bluuebunny/crossref_metadata_2025_split huggingface dataset:
K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes
Authors: Contreras‐Moreira Bruno , Filippi Carla V , Naamati Guy , García Girón Carlos , Allen James E , Flicek Paul 
Published: September 2021

AbstractThe annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole‐genome alignment, promoter analysis, or pangenome exploration. Although homology‐based annotation methods are computationally expensive, k‐mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two‐step approach, where repeats were first called by k‐mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k‐mer‐based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red‐masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant‐scripts.
Polymorphisms of the prion‐related protein gene are strongly associated with cervids’ susceptibility to chronic wasting disease
Authors: Roh In‐Soon , Kim Yong‐Chan , Kim Hyo‐Jin , Won Sae‐Young , Jeong Min‐Ju , Hwang Ji‐Yong , Kang Hae‐Eun , Sohn Hyun‐Joo , Jeong Byung‐Hoon 
Published: September 2021

AbstractBackgroundChronic wasting disease (CWD) is a cervid prion disease that is caused by abnormal prion protein (PrPSc). Recent studies have reported that prion family genes showed a strong association with the susceptibility of several types of prion diseases. To date, an association study of the prion‐related protein gene (PRNT) has not been performed in any type of cervid prion disease.MethodsIn the present study, we investigated PRNT polymorphisms in large deer, including 235 elk, 257 red deer and 150 sika deer. We compared genotype, allele and haplotype frequencies of PRNT polymorphisms between CWD‐negative animals and CWD‐positive animals to find an association of PRNT polymorphisms with the susceptibility of CWD.ResultsWe found a total of five novel single nucleotide polymorphisms (SNPs) in the cervid PRNT gene. Interestingly, we observed significantly different distributions of genotypes and allele frequencies of three PRNT SNPs, including c.108C>T, c.159+30C>T and c.159+32A>C, between CWD‐negative and CWD‐positive red deer. In addition, significant differences of two haplotype frequencies in red deer were found between the CWD‐negative and CWD‐positive groups. However, the association identified in the red deer was not found in elk and sika deer.ConclusionTo the best of our knowledge, this report is the first to describe the strong association of PRNT SNPs with the susceptibility of CWD.
Effects of a nutraceutical supplement in the management of mild equine squamous gastric disease in endurance horses
Authors: Lo Feudo Chiara Maria , Stucchi Luca , Conturba Bianca , Alberti Elena , Zucca Enrica , Ferrucci Francesco 
Published: September 2021

AbstractIntroductionEquine squamous gastric disease (ESGD) may require prolonged treatments with acid suppressants; therefore, interest in nutraceutical supplements with anti‐ulcerogenic properties has increased. This study aims to investigate the efficacy of Trophogast pellet for the treatment of ESGD in endurance horses.Material and methodsFifteen endurance horses were included based on their gastroscopic examination and randomly assigned to a treatment group, receiving Trophogast pellet for 30 days together with management changes, or to a control group, only subjected to management modifications. At the end of treatment, gastroscopy was repeated. Scores were assigned according to the Equine Gastric Ulcer Council scoring system. All horses were weighed at the beginning and at the end of the study. ESGD grades and weight before and after treatment were compared.ResultsAt enrolment, median ESGD score in the treatment group was 2, while in the control group it was 1. After the treatment period, a significant decrease in ESGD grade was observed in the treatment group (median 1,p = 0.0078), while there was no change in the control group (median 2). No significant weight change was observed in either group.ConclusionTrophogast pellet was effective at promoting healing of mild ESGD in endurance horses.
Anaesthetic management of a cheetah (Acinonyx jubatus) for caesarean section
Authors: Kadwa Abdur Rahmaan , Brown Geoffrey James , Henry O'Dell Jacques , Zeiler Gareth Edward , Buck Roxanne Kate 
Published: September 2021

AbstractAfter delivering a single stillborn cub, a 4‐year‐old, semi‐feral, captive cheetah (Acinonyx jubatus) presented at full‐term pregnancy with either suspension of labour or uterine inertia and a caesarean section was performed. The cheetah was sedated with 0.0357 mg/kg medetomidine intramuscularly, followed by intravenous induction with propofol to effect and maintenance on isoflurane inhalational anaesthesia. Each cub was administered a total of 0.15 mg atipamezole intramuscularly, in 0.05 mg increments, after delivery. The anaesthetic management of the cheetah focused on selecting anaesthetic drugs that would minimise neonatal drug exposure and ultimately maximise the chances of neonatal viability. Additionally, the drugs administered had to also provide sufficient sedation to ensure personnel safety. Finally, the anaesthesia of the cheetah had to be considered in context of the physiological changes that occur during pregnancy.
Detecting communities using social network analysis in online learning environments: Systematic literature review
Authors: Yassine Sahar , Kadry Seifedine , Sicilia Miguel‐Angel 
Published: September 2021

