bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovering novel cancer bio-markers in acquired lapatinib resistance using Bayesian methods
Authors: Azad A K M , Alyami Salem A
Published: March 2021

Signalling transduction pathways (STPs) are commonly hijacked by many cancers for their growth and malignancy, but demystifying their underlying mechanisms is difficult. Here, we developed methodologies with a fully Bayesian approach in discovering novel driver bio-markers in aberrant STPs given high-throughput gene expression (GE) data. This project, namely ‘PathTurbEr’ (Pathway Perturbation Driver) uses the GE dataset derived from the lapatinib (an EGFR/HER dual inhibitor) sensitive and resistant samples from breast cancer cell lines (SKBR3). Differential expression analysis revealed 512 differentially expressed genes (DEGs) and their pathway enrichment revealed 13 highly perturbed singalling pathways in lapatinib resistance, including PI3K-AKT, Chemokine, Hippo and TGF-$\beta $ singalling pathways. Next, the aberration in TGF-$\beta $ STP was modelled as a causal Bayesian network (BN) using three MCMC sampling methods, i.e. Neighbourhood sampler (NS) and Hit-and-Run (HAR) sampler that potentially yield robust inference with lower chances of getting stuck at local optima and faster convergence compared to other state-of-art methods. Next, we examined the structural features of the optimal BN as a statistical process that generates the global structure using $p_1$-model, a special class of Exponential Random Graph Models (ERGMs), and MCMC methods for their hyper-parameter sampling. This step enabled key drivers identification that drive the aberration within the perturbed BN structure of STP, and yielded 34, 34 and 23 perturbation driver genes out of 80 constituent genes of three perturbed STP models of TGF-$\beta $ signalling inferred by NS, HAR and MH sampling methods, respectively. Functional-relevance and disease-relevance analyses suggested their significant associations with breast cancer progression/resistance.
STREME: accurate and versatile sequence motif discovery
Authors: Bailey Timothy L
Published: March 2021

Motivation

Sequence motif discovery algorithms can identify novel sequence patterns that perform biological functions in DNA, RNA and protein sequences—for example, the binding site motifs of DNA- and RNA-binding proteins.

Results

The STREME algorithm presented here advances the state-of-the-art in ab initio motif discovery in terms of both accuracy and versatility. Using in vivo DNA (ChIP-seq) and RNA (CLIP-seq) data, and validating motifs with reference motifs derived from in vitro data, we show that STREME is more accurate, sensitive and thorough than several widely used algorithms (DREME, HOMER, MEME, Peak-motifs) and two other representative algorithms (ProSampler and Weeder). STREME’s capabilities include the ability to find motifs in datasets with hundreds of thousands of sequences, to find both short and long motifs (from 3 to 30 positions), to perform differential motif discovery in pairs of sequence datasets, and to find motifs in sequences over virtually any alphabet (DNA, RNA, protein and user-defined alphabets). Unlike most motif discovery algorithms, STREME reports a useful estimate of the statistical significance of each motif it discovers. STREME is easy to use individually via its web server or via the command line, and is completely integrated with the widely used MEME Suite of sequence analysis tools. The name STREME stands for ‘Simple, Thorough, Rapid, Enriched Motif Elicitation’.

Availability and implementation

The STREME web server and source code are provided freely for non-commercial use at http://meme-suite.org.

Supplementary information

Supplementary data are available at Bioinformatics online.
A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals
Authors: Zhao Haochen , Li Yaohang , Wang Jianxin
Published: March 2021

Motivation

The Anatomical Therapeutic Chemical (ATC) system is an official classification system established by the World Health Organization for medicines. Correctly assigning ATC classes to given compounds is an important research problem in drug discovery, which can not only discover the possible active ingredients of the compounds, but also infer theirs therapeutic, pharmacological and chemical properties.

Results

In this article, we develop an end-to-end multi-label classifier called CGATCPred to predict 14 main ATC classes for given compounds. In order to extract rich features of each compound, we use the deep Convolutional Neural Network and shortcut connections to represent and learn the seven association scores between the given compound and others. Moreover, we construct the correlation graph of ATC classes and then apply graph convolutional network on the graph for label embedding abstraction. We use all label embedding to guide the learning process of compound representation. As a result, by using the Jackknife test, CGATCPred obtain reliable Aiming of 81.94%, Coverage of 82.88%, Accuracy 80.81%, Absolute True 76.58% and Absolute False 2.75%, yielding significantly improvements compared to exiting multi-label classifiers.

Availability and implementation

The codes of CGATCPred are available at https://github.com/zhc940702/CGATCPred and https://zenodo.org/record/4552917.
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization
Authors: Yu Yue , Huang Kexin , Zhang Chao , Glass Lucas M , Sun Jimeng , Xiao Cao
Published: March 2021

Motivation

Thanks to the increasing availability of drug–drug interactions (DDI) datasets and large biomedical knowledge graphs (KGs), accurate detection of adverse DDI using machine learning models becomes possible. However, it remains largely an open problem how to effectively utilize large and noisy biomedical KG for DDI detection. Due to its sheer size and amount of noise in KGs, it is often less beneficial to directly integrate KGs with other smaller but higher quality data (e.g. experimental data). Most of existing approaches ignore KGs altogether. Some tries to directly integrate KGs with other data via graph neural networks with limited success. Furthermore most previous works focus on binary DDI prediction whereas the multi-typed DDI pharmacological effect prediction is more meaningful but harder task.

