bluuebunny/crossref_metadata_2025_split huggingface dataset:
A parameter-free deep embedded clustering method for single-cell RNA-seq data
Authors: Zeng Yuansong , Wei Zhuoyi , Zhong Fengqi , Pan Zixiang , Lu Yutong , Yang Yuedong 
Published: April 2022

Abstract
Clustering analysis is widely used in single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data to discover cell heterogeneity and cell states. While many clustering methods have been developed for scRNA-seq analysis, most of these methods require to provide the number of clusters. However, it is not easy to know the exact number of cell types in advance, and experienced determination is not always reliable. Here, we have developed ADClust, an automatic deep embedding clustering method for scRNA-seq data, which can accurately cluster cells without requiring a predefined number of clusters. Specifically, ADClust first obtains low-dimensional representation through pre-trained autoencoder and uses the representations to cluster cells into initial micro-clusters. The clusters are then compared in between by a statistical test, and similar micro-clusters are merged into larger clusters. According to the clustering, cell representations are updated so that each cell will be pulled toward centers of its assigned cluster and similar clusters, while cells are separated to keep distances between clusters. This is accomplished through jointly optimizing the carefully designed clustering and autoencoder loss functions. This merging process continues until convergence. ADClust was tested on 11 real scRNA-seq datasets and was shown to outperform existing methods in terms of both clustering performance and the accuracy on the number of the determined clusters. More importantly, our model provides high speed and scalability for large datasets.
HLAB: learning the BiLSTM features from the ProtBert-encoded proteins for the class I HLA-peptide binding prediction
Authors: Zhang Yaqi , Zhu Gancheng , Li Kewei , Li Fei , Huang Lan , Duan Meiyu , Zhou Fengfeng 
Published: April 2022

AbstractHuman Leukocyte Antigen (HLA) is a type of molecule residing on the surfaces of most human cells and exerts an essential role in the immune system responding to the invasive items. The T cell antigen receptors may recognize the HLA-peptide complexes on the surfaces of cancer cells and destroy these cancer cells through toxic T lymphocytes. The computational determination of HLA-binding peptides will facilitate the rapid development of cancer immunotherapies. This study hypothesized that the natural language processing-encoded peptide features may be further enriched by another deep neural network. The hypothesis was tested with the Bi-directional Long Short-Term Memory-extracted features from the pretrained Protein Bidirectional Encoder Representations from Transformers-encoded features of the class I HLA (HLA-I)-binding peptides. The experimental data showed that our proposed HLAB feature engineering algorithm outperformed the existing ones in detecting the HLA-I-binding peptides. The extensive evaluation data show that the proposed HLAB algorithm outperforms all the seven existing studies on predicting the peptides binding to the HLA-A*01:01 allele in AUC and achieves the best average AUC values on the six out of the seven k-mers (k=8,9,...,14, respectively represent the prediction task of a polypeptide consisting of k amino acids) except for the 9-mer prediction tasks. The source code and the fine-tuned feature extraction models are available at http://www.healthinformaticslab.org/supp/resources.php.
One among many: the enigmatic case of the Miocene mammal, Kolponomos newportensis
Authors: Modafferi Maria , Melchionna Marina , Castiglione Silvia , Tamagnini Davide , Maiorano Luigi , Sansalone Gabriele , Profico Antonio , Girardi Giorgia , Raia Pasquale 
Published: April 2022

Abstract
Kolponomos newportensis is an enigmatic Miocene mammal allied to stem Pinnipedimorpha. It has been suggested that Kolponomos fed on hard-shelled benthic marine invertebrates by using its mandible as a wedge to dislodge its prey from the sea bottom by means of strong pull and torque forces. This unique feeding style was thought to originate from a singular case of mosaic convergence in mandible biomechanics between Kolponomos and the sabretoothed cat Smilodon, which complied with similarly strong torque forces when grappling with prey. As such forces must have reflected on the cranium as well, we hypothesize that the convergence between Kolponomos and the sabretoothed cats could have affected its shape. To test this hypothesis, we looked for patterns of morphological convergence in cranial shape between Kolponomos and sabretoothed cats. We found that Kolponomos is not distinctly closer to Smilodon than a number of other pinnipeds. Yet, local areas of shape convergence with Smilodon are observed in the canine area and the posterior part of the cranium, that is where the bite applies and the temporalis muscle is located, respectively. These results indicate that the mosaic convergence present between the mandibles of Kolponomos and Smilodon is partially reflected in the cranium as well.
Terrestrialization in gastropods: lineages, ecological constraints and comparisons with other animals
Authors: Vermeij Geerat J , Watson-Zink Victoria M 
Published: April 2022

