bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light chaotic dynamics in the transformation from curved to flat surfaces
Authors: Xu Chenni , Dana Itzhack , Wang Li-Gang , Sebbah Patrick 
Published: March 2022

SignificanceExploring light dynamics and chaos on curved surfaces is one of the new challenges met in modern cosmology. To address this question and investigate chaotic dynamics of light on three-dimensional curved surfaces, we consider their connection under a conformal transformation with flat billiards with spatially varying refractive index. Through this connection, we demonstrate that these two systems share the same dynamics; the complexity of the problem simplifies, and well-known tools originating from chaos analysis in planar billiards can be used to explore chaotic dynamics on curved space. We discover that the degree of chaos is fully controlled by a single curvature-related geometrical parameter, providing a degree of freedom in chaos engineering, as well as potentialities to design nonuniform table billiards/cavities/resonators.
Contiguously hydrophobic sequences are functionally significant throughout the human exome
Authors: Lohia Ruchi , Hansen Matthew E. B. , Brannigan Grace 
Published: March 2022

Significance
Proteins rely on the hydrophobic effect to maintain structure and interactions with the environment. Surprisingly, natural selection on amino acid hydrophobicity has not been detected using modern genetic data. Analyses that treat each amino acid separately do not reveal significant results, which we confirm here. However, because the hydrophobic effect becomes more powerful as more hydrophobic molecules are introduced, we tested whether unbroken stretches of hydrophobic amino acids are under selection. Using genetic variant data from across the human genome, we find evidence that selection increases with the length of the unbroken hydrophobic sequence. These results could lead to improvements in a wide range of genomic tools as well as insights into protein-aggregation disease etiology and protein evolutionary history.
Ribosomal RNA 2′-O-methylations regulate translation by impacting ribosome dynamics
Authors: Khoshnevis Sohail , Dreggors-Walker R. Elizabeth , Marchand Virginie , Motorin Yuri , Ghalei Homa 
Published: March 2022

SignificanceThe presence of RNA chemical modifications has long been known, but their precise molecular consequences remain unknown. 2′-O-methylation is an abundant modification that exists in RNA in all domains of life. Ribosomal RNA (rRNA) represents a functionally important RNA that is heavily modified by 2′-O-methylations. Although abundant at functionally important regions of the rRNA, the contribution of 2′-O-methylations to ribosome activities is unknown. By establishing a method to disturb rRNA 2′-O-methylation patterns, we show that rRNA 2′-O-methylations affect the function and fidelity of the ribosome and change the balance between different ribosome conformational states. Our work links 2′-O-methylation to ribosome dynamics and defines a set of critical rRNA 2′-O-methylations required for ribosome biogenesis and others that are dispensable.
Cell size and polarization determine cytokinesis furrow ingression dynamics in mouse embryos
Authors: Paim Lia Mara Gomes , FitzHarris Greg 
Published: March 2022

Significance
The final step of cell division, termed cytokinesis, comprises the constriction of a furrow that divides the cytoplasm to form two daughter cells. Although cytokinesis is well studied in traditional cell systems, how cytokinesis is regulated in complex multicellular settings and during cell-fate decisions is less well understood. Here, using live imaging and physical and molecular interventions, we find that the emergence of cell polarity during mouse embryo morphogenesis dramatically impacts cytokinesis mechanisms. Specifically, the assembly of the apical domain in outer cells locally inhibits the cytokinetic machinery, leading to an unexpected laterally biased cytokinesis.
Obscene language and the renegotiation of gender roles in post-Soviet contexts
Authors: Lucchetti Cristiana 
Published: March 2022

