Results
Differences between FS and NFS were found in Peak V̇O2/BM (p < 0.001) and Max Power/BM (p < 0.001). FS were more likely to suffer from further persistent symptoms (p < 0.05). The exhaustion criterion Max. lactate was reached significantly more often by NFS individuals.

Conclusion
Although the aerobic performance (Max Power/BM) and the metabolic rate (Peak V̇O2/BM and Max. lactate) of FS were lower compared to NFS, they were equally able to reach objective exhaustion criteria. The decreased number of FS who reached the lactate criteria and the decreased V̇O2 peak indicates a change in metabolism. Other persistent post-COVID-19 symptoms besides fatigue may also impair performance, trainability and the ability to reach objective exhaustion.
Trial registration Trial registration: DRKS00023717; date of registration: 15.06.2021 (retrospectively registered).
The early negative bias of social semantics: evidence from behavioral and ERP studies
Authors: Fan Xinfang , Xu Qiang , Liu Juan , Xing Hongwei , Ning Liangyu , Chen Qingwei , Yang Yaping 
Published: August 2023

AbstractBackgroundCompared to nonsocial information, the human brain is more highly sensitive to social information. As a kind of typical social semantic information, the words describing person traits differ from the nonsocial semantic information describing inanimate objects in many ways. It remains to be seen whether the processing of trait words has a valence asymmetric and whether it differs from the processing of nonsocial semantic information in terms of behavioral responses and neural temporal processes.MethodTaking person and object names as priming stimuli and adjective words only used for describing humans or objects as target stimuli, the present study aimed to investigate the processing characteristics of social and nonsocial semantic information by recording both behavioral and ERP data.ResultsBehavioral results showed that the response times for negative words were significantly slower than those for positive words whether for social or nonsocial semantic information. The accuracy rates of negative words were significantly lower than those of positive words when the targets were social words which is contrary to the nonsocial words. The ERP results indicated that there was a negative bias effect on the processing of both types of information during the whole time course of brain neural activity; that is, the P2, N400, and LPP amplitudes elicited by negative words were larger than those elicited by positive words; However, the negative bias effect of social semantic information started at the early perceptual stage which was significantly earlier than the onset of negative bias of nonsocial semantic information, and was significantly affected by the prime type. In addition, there was a significant semantic conflict N400 effect only for nonsocial semantic information.ConclusionsOverall, the present study revealed the existence of an early negative bias of social information and provided evidence for the specificity of social information.
Artificial intelligence learning landscape of triple-negative breast cancer uncovers new opportunities for enhancing outcomes and immunotherapy responses
Authors: Li Shuyu , Zhang Nan , Zhang Hao , Zhou Ran , Li Zirui , Yang Xue , Wu Wantao , Li Hanning , Luo Peng , Wang Zeyu , Dai Ziyu , Liang Xisong , Wen Jie , Zhang Xun , Zhang Bo , Cheng Quan , Zhang Qi , Yang Zhifang 
Published: August 2023

AbstractTriple-negative breast cancer (TNBC) is a relatively aggressive breast cancer subtype due to tumor relapse, drug resistance, and multi-organ metastatic properties. Identifying reliable biomarkers to predict prognosis and precisely guide TNBC immunotherapy is still an unmet clinical need. To address this issue, we successfully constructed a novel 25 machine learning (ML) algorithms-based immune infiltrating cell (IIC) associated signature of TNBC (MLIIC), achieved by multiple transcriptome data of purified immune cells, TNBC cell lines, and TNBC entities. The TSI index was employed to determine IIC-RNAs that were accompanied by an expression pattern of upregulation in immune cells and downregulation in TNBC cells. LassoLR, Boruta, Xgboost, SVM, RF, and Pamr were utilized for further obtaining the optimal IIC-RNAs. Following univariate Cox regression analysis, LassoCox, CoxBoost, and RSF were utilized for the dimensionality reduction of IIC-RNAs from a prognostic perspective. RSF, Ranger, ObliqueRSF, Rpart, CoxPH, SurvivalSVM, CoxBoost, GlmBoost, SuperPC, StepwiseCox, Enet, LassoCox, CForest, Akritas, BlackBoost, PlsRcox, SurvReg, GBM, and CTree were used for determining the most potent MLIIC signature. Consequently, this MLIIC signature was correlated significantly with survival status validated by four independent TNBC cohorts. Also, the MLIIC signature had a superior predictive capability for TNBC prognosis, compared with 148 previously reported signatures. In addition, MLIIC signature scores developed by immunofluorescent staining of tissue arrays from TNBC patients showed a substantial prognostic value. In TNBC immunotherapy, the low MLIIC profile demonstrated significant immune-responsive efficacy in a dataset of multiple cancer types. MLIIC signature could also predict m6A epigenetic regulation which controls T cell homeostasis. Therefore, this well-established MLIIC signature is a robust predictive indicator for TNBC prognosis and the benefit of immunotherapy, thus providing an efficient tool for combating TNBC.
“I think there has to be a mutual respect for there to be value”: Evaluating patient engagement in a national clinical trial on de-implementation of low value care
Authors: Etchegary Holly , Linklater Stefanie , Duquette D.’Arcy , Wilkinson Gloria , Francis Vanessa , Gionet Erin , Patey Andrea M. , Grimshaw Jeremy M. 
Published: August 2023

