bluuebunny/crossref_metadata_2025_split huggingface dataset:
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata
Authors: Shokrof Moustafa , Brown C. Titus , Mansour Tamer A. 
Published: February 2021

AbstractBackgroundSpecialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can efficiently store k-mers with a skewed distribution.ResultHere, we present the mixed-counters quotient filter (MQF) as a new variant of the CQF with novel counting and labeling systems. The new counting system adapts to a wider range of data distributions for increased space efficiency and is faster than the CQF for insertions and queries in most of the tested scenarios. A buffered version of the MQF can offload storage to disk, trading speed of insertions and queries for a significant memory reduction. The labeling system provides a flexible framework for assigning labels to member items while maintaining good data locality and a concise memory representation. These labels serve as a minimal perfect hash function but are ~ tenfold faster than BBhash, with no need to re-analyze the original data for further insertions or deletions.ConclusionsThe MQF is a flexible and efficient data structure that extends our ability to work with high throughput sequencing data.
Evolutionary pattern of Macaca fascicularis in Southeast Asia inferred using Y-chromosomal gene
Authors: Rovie-Ryan Jeffrine J. , Khan Faisal Ali Anwarali , Abdullah Mohd Tajuddin 
Published: February 2021

AbstractBackgroundWe analyzed a combined segment (2032-bp) of the sex-determining region and the testis-specific protein of the Y-chromosome (Y-DNA) gene to clarify the gene flow and phylogenetic relationships of the long-tailed macaques (Macaca fascicularis) in Southeast Asia. Phylogenetic relationships were constructed using the maximum likelihood, Bayesian inference, and the median-joining network from a total of 164 adult maleM. fascicularisfrom 62 localities in Malaysia, including sequences from the other regions from previous studies.ResultsBased on Y-DNA, we confirm the presence of two lineages ofM. fascicularis: the Indochinese and Sundaic lineages. The Indochinese lineage is represented byM. fascicularislocated northwards of the Surat Thani-Krabi depression region and is introgressed by theMacaca mulattaY-DNA. The Sundaic lineage is free from such hybridization event, thus defined as the original carrier of theM. fascicularisY-DNA. We further revealed that the Sundaic lineage differentiated into two forms: the insular and the continental forms. The insular form, which represents the ancestral form ofM. fascicularis, consists of two haplotypes: a single homogenous haplotype occupying the island of Borneo, Philippines, and southern Sumatra; and the Javan haplotype.The more diverse continental form consists of 17 haplotypes in which a dominant haplotype was shared by individuals from southern Thai Peninsular (south of Surat Thani-Krabi depression), Peninsular Malaysia, and Sumatra. Uniquely, Sumatra contains both the continental and insular Y-DNA which can be explained by a secondary contact hypothesis.ConclusionsOverall, the findings in this study are important: (1) to help authority particularly in Malaysia on the population management activities including translocation and culling of conflictM. fascicularis, (2) to identify the unknown origin of captiveM. fascicularisused in biomedical research, and; (3) the separation between the continental and insular forms warrants for the treatment as separate management units.
Protecting the patches from the footprints: examining the land use factors associated with forest patches in Atewa range forest reserve
Authors: Agyemang-Duah Williams , Oduro Appiah Joseph , Adei Dina 
Published: February 2021

Abstract
Background
Land use practices are noted to contribute to changes in forest landscape composition. However, whereas studies have reported the intermix of land uses and forest patches and measured the direct impacts of land uses on forest patches, little is known regarding the spatially-explicit association between the most recent forest patches and land use footprints in protected areas. In this study, we use methods from GIS, remote sensing, and statistics to model the spatial relationship between footprints of land uses and patches of forest cover by drawing on geospatial data from the Atewa range forest reserve (ARFR).

Results
The study finds that forest patches that are within 1 km from agricultural land use footprints (AOR = 86.625, C.I. 18.057–415.563, P = 0.000), logging sites (AOR = 55.909, C.I. 12.032–259.804, P = 0.000), mine sites (53.571, C.I. 11.287–254.255, P = 0.000), access roads (AOR = 24.169, C.I. 5.544–105.357, P = 0.000), and human settlement footprints (AOR = 7.172, C.I. 1.969–26.128, P = 0.003) are significantly more likely to be less than the mean patch area (375,431.87 m2 = 37.54 ha) of forest cover. A ROC statistic of 0.995 achieved in this study suggests a high predictive power of the proposed model.

