bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CD70-CD27 axis in oncology: the new kids on the block
Authors: Flieswasser Tal , Van den Eynde Astrid , Van Audenaerde Jonas , De Waele Jorrit , Lardon Filip , Riether Carsten , de Haard Hans , Smits Evelien , Pauwels Patrick , Jacobs Julie 
Published: January 2022

AbstractThe immune checkpoint molecule CD70 and its receptor CD27 are aberrantly expressed in many hematological and solid malignancies. Dysregulation of the CD70-CD27 axis within the tumor and its microenvironment is associated with tumor progression and immunosuppression. This is in contrast to physiological conditions, where tightly controlled expression of CD70 and CD27 plays a role in co-stimulation in immune responses. In hematological malignancies, cancer cells co-express CD70 and CD27 promoting stemness, proliferation and survival of malignancy. In solid tumors, only expression of CD70 is present on the tumor cells which can facilitate immune evasion through CD27 expression in the tumor microenvironment. The discovery of these tumor promoting and immunosuppressive effects of the CD70-CD27 axis has unfolded a novel target in the field of oncology, CD70.In this review, we thoroughly discuss current insights into expression patterns and the role of the CD70-CD27 axis in hematological and solid malignancies, its effect on the tumor microenvironment and (pre)clinical therapeutic strategies.
Biomarkers for sepsis: more than just fever and leukocytosis—a narrative review
Authors: Barichello Tatiana , Generoso Jaqueline S. , Singer Mervyn , Dal-Pizzol Felipe 
Published: January 2022

AbstractA biomarker describes a measurable indicator of a patient's clinical condition that can be measured accurately and reproducibly. Biomarkers offer utility for diagnosis, prognosis, early disease recognition, risk stratification, appropriate treatment (theranostics), and trial enrichment for patients with sepsis or suspected sepsis. In this narrative review, we aim to answer the question, "Do biomarkers in patients with sepsis or septic shock predict mortality, multiple organ dysfunction syndrome (MODS), or organ dysfunction?" We also discuss the role of pro- and anti-inflammatory biomarkers and biomarkers associated with intestinal permeability, endothelial injury, organ dysfunction, blood–brain barrier (BBB) breakdown, brain injury, and short and long-term mortality. For sepsis, a range of biomarkers is identified, including fluid phase pattern recognition molecules (PRMs), complement system, cytokines, chemokines, damage-associated molecular patterns (DAMPs), non-coding RNAs, miRNAs, cell membrane receptors, cell proteins, metabolites, and soluble receptors. We also provide an overview of immune response biomarkers that can help identify or differentiate between systemic inflammatory response syndrome (SIRS), sepsis, septic shock, and sepsis-associated encephalopathy. However, significant work is needed to identify the optimal combinations of biomarkers that can augment diagnosis, treatment, and good patient outcomes.
Elevated plasma Galectin-3 is associated with major adverse kidney events and death after ICU admission
Authors: Boutin L. , Legrand M. , Sadoune M. , Mebazaa A. , Gayat E. , Chadjichristos C. E. , Dépret F. 
Published: January 2022

Abstract
Background
Galectin-3 (Gal-3) is a proinflammatory and profibrotic protein especially overexpressed after Acute Kidney Injury (AKI). The early renal prognostic value of Gal-3 after AKI in critically ill patients remains unexplored. The objective was to evaluate the prognostic value of plasma level of Gal-3 for Major Adverse Kidney Events (MAKE) and mortality 30 days after ICU admission across AKI stages.

Methods
This is an ancillary study of a prospective, observational, multicenter cohort (FROG-ICU). AKI was defined using KDIGO definition.

Results
Two thousand and seventy-six patients had a Gal-3 plasma level measurement at ICU admission. Seven hundred and twenty-three (34.8%) were females and the median age was 63 [51, 74] years. Eight hundred and seven (38.9%) patients developed MAKE, 774 (37.3%) had AKI and mortality rate at 30 days was 22.4% (N = 465). Patients who developed MAKE had higher Gal-3 level at admission compared to patients without (30.2 [20.8, 49.2] ng/ml versus 16.9 [12.7, 24.3] ng/ml, p < 0.001, respectively. The area under the receiver operating characteristic curve of Gal-3 to predict MAKE was 0.76 CI95% [0.74–0.78], p < 0.001. Gal-3 was associated with MAKE (OR 1.80 CI95% [1.68–1.93], p < 0.001, non-adjusted and OR 1.37 CI95% [1.27–1.49], p < 0.001, adjusted). The use of Gal-3 improved prediction performance of prediction model including SAPSII, Screatadm, pNGAL with a NRI of 0.27 CI95%(0.16–0.38), p < 0.001. Median Gal-3 was higher in non-survivors than in survivors at 30 days (29.2 [20.2, 49.2] ng/ml versus 18.8 [13.3, 29.2] ng/ml, p < 0.001, respectively).

