bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information
Authors: Yang Hangyuan , Wang Minghui , Liu Xia , Zhao Xing-Ming , Li Ao 
Published: July 2021

Abstract

Motivation
Phosphorylation is one of the most studied post-translational modifications, which plays a pivotal role in various cellular processes. Recently, deep learning methods have achieved great success in prediction of phosphorylation sites, but most of them are based on convolutional neural network that may not capture enough information about long-range dependencies between residues in a protein sequence. In addition, existing deep learning methods only make use of sequence information for predicting phosphorylation sites, and it is highly desirable to develop a deep learning architecture that can combine heterogeneous sequence and protein–protein interaction (PPI) information for more accurate phosphorylation site prediction.

Results
We present a novel integrated deep neural network named PhosIDN, for phosphorylation site prediction by extracting and combining sequence and PPI information. In PhosIDN, a sequence feature encoding sub-network is proposed to capture not only local patterns but also long-range dependencies from protein sequences. Meanwhile, useful PPI features are also extracted in PhosIDN by a PPI feature encoding sub-network adopting a multi-layer deep neural network. Moreover, to effectively combine sequence and PPI information, a heterogeneous feature combination sub-network is introduced to fully exploit the complex associations between sequence and PPI features, and their combined features are used for final prediction. Comprehensive experiment results demonstrate that the proposed PhosIDN significantly improves the prediction performance of phosphorylation sites and compares favorably with existing general and kinase-specific phosphorylation site prediction methods.

Availability and implementation
PhosIDN is freely available at https://github.com/ustchangyuanyang/PhosIDN.

Supplementary information
Supplementary data are available at Bioinformatics online.
The topology of data: opportunities for cancer research
Authors: Loughrey Ciara F , Fitzpatrick Padraig , Orr Nick , Jurek-Loughrey Anna 
Published: July 2021

Abstract

Motivation
Topological methods have recently emerged as a reliable and interpretable framework for extracting information from high-dimensional data, leading to the creation of a branch of applied mathematics called Topological Data Analysis (TDA). Since then, TDA has been progressively adopted in biomedical research. Biological data collection can result in enormous datasets, comprising thousands of features and spanning diverse datatypes. This presents a barrier to initial data analysis as the fundamental structure of the dataset becomes hidden, obstructing the discovery of important features and patterns. TDA provides a solution to obtain the underlying shape of datasets over continuous resolutions, corresponding to key topological features independent of noise. TDA has the potential to support future developments in healthcare as biomedical datasets rise in complexity and dimensionality. Previous applications extend across the fields of neuroscience, oncology, immunology and medical image analysis. TDA has been used to reveal hidden subgroups of cancer patients, construct organizational maps of brain activity and classify abnormal patterns in medical images. The utility of TDA is broad and to understand where current achievements lie, we have evaluated the present state of TDA in cancer data analysis.

Results
This article aims to provide an overview of TDA in Cancer Research. A brief introduction to the main concepts of TDA is provided to ensure that the article is accessible to readers who are not familiar with this field. Following this, a focussed literature review on the field is presented, discussing how TDA has been applied across heterogeneous datatypes for cancer research.
Accurate large-scale phylogeny-aware alignment using BAli-Phy
Authors: Gupta Maya , Zaharias Paul , Warnow Tandy 
Published: July 2021

AbstractMotivationBAli-Phy, a popular Bayesian method that co-estimates multiple sequence alignments and phylogenetic trees, is a rigorous statistical method, but due to its computational requirements, it has generally been limited to relatively small datasets (at most about 100 sequences). Here, we repurpose BAli-Phy as a ‘phylogeny-aware’ alignment method: we estimate the phylogeny from the input of unaligned sequences, and then use that as a fixed tree within BAli-Phy.ResultsWe show that this approach achieves high accuracy, greatly superior to Prank, the current most popular phylogeny-aware alignment method, and is even more accurate than MAFFT, one of the top performing alignment methods in common use. Furthermore, this approach can be used to align very large datasets (up to 1000 sequences in this study).Availability and implementationSee https://doi.org/10.13012/B2IDB-7863273_V1 for datasets used in this study.Supplementary informationSupplementary data are available at Bioinformatics online.
Cortical Morphology and White Matter Tractography of Three Phylogenetically Distant Primates: Evidence for a Simian Elaboration
Authors: Roumazeilles Lea , Lange Frederik J , Benn R Austin , Andersson Jesper L R , Bertelsen Mads F , Manger Paul R , Flach Edmund , Khrapitchev Alexandre A , Bryant Katherine L , Sallet Jérôme , Mars Rogier B 
Published: July 2021

