bluuebunny/crossref_metadata_2025 huggingface dataset:
Serum fibroblast growth factor-23 concentrations in young and mature adult cats with chronic kidney disease
Authors: Miyakawa Hirosumi , Hsu Huai-Hsun , Ogawa Mizuki , Akabane Ryota , Miyagawa Yuichi , Takemura Naoyuki
Published: August 2021

Objectives

The aim of this study was to investigate serum fibroblast growth factor (FGF)-23 concentrations in young and mature adult cats with chronic kidney disease (CKD).

Methods

The present study retrospectively investigated the serum samples and medical records of 1–8-year-old clinically healthy cats (control group, n = 7) and cats with CKD (n = 54). Cats with CKD were divided into four stages based on serum creatinine concentrations, according to the International Renal Interest Society (IRIS) CKD guidelines. Serum FGF-23 concentrations were compared between cats in the control group, IRIS stages 1, 2 and 3–4 CKD. Continuous variables were analysed using correlations and multiple linear regression.

Results

Serum FGF-23 concentrations were significantly higher in cats with IRIS stages 1, 2 and 3–4 CKD, compared with those in the control group ( P = 0.02, P = 0.002 and P = 0.002, respectively). Additionally, serum FGF-23 concentrations in cats with IRIS stages 3–4 CKD had higher serum FGF-23 concentrations than those with IRIS stages 1 and 2 CKD ( P = 0.04 and P = 0.02, respectively). In the multiple linear regression analysis, serum urea nitrogen concentration, serum phosphorus concentration and blood ionised calcium concentration were independent variables predicting serum FGF-23 concentration.

Conclusions and relevance

Serum FGF-23 concentrations in younger cats with CKD increased in early-stage CKD and were associated with mineral metabolic markers, as also occurs in geriatric cats.
Developing the Positive Identity of Minoritized Women Leaders in Higher Education: How can Multiple and Diverse Developers Help With Overcoming the Impostor Phenomenon?
Authors: Manongsong Ague Mae , Ghosh Rajashi
Published: August 2021

Minoritized women remain underrepresented in leadership positions, especially within higher education (HE). A key barrier to advancement for women of color is their susceptibility to impostor phenomenon (IP). A developmental network where the minoritized woman receives developmental support from multiple individuals is a potentially powerful intervention that can help them advance their careers, but there is a general lack of research on IP in the context of minoritized women’s leadership development and the role of developmental support, especially with regards to multiple diversified developmental relationships. Therefore, this paper integrates various literature streams (leader development for minoritized women in higher education, IP, mentoring) and offers a conceptual framework that utilizes a developmental network perspective. The propositions offered explain how multiple developers can help minoritized women address IP and develop positive leader identities, as well as how both parties can better anticipate and handle challenges related to diversified developmental relationships in HE.
Limitations of occasional reinforced extinction to alleviate spontaneous recovery and reinstatement effects: Evidence for a trial-signalling mechanism
Authors: Quintero María J , Flores Amanda , Gutiérrez-Huerta María T , Molina-Guerrero Patricia , López Francisco J , Morís Joaquín
Published: August 2021

Fear extinction is not permanent but is instead more vulnerable than the original fear memory, as traditionally shown by the return of fear phenomena. Because of this, techniques to mitigate the return of fear are needed in the clinical treatment of related psychological conditions. One promising strategy is the occasional reinforced extinction treatment, introducing a gradual and sparse number of conditioned stimulus–unconditioned stimulus (CS-US) pairings within the extinction treatment. We present the results of three experiments in which we used a threat conditioning procedure in humans. Our main aim was to evaluate whether occasional reinforced extinction could reduce two different forms of relapse: spontaneous recovery (Experiments 1 and 2) and reinstatement (Experiment 3). Contrary to our predictions and previous literature, the results indicate that an occasional reinforcement treatment did not mitigate relapse compared with standard extinction. From a theoretical standpoint, these results are more consistent with the idea that extinction entails the acquisition of new knowledge than with the idea that there are conditions in which extinction leads to a weakening of the original fear memory. These findings also question the generality of the potential benefits of using occasional reinforced extinction in clinical settings.
Tactile disgust: Post-contact can be more disgusting than contact
Authors: Saluja Supreet , Stevenson Richard J
Published: August 2021

Several studies have examined if disgust can be evoked by contacting an object—yet none have examined if reported disgust changes when the hand leaves the object. This is surprising given that post-contact tactile disgust is probably a driver of hand hygiene. We examined contact and post-contact tactile disgust and its sensory origins. Participants were asked to touch several objects, making sensory, disgust, and desire-to-handwash evaluations. These ratings were made at three stages-of-contact: object-contact (just touch), post-contact (just touch), and visual post-contact (touch, vision). Disgust was typically highest at post-contact (when the hand left the object). Stickiness and wetness were uniquely predictive of object-contact disgust. Only stickiness drove post-contact disgust, and only wetness visual post-contact disgust. Hand-washing desire was primarily driven by quantity of residue perceived on the hand. These findings suggest that tactile disgust is a multisensory and iterative process relating to object- and residue-adhesiveness.
Identification of the most effective muscles in landing impact forces
Authors: Mojaddarasil Marzieh , Sadigh Mohammad Jafar , Zahabi Sayed Jalal
Published: August 2021