Conclusion
Plasma levels of Gal-3 were strongly associated with renal function, with an increased risk of MAKE and death after ICU admission.
Trial registration ClinicalTrials.gov NCT01367093. Registered on 6 June 2011.

Graphical abstract
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
Authors: Davidson Nadia M. , Chen Ying , Sadras Teresa , Ryland Georgina L. , Blombery Piers , Ekert Paul G. , Göke Jonathan , Oshlack Alicia 
Published: January 2022

AbstractIn cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki.
Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice
Authors: Deng Li , Gao Baibai , Zhao Lun , Zhang Ying , Zhang Qing , Guo Minrong , Yang Yongqing , Wang Shuangqi , Xie Liang , Lou Hao , Ma Meng , Zhang Wei , Cao Zhilin , Zhang Qinghua , McClung C. Robertson , Li Guoliang , Li Xingwang 
Published: January 2022

AbstractBackgroundThe daily cycling of plant physiological processes is speculated to arise from the coordinated rhythms of gene expression. However, the dynamics of diurnal 3D genome architecture and their potential functions underlying the rhythmic gene expression remain unclear.ResultsHere, we reveal the genome-wide rhythmic occupancy of RNA polymerase II (RNAPII), which precedes mRNA accumulation by approximately 2 h. Rhythmic RNAPII binding dynamically correlates with RNAPII-mediated chromatin architecture remodeling at the genomic level of chromatin interactions, spatial clusters, and chromatin connectivity maps, which are associated with the circadian rhythm of gene expression. Rhythmically expressed genes within the same peak phases of expression are preferentially tethered by RNAPII for coordinated transcription. RNAPII-associated chromatin spatial clusters (CSCs) show high plasticity during the circadian cycle, and rhythmically expressed genes in the morning phase and non-rhythmically expressed genes in the evening phase tend to be enriched in RNAPII-associated CSCs to orchestrate expression. Core circadian clock genes are associated with RNAPII-mediated highly connected chromatin connectivity networks in the morning in contrast to the scattered, sporadic spatial chromatin connectivity in the evening; this indicates that they are transcribed within physical proximity to each other during the AM circadian window and are located in discrete “transcriptional factory” foci in the evening, linking chromatin architecture to coordinated transcription outputs.ConclusionOur findings uncover fundamental diurnal genome folding principles in plants and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.
Guided meditation for vision acuity training on adolescent myopia: study protocol for an open-label, prospective, multicenter, randomized controlled trial
Authors: Li Yibo , Zhu Lili , Wang Raoying , Yang Xingyue , Jiang Xinqi , Lu Tao 
Published: January 2022

Abstract
Background
Currently, the population with myopia climbs steadily, and is developing toward younger age, posing a great concern to the health of adolescents. Myopia in severe cases can cause irreversible consequences such as glaucoma, blindness, and other complications. At present, the solutions for myopia are glasses, medication, and surgery. This study aims to investigate the role of a physiotherapy category based on guided meditation for vision acuity training on adolescent myopia.

Methods
This is a prospective, randomized, multicenter clinical trial. One thousand one hundred forty primary and secondary school students aged 8–18 years old from 27 schools will be recruited and randomly divided into an experimental and a control group at a ratio of 2:1 in two phases, with a training period of 30 days in each phase and a follow-up period of 3 months. No interventions will be conducted during the follow-up period, nor will other interventions employed. Inclusion criteria will meet the diagnostic criteria for simple myopia and −6.00D ≤ spherical lenses ≤ −0.50D and cylindrical lenses ≤1.50D. The primary observation index will be to compare the statistical differences in distant visual acuity between the two groups; the secondary observation indexes will be ocular symptoms (mainly including eye fatigue, dryness, pain, double vision, neck pain, thought disorders, and lags in response), diopter, and astigmatism.

