bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and clinical characterization of Klebsiella pneumoniae carrying the pks island
Authors: Wang Zhiqian , Liu Yanjun , Liu Peilin , Jian Zijuan , Yan Qun , Tang Bin , Yang Awen , Liu Wenen 
Published: September 2023

BackgroundThe pks island and its production of the bacterial secondary metabolite genotoxin, colibactin, have attracted increasing attention. However, genomic articles focusing on pks islands in Klebsiella pneumoniae, as well as comparative genomic studies of mobile genetic elements, such as prophages, plasmids, and insertion sequences, are lacking. In this study, a large-scale analysis was conducted to understand the prevalence and evolution of pks islands, differences in mobile genetic elements between pks-negative and pks-positive K. pneumoniae, and clinical characteristics of infection caused by pks-positive K. pneumoniae.MethodsThe genomes of 2,709 K. pneumoniae were downloaded from public databases, among which, 1,422 were from NCBI and 1,287 were from the China National GeneBank DataBase (CNGBdb). Screening for virulence and resistance genes, phylogenetic tree construction, and pan-genome analysis were performed. Differences in mobile genetic elements between pks-positive and pks-negative strains were compared. The clinical characteristics of 157 pks-positive and 157 pks-negative K. pneumoniae infected patients were investigated.ResultsOf 2,709 K. pneumoniae genomes, 245 pks-positive genomes were screened. The four siderophores, type VI secretion system, and nutritional factor genes were present in at least 77.9% (191/245), 66.9% (164/245), and 63.3% (155/245) of pks-positive strains, respectively. The number and fragment length of prophage were lower in pks-positive strains than in pks-negative strains (p &lt; 0.05). The prevalence of the IS6 family was higher in pks-negative strains than in pks-positive strains, and the prevalence of multiple plasmid replicon types differed between the pks-positive and pks-negative strains (p &lt; 0.05). The detection rate of pks-positive K. pneumoniae in abscess samples was higher than that of pks-negative K. pneumoniae (p &lt; 0.05).ConclusionThe pks-positive strains had abundant virulence genes. There were differences in the distribution of mobile genetic elements between pks-positive and pks-negative isolates. Further analysis of the evolutionary pattern of pks island and epidemiological surveillance in different populations are needed.
Gait analysis patterns and rehabilitative interventions to improve gait in persons with hereditary spastic paraplegia: a systematic review and meta-analysis
Authors: Faccioli Silvia , Cavalagli Angela , Falocci Nicola , Mangano Giulia , Sanfilippo Irene , Sassi Silvia 
Published: September 2023

BackgroundHereditary spastic paraplegias (HSPs) are a group of inheritance diseases resulting in gait abnormalities, which may be detected using instrumented gait analysis. The aim of this systematic review was 2-fold: to identify specific gait analysis patterns and interventions improving gait in HSP subjects.MethodsA systematic review was conducted in PubMed, Cochrane Library, REHABDATA, and PEDro databases, in accordance with reporting guidelines of PRISMA statement and Cochrane's recommendation. The review protocol was recorded on the PROSPERO register. Patients with pure and complicated HSP of any age were included. All types of studies were included. Risk of bias, quality assessment, and meta-analysis were performed.ResultsForty-two studies were included: 19 were related to gait analysis patterns, and 24 were intervention studies. The latter ones were limited to adults. HSP gait patterns were similar to cerebral palsy in younger subjects and stroke in adults. Knee hyperextension, reduced range of motion at knee, ankle, and hip, reduced foot lift, and increased rapid trunk and arm movements were reported. Botulinum injections reduced spasticity but uncovered weakness and improved gait velocity at follow-up. Weak evidence supported intrathecal baclofen, active intensive physical therapy (i.e., robot-assisted gait training, functional exercises, and hydrotherapy), and functional electrical stimulation. Some improvements but adverse events were reported after transcranial magnetic stimulation, transcutaneous spinal direct current stimulation, and spinal cord stimulation implant.ConclusionKnee hyperextension, non-sagittal pelvic movements, and reduced ROM at the knee, ankle, and hip represent the most peculiar patterns in HSP, compared to diplegic cerebral palsy and stroke. Botulinum improved comfortable gait velocity after 2 months. Nonetheless, interventions reducing spasticity might result in ineffective functional outcomes unveiling weakness. Intensive active physical therapy and FES might improve gait velocity in the very short term.
A five-year observational prospective mono-center study of the efficacy of alemtuzumab in a real-world cohort of patients with multiple sclerosis
Authors: Sandgren Sofia , Novakova Lenka , Nordin Anna , Axelsson Markus , Malmeström Clas , Zetterberg Henrik , Lycke Jan 
Published: September 2023

