bluuebunny/crossref_metadata_2025_split huggingface dataset:
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories
Authors: Moco Vincent , Cazenave Damien , Garnier Maëlle , Pot Matthieu , Marcelino Isabel , Talarmin Antoine , Guyomard-Rabenirina Stéphanie , Breurec Sébastien , Ferdinand Séverine , Dereeper Alexis , Reynaud Yann , Couvin David 
Published: July 2022

Abstract
Background
Biological sequences are increasing rapidly and exponentially worldwide. Nucleotide sequence databases play an important role in providing meaningful genomic information on a variety of biological organisms.

Results
The getSequenceInfo software tool allows to access sequence information from various public repositories (GenBank, RefSeq, and the European Nucleotide Archive), and is compatible with different operating systems (Linux, MacOS, and Microsoft Windows) in a programmatic way (command line) or as a graphical user interface. getSequenceInfo or gSeqI v1.0 should help users to get some information on queried sequences that could be useful for specific studies (e.g. the country of origin/isolation or the release date of queried sequences). Queries can be made to retrieve sequence data based on a given kingdom and species, or from a given date. This program allows the separation between chromosomes and plasmids (or other genetic elements/components) by arranging each component in a given folder. Some basic statistics are also performed by the program (such as the calculation of GC content for queried assemblies). An empirically designed nucleotide ratio is calculated using nucleotide information in order to tentatively provide a “NucleScore” for studied genome assemblies. Besides the main gSeqI tool, other additional tools have been developed to perform various tasks related to sequence analysis.

Conclusion
The aim of this study is to democratize the use of public repositories in programmatic ways, and to facilitate sequence data analysis in a pedagogical perspective. Output results are available in FASTA, FASTQ, Excel/TSV or HTML formats. The program is freely available at: https://github.com/karubiotools/getSequenceInfo. getSequenceInfo and supplementary tools are partly available through the recently released Galaxy KaruBioNet platform (http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html).
Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands
Authors: Iwasaki Yuki , Ikemura Toshimichi , Wada Kennosuke , Wada Yoshiko , Abe Takashi 
Published: July 2022

Abstract
Background
Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it is important to characterize the bat genome from multiple perspectives. Unsupervised machine learning methods for extracting novel information from big sequence data without prior knowledge or particular models are highly desirable for obtaining unexpected insights. We previously established a batch-learning self-organizing map (BLSOM) of the oligonucleotide composition that reveals novel genome characteristics from big sequence data.

Results
In this study, using the oligonucleotide BLSOM, we conducted a comparative genomic study of humans and six bat species. BLSOM is an explainable-type machine learning algorithm that reveals the diagnostic oligonucleotides contributing to sequence clustering (self-organization). When unsupervised machine learning reveals unexpected and/or characteristic features, these features can be studied in more detail via the much simpler and more direct standard distribution map method. Based on this combined strategy, we identified the Mb-level enrichment of CG dinucleotide (Mb-level CpG islands) around the termini of bat long-scaffold sequences. In addition, a class of CG-containing oligonucleotides were enriched in the centromeric and pericentromeric regions of human chromosomes. Oligonucleotides longer than tetranucleotides often represent binding motifs for a wide variety of proteins (e.g., transcription factor binding sequences (TFBSs)). By analyzing the penta- and hexanucleotide composition, we observed the evident enrichment of a wide range of hexanucleotide TFBSs in centromeric and pericentromeric heterochromatin regions on all human chromosomes.

Conclusion
Function of transcription factors (TFs) beyond their known regulation of gene expression (e.g., TF-mediated looping interactions between two different genomic regions) has received wide attention. The Mb-level TFBS and CpG islands are thought to be involved in the large-scale nuclear organization, such as centromere and telomere clustering. TFBSs, which are enriched in centromeric and pericentromeric heterochromatin regions, are thought to play an important role in the formation of nuclear 3D structures. Our machine learning-based analysis will help us to understand the differential features of nuclear 3D structures in the human and bat genomes.
Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants’ stool samples in Argentina
Authors: Torrez Lamberti Mónica F. , Terán Lucrecia C. , Lopez Fabián E. , de las Mercedes Pescaretti María , Delgado Mónica A. 
Published: July 2022

Abstract
Background
Shigella specie is a globally important intestinal pathogen disseminated all over the world. In this study we analyzed the genome and the proteomic component of two Shigella flexneri 2a clinical isolates, collected from pediatric patients with gastroenteritis of the Northwest region of Argentina (NWA) in two periods of time, with four years of difference. Our goal was to determine putative changes at molecular levels occurred during these four years, that could explain the presence of this Shigella`s serovar as the prevalent pathogen in the population under study.