Discussion
The purpose of this two-phase trial is to compare the clinical effectiveness of focused vision-guided meditation with Chinese eye exercises that are also non-pharmacological, non-invasive interventions for myopia, and to maximize the benefit to the subjects. The results will indicate whether the training based on focused vision-guided meditation has the ability to improve distant visual acuity, relieve ocular symptoms, and ameliorate diopter. In addition, this trial will provide clinical efficacy of the training, which is expected to provide meaningful data for vision rehabilitation. At the same time, the vision acuity training method, which is permeated with the concept of Traditional Chinese Medicine (TCM) rehabilitation and health maintenance, will be applied to achieve the goal of preventing or alleviating myopic development and reducing myopia rate.

Trial registration
Chinese Clinical Trial Registry ChiCTR2000038642. Registered on 26 September 2020
Fasting before living-kidney donation: effect on donor well-being and postoperative recovery: study protocol of a multicenter randomized controlled trial
Authors: Oudmaijer C. A. J. , Minnee R. C. , Pol R. A. , van den Boogaard W. M. C. , Komninos D. S. J. , van de Wetering J. , van Heugten M. H. , Hoorn E. J. , Sanders J. S. F. , Hoeijmakers J. H. J. , Vermeij W. P. , IJzermans J. N. M. 
Published: January 2022

Abstract
Background
One of the main effectors on the quality of life of living-kidney donors is postoperative fatigue. Caloric restriction (CR) and short-term fasting (STF) are associated with improved fitness and increased resistance to acute stress. CR/STF increases the expression of cytoprotective genes, increases immunomodulation via increased anti-inflammatory cytokine production, and decreases the expression of pro-inflammatory markers. As such, nutritional preconditioning by CR or STF represents a non-invasive and cost-effective method that could mitigate the effects of acute surgery-induced stress and postoperative fatigue. To investigate whether preoperative STF contributes to a reduction in fatigue after living-kidney donation, a randomized clinical trial is indicated.

Methods
We aim to determine whether 2.5 days of fasting reduces postoperative fatigue score in subjects undergoing living-kidney donation. In this randomized study, the intervention group will follow a preoperative fasting regime for 2.5 days with a low-dose laxative, while the control group will receive standard care. The main study endpoint is postoperative fatigue, 4 weeks after living-kidney donation. Secondary endpoints include the effect of preoperative fasting on postoperative hospital admission time, the feasibility of STF, and the postoperative recovery of donor and recipient kidney function. This study will provide us with knowledge of the feasibility of STF and confirm its effect on postoperative recovery.

Discussion
Our study will provide clinically relevant information on the merits of caloric restriction for living-kidney donors and recipients. We expect to reduce the postoperative fatigue in living-kidney donors and improve the postoperative recovery of living-kidney recipients. It will provide evidence on the clinical merits and potential caveats of preoperative dietary interventions.

Trial registration
Netherlands Trial Register NL9262. EudraCT 2020-005445-16. MEC Erasmus MC MEC-2020-0778. CCMO NL74623.078.21
Variation in water contact behaviour and risk of Schistosoma mansoni (re)infection among Ugandan school-aged children in an area with persistent high endemicity
Authors: Trienekens Suzan C. M. , Faust Christina L. , Besigye Fred , Pickering Lucy , Tukahebwa Edridah M. , Seeley Janet , Lamberton Poppy H. L. 
Published: January 2022

Abstract
Background
Annual mass drug administration with praziquantel has reduced schistosomiasis transmission in some highly endemic areas, but areas with persistent high endemicity have been identified across sub-Saharan Africa, including Uganda. In these areas many children are rapidly reinfected post treatment, while some children remain uninfected or have low-intensity infections. The aim of this mixed-methods study was to better understand variation in water contact locations, behaviours and infection risk in school-aged children within an area with persistent high endemicity to inform additional control efforts.

Methods
Data were collected in Bugoto, Mayuge District, Uganda. Two risk groups were identified from a longitudinal cohort, and eight children with no/low-intensity infections and eight children with reinfections were recruited. Individual structured day-long observations with a focus on water contact were conducted over two periods in 2018. In all identified water contact sites, four snail surveys were conducted quarterly over 1 year. All observed Biomphalaria snails were collected, counted and monitored in the laboratory for Schistosoma mansoni cercarial shedding for 3 weeks.