Abstract

Mat is a specific domain of Russian obscene vocabulary including words related to sexuality. The first sociolinguistic
studies on mat emerged after the fall of the Soviet Union, concomitantly with the formation of Russian gender studies in the early
1990s (Tëmkina & Zdravomyslova 2003: 51). Until today, research on gender and taboo in Russian has been exiguous. Many
scholars claim that the use of mat is a male prerogative (Uspenskiĭ 1994: 56, Doleschal
& Schmid 2001: 274), whereas women’s use of mat is heavily sanctioned in society. Through data from a survey I carried out
with 772 participants, I illustrate that mat is strongly present in women’s language use and that stereotypical gender
conceptualizations are undergoing change. From the participants’ answers it emerges that discussions about the use of obscene
language play a critical role in the multifaceted process of renegotiation of gender roles in post-Soviet contexts.
Erratum: Measurement of (n, α) and (n, 2n) reaction cross sections at a neutron energy of 14.92 ± 0.02 MeV for potassium and copper with uncertainty propagation, [A. Gandhi, Aman Sharma, Rebecca Pachuau et al., Chin. Phys. C 46, 014002 (2022)]
Authors: Gandhi A. , Sharma Aman , Pachuau Rebecca , Singh Namrata , Danu L. S. , Suryanarayana S. V. , Nayak B. K. , Kumar A. 
Published: March 2022

Abstract
Experimentally measured neutron activation cross sections are presented for the

Cu(n, α)

Cu,

K(n, α)

Cl, and

Cu(n,2n)

Cu reactions with detailed uncertainty propagation. The neutron cross sections were measured at an incident energy of 14.92

0.02 MeV, and the neutrons were based on the t(d, n)α fusion reaction. The

Al(n, α)

Na reaction was used as a reference reaction for the normalization of the neutron flux. The pre-calibrated lead-shielded HPGe detector was used to detect the residues' γ-ray spectra. The data from the measured cross sections are compared to the previously measured cross sections from the EXFOR database, theoretically calculated cross sections using the TALYS and EMPIRE codes, and evaluated nuclear data.
NiO Supported on Porous Carbon From Merbau Wood: Synthesis and Characterization
Authors: Santi D , Triyono  , Trisunaryanti W , Falah I I 
Published: March 2022

Abstract
Nickel oxide catalyst supported on porous carbon (NiO/C), the materials support were synthesized from Merbau wood. The metals were loaded onto the carbon by the wet impregnation method. After drying and calcination, NiO/C was obtained. The prepared catalyst was evaluated for the hydrocracking of pyrolyzed α-cellulose. The catalyst was characterized by XRD, SEM-EDX, FT IR, SAA, and acidity test by NH3 base vapor adsorption determined gravimetrically and by FT IR. The XRD results showed that the carbonaceous of materials support were amorphous materials that characteristic for mesopore carbon. The impregnation of nickel into carbon results in difraktogram peaks that correspond to the presence of NiO, which was confirmed by EDX. The SEM image showed that the morphology of the catalyst samples was a honeycomb-like structure. The acidity test showed that the total acid amount of NiO/C samples was 3.05 mol/g, and the FT IR spectra indicated that there were Brönsted and Lewis acid sites on NiO/C catalyst. The SAA results showed that the specific surface area, total pore volume, and average pore diameter of the NiO/C catalyst were 520.41 m2/g, 0.27 cm3/g, and 2.083 nm, respectively.
Benchmarking Naïve Bayes and ID3 Algorithm for Prediction Student Scholarship
Authors: Karo I M K , Fajari M Y , Fadhilah N U , Wardani W Y 
Published: March 2022

Abstract
Student scholarship through Indonesian smart cards (ISC) is a cash donation scholarship for all student in range 6-21 years old as a solution of destitute child or potential dropouts. Currently the large student data stored in educational database. The data was used to determine feasible receiver ISC. Manual prediction by human take long time and potentially human error. This paper aim to predict feasible receiver ISC by using educational data mining. Source of data come from a senior high school database in Riau Province, Indonesia. In this paper we compared two algorithms (Naïve Bayes and ID3) to predict receiver ISC. Eighty percent process in this paper is data pre-processing. Information of other scholarship is the most influences variable to predict student scholarship. ID3 algorithm classification has accuracy 83 percent and f1 score 71 percent. While Naive Bayes Classification has accuracy 89 percent and f1 score 72 percent. In this case Naïve Bayes algorithm is better in ID3 algorithm.
Risk Assessment of Electronic Archive Services using Octave Allegro Method (Case Study: SIKN JIKN)
Authors: Herdianto R A , Ramli K , Suryanto Y 
Published: March 2022