The aim of this study was to evaluate the role of the main lower limb muscles in increasing or decreasing each lower limb joint impact force during drop landing. To do so, the body was modeled by a four-link musculoskeletal model consisting of eight main Hill-type muscles. Different drop landing scenarios were modeled by changing the activation levels of the considered muscles. In each landing simulation, the impact GRF and impact joint forces were obtained. In order to compare and rank the muscles with respect to their effect on each impact force, a computationally feasible zero-one (off-on) muscle activation analysis was proposed. The proposed approach revealed important features regarding the relation between different impact forces and muscle activations. Specifically, the results can be interpreted in terms of the role that each muscle potentially plays in causing or preventing certain injuries. Moreover, the results obtained from the analysis were further used to classify the muscles into four categories, depending on the effect they have on each impact force. The proposed theoretical analysis is seen to be a promising tool in predicting the role of muscles and their order of importance in the generation of lower limb impact forces in landing, without the need for experimental tests.
Multiparametric magnetic resonance imaging for bladder cancer: a comprehensive systematic review of the Vesical Imaging-Reporting and Data System (VI-RADS) performance and potential clinical applications
Authors: Séguier Denis , Puech Philippe , Kool Ronald , Dernis Léa , Gabert Héléna , Kassouf Wassim , Villers Arnauld , Marcq Gautier
Published: August 2021

Background:

The Vesical Imaging-Reporting and Data System (VI-RADS) score is a novel standardized approach to image and report bladder cancer (BC) with multiparametric MRI (mpMRI).

Objectives:

To describe and evaluate the performance of the VI-RADS score using mpMRI and assess its potential clinical applications and limitations.

Methods:

A systematic review was conducted using the MEDLINE and EMBASE electronic bibliographic databases between June 2020 and December 2020. All reports deemed relevant to describe the VI-RADS score and assess its performance and applications were retrieved. Results presentation stands as narrative, purely descriptive synthesis based on aggregate studies data.

Results:

A total of 20 relevant studies were retrieved: three meta-analyses, five prospective studies, and twelve retrospective studies. The retrospective studies covered 1676 patients, while the prospective studies included a total number of 468 patients. Pooled sensitivity, specificity to differentiate muscle-invasive from non-muscle-invasive bladder cancer, ranged from 74.1% to 97.3%, and 77% to 100%, respectively. The chosen VI-RADS score thresholds for this discrimination varied across studies. The interreader agreement ranged from 0.73 to 0.95. Currently, the potential clinical applications of VI-RADS consist of initial BC risk stratification, assessment of neoadjuvant therapies response, and bladder sparing approaches, although further validation is required.

Conclusions:

The VI-RADS score helps to discriminate muscle invasive from non-muscle invasive BC with good performance and reproducibility. A simple algorithm based on four basic questions may enhance its popularization. Further studies are required to validate the clinical applications.
Women’s Safety Concerns and Academia: How Safety Concerns Can Create Opportunity Gaps
Authors: Trawalter Sophie , Doleac Jennifer , Palmer Lindsay , Hoffman Kelly , Carter-Sowell Adrienne
Published: August 2021

The present work documents the safety concerns of men and women in academia and how these concerns can create opportunity gaps. Across five samples including undergraduate and graduate students, postdoctoral fellows, and faculty ( N = 1,812), women reported greater concerns about their safety than did men, and these concerns were associated with reduced work hours in libraries, offices, and/or labs afterhours. Additionally, although we were unable to manipulate safety concerns among women, in an experiment with men ( N = 117), increasing safety concerns decreased willingness to use the library afterhours. Finally, in an archival study of swipe access data ( N = 350,364 swipes), a crime event that made safety concerns salient for women was associated with a decreased likelihood that women worked in their office afterhours and a decreased likelihood that science, technology, engineering, and mathematics women worked in their labs later at night. Collectively, these data suggest that women’s safety concerns can restrict their work.
Raised C-reactive protein in medication overdose: A report of two cases
Authors: Arafat SM Yasir , Kar Sujita Kumar
Published: August 2021

Studies have been coming out focusing on the biological markers of suicide. Here, we present two cases with raised C-reactive protein who were admitted after attempts of suicide by overdose. There is a need to study the neuro-immuno-endocrinal changes in suicide systematically that will give insight into the biological underpinning.
Primary histiocytic sarcoma in the brain with renal metastasis causing internal ophthalmoparesis and external ophthalmoplegia in a Maine Coon cat
Authors: Monteiro Susana , Hughes Katherine , Genain Marie-Aude , Alves Lisa
Published: August 2021

Case summary

An 11-year-old neutered male Maine Coon cat was presented for investigation of anisocoria and depression. Neurological examination was consistent with a lesion at the level of the middle cranial fossa, and biochemistry was indicative of moderate renal functional impairment. MRI of the brain identified an extra-axial mass lesion at the level of the middle cranial fossa, T2-weighted hyperintense and strongly homogeneously contrast enhancing with dural tail. The cat was euthanased after 6 weeks of palliative treatment with corticosteroids. Histopathology and immunohistochemistry of the brain, the intra-cranial mass and the renal masses found on necropsy were consistent with histiocytic sarcoma.

