bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of open search methods based on theoretical mass spectra comparison
Authors: Lysiak Albane , Fertin Guillaume , Jean Géraldine , Tessier Dominique 
Published: April 2021

Abstract
Background
Mass spectrometry remains the privileged method to characterize proteins. Nevertheless, most of the spectra generated by an experiment remain unidentified after their analysis, mostly because of the modifications they carry. Open Modification Search (OMS) methods offer a promising answer to this problem. However, assessing the quality of OMS identifications remains a difficult task.

Methods
Aiming at better understanding the relationship between (1) similarity of pairs of spectra provided by OMS methods and (2) relevance of their corresponding peptide sequences, we used a dataset composed of theoretical spectra only, on which we applied two OMS strategies. We also introduced two appropriately defined measures for evaluating the above mentioned spectra/sequence relevance in this context: one is a color classification representing the level of difficulty to retrieve the proper sequence of the peptide that generated the identified spectrum ; the other, called LIPR, is the proportion of common masses, in a given Peptide Spectrum Match (PSM), that represent dissimilar sequences. These two measures were also considered in conjunction with the False Discovery Rate (FDR).

Results
According to our measures, the strategy that selects the best candidate by taking the mass difference between two spectra into account yields better quality results. Besides, although the FDR remains an interesting indicator in OMS methods (as shown by LIPR), it is questionable: indeed, our color classification shows that a non negligible proportion of relevant spectra/sequence interpretations corresponds to PSMs coming from the decoy database.

Conclusions
The three above mentioned measures allowed us to clearly determine which of the two studied OMS strategies outperformed the other, both in terms of number of identifications and of accuracy of these identifications. Even though quality evaluation of PSMs in OMS methods remains challenging, the study of theoretical spectra is a favorable framework for going further in this direction.
Euler diagrams drawn with ellipses area-proportionally (Edeap)
Authors: Wybrow Michael , Rodgers Peter , Dib Fadi K. 
Published: April 2021

AbstractBackgroundArea-proportional Euler diagrams are frequently used to visualize data from Microarray experiments, but are also applied to a wide variety of other data from biosciences, social networks and other domains.ResultsThis paper details Edeap, a new simple, scalable method for drawing area-proportional Euler diagrams with ellipses. We use a search-based technique optimizing a multi-criteria objective function that includes measures for both area accuracy and usability, and which can be extended to further user-defined criteria. The Edeap software is available for use on the web, and the code is open source. In addition to describing our system, we present the first extensive evaluation of software for producing area-proportional Euler diagrams, comparing Edeap to the current state-of-the-art; circle-based method, venneuler, and an alternative ellipse-based method, eulerr.ConclusionsOur evaluation—using data from the Gene Ontology database via GoMiner, Twitter data from the SNAP database, and randomly generated data sets—shows an ordering for accuracy (from best to worst) of eulerr, followed by Edeap and then venneuler. In terms of runtime, the results are reversed with venneuler being the fastest, followed by Edeap and finally eulerr. Regarding scalability, eulerr cannot draw non-trivial diagrams beyond 11 sets, whereas no such limitation is present in Edeap or venneuler, both of which draw diagrams up to the tested limit of 20 sets.
Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment
Authors: Chen Zhiwei , Zhou Longhua , Jiang Panpan , Lu Ruiju , Halford Nigel G. , Liu Chenghong 
Published: April 2021

AbstractBackgroundSucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies,SnRK1,SnRK2andSnRK3, of whichSnRK2andSnRK3are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe theSnRKgene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments.ResultsThe barleyHvSnRKgene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to theHvSnRK1subfamily, 10 toHvSnRK2and 34 toHvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50SnRKgenes in rice (fourOsSnRK1, 11OsSnRK2and 35OsSnRK3) and 39 in Arabidopsis (threeAtSnRK1, 10AtSnRK2and 26AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of theHvSnRKgenes responded to ABA, some positively, some negatively and some with complex time-dependent responses.ConclusionsThe barleyHvSnRKgene family is large, comprising 50 members, subdivided intoHvSnRK1(6 members),HvSnRK2(10 members) andHvSnRK3(34 members), showing differential positive and negative responses to ABA.
A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes
Authors: Strillacci Maria G. , Moradi-Shahrbabak Hossein , Davoudi Pourya , Ghoreishifar Seyed Mohammad , Mokhber Mahdi , Masroure Anoar Jamai , Bagnato Alessandro 
Published: April 2021

Abstract
Background
In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K.

Results
CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database.