Results
As previously reported, our findings support the idea of Shigella has a conserved “core” genome, since comparative studies of CI133 and CI172 genomes performed against 80 genomes obtained from the NCBI database, showed that there is a large number of genes shared among all of them. However, we observed that CI133 and CI172 harbors a small number of strain-specific genes, several of them present in mobile genetic elements, supporting the hypothesis that these isolates were established in the population by horizontal acquisition of genes. These differences were also observed at proteomic level, where it was possible to detect the presence of certain secreted proteins in a culture medium that simulates the host environment.

Conclusion
Great similarities were observed between the CI133 and CI172 strains, confirming the high percentage of genes constituting the “core” genome of S. flexneri 2. However, numerous strain specific genes were also determined. The presence of the here identified molecular elements into other strain of our culture collation, is currently used to develop characteristic markers of local pathogens. In addition, the most outstanding result of this study was the first description of a S. flexneri 2 producing Colicin E, as one of the characteristics that allows S. flexneri 2 to persist in the microbial community. These findings could also contribute to clarify the mechanism and the evolution strategy used by this pathogen to specifically colonize, survive, and cause infection within the NWA population.
1,25-dihydroxyvitamin D3 ameliorates lupus nephritis through inhibiting the NF-κB and MAPK signalling pathways in MRL/lpr mice
Authors: Li Xuewei , Liu Jie , Zhao Yingzhe , Xu Ning , Lv E. , Ci Chunzeng , Li Xiangling 
Published: July 2022

Abstract
Background
Lupus nephritis (LN) is a common and serious complication of systemic lupus erythematosus (SLE). However, the aetiology and pathogenesis of LN remain unknown. 1,25-dihydroxyvitamin D3 [1,25-(OH)2-VitD3] is the active form of vitamin D, and it has been shown to perform important functions in inflammatory and immune-related diseases. In this study, we investigated the time-dependent effects of 1,25-dihydroxyvitamin D3 and explored the underlying mechanism in MRL/lpr mice, a well-studied animal model of LN.

Methods
Beginning at 8 weeks of age, 24-h urine samples were collected weekly to measure the levels of protein in the urine. We treated female MRL/lpr mice with 1,25-dihydroxyvitamin D3 (4 μg/kg) or 1% DMSO by intraperitoneal injection twice weekly for 3 weeks beginning at the age of 11 weeks. The mice were separately sacrificed, and serum and kidney samples were collected at the ages of 14, 16, 18, and 20 weeks to measure creatinine (Cr) levels, blood urea nitrogen (BUN) levels, histological damage, immunological marker (A-ds DNA, C1q, C3, IgG, IgM) levels, and inflammatory factor (TNF-α, IL-17, MCP-1) levels. Furthermore, the nuclear factor kappa B (NF-κB) and the mitogen-activated protein kinase (MAPK) signalling pathways were also assessed to elucidate the underlying mechanism.

Results
We found that MRL/lpr mice treated with 1,25-dihydroxyvitamin D3 displayed significantly attenuated LN. VitD3-treated mice exhibited significantly improved renal pathological damage and reduced proteinuria, BUN, SCr, A-ds DNA antibody and immune complex deposition levels (P < 0.05) compared with untreated MRL/lpr mice. Moreover, 1,25-dihydroxyvitamin D3 inhibited the complement cascade, inhibited the release of proinflammatory cytokines, such as TNF-α, IL-17, and MCP-1, and inhibited NF-κB and MAPK activation (P < 0.05).