Relevance and novel information

Central nervous system histiocytic sarcoma is a rare finding in cats. This original case report describes the neurological presentation, novel MRI characteristics and pathological findings of suspected primary histiocytic sarcoma affecting the brain with renal metastasis in a cat.
Imagined Audiences, Emotions, and Feedback Expectations in Social Media Photo Sharing
Authors: Stsiampkouskaya Kseniya , Joinson Adam , Piwek Lukasz , Stevens Lorna
Published: August 2021

The present research explores the effects of imagined audiences, emotions, and feedback expectations on social media photo sharing. We focus on the audience-oriented approach to sharing and on how discrepancies between expected and received feedback might shape photo sharing behaviors. Twenty-four participants were interviewed using scenario-based semi-structured interview method. The participants were asked to develop an imagined story about two fictional individuals who decided to share a photo on their social media. The story was guided by questions about the characters’ motivations and incentives to post and explored three alternative scenarios representing the reception of usual feedback, better than usual feedback, and the absence of expected feedback, respectively. The results indicate that individuals often adopt their audience’s perspective when choosing a photo to post, and consider whether the chosen image would evoke sufficient interest to induce feedback. The participants believed that emotional photos engaged their audience and motivated the viewers to provide feedback. Furthermore, the study identified and analyzed the concept of feedback expectations. When received feedback exceeded the expectations, individuals experienced happiness. However, the replication of successful content was considered appropriate only if accompanied by a suitable caption and posted after a period of time. When received feedback failed to meet their expectations, individuals felt disconnected from their audiences and experienced disappointment. They employed rationalization and feedback dismissal as coping mechanisms and displayed two common behavioral responses to unsuccessful feedback; they attempted to repost the photo avoiding previous mistakes, and they changed the style of content they posted.
Biomechanical Comparison of a Novel Tibial Fixation Technique Versus Interference Screw Fixation for ACL Reconstruction Using Soft Tissue Grafts
Authors: Sun Tinghan , Zhang Hangzhou
Published: August 2021

Background:

Controversy remains regarding the optimal technique for tibial fixation of soft tissue grafts in anterior cruciate ligament (ACL) reconstruction.

Purpose/Hypothesis:

To compare the biomechanical outcomes of a novel transtibial tubercle fixation technique with those of a commonly utilized interference screw fixation at the tibial site. Our hypothesis was that transtibial tubercle fixation achieves higher ultimate failure loads than interference screw fixation.

Study Design:

Controlled laboratory study.

Methods:

We used 24 matched porcine tibias and digital extensor tendons, from which 12 grafts and tibial tunnels were prepared using the novel transtibial tubercle fixation technique and 12 were prepared using the interference screw fixation technique. The specimens underwent a cyclic loading test (50-250 N applied for 1000 cycles at a frequency of 1 Hz), followed by a load-to-failure test. The slippage, stiffness, and ultimate failure loads were compared between the techniques.

Results:

No differences in slippage were found during the cyclic loading test, and no graft fixation or tibial complex failures occurred during cyclic testing in either group. The transtibial tubercle fixation technique had higher ultimate failure loads (mean ± SD, 756.28 ± 123.43 N) as compared with interference screw fixation (602.15 ± 81.62 N; P < .05). The grafts in the transtibial tubercle fixation group were less stiff than those in the interference screw fixation group (84.43 vs 101.23 N/mm; P < .05).

Conclusion:

Transtibial tubercle fixation achieved higher ultimate failure loads than interference screw fixation in the load-to-failure test.

Clinical Relevance:

The novel transtibial tubercle fixation technique compared favorably with interference screw fixation during ACL reconstruction. This technique does not require hardware, has a low cost, theoretically eliminates the risk of complications associated with hardware implantation (eg, graft damage and pain attributed to retained hardware requiring removal), and is relatively easy to perform.
Youth Critical Data Practices in the COVID-19 Multipandemic
Authors: Calabrese Barton Angela , Greenberg Day , Turner Chandler , Riter Devon , Perez Melissa , Tasker Tammy , Jones Denise , Herrenkohl Leslie Rupert , Davis Elizabeth A.
Published: August 2021

This study investigates how youth from two cities in the United States engage in critical data practices as they learn about and take action in their lives and communities in relation to COVID-19 and its intersections with justice-related concerns. Guided by theories of critical data literacies and data justice, a historicized and future-oriented participatory methodological approach is used to center the lived lives and communities of participants through dialogic interviews and experience sampling method. Data were co-analyzed with participants using critical grounded theory. Findings illustrate how youth not only aimed to reveal the dynamic and human aspects of and relationships with data as they engage with/in the world as people who matter but also offered alternative infrastructures for counter data production and aggregation toward justice in the here and now and desired possible futures. Implications for studies of learning with/through data practices in everyday life in relation to issues of justice are discussed.
Neighborhoods with the Highest Eviction Filing Rates Have the Lowest Levels of COVID-19 Vaccination
Authors: Jin Olivia , Lemmerman Emily , Hepburn Peter , Desmond Matthew
Published: August 2021