Conclusions
This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo’s natural adaptive history together to a recent selection for milk used as primary food source from this species.
Draft genome of a biparental beetle species, Lethrus apterus
Authors: Nagy Nikoletta A. , Rácz Rita , Rimington Oliver , Póliska Szilárd , Orozco-terWengel Pablo , Bruford Michael W. , Barta Zoltán 
Published: April 2021

AbstractBackgroundThe lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality.Lethrus apterusis one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring.ResultsHere, we report the draft genome ofL. apterus, the first genome in the family Geotrupidae. The final assembly consisted of 286.93 Mbp in 66,933 scaffolds. Completeness analysis found the assembly contained 93.5% of the Endopterygota core BUSCO gene set. Ab initio gene prediction resulted in 25,385 coding genes, whereas homology-based analyses predicted 22,551 protein coding genes. After merging, 20,734 were found during functional annotation. Compared to other publicly available beetle genomes, 23,528 genes among the predicted genes were assigned to orthogroups of which 1664 were in species-specific groups. Additionally, reproduction related genes were found among the predicted genes based on which a reduction in the number of odorant- and pheromone-binding proteins was detected.ConclusionsThese genes can be used in further comparative and functional genomic researches which can advance our understanding of the genetic basis and hence the evolution of parental behaviour.
May direct-to-consumer genetic testing have an impact on general practitioners’ daily practice? a cross-sectional study of patients’ intentions towards this approach
Authors: Cohidon Christine , Cardinaux Regula , Cornuz Jacques , Chenal Robin , Desvergne Béatrice , Guessous Idris , Cerqui Daniela , Widmer Daniel 
Published: April 2021

AbstractBackgroundDirect-to-consumer genetic testing (DTCGT) offers individuals access to information on their probable risks of suffering from a wide range of chronic diseases. General practitioners (GPs) will probably play a major role in supporting its use, but patients’ perception of DTCGT remain unclear. This study aimed to describe those attitudes and expectations and how they might affect GPs’ daily practices.MethodsIn 2018–2019, a study related to the use of DTCGT for preventive care in general medicine was conducted among patients in Switzerland’s French-speaking areas. Data were collected in the waiting room using a self-administrated questionnaire about patients’ interest in DTCGT and what their attitudes might be if testing revealed an elevated risk of diabetes, colorectal cancer, or Alzheimer’s disease.ResultsAbout 40% of the 929 participating (participation rate about 80%) patients had heard about DTCGT and, once the test had been explained, 43% reported that they would be interested in being tested. If that testing suggested an elevated risk of disease, the majority of patients reported that they would change their lifestyle (65%–81%, depending on the disease), request more examinations (63%–77%), and expect changes in their GP’s follow-up (48%–59%). Personal characteristics such as sex, age, urbanity, marital status, and perceived health were factors predictive of patients’ attitudes.ConclusionFindings indicated that the generalization of DTCGT might affect GPs’ daily practices in terms of workload and knowledge about this approach. However, this result must be qualified by the fact that it is based on hypothetical situations.
Establishing content validity for a composite activities-specific risk of falls scale:linkage between fear of falling and physical activity
Authors: Wang Jing X. , Chen Lin Y. , Jiang Yan N. , Ni Ling , Sheng Jie M. , Shen Xia 
Published: April 2021

Abstract
Background
Fear of falling (FoF) and physical activity (PA) are important psychological and behavioral factors associated with falls. No instrument quantifies the link between these two factors to evaluate the risk of falls. We aimed to design a scale linking FoF with PA (Composite Activities-specific Risk of Falls Scale, CARFS) for people with various disability levels.

Methods
First, we designed a questionnaire comprising 40 balance-related activities from the International Classification of Functioning, Disability, and Health (ICF) for a pilot survey. Second, participants were interviewed about their activities-specific FoF degree and PA frequency. The participants comprised 30 community-dwelling older adults, hospitalized patients with strokes, and those with spinal cord injuries, each with different disability levels. Third, the content validity of the items was evaluated twice by 12 experienced rehabilitation professionals: one based on experience and the other on the survey responses. Items with a higher than moderate relevance in both evaluations were included in the CARFS. The panel of professionals discussed and voted on the contribution of FoF and PA on the CARF score. Finally, the scale sensitivity in distinguishing disability levels was analyzed to evaluate the population suitability to the CARFS.

Results
The CARFS included 14 activities. A five-point Likert scale was used to quantify degree of FoF (A) and frequency of PA (B). The CARF score (C), which was determined using the eq. C = A+(4-B) + A × B/2, reflected sensitivity to disability levels in most items.