Conclusion
The study findings suggest that to ensure sustainable land uses and ecological integrity, there is a need for land use policies and land management strategies that ensure responsible livelihood activities as well as further restrictions on logging and mining in the globally significant biodiversity area.
Nectar-dwelling microbes of common tansy are attractive to its mosquito pollinator, Culex pipiens L.
Authors: Peach D. A. H. , Carroll C. , Meraj S. , Gomes S. , Galloway E. , Balcita A. , Coatsworth H. , Young N. , Uriel Y. , Gries R. , Lowenberger C. , Moore M. , Gries G. 
Published: February 2021

AbstractBackgroundThere is widespread interkingdom signalling between insects and microbes. For example, microbes found in floral nectar may modify its nutritional composition and produce odorants that alter the floral odor bouquet which may attract insect pollinators. Mosquitoes consume nectar and can pollinate flowers. We identified microbes isolated from nectar of common tansy,Tanacetum vulgare, elucidated the microbial odorants, and tested their ability to attract the common house mosquito,Culex pipiens.ResultsWe collected 19 microbial isolates fromT. vulgarenectar, representing at least 12 different taxa which we identified with 16S or 26S rDNA sequencing as well as by biochemical and physiological tests. Three microorganisms (Lachancea thermotolerans, Micrococcus lactis,Micrococcus luteus) were grown on culture medium and tested in bioassays. Only the yeastL. thermotoleransgrown on nectar, malt extract agar, or in synthetic nectar broth significantly attractedCx. pipiensfemales. The odorant profile produced byL. thermotoleransvaried with the nutritional composition of the culture medium. All three microbes grown separately, but presented concurrently, attracted fewerCx. pipiensfemales thanL. thermotoleransby itself.ConclusionsFloral nectar ofT. vulgarecontains various microbes whose odorants contribute to the odor profile of inflorescences. In addition,L. thermotoleransproduced odorants that attractCx. pipiensfemales. As the odor profile ofL. thermotoleransvaried with the composition of the culture medium, we hypothesize that microbe odorants inform nectar-foraging mosquitoes about the availability of certain macro-nutrients which, in turn, affect foraging decisions by mosquitoes.
GCA: an R package for genetic connectedness analysis using pedigree and genomic data
Authors: Yu Haipeng , Morota Gota 
Published: February 2021

AbstractBackgroundGenetic connectedness is a critical component of genetic evaluation as it assesses the comparability of predicted genetic values across units. Genetic connectedness also plays an essential role in quantifying the linkage between reference and validation sets in whole-genome prediction. Despite its importance, there is no user-friendly software tool available to calculate connectedness statistics.ResultsWe developed the GCA R package to perform genetic connectedness analysis for pedigree and genomic data. The software implements a large collection of various connectedness statistics as a function of prediction error variance or variance of unit effect estimates. The GCA R package is available at GitHub and the source code is provided as open source.ConclusionsThe GCA R package allows users to easily assess the connectedness of their data. It is also useful to determine the potential risk of comparing predicted genetic values of individuals across units or measure the connectedness level between training and testing sets in genomic prediction.
Age-related changes of microbiota in midlife associated with reduced saccharolytic potential: an in vitro study
Authors: Chen Junkui , Pi Xionge , Liu Wei , Ding Qunfang , Wang Xin , Jia Weiguo , Zhu Liying 
Published: February 2021

Abstract
Background
Gut microbiota is critical in maintaining human health, of which diversity and abundance are subject to significantly reduce in seniors. Gut microbiota is reported to be stable across the long adulthood in general, but lack of careful examination, especially for the midlife people.

Results
To characterize the gut microbiota in midlife, we investigated the faecal microbiota between two groups of healthy people, young, 20–39 years old, n = 15; and midlife, 40–60 years old, n = 15. Metabolic responses of the microbiota were studied through in vitro batch fermentation model. Although no difference was observed in the diversity indices between the two age groups, a wide range taxonomic changes were found in the faecal microbiota. Furthermore, substantial Bifidobacterium reduction was also found in both faecal and fermented samples. The faecal SCFAs are similar in both groups, as well as starch fermentation broth. However, after inulin fermentation, the acetate concentration and inulin degradation rate decreased while the gas production increased in midlife group, suggesting a deficiency of saccharolytic potential in midlife, especially for non-digestible carbohydrate.

