bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential impacts of climate, land use and land cover changes on hydropower generation in West Africa: a review
Authors: Obahoundje Salomon , Diedhiou Arona
Published: March 2022

This study aims to review the existing literature on the past and future effects of climate, land use, and land cover changes on hydropower generation in West Africa (WA), based on listings in the Scopus and Google Scholar databases. This review shows that several African hydropower plants have experienced repeated power disruptions over the last three decades due to climate change and variability but it is less documented how increasing land use and land cover changes around the major dams have impacted the hydrological system and the hydropower generation. In the future, the risks of hydropower in WA may not be equally distributed within a country or region. Despite uncertainties in precipitation and on impacts on streamflow and water level in major basins, climate change is likely to reduce the available water over the range of 10%–20% (15%–40%) for the RCP4.5 (RCP8.5) scenario by 2050, which may considerably affect the water demand across all sectors, including hydropower. However, in the Kainji dam (Niger River basin), models project an increase in rainfall favorable to hydropower production for both RCP4.5 and RCP8.5. In contrast, within the Black Volta sub-basin, the intensification of land use is predicted to favor runoff and, consequently, an increase in the generation of Bui hydropower in the near future, even though models predict a rainfall decrease. This increase in land use for agriculture to feed a growing population has other adverse effects that need to be assessed, namely sedimentation and siltation, which are harmful to hydropower plants. Finally, the combined impact of climate and land use changes on the efficiency of hydroelectric infrastructure in WA is not well documented, while sustainable planning and investments in the hydropower sector require consideration of the nexus between climate, land use changes, and water.
Global markets and the commons: the role of imports in the US wild-caught shrimp market
Authors: Asche Frank , Oglend Atle , Smith Martin D
Published: March 2022

The commons literature focuses heavily on rules and the behavior of resource users but places less emphasis on the returns to individual effort. However, for most resource settings, market conditions and associated resource prices are key drivers of exploitation effort. In a globalized world, import competition can strongly influence the incentives for individual resource users, a topic largely unexplored in the commons literature. Import competition is especially salient for seafood, one of the most internationally traded food groups. We analyze the US shrimp market, which was once dominated by domestic catches but is now mostly supplied by imports. For domestic producers (users of the commons), lower revenues result, while US consumers eat more shrimp at lower prices. Globalization changed the sources of price risk and compensation that domestic producers face and altered incentives to exploit the commons. In a market dominated by domestic supply shocks, the price response to a shock moderates the effect on revenue and effort. In a market dominated by imports, domestic shocks are buffered by import adjustments, while price movements are determined by global shocks. Despite losses for the domestic fishery, globalization creates new incentives to coordinate effort and capture price premiums determined in the global market.
Mad/Utopian/Prehistoric: Black Powers of Speculation
Authors: Carrington André
Published: March 2022

Black life in the modern world makes incisive demands on the cultural politics of imaginative fiction as well as social movement rhetoric. Recent scholarship supplements the ongoing efflorescence of Afrofuturist art by reconstructing the history of speculative, utopian, and cautionary tales in Black writing. Isiah Lavender’s Afrofuturism Rising and Alex Zamalin’s Black Utopia join a growing body of intellectual history prepared for the task of historicizing fantastic Black aesthetics. Sami Schalk’s more contemporary intervention, Bodyminds Reimagined, demonstrates the integral value of Black women’s speculative fiction to rethinking the role of dis/ability—conspicuously including the radical difference signified by “madness”—in the panoply of power relations that stand to be transformed by Black radical thought in action.
deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning
Authors: Duhan Naveen , Norton Jeanette M , Kaundal Rakesh
Published: March 2022