BackgroundAlemtuzumab (ALZ) is a pulsed immune reconstitution therapy for multiple sclerosis (MS).ObjectiveTo assess basic characteristics, therapeutic effects, and prognostic biomarkers on clinical and imaging parameters of disease activity for relapsing–remitting MS (RRMS) patients selected for ALZ, in a real-world long-term setting.MethodsFifty-one RRMS patients [female = 31; mean age 36 (standard deviation 7.1) years; median expanded disability status scale (EDSS) 2 (interquartile range (IQR) 1.5)] initiating ALZ treatment, were consecutively included. Patients were assessed at baseline and thereafter annually for 5 years with clinical measures, symbol digit modality test (SDMT), and magnetic resonance imaging (MRI). Concentrations of glial fibrillary acidic protein (GFAP), reflecting astrogliosis, and neurofilament light (NfL), reflecting axonal damage, were measured in cerebrospinal fluid (CSF) and serum samples collected at baseline and after 2 years in CSF, and annually in serum. Control subjects were symptomatic controls (SCs, n = 27), who were examined at baseline and after 5 years without evidence of neurological disease.ResultsWhile the mean annualized relapse rate was significantly reduced from baseline at each year of follow-up, disability was essentially maintained at a median EDSS of 1.5 and IQR between 1.13 and 2.25. New MRI activity was recorded in 26 patients (53%) over 5 years. The proportion of patients who achieved no evidence of disease activity (NEDA-3), 6-months confirmed disability worsening (CDW), and 6-months confirmed disability improvement (CDI) at 5 years were 33, 31, and 31%, respectively. The SDMT score was reduced for patients (p &lt; 0.001), but unchanged for SCs. ALZ treatment did not change GFAP levels, whereas there was a significant decrease for RRMS patients in median CSF and serum NfL levels at follow-up [CSF month 24: 456 pg./mL (IQR 285.4) (p = 0.05); serum month 24: 6.7 pg/mL (IQR 4.7) (p &lt; 0.01); serum month 60: 7.2 pg/mL (IQR 4.7) (p &lt; 0.01)], compared to baseline [CSF: 1014 pg/mL (IQR 2832.5); serum 8.6 pg/mL (IQR 17.4)].ConclusionIn this real-world mono-center population, we observed a progression-free survival of 69%, cumulative NEDA-3 of 33%, and reduced NfL levels, over a five-year follow-up. This confirms ALZ as an effective pulsed immune reconstitution therapy that significantly reduces neuro axonal loss, and therefore has the potential to reduce long-term neurological disability. ALZ did not appear to affect astrogliosis.
Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration
Authors: Liang Jia , Fang Dong , Yao Fei , Chen Lu , Zou Zhenhua , Tang Xiangcheng , Feng Lujia , Zhuang Yijing , Xie Ting , Wei Pengxue , Li Pengfeng , Zheng Huiyan , Zhang Shaochong 
Published: September 2023