Abstract
Comparative neuroimaging has been used to identify changes in white matter architecture across primate species phylogenetically close to humans, but few have compared the phylogenetically distant species. Here, we acquired postmortem diffusion imaging data from ring-tailed lemurs (Lemur catta), black-capped squirrel monkeys (Saimiri boliviensis), and rhesus macaques (Macaca mulatta). We were able to establish templates and surfaces allowing us to investigate sulcal, cortical, and white matter anatomy. The results demonstrate an expansion of the frontal projections of the superior longitudinal fasciculus complex in squirrel monkeys and rhesus macaques compared to ring-tailed lemurs, which correlates with sulcal anatomy and the lemur’s smaller prefrontal granular cortex. The connectivity of the ventral pathway in the parietal region is also comparatively reduced in ring-tailed lemurs, with the posterior projections of the inferior longitudinal fasciculus not extending toward parietal cortical areas as in the other species. In the squirrel monkeys we note a very specific occipito-parietal anatomy that is apparent in their surface anatomy and the expansion of the posterior projections of the optical radiation. Our study supports the hypothesis that the connectivity of the prefrontal-parietal regions became relatively elaborated in the simian lineage after divergence from the prosimian lineage.
Reconstructing baselines: use of habitat suitability modelling to predict pre-fishing condition of a Vulnerable Marine Ecosystem
Authors: Downie Anna-Leena , Piechaud Nils , Howell Kerry , Barrio Froján Christopher , Sacau Mar , Kenny Andrew 
Published: July 2021

Abstract
As industrialized fishing activities have moved into deeper water, the recognition of Vulnerable Marine Ecosystems (VMEs) has become important for the protection of the deep-sea. Our limited knowledge on the past and present distribution of VMEs hinders our ability to manage bottom fisheries effectively. This study investigated whether accounting for bottom fishing intensity (derived from Vessel Monitoring System records) as a predictor in habitat suitability models can (1) improve predictions of, and (2) provide estimates for a pre-fishing baseline for the distribution and biomass of a VME indicator taxon. Random Forest models were applied to presence/absence and biomass of Geodia sponges and environmental variables with and without bottom fishing intensity. The models including fishing were further used to predict distribution and biomass of Geodia to a pre-fishing scenario. Inclusion of fishing pressure as a predictive term significantly improved model performance for both sponge presence and biomass. This study has demonstrated a way to produce a more accurate picture of the current distribution of VMEs in the study area. The pre-fishing scenario predictions also identified areas of suitable Geodia habitat that are currently impacted by fishing, suggesting that sponge habitat and biomass have been impacted by bottom trawling activities.
Controllability of second-order differential equations with state-dependent delay
Authors: Karthikeyan K , Tamizharasan D , Nieto J J , Nisar Kottakkaran Sooppy 
Published: July 2021

Abstract
The intention of this article is to analyse the existence of controllability of differential equations of second order with state-dependent delay by using the cosine function theory. Also, well-posedness of the solution to the problem is examined. In the end, examples are provided to represent the theory.
On Endomorphisms of Algebraic Varieties
Authors: Das Nilkantha 
Published: July 2021

Abstract
Consider an endomorphism of an algebraic variety over an algebraically closed field of characteristic zero that is injective on the complement of a proper closed subvariety. We prove that such an endomorphism is an automorphism, provided the morphism is quasi-finite. We also show that if the codimension of the subvariety is at least $2$, the endomorphism is an automorphism, provided the morphism is affine, or the variety is affine, or the variety has a normalization, which is locally factorial.
Post-transcriptional regulation of immunological responses by Regnase-1-related RNases
Authors: Uehata Takuya , Takeuchi Osamu 
Published: July 2021