Abstract
The National Archives Information System (SIKN) and the National Archives Information Network (JIKN) are the government national priority programs that aimed at providing web-based electronic archive treasury information facilities to the public. However, threat and disruption of critical information asset on electronic archives can cause interruption strategic objectives goals, vision, and mission of The National Archives of Indonesia (ANRI) in organizing archives that impact the network node, and the public. Therefore this research aims to analyze and identify risks in the SIKN JIKN electronic archive service and determine the potential risk of threats to important information assets. The OCTAVE Allegro method used to measure information security on five important information assets of the SIKN JIKN electronic archive information service. The results showed 64 areas of concerns analyzed, as many as 40 had to mitigate while the remaining 24 could be deferred or postponed. The conclusion of the risk assessment results in recommendations that must take to manage and protect critical assets in electronic archive services and supporting material for policymaking.
Forecasting of Freight Demand Transportation (Case Study in Lampung Province, Indonesia)
Authors: Junaedi T 
Published: March 2022

Abstract
Forecasting the volume of freight has a significant importance for future decisions for the entire economy, as well as its individual participants. The transportation of goods between Sumatra and Java using the highway mode that accumulate with local transportation will greatly burden roads in Lampung province. This research was conducted to predict the pattern and amount of movement of goods in the future. The modelling is conducted for the plan period up to 20 years based on growth predictions of geographical, social, economic and traffic flow. This study conducted a process of Sequential Demand Model (Planning Model 4 stages) by using software Transplan Version 8. Transportation patterns in 2040 is predicted will be dominated by continuous trips with domination of movement from Java to South Sumatra, or otherwise. Both the transportation between internal zones and external zone to internal zone have a significant increase. The most strategic main line freight in Lampung for today and in the future is along the Bakauheni-South Sumatra and Bengkulu-South Sumatra both through toll roads, national roads, and railways.
A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations
Authors: Milite Salvatore , Bergamin Riccardo , Patruno Lucrezia , Calonaci Nicola , Caravagna Giulio 
Published: March 2022

AbstractMotivationCancers are composed by several heterogeneous subpopulations, each one harbouring different genetic and epigenetic somatic alterations that contribute to disease onset and therapy response. In recent years, copy number alterations (CNAs) leading to tumour aneuploidy have been identified as potential key drivers of such populations, but the definition of the precise makeup of cancer subclones from sequencing assays remains challenging. In the end, little is known about the mapping between complex CNAs and their effect on cancer phenotypes.ResultsWe introduce CONGAS, a Bayesian probabilistic method to phase bulk DNA and single-cell RNA measurements from independent assays. CONGAS jointly identifies clusters of single cells with subclonal CNAs, and differences in RNA expression. The model builds statistical priors leveraging bulk DNA sequencing data, does not require a normal reference and scales fast thanks to a GPU backend and variational inference. We test CONGAS on both simulated and real data, and find that it can determine the tumour subclonal composition at the single-cell level together with clone-specific RNA phenotypes in tumour data generated from both 10× and Smart-Seq assays.Availability and implementationCONGAS is available as 2 packages: CONGAS (https://github.com/caravagnalab/congas), which implements the model in Python, and RCONGAS (https://caravagnalab.github.io/rcongas/), which provides R functions to process inputs, outputs and run CONGAS fits. The analysis of real data and scripts to generate figures of this paper are available via RCONGAS; code associated to simulations is available at https://github.com/caravagnalab/rcongas_test.Supplementary informationSupplementary data are available at Bioinformatics online.
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier
Authors: Kumar Ambuj , Khade Pranav M , Dorman Karin S , Jernigan Robert L 
Published: March 2022

