bluuebunny/crossref_metadata_2025_split huggingface dataset:
CCIP: predicting CTCF-mediated chromatin loops with transitivity
Authors: Wang Weibing , Gao Lin , Ye Yusen , Gao Yong 
Published: July 2021

Abstract

Motivation
CTCF-mediated chromatin loops underlie the formation of topological associating domains and serve as the structural basis for transcriptional regulation. However, the formation mechanism of these loops remains unclear, and the genome-wide mapping of these loops is costly and difficult. Motivated by the recent studies on the formation mechanism of CTCF-mediated loops, we studied the possibility of making use of transitivity-related information of interacting CTCF anchors to predict CTCF loops computationally. In this context, transitivity arises when two CTCF anchors interact with the same third anchor by the loop extrusion mechanism and bring themselves close to each other spatially to form an indirect loop.

Results
To determine whether transitivity is informative for predicting CTCF loops and to obtain an accurate and low-cost predicting method, we proposed a two-stage random-forest-based machine learning method, CTCF-mediated Chromatin Interaction Prediction (CCIP), to predict CTCF-mediated chromatin loops. Our two-stage learning approach makes it possible for us to train a prediction model by taking advantage of transitivity-related information as well as functional genome data and genomic data. Experimental studies showed that our method predicts CTCF-mediated loops more accurately than other methods and that transitivity, when used as a properly defined attribute, is informative for predicting CTCF loops. Furthermore, we found that transitivity explains the formation of tandem CTCF loops and facilitates enhancer–promoter interactions. Our work contributes to the understanding of the formation mechanism and function of CTCF-mediated chromatin loops.

Availability and implementation
The source code of CCIP can be accessed at: https://github.com/GaoLabXDU/CCIP.

Supplementary information
Supplementary data are available at Bioinformatics online.
What Influences Parents and Practitioners’ Decisions to Share Personal Information within an Early Help (Social Care) Context? Implications for Practice in Sharing Digital Data across Sectors
Authors: Smart Deborah , Jackson Katherine , Alderson Hayley , Foley Thomas , Foreman Stephen , Kaner Ben , Kaner Eileen , Lancaster Helen , Lingam Raghu , Rankin Judith , Rowlands Gill , Spencer Liam , McGovern Ruth 
Published: July 2021

AbstractMeeting the multiple and often complex needs of families (children, young people and adults) within ‘Early Help’ support is dependent upon practitioners from different sectors sharing relevant and timely information, after gaining a family’s voluntary consent to share information. This article reports on qualitative one-to-one interviews with adults in families (n = 32), one mother/father dyad interview (n = 2) and focus groups with practitioners (n = 47) in five local authority areas in North East England receiving or providing Early Help support. We explored experiences of providing consent to share personal information and consider the usefulness of a digital health data system when providing Early Help support to families. Communication Privacy Management theory was used as a framework to analyse the data. Key themes in participants’ accounts include the degree of need for help and support; the importance of trusting relationships; stronger and structured joint working practices; and understanding how information is shared. This work provides insights into current information sharing practices for some of the most vulnerable families and the wider social contexts. It has implications for the usefulness of a digital data system that shares GP health data with Early Help services and suggests the role this could have in the parent–practitioner relationship.
Bridging the energy gap of India’s residential buildings by using rooftop solar PV systems for higher energy stars
Authors: Dalal Rakesh , Bansal Kamal , Thapar Sapan 
Published: July 2021

