bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manure amendment acts as a recommended fertilization for improving carbon sequestration efficiency in soils of typical drylands of China
Authors: Liang Shuo , Sun Nan , Wang Shuhui , Colinet Gilles , Longdoz Bernard , Meersmans Jeroen , Wu Lianhai , Xu Minggang 
Published: May 2023

It is generally known that soil organic carbon (SOC) stocks tend to increase with an increase in C input, whereas the C sequestration efficiency (CSE), i.e., the conversion ratio of C input to SOC, differs depending on the amount and type of C input. However, there is still a need to better understand the impact of various fertilization practices on CSE. We studied the data from eight long-term experiments located in the main dryland region of China in order to comprehensively assess the key drivers of CSE in the plow layer considering nearly four decades of various fertilizer treatments, i.e., no fertilizer (CK); chemical nitrogen, phosphorus, and potassium (NPK/NP); chemical fertilizers plus manure (NPKM/NPM/NM); and straw (NPKS/NPS/NS). Our results showed that manure amendment had the most significant fertilization effect on SOC sequestration with an average CSE of 14.9%, which was significantly higher than that of chemical fertilization (9.0%) and straw return treatments (7.9%). In addition, manure amendment also had the highest average SOC increase rate of 684 kg C ha-1 yr-1. Variance partitioning analysis (VPA) illustrated that the CSE of the main dryland region of China was mostly controlled by edaphic characteristics (32.2%), especially the soil C/N ratio and clay content. VPA and structural equation modeling revealed that the magnitude and influencing factors driving CSE varied among different fertilizer treatments. Soil total N was the limiting factor for CSE in the CK treatment, whereas the soil C/N ratio and pH were the main explanatory factors for CSE in the long-term chemical NPK fertilizer treatment. The negative impact of C input from straw was the main driver of CSE under straw return treatments, though C input had a positive effect on the improvement of soil physical properties. However, when considering manure amendments, the improvement of soil nutrients and clay content controlled CSE, underlining the main positive direct effect of soil chemical properties. In a nutshell, our results recommend manure plus chemical fertilizers as a sustainable practice for improving the C sequestration rate and efficiency in dryland cropping systems.
Whole-exome identifies germline variants in families with obstructive sleep apnea syndrome
Authors: de Azevedo Pedro Guimarães , Guimarães Maria de Lourdes Rabelo , Albuquerque Anna Luiza Braga , Alves Rayane Benfica , Gomes Fernandes Bianca , Marques de Melo Flavia , Guimaraes Corrêa Do Carmo Lisboa Cardenas Raony , Friedman Eitan , De Marco Luiz , Bastos-Rodrigues Luciana 
Published: May 2023

Background: Obstructive sleep apnea syndrome (OSAS) (OMIM #107650) is characterized by complete or partial obstruction of the upper airways, resulting in periods of sleep associated apnea. OSAS increases morbidity and mortality risk from cardiovascular and cerebrovascular diseases. While heritability of OSAS is estimated at ∼40%, the precise underlying genes remain elusive. Brazilian families with OSAS that follows as seemingly autosomal dominant inheritance pattern were recruited.Methods: The study included nine individuals from two Brazilian families displaying a seemingly autosomal dominant inheritance pattern of OSAS. Whole exome sequencing of germline DNA were analyzed using Mendel, MD software. Variants selected were analyzed using Varstation® with subsequent analyses that included validation by Sanger sequencing, pathogenic score assessment by ACMG criteria, co-segregation analyses (when possible) allele frequency, tissue expression patterns, pathway analyses, effect on protein folding modeling using Swiss-Model and RaptorX.Results: Two families (six affected patients and three unaffected controls) were analyzed. A comprehensive multistep analysis yielded variants in COX20 (rs946982087) (family A), PTPDC1 (rs61743388) and TMOD4 (rs141507115) (family B) that seemed to be strong candidate genes for being OSAS associated genes in these families.Conclusion: Sequence variants in COX20, PTPDC1 and TMOD4 seemingly are associated with OSAS phenotype in these families. Further studies in more, ethnically diverse families and non-familial OSAS cases are needed to better define the role of these variants as contributors to OSAS phenotype.
Comparative analysis of tissue-specific genes in maize based on machine learning models: CNN performs technically best, LightGBM performs biologically soundest
Authors: Wang Zijie , Zhu Yuzhi , Liu Zhule , Li Hongfu , Tang Xinqiang , Jiang Yi 
Published: May 2023

