bluuebunny/crossref_metadata_2025_split huggingface dataset:
IonCRAM: a reference-based compression tool for ion torrent sequence files
Authors: Shokrof Moustafa , Abouelhoda Mohamed 
Published: September 2020

Abstract
Background
Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data. The flow signals occupy a big portion of the BAM file (about 75% for the human genome). Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. However, the tools for generating the CRAM formats are not designed to handle the flow signals. This missing feature has motivated us to develop a new program to improve the compression of the Ion Torrent files for long term archiving.

Results
In this paper, we present IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%.

Conclusions
Reducing the space consumption of NGS data reduces the cost of storage and data transfer. Therefore, developing efficient compression software for clinical NGS data goes beyond the computational interest; as it ultimately contributes to the overall cost reduction of the clinical test. The space saving achieved by our tool is a practical step in this direction. The tool is open source and available at Code Ocean, github, and http://ioncram.saudigenomeproject.com.
Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus)
Authors: Cruz-López Medardo , Fernández Guillermo , Hipperson Helen , Palacios Eduardo , Cavitt John , Galindo-Espinosa Daniel , Gómez del Angel Salvador , Pruner Raya , Gonzalez Oscar , Burke Terry , Küpper Clemens 
Published: September 2020

Abstract
Background
Understanding the structure and variability of adaptive loci such as the major histocompatibility complex (MHC) genes is a primary research goal for evolutionary and conservation genetics. Typically, classical MHC genes show high polymorphism and are under strong balancing selection, as their products trigger the adaptive immune response in vertebrates. Here, we assess the allelic diversity and patterns of selection for MHC class I and class II loci in a threatened shorebird with highly flexible mating and parental care behaviour, the Snowy Plover (Charadrius nivosus) across its broad geographic range.

Results
We determined the allelic and nucleotide diversity for MHC class I and class II genes using samples of 250 individuals from eight breeding population of Snowy Plovers. We found 40 alleles at MHC class I and six alleles at MHC class II, with individuals carrying two to seven different alleles (mean 3.70) at MHC class I and up to two alleles (mean 1.45) at MHC class II. Diversity was higher in the peptide-binding region, which suggests balancing selection. The MHC class I locus showed stronger signatures of both positive and negative selection than the MHC class II locus. Most alleles were present in more than one population. If present, private alleles generally occurred at very low frequencies in each population, except for the private alleles of MHC class I in one island population (Puerto Rico, lineage tenuirostris).

Conclusion
Snowy Plovers exhibited an intermediate level of diversity at the MHC, similar to that reported in other Charadriiformes. The differences found in the patterns of selection between the class I and II loci are consistent with the hypothesis that different mechanisms shape the sequence evolution of MHC class I and class II genes. The rarity of private alleles across populations is consistent with high natal and breeding dispersal and the low genetic structure previously observed at neutral genetic markers in this species.
Optimizing the genetic prediction of the eye and hair color for North Eurasian populations
Authors: Balanovska Elena , Lukianova Elena , Kagazezheva Janet , Maurer Andrey , Leybova Natalia , Agdzhoyan Anastasiya , Gorin Igor , Petrushenko Valeria , Zhabagin Maxat , Pylev Vladimir , Kostryukova Elena , Balanovsky Oleg 
Published: September 2020

Abstract
Background
Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been verified on the West and Central Europeans only, while populations from border regions between Europe and Asia (like Caucasus and Ural) also carry the light pigmentation phenotypes.

Results
We phenotyped 286 samples collected across North Eurasia, genotyped them by the standard HIrisPlex-S markers and found that predictive power in Caucasus/Ural/West Siberian populations is reasonable but lower than that in West Europeans. As these populations have genetic ancestries different from that of West Europeans, we hypothesized they may carry a somewhat different allele spectrum. Thus, for all samples we performed the exome sequencing additionally enriched with the 53 genes and intergenic regions known to be associated with the eye/hair color. Our association analysis replicated the importance of the key previously known SNPs but also identified five new markers whose eye color prediction power for the studied populations is compatible with the two major previously well-known SNPs. Four out of these five SNPs lie within the HERС2 gene and the fifth in the intergenic region. These SNPs are found at high frequencies in most studied populations. The released dataset of exomes from Russian populations can be further used for population genetic and medical genetic studies.