Nitrogen is essential for life and its transformations are an important part of the global biogeochemical cycle. Being an essential nutrient, nitrogen exists in a range of oxidation states from +5 (nitrate) to −3 (ammonium and amino-nitrogen), and its oxidation and reduction reactions catalyzed by microbial enzymes determine its environmental fate. The functional annotation of the genes encoding the core nitrogen network enzymes has a broad range of applications in metagenomics, agriculture, wastewater treatment and industrial biotechnology. This study developed an alignment-free computational approach to determine the predicted nitrogen biochemical network-related enzymes from the sequence itself. We propose deepNEC, a novel end-to-end feature selection and classification model training approach for nitrogen biochemical network-related enzyme prediction. The algorithm was developed using Deep Learning, a class of machine learning algorithms that uses multiple layers to extract higher-level features from the raw input data. The derived protein sequence is used as an input, extracting sequential and convolutional features from raw encoded protein sequences based on classification rather than traditional alignment-based methods for enzyme prediction. Two large datasets of protein sequences, enzymes and non-enzymes were used to train the models with protein sequence features like amino acid composition, dipeptide composition (DPC), conformation transition and distribution, normalized Moreau–Broto (NMBroto), conjoint and quasi order, etc. The k-fold cross-validation and independent testing were performed to validate our model training. deepNEC uses a four-tier approach for prediction; in the first phase, it will predict a query sequence as enzyme or non-enzyme; in the second phase, it will further predict and classify enzymes into nitrogen biochemical network-related enzymes or non-nitrogen metabolism enzymes; in the third phase, it classifies predicted enzymes into nine nitrogen metabolism classes; and in the fourth phase, it predicts the enzyme commission number out of 20 classes for nitrogen metabolism. Among all, the DPC + NMBroto hybrid feature gave the best prediction performance (accuracy of 96.15% in k-fold training and 93.43% in independent testing) with an Matthews correlation coefficient (0.92 training and 0.87 independent testing) in phase I; phase II (accuracy of 99.71% in k-fold training and 98.30% in independent testing); phase III (overall accuracy of 99.03% in k-fold training and 98.98% in independent testing); phase IV (overall accuracy of 99.05% in k-fold training and 98.18% in independent testing), the DPC feature gave the best prediction performance. We have also implemented a homology-based method to remove false negatives. All the models have been implemented on a web server (prediction tool), which is freely available at http://bioinfo.usu.edu/deepNEC/.
Translating cell therapies for neurodegenerative diseases: Huntington’s disease as a model disorder
Authors: Rosser Anne E. , Busse Monica E. , Gray William P. , Badin Romina Aron , Perrier Anselme L. , Wheelock Vicki , Cozzi Emanuele , Martin Unai Perpiña , Salado-Manzano Cristina , Mills Laura J. , Drew Cheney , Goldman Steven A. , Canals Josep M. , Thompson Leslie M.
Published: March 2022

There has been substantial progress in the development of regenerative medicine strategies for CNS disorders over the last decade, with progression to early clinical studies for some conditions. However, there are multiple challenges along the translational pipeline, many of which are common across diseases and pertinent to multiple donor cell types. These include defining the point at which the preclinical data are sufficiently compelling to permit progression to the first clinical studies; scaling-up, characterization, quality control and validation of the cell product; design, validation and approval of the surgical device; and operative procedures for safe and effective delivery of cell product to the brain. Furthermore, clinical trials that incorporate principles of efficient design and disease-specific outcomes are urgently needed (particularly for those undertaken in rare diseases, where relatively small cohorts are an additional limiting factor), and all processes must be adaptable in a dynamic regulatory environment.

Here we set out the challenges associated with the clinical translation of cell therapy, using Huntington’s disease as a specific example, and suggest potential strategies to address these challenges. Huntington’s disease presents a clear unmet need, but, importantly, it is an autosomal dominant condition with a readily available gene test, full genetic penetrance and a wide range of associated animal models, which together mean that it is a powerful condition in which to develop principles and test experimental therapeutics. We propose that solving these challenges in Huntington’s disease would provide a road map for many other neurological conditions. This white paper represents a consensus opinion emerging from a series of meetings of the international translational platforms Stem Cells for Huntington’s Disease and the European Huntington’s Disease Network Advanced Therapies Working Group, established to identify the challenges of cell therapy, share experience, develop guidance and highlight future directions, with the aim to expedite progress towards therapies for clinical benefit in Huntington’s disease.
A New Neural Distinguisher Considering Features Derived From Multiple Ciphertext Pairs
Authors: Chen Yi , Shen Yantian , Yu Hongbo , Yuan Sitong
Published: March 2022