Results

To fill the gaps, we propose a new method SumGNN: knowledge summarization graph neural network, which is enabled by a subgraph extraction module that can efficiently anchor on relevant subgraphs from a KG, a self-attention based subgraph summarization scheme to generate reasoning path within the subgraph, and a multi-channel knowledge and data integration module that utilizes massive external biomedical knowledge for significantly improved multi-typed DDI predictions. SumGNN outperforms the best baseline by up to 5.54%, and performance gain is particularly significant in low data relation types. In addition, SumGNN provides interpretable prediction via the generated reasoning paths for each prediction.

Availability and implementation

The code is available in Supplementary Material.

Supplementary information

Supplementary data are available at Bioinformatics online.
Do colour morphs of wall lizards express different personalities?
Authors: Sreelatha Lekshmi B , Carretero Miguel Angel , Pérez I De Lanuza Guillem , Klomp Danielle A , Boratyński Zbyszek
Published: March 2021

Colour morphs sometimes have different behavioural strategies which may be maintained by frequency or density dependence mechanisms. We investigated temporal changes in behavioural reaction to a novel environment among colour morphs (yellow, orange, white) of the European wall lizard (Podarcis muralis). Adult males were given two 15 min experimental trials, and their locomotion was highly consistent between the two trials. Boldness, freezing and escape behaviour were less repeatable. Colour morphs differed in their locomotion and freezing behaviour. Boldness was similar among the morphs, whereas escape behaviour was lowest in yellow morph. Consequently, yellow morph males tended to explore novel environments quickly and thus were more likely to move to potentially safe areas. Orange and white males showed more fear when exposed to a novel environment. Whether such alternative behavioural strategies can contribute to the maintenance of variable fitness optima among the morphs and ultimately to the maintenance of polymorphism remains open to further investigation.
Acute submassive pulmonary embolism after SARS-CoV-2 infection: a case report of reinfection or prolonged hypercoagulable state
Authors: Pow Timothy , Allen Sorcha , Brailovsky Yevgeniy , Darki Amir
Published: March 2021

Background

Coronavirus disease 19 (COVID-19) reinfection has been a topic of discussion with data still emerging. Viral antibodies are known to develop upon initial infection; however, it is unclear the amount of protection this confers against reinfection. Additionally, COVID-19-associated coagulopathy (CAC) is a well-documented phenomenon; however, there are no high-quality studies to support the treatment of outpatients beyond standard indications of venous thromboembolism (VTE) prophylaxis. This case describes a patient with either COVID-19 reinfection or prolonged course of CAC resulting in pulmonary embolism (PE).

Case summary

A 40-year-old healthy man presented with fever and cough. He tested positive for COVID-19 and was sent home to self-quarantine. His symptoms resolved and repeat COVID-19 testing returned negative. Two months later, he developed dyspnoea on exertion and syncope. Computed tomography with PE protocol demonstrated acute bilateral PE, and repeat COVID-19 testing returned positive. He was escalated to catheter-directed thrombolysis, but prior to the procedure went into cardiopulmonary arrest. Cardiopulmonary resuscitation was initiated and full-dose systemic alteplase was administered. Cardiothoracic surgery was consulted for consideration of veno-arterial extracorporeal membrane oxygenation; however, return of spontaneous circulation was unable to be achieved.

Discussion

This case raises the question of COVID-19 reinfection and prolonged risk of VTE due to CAC. We believe the patient was reinfected with COVID-19 provoking his PE; however, a single COVID-19 infection causing a prolonged course of CAC is possible. Until better data exists, decisions regarding outpatient prophylaxis must be individualized to weigh the risks of bleeding against the risk of thrombosis.
Fathers’ Job Flexibility and Mothers’ Return to Employment
Authors: Buchler Sandra , Lutz Katharina
Published: March 2021

One of the main drivers of gender inequality is the unequal distribution of paid work between men and women, in particular, after the birth of a child. In this study, we examine how a man’s employment flexibility, specifically his weekly hours of employment and schedule autonomy, influence his female partner’s return to employment after the birth of a first child using the German Socio-Economic Panel. Given women’s placement as primary but not solitary carers of young children, it is plausible that women’s attachment to the labour force will increase if their male partner is in a position to take on more of the responsibility for unpaid work. Results indicate that a father’s employment flexibility facilities a mother’s part-time employment. A return to full-time hours, however, is less contingent on the father’s employment circumstances or other external factors. The findings highlight the importance of employing couple-level analyses in examinations of the gender division of labour.
Signal time–frequency representation and decomposition using partial fractions
Authors: Ursin Bjorn , Porsani Milton J
Published: March 2021