Conclusions
This study demonstrated that precision of the established systems for eye/hair color prediction from a genotype is slightly lower for the populations from the border regions between Europe and Asia that for the West Europeans. However, this precision can be improved if some newly revealed predictive SNPs are added into the panel. We discuss that the replication of these pigmentation-associated SNPs on the independent North Eurasian sample is needed in the future studies.
GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data
Authors: Yang Xingyu , Tipton Christopher M. , Woodruff Matthew C. , Zhou Enlu , Lee F. Eun-Hyung , Sanz Inãki , Qiu Peng 
Published: September 2020

Abstract
Background
B cell affinity maturation enables B cells to generate high-affinity antibodies. This process involves somatic hypermutation of B cell immunoglobulin receptor (BCR) genes and selection by their ability to bind antigens. Lineage trees are used to describe this microevolution of B cell immunoglobulin genes. In a lineage tree, each node is one BCR sequence that mutated from the germinal center and each directed edge represents a single base mutation, insertion or deletion. In BCR sequencing data, the observed data only contains a subset of BCR sequences in this microevolution process. Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes.

Results
We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree nodes. Through comparison using simulated and real data, GLaMST outperforms existing algorithms in simulations with high rates of mutation, insertion and deletion, and generates lineage trees with smaller size and closer to ground truth according to tree features that highly correlated with selection pressure.

Conclusions
GLaMST outperforms state-of-art in reconstruction of the BCR lineage tree in both efficiency and accuracy. Integrating it into existing BCR sequencing analysis frameworks can significant improve lineage tree reconstruction aspect of the analysis.
Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species
Authors: Suntsova Maria V. , Buzdin Anton A. 
Published: September 2020

AbstractChimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5–7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species.
Griseococcin (1) from Bovistella radicata (Mont.) Pat and antifungal activity
Authors: Ye Yong , Zeng Qinghua , Zeng Qingmei 
Published: September 2020

Abstract
Background
To evaluate the antimicrobial and microbicidel activity of B. radicata fermentation broth, the broth was purified by DEAE-cellulose and sephadex LC-20 column. The compounds were submitted to spectral analyses (HPLC, FT-IR, 1D and 2D NMR etc.).

Results
The purified compounds were identified as the Griseococcin(s) which were naphthoquinone derivatives, the Chemical formula and MW of Griseococcin (1) was determined as C37O10H43N and 661 Da. only Griseococcin (1) has good antimicrobial activity among the Griseococcin(s). The zone of inhibition (ZOI), minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) or minimum fungicidal concentration (MFC) of Griseococcin (1) were used to investigate the antimicrobial activity. Antifungal activity of Griseococcin (1) was significant, especially for main pathogenic fungus Trichophyton rubrum and Trichophyton mentagrophytes, MFC/MIC of Griseococcin (1) was 1, while MFC/MIC of postive control was greater than 4, the fungicidal effect of Griseococcin (1) was better than that of positive control.

Conclusions
In this paper, the secondary metabolite compound Griseococcin (1) from B. radicata was purified. The purified compound can restrain main pathogens (T. rubrum and T. mentagrophytes) leading to tinea pedis. The antifungal activity of Griseococcin (1) was similar to that of the positive control and the fungicidal effect of Griseococcin (1) was better than that of positive control, it might be suitable for pharmaceutical industries.
‘Motivational work’: a qualitative study of preventive health dialogues in general practice
Authors: Broholm-Jørgensen Marie , Langkilde Siff Monrad , Tjørnhøj-Thomsen Tine , Pedersen Pia Vivian 
Published: September 2020

Abstract
Background
The aim of this article is to explore preventive health dialogues in general practice in the context of a pilot study of a Danish primary preventive intervention ‘TOF’ (a Danish acronym for ‘Early Detection and Prevention’) carried out in 2016. The intervention consisted of 1) a stratification of patients into one of four groups, 2) a digital support system for both general practitioners and patients, 3) an individual digital health profile for each patient, and 4) targeted preventive services in either general practice or a municipal health center.

Methods
The empirical material in this study was obtained through 10 observations of preventive health dialogues conducted in general practices and 18 semi-structured interviews with patients and general practitioners. We used the concept of ‘motivational work’ as an analytical lens for understanding preventive health dialogues in general practice from the perspectives of both general practitioners and patients.