Abstract
Evolutionary transitions from water to land are infrequent. The physical contrasts between these media are amplified by biological differences in the patterns of selection. A new compilation, based on published phylogenetic and fossil evidence, identifies 30 separate instances of terrestrial colonization by gastropods, at least 12 from the sea and 14 from freshwater. Pre-Cenozoic transitions, mainly from freshwater and all tropical, resulted in high terrestrial diversity. Most Cenozoic colonizations were local, especially on oceanic islands, and yielded few terrestrial species. An increasingly predator-rich terrestrial environment after the Cretaceous made colonization on land unlikely except in cryptic habitats and on islands. Colonization from the sea became possible only in the Cenozoic, when marine lineages became specialized for life on the upper seashore. The results are compared with terrestrial colonizations by other groups of plants and animals.
Training allows switching from limited-capacity manipulations to large-capacity perceptual processing
Authors: Malinovitch Tamar , Albouy Philippe , Zatorre Robert J , Ahissar Merav 
Published: April 2022

AbstractIn contrast to perceptual tasks, which enable concurrent processing of many stimuli, working memory (WM) tasks have a very small capacity, limiting cognitive skills. Training on WM tasks often yields substantial improvement, suggesting that training might increase the general WM capacity. To understand the underlying processes, we trained a test group with a newly designed tone manipulation WM task and a control group with a challenging perceptual task of pitch pattern discrimination. Functional magnetic resonance imaging (fMRI) scans confirmed that pretraining, manipulation was associated with a dorsal fronto-parietal WM network, while pitch comparison was associated with activation of ventral auditory regions. Training induced improvement in each group, which was limited to the trained task. Analyzing the behavior of the group trained with tone manipulation revealed that participants learned to replace active manipulation with a perceptual verification of the position of a single salient tone in the sequence presented as a tentative reply. Posttraining fMRI scans revealed modifications in ventral activation of both groups. Successful WMtrained participants learned to utilize auditory regions for the trained task. These observations suggest that the huge task-specific enhancement of WM capacity stems from a task-specific switch to perceptual routines, implemented in perceptual regions.
Catabolism of sialic acids in an environmental microbial community
Authors: Tomás-Martínez Sergio , Chen Le Min , Neu Thomas R , Weissbrodt David G , van Loosdrecht Mark C M , Lin Yuemei 
Published: April 2022

AbstractSialic acids are a family of nine-carbon negatively charged carbohydrates. In animals, they are abundant on mucosa surfaces as terminal carbohydrates of mucin glycoproteins. Some commensal and pathogenic bacteria are able to release, take up and catabolize sialic acids. Recently, sialic acids have been discovered to be widespread among most microorganisms. Although the catabolism of sialic acids has been intensively investigated in the field of host–microbe interactions, very limited information is available on microbial degradation of sialic acids produced by environmental microorganisms. In this study, the catabolic pathways of sialic acids within a microbial community dominated by ‘Candidatus Accumulibacter’ were evaluated. Protein alignment tools were used to detect the presence of the different proteins involved in the utilization of sialic acids in the flanking populations detected by 16S rRNA gene amplicon sequencing. The results showed the ability of Clostridium to release sialic acids from the glycan chains by the action of a sialidase. Clostridium and Chryseobacterium can take up free sialic acids and utilize them as nutrient. Interestingly, these results display similarities with the catabolism of sialic acids by the gut microbiota. This study points at the importance of sialic acids in environmental communities in the absence of eukaryotic hosts.
Theory-based implementation of physical activity programs in worksite health promotion settings: a systematic review
Authors: Grønningsæter Hilde , Kiland Charlotte 
Published: April 2022

