bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Clinical Prognostic Scoring System for Neurocysticercosis
Authors: Marquez-Romero Juan Manuel , Huerta-Franco María Raquel , Soto-Cabrera Elizabeth , Espinoza-López Dulce Anabel , Orrego Héctor , Martínez-Jurado Elizabeth , Zermeño-Pöhls Fernando , Guerrero-Juárez Vicente 
Published: January 2021

Abstract

Objectives In patients with neurocysticercosis (NCC), an accurate risk prediction would allow a better therapeutic approach; however, there are currently no tools that can enhance the accuracy of risk prediction. We designed a prognostic scoring system to be used by neurologists and other physicians managing patients with NCC.

Materials and Methods Using data from clinical records of patients from a third-level national reference center for neurological diseases, we assessed demographic, clinical, and tomographic variables among 293 patients diagnosed with NCC. Multivariable logistic regression analyses were used to develop a clinical prognostic scoring instrument. Patients with NCC were assessed for neurological impairment at 3 months after diagnosis.

Statistical Analysis Score accuracy was assessed by receiver operating characteristic (ROC) curve analysis. The primary outcome was the presence of neurological impairment, resulting in disability according to self-report or caregiver reports; this outcome was assessed during follow-up visits at 3 ± 1 months after discharge.

Results The most common symptoms at presentation were headache (67%) and seizure (63%). A six-item (total score from –4 to + 2) prognostic instrument was constructed on the basis of the presence of seizures/headache at presentation, a leukocyte count above 12x 109/dL, the presence of six to ten parasites, subarachnoid localization, and the use of anthelmintic drugs. Among 113 patients with negative scores, 79.6% developed neurological deficits. Among patients with scores of 1 to 2, 64.6% recovered completely, with an overall accuracy of prediction of 74.7% and area under the ROC curve = 0.722 (95% CI, 0.664–0.780, p < 0.0001).

Conclusions The clinical prognostic scoring system for NCC described in this study is a new instrument for use in daily clinical practice. It is simple to administer, and it has a prognostic accuracy of 75%. Its use has the potential to improve the quality of care by guiding appropriate decision-making and early management of patients with NCC.
Use of Hausdorff Distance and Computer Modelling to Evaluate Virtual Surgical Plans with Three-Dimensional Printed Guides against Freehand Techniques for Navicular Bone Repair in Equine Orthopaedics
Authors: Biedrzycki Adam H. , Kistler Hannah C. , Perez-Jimenez Erik E. , Morton Alison J. 
Published: January 2021

AbstractObjective The aim of this study was to evaluate the surgical execution of a virtual surgical plan (VSP) with three-dimensional (3D) guides against a freehand approach in the equine navicular bone using an automated in silico computer analysis technique.Study Design Eight pairs of cadaveric forelimb specimens of adult horses were used in an ex vivo experimental study design with in silico modelling. Limbs received either a 3.5 mm cortical screw according to a VSP or using an aiming device. Using computed tomography and computer segmentation, a comparison was made between the executed screw and the planned screw using the Hausdorff distance (HD).Results Navicular bone mean HD registration error was –0.06 ± 0.29 mm. The VSP with 3D printing demonstrated significantly superior accuracy with a mean deviation of 1.19 ± 0.42 mm compared with aiming device group (3.53 ± 1.24 mm, p = 0.0018). The VSP group was 5.0 times more likely to result in a mean aberration of less than 1.0 mm (95% confidence interval, 0.62–33.4). A 3.5 mm screw with an optimal entry point can have a maximum deviation angle of 3.23 ± 0.07, 2.70 ± 0.06 and 2.37 ± 0.10 degrees in a proximal, dorsal and palmar direction respectively, prior to violating one of the cortical surfaces.Conclusion Procedures performed using the 3D guides have a high degree of accuracy, with minimal mean deviations (<1 mm and <1 degree) of a VSP compared with those using the conventional aiming device. The use of VSP and the HD for evaluation of orthopaedic surgeries and outcome measures shows promise for simplifying and improving surgical accuracy.
Key comparison BIPM.RI(I)-K3 of the air-kerma standards of the VNIIM, Russian Federation, and the BIPM in medium-energy x-rays
Authors: Burns D T , Kessler C , Villevalde A Y , Grishin D , Oborin A V 
Published: January 2021