Conclusion
1,25-dihydroxyvitamin D3 exerts a protective effect against LN by inhibiting the NF-κB and MAPK signalling pathways, providing a potential treatment strategy for LN. Interestingly, the NF-κB and MAPK signalling pathways are time-dependent mediators of LN and may be associated with lupus activity.
Perioperative levetiracetam for seizure prophylaxis in seizure-naive brain tumor patients with focus on neurocognitive functioning
Authors: Konrath Elias , Marhold Franz , Kindler Wolfgang , Scheichel Florian , Popadic Branko , Blauensteiner Katrin , Calabek Bernadette , Freydl Elisabeth , Weber Michael , Ristl Robin , Hainz Katharina , Sherif Camillo , Oberndorfer Stefan 
Published: July 2022

Abstract
Introduction
In seizure-naive brain tumor patients, the efficacy of perioperative prophylactic antiepileptic drug treatment remains controversial. In case of administration, the common preferred drug is levetiracetam (LEV) because of its favorable pharmacological profile. Research to date has not sufficiently determined how LEV affects cognition in the short term, as is the case in the perioperative period. The objective of this prospective study was to examine the neurocognitive functioning of seizure-naive brain tumor patients after receiving LEV perioperatively.

Methods
Fortythree patients with supratentorial brain tumor scheduled for surgery received LEV three days before until six days after surgery as seizure prophylaxis. Cognitive functioning (NeuroCogFX), LEV plasma-levels, hematotoxicity, side-effects, as well as health-related quality of life (HRQoL, Qolie31), were recorded preoperatively before (Baseline) and after onset of LEV (Pre-Op), 4–6 days postoperatively (Post-Op) and 21 days postoperatively (Follow-Up).

Results
No significant changes in cognitive functioning and HRQoL were seen after onset of preoperative LEV. There was a significant improvement of NeuroCogFX total-score at Follow-Up (p = 0.004) compared to Baseline. The overall-score Qolie31 showed simultaneous improvement patterns as cognitive functioning (p < 0.001). The most frequent side effect related to study drug was somnolence (in 28.6% of patients).

Conclusions
A significant improvement of cognitive functioning, as well as an improvement in HRQoL, were detected postoperatively. This is presumably due to the debulking effect of the surgery. Nevertheless, LEV has no detrimental effect on cognitive functioning in the perioperative phase in seizure-naive brain tumor patients.

Trial registration
This study was registered prospectively (Date: 25/11/2015; EudraCT: 2015–003,916-19).
A 15-year retrospective review of urodynamic studies in children at Red Cross War Memorial Children’s Hospital, Cape town, South Africa
Authors: Mosalakatane Thembisile Dintle , McCulloch Mignon , Nourse Peter , Coetzee Ashton , Wright Anne , Raad Jeanette , Lazarus John , Howlett Justin 
Published: July 2022

Abstract
Background
Despite the undeniable diagnostic benefits of urodynamic studies (UDS), their adoption into clinical practice in Africa has been slow. This study aimed to review the use of invasive UDS in children at a tertiary paediatric hospital in South Africa.

Methods
A retrospective analysis of 1108 UDS was conducted. Patient demographic characteristics, primary diagnosis, indication and urodynamic outcomes were reviewed. Presence of urodynamic high-risk features were documented, and a comparison was made between the first study and follow-up study.

Results
This study revealed increasing trends in the use of UDS from 2015. Referrals were from Urology (37.7%), Spinal defects clinic (34.4%), Nephrology (20.8%) and other departments (7.0%). The most common reason for referral was review of medical treatment (36.5%). Spinal dysraphism (58.3%) accounted for the majority of conditions seen. Majority (59.1%) of the patients were receiving more than one type of bladder treatment at the time of their first study, with clean intermittent catheterisation (46.5%) being the most common form of bladder management. 97.5% of studies were performed using transurethral bladder catheterization. Urodynamic diagnosis was neurogenic in 74.0%, anatomical (12.2%), functional (8.8%) and normal (5.0%). There was statistically significant improvement in bladder compliance, detrusor leak point pressure and detrusor sphincter dyssynergia between the first study and a subsequent study following therapeutic intervention.