Summary
Worksites are important settings for implementing health promotion programs. Evidence for sustainable upscaling of physical activity (PA) programs and critical evaluation of the implementation process are scarce. In this article, we address the following research questions: (i) To what extent is the implementation process of PA programs theoretically informed? (ii) What characterizes the implementation process of PA programs in theory driven studies? (iii) Which facilitators and barriers are identified in the implementation process and at what level? We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. The databases Medline (Ovid) and Sportdiscuss (Ebsco) were searched for peer-reviewed original articles published in English (2000–2020), from a European, North American, New Zealand and Australian context. Reported implementation components and facilitators/barriers (F/Bs) were detected, interpreted and analyzed according to implementation theory. Appraisal of methodological quality on included studies was executed. Of 767 eligible studies, 17 studies were included, 11 of which conducted a theory-based process evaluation of the implementation. They implemented composite PA programs, at two or more levels with internal or mixed implementation teams. F/Bs were most frequently related to the implementation component ‘fidelity’, corresponding to organizational and implementer level, and the component ‘reach’ corresponding to program and participant level. Notably, only one study reported F/Bs on the socio-political level. Despite more frequent use in recent years of theory-based implementation, few studies reported implementation effectiveness. Major challenges regarding incoherent use of theoretical concepts and scarcity of empirically tested frameworks are discussed.
Evaluating ecosystem impacts of gear regulations in a data-limited fishery—comparing approaches to estimate predator–prey interactions in Ecopath with Ecosim
Authors: Rehren Jennifer , Coll Marta , Jiddawi Narriman , Kluger Lotta Clara , Omar Omar , Christensen Villy , Pennino Maria Grazia , Wolff Matthias 
Published: April 2022

Abstract
Ecosystem models, such as Ecopath with Ecosim (EwE), are useful tools for developing ecosystem-based management strategies. Model development, however, requires data for the estimation of input parameters including time series for calibration. Most small-scale fisheries lack such information, making it difficult to reliably use ecosystem models for management strategy exploration. This is the case for the Chwaka Bay fishery (Zanzibar), where an increase in dragnets has led to concerns for unsustainable development. While EwE could help to explore the impacts of gear regulations in the bay, this is hampered by the lack of time series to estimate the predator–prey interactions (vulnerabilities) in the model. Here, we explore available approaches for estimating the vulnerabilities to simulate the effects of a dragnet prohibition with and without reallocation of fishing effort. Simulations suggest that banning dragnets would be beneficial for the fishing community judged by the increase in biomass of functional groups and fishers’ profits, but not if dragnet fishers were to continue fishing in the bay by reallocating to other gears, indicated by the reduced fish biomass and fishers’ profits. The overall trend (decreasing or increasing) in the changes of functional groups, ecosystem indicators, and profits were relatively consistent across vulnerability settings, illustrating that an unfitted EwE model can be used for qualitative management strategy exploration.
High prevalence of straying in a wild brown trout (Salmo trutta) population in a fjord system
Authors: Källo Kristi , Baktoft Henrik , Kristensen Martin Lykke , Birnie-Gauvin Kim , Aarestrup Kim 
Published: April 2022

Abstract
Natal homing is a prevalent life-history strategy among salmonids. However, not all individuals return to their natal river, a behaviour known as straying. In this study, we investigated the prevalence of straying and its connection to different life-history characteristics in an anadromous brown trout (Salmo trutta) population. In total, 21 538 juvenile out-migrating brown trout were tagged with Passive Integrated Transponder (PIT) tags in two years. Individuals were grouped according to their developmental status (parr, pre-smolt, and smolt) at the time of out-migration to investigate the effect of such life-history characteristic on the likelihood of straying. High number of anadromous brown trout (36%) were detected in non-natal rivers. Individuals spending longer time at sea were less likely to stray. Additionally, the likelihood of straying was dependent on the developmental status during out-migration, with parr having lower likelihood to stray compared to pre-smolt and smolt. However, the latter is further dependent on length and timing of juvenile out-migration. These results indicate that straying is an inherent part of this anadromous brown trout population and it is influenced by several life-history characteristics at different life stages. This may have significant implications to genetic structure within and between populations and to population dynamics.
The fabrication and testing of a self-sensing MWCNT nanocomposite sensor for oil leak detection
Authors: Al-Bahrani Mohammed , Bouaissi Aissa , Cree Alistair 
Published: April 2022