Abstract
The residential-building sector in India consumes &gt;25% of the total electricity and is the third-largest consumer of electricity; consumption increased by 26% between 2014 and 2017. India has introduced a star-labelling programme for residential buildings that is applicable for all single- and multiple-dwelling units in the country for residential purposes. The Energy Performance Index (EPI) of a building (annual energy consumption in kilowatt-hours per square metre of the building) is taken as an indicator for awarding the star label for residential buildings. For gauging the EPI status of existing buildings, the electricity consumption of residential buildings (in kWh/m2/year) is established through a case study of the residential society. Two years of electricity bills are collected for an Indian residential society located in Palam, Delhi, analysed and benchmarked with the Indian residential star-labelling programme. A wide EPI gap is observed for existing buildings for five-star energy labels. Based on existing electricity tariffs, the energy consumption of residential consumers and the Bureau of Energy Efficiency (BEE)’s proposed building ENERGY STAR labelling, a grid-integrated rooftop solar photovoltaic (PV) system is considered for achieving a higher star label. This research study establishes the potential of grid-connected rooftop solar PV systems for residential buildings in Indian cities through a case study of Delhi. Techno-economic analysis of a grid-integrated 3-kWp rooftop solar PV plant is analysed by using RETScreen software. The study establishes that an additional two stars can be achieved by existing buildings by using a grid-integrated rooftop solar PV plant. Payback for retrofit of a 3-kWp rooftop solar PV plant for Indian cites varies from 3 to 7 years.
A case study in Delhi, India establishes the potential of grid-connected rooftop solar PV systems for residential buildings. Techno-economic analysis of grid integrated, 3 kWp rooftop solar systems estimates a payback period from 3 to 7 years.
Accuracy of Gastrointestinal Ultrasound and Calprotectin in the Assessment of Inflammation and its Location in Patients with an Ileoanal Pouch
Authors: Ardalan Zaid S , Friedman Antony B , Con Danny , Chandran Sujievvan , Gibson David , Pham Alan , De Cruz Peter , Tay Kwang , Bell Stephen , Rosella Ourania , Sparrow Miles P , Gibson Peter R 
Published: July 2021

Abstract

Background and Aims
In symptomatic patients with ileoanal pouches, pouchoscopy is needed for accurate diagnosis but is invasive. We aimed to assess the utility of non-invasive gastrointestinal ultrasound and faecal calprotectin in ileoanal pouch patients.

Methods
Patients with an ileoanal pouch were consecutively enrolled in this cross-sectional study from clinics in Victoria, Australia. The pouchitis disease activity index was used as a reference standard. Video-recorded pouchoscopies were reviewed by three gastroenterologists. Pouch, pre-pouch, and cuff biopsies were reviewed by a single pathologist. Ultrasound was performed by a single gastroenterologist transabdominally and transperineally. Faecal calprotectin was measured from morning stool samples. All examiners were blinded to patients’ clinical history.

Results
A total of 44 participants had a pouchoscopy, of whom 43 had a faecal calprotectin test and 42 had an ultrasound; 17 had pouchitis, 15 had pre-pouch ileitis, and 16 had cuffitis. Pouch wall thickness of &lt;3 mm was 88% sensitive in excluding pouchitis, and pouch wall thickness of ≥4 mm was 87% specific in diagnosing pouchitis. Transabdominal ultrasound had good utility [area under the curve: 0.78] in diagnosing moderate-severe pre-pouch ileitis. Transperineal ultrasound had good utility for the diagnosis of pouchitis [area under the curve: 0.79]. Faecal calprotectin differentiated inflammatory from non-inflammatory pouch disorders, such as irritable pouch syndrome, with an area under the curve of 0.90. Faecal calprotectin &lt;100 µg/g ruled out inflammatory pouch disorders with a sensitivity of 94%.

Conclusions
Faecal calprotectin and ultrasound are accurate and complementary tests to diagnose and localise inflammation of the ileoanal pouch. Prospective studies are needed to validate proposed sonographic indices and calprotectin levels.
Low-dose rivaroxaban and aspirin among patients with peripheral artery disease: a meta-analysis of the COMPASS and VOYAGER trials
Authors: Anand Sonia S , Hiatt Will , Dyal Leanne , Bauersachs Rupert , Berkowitz Scott D , Branch Kelley R H , Debus Sebastian , Fox Keith A A , Liang Yan , Muehlhofer Eva , Nehler Mark , Haskell Lloyd P , Patel Manesh , Szarek Michael , Yusuf Salim , Eikelboom John , Bonaca Marc P 
Published: July 2021

Abstract

Aims
Peripheral artery disease (PAD) patients suffer a high risk of major cardiovascular (CV) events, with athero-thrombo-embolism as the underlying pathophysiologic mechanism. Recently, two large randomized clinical trials evaluated the efficacy and safety of low-dose rivaroxaban twice daily plus aspirin in stable PAD outpatients and those immediately after peripheral revascularization. We sought to determine if the effects of low-dose rivaroxaban and aspirin compared to aspirin alone are consistent across this broad spectrum of PAD patients.