Conclusions
Our data demonstrate that gut microbiota begins to change as early as in midlife. The reduction in Bifidobacterium dominates the change of the microbiota composition in midlife resulting in attenuated saccharolytic capacity of inulin, possibly leading to insufficient acetate production which might be associated with healthy problems in this transition period from young to elderly.
Comparison of BCYEα+AB agar and MWY agar for detection and enumeration of Legionella spp. in hospital water samples
Authors: Ditommaso Savina , Giacomuzzi Monica , Memoli Gabriele , Garlasco Jacopo , Zotti Carla M. 
Published: February 2021

AbstractBackgroundThis study illustrates for the first time the performance (sensitivity and selectivity) of the selective medium BCYEα +AB suggested by the new edition of ISO 11731 for legionella isolation and enumeration. We compared the efficacy of the selective BCYEα +AB medium with that of the highly selective MWY medium.ResultsLegionellaspp.was detected in 48.2 and 47.1% of the samples by BCYEα +AB and MWY agar, respectively. For optimal detection ofLegionellaspp., most protocols recommend using selective media to reduce the number of non-Legionellabacteria. Agreement between the two media was 86.7%.ConclusionsAccording to the results, both media have a very similar performance and they both have advantages and disadvantages over each other. In AB medium there is the risk of being less selective so more interfering microbiota may grow but in MWY medium there is the risk of being too selective. The low selectivity of the AB medium could be resolved if other treatments are applied after filtration, e.g. acid and/or heat treatment, but it must be taken into account that these treatments still reduce the number of viableLegionella. In conclusion, we recommend using MWY as a selective medium for the detection ofLegionellaspp. as it is easier discern suspected colonies and facilitate the finalLegionellaspp. count.
The visually estimated blood volume in scaled canisters based on a simulation study
Authors: Gerdessen Lara , Neef Vanessa , Raimann Florian J. , Zacharowski Kai , Piekarski Florian 
Published: February 2021

Abstract
Background
The most common technique used worldwide to quantify blood loss during an operation is the visual assessment by the attending intervention team. In every operating room you will find scaled suction canisters that collect fluids from the surgical field. This scaling is commonly used by clinicians for visual assessment of intraoperative blood loss. While many studies have been conducted to quantify and improve the inaccuracy of the visual estimation method, research has focused on the estimation of blood volume in surgical drapes. The question whether and how scaling of canisters correlates with actual blood loss and how accurately clinicians estimate blood loss in scaled canisters has not been the focus of research to date.

Methods
A simulation study with four “bleeding” scenarios was conducted using expired whole blood donations. After diluting the blood donations with full electrolyte solution, the sample blood loss volume (SBL) was transferred into suction canisters. The study participants then had to estimate the blood loss in all four scenarios. The difference to the reference blood loss (RBL) per scenario was analyzed.

Results
Fifty-three anesthetists participated in the study. The median estimated blood loss was 500 ml (IQR 300/1150) compared to the RBL median of 281.5 ml (IQR 210.0/1022.0). Overestimations up to 1233 ml were detected. Underestimations were also observed in the range of 138 ml. The visual estimate for canisters correlated moderately with RBL (Spearman’s rho: 0.818; p < 0.001). Results from univariate nonparametric confirmation statistics regarding visual estimation of canisters show that the deviation of the visual estimate of blood loss is significant (z = − 10.95, p < 0.001, n = 220). Participants’ experience level had no significant influence on VEBL (p = 0.402).