IntroductionPhotoreceptor degenerative diseases are characterized by the progressive death of photoreceptor cells, resulting in irreversible visual impairment. However, the role of competing endogenous RNA (ceRNA) in photoreceptor degeneration is unclear. We aimed to explore the shared ceRNA regulation network and potential molecular mechanisms between primary and secondary photoreceptor degenerations.MethodsWe established animal models for both types of photoreceptor degenerations and conducted retina RNA sequencing to identify shared differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). Using ceRNA regulatory principles, we constructed a shared ceRNA network and performed function enrichment and protein–protein interaction (PPI) analyses to identify hub genes and key pathways. Immune cell infiltration and drug–gene interaction analyses were conducted, and hub gene expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR).ResultsWe identified 37 shared differentially expressed lncRNAs, 34 miRNAs, and 247 mRNAs and constructed a ceRNA network consisting of 3 lncRNAs, 5 miRNAs, and 109 mRNAs. Furthermore, we examined 109 common differentially expressed genes (DEGs) through functional annotation, PPI analysis, and regulatory network analysis. We discovered that these diseases shared the complement and coagulation cascades pathway. Eight hub genes were identified and enriched in the immune system process. Immune infiltration analysis revealed increased T cells and decreased B cells in both photoreceptor degenerations. The expression of hub genes was closely associated with the quantities of immune cell types. Additionally, we identified 7 immune therapeutical drugs that target the hub genes.DiscussionOur findings provide new insights and directions for understanding the common mechanisms underlying the development of photoreceptor degeneration. The hub genes and related ceRNA networks we identified may offer new perspectives for elucidating the mechanisms and hold promise for the development of innovative treatment strategies.
A cross-sectional study on the association between dietary inflammatory index and hyperuricemia based on NHANES 2005–2018
Authors: Wang Hao , Qin Shengmei , Li Feng , Zhang Huanhuan , Zeng Ling 
Published: September 2023

BackgroundHyperuricemia is a common condition that can lead to gout and other related diseases. It has been suggested that Inflammatory factors play important role in the development and progression of hyperuricemia. The dietary inflammatory index (DII) enables the assessment of the inflammatory potential of an individual’s diet. This study aimed to investigate the association between DII and hyperuricemia.MethodsThis study was performed based on a cross-sectional dataset from the National Health and Nutrition Examination Survey (NHANES) 2005–2018. Participants aged 18 years and above with dietary intake and serum uric acid level information were included. DII scores were calculated using dietary intake data, based on which participants were categorized into tertiles. Multivariable logistic regression analysis was adopted to investigate the association between DII and hyperuricemia.ResultsAmong a total of 31,781 participants in the analysis, 5,491 had hyperuricemia. After adjusting confounding factors, the odds of hyperuricemia are significantly higher in the second (OR 1.17, 95% CI 1.07–1.29) and third tertiles (OR 1.31, 95% CI 1.19–1.44) relative to the first one.ConclusionThis study suggested that diet with higher inflammatory potential, as measured by DII, is associated with increased hyperuricemia risk. These findings indicated that dietary modification may be a potential approach for hyperuricemia’s prevention and control.
High resting energy expenditure, less fat-free mass, and less muscle strength in HIV-infected children: a matched, cross-sectional study
Authors: Franco-Oliva Andrea , Pinzón-Navarro Beatriz Adriana , Martínez-Soto-Holguín Martha C. , León-Lara Ximena , Ordoñez-Ortega Javier , Pardo-Gutiérrez Ana Laura , Guevara-Cruz Martha , Avila-Nava Azalia , García-Guzmán Alda Daniela , Guevara-Pedraza Laura , Medina-Vera Isabel 
Published: September 2023