Results
While the health dialogues in TOF sought to reveal patients’ motivations, understandings, and priorities related to health behavior, we find that the dialogues were treatment-oriented and structured around biomedical facts, numeric standards, and risk factor guidance. Overall, we find that numeric standards and quantification of motivation lessens the dialogue and interaction between General Practitioner and patient and that contextual factors relating to the intervention framework, such as a digital support system, the general practitioners’ perceptions of their professional position as well as the patients’ understanding of prevention —in an interplay—diminished the motivational work carried out in the health dialogues.

Conclusion
The findings show that the influence of different kinds of context adds to the complexity of prevention in the clinical encounter which help to explain why motivational work is difficult in general practice.
Effectiveness of a health-social partnership program for discharged non-frail older adults: a pilot study
Authors: WONG Arkers Kwan Ching , WONG Frances Kam Yuet , NGAI Jenny Sau Chun , HUNG Shirley Yu Kan , LI Wah Chun 
Published: September 2020

Abstract
Background
Previous studies supporting discharged patients are hospital-based which admission criteria tend to include mainly those with complex needs and/or specific disease conditions. This study captured the service gap where these non-frail older patients might have no specific medical problem upon discharge but they might encounter residual health and social issues when returning home.

Methods
Discharged community-dwelling non-frail older adults from an emergency medical ward were recruited and randomized into either intervention (n = 37) or control (n = 38) group. The intervention group received a 12-week complex interventions that included structured assessment, health education, goal empowerment, and care coordination supported by a health-social team. The control group received usual discharge care and monthly social call. The primary outcome was health-related quality of life (HRQoL). Secondary outcomes included activities of daily living (ADL), the presence of depressive symptoms, and the use of health services. The outcomes were measured at pre-intervention (T1) and at three months post-intervention (T2). The independent t-test or the Mann-Whitney U test was used to analyze the group differences in HRQoL, ADL, and presence of depressive symptoms according to the normality of data.

Results
Analysis showed that the intervention group experienced a statistically significantly improvement in the mental component scale of quality of life (p = .036), activities of daily living (p = .005), and presence of depressive symptoms (p = .035) at T2 compared with at T1. No significant differences were found in the control group.

Conclusions
Supporting self-care is necessary to enable community-dwelling non-frail older adults to be independent to the fullest extent possible in the community. The promising results found in this pilot study suggested that the integration of the health-social partnership into transitional care practice is effective and can be sustained in the community. Future studies can draw on these findings and maximize the integrated care quality during the transition phase.

Trial registration
NCT04434742 (date: 17 June 2020, retrospectively registered).
Variation between nursing homes in drug use and in drug-related problems
Authors: Fog Amura Francesca , Mdala Ibrahimu , Engedal Knut , Straand Jørund 
Published: September 2020

Abstract
Background
Residents at nursing homes (NHs) are at particular risk for drug related harm. Regular medication reviews using explicit criteria for pharmacological inappropriateness and classification of drug related problems (DRPs) have recently been introduced as measures to improve the quality of medication use and for making the treatment more uniform across different institutions. Knowledge about variation in DRPs between NHs is scarce. To explore if increased attention towards more appropriate drug treatment in NHs have led to more uniform treatment, we have analyzed variations between different nursing homes’ drug use and DRPs.

Methods
Cross-sectional medication review study including 2465 long-term care residents at 41 NHs in Oslo, Norway. Regular drug use was retrieved from the patients’ medical records. DRPs were identified by using STOPP/START and NORGEP criteria and a drug-drug interactions database. NHs were grouped in quartiles based on average levels of drug use. The upper and lower quartiles were compared using independent samples t-test and associations between drug use and DRPs were tested by logistic regression.

Results
Patients’ mean age was 85.9 years, 74.2% were women.
Mean numbers of regular drugs per patient was 6.8 and varied between NHs from 4.8 to 9.3.
The proportion of patients within each NH using psychotropic and analgesic drugs varied largely: antipsychotics from three to 50%, benzodiazepines from 24 to 99%, antidepressants from nine to 75%, anti-dementia drugs from no use to 42%, opioids from no use to 65% and paracetamol from 16 to 74%.
Mean DRPs per patient was 2.0 and varied between NHs from 0.5 to 3.4.
The quartiles of NHs with highest and lowest mean drugs per patient (7.7 vs. 5.7, p < 0.001) had comparable mean number of DRPs per patient (2.2 vs. 1.8, p = 0.2). Using more drugs and the use of opioids, antipsychotics, benzodiazepines and antidepressants were associated with more DRPs.