Conclusion
The discrepancies between the visual estimate of canisters and the actual blood loss are enormous despite the given scales. Therefore, we do not recommend estimating the blood loss visually in scaled suction canisters. Colorimetric blood loss estimation could be a more accurate option.
The impact of vildagliptin on the daily glucose profile and coronary plaque stability in impaired glucose tolerance patients with coronary artery disease: VOGUE—A multicenter randomized controlled trial
Authors: Yamamoto Hiroyuki , Konishi Akihide , Shinke Toshiro , Otake Hiromasa , Kuroda Masaru , Osue Tsuyoshi , Sawada Takahiro , Takaya Tomofumi , Kawai Hiroya , Hashimoto Naoko , Ohara Takeshi , Hirota Yushi , Sakaguchi Kazuhiko , Omori Takashi , Ogawa Wataru , Hirata Ken-ichi 
Published: February 2021

Abstract
Background
The impact of reduction in glycemic excursion on coronary plaques remains unknown. This study aimed to elucidate whether a dipeptidyl peptidase 4 inhibitor could reduce the glycemic excursion and stabilize the coronary plaques compared with conventional management in coronary artery disease (CAD) patients with impaired glucose tolerance (IGT).

Methods
This was a multicenter, randomized controlled trial including CAD patients with IGT under lipid-lowering therapy receiving either vildagliptin (50 mg once a day) or no medication (control group) regarding glycemic treatment. The primary endpoint was changes in the minimum fibrous cap thickness and lipid arc in non-significant native coronary plaques detected by optical coherence tomography at 6 months after intervention. Glycemic variability expressed as the mean amplitude of glycemic excursion (MAGE) measured with a continuous glucose monitoring system was evaluated before and 6 months after intervention.

Results
A total of 20 participants with 47 lesions were allocated to either the vildagliptin group (10 participants, 22 lesions) or the control group (10 participants, 25 lesions). The adjusted difference of mean changes between the groups was − 18.8 mg/dl (95% confidence interval, − 30.8 to − 6.8) (p = 0.0064) for the MAGE (vildagliptin, − 20.1 ± 18.0 mg/dl vs. control, 2.6 ± 12.7 mg/dl), − 22.8° (− 40.6° to − 5.1°) (p = 0.0012) for the mean lipid arc (vildagliptin, − 9.0° ± 25.5° vs. control, 15.8° ± 16.8°), and 42.7 μm (15.3 to 70.1 μm) (p = 0.0022) for the minimum fibrous cap thickness (vildagliptin, 35.7 ± 50.8 μm vs. control, − 15.1 ± 25.2 μm).

Conclusions
Vildagliptin could reduce the MAGE at 6 months and may be associated with the decreased lipid arc and increased minimum FCT of the coronary plaques in CAD patients with IGT as compared with the control group. These findings may represent its potential stabilization effect on coronary plaques, which are characteristic in this patient subset.
Trial registration Registered in the UMIN clinical trial registry (UMIN000008620), Name of the registry: VOGUE trial, Date of registration: Aug 6, 2012, URL: https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000010058
Assessment of the ability of the CHA2DS2-VASc scoring system to grade left atrial function by 2D speckle-tracking echocardiography
Authors: Hadadi Marjan , Mohseni-Badalabadi Reza , Hosseinsabet Ali 
Published: February 2021

AbstractBackgroundThe CHA2DS2-VASc scoring system is correlated with left atrial (LA) reservoir function in patients with atrial fibrillation (AF) rhythm or paroxysmal AF. We assessed the ability of CHA2DS2-VASc to grade LA function in patients with sinus rhythm who were candidates for coronary artery bypass grafting (CABG).MethodsThis cross-sectional study recruited 340 consecutive candidates for CABG and categorized them according to their CHA2DS2-VASc scores as mild-, moderate-, and high-risk score groups with 34 (10%), 83 (24%), and 223 (66%) patients, respectively. LA function was evaluated via 2D speckle-tracking echocardiography in terms of global longitudinal strain and strain rate during the reservoir, conduit, and contraction phases. In-hospital mortality, postoperative AF, prolonged intensive care unit (ICU) stay, and prolonged mechanical ventilation were assessed.ResultsLA strain and strain rate during the reservoir phase was statistically significantly lower in the high-risk score group than the low- and moderate-risk score groups (27.8 ± 6.9% vs 31.0 ± 5.0% vs 29.8 ± 6.1%, respectively;P = 0.004 and 2.6 ± 0.7 s−1vs 2.9 ± 0.6 s−1vs 2.9 ± 0.6 s−1, correspondingly;P = 0.009) and regarding LA strain and strain rate during the conduit phase (9.7 [7.1–12.5]% vs 12.9 [9.4–15.1]% vs 11.5 [9.1–13.8]%, correspondingly;P < 0.001 and 2.1 [1.6–2.7] s−1vs 2.8 [2.4–3.6] s−1vs 2.6 [2.2–3.0] s−1, respectively;P < 0.001). In addition, LA strain rate during the conduit phase was lower in the moderate-risk score group than the low-risk score group. After adjustments for possible confounders, these differences remained statistically significant. The risk of postoperative AF and prolonged ICU stay was highest in the high-risk score group (relative risk = 9.67 (1.31–71.43) and 8.05 (1.08–60.16), respectively;P = 0.026 andP = 0.042, respectively).ConclusionsLA reservoir and conduit functions decreased in the high-risk score group, which was accompanied by an increased risk of postoperative AF and prolonged ICU stay.
Family satisfaction in the intensive care unit, a cross-sectional study from Norway
Authors: Haave Randi Olsson , Bakke Hilde Hammerud , Schröder Agneta 
Published: February 2021