Abstract
Oil spillage, due to either direct or indirect accidents, can cause major environmental and economic issues if not detected and remedied immediately. In this study, the unique properties of carbon nanotubes have shown a substantial sensing capability for such a purpose when incorporated into a nanostructured composite material. A high-efficiency self-sensing nanocomposite sensor was fabricated by inserting highly conductive multi-walled carbon nanotubes (MWCNTs) into an elastomeric polymer substrate. The microstructure of the nanocomposite sensor was studied using scanning electronic microscopy and Raman spectroscopy. The response rate of the sensor was evaluated against different MWCNT concentrations, geometrical thickness and applied strains (causing by stretching). The results indicated that the response rate of the sensor (β) decreased with increasing MWCNT concentration and showed the strongest response when the sensor contained a 1.0 wt % concentration of MWCNTs. Additionally, it was found that the response time of the self-sensing nanocomposite sensors decreased in keeping with decreases in the sensor thickness. Moreover, when the sensor was subjected to strain, while immersed in an oil bath, it was found that the response rate (β) of the unstretched self-sensing nanocomposite sensor was significantly lower than that of the stretched one. The sensors given a 3% applied strain presented a response rate (β) ≈ 7.91 times higher than of the unstretched one. The self-sensing nanocomposite sensor described here shows good potential to be employed for oil leakage detection purposes due to its effective self-damage sensing capability and high sensing efficiency and low power consumption.
Pancreatic Ductal Carcinoma Risk Associated With Hereditary Cancer-Risk Genes
Authors: Gardiner Anna , Kidd John , Elias Maria C , Young Kayla , Mabey Brent , Taherian Nassim , Cummings Shelly , Malafa Mokenge , Rosenthal Eric , Permuth Jennifer B 
Published: April 2022

AbstractBackgroundAlthough several hereditary cancer predisposition genes have been implicated in pancreatic ductal adenocarcinoma (PDAC) susceptibility, gene-specific risks are not well defined and are potentially biased because of the design of previous studies. More precise and unbiased risk estimates can result in screening and prevention better tailored to genetic findings.MethodsThis is a retrospective analysis of 676 667 individuals, 2445 of whom had a personal diagnosis of PDAC, who received multigene panel testing between 2013 and 2020 from a single laboratory. Clinical data were obtained from test requisition forms. Multivariable logistic regression models determined the increased risk of PDAC because of pathogenic variants (PVs) in various genes as adjusted odds ratios (ORs) with 95% confidence intervals (CIs). Multivariable odds ratios were adjusted for age, personal and/or family cancer history, and ancestry.ResultsOverall, 11.1% of patients with PDAC had a PV. Statistically significantly elevated PDAC risk (2-sided P &lt; .05) was observed for CDK2NA (p16INK4a) (OR = 8.69, 95% CI = 4.69 to 16.12), ATM (OR = 3.44, 95% CI = 2.58 to 4.60), MSH2 (OR = 3.17, 95% CI = 1.70 to 5.91), PALB2 (OR = 3.09, 95% CI = 2.02 to 4.74), BRCA2 (OR = 2.55, 95% CI = 1.99 to 3.27), and BRCA1 (OR = 1.62, 95% CI = 1.07 to 2.43).ConclusionsThis study provides PDAC risk estimates for 6 genes commonly included in multigene panel testing for hereditary cancer risk. These estimates are lower than those from previous studies, possibly because of adjustment for family history, and support current recommendations for germline testing in all PDAC patients, regardless of a personal or family history of cancer.
Circular RNA hsa_circ_0026344 suppresses gastric cancer cell proliferation, migration and invasion via the miR-590-5p/PDCD4 axis
Authors: Lv Long , Du Jinghu , Wang Daorong , Yan Zeqiang 
Published: April 2022

Abstract

Objectives
Circular RNA (CircRNA) is a class of non-coding RNA transcripts, with multiple pathophysiological functions. Instead, the mechanism and function of circRNA in gastric cancer (GC) are not fully deciphered.

