bluuebunny/crossref_metadata_2025_split huggingface dataset:
On how to generalize species-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome
Authors: García S. Alberto , Casamayor Juan Carlos 
Published: September 2021

Abstract
Background
Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and idiosyncrasy of genomic use cases mean that conceptual modeling techniques are used to generate conceptual schemes that focus on too specific scenarios (i.e., they are species-specific conceptual schemes). Our research group developed two different conceptual schemes. The first one is the Conceptual Schema of the Human Genome, which is intended to improve Precision Medicine and genetic diagnosis. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field.

Methods
Our two conceptual schemes have been ontologically compared to identify their similarities and differences. Based on this comparison, several changes have been performed in the Conceptual Schema of the Human Genome in order to obtain the first version of a species-independent Conceptual Schema of the Genome. Identifying the different genome information items used in each genomic case study has been essential in achieving our goal. The changes needed to provide an expanded, more generic version of the Conceptual Schema of the Human Genome are analyzed and discussed.

Results
This work presents a new CS called the Conceptual Schema of the Genome that is ready to be adapted to any specific working genome-based context (i.e., species-independent).

Conclusion
The generated Conceptual Schema of the Genome works as a global, generic element from which conceptual views can be created in order to work with any specific species. This first working version can be used in the human use case, in the citrus use case, and, potentially, in more use cases of other species.
Genetic identification and characterization of chromosomal regions for kernel length and width increase from tetraploid wheat
Authors: Zhou Jieguang , Li Cong , You Jianing , Tang Huaping , Mu Yang , Jiang Qiantao , Liu Yaxi , Chen Guoyue , Wang Jirui , Qi Pengfei , Ma Jun , Gao Yutian , Habib Ahsan , Wei Yuming , Zheng Youliang , Lan Xiujin , Ma Jian 
Published: September 2021

Abstract
Background
Improvement of wheat gercTriticum aestivum L.) yield could relieve global food shortages. Kernel size, as an important component of 1000-kernel weight (TKW), is always a significant consideration to improve yield for wheat breeders. Wheat related species possesses numerous elite genes that can be introduced into wheat breeding. It is thus vital to explore, identify, and introduce new genetic resources for kernel size from wheat wild relatives to increase wheat yield.

Results
In the present study, quantitative trait loci (QTL) for kernel length (KL) and width (KW) were detected in a recombinant inbred line (RIL) population derived from a cross between a wild emmer accession ‘LM001’ and a Sichuan endemic tetraploid wheat ‘Ailanmai’ using the Wheat 55 K single nucleotide polymorphism (SNP) array-based constructed linkage map and phenotype from six different environments. We identified eleven QTL for KL and KW including two major ones QKL.sicau-AM-3B and QKW.sicau-AM-4B, the positive alleles of which were from LM001 and Ailanmai, respectively. They explained 17.57 to 44.28% and 13.91 to 39.01% of the phenotypic variance, respectively. For these two major QTL, Kompetitive allele-specific PCR (KASP) markers were developed and used to successfully validate their effects in three F3 populations and two natural populations containing a panel of 272 Chinese wheat landraces and that of 300 Chinese wheat cultivars, respectively. QKL.sicau-AM-3B was located at 675.6–695.4 Mb on chromosome arm 3BL. QKW.sicau-AM-4B was located at 444.2–474.0 Mb on chromosome arm 4BL. Comparison with previous studies suggested that these two major QTL were likely new loci. Further analysis indicated that the positive alleles of QKL.sicau-AM-3B and QKW.sicau-AM-4B had a great additive effect increasing TKW by 6.01%. Correlation analysis between KL and other agronomic traits showed that KL was significantly correlated to spike length, length of uppermost internode, TKW, and flag leaf length. KW was also significantly correlated with TKW. Four genes, TRIDC3BG062390, TRIDC3BG062400, TRIDC4BG037810, and TRIDC4BG037830, associated with kernel development were predicted in physical intervals harboring these two major QTL on wild emmer and Chinese Spring reference genomes.