The aim of this visualization is to determine whether populations at greatest risk for eviction have been vaccinated against COVID-19 prior to the end of the U.S. federal eviction moratorium. The authors identified nine jurisdictions in which both records of recent eviction filings and data on COVID-19 vaccination were available at the ZIP code level. In every jurisdiction, the ZIP codes with the highest rates of eviction filing during the pandemic had the lowest vaccination rates. These areas are also disproportionately home to majority Black and Hispanic populations. Given previous research demonstrating links between eviction and the spread of COVID-19, the present findings support the continuation of eviction protections. Communities at risk for eviction should be prioritized in vaccination campaigns.
‘La Città ideale’ as a Set of New Institutionalized Resources Integration Practices—Insights from a Pilot Project of the Sicily Region
Authors: Fulco Irene , Carrubbo Luca , Megaro Antonietta , Liani Francesca
Published: August 2021

This study aims to investigate whether and how institutions can contribute to generate value at a territorial level and in which way this value may fit with value-in-business. Starting from the conceptualization of value generation and its relationship with territorial development according to service ecosystem perspective, this study aims to present and discuss an experimental project carried out in a specific Italian area to better understand these main theoretical issues. Specifically, the Sicily region is significant for the genetic factors of the context, linked to a social and cultural structure which, despite the presence of numerous obstacles to socio-economic development, strengthen the path of ‘multi-actor and multi-level’ involvement, which implies the active participation of a plurality of local actors essential to generate value for the territory and for business.
Celebrating the End of Enlightenment: Organization Theory in the Age of the Anthropocene and Gaia (and why neither is the solution to our ecological crisis)
Authors: Banerjee Subhabrata Bobby , Arjaliès Diane-Laure
Published: August 2021

This article aims to change the terms of the conversation about the ecological crisis. We argue that the human–nature dualism, a product of Enlightenment thought and primarily responsible for the ecological crisis, cannot be the basis for any meaningful solutions. We show how more recent Western imaginaries like the Anthropocene and Gaia proposed to overcome the separation of nature from culture are also based on exclusions that reflect Enlightenment rationality and legacies of colonialism. In sharp contrast, we show that Indigenous philosophies that preceded the Enlightenment by thousands of years have developed systems of knowledge based on a relational ontology that reflects profound connections between humans and nature. We demonstrate that such forms of knowledge have been systematically subjugated by Western scholarship based on arguments inspired by Enlightenment ideals of rationality and empiricism. A decolonial imagination will be able to generate new insights into understanding and addressing the ecological crisis. We therefore call for organization and management scholars to challenge the anthropomorphic biases and the economism that dominates our field through a respectful engagement with Indigenous worldviews.
Torque teno mini virus as a cause of childhood acute promyelocytic leukemia lacking PML/RARA fusion
Authors: Astolfi Annalisa , Masetti Riccardo , Indio Valentina , Bertuccio Salvatore Nicola , Messelodi Daria , Rampelli Simone , Leardini Davide , Carella Matteo , Serravalle Salvatore , Libri Virginia , Bandini Jessica , Volinia Stefano , Candela Marco , Pession Andrea
Published: August 2021

Astolf et al provide the first report of acute promyelocytic leukemia driven by viral insertion into the RARA locus. This represents a clear demonstration of a pathology driven by the member of the anelloviruses, a group of viruses otherwise thought to have minimal or no pathogenic potential.
TLR7 ligation augments hematopoiesis in Rps14 (uS11) deficiency via paradoxical suppression of inflammatory signaling
Authors: Peña Oscar A. , Lubin Alexandra , Hockings Catherine , Rowell Jasmine , Jung Youngrock , Hoade Yvette , Dace Phoebe , Valdivia Leonardo E. , Tuschl Karin , Böiers Charlotta , Virgilio Maria C. , Richardson Simon , Payne Elspeth M.
Published: August 2021

Myelodysplastic syndrome (MDS) is a hematological malignancy characterized by blood cytopenias and predisposition to acute myeloid leukemia (AML). Therapies for MDS are lacking, particularly those that have an impact in the early stages of disease. We developed a model of MDS in zebrafish with knockout of Rps14, the primary mediator of the anemia associated with del(5q) MDS. These mutant animals display dose- and age-dependent abnormalities in hematopoiesis, culminating in bone marrow failure with dysplastic features. We used Rps14 knockdown to undertake an in vivo small-molecule screening, to identify compounds that ameliorate the MDS phenotype, and we identified imiquimod, an agonist of Toll-like receptor-7 (TLR7) and TLR8. Imiquimod alleviates anemia by promoting hematopoietic stem and progenitor cell expansion and erythroid differentiation, the mechanism of which is dependent on TLR7 ligation and Myd88. TLR7 activation in this setting paradoxically promoted an anti-inflammatory gene signature, indicating cross talk via TLR7 between proinflammatory pathways endogenous to Rps14 loss and the NF-κB pathway. Finally, in highly purified human bone marrow samples from anemic patients, imiquimod led to an increase in erythroid output from myeloerythroid progenitors and common myeloid progenitors. Our findings have both specific implications for the development of targeted therapeutics for del(5q) MDS and wider significance identifying a potential role for TLR7 ligation in modifying anemia.
Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case
Authors: Penter Livius , Gohil Satyen H. , Huang Teddy , Thrash Emily M. , Schmidt Dominik , Li Shuqiang , Severgnini Mariano , Neuberg Donna , Hodi F. Stephen , Livak Kenneth J. , Zeiser Robert , Bachireddy Pavan , Wu Catherine J.
Published: August 2021