Methods
CircRNA_0026344 (circ_0026344), microRNA (miR)-590-5p and programmed cell death 4 (PDCD4) mRNA expression levels in GC tissues and cells were probed by quantitative real-time PCR. Cell viability, migration and aggressiveness were examined by cell counting kit-8 and transwell assays. Additionally, the interplay among circ_0026344, miR-590-5p and PDCD4 was verified with bioinformatics and dual-luciferase reporter gene assay. Western blot was conducted to probe PDCD4 protein expression.

Key findings
Circ_0026344 expression was underexpressed in GC tissues and cells, which was associated with clinicopathological characteristics such as tumour size, tumor-node-metastasis stage and lymph node metastasis. Circ_0026344 overexpression restrained the malignant biological behaviours of GC cells, while circ_0026344 knockdown functioned oppositely. Circ_0026344 could act as a competing endogenous RNA of miR-590-5p to negatively modulate its expression, and this miRNA could mitigate the impact of circ_0026344 on GC cells. In addition, PDCD4 was identified as the downstream target of miR-590-5p, and PDCD4 expression was positively modulated by circ_0026344.

Conclusions
Circ_0026344 up-regulates PDCD4 expression via sponging miR-590-5p, thus inhibiting the progression of GC. This study further expounds the underlying molecular mechanism in the GC progression.
Clinical outcomes of extended intralesional curettage with cementation without implant augmentation in non-fracture giant cell tumor of bone around the knee
Authors: Sukpanichyingyong Sermsak , Salang Krits , Sangkomkamhang Thananit 
Published: April 2022

Abstract
There remains a lack of consensus regarding the necessity of implant augmentation or fixation after intralesional curettage in giant cell tumor of bone (GCTB) around the knee. This study assessed whether cementation alone is effective and safe in GCTB with a non-fracture around the knee. We retrospectively examined clinical data from 14 GCTB patients treated from 2012 to 2022. Outcome parameters were Musculoskeletal Tumor Society (MSTS) score, postoperative fracture, metastases, recurrence and complications. Of the 14 GCTB cases examined, 10 were at the distal femur and four were at the proximal tibia. Mean patient age was 32 years, and follow-up time was 61 months. Mean tumor size was 61 × 79 × 50 mm, and MSTS score was 89.2%. There were no cases of postoperative fracture. Defect reconstruction with cementation alone may be strong enough to provide immediate stability and prevent postoperative fracture in GCTB around the knee.
Laparoscopic cholecystectomy for acalculous, gangrenous cholecystitis on an outpatient COVID-19 adult: a case report
Authors: Liapis Stavros Chrysovalantis , Stavrou Alexios , Perivoliotis Konstantinos , Christodoulou Prokopis , Kalodimos Georgios , Kitsakis Georgios , Kapatou Kassiani , Ziamas Dimitrios , Lytras Dimitrios 
Published: April 2022

Abstract
We report the rare case of an acalculous, gangrenous cholecystitis on a, previously healthy, outpatient COVID-19 adult. The 53-year-old patient presented to the emergency department due to epigastric pain and fever and was admitted to the COVID-19 department. Due to clinical and laboratory deterioration, a computed tomography scan was performed that confirmed the diagnosis of acalculous cholecystitis. The patient was submitted to laparoscopic cholecystectomy. Intraoperatively, a gangrenous gallbladder was identified. Immunohistology validated the presence of specimen wall vasculitis and vessel thrombosis.