Conclusions
The use of psychotropic and analgesic drugs was high and varied substantially between different NHs. Even if the use of more drugs, opioids and psychotropic drugs was associated with DRPs, no difference was found in DRPs between the NHs with highest vs. lowest drug use.
Adherence to World Health Organisation guidelines for treatment of early onset neonatal sepsis in low-income settings; a cohort study in Nepal
Authors: Ekman Beatrice , Paudel Prajwal , Basnet Omkar , KC Ashish , Wrammert Johan 
Published: September 2020

Abstract
Background
Neonatal sepsis is one of the major causes of death during the first month of life and early empirical treatment with injectable antibiotics is a life-saving intervention. Adherence to World Health Organisation guidelines on first line antibiotics is crucial to mitigate the risks of increased antimicrobial resistance. The aim of this paper was to evaluate if treatment of early onset neonatal sepsis in a low-income facility setting observe current guidelines and if compliance is influenced by contextual factors.

Methods
This cohort study used data on antimicrobial treatment of neonatal sepsis onset within 72 h of life from 12 regional hospitals participating in a scale-up trial of a neonatal resuscitation quality improvement package intervention in Nepal. Infants treated according to guidelines were compared with those receiving other antimicrobials. A multiple logistic regression analysis adjusted for the intervention and time trend was applied.

Results
1564 infants with a preliminary diagnosis of early onset sepsis were included. A majority (74.9%) were treated according to guidelines and adherence was increasing over time. Infants born at larger facilities (adjusted Odds Ratio 5.6), those that were inborn (adjusted Odds Ratio 1.97) or belonging to a family of dis-advantaged caste (adjusted Odds Ratio 2.15) had higher odds for treatment according to guidelines. A clinical presentation of lethargy or tachypnoea was associated with adherence to guidelines.

Conclusion
Adherence to guidelines for antibiotic treatment of early neonatal sepsis was moderately high in this low-income setting. Odds for observing guidelines increased with facility size, for inborn infants and if the family belonged to a dis-advantaged caste. Cefotaxime was a common alternative choice when guidelines were not followed, highly relevant for the risk of increased antimicrobial resistance.

Trial registration
ISRCTN, ISRCTN30829654, registered 17th of May, 2017.
Retrospective accuracy analysis of MRI based lesion size measurement in neuroblastic tumors: which sequence should we choose?
Authors: Gassenmaier Sebastian , Tsiflikas Ilias , Maennlin Simon , Urla Cristian , Warmann Steven W. , Schaefer Juergen F. 
Published: September 2020

Abstract
Background
MR imaging of neuroblastic tumors is widely used for assessing the effect of chemotherapy on tumor size. However, there are some concerns that MRI might falsely estimate lesion diameters due to calcification and fibrosis. Therefore, the aim of our study was to compare neuroblastic tumor size based on MRI measurements to histopathology measurements of the resected specimens as standard of reference.

Methods
Inclusion criteria were diagnosis of a neuroblastic tumor, MR imaging within 100 days to surgery and gross total resection without fragmentation of the tumor between 2008 and 2019. Lesion diameters were measured by two radiologists according to RECIST 1.1 in axial plane in T2w turbo spin echo (TSE), diffusion-weighted imaging (DWI), and in T1w pre- and postcontrast sequences. Furthermore, the largest lesion size in three-dimensions was noted. The largest diameter of histopathology measurements of each specimen was used for comparison with MRI.

Results
Thirty-seven patients (mean age: 5 ± 4 years) with 38 lesions (neuroblastoma: n = 17; ganglioneuroblastoma: n = 11; ganglioneuroma: n = 10) were included in this retrospective study. There was excellent intra-class correlation coefficient between both readers for all sequences (> 0.9) Tumor dimensions of reader 1 based on axial MRI measurements were significantly smaller with the following median differences (cm): T1w precontrast − 1.4 (interquartile range (IQR): 1.8), T1w postcontrast − 1.0 (IQR: 1.9), T2w TSE: -1.0 (IQR: 1.6), and DWI -1.3 (IQR: 2.2) (p < 0.001 for all sequences). However, the evaluation revealed no significant differences between the three-dimensional measurements and histopathology measurements of the resected specimens regardless of the applied MRI sequence.

Conclusions
Axial MRI based lesion size measurements are significantly smaller than histopathological measurements. However, there was no significant difference between three-dimensional measurements and histopathology measurements of the resected specimens. T2w TSE and T1w postcontrast images provided the lowest deviation and might consequently be preferred for measurements.