Results
Children came into contact with water for a range of purposes, either directly at the water sources or by coming into contact with water collected previously. Although some water contact practices were similar between the risk groups, only children with reinfection were observed fetching water for commercial purposes and swimming in water sources; this latter group of children also came into contact with water at a larger variety and number of sites compared to children with no/low-intensity infection. Households with children with no/low-intensity infections collected rainwater more often. Water contact was observed at 10 sites throughout the study, and a total of 9457 Biomphalaria snails were collected from these sites over four sampling periods. Four lake sites had a significantly higher Biomphalaria choanomphala abundance, and reinfected children came into contact with water at these sites more often than children with no/low-intensity infections. While only six snails shed cercariae, four were from sites only contacted by reinfected children.

Conclusions
Children with reinfection have more high-risk water contact behaviours and accessed water sites with higher B. choanomphala abundance, demonstrating that specific water contact behaviours interact with environmental features to explain variation in risk within areas with persistent high endemicity. Targeted behaviour change, vector control and safe water supplies could reduce reinfection in school-aged children in these settings.

Graphical Abstract
Regional heterogeneity and unexpectedly high abundance of Cooperia punctata in beef cattle at a northern latitude revealed by ITS-2 rDNA nemabiome metabarcoding
Authors: De Seram Eranga Lakshitha , Redman Elizabeth Mary , Wills Felicity Kaye , de Queiroz Camila , Campbell John Ross , Waldner Cheryl Lynne , Parker Sarah Elizabeth , Avramenko Russell William , Gilleard John Stuart , Uehlinger Fabienne Dominique 
Published: January 2022

Abstract
Background
The species composition of cattle gastrointestinal nematode (GIN) communities can vary greatly between regions. Despite this, there is remarkably little large-scale surveillance data for cattle GIN species which is due, at least in part, to a lack of scalable diagnostic tools. This lack of regional GIN species-level data represents a major knowledge gap for evidence-based parasite management and assessing the status and impact of factors such as climate change and anthelmintic drug resistance.

Methods
This paper presents a large-scale survey of GIN in beef herds across western Canada using ITS-2 rDNA nemabiome metabarcoding. Individual fecal samples were collected from 6 to 20 randomly selected heifers (n = 1665) from each of 85 herds between September 2016 and February 2017 and 10–25 first season calves (n = 824) from each of 42 herds between November 2016 and February 2017.

Results
Gastrointestinal nematode communities in heifers and calves were similar in Alberta and Saskatchewan, with Ostertagia ostertagi and Cooperia oncophora being the predominant GIN species in all herds consistent with previous studies. However, in Manitoba, Cooperia punctata was the predominant species overall and the most abundant GIN species in calves from 4/8 beef herds.

Conclusions
This study revealed a marked regional heterogeneity of GIN species in grazing beef herds in western Canada. The predominance of C. punctata in Manitoba is unexpected, as although this parasite is often the predominant cattle GIN species in more southerly latitudes, it is generally only a minor component of cattle GIN communities in northern temperate regions. We hypothesize that the unexpected predominance of C. punctata at such a northerly latitude represents a range expansion, likely associated with changes in climate, anthelmintic use, management, and/or animal movement. Whatever the cause, these results are of practical concern since C. punctata is more pathogenic than C. oncophora, the Cooperia species that typically predominates in cooler temperate regions. Finally, this study illustrates the value of ITS-2 rDNA nemabiome metabarcoding as a surveillance tool for ruminant GIN parasites.

Graphical Abstract
Chromatin alterations during the epididymal maturation of mouse sperm refine the paternally inherited epigenome
Authors: Bedi Yudhishtar S. , Roach Alexis N. , Thomas Kara N. , Mehta Nicole A. , Golding Michael C. 
Published: January 2022

Abstract
Background
Paternal lifestyle choices and male exposure history have a critical influence on the health and fitness of the next generation. Accordingly, defining the processes of germline programming is essential to resolving how the epigenetic memory of paternal experiences transmits to their offspring. Established dogma holds that all facets of chromatin organization and histone posttranslational modification are complete before sperm exits the testes. However, recent clinical and animal studies suggest that patterns of DNA methylation change during epididymal maturation. In this study, we used complementary proteomic and deep-sequencing approaches to test the hypothesis that sperm posttranslational histone modifications change during epididymal transit.