The Z-transform of a complex time signal (or the analytic signal of a real signal) is equal to the Z-transform of a prediction error divided by the Z-transform of the prediction error operator. This inverse is decomposed into a sum of partial fractions, which are used to obtain impulse response operators formed by non-causal filters that complex-conjugate symmetric coefficients. The time components are obtained by convolving the filters with the original signal, and the peak frequencies, corresponding to the poles of the prediction error operator, are used for mapping the time components into frequency components. For non-stationary signals, this decomposition is done in sliding time windows, and the signal component values, in the middle of each window, are attributed to the peak value of its frequency response that corresponds to the pole of this partial fraction component. The result is an exact, but non-unique, time–frequency representation of the input signal. A sparse signal decomposition can be obtained by summing along the frequency axis in patches with similar characteristics in the time–frequency domain. The peak amplitude frequency of each new time component is obtained by computing a scalar prediction error operator in sliding time windows, resulting in a sparse time–frequency representation. In both cases, the result is a time–frequency matrix where an estimate of the frequency content of the input signal can be obtained by summation over the time variable. The performance of the new method is demonstrated with excellent results on a synthetic time signal, the LIGO gravitational wave signal and seismic field data.
The effect of a warmer climate on the salmon lice infection pressure from Norwegian aquaculture
Authors: Sandvik Anne D , Dalvin Sussie , Skern-Mauritzen Rasmus , Skogen Morten D
Published: March 2021

Climate change can hamper sustainable growth in the aquaculture industry by amplifying and adding to other environmental challenges. In Norway, salmon lice-induced mortality in wild salmonid populations is identified as a major risk factor for further expansion. Higher temperatures will induce increased production of salmon lice larvae, decreased developmental time from non-infective nauplii to infectious copepods, and higher infectivity of copepodids. In a warmer climate, a modelling exercise shows how these three factors lead to a significant increase in the infection pressure from farmed to wild salmonids, where the infectivity of copepodids is the term with the highest sensitivity to temperature changes. The total infection pressure gradually increases with increasing temperature, with an estimated twofold if the temperature increases from 9°C to 11°C. Thus, making it even harder to achieve a sustainable expansion of the industry with rising water temperature. This study demonstrates how bio-hydrodynamic models might be used to assess the combined effects of future warmer climate and infection pressure from salmon lice on wild salmonids. The results can be used as an early warning for the fish-farmers, conservation stakeholders and the management authorities, and serve as a tool to test mitigation strategies before implementation of new management plans.
Supplementing organic-complexed or inorganic Co, Cu, Mn, and Zn to beef cows during gestation: physiological and productive response of cows and their offspring until weaning
Authors: Harvey Kelsey M , Cooke Reinaldo F , Colombo Eduardo A , Rett Bruna , de Sousa Osvaldo A , Harvey Lorin M , Russell Jason R , Pohler Ky G , Brandão Alice P
Published: March 2021

One hundred and ninety non-lactating, pregnant beef cows (three-fourth Bos taurus and one-fourth Bos indicus; 138 multiparous and 52 primiparous) were assigned to this experiment at 117 ± 2.2 d of gestation (day 0). Cows were ranked by parity, pregnancy type (artificial insemination = 102 and natural service = 88), body weight (BW), and body condition score (BCS) and assigned to receive a supplement containing: 1) sulfate sources of Cu, Co, Mn, and Zn (INR; n = 95) or 2) an organic-complexed source of Cu, Mn, Co, and Zn (AAC; Availa 4; Zinpro Corporation, Eden Prairie, MN; n = 95). The INR and AAC provided the same daily amount of Cu, Co, Mn, and Zn, based on 7 g of the AAC source. From day 0 to calving, cows were maintained in a single pasture and were segregated three times weekly into 1 of the 24 individual feeding pens to receive treatments. Cow BW and BCS were recorded on days −30, 97, upon calving, and at weaning (day 367). Milk production was estimated at 42 ± 0.5 d postpartum via weigh–suckle–weigh (WSW) method. Liver biopsies were performed in 30 cows per treatment on days −30, 97, upon calving, and the day after WSW. Calf BW was recorded at birth and weaning. Liver and longissimus muscle (LM) biopsies were performed in 30 calves per treatment upon calving and 24 h later, the day after WSW, and at weaning. No treatment effects were detected (P ≥ 0.49) for cow BCS during gestation, despite AAC cows having greater (P = 0.04) BW on day 97. Liver Co concentrations were greater (P < 0.01) for AAC compared with INR cows, and liver concentrations of Cu were greater (P = 0.02) for INR compared with AAC cows on day 97. Upon calving, INR cows had greater (P ≤ 0.01) liver Cu and Zn concentrations compared with AAC cows. No other treatment differences were noted (P ≥ 0.17) for cow and calf liver trace mineral concentrations. Cows receiving AAC had greater (P = 0.04) hepatic mRNA expression of metallothionein 1A at calving, and their calves had greater (P = 0.04) hepatic mRNA expression of superoxide dismutase at weaning. Milk production did not differ between AAC and INR cows (P = 0.70). No treatment effects were detected (P ≥ 0.29) for mRNA expression of LM genes associated with adipogenic or muscle development activities in calves at birth and weaning. Calf birth and weaning BW also did not differ (P ≥ 0.19) between treatments. In summary, supplementing AAC or INR to beef cows during the last 5 mo of gestation yielded similar cow–calf productive responses until weaning.
Direct and Knock-on Effects of Water Stress on the Nutrient Contents ofTriticum aestivum(Poales: Poaceae) and Population Growth ofRhopalosiphum padi(Hemiptera: Aphididae)
Authors: Lin Ya-Ying , Liu Wei-Cheng , Hsu Yi-Ting , Hsu Ching-Hsin , Hu Chi-Chieh , Saska Pavel , Skuhrovec Jiří , Tuan Shu-Jen
Published: March 2021