Conclusions
The CARFS has strong content validity for measuring risk of falls in relation to the FoF and PA of people with various disability levels. It has a potential to provide a guide for designing individualized exercise- and behavior-focused fall prevention programs and enable the precise trtrun 0acking of program effectiveness as a multidimensional outcome measure.
Retrospective study revealed that Zn relate to improvement of swallowing function in the older adults
Authors: Seki Yumika , Ishizawa Kota , Akaishi Tetsuya , Abe Michiaki , Okamoto Koji , Tanaka Junichi , Arita Ryutaro , Takayama Shin , Kikuchi Akiko , Miyazaki Mariko , Harigae Hideo , Sato Mayumi , Hoshi Masaya , Hatsugai Kazuaki , Ishii Tadashi 
Published: April 2021

Abstract
Background
Zinc is an essential micronutrient for maintaining biological activity. The level of zinc in the blood is known to decrease with age, especially in those over 75 years of age. In older adults patients with impaired functional status, aspiration pneumonia based on dysphagia often becomes problematic. However, the relationship between zinc deficiency and swallowing function has not been studied before.

Methods
A total of 52 older adults subjects (15 males and 37 females) living in a nursing home were enrolled for this study. At the time of enrollment, data of gender, age, body weight, serum zinc levels, serum albumin levels, and the time in a simple 2-step swallowing provocation test (S-SPT) were collected. In patients with serum zinc levels < 60 μg/dL, we initiated 2 months of oral zinc supplementation therapy with a 34 mg/day zinc load. Those who underwent zinc supplementation were re-evaluated after the treatment period and serum zinc levels and S-SPT time were measured.

Results
At the time of enrollment, serum zinc level was significantly correlated with serum albumin levels (Pearson’s R = 0.58, p < 0.0001) and time in the S-SPT (Spearman’s rho = − 0.32, p = 0.0219). Twenty-five of the 52 patients had zinc deficiency with a serum zinc level < 60 μg/dL. After 2 months of oral zinc supplementation, both serum zinc levels (p < 0.0001) and time in the S-SPT (p = 0.04) significantly improved. Meanwhile, serum albumin level (p = 0.48) or body weight (p = 0.07) did not significantly change following zinc supplementation. Zinc supplementation significantly improved swallowing function, especially in the older adults who had comorbid dysphagia and zinc deficiency.

Conclusions
Zinc deficiency is associated with compromised swallowing function in older adults patients with impaired general functions. Oral zinc supplementation can alleviate dysphagia in older adults patients with zinc deficiency even though this is a retrospective study. Further study will be needed to confirm this positive effect.
Diagnostic value of neutrophil CD64, procalcitonin, and interleukin-6 in sepsis: a meta-analysis
Authors: Cong Shan , Ma Tiangang , Di Xin , Tian Chang , Zhao Min , Wang Ke 
Published: April 2021

Abstract
Background
The aim of the study was to conduct a meta-analysis to evaluate the accuracy of neutrophil CD64, procalcitonin (PCT), and interleukin-6 (IL-6) as markers for the diagnosis of sepsis in adult patients.

Methods
Various databases were searched to collect published studies on the diagnosis of sepsis in adult patients using neutrophil CD64, PCT, and IL-6 levels. Utilizing the Stata SE 15.0 software, forest plots and the area under the summary receiver operating characteristic curves were drawn. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the curve (AUC) were calculated.

Results
Fifty-four articles were included in the study. The pooled sensitivity, specificity, and AUC of neutrophil CD64 for the diagnosis of sepsis were 0.88 (95% confidence interval [CI], 0.81–0.92), 0.88 (95% CI, 0.83–0.91), and 0.94 (95% CI, 0.91–0.96), respectively. The pooled sensitivity, specificity, and AUC of PCT for the diagnosis of sepsis were 0.82 (95% CI, 0.78–0.85), 0.78 (95% CI, 0.74–0.82), and 0.87 (95% CI, 0.83–0.89), respectively. Subgroup analysis showed that the AUC for PCT diagnosis of intensive care unit (ICU) sepsis was 0.86 (95% CI, 0.83–0.89) and the AUC for PCT diagnosis of non-ICU sepsis was 0.82 (95% CI, 0.78–0.85). The pooled sensitivity, specificity, and AUC of IL-6 for the diagnosis of sepsis were 0.72 (95% CI, 0.65–0.78), 0.70 (95% CI, 0.62–0.76), and 0.77 (95% CI, 0.73–0.80), respectively.

