bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scandcleft randomized trials of primary surgery for unilateral cleft lip and palate: impact of maxillary dental agenesis on craniofacial growth and dental arch relationship in 8 year olds
Authors: Rizell Sara , Küseler Annelise , Heliövaara Arja , Skaare Pål , Brinck Eli , Bellardie Haydn , Mooney Jeanette , Mølsted Kirsten , Karsten Agneta , Sæle Paul , Chalien Midia Najar , Marcusson Agneta , Eyres Philip , Shaw William , Semb Gunvor 
Published: February 2021

Summary

Background
It is suggested that dental agenesis affects maxillary protrusion and dental arch relationship in children with unilateral cleft lip and palate (UCLP). In addition, an association between the need for orthognathic surgery and dental agenesis is reported.

Aim
The aim was to study the impact of maxillary dental agenesis on craniofacial growth and dental arch relationship in 8-year-old children with UCLP.

Subjects and methods
The sample consisted of individuals with UCLP from Scandcleft randomized trials. The participants had available data from diagnosis of maxillary dental agenesis as well as cephalometric measurements (n = 399) and GOSLON assessment (n = 408) at 8 years of age.

Results
A statistically significant difference was found for ANB between individuals with agenesis of two or more maxillary teeth (mean 1.52°) in comparison with those with no or only one missing maxillary tooth (mean 3.30° and 2.70°, respectively). Mean NSL/NL was lower among individuals with agenesis of two or more maxillary teeth (mean 9.90°), in comparison with individuals with no or one missing maxillary tooth (mean 11.46° and 11.45°, respectively). The number of individuals with GOSLON score 4–5 was 47.2% in the group with two or more missing maxillary teeth and 26.1% respectively 26.3% in the groups with no or one missing maxillary tooth. No statistically significant difference was found in the comparison between individuals with no agenesis or with agenesis solely of the cleft-side lateral.

Conclusion
Maxillary dental agenesis impacts on craniofacial growth as well as dental arch relationship and should be considered in orthodontic treatment planning.
An RNA-interference screen in Drosophila to identify ZAD-containing C2H2 zinc finger genes that function in female germ cells
Authors: Shapiro-Kulnane Laura , Bautista Oscar , Salz Helen K 
Published: February 2021

Abstract
The zinc finger-associated domain (ZAD) is present in over 90 C2H2 zinc finger (ZNF) proteins. Despite their abundance, only a few ZAD-ZNF genes have been characterized to date. Here, we systematically analyze the function of 68 ZAD-ZNF genes in Drosophila female germ cells by performing an in vivo RNA-interference screen. We identified eight ZAD-ZNF genes required for oogenesis, and based on further characterization of the knockdown phenotypes, we uncovered defects broadly consistent with functions in germ cell specification and/or survival, early differentiation, and egg chamber maturation. These results provide a candidate pool for future studies aimed at functionalization of this large but poorly characterized gene family.
Genome assembly and annotation of the California harvester antPogonomyrmex californicus
Authors: Bohn Jonas , Halabian Reza , Schrader Lukas , Shabardina Victoria , Steffen Raphael , Suzuki Yutaka , Ernst Ulrich R , Gadau Jürgen , Makałowski Wojciech 
Published: February 2021

AbstractThe harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America. The California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in North America. Pogonomyrmex californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present a genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in agreement with the previously estimated genome size. We were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness at a 95% level. The presented P. californicus genome assembly will pave the way for investigations of the genomic underpinnings of social polymorphism in the number of queens, regulation of aggression, and the evolution of adaptations to dry habitats.
Roles for RNA export factor, Nxt1, in ensuring muscle integrity and normal RNA expression in Drosophila
Authors: van der Graaf Kevin , Jindrich Katia , Mitchell Robert , White-Cooper Helen 
Published: February 2021