Conclusions
Two stable and major QTL for KL and KW across six environments were detected and verified in three biparental populations and two natural populations. Significant relationships between kernel size and yield-related traits were identified. KASP markers tightly linked the two major QTL could contribute greatly to subsequent fine mapping. These results suggested the application potential of wheat related species in wheat genetic improvement.
Chi-square test under indeterminacy: an application using pulse count data
Authors: Aslam Muhammad 
Published: September 2021

AbstractBackgroundThe data obtained from the counting process is known as the count data. In practice, the counting can be done at the same time or the time of the count is not the same. To test either the K counts are differed significantly or not, the Chi-square test for K counts is applied.ResultsThe paper presents the Chi-square tests for K counts under neutrosophic statistics. The test statistic of the proposed test when K counts are recorded at the same time and different time are proposed. The testing procedure of the proposed test is explained with the help of pulse count data.ConclusionsFrom the analysis of pulse count data, it can be concluded that the proposed test suggests the cardiologists use different treatment methods on patients. In addition, the proposed test gives more information than the traditional test under uncertainty.
LncRNA MCF2L-AS1 aggravates the malignant development of colorectal cancer via targeting miR-105-5p/RAB22A axis
Authors: Kong Wencheng , Li Hui , Xie Lesi , Cui Guangxing , Gu Weigang , Zhang Hongchen , Ma Wencong , Zhou Yifeng 
Published: September 2021

Abstract
Background
Colorectal cancer (CRC) represents one of the major malignant cancers in the world. It has been demonstrated that long non-coding RNAs (lncRNAs) can cause great influences on various human cancers. Though MCF.2 cell line derived transforming sequence like antisense RNA 1 (MCF2L-AS1) and its carcinogenic effect in CRC has been elucidated by several previous researches, the underlying mechanism remains unknown.

Aim
We aimed at exploring the function and regulatory mechanism of MCF2L-AS1 in CRC.

Methods
MCF2L-AS1 expression in CRC cells was tested via RT-qPCR assay. The effects of MCF2L-AS1 on the biological properties of CRC cells were testified through functional experiments. The molecular mechanism of MCF2L-AS1 was verified through mechanism experiments.

Results
MCF2L-AS1 was highly expressed in CRC cells, and it could enhance the proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) process of CRC cells. MiR-105-5p was sponged by MCF2L-AS1 in CRC cells and Ras-related protein Rab-22A (RAB22A) was verified to be the downstream target of miR-105-5p. It was verified through rescue assays that RAB22A overexpression or miR-105-5p silencing could reverse the repressive impact of MCF2L-AS1 silencing on CRC progression.

Conclusion
MCF2L-AS1 accelerated the malignant development of CRC cells by targeting the miR-105-5p/RAB22A axis.
Iranian healthcare professionals’ knowledge, attitudes, and use of complementary and alternative medicine: a cross sectional study
Authors: Jafari Alireza , Zanganeh Mohaddeseh , Kazemi Zahra , Lael-Monfared Elaheh , Tehrani Hadi 
Published: September 2021

Abstract
Background
The present study aims to investigate the knowledge, attitude, and performance of Iranian Healthcare Professionals (HP) about Complementary and Alternative Medicine (CAM) modalities.

Methods
This cross-sectional study was carried out on 210 HP in 2019. Samples were selected from healthcare centers, clinics, and hospitals using census sampling. Data collection tools included demographic information, attitude, knowledge, and the amount of use of CAM modalities. Data analysis was performed using SPSS ver. 24.

Results
In this study, the response rate was 85.3% (n=209). A majority of respondents had a positive attitude toward CAM (n=166, 79%), but their level of knowledge was limited (n=154, 73.6%). The most commonly used CAM modalities were herbal medicine (93.2%), exercise therapy (75.4%), and hydrotherapy (75.2%), respectively, and the least commonly used ones were magnetic therapy (2.9%) and hypnosis (4.8%). The most important reasons for the use of CAM modalities by HP included fewer side effects than medical treatments (57.4%), its lowest cost than medical treatments (34.9%), non-serious disease with no need for referral to a clinic (32.1%), and its more convenient access than medical treatments (30.6%). The results showed that there was a significant relationship between the education level and the use of CAM modalities (p<0.05). There was also a significant relationship between the suggestion of CAM modalities and the amount of use of these modalities, and those who used these modalities would also have recommended them to their clients more frequently (p<0.05).