Relapse of myeloproliferative neoplasms (MPNs) after allogeneic hematopoietic stem cell transplantation (HSCT) is associated with poor outcomes, as therapeutic approaches to reinstate effective graft-versus-leukemia (GVL) responses remain suboptimal. Immune escape through overexpression of PD-L1 in JAK2V617F-mutated MPN provides a rationale for therapeutic PD-1 blockade, and indeed, clinical activity of nivolumab in relapsed MPN post-HSCT has been observed. Elucidation of the features of response following PD-1 blockade in such patients could inform novel therapeutic concepts that enhance GVL. Here, we report an integrated high-dimensional analysis using single-cell RNA sequencing, T-cell receptor sequencing, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and assay for transposase-accessible chromatin using sequencing (scATAC-seq), together with mass cytometry, in peripheral blood mononuclear cells collected at 6 timepoints before, during, and after transient response to PD-1 blockade from an index case of relapsed MPN following HSCT. Before nivolumab infusion, acute myeloid leukemia (AML) blasts demonstrated high expression of chemokines, and T cells were characterized by expression of interferon-response genes. This baseline inflammatory signature disappeared after nivolumab infusion. Clinical response was characterized by transient expansion of a polyclonal CD4+ T-cell population and contraction of an AML subpopulation that exhibited megakaryocytic features and elevated PD-L1 expression. At relapse, the proportion of the AML subpopulation with progenitor-like features progressively increased, suggesting coevolution of AML blasts and donor-derived T cells. We thus demonstrate how single-cell technologies can provide complementary insight into cellular mechanisms underlying response to PD-1 blockade, motivating future longitudinal high-dimensional single-cell studies of GVL responses in relapsed myeloid disease.
Fast and SNP-aware short read alignment with SALT
Authors: Quan Wei , Liu Bo , Wang Yadong
Published: August 2021

Background

DNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies. The accuracy of sequence alignments directly affects the accuracy of downstream analyses, such as variant calling and quantitative analysis of transcriptome; therefore, rapidly and accurately mapping reads to a reference genome is a significant topic in bioinformatics. Conventional DNA read aligners map reads to a linear reference genome (such as the GRCh38 primary assembly). However, such a linear reference genome represents the genome of only one or a few individuals and thus lacks information on variations in the population. This limitation can introduce bias and impact the sensitivity and accuracy of mapping. Recently, a number of aligners have begun to map reads to populations of genomes, which can be represented by a reference genome and a large number of genetic variants. However, compared to linear reference aligners, an aligner that can store and index all genetic variants has a high cost in memory (RAM) space and leads to extremely long run time. Aligning reads to a graph-model-based index that includes all types of variants is ultimately an NP-hard problem in theory. By contrast, considering only single nucleotide polymorphism (SNP) information will reduce the complexity of the index and improve the speed of sequence alignment.

Results

The SNP-aware alignment tool (SALT) is a fast, memory-efficient, and SNP-aware short read alignment tool. SALT uses 5.8 GB of RAM to index a human reference genome (GRCh38) and incorporates 12.8M UCSC common SNPs. Compared with a state-of-the-art aligner, SALT has a similar speed but higher accuracy.

Conclusions

Herein, we present an SNP-aware alignment tool (SALT) that aligns reads to a reference genome that incorporates an SNP database. We benchmarked SALT using simulated and real datasets. The results demonstrate that SALT can efficiently map reads to the reference genome with significantly improved accuracy. Incorporating SNP information can improve the accuracy of read alignment and can reveal novel variants. The source code is freely available at https://github.com/weiquan/SALT.
TLGP: a flexible transfer learning algorithm for gene prioritization based on heterogeneous source domain
Authors: Wang Yan , Xia Zuheng , Deng Jingjing , Xie Xianghua , Gong Maoguo , Ma Xiaoke
Published: August 2021

Background

Gene prioritization (gene ranking) aims to obtain the centrality of genes, which is critical for cancer diagnosis and therapy since keys genes correspond to the biomarkers or targets of drugs. Great efforts have been devoted to the gene ranking problem by exploring the similarity between candidate and known disease-causing genes. However, when the number of disease-causing genes is limited, they are not applicable largely due to the low accuracy. Actually, the number of disease-causing genes for cancers, particularly for these rare cancers, are really limited. Therefore, there is a critical needed to design effective and efficient algorithms for gene ranking with limited prior disease-causing genes.