Abstract
The mRNA export pathway is responsible for the transport of mRNAs from the nucleus to the cytoplasm, and thus is essential for protein production and normal cellular functions. A partial loss of function allele of the mRNA export factor Nxt1 in Drosophila shows reduced viability and sterility. A previous study has shown that the male fertility defect is due to a defect in transcription and RNA stability, indicating the potential for this pathway to be implicated in processes beyond the known mRNA transport function. Here we investigate the reduced viability of Nxt1 partial loss of function mutants, and describe a defect in growth and maintenance of the larval muscles, leading to muscle degeneration. RNA-seq revealed reduced expression of a set of mRNAs, particularly from genes with long introns in Nxt1 mutant carcass. We detected differential expression of circRNA, and significantly fewer distinct circRNAs expressed in the mutants. Despite the widespread defects in gene expression, muscle degeneration was rescued by increased expression of the costamere component tn (abba) in muscles. This is the first report of a role for the RNA export pathway gene Nxt1 in the maintenance of muscle integrity. Our data also links the mRNA export pathway to a specific role in the expression of mRNA and circRNA from common precursor genes, in vivo.
AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology
Authors: Min Daniel , Doxey Andrew C , Neufeld Josh D 
Published: February 2021

Abstract

Background
Advances in high-throughput sequencing accessibility have democratized small subunit ribosomal RNA gene sequence data collection, coincident with an increasing availability of computational tools for sequence data processing, multivariate statistics, and data visualization. However, existing tools often require programming ability and frequent user intervention that may not be suitable for fast-paced and large-scale data analysis by end user microbiologists who are unfamiliar with the Linux command line environment or who prefer interactions with a GUI. Here we present AXIOME3, which is a completely redeveloped AXIOME pipeline that streamlines small subunit ribosomal RNA data analysis by managing QIIME2, R, and Python-associated analyses through an interactive web interface.

Findings
AXIOME3 comes with web GUI to improve usability by simplifying configuration processes and task status tracking. Internally, it uses an automated pipeline that is wrapped around QIIME2 to generate a range of outputs including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations. The extension module for AXIOME3 provides advanced data visualization tools such as principal coordinate analysis, bubble plots, and triplot ordinations that can be used to visualize interactions between a distance matrix, amplicon sequence variant taxonomy, and sample metadata.

Conclusions
Because repeat analysis of small subunit ribosomal RNA amplicon sequence data is challenging for those who have limited experience in command line environments, AXIOME3 now offers rapid and user-friendly options within an automated pipeline, with advanced data visualization tools and the ability for users to incorporate additional analyses easily through extension. AXIOME3 is completely open source (https://github.com/neufeld/AXIOME3, https://github.com/neufeld/AXIOME3-GUI), and researchers are encouraged to modify and redistribute the package.
High-resolution Bayesian spatial autocorrelation (SPAC) quasi-3-D Vs model of Utah FORGE site with a dense geophone array
Authors: Zhang Hao , L. Pankow Kristine 
Published: February 2021

SUMMARY
We expand the application of spatial autocorrelation (SPAC) from typical 1-D Vs profiles to quasi-3-D imaging via Bayesian Monte Carlo inversion (BMCI) using a dense nodal array (49 nodes) located at the Utah Frontier Observatory for Research in Geothermal Energy (FORGE) site. Combinations of 4 and 9 geophones in subarrays provide for 36 and 25 1-D Vs profiles, respectively. Profiles with error bars are determined by calculating coherency functions that fit observations in a frequency range of 0.2–5 Hz. Thus, a high-resolution quasi-3-D Vs model from the surface to 2.0 km depth is derived and shows that surface-parallel sedimentary strata deepen to the west, consistent with a 3-D seismic reflection survey. Moreover, the resulting Vs profile is consistent with a Vs profile derived from distributed acoustic sensing (DAS) data located in a borehole at the FORGE site. The quasi-3-D velocity model shows that the base of the basin dips ∼22° to the west and topography on the basement interface coincident with the Mag Lee Wash suggests that the bedrock interface is an unconformity.
The Crime of Genocide in General Assembly Resolutions: Legal Foundations and Effects
Authors: Ramsden Michael 
Published: February 2021