Introduction: With the advancement of RNA-seq technology and machine learning, training large-scale RNA-seq data from databases with machine learning models can generally identify genes with important regulatory roles that were previously missed by standard linear analytic methodologies. Finding tissue-specific genes could improve our comprehension of the relationship between tissues and genes. However, few machine learning models for transcriptome data have been deployed and compared to identify tissue-specific genes, particularly for plants.Methods: In this study, an expression matrix was processed with linear models (Limma), machine learning models (LightGBM), and deep learning models (CNN) with information gain and the SHAP strategy based on 1,548 maize multi-tissue RNA-seq data obtained from a public database to identify tissue-specific genes. In terms of validation, V-measure values were computed based on k-means clustering of the gene sets to evaluate their technical complementarity. Furthermore, GO analysis and literature retrieval were used to validate the functions and research status of these genes.Results: Based on clustering validation, the convolutional neural network outperformed others with higher V-measure values as 0.647, indicating that its gene set could cover as many specific properties of various tissues as possible, whereas LightGBM discovered key transcription factors. The combination of three gene sets produced 78 core tissue-specific genes that had previously been shown in the literature to be biologically significant.Discussion: Different tissue-specific gene sets were identified due to the distinct interpretation strategy for machine learning models and researchers may use multiple methodologies and strategies for tissue-specific gene sets based on their goals, types of data, and computational resources. This study provided comparative insight for large-scale data mining of transcriptome datasets, shedding light on resolving high dimensions and bias difficulties in bioinformatics data processing.
Pembrolizumab-induced optic neuropathy – a case report
Authors: Daetwyler Eveline , Zippelius Alfred , Meyer Peter , Läubli Heinz 
Published: May 2023

BackgroundImmune checkpoint inhibitor (ICI) treatment has become important for treating various cancer types, including Hodgkin’s lymphoma. However, ICI can overstimulate the immune system, leading to a broad range of immunological side effects, known as immune-related adverse events (irAEs). Here, we report a case of optic neuropathy caused by pembrolizumab.Case presentationA patient with Hodgkin’s lymphoma received pembrolizumab every three weeks. Twelve days after the sixth cycle of pembrolizumab, the patient was admitted to the emergency department with blurred vision, visual field impairment and altered color perception affecting the right eye. The diagnosis of immune-related optic neuropathy was established. Pembrolizumab was stopped permanently and high-dose steroid treatment was immediately started. This emergency treatment led to a satisfactory binocular vision and an improvement of visual acuity testing results. After another 7 months, the left eye was affected with the same symptoms. At this time, only an extended immunosuppressive therapy consisting of high-dose steroid treatment, plasmapheresis, immunoglobulin treatment, retrobulbar injection of steroids and mycophenolate mofetil, successfully reduced the symptoms.ConclusionsThis case highlights the need for prompt recognition and treatment of rare irAEs, such as optic neuropathy. Urgent treatment with initial high-dose steroid treatment is required to avoid persistent loss of visual acuity. Options for further treatment are mainly based on small case series and case reports. In our case, a retrobulbar injection of steroids in combination with mycophenolate mofetil showed significant success in treating steroid-refractory optic neuropathy.
Development and validation of urinary exosomal microRNA biomarkers for the diagnosis of acute rejection in kidney transplant recipients
Authors: Seo Jung-Woo , Lee Yu Ho , Tae Dong Hyun , Kim Yang Gyun , Moon Ju-Young , Jung Su Woong , Kim Jin Sug , Hwang Hyeon Seok , Jeong Kyung-Hwan , Jeong Hye Yun , Lee So-Young , Chung Byung Ha , Kim Chan-Duck , Park Jae Berm , Seok Junhee , Kim Yeong Hoon , Lee Sang-Ho 
Published: May 2023