Main text
A key comparison has been made between the air-kerma standards of the VNIIM and the BIPM in the medium-energy x-ray range. The results show the standards to be in agreement at the level of the standard uncertainty of the comparison of 1.9 parts in 103. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.
To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
How quality improvement collaboratives work to improve healthcare in care homes: a realist evaluation
Authors: Devi Reena , Chadborn Neil H , Meyer Julienne , Banerjee Jay , Goodman Claire , Dening Tom , Gladman John R F , Hinsliff-Smith Kathryn , Long Annabelle , Usman Adeela , Housley Gemma , Lewis Sarah , Glover Matthew , Gage Heather , Logan Philippa A , Martin Finbarr C , Gordon Adam L 
Published: January 2021

Abstract

Background
Quality improvement collaboratives (QICs) bring together multidisciplinary teams in a structured process to improve care quality. How QICs can be used to support healthcare improvement in care homes is not fully understood.

Methods
A realist evaluation to develop and test a programme theory of how QICs work to improve healthcare in care homes. A multiple case study design considered implementation across 4 sites and 29 care homes. Observations, interviews and focus groups captured contexts and mechanisms operating within QICs. Data analysis classified emerging themes using context-mechanism-outcome configurations to explain how NHS and care home staff work together to design and implement improvement.

Results
QICs will be able to implement and iterate improvements in care homes where they have a broad and easily understandable remit; recruit staff with established partnership working between the NHS and care homes; use strategies to build relationships and minimise hierarchy; protect and pay for staff time; enable staff to implement improvements aligned with existing work; help members develop plans in manageable chunks through QI coaching; encourage QIC members to recruit multidisciplinary support through existing networks; facilitate meetings in care homes and use shared learning events to build multidisciplinary interventions stepwise. Teams did not use measurement for change, citing difficulties integrating this into pre-existing and QI-related workload.

Conclusions
These findings outline what needs to be in place for health and social care staff to work together to effect change. Further research needs to consider ways to work alongside staff to incorporate measurement for change into QI.
Blue flower coloration of Corydalis ambigua requires ferric ion and kaempferol glycoside
Authors: Yoshida Kumi , Oniduka Takeya , Oyama Kin-ichi , Kondo Tadao 
Published: January 2021

Abstract
Corydalis ambigua (Japanese name, Ezoengosaku) flowers bloom with blue to purplish petals in early spring in Hokkaido prefecture. In this study, a mechanism for blue petal coloration by ferric ions and keampferol glycoside was elucidated. Blue petals and cell sap exhibited similar visible (Vis) spectra, with λmax at approximately 600 nm and circular dichroism (CD) with positive exciton-type Cotton effects in the Vis region. Analysis of the organic components of the petals confirmed cyanidin 3-O-sambubioside and kaempferol 3-O-sambubioside as the major flavonoids. Mg, Al, and Fe were detected in petals using atomic emission spectroscopy. Color, Vis absorption, and CD consistent with those of blue petals were reproduced by mixing cyanidin 3-O-sambubioside, kaempferol 3-O-sambubioside, and Fe3+ in a buffered aqueous solution at pH 6.5. Both Fe3+ and flavonol were essential for blue coloration.
Biosynthetic pathways and enzymes involved in the production of phosphonic acid natural products
Authors: Shiraishi Taro , Kuzuyama Tomohisa 
Published: January 2021

Abstract
Phosphonates are organophosphorus compounds possessing a characteristic C−P bond in which phosphorus is directly bonded to carbon. As phosphonates mimic the phosphates and carboxylates of biological molecules to potentially inhibit metabolic enzymes, they could be lead compounds for the development of a variety of drugs. Fosfomycin (FM) is a representative phosphonate natural product that is widely used as an antibacterial drug. Here, we review the biosynthesis of FM, which includes a recent breakthrough to find a missing link in the biosynthetic pathway that had been a mystery for a quarter-century. In addition, we describe the genome mining of phosphonate natural products using the biosynthetic gene encoding an enzyme that catalyzes C–P bond formation. We also introduce the chemoenzymatic synthesis of phosphonate derivatives. These studies expand the repertoires of phosphonates and the related biosynthetic machinery. This review mainly covers the years 2012-2020.
Phenazine-1-carboxylic acid (PCA) produced by Paraburkholderia phenazinium CK-PC1 aids postgermination growth of Xyris complanata seedlings with germination induced by Penicillium rolfsii Y-1
Authors: Hane Masataka , Wijaya Hanny C , Nyon Yanetri A , Sakihama Yasuko , Hashimoto Makoto , Matsuura Hideyuki , Hashidoko Yasuyuki 
Published: January 2021

