bluuebunny/crossref_metadata_2025_split huggingface dataset:
HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data
Authors: Wang Jiankang , Nakato Ryuichiro 
Published: November 2021

Abstract
Eukaryotic genomes are organized in a three-dimensional spatial structure. In this regard, the development of chromosome conformation capture methods has enabled studies of chromosome organization on a genomic scale. Hi-C, the high-throughput chromosome conformation capture method, can reveal a population-averaged, hierarchical chromatin structure. The typical Hi-C analysis uses a two-dimensional (2D) contact matrix that indicates contact frequencies between all possible genomic position pairs. Oftentimes, however, such a 2D matrix is not amenable to handling quantitative comparisons, visualizations and integrations across multiple datasets. Although several one-dimensional (1D) metrics have been proposed to depict structural information in Hi-C data, their effectiveness is still underappreciated. Here, we first review the currently available 1D metrics for individual Hi-C samples or two-sample comparisons and then discuss their validity and suitable analysis scenarios. We also propose several new 1D metrics to identify additional unique features of chromosome structures. We highlight that the 1D metrics are reproducible and robust for comparing and visualizing multiple Hi-C samples. Moreover, we show that 1D metrics can be easily combined with epigenome tracks to annotate chromatin states in greater details. We develop a new framework, called HiC1Dmetrics, to summarize all 1D metrics discussed in this study. HiC1Dmetrics is open-source (github.com/wangjk321/HiC1Dmetrics) and can be accessed from both command-line and web-based interfaces. Our tool constitutes a useful resource for the community of chromosome-organization researchers.
Deep graph learning of inter-protein contacts
Authors: Xie Ziwei , Xu Jinbo 
Published: November 2021

Abstract

Motivation
Inter-protein (interfacial) contact prediction is very useful for in silico structural characterization of protein–protein interactions. Although deep learning has been applied to this problem, its accuracy is not as good as intra-protein contact prediction.

Results
We propose a new deep learning method GLINTER (Graph Learning of INTER-protein contacts) for interfacial contact prediction of dimers, leveraging a rotational invariant representation of protein tertiary structures and a pretrained language model of multiple sequence alignments. Tested on the 13th and 14th CASP-CAPRI datasets, the average top L/10 precision achieved by GLINTER is 54% on the homodimers and 52% on all the dimers, much higher than 30% obtained by the latest deep learning method DeepHomo on the homodimers and 15% obtained by BIPSPI on all the dimers. Our experiments show that GLINTER-predicted contacts help improve selection of docking decoys.

Availability and implementation
The software is available at https://github.com/zw2x/glinter. The datasets are available at https://github.com/zw2x/glinter/data.

Supplementary information
Supplementary data are available at Bioinformatics online.
Climate-Friendly Seafood: The Potential for Emissions Reduction and Carbon Capture in Marine Aquaculture
Authors: Jones Alice R , Alleway Heidi K , McAfee Dominic , Reis-Santos Patrick , Theuerkauf Seth J , Jones Robert C 
Published: November 2021

Abstract
Aquaculture is a critical food source for the world's growing population, producing 52% of the aquatic animal products consumed. Marine aquaculture (mariculture) generates 37.5% of this production and 97% of the world's seaweed harvest. Mariculture products may offer a climate-friendly, high-protein food source, because they often have lower greenhouse gas (GHG) emission footprints than do the equivalent products farmed on land. However, sustainable intensification of low-emissions mariculture is key to maintaining a low GHG footprint as production scales up to meet future demand. We examine the major GHG sources and carbon sinks associated with fed finfish, macroalgae and bivalve mariculture, and the factors influencing variability across sectors. We highlight knowledge gaps and provide recommendations for GHG emissions reductions and carbon storage, including accounting for interactions between mariculture operations and surrounding marine ecosystems. By linking the provision of maricultured products to GHG abatement opportunities, we can advance climate-friendly practices that generate sustainable environmental, social, and economic outcomes.
A novel stroke lesion network mapping approach: improved accuracy yet still low deficit prediction
Authors: Pini Lorenzo , Salvalaggio Alessandro , De Filippo De Grazia Michele , Zorzi Marco , Thiebaut de Schotten Michel , Corbetta Maurizio 
Published: November 2021