Abstract
Regulation of messenger RNA (mRNA) decay plays a crucial role in the control of gene expression. Canonical mRNA decay pathways are initiated by deadenylation and decapping and are followed by exonucleolytic degradation. However, recent studies revealed that endoribonucleolytic cleavage also mediates mRNA decay, and both exoribonucleolytic and endoribonucleolytic decay pathways are important for the regulation of immune responses. Regnase-1 functions as an endoribonuclease to control immunity by damping mRNAs. Particularly, Regnase-1 controls cytokines and other inflammatory mediators by recognizing their mRNAs via stem–loop structures present in the 3′ untranslated regions. Regnase-1 was found to be critical for human inflammatory diseases such as ulcerative colitis and idiopathic pulmonary fibrosis. Furthermore, a set of Regnase-1-related RNases contribute to immune regulation as well as antiviral host defense. In this review, we provide an overview of recent findings as to immune-related RNA-binding proteins (RBPs) with an emphasis on stem–loop-mediated mRNA decay via Regnase-1 and related RNases and discuss how the function of these RBPs is regulated and contributes to inflammatory disorders.
Clinic, community, and in-between: the influence of space on real-time translation of medical expertise by frontline healthcare professionals in marginal tribal communities
Authors: Tripathi Vinayak R , Jha Harsh Kumar , Popli Manish , Shah Pankaj , Desai Gayatri 
Published: July 2021

AbstractIn this article, we explore real-time translation work undertaken by frontline healthcare professionals as they interact with marginal tribal communities in Western India. Our 1-year ethnographic study of a healthcare organization delivering obstetric and gynaecological care to tribal communities helps us understand how obstetric counsellors translate allopathic medical expertise across epistemological boundaries to the tribal community they serve, in localized comprehensible forms. We identify four distinct mechanisms of translation work—Interpreting, Annotating, Norming, and Justifying—which differentially deploy and integrate elements of tribal vocabulary, symbols, knowledge, and imaginations of health and body with specific aspects of clinical diagnosis and prescription, making the latter meaningful and actionable in the process. Furthermore, we use configurational approach—Qualitative Comparative Analysis—to investigate how the type of space where the interaction between the counsellors and tribal women patients happens influences the translation work undertaken. We find that counsellors engage in spatially differentiated translation work. They predominantly use justifying and norming in clinical space (hospital); interpreting and annotating in community space (village or school); and interpreting and norming in the overlapping in-between space (outdoor patient department). Our study contributes to translation literature by showing how real-time translation is undertaken in practice, especially in a setting representing high-stakes institutional translation, and how translation work is influenced by the type of space in which interactions happen.
Right-sided Bochdalek hernia in an adult: a case report
Authors: Pun Ashis , Dhoubhadel Pratibha , Dawadi Kamal 
Published: July 2021

Abstract
Bochdalek hernia (BH) is the most common type of congenital diaphragmatic hernia and is usually left-sided. It typically presents in neonates and diagnosis in adults is a rarity. To date only 34 reported cases of right-sided BH have been surgically managed in adults in literature. We review a 21-year-old female with a right-sided BH diagnosed as acute calculus cholecystitis and underwent laparoscopic cholecystectomy. The diagnosis of BH was made incidentally during surgery. The hernia did not have a sac with no hernial contents. It was treated via laparoscopic intracorporeal suturing and patient postoperative period was uneventful. Right-sided BH is rare. Regardless of the symptoms surgical treatment should be done to avoid risk of visceral strangulation.
A phosphate binding pocket is a key determinant of exo- versus endo-nucleolytic activity in the SNM1 nuclease family
Authors: Baddock Hannah T , Newman Joseph A , Yosaatmadja Yuliana , Bielinski Marcin , Schofield Christopher J , Gileadi Opher , McHugh Peter J 
Published: July 2021