Abstract
Symbiosis of Penicillium rolfsii Y-1 is essential for the seed germination of Hawaii yellow-eyed grass (Xyris complanata). However, the local soil where the plants grow naturally often suppresses the radicle growth of the seedlings. This radicle growth was drastically restored by coinoculation of Paraburkholderia phenazinium isolate CK-PC1, which is a rhizobacterium of X. complanata. It was found that the isolate CK-PC1 produced phenazine-1-carboxylic acid (PCA, 1) as a major metabolite. The biological effects of PCA (1) were investigated using the seeds of X. complanata and Mung bean (Vigna radiata) and it was uncovered that the symbiosis of the isolate CK-PC1was essential for the postgermination growth of X. complanata and the metabolite PCA (1) might partially contribute to promote the growth of the plants.
Substrate specificity of two cytochrome P450 monooxygenases involved in lankamycin biosynthesis
Authors: Teshima Aiko , Kondo Hisashi , Tanaka Yu , Nindita Yosi , Misaki Yuya , Konaka Yuji , Itakura Yasuhiro , Tonokawa Tsugumi , Kinashi Haruyasu , Arakawa Kenji 
Published: January 2021

Abstract
To elucidate the gross lankamycin biosynthetic pathway including two cytochrome P450 monooxygenases, LkmK and LkmF, we constructed two double mutants of P450 genes in combination with glycosyltransferase genes, lkmL and lkmI. An aglycon 8,15-dideoxylankanolide, a possible substrate for LkmK, was prepared from an lkmK–lkmL double mutant, while a monoglycoside 3-O-l-arcanosyl-8-deoxylankanolide, a substrate for LkmF, was from an lkmF–lkmI double mutant. Bioconversion of lankamycin derivatives was performed in the Escherichia coli recombinant for LkmK and the Streptomyces lividans recombinant for LkmF, respectively. LkmK catalyzes the C-15 hydroxylation on all 15-deoxy derivatives, including 8,15-dideoxylankanolide (a possible substrate), 8,15-dideoxylankamycin, and 15-deoxylankamycin, suggesting the relaxed substrate specificity of LkmK. On the other hand, LkmF hydroxylates the C-8 methine of 3-O-l-anosyl-8-deoxylankanolide. Other 8-deoxy lankamycin/lankanolide derivatives were not oxidized, suggesting the importance of a C-3 l-arcanosyl moiety for substrate recognition by LkmF in lankamycin biosynthesis. Thus, LkmF has a strict substrate specificity in lankamycin biosynthesis.
CapiPy: python-based GUI-application to assist in protein immobilization
Authors: Roura Padrosa David , Marchini Valentina , Paradisi Francesca 
Published: January 2021

Abstract

Summary
Protein immobilization, while widespread to unlock enzyme potential in biocatalysis, remains tied to a trial an error approach. Nonetheless, several databases and computational methods have been developed for protein characterization and their study. CapiPy is a user-friendly application for protein model creation and subsequent analysis with a special focus on the ease of use and interpretation of the results to help the users to make an informed decision on the immobilization approach which should be ideal for a protein of interest. The package has been tested with three separate random sets of 150 protein sequences from Uniprot with more than a 70% overall success rate (see Supplementary information and Supplementary Dataset).

Availability and implementation
The package is free to use under the GNU General Public License v3.0. All necessary files can be downloaded from https://github.com/drou0302/CapiPy or https://pypi.org/project/CapiPy/. All external requirements are also freely available, with some restrictions for non-academic users.

Supplementary information
Supplementary data are available at Bioinformatics online.
HIVID2: an accurate tool to detect virus integrations in the host genome
Authors: Zeng Xi , Zhao Linghao , Shen Chenhang , Zhou Yi , Li Guoliang , Sung Wing-Kin 
Published: January 2021

Abstract

Motivation
Virus integration in the host genome is frequently reported to be closely associated with many human diseases, and the detection of virus integration is a critically challenging task. However, most existing tools show limited specificity and sensitivity. Therefore, the objective of this study is to develop a method for accurate detection of virus integration into host genomes.