Methods and results
We conducted a random-effects meta-analysis of the COMPASS and VOYAGER randomized trials among 11 560 PAD patients (4996 from COMPASS and 6564 from VOYAGER) in the primary analysis and 9332 (2768 from COMPASS and 6564 from VOYAGER) with lower extremity (LE)-PAD in the secondary analysis. The hazard ratio (HR) for the composite of CV death, myocardial infarction, ischaemic stroke, acute limb ischaemia, or major vascular amputation was 0.79 (95% confidence interval, CI: 0.65–0.95) comparing low-dose rivaroxaban plus aspirin to aspirin alone. While the risk of major bleeding was increased with low-dose rivaroxaban plus aspirin compared to aspirin alone [HR: 1.51 (95% CI: 1.22–1.87)], there was no significant increase in severe bleeding [HR: 1.18 (95% CI: 0.79–1.76)]. Similar effects were observed in the subset with symptomatic LE-PAD.

Conclusions
Among PAD patients, low-dose rivaroxaban plus aspirin is superior to aspirin alone in reducing CV and limb outcomes including acute limb ischaemia and major vascular amputation. This reduction is offset by a relative increase in major bleeding, but not by an excess of fatal or critical organ bleeding. The consistency of findings of these trials supports the use of combination low-dose rivaroxaban plus aspirin in PAD patients across a broad spectrum of disease.
Applications of virus-induced gene silencing for identification of gene function in fruit
Authors: Liu Gangshuai , Li Hongli , Fu Daqi 
Published: July 2021

AbstractWith the development of bioinformatics, it is easy to obtain information and data about thousands of genes, but the determination of the functions of these genes depends on methods for rapid and effective functional identification. Virus-induced gene silencing (VIGS) is a mature method of gene functional identification developed over the last 20 years, which has been widely used in many research fields involving many species. Fruit quality formation is a complex biological process, which is closely related to ripening. Here, we review the progress and contribution of VIGS to our understanding of fruit biology and its advantages and disadvantages in determining gene function.
Chemical rescue of mutant proteins in livingSaccharomyces cerevisiaecells by naturally occurring small molecules
Authors: Hassell Daniel S , Steingesser Marc G , Denney Ashley S , Johnson Courtney R , McMurray Michael A 
Published: July 2021

AbstractIntracellular proteins function in a complex milieu wherein small molecules influence protein folding and act as essential cofactors for enzymatic reactions. Thus protein function depends not only on amino acid sequence but also on the concentrations of such molecules, which are subject to wide variation between organisms, metabolic states, and environmental conditions. We previously found evidence that exogenous guanidine reverses the phenotypes of specific budding yeast septin mutants by binding to a WT septin at the former site of an Arg side chain that was lost during fungal evolution. Here, we used a combination of targeted and unbiased approaches to look for other cases of “chemical rescue” by naturally occurring small molecules. We report in vivo rescue of hundreds of Saccharomyces cerevisiae mutants representing a variety of genes, including likely examples of Arg or Lys side chain replacement by the guanidinium ion. Failed rescue of targeted mutants highlight features required for rescue, as well as key differences between the in vitro and in vivo environments. Some non-Arg mutants rescued by guanidine likely result from “off-target” effects on specific cellular processes in WT cells. Molecules isosteric to guanidine and known to influence protein folding had a range of effects, from essentially none for urea, to rescue of a few mutants by DMSO. Strikingly, the osmolyte trimethylamine-N-oxide rescued ∼20% of the mutants we tested, likely reflecting combinations of direct and indirect effects on mutant protein function. Our findings illustrate the potential of natural small molecules as therapeutic interventions and drivers of evolution.
“When I Need to Travel, I Feel Feverish”: Everyday Experiences of Transport Inequalities Among Older Adults in Dhaka, Bangladesh
Authors: Jahangir Selim , Bailey Ajay , Hasan Musleh Uddin , Hossain Shanawez , Helbich Marco , Hyde Martin 
Published: July 2021