Abstract
The past decade has seen increased scholarly attention on the practice and latent potential of the United Nations General Assembly (‘Assembly’) to secure accountability for atrocity crimes. This increased focus has arisen primarily due to growing frustration over permanent member deadlock in the Security Council in the face of documented atrocities. One aspect of this nascent research agenda yet to be analysed is the invocation of the crime of genocide in Assembly resolutions and practice. Studies have shown the Security Council to have applied the genocide label selectively and only where aligned with the permanent members’ interests. Can the same be said about the Assembly? This article tracks the use of the genocide norm in Assembly resolutions, revealing two major functions: prescriptive and quasi-judicial. It notes that Resolution 96(I) (1946) has had a pervasive influence on the development of the crime of genocide. Still, later attempts in the Assembly to develop the genocide definition have enjoyed less success. Although the Assembly has been beset with political selectivity in the use of the genocide label, the rise of commissions of inquiry in UN practice can usefully augment a closer dialogue between their outputs and Assembly resolutions, as recent resolutions concerning alleged crimes against the Rohingya show.
Density-independent mortality at early life stages increases the probability of overlooking an underlying stock–recruitment relationship
Authors: Zimmermann Fabian , Enberg Katja , Mangel Marc 
Published: February 2021

Abstract
Beverton and Holt’s (1957. On the dynamics of exploited fish populations. UK Ministry of Agriculture, Fisheries and Food. Fisheries Investigations, 2: 533 pp.) monograph contributed a widely used stock–recruitment relationship (BH-SRR) to fisheries science. However, because of variation around a presumed relationship between spawning biomass and recruits, the BH-SRR is often considered inadequate and approached merely as a curve-fitting exercise. The commonly used and simplified version of the BH-SRR has eclipsed the fact that in their classic monograph, the derivation accounted for mechanistic recruitment processes, including multi-stage recruitment with explicit cohort-dependent and -independent mortality terms that represent competition between recruits and extrinsic, cohort-independent factors such as the environment or predation as two independent sources of mortality. The original BH-SRR allows one to recreate recruitment patterns that correspond to observed ones. Doing so shows that variation in density-independent mortality increases the probability of overlooking an underlying stock–recruitment relationship. Intermediate coefficients of variation in mortality (75–100%) are sufficient to mask stock–recruitment relationships and recreate recruitment time series most similar to empirical data. This underlines the importance of variation in survival for recruitment and that Beverton and Holt’s work still provides a fundamental and useful tool to model the dynamics of populations.
Invariant Subvarieties With Small Dynamical Degree
Authors: Matsuzawa Yohsuke , Meng Sheng , Shibata Takahiro , Zhang De-Qi , Zhong Guolei 
Published: February 2021

AbstractLet $f:X\to X $ be a dominant self-morphism of an algebraic variety. Consider the set $\Sigma _{f^{\infty }}$ of $f$-periodic subvarieties of small dynamical degree (SDD), the subset $S_{f^{\infty }}$ of maximal elements in $\Sigma _{f^{\infty }}$, and the subset $S_f$ of $f$-invariant elements in $S_{f^{\infty }}$. When $X$ is projective, we prove the finiteness of the set $P_f$ of $f$-invariant prime divisors with SDD and give an optimal upper bound $$\begin{align*} &\sharp P_{f^n}\le d_1(f)^n(1+o(1))\end{align*}$$as $n\to \infty $, where $d_1(f)$ is the 1st dynamic degree. When $X$ is an algebraic group (with $f$ being a translation of an isogeny), or a (not necessarily complete) toric variety, we give an optimal upper bound $$\begin{align*} &\sharp S_{f^n}\le d_1(f)^{n\cdot\dim(X)}(1+o(1))\end{align*}$$as $n \to \infty $, which slightly generalizes a conjecture of S.-W. Zhang for polarized $f$.
Adapting sorghum sowing date and genotype maturity to seasonal rainfall variation in a temperate region
Authors: Carcedo Ana J P , Cejas Emilia , Gambin Brenda L 
Published: February 2021