To ascertain the direct effects of water stress upon wheat plants (Triticum aestivum L.) and how these effects, in turn, influence the population growth of the bird cherry-oat aphid (Rhopalosiphum padi L.), we conducted a physiological analysis of wheat seedlings grown under three different watering regimes and subsequently determined the population parameters of the aphid using the age-stage, two-sex life table. A significantly higher content of free amino acids and soluble sugars were observed in wheat seedlings exposed to drought stress compared to seedlings that were well-watered and those that were grown under waterlogged conditions. Extended phloem salivation and stylet penetration with shorter duration of sustained ingestion from phloem was observed in an electrical penetration graph (EPG) of R. padi on drought-stressed wheat seedlings. This suggested that the aphid’s feeding activity, as well as nutrient intake, were impeded. The significantly higher percentage of essential amino acids found in wheat seedlings grown under waterlogged conditions promoted significantly higher fecundity and intrinsic rate of increase in R. padi populations compared to aphids fed on drought-treated or well-watered wheat seedlings. Our findings suggest that wheat seedling responses to water stress involve changes in sap composition that are responsible for altering the aphids’ nutrient intake and consequently affect their population growth. From a grower’s perspective, extending wheat cultivation in a rice–wheat rotation paddy field during the winter season may not be economically profitable if the fields are chronically waterlogged, since this may potentially lead to a higher infestation of cereal aphids.
Impact of Insecticide Treatments for Phyllocnistis citrella (Lepidoptera: Gracillariidae) on Growth and Yield of Young Citrus reticulata Mandarins
Authors: Grafton-Cardwell E E , Daugherty M P
Published: March 2021

The citrus leafminer, Phyllocnistis citrella Stainton, is an invasive pest of citrus whose larvae damage developing leaves, which can impact tree photosynthetic capacity and may ultimately reduce tree growth and yield. Damage is most pronounced in young trees due to their greater propensity for production of new foliage, which supports P. citrella oviposition and larval development. We studied P. citrella damage and tree growth and yield among different insecticide treatment regimes to gauge their effectiveness at protecting young citrus trees. Three levels of insecticide treatments were applied over 3 yr to ‘Tango’ mandarin (Citrus reticulata Blanco) citrus trees planted in the prior summer, which were inspected regularly along with untreated trees. Leaves suitable for oviposition by P. citrella were available during all census dates, though their numbers fluctuated in the summer months. Phyllocnistis citrella were suppressed for 2–3 wk by systemic or foliar treatments of insecticides. The higher number of treatments provided more sustained suppression of larvae. Trunk diameter was unchanged and canopy volume affected by only the most aggressive treatment regime. However, citrus yield was 2–2.5 times higher following the second year of treatments and 1.2- to 1.8-fold times following the third year of treatments for trees in the treatment regimes that included systemic imidacloprid plus 2–3 or 4–5 foliar applications, respectively, relative to untreated controls. Suitable leaf flush and larval densities declined over the 3 yr of the study. These data support the use of insecticidal control of P. citrella to protect young ‘Tango’ mandarin trees, but demonstrated that frequent applications are necessary to suppress populations.
Educational and migration aspirations among children of Mexican migrant returnees in a border context
Authors: Vargas-Valle Eunice D , Glick Jennifer E
Published: March 2021

There has been a significant increase in migrant children from the USA living in Mexico in the last two decades. This article analyses the association between transnational schooling and the education and migration aspirations (the country one wishes to live or work in) of lower secondary students in Tijuana, a border city with very high return migration. This article also addresses how education and migration aspirations are connected and the extent to which these aspirations are mediated by US-specific capital (US citizenship, having family members in the USA, English proficiency, and cultural identification with the USA). The analyses draw from the 2017 School Integration and Migration Survey, conducted among students in 86 lower secondary schools, and 38 follow-up semi-structured interviews with transnational students. The results indicate that students with US school experience were more likely to aspire to study a two-year college or technical degree than nontransnational students. Transnational schooling was also directly associated with aspiring to migrate or engage in cross-border employment. Interviews elucidate the ways tertiary education plans were subordinate to intentions to work in the USA as funding their education became part of transnational students’ life projects. US schools were essential conduits through which education values, English skills, and national identities became ingrained in Mexican migrant children. Students’ migratory aspirations were nurtured by their experience in US schools and transnational social networks, in addition to their US citizenship. The public policy implications of these findings are also discussed.
Foundational Grounding and Creaturely Freedom
Authors: Pearce Kenneth L
Published: March 2021