Abstract
Background
The evaluation of patient engagement in research is understudied and under-reported, making it difficult to know what engagement strategies work best and when. We provide the results of an evaluation of patient engagement in a large Canadian research program focused on the de-implementation of low-value care. We aimed to evaluate the experience and impact of patient engagement in the study.

Methods
An online cross-sectional survey was administered using Microsoft Forms to (1) researchers and study staff and (2) patient partners. The survey was developed following iterative reviews by the project’s patient partnership council and evaluation committee. Survey content areas included opinions on patient engagement to date, including challenges to engagement and suggestions for improvement. Patient partners also evaluated the partnership council. Descriptive statistics including counts and percentages described Likert scale survey items, while open comments were analyzed using descriptive content analysis.

Results
The survey response rate was 46% (17/37). There were positive attitudes about the value of patient engagement in this project. There was also a high degree of willingness to be involved with patient engagement in future projects, whether as a patient partner or as a researcher including patients on the research team. Most patient partners felt their contributions to the project were valued by researchers and study research staff. Open comments revealed that a co-design approach and full inclusion on the research team were integral to demonstrating the value of patient partner input. Areas for improvement included more frequent and ongoing communication among all team members, as well as earlier training about patient engagement, particularly addressing role expectations and role clarity.

Conclusions
Our data revealed that despite some challenges, team members recognized the value of patient engagement in research and agreed project decisions had been impacted by patient partner input. Ongoing communication was highlighted as an area for improvement, as well as earlier training and ongoing support for all team members, but particularly researchers and study staff. In response to evaluation data, the team has reinstated a quarterly newsletter and plans to use specific patient engagement planning templates across study sites for all project activities. These tools should help make expectations clear for all team members and contribute to a positive patient engagement experience. Findings can inform patient engagement planning and evaluation for other health research projects.
Vitamin D Binding Protein and Postsurgical Outcomes and Tissue Injury Markers After Hip Fracture: A Prospective Study
Authors: Meng Lingqiong , Wang Xiangbing , Carson Jeffrey L , Schlussel Yvette , Shapses Sue A 
Published: August 2023

Abstract

Context
Hip fracture is a serious injury that can lead to increased morbidity and mortality. Vitamin D binding protein (DBP) is a potential prognostic indicator of outcomes since it is important for actin scavenging and inflammation after tissue injury.

Objective
To determine whether circulating DBP is associated with mobility or mortality after hip fracture and its association with acute tissue injury markers.

Methods
Post hoc analysis of a multisite North American prospective study of 260 patients with hip fracture; mobility assessed at 30 and 60 days and mortality at 60 days after repair surgery. Biochemical markers were measured before, and 2 to 4 days after surgery. Tissue injury markers were measured in 100 randomly selected patients and controls. The primary outcome was mobility and mortality by DBP tertiles. Secondary outcomes were assessment of pre- and postoperative biomarkers.

Results
Among all patients (81 ± 9 years, BMI 25 ± 4 kg/m2; 72% female), the highest DBP tertile had greater mobility at 30 (OR: 2.66; 95% CI: 1.43, 4.92; P = .002) and 60 days (OR: 2.31; 95% CI: 1.17, 4.54; P = .014) and reduced mortality (OR: 0.18; 95% CI: 0.04, 0.86; P = .032) compared with the lowest DBP tertile (&lt;28.0 mg/dL). Total 25-hydroxyvitamin-D did not differ between tertiles (22.0 ± 9.5 ng/mL). Circulating DBP and gelsolin were lower and interleukin-6, C-reactive protein, and F-actin were higher (P &lt; .01) in patients vs controls, and worsened (P &lt; .01) after surgery.