Abstract
The SNM1 nucleases which help maintain genome integrity are members of the metallo-β-lactamase (MBL) structural superfamily. Their conserved MBL-β-CASP-fold SNM1 core provides a molecular scaffold forming an active site which coordinates the metal ions required for catalysis. The features that determine SNM1 endo- versus exonuclease activity, and which control substrate selectivity and binding are poorly understood. We describe a structure of SNM1B/Apollo with two nucleotides bound to its active site, resembling the product state of its exonuclease reaction. The structure enables definition of key SNM1B residues that form contacts with DNA and identifies a 5′ phosphate binding pocket, which we demonstrate is important in catalysis and which has a key role in determining endo- versus exonucleolytic activity across the SNM1 family. We probed the capacity of SNM1B to digest past sites of common endogenous DNA lesions and find that base modifications planar to the nucleobase can be accommodated due to the open architecture of the active site, but lesions axial to the plane of the nucleobase are not well tolerated due to constriction around the altered base. We propose that SNM1B/Apollo might employ its activity to help remove common oxidative lesions from telomeres.
Soft and disordered hyperuniform elastic metamaterials for highly efficient vibration concentration
Authors: Tang Hanchuan , Hao Zhuoqun , Liu Ying , Tian Ye , Niu Hao , Zang Jianfeng 
Published: July 2021

Abstract
Vibrations, which widely exist throughout the world, could be a nearly endless and locally obtained green energy source. It has been a long-standing challenge to efficiently utilize dispersed vibration energy, especially within the high-frequency range, since the amplitudes of high-frequency vibrations in local parts of objects are relatively weak. Here, for the first time, we propose a soft and disordered hyperuniform elastic metamaterial (DHEM), achieving a remarkable concentration of vibrations in broad frequency bands by a maximum enhancement factor of ∼4000 at 1930 Hz. The DHEM, with rational sizes from ∼1 cm to ∼1000 cm, covers a broad range of frequencies from ∼10 Hz to ∼10 kHz, which are emitted by many vibration sources including domestic appliances, factories and transportation systems, for example. Moreover, the performance of the soft DHEM under deformation is validated, enabling conformal attachments on uneven objects. Our findings lay the groundwork for reducing traditional energy consumption by recovering some of the energy dissipated by devices in the working world.
Accurate and broadband manipulations of harmonic amplitudes and phases to reach 256 QAM millimeter-wave wireless communications by time-domain digital coding metasurface
Authors: Chen Ming Zheng , Tang Wankai , Dai Jun Yan , Ke Jun Chen , Zhang Lei , Zhang Cheng , Yang Jin , Li Lianlin , Cheng Qiang , Jin Shi , Cui Tie Jun 
Published: July 2021

Abstract
We propose a theoretical mechanism and new coding strategy to realize extremely accurate manipulations of nonlinear electromagnetic harmonics in ultrawide frequency band based on a time-domain digital coding metasurface (TDCM). Using the proposed mechanism and coding strategy, we design and fabricate a millimeter-wave (mmWave) TDCM, which is composed of reprogrammable meta-atoms embedded with positive-intrinsic-negative diodes. By controlling the duty ratios and time delays of the digital coding sequences loaded on a TDCM, experimental results show that both amplitudes and phases of different harmonics can be engineered at will simultaneously and precisely in broad frequency band from 22 to 33 GHz, even when the coding states are imperfect, which is in good agreement with theoretical calculations. Based on the fabricated high-performance TDCM, we further propose and experimentally realize a large-capacity mmWave wireless communication system, where 256 quadrature amplitude modulation, along with other schemes, is demonstrated. The new wireless communication system has a much simpler architecture than the currently used mmWave wireless systems, and hence can significantly reduce the hardware cost. We believe that the proposed method and system architecture can find vast application in future mmWave and terahertz-wave wireless communication and radar systems.
English Overseas Empire
Authors: Roper L. H. 
Published: July 2021