Results
Herein, we report a novel method termed HIVID2 that is a significant upgrade of HIVID. HIVID2 performs a paired-end combination (PE-combination) for potentially integrated reads. The resulting sequences are then remapped onto the reference genomes, and both split and discordant chimeric reads are used to identify accurate integration breakpoints with high confidence. HIVID2 represents a great improvement in specificity and sensitivity, and predicts breakpoints closer to the real integrations, compared with existing methods. The advantage of our method was demonstrated using both simulated and real datasets. HIVID2 uncovered novel integration breakpoints in well-known cervical cancer-related genes, including FHIT and LRP1B, which was verified using protein expression data. In addition, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations. By analyzing the simulated data and real data tests, we demonstrated that HIVID2 is not only more accurate than HIVID but also better than other existing programs with respect to both sensitivity and specificity. We believe that HIVID2 will help in enhancing future research associated with virus integration.

Availabilityand implementation
HIVID2 can be accessed at https://github.com/zengxi-hada/HIVID2/.

Supplementary information
Supplementary data are available at Bioinformatics online.
CoRC: the COPASI R Connector
Authors: Förster Jonas , Bergmann Frank T. , Pahle Jürgen 
Published: January 2021

Abstract

Motivation
COPASI is a biochemical simulator and model analyzer which has found widespread use in academic research, teaching and beyond. One of COPASI’s strengths is its graphical user interface, and this is what most users work with. COPASI also provides a command-line tool. So far, an intuitive scripting interface that allows the creation and documentation of systems biology workflows was missing though.

Results
We have developed CoRC, the COPASI R Connector, an R package which provides a high-level scripting interface for COPASI. It closely mirrors the thought process of a (graphical interface) user and should therefore be very easy to use. This allows for complex workflows to be reproducibly scripted, utilizing COPASI’s powerful analytic toolset in combination with R’s extensive analysis and package ecosystem.

Availability and implementation
CoRC is a free and open-source R package, available via GitHub at https://jpahle.github.io/CoRC/ under the Artistic-2.0 license.

Supplementary information
We provide tutorial articles as well as several example scripts on the project’s website.
Off-label underdosed apixaban use in Asian patients with non-valvular atrial fibrillation
Authors: Lee So-Ryoung , Choi Eue-Keun , Park Sang-Hyun , Jung Jin-Hyung , Han Kyung-Do , Oh Seil , Lip Gregory Y H 
Published: January 2021

Abstract

Aims
To compare the effectiveness and safety of off-label underdosed apixaban with on-label standard dose apixaban in Asian patients with atrial fibrillation (AF).

Methods and results
Using the Korean nationwide claims database, we identified patients who were prescribed apixaban and did not fulfil the dose reduction criteria for apixaban between January 2015 and December 2017. A multivariable Cox hazard regression model was performed, and hazard ratios (HRs) for ischaemic stroke, major bleeding (MB), all-cause death, and composite outcome were analysed. Compared to patients prescribed on-label standard dose apixaban (n = 4194), patients prescribed off-label underdosed apixaban (n = 2890) showed a higher risk of ischaemic stroke [adjusted HR (aHR) 1.38, 95% confidence interval (CI) 1.06–1.81], all-cause death (aHR 1.19, 95% CI 1.01–1.39), and the composite outcome (aHR 1.17, 95% CI 1.03–1.34), but with no significant differences in MB between the two groups. Among the patients who did not meet any dose reduction criteria, off-label underdosed apixaban use was associated with a significantly higher risk of ischaemic stroke than on-label standard dose apixaban use (aHR 1.85, 95% CI 1.25–2.73). Among the patients who met a single dose reduction criterion, off-label underdosed apixaban use was associated with a higher risk of all-cause death than on-label standard dose apixaban (aHR 1.32, 95% CI 1.07–1.64).

Conclusion
The off-label underdosed apixaban group showed higher risks of ischaemic stroke, all-cause death, and composite clinical outcomes than the on-label standard dose apixaban group, but both showed comparable risks of MB. Label adherence to apixaban dosing should be emphasized to achieve the best clinical outcomes for Asian patients with AF.
Two genetic elements regulate murine beta-glucuronidase synthesis following transcript accumulation.
Authors: Wawrzyniak C J , Meredith S A , Ganschow R E 
Published: January 2021