Results

In this study, we propose a transfer learning based algorithm for gene prioritization (called TLGP) in the cancer (target domain) without disease-causing genes by transferring knowledge from other cancers (source domain). The underlying assumption is that knowledge shared by similar cancers improves the accuracy of gene prioritization. Specifically, TLGP first quantifies the similarity between the target and source domain by calculating the affinity matrix for genes. Then, TLGP automatically learns a fusion network for the target cancer by fusing affinity matrix, pathogenic genes and genomic data of source cancers. Finally, genes in the target cancer are prioritized. The experimental results indicate that the learnt fusion network is more reliable than gene co-expression network, implying that transferring knowledge from other cancers improves the accuracy of network construction. Moreover, TLGP outperforms state-of-the-art approaches in terms of accuracy, improving at least 5%.

Conclusion

The proposed model and method provide an effective and efficient strategy for gene ranking by integrating genomic data from various cancers.
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data
Authors: Untergasser Andreas , Ruijter Jan M. , Benes Vladimir , van den Hoff Maurice J. B.
Published: August 2021

Background

The analyses of amplification and melting curves have been shown to provide valuable information on the quality of the individual reactions in quantitative PCR (qPCR) experiments and to result in more reliable and reproducible quantitative results.

Implementation

The main steps in the amplification curve analysis are (1) a unique baseline subtraction, not using the ground phase cycles, (2) PCR efficiency determination from the exponential phase of the individual reactions, (3) setting a common quantification threshold and (4) calculation of the efficiency-corrected target quantity with the common threshold, efficiency per assay and Cq per reaction. The melting curve analysis encompasses smoothing of the observed fluorescence data, normalization to remove product-independent fluorescence loss, peak calling and assessment of the correct peak by comparing its melting temperature with the known melting temperature of the intended amplification product.

Results

The LinRegPCR web application provides visualization and analysis of a single qPCR run. The user interface displays the analysis results on the amplification curve analysis and melting curve analysis in tables and graphs in which deviant reactions are highlighted. The annotated results in the tables can be exported for calculation of gene-expression ratios, fold-change between experimental conditions and further statistical analysis. Web-based LinRegPCR addresses two types of users, wet-lab scientists analyzing the amplification and melting curves of their own qPCR experiments and bioinformaticians creating pipelines for analysis of series of qPCR experiments by splitting its functionality into a stand-alone back-end RDML (Real-time PCR Data Markup Language) Python library and several companion applications for data visualization, analysis and interactive access. The use of the RDML data standard enables machine independent storage and exchange of qPCR data and the RDML-Tools assist with the import of qPCR data from the files exported by the qPCR instrument.

Conclusions

The combined implementation of these analyses in the newly developed web-based LinRegPCR (https://www.gear-genomics.com/rdml-tools/) is platform independent and much faster than the original Windows-based versions of the LinRegPCR program. Moreover, web-based LinRegPCR includes a novel statistical outlier detection and the combination of amplification and melting curve analyses allows direct validation of the amplification product and reporting of reactions that amplify artefacts.
Integrative analysis of metabolome and transcriptome profiles provides insight into the fruit pericarp pigmentation disorder caused by ‘Candidatus Liberibacter asiaticus’ infection
Authors: Wang Feiyan , Wu Yunli , Wu Wen , Huang Yongjing , Zhu Congyi , Zhang Ruimin , Chen Jiezhong , Zeng Jiwu
Published: August 2021

Background

Mandarin ‘Shatangju’ is susceptible to Huanglongbing (HLB) and the HLB-infected fruits are small, off-flavor, and stay-green at the maturity period. To understand the relationship between pericarp color and HLB pathogen and the effect mechanism of HLB on fruit pericarp coloration, quantitative analyses of HLB bacterial pathogens and carotenoids and also the integrative analysis of metabolome and transcriptome profiles were performed in the mandarin ‘Shatangju’ variety with four different color fruits, whole green fruits (WGF), top-yellow and base-green fruits (TYBGF), whole light-yellow fruits (WLYF), and whole dark-yellow fruits (WDYF) that were infected with HLB.

Results

the HLB bacterial population followed the order WGF > TYBGF > WLYF > WDYF. And there were significant differences between each group of samples. Regarding the accumulation of chlorophyll and carotenoid, the chlorophyll-a content in WGF was the highest and in WDYF was the lowest. The content of chlorophyll-b in WGF was significantly higher than that in other three pericarps. There were significant differences in the total content of carotenoid between each group. WGF and TYBGF pericarps were low in phytoene, γ-carotene, β-cryptoxanthin and apocarotenal, while other kinds of carotenoids were significantly higher than those in WDYF. And WLYF was only short of apocarotenal. We comprehensively compared the transcriptome and metabolite profiles of abnormal (WGF, TYBGF and WLYF) and normal (WDYF, control) pericarps. In total, 2,880, 2,782 and 1,053 differentially expressed genes (DEGs), including 121, 117 and 43 transcription factors were identified in the three comparisons, respectively. The qRT-PCR confirmed the expression levels of genes selected from transcriptome. Additionally, a total of 77 flavonoids and other phenylpropanoid-derived metabolites were identified in the three comparisons. Most (76.65 %) showed markedly lower abundances in the three comparisons. The phenylpropanoid biosynthesis pathway was the major enrichment pathway in the integrative analysis of metabolome and transcriptome profiles.