Conclusion
High circulating DBP concentrations are associated with better mobility and reduced mortality after hip fracture surgery. The role of DBP as an acute phase reactant to tissue injury and clinical outcomes should be addressed in future study.
Hirschsprung's Disease - Review of Clinical Features, Diagnosis and Treatment
Authors: Tkaczyk Rafał , Świątek Gabriela , Tomczyk Jakub , Sosnowska Weronika , Tomkiewicz Maria , Taracha Kalina , Tomkiewicz Maciej , Brzozowska Aleksandra , Trusz Kornelia , Wanat Iwona 
Published: August 2023

Introduction and purpose: Hirschsprung's disease, also known as congenital aganglionic megacolon, is a rare congenital disorder that affects the large intestine. Due to the absence of ganglion cells, the affected segment of the colon becomes narrow and unable to relax. The disease is present from birth but may not always be immediately apparent. In this paper, we will attempt to present the current state of knowledge regarding the diagnosis and treatment of Hirschsprung's disease, based on the analysis of literature available on the PubMed platform.
Description of the state of knowledge: Hirschsprung's disease (HSCR), also known as congenital aganglionosis of the colon, involves abnormal migration, proliferation, and differentiation of neural crest cells, leading to the absence of autonomic nerve ganglia within the colon. HSCR is associated with mutations in several genes, with RET, GDNF, EDNRB and SOX10 being identified as the main causes of the disease. Mutations in the RET gene are associated with the hereditary form of Hirschsprung's disease. Symptoms of HSCR appear in newborns and may include bilious vomiting, diarrhea associated with enterocolitis, failure to pass meconium within the first 24 hours of life, impaired peristalsis, jaundice, feeding difficulties, and progressive abdominal distension.
Summary: Diagnosis is typically made based on clinical presentation, imaging studies, and biopsy. Treatment usually involves surgery to remove the affected segment of the colon and reconnect the healthy portions. Although postoperative complications are relatively common, long-term studies suggest that the majority of children with Hirschsprung's disease function well in society.
Is Splenectomy still the best treatment for Autoimmune hemolytic anemia
Authors: Chomicz Malwina , Puszkarz Aleksandra , Łukaszewska Anna , Łukaszewska Ewa , Bąk Mateusz , Guzik Natalia , Bik Tomasz , Gaj Łukasz , Drozdowska Katarzyna , Łukaszewska-Stanik Katarzyna 
Published: August 2023

Introduction:
Autoimmune hemolytic anemia (AIHA) is an acquired, heterogeneous group of diseases that includes AIHA with warm type antibodies, cold agglutinin disease (CAD), mixed type AIHA, paroxysmal cold hemoglobinuria, and atypical AIHA.
Currently CAD is defined as chronic, clonal lymphoproliferative disease, while presence of cold agglutinin in gastrointestinal tract is known as cold agglutinin syndrome. AIHA is mediated by autoantibodies against red blood cells (RBCs), these antibodies cause premature destruction of erythrocytes. The pathogenesis of AIHA is complex and still not yet fully understood.
Aim of study:
The purpose of the study was to review the literature on the treatment options for Autoimmune Hemolytic Anemia
Materials and methods: A systemic review was conducted using PubMed, ScienceDirect, Google Scholar databases. The search strategy was based on following terms: Aiha, splenectomy autoimmune anemia, aiha treatment,
Results and Conclusions:
Based on the review of the medical literature, we believe that Splenectomy is no longer the most effective method of treating any type of AIHA and the Rituximab treatment presented by us seems to be safer and definitely less burdensome for the patient.
Of course, splenectomy is still used in AIHA - but nowadays it is more limited due to the very high effectiveness of the described non-surgical treatment
Rosacea – a modern view of diagnostics and treatment
Authors: Gawęda Agnieszka , Babiak Rafał , Bajak Karolina , Czuchryta Paulina , Domańska Anastazja , Grabek Agata , Rutkowska Julia , Rzęsa-Tokarczyk Żaneta , Skorek Klaudia , Urbańczyk Agnieszka 
Published: August 2023