Conclusions
The unique ability of UDS to demonstrate changes in detrusor pressures, which is a common reason for therapy failure, makes UDS an invaluable tool in the diagnosis and management of children with lower urinary tract dysfunction.
A bifactor model of personality organization in adolescence: the validity of a brief screening measure assessing severity and core domains of functioning
Authors: Biberdzic M. , Grenyer B. F. , Normandin L. , Ensink K. , Clarkin J. F. 
Published: July 2022

Abstract
Background
Both the latest edition of the DSM-5 as well as the new ICD-11 have established a new focus in the diagnosis of personality disorders: the assessment of personality functioning. This recent shift in focus converges with long-standing psychodynamic conceptualizations of personality pathology, particularly Kernberg’s object relations model. Although a significant amount of research supports these models in adults, much less is known about the validity of these frameworks in youth. Considering the paucity of brief measures of personality functioning in adolescents, the current study aimed to develop and investigate the validity of the Inventory of Personality Organization for Adolescents—Short Form, a theoretically-informed measure assessing severity and core domains of functioning in adolescents.

Methods
A total sample of N = 525 adolescents aged 13 to 19 years were recruited through a community University-Health Psychology Clinic as current patients (n = 94) or who responded to an online research call (n = 431).

Results
Results indicate that a bifactor model provided the best fit to the data and consisted of a general factor reflecting core self-other functioning and three specific factors, representing additional dimensions of personality organization.

Conclusions
A brief 15-item version of the IPO-A was successfully derived for time-efficient screening of personality pathology in youth. Similarities with the ICD-11 framework are discussed.
Predicting accidental drug overdose as the cause of fatality in near real-time using the Suspected Potential Overdose Tracker (SPOT): public health implications
Authors: Hochstatter Karli R. , Rastogi Sonal , Klein Kathryn , Tait-Ozer Cameron , El-Bassel Nabila , Graham Jason 
Published: July 2022

Abstract
Background
Effective responses to the worsening drug overdose epidemic require accurate and timely drug overdose surveillance data. The objectives of this paper are to describe the development, functionality, and accuracy of the Suspected Potential Overdose Tracker (SPOT) for predicting accidental drug overdose as the cause and manner of death in near real-time, and public health implications of adopting the tool.

Methods
SPOT was developed to rapidly identify overdose deaths through a simple and duplicable process using data collected by death investigators. The tool assigns each death a ranking of 1 through 3 based on the likelihood of it being an unintentional drug overdose, with 1 representing the highest likelihood that the death will be confirmed as an unintentional drug overdose and 3 representing the lowest. We measured the accuracy of the tool for predicting overdose deaths by comparing potential overdose deaths in New York City from 2018–2020 that were identified using SPOT to finalized death certificates. We also calculated the proportion of death certificate-confirmed overdoses that were missed by the SPOT tool and the proportion of type 1 errors.

Results
SPOT captured up to 77% of unintentional drug overdose deaths using data collected within 72 h of fatality. The tool predicted unintentional drug overdose from 2018 to 2020 with 93–97% accuracy for cases assigned a ranking of 1, 87–91% accuracy for cases assigned a ranking of 2, and 62–73% accuracy for cases assigned a ranking of 3. Among all unintentional overdose deaths in 2018, 2019, and 2020, 21%, 28%, and 33% were missed by the SPOT tool, respectively. During this timeframe, the proportion of type 1 errors ranged from 15%-23%.

Conclusions
SPOT may be used by health departments, epidemiologists, public health programs, and others to monitor overdose fatalities before death certificate data becomes available. Improved monitoring of overdose fatalities allows for rapid data-driven decision making, identification of gaps in public health and public safety overdose response, and evaluation and response to overdose prevention interventions, programs, and policies.
Perioperative stroke in patients undergoing spinal surgery: a retrospective cohort study
Authors: Yan Xin , Pang Ying , Yan Lirong , Ma Zhigang , Jiang Ming , Wang Weiwei , Chen Jie , Han Yangtong , Guo Xiaolei , Hu Hongtao 
Published: July 2022

Abstract
Background
The incidence of perioperative stroke following spinal surgery, including ischemic and hemorrhagic stroke, has not been fully investigated in the Chinese population. Whether specific spinal or emergency/elective procedures are associated with perioperative stroke remains controversial. This study aimed to investigate the incidence of perioperative stroke, health economic burden, clinical outcomes, and associated risk factors.