Conclusion
The results showed that most of HP used at least one of the CAM modalities and had a positive attitude towards CAM. As the level of knowledge was limited, training courses should be implemented to increase health practitioner’s level of knowledge on CAM.
Scaling production of GFP1-10 detector protein in E. coli for secretion screening by split GFP assay
Authors: Müller Carolin , Igwe Chika L. , Wiechert Wolfgang , Oldiges Marco 
Published: September 2021

Abstract
Background
The split GFP assay is a well-known technology for activity-independent screening of target proteins. A superfolder GFP is split into two non-fluorescent parts, GFP11 which is fused to the target protein and GFP1-10. In the presence of both, GFP1-10 and the GFP11-tag are self-assembled and a functional chromophore is formed. However, it relies on the availability and quality of GFP1-10 detector protein to develop fluorescence by assembly with the GFP11-tag connected to the target protein. GFP1-10 detector protein is often produced in small scale shake flask cultivation and purified from inclusion bodies.

Results
The production of GFP1-10 in inclusion bodies and purification was comprehensively studied based on Escherichia coli as host. Cultivation in complex and defined medium as well as different feed strategies were tested in laboratory-scale bioreactor cultivation and a standardized process was developed providing high quantity of GFP1-10 detector protein with suitable quality. Split GFP assay was standardized to obtain robust and reliable assay results from cutinase secretion strains of Corynebacterium glutamicum with Bacillus subtilis Sec signal peptides NprE and Pel. Influencing factors from environmental conditions, such as pH and temperature were thoroughly investigated.

Conclusions
GFP1-10 detector protein production could be successfully scaled from shake flask to laboratory scale bioreactor. A single run yielded sufficient material for up to 385 96-well plate screening runs. The application study with cutinase secretory strains showed very high correlation between measured cutinase activity to split GFP fluorescence signal proofing applicability for larger screening studies.
Polydopamine-coated UiO-66 nanoparticles loaded with perfluorotributylamine/tirapazamine for hypoxia-activated osteosarcoma therapy
Authors: Chen Hongfang , Fu You , Feng Kai , Zhou Yifan , Wang Xin , Huang Haohan , Chen Yan , Wang Wenhao , Xu Yuanjing , Tian Haijun , Mao Yuanqing , Wang Jinwu , Zhang Zhiyuan 
Published: September 2021

Abstract
Background
Hypoxia is a characteristic of solid tumors that can lead to tumor angiogenesis and early metastasis, and addressing hypoxia presents tremendous challenges. In this work, a nanomedicine based on oxygen-absorbing perfluorotributylamine (PFA) and the bioreductive prodrug tirapazamine (TPZ) was prepared by using a polydopamine (PDA)-coated UiO-66 metal organic framework (MOF) as the drug carrier.

Results
The results showed that TPZ/PFA@UiO-66@PDA nanoparticles significantly enhanced hypoxia, induced cell apoptosis in vitro through the oxygen-dependent HIF-1α pathway and decreased oxygen levels in vivo after intratumoral injection. In addition, our study demonstrated that TPZ/PFA@UiO-66@PDA nanoparticles can accumulate in the tumor region after tail vein injection and effectively inhibit tumor growth when combined with photothermal therapy (PTT). TPZ/PFA@UiO-66@PDA nanoparticles increased HIF-1α expression while did not promote the expression of CD31 in vivo during the experiment.

Conclusions
By using TPZ and PFA and the enhanced permeability and retention effect of nanoparticles, TPZ/PFA@UiO-66@PDA can target tumor tissues, enhance hypoxia in the tumor microenvironment, and activate TPZ. Combined with PTT, the growth of osteosarcoma xenografts can be effectively inhibited.

Graphic abstract
Genetic interference exerted by Salmonella-delivered CRISPR/Cas9 significantly reduces the pathological burden caused by Marek’s disease virus in chickens
Authors: Senevirathne Amal , Hewawaduge Chamith , Lee John Hwa 
Published: September 2021