Introduction: Rosacea is a chronic inflammatory skin disease affecting central region of the face. Main symptoms consist of erythema, flushing, telangiectasia, phymatous changes and inflammatory papules and pustules. It can also affect eyes, causing blepharitis, conjunctivitis, keratitis or lid margin telangiectasia. Rosacea can negatively affect the quality of life, causing low self-esteem, avoidance of social interactions and mental health issues such as anxiety and depression. There are two classifications of rosacea, one from 2002 focusing on subtypes, and new phenotype-based classification. Phenotype-based approach allows individual management of each patient instead of categorizing by predefined subtype. Due to increased frequency of Demodex infestation in patients with rosacea, diagnosis and treatment of demodicosis can be helpful in management of rosacea. General treatment of rosacea consists of combination of oral and topical therapies, choosing adequate skincare cosmetics, laser therapies and avoidance of identified trigger factors specific for the patient.
The aim of the study: This study aims to gather current knowledge about classification, diagnostics, skincare and treatment of rosacea.
Materials and methods: This review was based on available data collected in the PubMed database, using the keywords: ‘rosacea’, ‘ocular rosacea’, ‘rosacea treatment’.
Conclusions: The treatment of rosacea requires selection of appropriate treatment depending on symptoms specific for the patient. Because of increased Demodex infestation present in some of the patients with rosacea, eradication can mitigate rosacea symptoms. Identification and avoidance of trigger factors and assortment of adequate skincare products are also substantial parts of management of rosacea and can alleviate rosacea symptoms.
Extrinsic allergic pneumonitis - classification, pathogenesis, diagnosis
Authors: Brzyska Anna , Kopiec Dominika , Kuzioła Karolina 
Published: August 2023

Introduction and objective: Extrinsic allergic pneumonitis (AZPP) is an inflammatory disease of the lung parenchyma and bronchioles, caused by inhalation of organic and inorganic antigens. The pathhomechanism of the disease is based on the binding of the antigen with precipitins to form immune complexes that are responsible for the formation of acute inflammation in the lung tissue. The resulting inflammation is a type III and type IV hypersensitivity reaction. In the clinical course, azpp is divided into acute, subacute and chronic phases. The course of the disease varies depending on the type and duration of exposure to the antigen. It is most often manifested by shortness of breath, coughing and the progression of the disease leads to respiratory failure.
Review methods: While writing the thesis, a database was used, ie Pubmed and Google Scholar.
Brief description of the stage of knowledge: Extrinsic allergic pneumonitis requires a thorough differential diagnosis, which includes laboratory tests, functional tests, imaging tests, inhalation provocation tests and lung biopsy. The mainstay of treatment is to avoid exposure to the antigen. In severe disease, systemic corticosteroid therapy is indicated.
Summary: Correct diagnosis is a big problem because of the differences in symptoms and the severity of the disease among patients. Expanding the knowledge about the clinical course of the disease or its pathogenesis will affect the effectiveness of diagnostics and help to develop new methods of treatment.
Supplementation with Omega-3 fatty acids in the supportive treatment of depression – systematic review
Authors: Chmielarz Karolina , Zapała Magdalena , Hunek Adrian , Kaziród Karolina , Wiśniewska-Skomra Joanna , Tylutka Kinga , Hapon Anna 
Published: August 2023

Omega-3 is a polyunsaturated fatty acid (PUFA) with a double bond present at the ω-3 carbon atom. Recently, many neurobiologists and psychiatrists have been studying the involvement of inflammatory factors and mechanisms in the pathogenesis of depression, including factors like an improper diet with an excess of omega-6, gut dysbiosis, obesity, and autoimmune diseases. The present study focuses on the impact of unsaturated fatty acids on mood improvement and cognitive processes in elderly patients with major depressive disorder (MDD) resistant to standard treatment. This form of depression is often associated with autoimmune diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus, and inflammatory bowel diseases. The influence of omega-3 supplementation on depression prevention and its effects on childhood depression were also examined. It should be noted that some publications do not confirm the antidepressant effects of omega-3. However, this article provides evidence of the supportive role of omega-3 in depression treatment, based on neuroendocrine, metabolic, and immunological reactions.
Objective: Literature review on the impact of omega-3 on depression treatment, considering its forms, inflammatory mechanisms, neuroendocrine factors, diet, lifestyle, and age.
Materials and Methods: Literature review based on available sources from PubMed and Google Scholar.
Conclusions: Omega-3 is a polyunsaturated fatty acid that positively affects the functioning of the body. Many research studies confirm its antidepressant and anti-inflammatory effects, making it a potential adjunctive treatment for depression, especially in elderly patients with major treatment-resistant depression (MDD) coexisting with other chronic diseases. The results of studies on the relationship between omega-3 and antidepressant action also depend on various environmental factors and lifestyle choices.