AbstractUncovering community structure has made a significant advancement in explaining, analyzing, and forecasting behaviors and dynamics of networks related to different fields in sociology, criminology, biology, medicine, communication, economics, and academia. Detecting and clustering communities is a powerful step toward identifying the structural properties and the behavioral patterns in social networks. Recently, online learning has been progressively adopted by a lot of educational practices which raise many questions about assessing the learners' engagement, collaboration, and behaviors in the new emerging learning communities. This systematic literature review aims to assess the use of community detection techniques in analyzing the network's structure in online learning environments. It provides a comprehensive overview of the existing research that adopted those techniques with identifying the educational objectives behind their application as well as suggesting possible future research directions. Our analysis covered 65 studies that found in the literature and applied different community discovery techniques on various types of online learning environments to analyze their users' interactions patterns. Our review revealed the potential of this field in improving educational practices and decisions and in utilizing the massive amount of data generated from interacting with those environments. Finally, we highlighted the need to include automated community discovery techniques in online learning environments to facilitate and enhance their use as well as we stressed on the urge for further advance research to uncover a lot of hidden opportunities.This article is categorized under:
Algorithmic Development > Statistics
Algorithmic Development > Web Mining
Application Areas > Education and Learning
The dynamic responses of an infinite plate resting on a poroelastic layered half‐space soil medium with imperfect interface to a moving load
Authors: Zheng Yuanxun , Luo Cunxin , Liu Heng , Du Chaowei 
Published: September 2021

AbstractThe present study deals with the dynamic responses of an infinite plate resting on a poroelastic layered half‐space soil medium with imperfect interfaces to a moving load. Kirchhoff thin plate theory is employed to analyze the plate, while Biot's fully dynamic poroelastic theory is used to characterize the poroelastic half‐space. Applying the Fourier transform and vector functions, the completely coupled system of equations of motion for the layered system are reduced to a system of decoupled ordinary differential equations which could be solved semi‐analytically. The propagation relationships for the layered structure with imperfect interfaces are derived by the novel and efficient dual variable and position (DVP) method. In so doing, the calculated expansion coefficients in the transformed domain are utilized to calculate the unknowns in the physical domain by integration at each field point. Numerical analyses validate the obtained results by comparing with the existing work, and soil vertical displacements, accelerations and pore water pressures induced by moving load are calculated. Moreover, the effects of the different factors are investigated. Computed result shows apparent influences of load velocity, intrinsic permeability and imperfect bonded condition of the soil medium on the dynamic responses of the whole system.
Application to a Case Study
Authors: Rey Emmanuel , Laprise Martine , Lufkin Sophie 
Published: September 2021

AbstractWe present an application of the operational monitoring tool SIPRIUS+ to an ongoing case study representative of urban brownfield regeneration projects: the Pôle Viotte neighbourhood, located in Besançon (France). We start with a description of the brownfield site, followed by the regeneration project. Then, we evaluate 52 indicators linked to the context, project, and governance. Each monitoring result is illustrated by a graph showing the evolution of the performances. Then, we analyse the overall results, which allows us to assess the sustainability strategy of the regeneration project. Through this analysis, we identify four actions to improve sustainability objectives. Finally, we conclude that SIPRIUS+ has the potential to contribute to the integration of sustainability issues into the dynamics of neighbourhoods in transition. The operational monitoring tool is expected to contribute to decision-making in a multi-disciplinary manner, without giving ready-made solutions. Interactions with project stakeholders reveal that, while the use of such a tool would require a change in project management, the evolutions to adopt to include this practice appear not only feasible but realistic and desired.
Compactifying 5d superconformal field theories to 3d
Authors: Sacchi Matteo , Sela Orr , Zafrir Gabi 
Published: September 2021

Abstract
Building on recent progress in the study of compactifications of 6d (1, 0) superconformal field theories (SCFTs) on Riemann surfaces to 4d$$ \mathcal{N} $$
N
= 1 theories, we initiate a systematic study of compactifications of 5d$$ \mathcal{N} $$
N
= 1 SCFTs on Riemann surfaces to 3d$$ \mathcal{N} $$
N
= 2 theories. Specifically, we consider the compactification of the so-called rank 1 Seiberg $$ {E}_{N_f+1} $$

E

N
f

+
1

SCFTs on tori and tubes with flux in their global symmetry, and put the resulting 3d theories to various consistency checks. These include matching the (usually enhanced) IR symmetry of the 3d theories with the one expected from the compactification, given by the commutant of the flux in the global symmetry of the corresponding 5d SCFT, and identifying the spectrum of operators and conformal manifolds predicted by the 5d picture. As the models we examine are in three dimensions, we encounter novel elements that are not present in compactifications to four dimensions, notably Chern-Simons terms and monopole superpotentials, that play an important role in our construction. The methods used in this paper can also be used for the compactification of any other 5d SCFT that has a deformation leading to a 5d gauge theory.
Strings in bimetric spacetimes
Authors: Yan Ziqi 
Published: September 2021