IntroductionAcute rejection (AR) continues to be a significant obstacle for short- and long-term graft survival in kidney transplant recipients. Herein, we aimed to examine urinary exosomal microRNAs with the objective of identifying novel biomarkers of AR.Materials and methodsCandidate microRNAs were selected using NanoString-based urinary exosomal microRNA profiling, meta-analysis of web-based, public microRNA database, and literature review. The expression levels of these selected microRNAs were measured in the urinary exosomes of 108 recipients of the discovery cohort using quantitative real-time polymerase chain reaction (qPCR). Based on the differential microRNA expressions, AR signatures were generated, and their diagnostic powers were determined by assessing the urinary exosomes of 260 recipients in an independent validation cohort.ResultsWe identified 29 urinary exosomal microRNAs as candidate biomarkers of AR, of which 7 microRNAs were differentially expressed in recipients with AR, as confirmed by qPCR analysis. A three-microRNA AR signature, composed of hsa-miR-21-5p, hsa-miR-31-5p, and hsa-miR-4532, could discriminate recipients with AR from those maintaining stable graft function (area under the curve [AUC] = 0.85). This signature exhibited a fair discriminative power in the identification of AR in the validation cohort (AUC = 0.77).ConclusionWe have successfully demonstrated that urinary exosomal microRNA signatures may form potential biomarkers for the diagnosis of AR in kidney transplantation recipients.
Racehorses from a breeding farm in Tropical Ecuador have a high seroprevalence of anti-Leptospira spp. antibodies: a paradigm for leptospirosis management from a One Health perspective
Authors: Orlando Solon Alberto , Paez Martinez Katherine , Sanchez Ericka , de la Cruz Carmen , Calderon Joselyn , Arcos Fabrizio , Torres-Lasso Pablo , Calvopiña Manuel , Garcia-Bereguiain Miguel Angel 
Published: May 2023

BackgroundLeptospirosis is a zoonotic disease of worldwide distribution that affects humans and domestic and wild animals, and it is highly endemic in Ecuador. However, no reports of infections affecting horses have been published in the country.MethodsThis study evaluates the prevalence of anti-Leptospira spp. antibodies in racing horses from a breeding farm in the coastal Santa Elena province, southwest Ecuador. Sera were collected from 108 non-vaccinated horses and evaluated for 24 serovars of Leptospira spp. using the microscopic agglutination test (MAT).ResultsIt was found that 100% of horses were reactive for Leptospira spp., most of them for multiple serovars. The most prevalent serovars were Leptospira kirschneri serovar Grippotyphosa (100%; 95% CI 99.9% to 100.1%); L. interrogans serovars Sejroe (96.3%; 95% CI 96.2% to 96.4%), Saxkoebing (95.4%; 95% CI 95.3% to 95.5%), Canicola (90.7%; 95% CI 90.5% to 90.9%), Icterohaemorrhagiae (80.5%; 95% CI 80.4% to 80.6%), Bataviae (73.1%; 95% CI 73.0% to 73.2%), Australis (75.0%; 95% CI 74.9% to 75.1%), and Bratislava (71.2%; 95% CI 71.1% to 71.4%); and L. borgpetersenii serovar Tarassovi (76.8%; 95% CI 76.6% to 77.0%).ConclusionsWe found a high prevalence of anti-Leptospira spp. seropositivity in racehorses from a breeding farm in Ecuador. This is the first serologic report for leptospirosis in horses in Ecuador. “One Health”-based sanitary practices for horse-breeding farms are recommended to improve animal and human health.
Global ocean reanalysis CORA2 and its inter comparison with a set of other reanalysis products
Authors: Fu Hongli , Dan Bo , Gao Zhigang , Wu Xinrong , Chao Guofang , Zhang Lianxin , Zhang Yinquan , Liu Kexiu , Zhang Xiaoshuang , Li Wei 
Published: May 2023