Conclusions

Synthesizing the above analytical results, this study indicated that different color pericarps were associated with the reduced levels of some carotenoids and phenylpropanoids derivatives products and the down-regulation of proteins in flavonoids, phenylpropanoids derivatives biosynthesis pathway and the photosynthesis-antenna proteins.
Positive DAT-SCAN in SPG7: a case report mimicking possible MSA-C
Authors: Bellini Gabriele , Del Prete Eleonora , Unti Elisa , Frosini Daniela , Siciliano Gabriele , Ceravolo Roberto
Published: August 2021

Background

Spastic Paraplegia type 7 (SPG7) is one of the most common autosomal recessive Hereditary Spastic Paraplegias (HSP); Spastic Paraplegias (SPGs) can present as hereditary ataxias. However, ataxia is frequently the symptom of presentation of many other hereditary/sporadic disorders, such as Multiple system atrophy type C (MSA-C), an α-synuclein sporadic neurodegenerative disorder, in which cerebellar ataxia is one of the main clinical features. Dopamine Transporter imaging (DAT-SCAN), associated with clinical features, can be a helpful tool in order to distinguish MSA-C from other causes of ataxia.

Case-presentation

We present the case of a 70-year-old man with gait difficulties over a period of 3 years and frequent backward/lateral falls. He also reported urinary urge incontinence, but no symptoms that are compatible with orthostatic hypotension. On neurological examination he showed ataxic gait, spasticity in the left lower limb and trunk and limb ataxia, especially on the left side. Mild hypokinesia was found in all 4 limbs, especially in the left foot. MRI revealed atrophy of the cerebellar hemispheres and vermis. DAT-SCAN imaging revealed bilateral nigro-striatal degeneration, which was compatible with a diagnosis of possible MSA-C. Considering the atypical disease course (the patient walked without any support after 3 years), we carried out a genetic investigation for Ataxia, and a mutation in SPG7 was found.

Conclusions

DAT-SCAN imaging, evaluated together with the clinical findings, can be useful for differentiating MSA from other possible causes of adult-onset Ataxia. Indeed, patients with MSA-C generally show a decreased uptake of dopamine transporters in DAT-SCAN imaging. Ours is the first case reported in the literature of a patient with SPG7 mutation with nigrostriatal degeneration and a clinical presentation of a possible MSA-C. Performing genetic investigations in patients with an atypical disease course is important to avoid MSA-mimicries.

Identifying the correct diagnosis is important not only for prognostic reasons, but also for possible future genetic therapies.
Comprehensive analysis of coagulation indices for predicting survival in patients with biliary tract cancer
Authors: Ke Xindi , Jin Bao , You Wen , Chen Yang , Xu Haifeng , Zhao Haitao , Lu Xin , Sang Xinting , Zhong Shouxian , Yang Huayu , Mao Yilei , Du Shunda
Published: August 2021

Background

Abnormal activation of the coagulation system has been reported in patients with malignancies, but its prognostic significance in biliary tract cancer (BTC) remains unclear. This study aims to analyze and compare the prognostic value of coagulation indices in patients with BTC.

Methods

The medical records of 450 patients with BTC who underwent surgical resection at our hospital between 2003 and 2017 were retrospectively analyzed. Time-dependent receiver operating characteristic curves were plotted to compare the predictive accuracy of coagulation indices. A predictive nomogram for overall survival (OS) was established based on the Cox regression analysis and validated in both the training and validation cohorts. A novel stratification model was created according to the total points of the nomogram.

Results

Fibrinogen and international normalized ratio (INR) had the best predictive accuracy among the coagulation indices considered and were also the independent prognostic factors for OS. The nomogram and the novel stratification model had satisfactory performance and outperformed TNM staging.

Conclusions

The study demonstrated that coagulation indices are valuable in predicting OS in BTC, with fibrinogen and INR having the best predictive ability. The nomogram and the novel stratification model could be applied to predict survival for patients with BTC.
Prognostic role of DFNA5 in head and neck squamous cell carcinoma revealed by systematic expression analysis
Authors: Liu Zhiguo , Liu Hongyan , Dong Qian , Li Hongyu , Zhang Bin , Liu Yufeng , Zhong Limei , Tang Haikuo
Published: August 2021

Background

The gasdermin E gene (GSDME, also known as DFNA5) is mutated in familial aging-related hearing loss. Recent studies have also revealed that the expression of DFNA5 is suppressed in many cancer types; however, little is known about the function of DFNA5 in head and neck squamous cell carcinoma (HNSCC). Accordingly, the aim of the present study was to evaluate the expression of DFNA5 and explore its prognostic value in HNSCC.