Abstract

Summary
A new dynamic community identifier (DCI) is presented that relies upon protein residue dynamic cross-correlations generated by Gaussian elastic network models to identify those residue clusters exhibiting motions within a protein. A number of examples of communities are shown for diverse proteins, including GPCRs. It is a tool that can immediately simplify and clarify the most essential functional moving parts of any given protein. Proteins usually can be subdivided into groups of residues that move as communities. These are usually densely packed local sub-structures, but in some cases can be physically distant residues identified to be within the same community. The set of these communities for each protein are the moving parts. The ways in which these are organized overall can aid in understanding many aspects of functional dynamics and allostery. DCI enables a more direct understanding of functions including enzyme activity, action across membranes and changes in the community structure from mutations or ligand binding. The DCI server is freely available on a web site (https://dci.bb.iastate.edu/).

Supplementary information
Supplementary data are available at Bioinformatics online.
hacksig: a unified and tidy R framework to easily compute gene expression signature scores
Authors: Carenzo Andrea , Pistore Federico , Serafini Mara S , Lenoci Deborah , Licata Armando G , De Cecco Loris 
Published: March 2022

Abstract

Summary
Hundreds of gene expression signatures have been developed during the last two decades. However, due to the multitude of development procedures and sometimes a lack of explanation for their implementation, it can become challenging to apply the original method on custom data. Moreover, at present, there is no unified and tidy interface to compute signature scores with different single sample enrichment methods. For these reasons, we developed hacksig, an R package intended as a unified framework to obtain single sample scores with a tidy output as well as a collection of manually curated gene signatures and methods from cancer transcriptomics literature.

Availability and implementation
The hacksig R package is freely available on CRAN (https://CRAN.R-project.org/package=hacksig) under the MIT license. The source code can be found on GitHub at https://github.com/Acare/hacksig.

Supplementary information
Supplementary data are available at Bioinformatics online.
Compromised future thinking: another cognitive cost of temporal lobe epilepsy
Authors: Rayner Genevieve , Antoniou Mariana , Jackson Graeme , Tailby Chris 
Published: March 2022

AbstractThe ability to mentally travel forward through time allows humans to envisage a diverse array of possible events taking place in the future, helping us to choose which pathway to take in life. In epilepsy, we assume that patients use this cognitive ability when deciding between various treatment options, but this assumption has not been robustly tested. The temporal lobes are key contributors to this ‘future thinking’ and its building blocks include cognitive functions commonly impaired in temporal lobe epilepsy such as memory and language, giving rise to a hypothesis that ‘future thinking’ is impaired in this patient cohort. Participants were 68 adults: 37 with neurosurgically-naïve, unilateral temporal lobe epilepsy (51% right lateralized) and 31 healthy controls of similar age, sex and intellectual ability to the participants with epilepsy. Future thinking was measured using an imagined experiences task validated in other neurological populations. Tools well-established in temporal lobe epilepsy were used to measure potential cognitive correlates of future thinking. Analysis of variance revealed significantly impoverished future thinking in both left and right temporal lobe epilepsy relative to controls (P = 0.001, ηp2=0.206), with no difference between temporal lobe epilepsy groups (P &gt; 0.05). Future thinking deficits in left temporal lobe epilepsy were paralleled by deficits in scene construction, whereas impoverished future thinking in right temporal lobe epilepsy occurred in the setting of intact scene construction. Deficits in future thinking were associated with reductions in lexical access and episodic autobiographic memory in both epilepsy groups. In sum, future thinking is compromised in both left and right temporal lobe epilepsy. The deficit in left temporal lobe epilepsy is largely explainable by dysfunction in verbal cognitive processes including scene construction. While the basis of the deficits observed with right temporal foci shares features with that of left temporal lobe epilepsy, their intact scene construction raises questions about the role of the left and right temporal lobes in future thinking and scene construction and the relationship between these two constructs, including whether right temporal lobe might play a specific role in future thinking in terms of creative processing. Clinicians should take impaired future thinking into account when counselling temporal lobe epilepsy patients about various treatment options, as they may struggle to vividly imagine what different outcomes might mean for their future selves.
Longitudinal tracking of axonal loss using diffusion magnetic resonance imaging in multiple sclerosis
Authors: Boonstra Frederique M. , Clough Meaghan , Strik Myrte , van der Walt Anneke , Butzkueven Helmut , White Owen B. , Law Meng , Fielding Joanne , Kolbe Scott C. 
Published: March 2022