AbstractBackground and ObjectivesBuses are the most common form of public transport for older adults in developing countries. With over 37% of total trips, buses are the principal mode of transport in Dhaka. The majority of older adults are dependent on buses because of their affordability relative to other modes such as auto-rickshaws, rideshares, and taxis. This study aims to investigate key barriers in accessing buses in Dhaka and the consequences of these barriers to the everyday mobility of older adults.Research Design and MethodsThirty participants aged 60 and older were recruited from 2 socioeconomically different neighborhoods in Dhaka. We employed a thematic analysis of visual surveys and in-depth interviews to understand older adults’ spatial and cultural context and their experiences using buses in their everyday lives.ResultsBoarding and deboarding buses were common barriers for older adults due to overcrowding and traffic congestion. In addition, older adults faced challenges such as ageism, gender discrimination, and undesirable behavior by transport personnel and co-passengers. These barriers affected their independent mobility and influenced their access to work and social life, contributing to their social exclusion.Discussion and ImplicationsThis study illustrates the challenges faced by older adults when accessing public transport and the need to improve access to work, health care, and social life. Inclusive transport policies are essential in low- and middle-income countries to improve the well-being of older adults.
A unified description of surface waves and guided waves with relative amplitude dispersion maps
Authors: Sun Chengyu , Wang Zhinong , Wu Dunshi , Cai Ruiqian , Wu Han 
Published: July 2021

SUMMARYCompared with surface waves, guided waves are rarely applied in near-surface investigation. The main reason may lie in the complexity of their dispersion curves. Besides, the study and understanding of guided wave dispersion characteristics are now also inadequate and not deep enough. In this paper, we derived the complete theoretical dispersion curves of P–SV-wave and pure P-wave systems in layered media based on the transmission matrix method and obtained the relative displacement amplitude coefficients at the free surface as a function of frequency and phase velocity for both surface and guided waves. By assigning the value of relative displacement amplitude coefficient to the corresponding point (f,v) on dispersion curve, we got a multi-information diagram called relative amplitude dispersion map (RADM). As a unified description of surface and guided waves, RADM not only shows the velocity–frequency relationship but also represents the polarized energy ratio at the free surface by display colours. The accuracy of RADM was proved by synthetic seismic records, in which RADMs fit well with the corresponding dispersion energy of surface and guided waves. In addition, we designed six models with different Poisson's ratio (PR) and different layer numbers for comparison. It shows that the dispersive vertical-to-horizontal amplitude ratio of guided waves is complex and discontinuous in RADM, which brings great difficulty for mode identification and even affects the subsequent inversion. Tests also show that for high PR layers, the trends of guided P–SV-wave dispersion curves are basically consistent with those of pure P wave. With the decrease of PR, dispersion curves of guided P–SV wave gradually deviate from those of pure P wave. However, RADMs can be greatly consistent with the dispersion energy in either case. This is of great significance for the inversion of near-surface P and S velocities by using dispersion relationships of multimode surface and guided waves.
A systematic investigation of piercing-point-dependent seismic azimuthal anisotropy
Authors: Jia Yan , Liu Kelly H , Kong Fansheng , Liu Lin , Gao Stephen S 
Published: July 2021