Abstract
Reducing sorghum yield gaps depends on the capacity to identify combinations of genetics and management that best suit region and seasonal conditions. Using simulated and empirical data, we explored how the combination of different sowing dates and genotype maturity respond to specific water stress patterns common across a temperate region (Argentina Pampas). This region was recently characterized by three water stress patterns (or environmental types, ENVTs). These ENVTs are: pre-flowering stress, low terminal stress and grain-filling stress. In the north and central regions, significant ENVT × sowing date interaction for yield (P &lt; 0.05) indicated that sowing date should be chosen depending on the prevailing seasonal ENVT. This drought escape strategy increased yields by 4068–5049 kg ha−1. In the southern region, early sowings had the highest yields independently of the ENVT. Genotype maturity effect was less important, although early materials increased yield by 438–923 kg ha−1 (5–25 %) relative to the intermediate genotype, depending on the region. Under low terminal or grain-filling stress, early sowings gave the highest yields via increased accumulated biomass and/or harvest index. Under pre-flowering stress, delaying the sowing dates increased final yields via improved harvest index. Later sowings provided a conservative strategy for reducing risk in the north and central east regions, while for the central west and southern regions the sowing date should be as early as possible. We provided information to improve sorghum management decisions and guide breeding in temperate regions.
PRO: Carbapenems should be used for ALL infections caused by ceftriaxone-resistant Enterobacterales
Authors: Paterson David L , Isler Burcu , Harris Patrick N A 
Published: February 2021

Abstract
Ceftriaxone resistance in the Enterobacterales is typically the result of production of ESBLs or AmpC β-lactamases. The genes encoding these enzymes are often co-located with other antibiotic resistance genes leading to resistance to aminoglycosides, quinolones and trimethoprim/sulfamethoxazole. Carbapenems are stable to ESBLs and AmpC giving them reliable in vitro activity against producers of these β-lactamases. In contrast, piperacillin/tazobactam and amoxicillin/clavulanate are compromised by co-production of OXA-1, which is not inhibited by tazobactam or clavulanate. These in vitro findings provide an explanation for the MERINO trial outcomes, where 3.7% (7/191) randomized to meropenem died compared with 12.3% (23/187) randomized to piperacillin/tazobactam as definitive treatment of bloodstream infection due to ceftriaxone-resistant organisms. No randomized trials have yet put cefepime and carbapenems head to head, but some observational studies have shown worse outcomes with cefepime. We argue that carbapenems are the antibiotics of choice for ceftriaxone-resistant Enterobacterales.
Measurement of Available Carbohydrates in Cereal and Cereal Products, Dairy Products, Vegetables, Fruit, and Related Food Products and Animal Feeds: First Action 2020.07
Authors: McCleary Barry V , McLoughlin Ciara 
Published: February 2021

Abstract

Background
The level of available carbohydrates in our diet is directly linked to two major diseases: obesity and Type II diabetes. Despite this, to date there is no method available to allow direct and accurate measurement of available carbohydrates in human and animal foods.

Objective
The aim of this research was to develop a method that would allow simple and accurate measurement of available carbohydrates, defined as non-resistant starch, maltodextrins, maltose, isomaltose, sucrose, lactose, glucose, fructose, and galactose.

Method
Non-resistant (digestible) starch is hydrolyzed to glucose and maltose by pancreatic α-amylase (PAA) and amyloglucosidase at pH 6.0 with shaking or stirring at 37°C for 4 h. Sucrose, lactose, maltose, and isomaltose are completely hydrolyzed by specific enzymes to their constituent monosaccharides, which are then measured using pure enzymes in a single reaction cuvette.

Results
A method has been developed that allows the accurate measurement of available carbohydrates in all cereal, vegetable, fruit, food, and feed products, including dairy products.

Conclusions
A single-laboratory validation was performed on a wide range of food and feed products. The inter-day repeatability (RSDr, %) was &lt;3.58% (w/w) across a range of samples containing 44.1–88.9% available carbohydrates. The LOD and LOQ obtained were 0.054% (w/w) and 0.179% (w/w), respectively. The method is all inclusive, specific, robust, and simple to use.

Highlights
A unique method has been developed for the direct measurement of available carbohydrates, entailing separate measurement of glucose, fructose, and galactose, information of value in determining the glycemic index of foods.
Determination of Enzymatic Hydrolysis Efficiency in Detection of Cannabis Use by UPLC–MS-MS
Authors: Kul Aykut , Sagirli Olcay 
Published: February 2021