AbstractEfficient in vivo delivery of a CRISPR/Cas9 plasmid is of paramount importance for effective therapy. Here, we investigated the usability of Salmonella as a plasmid carrier for in vivo therapy against virus-induced cancer using Marek’s disease virus (MDV) as a model for study in chickens. A green fluorescent protein-expressing CRISPR/Cas9 plasmid encoding the virulence gene pp38 was constructed against Marek’s disease virus. Therapeutic plasmids were transformed into Salmonella carrying lon and sifA gene deletions. The animals in 5 groups were intraperitoneally inoculated with phosphate-buffered saline, vector control, or Salmonella before or after MDV infection, or left uninfected as a naïve control. Therapeutic effectiveness was evaluated by observing disease outcomes and the viral copy number in peripheral blood mononuclear cells. The efficacy of plasmid delivery by Salmonella was 13 ± 1.7% in the spleen and 8.0 ± 1.8% in the liver on the 6th day post-infection. The Salmonella-treated groups showed significant resistance to MDV infection. The maximum effect was observed in the group treated with Salmonella before MDV infection. None of the chickens fully recovered; however, the results suggested that timely delivery of Salmonella could be effective for in vivo CRISPR/Cas9-mediated genetic interference against highly pathogenic MDV. The use of Salmonella in CRISPR systems provides a simpler and more efficient platform for in vivo therapy with CRISPR than the use of conventional in vivo gene delivery methods and warrants further development.
Correlation between estradiol levels on day of HCG trigger and the number of mature follicles, number of oocytes retrieved, and the number of mature oocytes (M2) after oocyte aspiration in ICSI cycles
Authors: Malathi Anitha , Balakrishnan Sheila , B. S. Lakshmi 
Published: September 2021

AbstractBackgroundEstradiol is an important marker of ovarian response to ovarian stimulation in ART cycles. The study tries to find the correlation of serum estradiol on the day of HCG trigger to the number of follicles, the number of oocytes retrieved, and the number of mature oocytes, and also, to correlate estradiol per follicle and estradiol per oocyte on the day of HCG, to the number of oocytes retrieved, and to the number of mature oocytes. It is a cross sectional study using retrospective data.ResultsThe data of 232 patients were analyzed. Our study showed a positive correlation between estradiol levels and the number of follicles (NF) (r= 0.592,p< 0.001), number of retrieved oocytes (NRO) (r= 0.576,p< 0.001), and number of mature oocytes (NMO) (r= 0.554,p< 0.001). E/follicle ratio did not have a significant correlation with NRO and NMO. E/Oocyte ratio had a strong negative correlation with NMO (r= −0.280,p< 0.001)ConclusionsSerum estradiol had a positive correlation with NF, NRO, and NMO. But E/O had a strong negative correlation with NMO. These results indicate that estradiol levels can be used as an important clinical tool in the prediction of oocyte and mature oocyte yield in ART cycles. Reproductive outcome in ART cycles is largely dependent on the number of oocytes and mature oocyte yield. Estradiol levels on the day of HCG appear to strongly correlate with the outcome of ART cycles.
Perioperative Electroencephalogram Spectral Dynamics Related to Postoperative Delirium in Older Patients
Authors: Koch Susanne , Windmann Victoria , Chakravarty Sourish , Kruppa Jochen , Yürek Fatima , Brown Emery N. , Winterer Georg , Spies Claudia 
Published: September 2021

BACKGROUND:
Intraoperative electroencephalography (EEG) signatures related to the development of postoperative delirium (POD) in older patients are frequently studied. However, a broad analysis of the EEG dynamics including preoperative, postinduction, intraoperative and postoperative scenarios and its correlation to POD development is still lacking. We explored the relationship between perioperative EEG spectra-derived parameters and POD development, aiming to ascertain the diagnostic utility of these parameters to detect patients developing POD.

METHODS:
Patients aged ≥65 years undergoing elective surgeries that were expected to last more than 60 minutes were included in this prospective, observational single center study (Biomarker Development for Postoperative Cognitive Impairment [BioCog] study). Frontal EEGs were recorded, starting before induction of anesthesia and lasting until recovery of consciousness. EEG data were analyzed based on raw EEG files and downloaded excel data files. We performed multitaper spectral analyses of relevant EEG epochs and further used multitaper spectral estimate to calculate a corresponding spectral parameter. POD assessments were performed twice daily up to the seventh postoperative day. Our primary aim was to analyze the relation between the perioperative spectral edge frequency (SEF) and the development of POD.