We present the China Ocean ReAnalysis version 2 (CORA2) in this paper. We compare CORA2 with its predecessor, CORA1, and with other ocean reanalysis products created between 2004 and 2019 [GLORYS12v1 (Global Ocean reanalysis and Simulation), HYCOM (HYbrid Coordinate Ocean Model), GREP (Global ocean Reanalysis Ensemble Product), SODA3 (Simple Ocean Data Assimilation, version 3), and ECCO4 (Estimating the Circulation and Climate of the Ocean, version 4)], to demonstrate its improvements and reliability. In addition to providing tide and sea ice signals, the accuracy and eddy kinetic energy (EKE) of CORA2 are also improved owing to an enhanced resolution of 9 km and updated data assimilation scheme compared with CORA1. Error analysis shows that the root-mean-square error (RMSE) of CORA2 sea-surface temperature (SST) remains around 0.3°C, which is comparable to that of GREP and smaller than those of the other products studied. The subsurface temperature (salinity) RMSE of CORA2, at 0.87°C (0.15 psu), is comparable to that of SODA3, smaller than that of ECCO4, and larger than those of GLORYS12v1, HYCOM, and GREP. CORA2 and GLORYS12v1 can better represent sub-monthly-scale variations in subsurface temperature and salinity than the other products. Although the correlation coefficient of sea-level anomaly (SLA) in CORA2 does not exceed 0.8 in the whole region, as those of GREP and GLORYS12v1 do, it is more effective than ECCO4 and SODA3 in the Indian Ocean and Pacific Ocean. CORA2 can reproduce the variations in steric sea level and ocean heat content (OHC) on the multiple timescales as the other products. The linear trend of the steric sea level of CORA2 is closer to that of GREP than that of the other products, and the long-term warming trends of global OHC in the high-resolution CORA2 and GLORYS12v1 are greater than those in the low-resolution EN4 and GREP. Although CORA2 shows overall poorer performance in the Atlantic Ocean, it still achieves good results from 2009 onward. We plan to further improve CORA2 by assimilating the best available observation data using the incremental analysis update (IAU) procedure and improving the SLA assimilation method.
g-C3N4/Fe3O4 composites synthesized via solid-state reaction and photocatalytic activity evaluation of methyl blue degradation under visible light irradiation
Authors: Ali Asghar , Amin Muhammad , Tahir Muhammad , Ali S. S. , Hussain Asif , Ahmad Imtiaz , Mahmood Asif , Farooq M. Umer , Farid Muhammad Asim 
Published: May 2023

This study applied the solid-state reaction technique to synthesize g-C3N4, Fe3O4, and g-C3N4/Fe3O4composites in various ratios. XRD confirmed the formation of g-C3N4, Fe3O4, and a g-C3N4/Fe3O4heterostructure. SEM confirmed the rod-shaped structure of Fe2O3and the layered-like fabrication of g-C3N4. The Egof g-C3N4/Fe3O4was approximately 1.9 eV, making it a beneficial composite material for visible response in photocatalysis activity, which was confirmed by UV-Vis spectroscopy. Dielectrics were used to study ferrite nanoparticles and provide information on the mechanism of conductivity in the parts of the dielectric that responded to an applied alternating electric field. In polycrystalline ceramics, the resistive and capacitive grains, contributions, electrode specimen interfaces, and grain boundaries may all be distinguished using impedance analysis, a crucial tool for the study of complicated electrical performance. The g-C3N4/Fe3O4composite material showed high photocatalytic activity against methylene blue (MB) dye.
A novel homozygous variant of TMEM260 induced cardiac malformation and neurodevelopmental abnormality: case report and literature review
Authors: Peng Mou , Jing Siyuan , Duan Sichen , Lu Guoyan , Zhou Kaiyu , Hua Yimin , Wang Tao , Yue Peng , Li Yifei 
Published: May 2023