Background and aimsMany improvements have been made in the treatment of human immunodeficiency virus (HIV) in pediatric patients; however, challenges remain in terms of achieving normal growth, body composition, and metabolism during treatment, etc. Current nutritional recommendations are based on studies performed in adults, with limited data on the HIV-infected pediatric population. Therefore, this study aimed to compare the resting energy expenditure (REE) of asymptomatic HIV-infected pediatric patients with healthy counterparts and to compare body composition, dietary intake, and physical activity between the two groups.MethodsThis was a cross-sectional study of asymptomatic HIV-infected children who were receiving antiretroviral therapy; the infected group was compared with the uninfected group, matched by age (± 6 months), sex, and body mass index (± 0.5 z-score). Participants were recruited between 2021 and 2022, as outpatients. In both groups, REE was determined by indirect calorimetry and body composition by bioelectrical impedance analysis and hand strength, measured using a hydraulic hand dynamometer.ResultsSeventy-eight participants were enrolled, where n = 39 HIV-infected children and n = 39 controls, with a mean age of 11.6 ± 3.4 years old. REE was significantly higher in the HIV group (1254.4 ± 334.7 kcal/day vs. 1124.7 ± 321 kcal/day, p = 0.013) than in the control group. Fat-free mass (FFM) was lower in the HIV group (28.2 ± 10.5 kg vs. 32 ± 11.2 kg, p = 0.001); this trend continued when the index skeletal muscle was evaluated (7.2 ± 1.2 vs. 7.6 ± 1.5, p = 0.04). The strength of the dominant hand was also lower in the HIV group (12 (8–18) kg vs. 20 (10.5–26) kg, p &lt; 0.0001).ConclusionsChildren with asymptomatic HIV infection have higher REE than their uninfected peers. They also present decreased FFM, skeletal muscle mass index, and muscle strength. These parameters should be considered during nutritional assessment in this population to have a favorable impact on nutritional status and growth.
MRI and amino acid PET detection of whole-brain tumor burden
Authors: Chen Peng , Scarpelli Matthew L. , Healey Debbie R. , Mehta Shwetal , Quarles C. Chad 
Published: September 2023

Background[18F]fluciclovine amino acid PET has shown promise for detecting brain tumor regions undetected on conventional anatomic MRI scans. However, it remains unclear which of these modalities provides a better assessment of the whole brain tumor burden. This study quantifies the performance of [18F]fluciclovine PET and MRI for detecting the whole brain tumor burden.MethodsThirteen rats were orthotopically implanted with fluorescently transduced human glioblastoma cells. Rats underwent MRI (T1- and T2-weighted) and [18F]fluciclovine PET. Next brains were excised, optically cleared, and scanned ex vivo with fluorescence imaging. All images were co-registered using a novel landmark-based registration to enable a spatial comparison. The tumor burden identified on the fluorescent images was considered the ground truth for comparison with the in vivo imaging.ResultsAcross all cases, the PET sensitivity for detecting tumor burden (median 0.67) was not significantly different than MRI (combined T1+T2-weighted) sensitivity (median 0.61; p=0.85). However, the combined PET+MRI sensitivity (median 0.86) was significantly higher than MRI alone (41% higher; p=0.004) or PET alone (28% higher; p=0.0002). The specificity of combined PET+MRI (median=0.91) was significantly lower compared with MRI alone (6% lower; p=0.004) or PET alone (2% lower; p=0.002).ConclusionIn these glioblastoma xenografts, [18F]fluciclovine PET did not provide a significant increase in tumor burden detection relative to conventional anatomic MRI. However, a combined PET and MRI assessment did significantly improve detection sensitivity relative to either modality alone, suggesting potential value in a combined assessment for some tumors.
Research hotspots and trend analysis of abdominal pain in inflammatory bowel disease: a bibliometric and visualized analysis
Authors: Peng Shuai , Xia Yuan , Wang Ying , Yu Xiaoyun , Wu Zunan , Zhang Li , Xu Ke , Shen Lei , Luo Hesheng 
Published: September 2023

Aims: The study aimed to provide a bibliometric and visual analysis of research on abdominal pain in inflammatory bowel disease and discuss the current status, research hotspots, and future developments.Methods: We used the Web of Science Core Collection to comprehensively search the literature on abdominal pain-related research in IBD published between 2003 and 2022. The bibliometric and visual analysis was performed through CiteSpace, VOSviewer software, R language, and the bibliometric online analysis platform, including authors, institutions, countries, journals, references, and keywords in the literature.Results: A total of 3,503 relevant articles are included, indicating that the number of articles in this field has increased in recent years. The United States leads the way with a dominant position in terms of article output, followed by China and JAPAN. United States (967 articles), University of Calgary (98 articles), and World Journal of Gastroenterology (127 articles) are the top publishing countries, institutions, and journals, respectively; keyword analysis shows that gut microbiota, depression, stress, visceral hypersensitivity, and multidisciplinary approach are the hot spots and trends in this research area.Conclusion: Abdominal pain-related studies in IBD have received increasing attention in the past two decades. This study provides the first bibliometric analysis of papers in this research area using visualization software and data information mining. It provides insights into this field’s current status, hot spots, and trends. However, many outstanding issues in this research area still need further exploration to provide a theoretical basis for its clinical application.
Effects of Eimeria maxima infection doses on growth performance and gut health in dual-infection model of necrotic enteritis in broiler chickens
Authors: Goo Doyun , Choi Janghan , Ko Hanseo , Choppa Venkata Sesha Reddy , Liu Guanchen , Lillehoj Hyun Soon , Kim Woo Kyun 
Published: September 2023