Neural-aided cryptanalysis is a challenging topic, in which the neural distinguisher ($\mathcal{ND}$) is a core module. In this paper, we propose a new $\mathcal{ND}$ considering multiple ciphertext pairs simultaneously. Besides, multiple ciphertext pairs are constructed from different keys. The motivation is that the distinguishing accuracy can be improved by exploiting features derived from multiple ciphertext pairs. To verify this motivation, we have applied this new $\mathcal{ND}$ to five different ciphers. Experiments show that taking multiple ciphertext pairs as input indeed brings accuracy improvement. Then, we prove that our new $\mathcal{ND}$ applies to two different neural-aided key recovery attacks. Moreover, the accuracy improvement is helpful for reducing the data complexity of the neural-aided statistic attack. The code is available at https://github.com/AI-Lab-Y/ND_mc.
RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history
Authors: Baar Till , Dümcke Sebastian , Gressel Saskia , Schwalb Björn , Dilthey Alexander , Cramer Patrick , Tresch Achim
Published: March 2022

Alu elements are one of the most successful groups of RNA retrotransposons and make up 11% of the human genome with over 1 million individual loci. They are linked to genetic defects, increases in sequence diversity, and influence transcriptional activity. Still, their RNA metabolism is poorly understood yet. It is even unclear whether Alu elements are mostly transcribed by RNA Polymerase II or III. We have conducted a transcription shutoff experiment by α-amanitin and metabolic RNA labeling by 4-thiouridine combined with RNA fragmentation (TT-seq) and RNA-seq to shed further light on the origin and life cycle of Alu transcripts. We find that Alu RNAs are more stable than previously thought and seem to originate in part from RNA Polymerase II activity, as previous reports suggest. Their expression however seems to be independent of the transcriptional activity of adjacent genes. Furthermore, we have developed a novel statistical test for detecting the expression of quantitative trait loci in Alu elements that relies on the de Bruijn graph representation of all Alu sequences. It controls for both statistical significance and biological relevance using a tuned k-mer representation, discovering influential sequence features missed by regular motif search. In addition, we discover several point mutations using a generalized linear model, and motifs of interest, which also match transcription factor-binding motifs.
Coupled body and surface wave sensitivity kernels for coda-wave interferometry in a three-dimensional scalar scattering medium
Authors: Barajas Andres , Margerin Ludovic , Campillo Michel
Published: March 2022

Analysis of long recordings of ambient seismic noise has shown to be effective for estimation of seismic responses between points located on the surface. This includes both the ballistic and the coda part of the waveforms. Passive image interferometry is used to analyse perturbations in the reconstructed coda, to detect and locate changes in the medium. This method has been shown to be effective in monitoring variations in seismic velocity produced by a wide range of phenomena. However, localization of the sources of these changes is still an open problem for a 3-D half-space, given the difficulties of integrating body and surface waves within the same framework. In this study, we approach this problem by developing the sensitivity kernels of a scalar model that integrates the body and surface scalar waves. First, we establish a parallel between the penetration depth of the surface waves for the elastic and scalar cases, which equips the latter with a natural scaling with frequency that is otherwise not included in the model. Next, using a variational approach, we quantify how a velocity perturbation in the medium affects the propagation velocity of the surface waves. Based on these results, we extend the sensitivity theory to include the body and surface waves as modes of propagation and detection, as restricted to a 1-D depth-dependent perturbation description, for simplicity. The obtained kernel can be expressed as the sum of a surface and a body waves sensitivity kernels, which are inter-dependent through a set of traveltime distributions. These distributions are estimated with Monte Carlo simulations based on the radiative transfer equations of the system, with the source and the receiver located in the same position at the surface. The sensitivity at depth is in good agreement with previous results based on full wavefield elastic simulations in 3-D inhomogeneous half-space. The temporal evolution of the body and surface waves sensitivity is quantified, as well as the contribution of all the possible modes of propagation and detection to each of these sensitivities. We show how the position of the source affects the sensitivity between the two types of waves. We find that the efficacy of energy conversion from surface to body waves is controlled by the ratio between the surface wave penetration depth and the mean free path, a feature that has not been reported in previous studies. This means that configurations that share this ratio have the same sensitivity as long as all the spatial and temporal variables (e.g. elapsed time, depth) are non-dimensionalized with the mean free path and the mean free time, respectively.
Absenteeism among family planning providers: a mixed-methods study in western Kenya
Authors: Tumlinson Katherine , Britton Laura E , Williams Caitlin R , Wambua Debborah Muthoki , Onyango Dickens Otieno
Published: March 2022