AbstractLesion network mapping estimates functional network abnormalities caused by a focal brain lesion. The method requires embedding the volume of the lesion into a normative functional connectome and using the average functional magnetic resonance imaging signal from that volume to compute the temporal correlation with all other brain locations. Lesion network mapping yields a map of potentially functionally disconnected regions. Although promising, this approach does not predict behavioural deficits well. We modified lesion network mapping by using the first principal component of the functional magnetic resonance imaging signal computed from the voxels within the lesioned area for temporal correlation. We measured potential improvements in connectivity strength, anatomical specificity of the lesioned network and behavioural prediction in a large cohort of first-time stroke patients at 2-weeks post-injury (n = 123). This principal component functional disconnection approach localized mainly cortical voxels of high signal-to-noise; and it yielded networks with higher anatomical specificity, and stronger behavioural correlation than the standard method. However, when examined with a rigorous leave-one-out machine learning approach, principal component functional disconnection approach did not perform better than the standard lesion network mapping in predicting neurological deficits. In summary, even though our novel method improves the specificity of disconnected networks and correlates with behavioural deficits post-stroke, it does not improve clinical prediction. Further work is needed to capture the complex adjustment of functional networks produced by focal damage in relation to behaviour.
Multiplex connectome changes across the alzheimer’s disease spectrum using gray matter and amyloid data
Authors: Canal-Garcia Anna , Gómez-Ruiz Emiliano , Mijalkov Mite , Chang Yu-Wei , Volpe Giovanni , Pereira Joana B ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2021

AbstractThe organization of the Alzheimer’s disease (AD) connectome has been studied using graph theory using single neuroimaging modalities such as positron emission tomography (PET) or structural magnetic resonance imaging (MRI). Although these modalities measure distinct pathological processes that occur in different stages in AD, there is evidence that they are not independent from each other. Therefore, to capture their interaction, in this study we integrated amyloid PET and gray matter MRI data into a multiplex connectome and assessed the changes across different AD stages. We included 135 cognitively normal (CN) individuals without amyloid-β pathology (Aβ−) in addition to 67 CN, 179 patients with mild cognitive impairment (MCI) and 132 patients with AD dementia who all had Aβ pathology (Aβ+) from the Alzheimer’s Disease Neuroimaging Initiative. We found widespread changes in the overlapping connectivity strength and the overlapping connections across Aβ-positive groups. Moreover, there was a reorganization of the multiplex communities in MCI Aβ + patients and changes in multiplex brain hubs in both MCI Aβ + and AD Aβ + groups. These findings offer a new insight into the interplay between amyloid-β pathology and brain atrophy over the course of AD that moves beyond traditional graph theory analyses based on single brain networks.
Frontopolar tDCS induces frequency-dependent changes of spontaneous low-frequency fluctuations: a resting-state fMRI study
Authors: Ren Ping , Ma Manxiu , Wu Donghui , Ma Yuanye 
Published: November 2021

Abstract
Transcranial direct current stimulation (tDCS) is a noninvasive neuromodulation technique that can modulate cortical excitability and behavioral performance. However, its effects on spontaneous low-frequency fluctuations of brain activity are still poorly understood. Here, we systematically investigated the frontopolar tDCS effects on resting-state brain activity and connectivity. Twelve healthy participants were recruited and received anode, cathode, and sham stimulation in a randomized order. Resting-state functional magnetic resonance imaging was performed before and after stimulation. Functional connectivity was calculated to examine tDCS effects within and beyond the frontopolar network. To assess the frequency-dependent changes of brain activity, fractional amplitude of low-frequency fluctuations (fALFF) was computed in the slow-4 (0.027–0.073 Hz) and slow-5 (0.01–0.027 Hz) bands. The results showed anodal tDCS-induced widespread connectivity reduction within and beyond the frontopolar network. Regardless of tDCS polarity, stimulation effect on fALFF was significantly larger in slow-5 band compared with the slow-4. Notably, anodal tDCS-induced connectivity changes were associated with pre-tDCS fALFF in slow-4 band, showing positive correlations in the frontal regions and negative correlations in the temporal regions. Our findings imply that tDCS-induced brain alterations may be frequency-dependent, and pre-tDCS regional brain activity could be used to predict post-tDCS connectivity changes.
Constitutional Theories of International Organisations: Beyond the West
Authors: Peters Anne 
Published: November 2021