Abstract
Cannabis is still the most widely used illegal plant in the world. However, cannabis use is prohibited in many countries. After cannabis use, Δ9-tetrahydrocannabinol is metabolized in the liver to 11-nor-9-carboxy-Δ9-tetrahydrocannabinol (THC-COOH) and most undergo glucuronidation. THC-COOH and THC-COOH glucuronide are excreted in the urine. The total concentration of THC-COOH in the urine sample is measured to determine cannabis use. The total concentration is determined after enzymatic or alkaline hydrolysis. In this study, comparing enzymatic hydrolysis efficiency is presented comprehensively together with the method developed for the determination of total THC-COOH in the urine. Also, the method was validated according to the European Medicines Agency Guidelines on bioanalytical method validation. The method has rapid hydrolysis time (20 min), rapid analysis time (5 min) and simple sample preparation. The lower limit of quantitation of the developed method was 1 ng/mL for THC-COOH. The calibration curve of THC-COOH was between 1 and 2,000 ng/mL with a correlation coefficient &gt;0.99. Also, the method was applied to real patient’s urine. We think that the results will provide a new perspective on enzymatic hydrolysis optimization studies.
Increasing Prevalence and Direct Health Care Cost of Inflammatory Bowel Disease Among Adults: A Population-Based Study From a Western Canadian Province
Authors: Osei Jessica Amankwah , Peña-Sánchez Juan Nicolás , Fowler Sharyle A , Muhajarine Nazeem , Kaplan Gilaad G , Lix Lisa M 
Published: February 2021

Abstract

Objectives
Our study aimed to calculate the prevalence and estimate the direct health care costs of inflammatory bowel disease (IBD), and test if trends in the prevalence and direct health care costs of IBD increased over two decades in the province of Saskatchewan, Canada.

Methods
We conducted a retrospective population-based cohort study using administrative health data of Saskatchewan between 1999/2000 and 2016/2017 fiscal years. A validated case definition was used to identify prevalent IBD cases. Direct health care costs were estimated in 2013/2014 Canadian dollars. Generalized linear models with generalized estimating equations tested the trend. Annual prevalence rates and direct health care costs were estimated along with their 95% confidence intervals (95%CI).

Results
In 2016/2017, 6468 IBD cases were observed in our cohort; Crohn’s disease: 3663 (56.6%), ulcerative colitis: 2805 (43.4%). The prevalence of IBD increased from 341/100,000 (95%CI 340 to 341) in 1999/2000 to 664/100,000 (95%CI 663 to 665) population in 2016/2017, resulting in a 3.3% (95%CI 2.4 to 4.3) average annual increase. The estimated average health care cost for each IBD patient increased from $1879 (95%CI 1686 to 2093) in 1999/2000 to $7185 (95%CI 6733 to 7668) in 2016/2017, corresponding to an average annual increase of 9.5% (95%CI 8.9 to 10.1).

Conclusions
Our results provide relevant information and analysis on the burden of IBD in Saskatchewan. The evidence of the constant increasing prevalence and health care cost trends of IBD needs to be recognized by health care decision-makers to promote cost-effective health care policies at provincial and national levels and respond to the needs of patients living with IBD.
Predicting cybersickness based on user’s gaze behaviors in HMD-based virtual reality
Authors: Chang Eunhee , Kim Hyun Taek , Yoo Byounghyun 
Published: February 2021

AbstractCybersickness refers to a group of uncomfortable symptoms experienced in virtual reality (VR). Among several theories of cybersickness, the subjective vertical mismatch (SVM) theory focuses on an individual’s internal model, which is created and updated through past experiences. Although previous studies have attempted to provide experimental evidence for the theory, most approaches are limited to subjective measures or body sway. In this study, we aimed to demonstrate the SVM theory on the basis of the participant’s eye movements and investigate whether the subjective level of cybersickness can be predicted using eye-related measures. 26 participants experienced roller coaster VR while wearing a head-mounted display with eye tracking. We designed four experimental conditions by changing the orientation of the VR scene (upright vs. inverted) or the controllability of the participant’s body (unrestrained vs. restrained body). The results indicated that participants reported more severe cybersickness when experiencing the upright VR content without controllability. Moreover, distinctive eye movements (e.g. fixation duration and distance between the eye gaze and the object position sequence) were observed according to the experimental conditions. On the basis of these results, we developed a regression model using eye-movement features and found that our model can explain 34.8% of the total variance of cybersickness, indicating a substantial improvement compared to the previous work (4.2%). This study provides empirical data for the SVM theory using both subjective and eye-related measures. In particular, the results suggest that participants’ eye movements can serve as a significant index for predicting cybersickness when considering natural gaze behaviors during a VR experience.