According to classical theism, the universe depends on God in a way that goes beyond mere (efficient) causation. I have previously argued that this ‘deep dependence’ of the universe on God is best understood as a type of grounding. In a recent paper in this journal, Aaron Segal argues that this doctrine of deep dependence causes problems for creaturely free will: if our choices are grounded in facts about God, and we have no control over these facts, then we do not control our choices and are therefore not free. This amounts to a grounding analogue of the Consequence Argument for the incompatibility of free will and determinism. If successful, it would have application beyond classical theism: similar concerns would apply to any view that takes our choices to be grounded in a deeper reality which is beyond our control. However, I show that the argument is not successful. Segal’s Grounding Consequence Argument is so closely analogous to the Causal Consequence Argument that any response to the one provides a response to the other. As a result, if you don’t think that prior causes (whether deterministic or indeterministic) undermine free will, you shouldn’t think that prior grounds undermine free will.
A polarization census of bright pulsars using the ultrawideband receiver on the Parkes radio telescope
Authors: Sobey C , Johnston S , Dai S , Kerr M , Manchester R N , Oswald L S , Parthasarathy A , Shannon R M , Weltevrede P
Published: March 2021

We present high signal-to-noise ratio, full polarization pulse profiles for 40 bright, ‘slowly’ rotating (non-recycled) pulsars using the new ultrawideband low-frequency (UWL; 704–4032 MHz) receiver on the Parkes radio telescope. We obtain updated and accurate interstellar medium parameters towards these pulsars (dispersion measures and Faraday rotation measures), and reveal Faraday dispersion towards PSR J1721–3532 caused by interstellar scattering. We find general trends in the pulse profiles including decreasing fractional linear polarization and increasing degree of circular polarization with increasing frequency, consistent with previous studies, while also revealing new features and frequency evolution. This demonstrates results that can be obtained using UWL monitoring observations of slow pulsars, which are valuable for improving our understanding of pulsar emission and the intervening interstellar medium. The calibrated data products are publicly available.
Understanding X-ray and optical selection of galaxy clusters: a comparison of the XXL and CAMIRA cluster catalogues obtained in the common XXL-HSC SSP area
Authors: Willis J P , Oguri M , Ramos-Ceja M E , Gastaldello F , Sereno M , Adami C , Alis S , Altieri B , Chiappetti L , Corasaniti P S , Eckert D , Ettori S , Garrel C , Giles P , Lefevre J , Faccioli L , Fotopoulou S , Hamabata A , Koulouridis E , Lieu M , Lin Y-T , Maughan B , Nishizawa A J , Okabe T , Okabe N , Pacaud F , Paltani S , Pierre M , Plionis M , Poggianti B , Pompei E , Sadibekova T , Umetsu K , Valageas P
Published: March 2021

Large samples of galaxy clusters provide knowledge of both astrophysics in the most massive virialized environments and the properties of the cosmological model that defines our Universe. However, an important issue that affects the interpretation of galaxy cluster samples is the role played by the selection waveband and the potential for this to introduce a bias in the physical properties of clusters thus selected. We aim to investigate waveband-dependent selection effects in the identification of galaxy clusters by comparing the X-ray MultiMirror (XMM) Ultimate Extra-galactic Survey (XXL) and Subaru Hyper Suprime-Cam (HSC) CAMIRA cluster samples identified from a common 22.6 deg2 sky area. We compare 150 XXL and 270 CAMIRA clusters in a common parameter space defined by X-ray aperture brightness and optical richness. We find that 71/150 XXL clusters are matched to the location of a CAMIRA cluster, the majority of which (67/71) display richness values N > 15 that exceed the CAMIRA catalogue richness threshold. We find that 67/270 CAMIRA clusters are matched to the location of an XXL cluster (defined within XXL as an extended X-ray source). Of the unmatched CAMIRA clusters, the majority display low X-ray fluxes consistent with the lack of an XXL counterpart. However, a significant fraction (64/107) CAMIRA clusters that display high X-ray fluxes are not associated with an extended source in the XXL catalogue. We demonstrate that this disparity arises from a variety of effects including the morphological criteria employed to identify X-ray clusters and the properties of the XMM PSF.
Astraeus – III. The environment and physical properties of reionization sources
Authors: Hutter Anne , Dayal Pratika , Legrand Laurent , Gottlöber Stefan , Yepes Gustavo
Published: March 2021