Abstract
The Joint Statement by the Foreign Ministers of China and Russia on Certain Aspects of Global Governance in Modern Conditions of 23 March 2021 calls for “the establishment of a fairer, more democratic and rational multipolar world order.” The paper inquires how constitutional theories of international organisations have in the past and present sought to contribute to world order. It identifies three waves of such theory since the 1960s. Looking in more detail at the ongoing third wave, it identifies and seeks to pull out further a constitutional model which upscales the proto-democratic practices in international organisations by strengthening forums for participation and contestation, which rectifies to the north-south imbalance inter alia rooted in the colonial heritage by involving more actors from the global south, and which tackles the global social question upfront.
Identification and Functional Characterization of Antifreeze Protein and Its Mutants in Dendroctonus armandi (Coleoptera: Curculionidae: Scolytinae) Larvae Under Cold Stress
Authors: Fu Danyang , Sun Yaya , Gao Haiming , Liu Bin , Kang Xiaotong , Chen Hui 
Published: November 2021

Abstract
Dendroctonus armandi (Tsai and Li) (Coleoptera: Curculionidae: Scolytinae) is considered to be the most destructive forest pest in the Qinling and Bashan Mountains of China. Low winter temperatures limit insect’s populations, distribution, activity, and development. Insects have developed different strategies such as freeze-tolerance and freeze-avoidance to survive in low temperature conditions. In the present study, we used gene cloning, real-time polymerase chain reaction (PCR), RNA interference (RNAi), and heterologous expression to study the function of the D. armandi antifreeze protein gene (DaAFP). We cloned the 800 bp full-length cDNA encoding 228 amino acids of DaAFP and analyzed its structure using bioinformatics analysis. The DaAFP amino acid sequence exhibited 24–86% similarity with other insect species. The expression of DaAFP was high in January and in the larvae, head, and midgut of D. armandi. In addition, the expression of DaAFP increased with decreasing temperature and increasing exposure time. RNAi analysis also demonstrated that AFP plays an important role in the cold tolerance of overwintering larvae. The thermal hysteresis and antifreeze activity assay of DaAFP and its mutants indicated that the more regular the DaAFP threonine-cystine-threonine (TXT) motif, the stronger the antifreeze activity. These results suggest that DaAFP plays an essential role as a biological cryoprotectant in overwintering D. armandi larvae and provides a theoretical basis for new pest control methods.
Impact of ascending aortic prosthetic grafts on early postoperative descending aortic biomechanics on cardiac magnetic resonance imaging
Authors: Palumbo Maria C , Redaelli Alberto , Wingo Matthew , Tak Katherine A , Leonard Jeremy R , Kim Jiwon , Rong Lisa Q , Park Christine , Mitlak Hannah W , Devereux Richard B , Roman Mary J , RoyChoudury Arindam , Lau Christopher , Gaudino Mario F L , Girardi Leonard N , Weinsaft Jonathan W 
Published: November 2021

Abstract

OBJECTIVES
Among patients with ascending thoracic aortic aneurysms, prosthetic graft replacement yields major benefits but risk for recurrent aortic events persists for which mechanism is poorly understood. This pilot study employed cardiac magnetic resonance to test the impact of proximal prosthetic grafts on downstream aortic flow and vascular biomechanics.

METHODS
Cardiac magnetic resonance imaging was prospectively performed in patients with thoracic aortic aneurysms undergoing surgical (Dacron) prosthetic graft implantation. Imaging included time resolved (4-dimensional) phase velocity encoded cardiac magnetic resonance for flow quantification and cine-cardiac magnetic resonance for aortic wall distensibility/strain.