BackgroundCongenital heart disease (CHD) represents the most widespread congenital birth defect among neonates worldwide, leading to substantial expenses and contributing significantly to premature death caused by birth defects. Despite the significance of CHD, research on its etiology remains limited and has failed to provide substantial evidence for the molecular basis of the disease. With the advancement of next-generation sequencing (NGS), genetic screening has become increasingly accessible, offering a greater capability for identifying potential genetic variants associated with CHD.Case presentationExome sequencing and variant analysis of TMEM260 were performed to obtain genetic data, and clinical characteristics were determined. A complex and severe form of CHD, comprising a persistent truncus arteriosus type I, ventricular septal defect, right aortic arch, as well as critical neurodevelopmental delay and neurological dysfunction, was observed in a patient. This proband presented global muscle hypotonia and a significant delay in gross and fine motor development. Cranial computed tomography scanning showed the presence of bilateral apical, occipital, and temporal subdural effusions; slightly wider bilateral lateral ventricles and annular cisterns; and bilateral cerebral hemispheric parenchyma atrophy. Upon genetic analysis of the patient, a novel homozygous mutation was identified in the TMEM260 gene. The mutation, c.1336_1339DEL, was found to be homozygous and resulted in a frameshift mutation, causing a p.L447Vfs*9 amino acid change. This mutation led to the deletion of a TCTC sequence from positions 1336 to 1339 in the TMEM260 gene, changing leucine to valine at amino acid 447 and introducing a stop codon after the ninth amino acid. This structural deletion in the TMEM260 protein resulted in the loss of gene function.ConclusionThis case report presents a newly discovered variant site in the TMEM260 gene and reinforces the relationship between TMEM260 molecular function and differentiation of mesoderm and ectoderm. Furthermore, our findings broaden the spectrum of variants in the TMEM260 gene and contribute to advancing the genetic understanding of CHD.
The impact of guided self-study on knowledge and skills in Swiss pre-clinical physiotherapy students – a feasibility study protocol
Authors: Schenk Elisabeth , Taeymans Jan , Rogan Slavko 
Published: May 2023

Physiotherapy education in Europe must incorporate self-study units in the curriculum due to the bologna reform. Studies investigating the impact of guided self-study (G-SS) on knowledge and skills in pre-clinical Swiss physiotherapy students are scarce. This study protocol describes a prospective randomized feasibility education study that will primarily examine the feasibility of establishing G-SS using retired physiotherapists as tutors in undergraduate physiotherapy students at the Bern University of Applied Sciences, School of Health Professions. Secondary objective will be to evaluate the effectiveness of six G-SS cycles with retired physiotherapists as tutors on knowledge and skills of pre-clinical undergraduate physiotherapy students. Students of the physiotherapy degree course will be allocated into a G-SS group or control group (CG). G-SS consists of an 8-day cycle. Feasibility outcome are the fidelity of implementation that include exposure dosage and students’ responsiveness, and the degree of acceptability. Success criteria of feasibility are (1) exposure dosage calculated as the number of 90-min presentations that are conducted, and the content of cases and competences and (2) students’ responsiveness, with at least a 83% willingness to participate. Acceptability of intervention from the undergraduate students’ perspective will be evaluated by a questionnaire with open, semi-structured questions (post intervention). This study will provide new information regarding the feasibility of embedding G-SS in the curriculum and about the students’ responsiveness and their acceptability for G-SS.Study protocol version 1Trial registration:German Register of Clinical Studies (DKRS: DRKS00015518).
Maternal HIV infection drives altered placental Mtb-specific antibody transfer
Authors: Nziza Nadege , Jung Wonyeong , Mendu Maanasa , Chen Tina , McNamara Ryan P. , Fortune Sarah M. , Franken Kees L. M. C. , Ottenhoff Tom H. M. , Bryson Bryan , Ngonzi Joseph , Bebell Lisa M. , Alter Galit 
Published: May 2023

IntroductionPlacental transfer of maternal antibodies is essential for neonatal immunity over the first months of life. In the setting of maternal HIV infection, HIV-exposed uninfected (HEU) infants are at higher risk of developing severe infections, including active tuberculosis (TB). Given our emerging appreciation for the potential role of antibodies in the control of Mycobacterium tuberculosis (Mtb), the bacteria that causes TB, here we aimed to determine whether maternal HIV status altered the quality of Mtb-specific placental antibody transfer.MethodsAntigen-specific antibody systems serology was performed to comprehensively characterize the Mtb-specific humoral immune response in maternal and umbilical cord blood from HIV infected and uninfected pregnant people in Uganda.ResultsSignificant differences were noted in overall antibody profiles in HIV positive and negative maternal plasma, resulting in heterogeneous transfer of Mtb-specific antibodies. Altered antibody transfer in HIV infected dyads was associated with impaired binding to IgG Fc-receptors, which was directly linked to HIV viral loads and CD4 counts.ConclusionsThese results highlight the importance of maternal HIV status on antibody transfer, providing clues related to alterations in transferred maternal immunity that may render HEU infants more vulnerable to TB than their HIV-unexposed peers.