In this work, we use the astraeus (seminumerical rAdiative tranSfer coupling of galaxy formaTion and Reionization in N-body dArk mattEr simUlationS) framework that couples galaxy formation and reionization in the first billion years. Exploring a number of models for reionization feedback and the escape fraction of ionizing radiation from the galactic environment (fesc), we quantify how the contribution of star-forming galaxies (with halo masses $M_\mathrm{ h}\gt 10^{8.2}\, {\rm \rm M_\odot }$) to reionization depends on the radiative feedback model, fesc, and the environmental overdensity. Our key findings are: (i) for constant fesc models, intermediate-mass galaxies (with halo masses of $M_\mathrm{ h}\simeq 10^{9-11}\, {\rm \rm M_\odot }$ and absolute UV magnitudes of MUV ∼ −15 to −20) in intermediate-density regions (with overdensity log10(1 + δ) ∼ 0−0.8 on a 2 comoving Mpc spatial scale) drive reionization; (ii) scenarios where fesc increases with decreasing halo mass shift, the galaxy population driving reionization to lower mass galaxies ($M_\mathrm{ h}\lesssim 10^{9.5}\, {\rm \rm M_\odot }$) with lower luminosities (MUV ≳ −16) and overdensities [log10(1 + δ) ∼ 0−0.5 on a 2 comoving Mpc spatial scale]; (iii) reionization imprints its topology on the ionizing emissivity of low-mass galaxies ($M_h\lesssim 10^{9}\, {\rm \rm M_\odot }$] through radiative feedback. Low-mass galaxies experience a stronger suppression of star formation by radiative feedback and show lower ionizing emissivities in overdense regions; (iv) a change in fesc with galaxy properties has the largest impact on the sources of reionization and their detectability, with the radiative feedback strength and environmental overdensity playing a sub-dominant role; (v) James Webb Space Telescope-surveys (with a limiting magnitude of MUV = −16) will be able to detect the galaxies providing ${\sim}60{-}70{{\ \rm per\ cent}}$ (${\sim}10{{\ \rm per\ cent}}$) of reionization photons at z = 7 for constant fesc models (scenarios where fesc increases with decreasing halo mass).
On the duration of the embedded phase of star formation
Authors: Kim Jaeyeon , Chevance Mélanie , Kruijssen J M Diederik , Schruba Andreas , Sandstrom Karin , Barnes Ashley T , Bigiel Frank , Blanc Guillermo A , Cao Yixian , Dale Daniel A , Faesi Christopher M , Glover Simon C O , Grasha Kathryn , Groves Brent , Herrera Cinthya , Klessen Ralf S , Kreckel Kathryn , Lee Janice C , Leroy Adam K , Pety Jérôme , Querejeta Miguel , Schinnerer Eva , Sun Jiayi , Usero Antonio , Ward Jacob L , Williams Thomas G
Published: March 2021

Feedback from massive stars plays a key role in molecular cloud evolution. After the onset of star formation, the young stellar population is exposed by photoionization, winds, supernovae, and radiation pressure from massive stars. Recent observations of nearby galaxies have provided the evolutionary timeline between molecular clouds and exposed young stars, but the duration of the embedded phase of massive star formation is still ill-constrained. We measure how long massive stellar populations remain embedded within their natal cloud, by applying a statistical method to six nearby galaxies at $20{-}100~\mbox{${\rm ~pc}$}$ resolution, using CO, Spitzer 24$\rm \, \mu m$, and H α emission as tracers of molecular clouds, embedded star formation, and exposed star formation, respectively. We find that the embedded phase (with CO and 24$\rm \, \mu m$ emission) lasts for 2−7 Myr and constitutes $17{-}47{{\ \rm per\ cent}}$ of the cloud lifetime. During approximately the first half of this phase, the region is invisible in H α, making it heavily obscured. For the second half of this phase, the region also emits in H α and is partially exposed. Once the cloud has been dispersed by feedback, 24$\rm \, \mu m$ emission no longer traces ongoing star formation, but remains detectable for another 2−9 Myr through the emission from ambient CO-dark gas, tracing star formation that recently ended. The short duration of massive star formation suggests that pre-supernova feedback (photoionization and winds) is important in disrupting molecular clouds. The measured time-scales do not show significant correlations with environmental properties (e.g. metallicity). Future JWST observations will enable these measurements routinely across the nearby galaxy population.
3D reconstruction of genomic regions from sparse interaction data
Authors: Mendieta-Esteban Julen , Di Stefano Marco , Castillo David , Farabella Irene , Marti-Renom Marc A
Published: March 2021

Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterize short- and long-range enhancer–promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organization from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalization, detection of significant interactions and reconstruction of the full 3D organization of the genomic region despite of the data sparseness. Specifically, it builds, with as low as the 2–3% of the data from the matrix, reliable 3D models of similar accuracy of those based on dense interaction matrices. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organizational features such as the formation of different networks of active gene communities.
Credit Supply and Housing Speculation
Authors: Mian Atif , Sufi Amir
Published: March 2021

Credit supply expansion boosts housing speculation and amplifies the housing cycle. The surge in private-label mortgage securitization in 2003 fueled a large expansion in mortgage credit supply by lenders financed with noncore deposits. Areas more exposed to these lenders experienced a large relative rise in transaction volume driven by a small group of speculators, and these areas simultaneously witnessed an amplified housing boom and bust. Consistent with the importance of belief heterogeneity, house price growth expectations of marginal buyers rose during the boom, while housing market pessimism among the general population increased.
Fear of COVID-19 and its associations with perceived personal and family benefits and harms in Hong Kong
Authors: Sit Shirley Man-Man , Lam Tai-Hing , Lai Agnes Yuen-Kwan , Wong Bonny Yee-Man , Wang Man-Ping , Ho Sai-Yin
Published: March 2021