RESULTS
Twenty-nine patients with thoracic aortic aneurysms undergoing proximal aortic graft replacement were studied; cardiac magnetic resonance was performed pre- [12 (4, 21) days] and postoperatively [6.4 (6.2, 7.2) months]. Postoperatively, flow velocity and wall shear stress increased in the arch and descending aorta (P &lt; 0.05); increases were greatest in hereditary aneurysm patients. Global circumferential strain correlated with wall shear stress (r = 0.60–0.72, P &lt; 0.001); strain increased postoperatively in the native descending and thoraco-abdominal aorta (P &lt; 0.001). Graft-induced changes in biomechanical properties of the distal native ascending aorta were associated with post-surgical changes in descending aortic wall shear stress, as evidenced by correlations (r = −0.39–0.52; P ≤ 0.05) between graft-induced reduction of ascending aortic distensibility and increased distal native aortic wall shear stress following grafting.

CONCLUSIONS
Prosthetic graft replacement of the ascending aorta increases downstream aortic wall shear stress and strain. Postoperative increments in descending aortic wall shear stress correlate with reduced ascending aortic distensibility, suggesting that grafts provide a nidus for high energy flow and adverse distal aortic remodelling.
Contesting Homogeneity: Stereotypes and Heteronormativity in Aruni Kashyap’s His Father’s Disease
Authors: Biswas Debajyoti 
Published: November 2021

Abstract
This article analyses Aruni Kashyap’s short story collection His Father’s Disease. Kashyap challenges hegemonic structures through an emerging writing area tentatively classified as ‘Anglophone fiction from Northeast India’. By engaging with Foucault’s reading of Power/Knowledge this article examines the disciplining of literary regionalism (Anglophone literature from Northeast India), territory and sexuality encapsulated in Kashyap’s exposition of heteronormative societies across cultures. Through the stories Kashyap weaves a dialogic space within the narrative world that challenges various forms of stereotypes relating to regional representation in literary works as well as regional identity and sexuality prevailing in the contemporary world’s existing social and literaryscape. Therefore, it becomes pertinent to observe how Kashyap’s text becomes a site of contention where on one hand the stereotype is accommodated within the power structure, hence controlled and regulated by various agencies, and on the other hand the same knowledge is appropriated by the author as a counter-narrative/reverse-discourse.
The Cardiology Society of India-Kerala Acute Heart Failure Registry: poor adherence to guideline-directed medical therapy
Authors: Joseph Stigi , Panniyammakal Jeemon , Abdullakutty Jabir , S Sujithkumar , Vaikathuseril L Jayaprakash , Joseph Johny , Mattummal Shaffeq , Punnose Eapen , Unni Govindan , Natesan Syam , Sivadasanpillai Harikrishnan 
Published: November 2021

Abstract

Aims
Data on the burden of acute heart failure (AHF) admissions, practice patterns, and outcomes are rare from India and other low- and middle-income countries. We aimed to describe the baseline characteristics, guideline-directed medical therapy (GDMT) prescribing patterns and 90-day mortality rates in patients admitted with AHF in Kerala, India.

Methods and results
The Cardiology Society of India-Kerala Acute Heart Failure Registry (CSI-KHFR) is an observational registry from 50 hospitals in Kerala, India, with prospective follow-up. Consecutive patients with AHF, who consented to participate, were enrolled. The 2016 European Society of Cardiology criteria were used for the diagnosis of AHF. Kaplan–Meier survival analysis and Cox-proportional hazard models were used for data analysis. The variables in the MAGGIC risk score were used in the multivariable model. A total of 7507 patients with AHF (37% female) participated in the CSI-KHFR. The mean age was 64.3 (12.9) years. More than two-third had reduced ejection fraction (EF) (67.5%). Nearly one-fourth (28%) of patients with heart failure (HF) with reduced EF received GDMT. Overall, in-hospital and 90-day mortality rates were 7% and 11.6%, respectively. Prescriptions of different components of GDMT were independently associated with 90-day mortality.

Conclusion
The CSI-KHFR recorded an in-hospital and 90-day mortality of 7% and 11.6%, respectively. Only one of four patients received GDMT. AHF mortality was independently associated with GDMT initiation. Quality improvement initiatives that focus on increasing GDMT prescription may improve the survival of HF patients in India.
Barriers to care for perinatal patients with opioid use disorder: family physician perspectives
Authors: St. Louis Joshua , Barreto Tyler , Taylor Melina , Kane Claire , Worringer Emma , Eden Aimee R 
Published: November 2021

Abstract

Background
While barriers to care for pregnant patients with opioid use disorder (OUD) have been described, the experiences and challenges of the physicians providing care to these patients are poorly understood.