Abstract
We put forward a two-dimensional nonlinear sigma model that couples (bosonic) matter fields to topological Hořava gravity on a nonrelativistic worldsheet. In the target space, this sigma model describes classical strings propagating in a curved spacetime background, whose geometry is described by two distinct metric fields. We evaluate the renormalization group flows of this sigma model on a flat worldsheet and derive a set of beta-functionals for the bimetric fields. Imposing worldsheet Weyl invariance at the quantum level, we uncover a set of gravitational field equations that dictate the dynamics of the bimetric fields in the target space, where a unique massless spin-two excitation emerges. When the bimetric fields become identical, the sigma model gains an emergent Lorentz symmetry. In this single metric limit, the beta-functionals of the bimetric fields reduce to the Ricci flow equation that arises in bosonic string theory, and the bimetric gravitational field equations give rise to Einstein’s gravity.
Modular flow of excited states
Authors: Lashkari Nima , Liu Hong , Rajagopal Srivatsan 
Published: September 2021

AbstractWe develop new techniques for studying the modular and the relative modular flows of general excited states. We show that the class of states obtained by acting on the vacuum (or any cyclic and separating state) with invertible operators from the algebra of a region is dense in the Hilbert space. This enables us to express the modular and the relative modular operators, as well as the relative entropies of generic excited states in terms of the vacuum modular operator and the operator that creates the state. In particular, the modular and the relative modular flows ofanystate can be expanded in terms of the modular flow of operators in vacuum. We illustrate the formalism with simple examples including states close to the vacuum, and coherent and squeezed states in generalized free field theory.
Rapid closure technique in suboccipital decompression
Authors: Vychopen Martin , Hadjiathanasiou Alexis , Brandecker Simon , Borger Valeri , Schuss Patrick , Vatter Hartmut , Güresir Erdem 
Published: September 2021

Abstract
Objective
Suboccipital decompression has been established as standard therapeutic procedure for raised intracranial pressure caused by mass-effect associated pathologies in posterior fossa. Several different surgical techniques of dural closure have been postulated to achieve safe decompression. The aim of this study was to examine the differences between fibrin sealant patch (FSP) and dural reconstruction (DR) in suboccipital decompression for acute mass-effect lesions.

Methods
We retrospectively analyzed our institutional data of patients who underwent suboccipital decompression due to spontaneous intracerebellar hemorrhage, cerebellar infarction and acute traumatic subdural hematoma between 2010 and 2019. Two different dural reconstruction techniques were performed according to the attending neurosurgeon: (1) fibrin sealant patch (FSP), and (2) dural reconstruction (DR) including the use of dural patch. Complications, operative time, functional outcome and the necessity of a ventriculoperitoneal shunt (VP Shunt) were assessed and further analyzed.

Results
Overall, 87 patients were treated at the authors’ institution (44 in FSP group, 43 in DR group). Glasgow coma scale on admission and preoperative coagulation state did not differ between the groups. Postoperatively, we found no difference in cerebrospinal fluid leakage or chronic hydrocephalus between the groups (p = 0.47). Revision rates were 2.27% (1/44 patients) in the FSP group, compared to 16.27% (7/43) in the DR group (p < 0.023). Operative time was significantly shorter in the FSP group (90.3 ± 31.0 min vs. 199.0 ± 48.8 min, p < 0.0001).

Conclusion
Rapid closure technique in suboccipital decompression is feasible and safe. Operative time is hereby reduced, without increasing complication rates.
Optical inline monitoring of the burnish surface in the punching process
Authors: Lorenz Maximilian , Menzl Matthias , Donhauser Christian , Layh Michael , Pinzer Bernd R. 
Published: September 2021

AbstractPunching is a wide-spread production process, applied when massive amounts of the ever-same cheap parts are needed. The punching process is sensitive to a multitude of parameters. Unfortunately, the precise dependencies are often unknown. A prerequisite for optimal, reproducible and transparent process alignment is the knowledge of how exactly parameters influence the quality of a punching part, which in turn requires a quantitative description of the quality of a part. We developed an optical inline monitoring system, which consists of a combined imaging and triangulation sensor as well as subsequent image processing. We show that it is possible to capture images of the cutting surface for every part within production. We automatically derive quality parameters using the example of the burnish height from 2D images. In addition, the 3D parameters are calculated and verified from the triangulation images. As an application, we show that the status of tool wear can be inferred by monitoring the burnish height, with immediate consequences for predictive maintenance. Although limited by slow images processing in our prototype, we conclude that connecting machine and process parameters with quality metrics in real time for every single part enables data-driven process modelling and ultimately the implementation of intelligent punching machines.
The value of bacterial metagenomic analysis in post-surgical examination of gallstones
Authors: Ploszaj T. , Brauncajs M. , Traczyk-Borszynska M. , Matyjas T. , Pomorski L. , Wasiak T. , Borowiec M. 
Published: September 2021