Public-sector healthcare providers are on the frontline of family planning service delivery in low- and middle-income countries like Kenya, yet research suggests public-sector providers are frequently absent. The current prevalence of absenteeism in Western Kenya, as well as the impact on family planning clients, is unknown. The objective of this paper is to quantify the prevalence of public-sector healthcare provider absenteeism in this region of Kenya, to describe the potential impact on family planning uptake and to source locally grounded solutions to provider absenteeism. We used multiple data collection methods including unannounced visits to a random sample of 60 public-sector healthcare facilities in Western Kenya, focus group discussions with current and former family planning users, key informant interviews (KIIs) with senior staff from healthcare facilities and both governmental and non-governmental organizations and journey mapping activities with current family planning providers and clients. We found healthcare providers were absent in nearly 60% of unannounced visits and, among those present, 19% were not working at the time of the visit. In 20% of unannounced visits, the facility had no providers present. Provider absenteeism took many forms including providers arriving late to work, taking an extended lunch break, not returning from lunch or being absent for the entire day. While 56% of provider absences resulted from sanctioned activities such as planned vacation, sick leave or off-site work responsibilities, nearly half of the absences were unsanctioned, meaning providers were reportedly running personal errands, intending to arrive later or no one at the facility could explain the absence. Key informants and focus group participants reported high provider absence is a substantial barrier to contraceptive use, but solutions for resolving this problem remain elusive. Identification and rigorous evaluation of interventions designed to redress provider absenteeism are needed.
Influencing and implementing mandatory alcohol pregnancy warning labels in Australia and New Zealand
Authors: Heenan Maddie , Shanthosh Janani , Cullerton Katherine , Jan Stephen
Published: March 2022

Alcohol labelling laws and policy are contentious and highly politicized. Very few countries have been able to implement health warnings on alcohol labels due to complex legal and governance systems and coordinated industry lobbying. In 2020, Australia and New Zealand implemented a mandatory and evidence-based legal standard for pregnancy warning labels on alcohol products. This article discusses some of the challenges faced in achieving policy change and how these barriers were overcome by public health advocacy groups to build the evidence, counter industry conflicts of interest, consumer test health messages, mobilize community support and gather political support. Reflecting on the decades of ineffective regulation and politicization of this health issue, lessons for other countries include the importance of creating and maintaining relationships with decision makers and regularly updating them with evidence and recommendations, highlighting industry failures and tactics, building broad-based coalitions and sharing lived-experiences.
Turning reference points inside out: comparing MSY reference points estimated inside and outside the assessment model
Authors: Trijoulet Vanessa , Berg Casper W , Miller David C M , Nielsen Anders , Rindorf Anna , Albertsen Christoffer Moesgaard
Published: March 2022