Objectives
To describe the experiences of family physicians providing comprehensive care to pregnant people with OUD and the challenges they face in providing such care.

Methods
Qualitative thematic analysis of 17 semistructured interviews conducted from July 2019 to September 2020 with family physicians who possess a Drug Enforcement Administration “X” waiver and provide care to pregnant patients.

Results
Seventeen family physicians practicing in the United States who care for pregnant people with OUD were interviewed. They described physician-, patient-, and systems-level barriers to providing and accessing care for this patient population. Of the 12 interrelated themes regarding challenges to delivering and accessing this care, 3 were particularly salient: the pervasive effects of social determinants of health, a lack of adequately trained providers, and social stigma associated with pregnant people with OUD.

Conclusion
A comprehensive, multilevel, and multidisciplinary approach is necessary to address these barriers and move towards health equity for this vulnerable patient population.
The spread of the plasmid RP4 in a synthetic bacterial community is dependent on the particular donor strain
Authors: Heß Stefanie , Kneis David , Virta Marko , Hiltunen Teppo 
Published: November 2021

ABSTRACT
The rapid spread of antibiotic resistance challenges modern medicine. So far, mechanistic and quantitative knowledge concerning the spread of resistance genes mainly relies on laboratory experiments with simplified setups, e.g. two strain communities. Thus, the transferability of the obtained process rates might be limited. To investigate the role of a diverse community concerning the dissemination of the multidrug resistance plasmid RP4, an Escherichia coli harboring RP4 invaded a microbial community consisting of 21 species. Changes in the community composition as well as plasmid uptake by community members were monitored for 22 days. Special focus was laid on the question of whether the observed changes were dependent on the actual invading donor isolate and the ambient antibiotic concentration. In our microcosm experiment, the community composition was primarily influenced by the given environmental variables and only secondarily by the particular invader E. coli. The establishment of resistance within the community, however, was directly dependent on the donor identity. The extent to which ambient conditions influence the spread of RP4 depended on the E. coli donor strain. These results emphasize that even within one species there are great differences in the ability to conquer an ecological niche and to spread antibiotic resistance.
High Temperature Requirement A (HtrA) protease ofListeria monocytogenesand its interaction with extracellular matrix molecules
Authors: Radhakrishnan Deepthi , M C Amrutha , Hutterer Evelyn , Wessler Silja , Ponnuraj Karthe 
Published: November 2021

ABSTRACTHigh Temperature Requirement A (HtrA) was identified as a secreted virulence factor in many pathogenic bacteria, including Listeria monocytogenes. Recently, it was discovered that Helicobacter pylori and Campylobacter jejuni HtrAs can directly cleave the human cell-adhesion molecule E-cadherin, which facilitates bacterial transmigration. HtrAs also interact with extracellular matrix (ECM) molecules. However, only a limited number of studies have been carried out in this regard. In the present study, the protease and ECM binding properties of L. monocytogenes HtrA (LmHtrA) were studied using native rLmHtrA, catalytically inactive rLmHtrA(S343A) and rLmHtrA lacking the PDZ domain (∆PDZ) to gain more insights into HtrA–ECM molecule interaction. The results show that (1) native rLmHtrA cleaves fibrinogen, fibronectin, plasminogen and casein in a time and temperature dependent manner, (2) interaction of rLmHtrA with various host proteins was found in the micromolar to nanomolar range, (3) in the absence of PDZ domain, rLmHtrA exhibits no drastic change in binding affinity toward the host molecules when compared with native rLmHtrA and (4) the PDZ domain plays an important role in the substrate cleavage as rLmHtrA1-394∆PDZ cleaves the substrates only under certain conditions. The proteolysis of various ECM molecules by rLmHtrA possibly highlights the role of HtrA in L. monocytogenes pathogenesis involving ECM degradation.