Result

We used a set of bioinformatics tools, including Oncomine, TIMER, TISIDB, cBioPortal, and GEPIA, to analyze the expression of DFNA5 in patients with HNSCC from public databases. Kaplan-Meier plotter was used to evaluate the potential prognostic significance of DFNA5. DFNA5 mRNA levels were significantly higher in HNSCC tissues than in normal tissues, and high DFNA5 expression was correlated with worse survival. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that DFNA5 expression has a strong positive correlation with cell adhesion and the integrin signaling pathway, whereas its expression was negatively correlated with the levels of infiltrating B cells (cor = − 0.223, P = 8.57e-07) and CD8 T cells (cor = − 0.223, P = 2.99e-07).

Conclusion

This study demonstrates that DFNA5 expression has prognostic value for HNSCC patients. Moreover, these results suggest that regulation of lymphocyte infiltration is the mechanism underlying the function of DFNA5 in HNSCC.
Physical growth and neurodevelopment during the first year of life: a cohort study of the Japan Environment and Children’s Study
Authors: Sanefuji Masafumi , Sonoda Yuri , Ito Yoshiya , Ogawa Masanobu , Tocan Vlad , Inoue Hirosuke , Ochiai Masayuki , Shimono Masayuki , Suga Reiko , Senju Ayako , Honjo Satoshi , Kusuhara Koichi , Ohga Shouichi ,   Japan Environment and Children’s Study Group, Kamijima Michihiro , Yamazaki Shin , Ohya Yukihiro , Kishi Reiko , Yaegashi Nobuo , Hashimoto Koichi , Mori Chisato , Ito Shuichi , Yamagata Zentaro , Inadera Hidekuni , Nakayama Takeo , Iso Hiroyasu , Shima Masayuki , Kurozawa Youichi , Suganuma Narufumi , Kusuhara Koichi , Katoh Takahiko
Published: August 2021

Background

The association between a slower physical growth and poorer neurodevelopment has been established in infants born preterm or small for gestational age. However, this association is inconsistent in term-born infants, and detailed investigations in infancy, when intervention is most beneficial for improving outcomes, are lacking. We therefore examined this association separately by sex during the first year of life in term-born infants.

Methods

Using data collected until children reached 12 months old in an ongoing prospective cohort of the Japan Environment and Children’s Study, we analyzed 44,264 boys and 42,541 girls with singleton term-birth. The exposure variables were conditional variables that disentangle linear growth from weight gain relative to linear growth, calculated from the length and weight at birth and 4, 7 and 10 months old. Neurodevelopmental delay was identified using the Japanese-translated version of Ages & Stages Questionnaires, third edition.

Results

A reduced risk of neurodevelopmental delay at 6 months old was observed in children with a higher birth weight (adjusted relative risks [aRRs]: 0.91 and 0.93, 95 % confidence intervals [95 % CIs]: 0.87–0.96 and 0.88–0.98 in boys and girls, respectively) and increased linear growth between 0 and 4 months old (aRRs: 0.85 and 0.87, 95 % CIs: 0.82–0.88 and 0.83–0.91 in boys and girls, respectively). A reduced risk at 12 months was found in children with an increased linear growth between 0 and 4 months (aRRs: 0.92 and 0.90, 95 % CIs: 0.87–0.98 and 0.84–0.96 in boys and girls, respectively), boys with an increased relative weight gain between 0 and 4 months (aRR: 0.90, 95 % CI: 0.84–0.97), and girls with a higher birth weight (aRR: 0.89, 95 % CI: 0.83–0.96).

Conclusions

These results suggest that a slow physical growth by four months old may be a predictor of neurodevelopmental delay during infancy.
Analysis of tweets on toothache during the COVID-19 pandemic using the CrystalFeel algorithm: a cross-sectional study
Authors: Altan Halenur , Coşgun Alem
Published: August 2021

Background

Reasons such as the lack of information on the COVID-19 disease, lack of proven treatment for it, uncertainty about the duration of the pandemic, or social isolation affect people’s mental health. This study aimed to analyze the emotional type and intensity in tweets on toothache posted during the COVID-19 pandemic.

Methods

Using the Twitter Search API, we collected tweets in English associated with the keywords “Corona, Toothache” “Corona, Tooth, Pain” “Corona, Dental Pain” “Covid-19, Toothache” “Covid-19, Tooth, Pain” and “Covid-19, Dental Pain” posted between March 11, 2020 and June 30, 2020 all around the world. After the relevant inclusion and exclusion criteria were applied, 426 posts were selected and analyzed using the CrystalFeel algorithm, a sensitivity analytical technology with proven accuracy. The chi-square test (SPSS v23, IBM) was used to compare emotions and emotional intensities according to the words used.

Results

It was determined that 80.3% of the participants experienced fear and 61.7% had a negative emotional intensity. There was no statistically significant difference between the distributions of emotions according to the words without time distinction (p = 0.136). There was a statistically significant difference between the distributions of emotional intensity according to the words without time distinction (p = 0.006). The keyword “Corona, Toothache” was used the most frequently by 30.8% of the participants.

Conclusions

This study is the first to analyze the emotional reactions of individuals who experienced toothaches during the COVID-19 pandemic using the CrystalFeel algorithm. Monitoring the social media posts of individuals experiencing toothache during the pandemic will help reduce fear and anger emotions and design public information messages that are compatible with the target group’s needs.