Reference points are used in fisheries management to infer stock status and inform future fishing opportunities. They can be estimated externally to the assessment model assuming attributes such as stock size to be known without error, or internally where the uncertainty can be accounted for in the estimation. Little is known about the effect of choosing one approach over another on reference point estimates. We compare maximum sustainable yield (MSY) reference points obtained internally in the assessment model (SAM) with those obtained by external estimation (EqSim) via simulations using 11 stocks with known and unknown stock–recruitment relationships (SRRs). Internal estimation of reference points does better on average than external estimation in terms of bias, variance, and SRR selection. Coverage probability of the reference point confidence intervals is good for the internal approach. Stochasticity considerations via re-sampling in the external approach can lead to bias. Bias in reference points have consequences on future yield, stock development, and status. However, it is difficult to predict them by solely looking at bias because they depend on current stock status, recruitment, and extent of bias, but also bias direction since a harvest control rule might compensate for the bias in the future.
A Tale of Two Systems: The Public and Private Faces of Investor-State Dispute Settlement
Authors: Menon Sundaresh
Published: March 2022

It seems fair to say that the system of investor-state dispute settlement (ISDS) now faces something of a ‘legitimacy crisis’. States complain of what they perceive to be an unjustified encroachment into their regulatory space. Investors bemoan the fragmentation of investment law. And the public resents the fact that an anonymous panel of lawyers sitting behind closed doors are making decisions with significant implications for their well-being and livelihoods through a process in which they are neither seen nor heard. These criticisms of ISDS raise serious questions as to the adequacy of the procedural design of the ISDS system and how this might be affecting perceptions of ISDS’s legitimacy as a means of dispute resolution. It is suggested that ISDS’s legitimacy crisis can be traced, at least in part, to its failure to uphold certain core values and principles of the Rule of Law – in particular, transparency, accountability and consistency – which are of especial importance in the ISDS context. It is argued that the reason why investment arbitration struggles to uphold these values lies in the dissonance between the public face of ISDS – meaning the public nature and significance of investment disputes – and its private face – meaning the private arbitral process by which investment disputes are resolved. Efforts at reform should be directed at resolving that dissonance, and whilst there is much to commend an incremental reform of the system of arbitration, it seems clear that that can only be an interim step on the path to deeper process reform.
‘We Are Not Our Parents’ – beyond Political Transition: Historical Failings, Present Angst and Future Yearnings of South African Youth
Authors: Maringira Godfrey , Ndelu Sandile , Gukurume Simbarashe , Langa Malose
Published: March 2022

The story of South Africa’s liberation struggle, from apartheid to constitutional democracy, is writ large with in-depth contributions from young people. Despite their historical involvement, young people have been noticeably absent from the transitional processes ushering in South Africa’s postapartheid dispensation. Their absence has created a crisis of legitimacy, particularly among those disillusioned young people who are unsentimental about the transition and who are growing increasingly impatient and frustrated with the slow pace of transformation in postapartheid South Africa, in particular within institutions of higher learning. Internationally, South Africa is widely considered as a role model for transitional justice, largely due to its peaceful transference of power from minority rule to the current democratic system. Domestically, however, South Africa’s transition has come under fire for prioritizing reconciliation without simultaneously addressing the social, institutional, political and economic injustices of the past. This article uses the ‘#FeesMustFall’ student protests that swept across South African universities from 2015 to 2017 as a case study for critically discussing whether young people feel South Africa’s transition has been transformative in terms of addressing its colonial and apartheid legacy. Conceptually, the article is rooted within institutional and decolonial transformative justice literature that identifies how the failure of transitional processes to address colonial civil-political and socioeconomic rights can lead to violence. It is argued that the #FeesMustFall protests represented a call for inclusive transitional justice processes that address past inequalities which continue to manifest in the present, including unequal access to free, quality and decolonized education.
Holonomic Approximation Through Convex Integration
Authors: Massot Patrick , Theillière Mélanie
Published: March 2022