The objective of this study was to investigate the effects of the different doses of Eimeria maxima (EM) oocysts on growth performance and intestinal health in broiler chickens challenged with a dual infection model of necrotic enteritis (NE) using EM and NetB+Clostridium perfringens (CP). A total of 432 fourteen-d-old male Cobb 500 broiler chickens were divided into 6 groups with 6 replicates each. The six different groups were as follows: Control, non-challenged; T0+, challenged with CP at 1 × 109 colony forming unit; T5K+, T0+ + 5,000 EM oocysts; T10K+, T0+ + 10,000 EM oocysts; T20K+; T0+ + 20,000 EM oocysts; and T40K+; T0+ + 40,000 EM oocysts. The challenge groups were orally inoculated with EM strain 41A on d 14, followed by NetB+CP strain Del-1 on 4 days post inoculation (dpi). Increasing EM oocysts decreased d 21 body weight, body weight gain, feed intake (linear and quadratic, p &lt; 0.001), and feed efficiency (linear, p &lt; 0.001) from 0 to 7 dpi. Increasing EM oocysts increased jejunal NE lesion score and intestinal permeability on 5, 6, and 7 dpi (linear, p &lt; 0.05). On 7 dpi, increasing the infection doses of EM oocysts increased jejunal CP colony counts (linear, p &lt; 0.05) and increased fecal EM oocyst output (linear and quadratic, p &lt; 0.001). Furthermore, increasing the infection doses of EM oocysts decreased the villus height to crypt depth ratios and the goblet cell counts (linear, p &lt; 0.05) on 6 dpi. Increasing EM oocysts downregulated the expression of MUC2, B0AT, B0,+AT, PepT1, GLUT2, AvBD3 and 9, LEAP2, and TLR4, while upregulating CLDN1, CATHL3, IL-1β, IFN-γ, TNFSF15, TNF-α, IL-10, and Gam56 and 82 on 6 dpi (linear, p &lt; 0.05). Additionally, increasing EM oocysts decreased Pielou’s evenness and Shannon’s entropy (linear, p &lt; 0.01). In conclusion, increasing the infection doses of EM significantly aggravated the severity of NE and exerted negative impact on intestinal health from 5 to 7 dpi.
What predicts the alleviation of Covid-related future anxiety in schoolchildren 6 to 9 months into the pandemic?
Authors: Voltmer Katharina , von Salisch Maria 
Published: September 2023

IntroductionAlthough the first COVID-19-related lockdown in the Spring of 2020 has contributed to an increase in mental health problems in many children worldwide, less is known about the longer-term effects of the pandemic on their (future) anxiety. This article examines resilience factors against children’s Covid-relatedfut ure anxiety (CRFA).MethodsN = 140 children (48,6% female) in 3rd and 4th grade classrooms in Northern Germany were asked to self-report about their CRFA, their anxiety, and the social climate in their classrooms in September (T1) and December 2020 (T2).ResultsResults indicate that 18.6% of the children experienced CRFA “often” in at least one item of the CRFA scale at T1. CRFA was more pronounced in girls and in children from immigrant families. Changes in children’s CRFA between T1 and T2 were predicted by changes in their anxiety and changes in classroom climate. Children in classrooms with increasing levels of peer support tended to have decreasing levels of CRFA, whereas their agemates’ CRFA in less supportive classrooms tended to increase over time.DiscussionThese results suggest that peer and teacher social support may bolster children’s resilience against future anxiety in challenging times. Implications for teachers and schools are discussed.