RESULTS:
Of the 237 included patients, 41 (17%) patients developed POD. The preoperative EEG in POD patients was associated with lower values in both SEF (POD 13.1 ± 4.6 Hz versus no postoperative delirium [NoPOD] 17.4 ± 6.9 Hz; P = .002) and corresponding γ-band power (POD −24.33 ± 2.8 dB versus NoPOD −17.9 ± 4.81 dB), as well as reduced postinduction absolute α-band power (POD −7.37 ± 4.52 dB versus NoPOD −5 ± 5.03 dB). The ratio of SEF from the preoperative to postinduction state (SEF ratio) was ~1 in POD patients, whereas NoPOD patients showed a SEF ratio >1, thus indicating a slowing of EEG with loss of unconscious. Preoperative SEF, preoperative γ-band power, and SEF ratio were independently associated with POD (P = .025; odds ratio [OR] = 0.892, 95% confidence interval [CI], 0.808–0.986; P = .029; OR = 0.568, 95% CI, 0.342–0.944; and P = .009; OR = 0.108, 95% CI, 0.021–0.568, respectively).

CONCLUSIONS:
Lower preoperative SEF, absence of slowing in EEG while transitioning from preoperative state to unconscious state, and lower EEG power in relevant frequency bands in both these states are related to POD development. These findings may suggest an underlying pathophysiology and might be used as EEG-based marker for early identification of patients at risk to develop POD.
Are the Placement, Maintenance, and Removal of Femoral and Sciatic Catheters Associated With Bleeding Complications in Vascular Patients on Antithrombotics? A Single-Center, Retrospective Cohort Study
Authors: Wardhan Richa , Michel Ralph , Vasilopoulos Terrie , Yen Erin 
Published: September 2021

BACKGROUND:
Information on the safety of placement, maintenance, and removal of peripheral nerve blocks in the presence of therapeutic or prophylactic antithrombotics is limited to case reports.

METHODS:
In this retrospective, descriptive study, we examined the use of femoral and gluteal or subgluteal sciatic perineural catheters in 146 patients on antithrombotics who received lower limb amputation (LLA) above or below the knee at the University of Florida Health Shands Hospital between January 2015 and December 2019. We searched patient surgical records for complications such as bleeding, nerve damage, infection, and hematoma during placement, maintenance, and removal of the perineural catheters.

RESULTS:
In this cohort of 146 patients on antithrombotics, there was 1 episode of hematoma with an estimated incidence of 1 of 146 (0.68%, 95% confidence interval [CI], 0.02–3.76). This patient developed a hematoma at the location of the femoral catheter and required a blood transfusion. This patient was on aspirin daily and subcutaneous heparin 3 times per day and had a normal coagulation profile during their hospital stay.

CONCLUSIONS:
This report investigates bleeding complications of femoral and sciatic perineural catheters in patients undergoing LLA on antithrombotics. We found that, except for 1 patient, most patients on varying combinations of antithrombotics did not experience bleeding complications related to the femoral and sciatic perineural catheters.
Optimising access and provision of interventional radiology service to patients by utilising a new referral system
Authors: Diamantopoulos Athanasios , Theodoulou Iakovos , Ghobrial Stephanos , Taliadoros Vasilis , Thulasidasan Narayanan , Raja Usman , Nourzaie Romman , Karunanithy Narayan , Cronin Bernadette 
Published: September 2021

Objective:
Implementing a streamlined interventional radiology (IR) service in the UK has been a challenge. This study aims to review a set of changes introduced in IR at a tertiary centre, including a new referral process and the designation of IR clinical nurse specialists.

Methods:
A new process of referring patients to IR using a single generic referral pathway was implemented, replacing an order dropdown-based system. A qualitative survey was designed and distributed as a single-use web link in order to assess the satisfaction and impact of this new process. Responses were based on Likert scale and pertained to perceived qualities of the new referral process. Data analysis was performed to identify specialty and grade-specific trends and possible differences amongst groups.

Results:
Findings from 98 respondents revealed a strong overall satisfaction with the new referral method and support for its continuation. Subgroup analysis by specialty, concluded medical specialties rated the new referral system more favourably than surgical specialties across all aspects: time efficiency, ease of use, periprocedural support and overall user experience. The new system also increased departmental productivity with an increase in the number of patients treated by 11.2%.

Conclusion:
Micropolicy changes within individual IR departments such as the replacement of a request-based referral system to one which puts IR in control of vetting and patient flow is one of many changes that reinforce the transformational phase of this specialty.

Advances in knowledge:
Micropolicy changes within IR departments are key in the progression and widespread recognition of the specialty.