Convex integration and the holonomic approximation theorem are two well-known pillars of flexibility in differential topology and geometry. They may each seem to have their own flavor and scope. The goal of this paper is to bring some new perspective on this topic. We explain how to prove the holonomic approximation theorem for first-order jets using convex integration. More precisely, we first prove that this theorem can easily be reduced to proving flexibility of some specific relation. Then we prove this relation is open and ample, hence its flexibility follows from off-the-shelf convex integration.
Initiation of antiretroviral therapy in treatment-naive adults with HIV infection at the first specialist appointment
Authors: Al-Hayani Aws Waleed M. , Cabello-Úbeda Alfonso , Del Palacio-Tamarit Marta , Rodríguez-Alonso Blanca , Carrillo-Acosta Irene , Álvarez-Álvarez Beatriz , Prieto-Pérez Laura , Fernández Quintela Laura , Fuensalida Gema , Téllez Raquel , Luis-Castaño Ángel , Hernández-Segurado Marta , Becares Javier , Benito José Miguel , Rallón Norma , Górgolas Miguel
Published: March 2022

Background

Fast initiation of ART has been associated with higher rates of retention in HIV care and viral suppression at 48 weeks and with lower mortality rates. However, scarce evidence exists in our setting, where diagnosis and treatment are carried out in different contexts.

Methods

An observational retrospective study evaluating efficacy and safety of ART prescribed at the first specialist appointment, without baseline laboratory data, in a tertiary hospital in downtown Madrid. Individuals with a new diagnosis of HIV infection who initiated treatment at their first appointment with an infectious diseases specialist before receiving baseline laboratory results were included, irrespective of the ART regimen chosen.

Results

One hundred and eight participants were included. The majority (99.1%) were MSM who had acquired infection during sexual intercourse. The efficacy of ART, without baseline laboratory results at the time of initiation, was 85.2% (92/108) in the ITT analysis and 91.7% (99/108) in the treatment-related discontinuation equals failure analysis. All but nine patients presented an undetectable viral load (<50 copies/mL) at 48 weeks from starting ART. No serious adverse effects associated with the strategy were observed. In total, 101 participants continued care at 48 weeks with retention in HIV care rate of 93.5% (101/108).

Conclusions

Initiating ART at the first available opportunity without baseline laboratory data does not reduce efficacy or safety of ART and achieves rapid virological control with high rates of retention in HIV care.
Effect of dihydroartemisinin/piperaquine for malaria intermittent preventive treatment on dolutegravir exposure in pregnant women living with HIV
Authors: Banda Clifford G. , Nkosi Dumisile , Allen Elizabeth , Workman Lesley , Madanitsa Mwayiwawo , Chirwa Marumbo , Kapulula Mayamiko , Muyaya Sharon , Munharo Steven , Wiesner Lubbe , Phiri Kamija S. , Mwapasa Victor , Ter Kuile Feiko O. , Maartens Gary , Barnes Karen I.
Published: March 2022

Background

In sub-Saharan Africa, the burdens of malaria and HIV infections overlap. In settings with moderate-to-high malaria transmission intensity, pregnant women living with HIV (PLWH) require both ART and malaria intermittent preventive treatment (IPTp). Dihydroartemisinin/piperaquine has been identified as a promising alternative to sulfadoxine/pyrimethamine for IPTp. However, another antimalarial drug, artesunate/amodiaquine, similar to dihydroartemisinin/piperaquine, was previously shown to reduce dolutegravir exposure in non-pregnant adults.

Objectives

To investigate the effect of dihydroartemisinin/piperaquine on dolutegravir plasma exposure in pregnant women on dolutegravir-based ART.

Methods

We conducted an open-label, non-randomized, fixed-sequence, pharmacokinetic study in PLWH in Malawi. Dolutegravir concentrations were measured over a 24 h period, before and after the recommended 3 day treatment dose of dihydroartemisinin/piperaquine in 12 pregnant women in their second or third trimester. Non-compartmental analysis was performed, and geometric mean ratios (GMRs) and 90% CIs were generated to compare dolutegravir pharmacokinetic parameters between the two treatment periods.

Results

Co-administration of dihydroartemisinin/piperaquine and dolutegravir increased dolutegravir’s overall exposure (AUC0–24) and Cmax by 30% (GMR 1.30; 90% CI 1.11–1.52) and 31% (GMR 1.31; 90% CI 1.13–1.51), respectively. The dolutegravir trough (C24) concentration increased by 42% (GMR 1.42; 90% CI 1.09–1.85). The combined treatments were well tolerated with no serious adverse events observed.