The English (after the Union of England, Scotland, and Wales in 1707, the British) Overseas Empire famously encompassed the globe. The range of scholarship related to this phenomenon stretches accordingly. This article focuses on contributions that consider the period prior to c. 1700 but provides links to other Oxford Bibliographies articles that include entries on non-English perspectives on the expansion of English overseas interests more fully, entries on the cultural interactions generated by that expansion, entries that relate to the later period, and entries that provide additional references to the topics discussed here. The emergence of an English Overseas Empire might be regarded as one of the most significant yet one of the more unlikely consequences of the Reformation and the Renaissance. In the fifteenth century, England suffered civil war and had its overseas territory reduced to Calais and the Pale of Dublin while its foreign mercantile sphere concentrated on the Baltic region, Antwerp, and Seville. The English break with Rome severed longstanding Anglo-Iberian economic ties and provided the religious-ideological frame for trading, plundering, and colonizing forays against the “popish” Iberians the success of whose initiatives had left the English scandalously behind in the minds of early imperial cheerleaders. By the 1640s, English “private” initiatives had established presences in Africa, America, and Asia, although the scale of these operations eventually proved beyond the capacity of these projectors, thus necessitating governmental intervention. After 1689, France replaced Spain as the imperial bogey, but an anti-Catholic imperial ideology, which employed a language of liberty and virtue derived from humanism, intensified as English political and economic ambitions expanded and direct government involvement in empire increased. Both this expansion and the cultural interactions it generated tracked changing English cultural and political sensibilities: contemporary authors and artists acclaimed English overseas endeavor as a hallmark of civilization, modernity, capitalism, and progress; the stridency of this celebratory view accompanied a seemingly inexorable coloring of the globe pink prior to World War II. English overseas expansion also entailed deep involvement in the enslavement of Africans—in terms of both exporting enslaved persons from sub-Saharan Africa throughout the Western Hemisphere and importing these people to labor on English plantations—a reality that has begun to receive significant attention only recently. It also involved the often-nasty subjugation of societies in situ, another reality that has also received a recent intensive rethink in the postcolonial era that began in the 1960s. The careful treatment of the responses of those societies to British incursions has become another recent and welcome development.
Death From Primary Amebic Meningoencephalitis After Recreational Water Exposure During Recent Travel to India—Santa Clara County, California, 2020
Authors: Harris Glenn R , Karmarkar Ellora N , Quenelle Rebecca , Chaille Lyndsey , Madhok Jai , Tien Vivian , Gupta Jyoti , Jain Seema , Liu Maria , Roy Shantanu , Narasimhan Supriya , Kimura Akiko , Cope Jennifer R , Ali Ibne Karim M 
Published: July 2021

Abstract

Background
In February 2020, a man returned to the United States after an 11-day trip to India and died of primary amebic meningoencephalitis (PAM), caused by nasal exposure to the free-living ameba Naegleria fowleri found in warm water. We identified potential exposures, confirmed etiology, and described the molecular epidemiology of the infection.

Methods
We reviewed medical records to describe his clinical course and interviewed his family to determine water exposures. Genotyping was performed on the N. fowleri strain and compared with North American strains through repetitive nonpolymorphic nuclear loci analysis to identify differences. We reviewed N. fowleri strains in the National Center for Biotechnology Information database (GenBank) to determine genotypes present in India.

Results
The patient became acutely encephalopathic 3 days after returning; the only known nasal water exposure was at an indoor swimming pool in India 5 days earlier. Cerebrospinal fluid (CSF) testing demonstrated neutrophil-predominant pleocytosis and low glucose, but negative gram stain and culture. CSF microscopy revealed trophozoites; N. fowleri was detected by real-time polymerase chain reaction. Classical genotyping confirmed genotype I, common in the United States and among Indian strains in GenBank. The North American N. fowleri strains and the patient’s strain varied at 5 nonpolymorphic loci.

Conclusions
A man died from PAM after likely exposure at a vacation rental pool in India. We recommend including PAM in the differential diagnosis when CSF studies suggest bacterial meningitis but gram stain is negative. Genotyping can advance our understanding of N. fowleri molecular epidemiology and support future investigations.