AbstractGallstone disease is one of the most common causes of hospitalization for gastrointestinal diseases in the world. Recent studies have examined the presence of bacteria in the formation of stones. Our main goal was to determine the overall composition of gallstone microflora. Gallstones were obtained from 24 patients during laparoscopic cholecystectomy from which DNA were extracted. Composition of bacterial flora was evaluated on 16 s rDNA sequencing technique. In the vast majority of samples, bacteria were present, and four groups could be differentiated regarding the flora. Overall composition shows that 87% of the stones were cholesterol/mixed type of gallstone. Additionally, potentially harmful microorganisms (Streptococcus, ClostridiumandKocuria) that could cause post-surgery complications were identified in several patients. The obtained results indicate that this technique may be useful in analyzing the type of stones and in pinpointing the presence of pathogenic bacteria.
Functional interaction of H2-receptors and 5HT4-receptors in atrial tissues isolated from double transgenic mice and from human patients
Authors: Neumann Joachim , Schwarzer Denise , Fehse Charlotte , Schwarz Rebecca , Marusakova Margareta , Kirchhefer Uwe , Hofmann Britt , Gergs Ulrich 
Published: September 2021

AbstractIn the past, we generated transgenic mice that overexpress the human histamine 2 (H2)-receptor (H2-TG) or that overexpress the human serotonin 4 (5-HT4)-receptor (5-HT4-TG) in the heart. Here, we crossbred these lines of mice to generate double transgenic mice that overexpress both receptors (DT). This was done to study a conceivable interaction between these receptors in the mouse heart as a model for the human heart. When in left atria, initially, force of contraction was elevated maximally with 1 µM serotonin, and subsequently, histamine was cumulatively applied; a biphasic effect of histamine was noted: the force of contraction initially decreased, maximally at 10 nM histamine, and thereafter, the force of contraction increased again at 1 µM histamine. Notably, functional interaction between 5-HT and histamine was also identified in isolated electrically stimulated trabeculae carneae from human right atrium (obtained during cardiac surgery). These functional and biochemical data together are consistent with a joint overexpression of inotropically active H2-receptors and 5-HT4-receptors in the same mouse heart. We also describe an antagonistic interaction on the force of contraction of both receptors in the mouse atrium (DT) and in the human atrial muscle strips. We speculate that via this interaction, histamine might act as a “brake” on the cardiac actions of 5-HT via inhibitory GTP-binding proteins acting on the activity of adenylyl cyclase.
The mid-term effects of carotid endarterectomy on cognition and regional neural activity analyzed with the amplitude of low frequency fluctuations technique
Authors: Porcu Michele , Cocco Luigi , Cau Riccardo , Suri Jasjit S. , Mannelli Lorenzo , Yang Qi , Defazio Giovanni , Wintermark Max , Saba Luca 
Published: September 2021

AbstractPurposeThe study aims to evaluate the mid-term effects of carotid endarterectomy (CEA) on cognition and resting-state functional magnetic resonance imaging (rs-fMRI) using the Amplitude of Low Frequency Fluctuations (ALFF) technique.MethodsIn this observational study, patients eligible for CEA were prospectively included. On the same day, within 1 week of the CEA procedure performed and 12 months after the CEA procedure, all patients underwent (i) an MRI examination for rs-fMRI analysis and (ii) a cognitive evaluation using the Italian version of the Mini-Mental State Examination (MMSE) corrected for age and schooling. Pre-CEA and post-CEA MMSE scores were evaluated using paired samplet-tests, adopting ap-value < 0.05 as statistical threshold. The ALFF technique was used for analyzing the differences between pre-CEA and post-CEA rs-fMRI scans in terms of regional neural activation. This was accomplished by applying non-parametric statistics based on randomization/permutation for cluster-level inferences, adopting a cluster-massp-value corrected for false discovery < 0.05 for cluster threshold, and ap-uncorrected < 0.01 for the voxel threshold.ResultsTwenty asymptomatic patients were enrolled. The mean MMSE score resulted improved following CEA procedure (p-value = 0.001). The ALFF analysis identified a single cluster of 6260 voxels of increased regional neural activity following CEA, and no cluster of reduced activity. The majority of voxels covered the right precentral gyrus, the right middle frontal gyrus, and the anterior division of the cingulate gyrus.ConclusionMid-term cognitive improvements observed after CEA are associated to increased regional neural activity of several cerebral regions.