Abstract
Mutant alleles of two genetic regulatory elements, which underlie a three- to sixfold reduction in beta-glucuronidase (GUS) activity levels, distinguish mice of the H haplotype from those of the other two common GUS haplotypes, A and B. Both elements are tightly linked to the GUS structural gene over which they exert control. One (Gus-u) exerts a cis-active effect upon GUS activity levels in all tissues at all times while the other (Gus-t) regulates GUS activity in trans after the 12th postnatal day in certain tissues. While previous studies show that differences in the rate of GUS synthesis account for the combined effects of these two elements in liver of adult mice, we demonstrate the separate effects of each on GUS synthesis at times during early postnatal development when their individual expressions can be distinguished. Assessments of the relative levels of S1 nuclease protection of a radiolabeled GUS antisense RNA probe after hybridization with total liver RNA preparations from adult mice of A and H haplotypes reveal no differences. These results argue that Gus-u and Gus-t exert their control of GUS expression subsequent to the accumulation of processed GUS transcripts.
The Tc3 family of transposable genetic elements in Caenorhabditis elegans.
Authors: Collins J , Forbes E , Anderson P 
Published: January 2021

Abstract
We describe genetic and molecular properties of Tc3, a family of transposable elements in Caenorhabditis elegans. About 15 Tc3 elements are present in the genomes of several different wild-type varieties of C. elegans, but Tc3 transposition and excision are not detected in these strains. Tc3 transposition and excision occur at high frequencies, however, in strain TR679, a mutant identified because of its highly active Tc1 elements. In TR679, Tc3 is responsible for several spontaneous mutations affecting the unc-22 gene. Tc3-induced mutations are unstable, and revertants result from precise or nearly precise excision of Tc3. Although Tc3 is very active in TR679, it is not detectably active in several other mutator mutants, all of which exhibit high levels of Tc1 activity. Tc3 is 2.5 kilobases long, and except for sequences near its inverted repeat termini, it is unrelated to Tc1. The termini of Tc3 are inverted repeats of at least 70 base pairs; the terminal 8 nucleotides of Tc3 are identical to 8 of the terminal 9 nucleotides of Tc1.
Phage lambda Cro protein and cI repressor use two different patterns of specific protein-DNA interactions to achieve sequence specificity in vivo.
Authors: Benson N , Youderian P 
Published: January 2021

Abstract
By assaying the binding of wild-type Cro to a set of 40 mutant lambda operators in vivo, we have determined that the 14 outermost base pairs of the 17 base pair, consensus lambda operator are critical for Cro binding. Cro protein recognizes 4 base pairs in a lambda operator half-site in different ways than cI repressor. The sequence determinants of Cro binding at these critical positions in vivo are nearly perfectly consistent with the model proposed by W. F. ANDERSON, D. H. OHLENDORF, Y. TAKEDA and B. W. MATTHEWS and modified by Y. TAKEDA, A. SARAI and V. M. RIVERA for the specific interactions between Cro and its operator, and explain the relative order of affinities of the six natural lambda operators for Cro. Our data call into question the idea that lambda repressor and Cro protein recognize the consensus lambda operator by nearly identical patterns of specific interactions.
IS103, a new insertion element in Escherichia coli: characterization and distribution in natural populations.
Authors: Hall B G , Parker L L , Betts P W , DuBose R F , Sawyer S A , Hartl D L 
Published: January 2021

Abstract
IS103 is a previously unknown insertion sequence found in Escherichia coli K12. We have sequenced IS103 and find that it is a 1441-bp element that consists of a 1395-bp core flanked by imperfect 23-bp inverted repeats. IS103 causes a 6-bp duplication of the target sequence into which it inserts. There is a single copy of IS103 present in wild-type E. coli K12 strain HfrC. In strain X342 and its descendents there are two additional copies, one of which is located within the bglF gene. IS103 is capable of excising from within bglF and restoring function of that gene. IS103 exhibits 44% sequence identity with IS3, suggesting that the two insertion sequences are probably derived from a common ancestor. We have examined the distribution of IS103 in the chromosomes and plasmids of the ECOR collection of natural isolates of E. coli. IS103 is found in 36 of the 71 strains examined, and it strongly tends to inhabit plasmids rather than chromosomes. Comparison of the observed distribution of IS103 with distributions predicted by nine different models for the regulation of transposition according to copy number and of the effects of copy number on fitness suggest that transposition of IS103 is strongly regulated and that it has only minor effects on fitness. The strong clustering of IS103 within one phylogenetic subgroup of the E. coli population despite its presence on plasmids suggests that plasmids tend to remain within closely related strains and that transfer to distantly related strains is inhibited.