SUMMARYThe vast majority of teleseismic XKS (including SKS, SKKS and PKS) shear wave splitting studies interpret the observed splitting parameters (fast orientation and splitting time) based on the assumption of a spatially invariant anisotropy structure in the vicinity of a recording station. For such anisotropy structures the observed splitting parameters are either independent of the arriving azimuth of the seismic ray paths if the medium traversed by the ray paths can be represented by a single layer of anisotropy with a horizontal axis of symmetry (i.e. simple anisotropy), or demonstrate a periodic variation with respect to the arriving azimuth for a more complicated structure of anisotropy (e.g. multiple layers with a horizontal axis of symmetry, or a single layer with a dipping axis). When a recording station is located near the boundary of two or more regions with different anisotropy characteristics, the observed splitting parameters are dependent on the location of the ray piercing points. Such a piercing-point dependence is clearly observed using a total of 360 pairs of XKS splitting parameters at three stations situated near the northeastern edge of the Sichuan Basin in central China. For a given station, the fast orientations differ as much as 90°, and the azimuthal variation of the fast orientations lacks a 90° or 180° periodicity which is expected for double-layered or dipping axis anisotropy. The observed splitting parameters from the three stations are spatially most consistent when they are projected at a depth of ∼250 km, and can be explained by shear strain associated with the absolute plate motion and mantle flow deflected by the cone-shaped lithospheric root of the Sichuan Basin.
A spatial analysis of out-of-pocket payments for healthcare in Malawi
Authors: Mwale Martin Limbikani , Mchenga Martina , Chirwa Gowokani Chijere 
Published: July 2021

Abstract
Out-of-pocket (OOP) expenditures on health remain high in many low- and middle-income countries despite policy efforts aiming to reduce these health costs by targeting their hotspots. Hotspot targeting remains inadequate, particularly where the OOP expenditures are related across geographic regions due to unequal demand, supply and prices of healthcare services. In this paper, we investigate the existence of geographical correlations in OOP health expenditures by employing a spatial Durbin model on data from 778 clusters obtained from the 2016 Malawi’s Integrated Household Survey. Results reveal that Malawian communities face geographical spillovers of OOP health expenditures. Furthermore, we find that factors including household size, education and geographical location are important drivers of the OOP health expenditure’s spatial dependency. The paper calls for policy in low-income countries to improve the quality and quantity of healthcare services in both OOP hotspots and their neighbouring communities.
Discovery of genomic variation across a generation
Authors: Trost Brett , Loureiro Livia O , Scherer Stephen W 
Published: July 2021

Abstract
Over the past 30 years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared with the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA—approximately 30 megabase pairs (Mb)—being ‘structurally variable’, mostly in the form of indels and copy number changes. Additional large-scale variations include balanced inversions (average of 18 Mb) and complex, difficult-to-resolve alterations. Collectively, ~1% of an individual’s genome will differ from the human reference sequence. When comparing across a generation, fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child’s genome. Driven by increasingly higher-resolution and higher-throughput sequencing technologies, newer and more accurate databases of genetic variation (for instance, more comprehensive structural variation data and phasing of combinations of variants along chromosomes) of worldwide populations will emerge to underpin the next era of discovery in human molecular genetics.
A long road to recovery: dynamics and ecology of the marbled rockcod (Notothenia rossii, family: Nototheniidae) at South Georgia, 50 years after overexploitation
Authors: Hollyman Philip R , Hill Simeon L , Laptikhovsky Vladimir V , Belchier Mark , Gregory Susan , Clement Alice , Collins Martin A 
Published: July 2021

Abstract
Exploitation is one of the major drivers of change in marine ecosystems. Following discovery in 1775, South Georgia saw sequential overexploitation of living resources, including seals, whales, and fish. Although exploitation is now tightly regulated, the ecosystem is still recovering. Marbled rockcod, Notothenia rossii (Richardson 1844), was the first fish species to be commercially exploited and high catches between 1967 and 1972 resulted in dramatic stock decline. Here, we use 30 years of trawl survey data to provide the first evidence of a sustained increase in the N. rossii population starting two decades after the prohibition of targeted fishing in 1985. The way species respond to change is mediated in part by trophic relationships with other organisms. We present the first multi-year, spatially-resolved comparison of adult N. rossii diet at South Georgia, highlighting a variable diet with less reliance on Antarctic krill than previously thought. Life history factors and possible heavy predation on early life stages might have delayed their recovery while diet plasticity potentially supported recent population growth. Due to the dynamic ecosystem at South Georgia and questions over catch reports from the period of heaviest exploitation, it is unlikely the current ecosystem could support a recovery to estimated pre-exploitation levels.