AbstractBackgroundBecoming critically ill represents not just a great upheaval for the patient in question, but also for the patient’s closest family. In recent years, there has been a change in how the quality of the public health service is measured. There is currently a focus on how patients and their families perceive the quality of treatment and care. It can be challenging for patients to evaluate their stay in an intensive care unit (ICU) due to illness and treatment. Earlier studies show that the perceptions of the family and the patient may concur. It is important, therefore, to ascertain the family’s level of satisfaction with the ICU stay.The aim of the study was to describe how the family evaluate their satisfaction with the ICU stay. A further aim was to identify which demographic variables were associated with differences in family satisfaction.MethodThe study had a cross-sectional design. A sample of 57 family members in two ICUs in Norway completed the questionnaire: Family satisfaction in the intensive care unit 24 (FS-ICU 24). Statistical analysis was conducted using the Mann-Whitney U test (U), Kruskal Wallis, Spearman rho and a performance-importance plot.ResultsThe results showed that families were very satisfied with a considerable portion of the ICU stay. Families were less satisfied with the information they received and the decision-making processes than with the nursing and care performed during the ICU stay. The results revealed that two demographic variables – relation to the patient and patient survival – significantly affected family satisfaction.ConclusionAlthough families were very satisfied with the ICU stay, several areas were identified as having potential for improvement. The results showed that some of the family demographic variables were significant for family satisfaction. The findings are clinically relevant since the results can strengthen intensive care nurses’ knowledge when meeting the family of the intensive care patient.
Regression models for interval censored data using parametric pseudo-observations
Authors: Johansen Martin Nygård , Lundbye-Christensen Søren , Larsen Jacob Moesgaard , Parner Erik Thorlund 
Published: February 2021

Abstract
Background
Time-to-event data that is subject to interval censoring is common in the practice of medical research and versatile statistical methods for estimating associations in such settings have been limited. For right censored data, non-parametric pseudo-observations have been proposed as a basis for regression modeling with the possibility to use different association measures. In this article, we propose a method for calculating pseudo-observations for interval censored data.

Methods
We develop an extension of a recently developed set of parametric pseudo-observations based on a spline-based flexible parametric estimator. The inherent competing risk issue with an interval censored event of interest necessitates the use of an illness-death model, and we formulate our method within this framework. To evaluate the empirical properties of the proposed method, we perform a simulation study and calculate pseudo-observations based on our method as well as alternative approaches. We also present an analysis of a real dataset on patients with implantable cardioverter-defibrillators who are monitored for the occurrence of a particular type of device failures by routine follow-up examinations. In this dataset, we have information on exact event times as well as the interval censored data, so we can compare analyses of pseudo-observations based on the interval censored data to those obtained using the non-parametric pseudo-observations for right censored data.

Results
Our simulations show that the proposed method for calculating pseudo-observations provides unbiased estimates of the cumulative incidence function as well as associations with exposure variables with appropriate coverage probabilities. The analysis of the real dataset also suggests that our method provides estimates which are in agreement with estimates obtained from the right censored data.

Conclusions
The proposed method for calculating pseudo-observations based on the flexible parametric approach provides a versatile solution to the specific challenges that arise with interval censored data. This solution allows regression modeling using a range of different association measures.