Fear of COVID-19 is associated with public health compliance but also with negative well-being; however, no articles have reported associations of such fear with perceived benefits and harms. We assessed the level of fear of COVID-19 in Hong Kong adults and its associations with sociodemographic factors and perceived benefits and harms of COVID-19. In a 6-day population-based cross-sectional online survey in May 2020, 4,890 adults provided data on fear and perceived benefits and harms, personal happiness and family well-being, and sociodemographic characteristics. Linear regression was used to analyze associations. The level of fear was moderate (mean score 6.3/10). Fewer respondents reported perceived benefits (10.6%–21.7%) than harms (13.4%–43.5%). Females, younger age groups, and respondents with lower education or more cohabitants had greater fear. Fear was associated with perceived personal (increased knowledge of personal epidemic prevention) and family benefits (improved family hygiene), both with a very small effect size (Cohen’s d = 0.03). Fear was also associated with lower personal happiness and perceived personal (increased negative emotions, feeling depressed and anxious, decreased income, and decreased work efficiency) and family harms (increased conflicts and negative emotions among family members), with small effect sizes (0.08–0.37). We have first shown sociodemographic differences in the fear of COVID-19 and such fear was associated with both perceived personal and family benefits and harms of COVID-19. Our findings may guide the management of fear to reduce sociodemographic differences, and maximize benefits and minimize harms.
Shifting Prevalence of Plant-Parasitic Nematodes in Orchards and Vineyards of the Okanagan Valley, British Columbia
Authors: Forge Thomas , Munro Paige , Midwood Andrew J. , Philips Lori , Hannam Kirsten , Neilsen Denise , Powers Tom , Zasada Inga
Published: March 2021

Fruit production in the Okanagan Valley of British Columbia is dominated by apple, sweet cherry, and wine grape. The relative importance of sweet cherry and grape has increased in recent decades, but little was known of the plant-parasitic nematodes associated with those crops. Soil samples analyzed for plant-parasitic nematodes were collected from a total of 39 apple orchards, 61 cherry orchards, and 57 vineyards; most were collected in 2018, but 36 cherry orchards were sampled in 2012. Soil properties were also assessed and related to nematode population densities. Nematode genera of potential significance were, in order of prevalence, Pratylenchus, Mesocriconema, Xiphinema, Paratylenchus, Paratrichodorus, Hemicycliophora, and Meloidogyne. Pratylenchus were found in 79, 98, and 81% of the apple, cherry, and grape plantings, respectively; Mesocriconema were found in 51, 79, and 82%; and Xiphinema were found in 59, 51, and 77%. Population densities of the three dominant genera were influenced more by soil texture than any other soil characteristics, with Pratylenchus being negatively correlated with percentage clay, Mesocriconema positively correlated with percentage sand, and Xiphinema positively correlated with percentage silt. The high prevalence of Mesocriconema in cherry orchards and vineyards in this region is significant because Mesocriconema is known to be an important pest of other Prunus crop species and grapevines in other regions. This study therefore provides a rationale for increasing grower awareness and research efforts on the impacts and management of Mesocriconema and other plant-parasitic nematodes in orchards and vineyards in the region.
COVID-19-related smell and taste disorders
Authors: Lindsay Leasha
Published: March 2021

Olfactory impairment is recognized as a hallmark of COVID-19. This article highlights dysfunction of smell and taste associated with COVID-19 and discusses implications for nursing practice.
The Effect of Epidural Nalbuphine Combined With Ropivacaine on Epidural Analgesia During Labor
Authors: Sun Xingfeng , Zhou Qun , Zhou Min , Cao Rong , Chen Zuolei , Tang Songjiang , Huang Shaoqiang
Published: March 2021

Objectives:

The addition of a small dose of opioids during epidural labor analgesia can enhance the local analgesic effect, reduce the dose of local anaesthetic required, and minimize motor blockade. For the treatment of visceral pain, studies have shown that κ-opioid receptor agonist are more effective than μ-receptor agonists. This study compared the effectiveness of epidural nalbuphine and sufentanil in combination with ropivacaine for labor analgesia, respectively.

Materials and Methods:

We conducted a prospective, randomized, double-blind, multicentre clinical trial. Parturients who requested labor pain relief were randomly assigned to either the nalbuphine group or sufentanil group. After 5 minutes of initial dose, parturients in nalbuphine group received 10 mL 0.1% ropivacaine plus 0.3 mg/mL nalbuphine solution. The sufentanil group received the same ropivacaine dose plus 0.3 μg/mL sufentanil. The primary outcome was the duration of analgesia (the time to the first requirement for additional medication). Secondary outcomes included the ropivacaine dose per hour, and adverse reactions.

Results:

Between November 2018 and February 2019, 180 parturients were recruited for the study. The study showed that the duration of analgesia was shorter in the nalbuphine group as compared with the sufentanil group (P=0.040). The ropivacaine dose per hour in nalbuphine group 9.3 (2.4) mg was significantly greater versus sufentanil group 8.4 (2.5) mg (P=0.024). No serious adverse events directly associated with the analgesics were observed.