Conclusions
Of the three biomarkers studied, neutrophil CD64 showed the highest diagnostic value for sepsis, followed by PCT, and IL-6. On the other hand, PCT showed a better diagnostic potential for the diagnosis of sepsis in patients with severe conditions compared with that in patients with non-severe conditions.
The frequency of cytomegalovirus non-ELR UL146 genotypes in neonates with congenital CMV disease is comparable to strains in the background population
Authors: Berg Christian , Rosenkilde Mette M. , Benfield Thomas , Nielsen Lene , Sundelin Thomas , Lüttichau Hans R. 
Published: April 2021

Abstract
Background
Congenital cytomegalovirus disease (cCMV) is common and can be fatal or cause severe sequelae. Circulating strains of cytomegalovirus carry a high number of variable or disrupted genes. One of these is UL146, a highly diverse gene with 14 distinct genotypes encoding a CXC-chemokine involved in viral dissemination. UL146 genotypes 5 and 6 lack the conserved ELR motif, potentially affecting strain virulence. Here, we investigate whether UL146 genotypes 5 and 6 were associated with congenital CMV infection.

Methods
Viral DNA was extracted and UL146 sequenced from 116 neonatal dried blood spots (DBS) stored in the Danish National Biobank since 1982 and linked to registered cCMV cases through a personal identifier. These sequences were compared to UL146 control sequences obtained from CMV DNA extracted from 83 urine samples from children with suspected bacterial urinary tract infections.

Results
Three non-ELR UL146 genotypes (5 and 6) were observed among the cases (2.6%) and two were observed among the controls (2.4%; P > 0.99). Additionally, no significant association with cCMV was found for the other 12 genotypes in a post-hoc analysis, although genotype 8 showed a tendency to be more frequent among cases with 12 observations against three (P = 0.10). All fourteen genotypes were found to have little intra-genotype variation. Viral load, gender, and sample age were not found to be associated with any particular UL146 genotype.

Conclusions
No particular UL146 genotype was associated with cCMV in this nationwide retrospective case-control study. Associations between CMV disease and disrupted or polymorph CMV genes among immunosuppressed people living with HIV/AIDS and transplant recipients should be investigated in future studies.
Whole-tumour evaluation with MRI and radiomics features to predict the efficacy of S-1 for adjuvant chemotherapy in postoperative pancreatic cancer patients: a pilot study
Authors: Liang Liang , Ding Ying , Yu Yiyi , Liu Kai , Rao Shengxiang , Ge Yingqian , Zeng Mengsu 
Published: April 2021

Abstract
Background
Multiple guidelines for pancreatic ductal adenocarcinoma (PDAC) suggest that all stages of patients need to receive postoperative adjuvant chemotherapy. S-1 is a recently emerged oral antitumour agent recommended by the guidelines. However, which population would benefit from S-1 needs to be determined, and predictors of chemotherapy response are needed for personalized precision medicine. This pilot study aimed to initially identify whether whole-tumour evaluation with MRI and radiomics features could be used for predicting the efficacy of S-1 and to find potential predictors of the efficacy of S-1 as evidence to assist personalized precision treatment.

Methods
Forty-six patients with PDAC (31 in the primary cohort and 15 in the validation cohort) who underwent curative resection and subsequently adjuvant chemotherapy with S-1 were included. Pre-operative abdominal contrast-enhanced MRI was performed, and radiomics features of the whole PDAC were extracted from the primary cohort. After univariable analysis and radiomics features selection, a multivariable Cox regression model for survival analysis was subsequently used to select statistically significant factors associated with postoperative disease-free survival (DFS). Predictive capacities of the factors were tested on the validation cohort by using Kaplan–Meier method.

Results
Multivariable Cox regression analysis identified the probability of T1WI_NGTDM_Strength and tumour location as independent predictors of the efficacy of S-1 for adjuvant chemotherapy of PDAC (p = 0.005 and 0.013) in the primary cohort, with hazard ratios (HRs) of 0.289 and 0.293, respectively. Further survival analysis showed that patients in the low-T1WI_NGTDM_Strength group had shorter DFS (median = 5.1 m) than those in the high-T1WI_NGTDM_Strength group (median = 13.0 m) (p = 0.006), and patients with PDAC on the pancreatic head exhibited shorter DFS (median = 7.0 m) than patients with tumours in other locations (median = 20.0 m) (p = 0.016). In the validation cohort, the difference in DFS between patients with low-T1WI_NGTDM_Strength and high-T1WI_NGTDM_Strength and the difference between patients with PDAC on the pancreatic head and that in other locations were approved, with marginally significant (p = 0.073 and 0.050), respectively.

Conclusions
Whole-tumour radiomics feature of T1WI_NGTDM_Strength and tumour location were potential predictors of the efficacy of S-1 and for the precision selection of S-1 as adjuvant chemotherapy regimen for PDAC.