Abstract
Axonal loss in the CNS is a key driver of progressive neurological impairments in people with multiple sclerosis. Currently, there are no established methods for tracking axonal loss clinically. This study aimed to determine the sensitivity of longitudinal diffusion MRI-derived fibre-specific measures of axonal loss in people with multiple sclerosis. Fibre measures were derived from diffusion MRI acquired as part of a standard radiological MRI protocol and were compared (i) to establish measures of neuro-axonal degeneration: brain parenchymal fraction and retinal nerve fibre layer thickness and (ii) between different disease stages: clinically isolated syndrome and early/late relapsing–remitting multiple sclerosis. Retrospectively identified data from 59 people with multiple sclerosis (18 clinically isolated syndrome, 22 early and 19 late relapsing–remitting) who underwent diffusion MRI as part of their routine clinical monitoring were collated and analysed. Twenty-six patients had 1-year and 14 patients had a 2-year follow-up. Brain parenchymal fraction was calculated from 3D MRI scans, and fibre-specific measures were calculated from diffusion MRI using multi-tissue constrained spherical deconvolution. At each study visit, patients underwent optical coherence tomography to determine retinal nerve fibre layer thickness, and standard neurological assessment expanded the disability status scale. We found a significant annual fibre-specific neuro-axonal degeneration (mean ± SD = −3.49 ± 3.32%, P &lt; 0.001) that was ∼7 times larger than the annual change of brain parenchymal fraction (−0.53 ± 0.95%, P &lt; 0.001), and more than four times larger than annual retinal nerve fibre layer thinning (−0.75 ± 2.50% P = 0.036). Only fibre-specific measures showed a significant difference in annual degeneration between the disease stages (P = 0.029). Reduced brain parenchymal fraction, retinal nerve fibre layer thickness and fibre-specific measures were moderately related to higher expanded disability status scale (rho = −0.368, rho = −0.408 and rho = −0.365, respectively). Fibre-specific measures can be measured from data collected within a standard radiological multiple sclerosis study and are substantially more sensitive to longitudinal change compared with brain atrophy and retinal nerve fibre layer thinning.
Methods for the identification and characterization of extracellular vesicles in cardiovascular studies: from exosomes to microvesicles
Authors: Davidson Sean M , Boulanger Chantal M , Aikawa Elena , Badimon Lina , Barile Lucio , Binder Christoph J , Brisson Alain , Buzas Edit , Emanueli Costanza , Jansen Felix , Katsur Miroslava , Lacroix Romaric , Lim Sai Kiang , Mackman Nigel , Mayr Manuel , Menasché Philippe , Nieuwland Rienk , Sahoo Susmita , Takov Kaloyan , Thum Thomas , Vader Pieter , Wauben Marca H M , Witwer Kenneth , Sluijter Joost P G 
Published: March 2022

Abstract
Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are released from cells of the cardiovascular system, and are considered important mediators of intercellular and extracellular communications. Two types of EVs of particular interest are exosomes and microvesicles, which have been identified in all tissue and body fluids and carry a variety of molecules including RNAs, proteins, and lipids. EVs have potential for use in the diagnosis and prognosis of cardiovascular diseases and as new therapeutic agents, particularly in the setting of myocardial infarction and heart failure. Despite their promise, technical challenges related to their small size make it challenging to accurately identify and characterize them, and to study EV-mediated processes. Here, we aim to provide the reader with an overview of the techniques and technologies available for the separation and characterization of EVs from different sources. Methods for determining the protein, RNA, and lipid content of EVs are discussed. The aim of this document is to provide guidance on critical methodological issues and highlight key points for consideration for the investigation of EVs in cardiovascular studies.