Method
A retrospective cohort study using an electronic hospital information system database was conducted from Jan 1, 2015, to Jan 1, 2021, in a tertiary hospital in China. Patients aged ≥18 years who had undergone spinal surgery were included in the study. We recorded patient demographics, comorbidities, and health economics data. Clinical outcomes included perioperative stroke during hospitalization and associated risk factors. The patients’ operative data, anesthetic data, and clinical manifestations were recorded.

Result
A total of 17,408 patients who had undergone spinal surgery were included in this study. Twelve patients had perioperative stroke, including seven ischemic stroke (58.3%) and five hemorrhagic stroke (41.7%). The incidence of perioperative stroke was 0.07% (12/17,408). In total, 12 stroke patients underwent spinal fusion. Patients with perioperative stroke were associated with longer hospital stay (38.33 days vs. 9.78 days, p < 0.001) and higher hospital expenses (RMB 175,642 vs. RMB 81,114, p < 0.001). On discharge, 50% of perioperative patients had severe outcomes. The average onset time of perioperative stroke was 1.3 days after surgery. Stroke history (OR 146.046, 95% CI: 28.102–759.006, p < 0.001) and hyperlipidemia (OR 4.490, 95% CI: 1.182–17.060, p = 0.027) were associated with perioperative stroke.

Conclusion
The incidence of perioperative stroke of spinal surgery in a tertiary hospital in China was 0.07%, with a high proportion of hemorrhagic stroke. Perioperative stroke patients experienced a heavy financial burden and severe outcomes. A previous stroke history and hyperlipidemia were associated with perioperative stroke.
Effect of oral health promotion interventions on pregnant women dental caries: a field trial
Authors: Deghatipour Marzie , Ghorbani Zahra , Mokhlesi Amir Hossein , Ghanbari Shahla , Namdari Mahshid 
Published: July 2022

Abstract
Background
Dental caries is a costly and very common disease, especially in pregnant women. Reasons such as not paying attention to oral health, poor diet and also lack of adequate education in this regard cause this to happen. Performing well-designed educational interventions using primary health system’s forces, can improve oral health of pregnant women and help control this disease. We conducted this study to evaluate the effectiveness of some oral health interventions on pregnant women dental caries.

Methods
A field trial study was done in comprehensive Health Centers in Varamin, Tehran, Iran to assess 439 mothers’ dental health status from pregnancy up to 2 years after delivery in intervention (n = 239) and control groups (n = 200). Mothers in intervention groups received oral health-related education consisted of nutritional and behavioral messages via either of four methods: A: comprehensive method including all following methods together (n = 74), B: group discussion by dentists (n = 59), C: face to face education by primary health care providers (n = 53), and D: social network applications (n = 53); while those in control group only received routine maternal and oral health care. We used a questionnaire to collect mothers’ demographic, socioeconomic and dental care behavior data and also performed oral examinations to assess their DMFT at baseline and 24 months after delivery to evaluate the effectiveness of these educational oral health interventions.

Results
From 454 mothers participated the examination session, 18 pregnant women discontinued during the follow-ups and 439 were remained with mean age of 27.47. In the intervention group, the frequency of daily brushing among women increased from 64% at baseline to 85.6% at the last follow-up and the mean D significantly decreased nearly 1unit at same period (P < 0.05). Most and least dental caries changes were in comprehensive intervention group and social network intervention group compared to other intervention groups, respectively.

Conclusions
Performing educational interventions during and after pregnancy using various message delivery methods and messengers (oral health professionals and trained PHCPs), could improve oral health status and behaviors of pregnant and lactating mothers in a feasible and applicable manner.