Discussion:

The analgesia effects of 0.3 mg/mL nalbuphine with ropivacaine are inferior to 0.3 μg/mL sufentanil with ropivacaine in labor analgesia. No serious side effects, either in the mother or in the fetus, were observed.
Association of Gestational Age with Postpartum Hemorrhage: An International Cohort Study
Authors: Butwick Alexander J. , Liu Can , Guo Nan , Bentley Jason , Main Elliot K. , Mayo Jonathan A. , Shaw Gary M. , Stephansson Olof
Published: March 2021

Background

Risk factors for postpartum hemorrhage, such as chorioamnionitis and multiple gestation, have been identified in previous epidemiologic studies. However, existing data describing the association between gestational age at delivery and postpartum hemorrhage are conflicting. The aim of this study was to assess the association between gestational age at delivery and postpartum hemorrhage.

Methods

The authors conducted a population-based retrospective cohort study of women who underwent live birth delivery in Sweden between 2014 and 2017 and in California between 2011 and 2015. The primary exposure was gestational age at delivery. The primary outcome was postpartum hemorrhage, classified using International Classification of Diseases, Ninth Revision—Clinical Modification codes for California births and a blood loss greater than 1,000 ml for Swedish births. The authors accounted for demographic and obstetric factors as potential confounders in the analyses.

Results

The incidences of postpartum hemorrhage in Sweden (23,323/328,729; 7.1%) and in California (66,583/2,079,637; 3.2%) were not comparable. In Sweden and California, the incidence of postpartum hemorrhage was highest for deliveries between 41 and 42 weeks’ gestation (7,186/75,539 [9.5%] and 8,921/160,267 [5.6%], respectively). Compared to deliveries between 37 and 38 weeks, deliveries between 41 and 42 weeks had the highest adjusted odds of postpartum hemorrhage (1.62 [95% CI, 1.56 to 1.69] in Sweden and 2.04 [95% CI, 1.98 to 2.09] in California). In both cohorts, the authors observed a nonlinear (J-shaped) association between gestational age and postpartum hemorrhage risk, with 39 weeks as the nadir. In the sensitivity analyses, similar findings were observed among cesarean deliveries only, when postpartum hemorrhage was classified only by International Classification of Diseases, Tenth Revision—Clinical Modification codes, and after excluding women with abnormal placentation disorders.

Conclusions

The postpartum hemorrhage incidence in Sweden and California was not comparable. When assessing a woman’s risk for postpartum hemorrhage, clinicians should be aware of the heightened odds in women who deliver between 41 and 42 weeks’ gestation.

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Suture-button Versus Screw Fixation in Adolescent Syndesmotic Injuries: Functional Outcomes and Maintenance of Reduction
Authors: Lurie Benjamin M. , Paez Conner J. , Howitt Shayna R. , Pennock Andrew T.
Published: March 2021

Background:

Fixation of the tibiofibular syndesmosis is often performed with a trans-syndesmotic screw (SS) or suture-button (SB). SB fixation has been shown to have lower rates of postoperative syndesmotic malreduction, late diastasis, and implant removal, though some studies have found complications related to infection and implant subsidence. The purpose of this study was to compare maintenance of reduction, complications, implant removal and functional outcomes of SB versus SS fixation in adolescents.

Methods:

A retrospective chart review identified patients who underwent syndesmotic fixation from 2010 to 2019 at a single institution. Loss of syndesmotic reduction (diastasis) was defined as either a >2 mm increase in tibiofibular clear space or >2 mm decrease in tibiofibular overlap, and corresponding incongruence of the ankle mortise (medial clear space 1 millimeter greater than superior clear space). Functional outcomes were collected at a minimum of 1 year postsurgery using the Foot and Ankle Ability Measure (FAAM).

Results:

Seventy-seven adolescents (45 SS, 32 SB) were included (mean age: 16±1.5 y). Forty-five patients had Weber C fibula fractures, 27 Weber B fractures, and 5 had isolated syndesmotic injuries or small posterior malleolus fractures. Fifty-one patients (66%) had functional outcomes available. There was no significant difference in mean FAAM Sports score between the 2 groups (SB=94.8%, SS=89.8%) at mean follow-up of 4.0±2.1 years. Syndesmotic implant removal occurred in 36/45 patients (80%) in the SS group compared with 4/32 patients (13%) in the SB group. There was 1 case of syndesmotic malreduction requiring revision surgery in the SS group, and no cases of postoperative malreduction or diastasis in the SB group. Nine patients in the SB group and 8 in the SS group weighed over 100 kilograms, with no cases of diastasis in these larger patients. There were 4 superficial infections and 1 deep infection in the screw group, with 1 superficial infection in the SB group.

Conclusions:

While both SB and screw fixation maintained syndesmotic reduction, SB fixation led to lower rates of implant removal surgery. SB fixation was equally effective at preventing recurrent diastasis in adolescents weighing over 100 kilograms, and functional outcomes were at least equivalent to screw-fixation at mean follow-up of 4.0 years.

Level of Evidence:

Level III.
Management of Highly Comminuted Intra-articular Fracture Subluxations at the Proximal Interphalangeal Joint by Subchondral Buttress Fixation and Early Mobilization
Authors: El-Haj Madi , Turker Tolga , Thirkannad Sunil M.
Published: March 2021

This article describes our technique of managing highly comminuted intra-articular fracture subluxations at the proximal interphalangeal joint by subchondral buttress fixation followed by early mobilization. This technique has proven to be reliable and all patients have been able to return to their preinjury level of activity.