Results
Using proteomic analysis to contrast immature spermatozoa and mature sperm isolated from the mouse epididymis, we find progressive changes in multiple histone posttranslational modifications, including H3K4me1, H3K27ac, H3K79me2, H3K64ac, H3K122ac, H4K16ac, H3K9me2, and H4K20me3. Interestingly, some of these changes only occurred on histone variant H3.3, and most involve chromatin modifications associated with gene enhancer activity. In contrast, the bivalent chromatin modifications, H3K4me3, and H3K27me3 remained constant. Using chromatin immunoprecipitation coupled with deep sequencing, we find that changes in histone h3, lysine 27 acetylation (H3K27ac) involve sharpening broad diffuse regions into narrow peaks centered on the promoter regions of genes driving embryonic development. Significantly, many of these regions overlap with broad domains of H3K4me3 in oocytes and ATAC-seq signatures of open chromatin identified in MII oocytes and sperm. In contrast, histone h3, lysine 9 dimethylation (H3K9me2) becomes enriched within the promoters of genes driving meiosis and in the distal enhancer regions of tissue-specific genes sequestered at the nuclear lamina. Maturing sperm contain the histone deacetylase enzymes HDAC1 and HDAC3, suggesting the NuRD complex may drive some of these changes. Finally, using Western blotting, we detected changes in chromatin modifications between caput and caudal sperm isolated from rams (Ovis aries), inferring changes in histone modifications are a shared feature of mammalian epididymal maturation.

Conclusions
These data extend our understanding of germline programming and reveal that, in addition to trafficking noncoding RNAs, changes in histone posttranslational modifications are a core feature of epididymal maturation.
Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial
Authors: Hong Jung Yong , Cho Hee Jin , Sa Jason K. , Liu Xiaoqiao , Ha Sang Yun , Lee Taehyang , Kim Hajung , Kang Wonseok , Sinn Dong Hyun , Gwak Geum-Youn , Choi Moon Seok , Lee Joon Hyeok , Koh Kwang Cheol , Paik Seung Woon , Park Hee Chul , Kang Tae Wook , Rhim Hyunchul , Lee Su Jin , Cristescu Razvan , Lee Jeeyun , Paik Yong Han , Lim Ho Yeong 
Published: January 2022

AbstractBackgroundA limited number of studies have characterized genomic properties of hepatocellular carcinoma (HCC) patients in response to anti-PD-1 immunotherapy.MethodsHerein, we performed comprehensive molecular characterization of immediate (D-42 to D-1) pre-treatment tumor biopsy specimens from 60 patients with sorafenib-failed HCC in a single-arm prospective phase II trial of pembrolizumab. Objective response rate was the primary efficacy endpoint. We used whole-exome sequencing, RNA sequencing, and correlative analysis. In addition, we performed single-cell RNA sequencing using peripheral blood mononuclear cells.ResultsThe overall response rate of pembrolizumab in sorafenib-failed HCC patients was 10% ([6/60]95% CI, 2.4–17.6). In a univariate analysis using clinicopathological features, female gender, PD-L1 positivity, and low neutrophil-to-lymphocyte ratio (NLR) were identified as contributing factors to pembrolizumab response. Somatic mutations in CTNNB1 and genomic amplifications in MET were found only in non-responders. Transcriptional profiles through RNA sequencing identified that pembrolizumab responders demonstrated T cell receptor (TCR) signaling activation with expressions of MHC genes, indicating increased levels of T cell cytotoxicity. In single-cell sequencing from 10 pre- and post-treatment peripheral blood mononuclear cells (PBMCs), patients who achieved a partial response or stable disease exhibited immunological shifts toward cytotoxic CD8+ T cells. Conversely, patients with progressive disease showed an increased number of both CD14+ and CD16+ monocytes and activation of neutrophil-associated pathways.ConclusionsTaken together, HCC patients with infiltration of cytotoxic T cells, along with increased active circulating CD8+ T cells during pembrolizumab treatment and down-regulation of neutrophil-associated markers, significantly benefited from pembrolizumab treatment.Trial registrationNCT#03163992(first posted: May 23, 2017)