Conclusions

Dihydroartemisinin/piperaquine may be administered with dolutegravir-based ART in pregnant women as the modest increase in dolutegravir exposure, similar to pharmacokinetic parameter values published previously, ensures its efficacy without any clinically significant adverse events observed in this small study.
The UK Joint Committee on Human Rights and the United Nations Universal Periodic Review: A Critical Appraisal
Authors: Lane Michael
Published: March 2022

This article critically appraises the extent that the UK Parliament’s Joint Committee on Human Rights has engaged with the UN’s Universal Periodic Review and its recommendations on the UK’s human rights situation. It initially explores the Universal Periodic Review process, the UK’s implementation of its recommendations, and posits that a contributing factor to poor implementation is a lack of mobilization of domestic actors. The UK’s Parliament, and its Joint Committee on Human Rights, it is argued, are central domestic actors in this regard. By reviewing existing research as well as a range of documentary sources, this article identifies several shortcomings in the Joint Committee on Human Rights’ engagement with the Universal Periodic Review and, drawing from the available evidence, articulates possible reasons for these. This article closes by making proposals on how the Joint Committee on Human Rights’ participation in the Universal Periodic Review process may be enhanced. Thus, it will make a modest contribution to the successful realization of human rights in the UK, and to the growing scholarship on parliaments’ roles in the international human rights framework.
Plant growth ability, rather than phylogenetic relatedness, predicts the effect of soil biota from an abandoned field on native and exotic plants
Authors: Wei Chunqiang , Jia Bingbing , Gao Lunlun , Liu Zhen , Liang Yuming , Zhang Xin , Lu Xinmin
Published: March 2022

Soil biota, as legacy effects of previous species in natural ecosystems, profoundly affects plant performance in new habitats and, in turn, plant community. However, how soil biota, as legacy effects of agricultural crops, affects the likelihood of establishment of exotic and native plants in newly abandoned farmland remains poorly understood, which may hinder effective management of agricultural weeds. Here, we grew 58 plant species (28 exotic species and 30 native species) common in Central China in sterilized vs. nonsterilized soils collected from a newly abandoned maize field. We (i) estimated the effects of soil biota on plant shoot, root and total mass, (ii) explored the dependence of soil effects on the plants’ phylogenetic distance to maize, origin (native vs. exotic) and life history (annual vs. perennial) and (iii) tested which plant traits could predict soil effects. Soil biota, in general, decreased plant mass, suggesting a dominant role of enemies. The effect of the soil biota on plant total mass was unrelated to the phylogenetic distance of the plants to maize and decreased linearly with increasing plant intrinsic growth ability. Moreover, the soil biota on average had greater negative impacts on the total mass of exotic plants, particularly perennial species, than on that of native plants. Our results suggest that plant intrinsic growth ability, rather than phylogenetic relatedness, is a reliable predictor of soil effects. Additionally, native plants can benefit from plant–soil interactions in competing with exotic perennial plants when initially established in newly abandoned farmlands.
Structure, diversity and the conservation value of tropical dry forests in highly fragmented landscapes
Authors: Lanuza Oscar R , Casanoves Fernando , Vílchez-Mendoza Sergio , Espelta Josep Maria , Peñuelas Josep , Peguero Guille
Published: March 2022

Although tropical dry forests are among the most degraded and fragmented biomes in the world, we still have a poor understanding of their basic ecological features and conservation status, particularly in the Neotropics. Here, we assess the diversity, composition, structure and conservation value of tropical dry forests in a highly fragmented landscape in Nicaragua. We established 31 plots and transects in and along river corridors, secondary forests, living fences and pasture-woodlands. We recorded all trees with diameters at breast height ≥ 2.5 cm using Hill numbers (qD, where q = 0, 1 or 2) and estimated the richness and diversity of trees in each forest type. We calculated the Importance Value Index (IVI) to species and family levels and, finally, performed a Non-Metric Multidimensional Scaling (NMDS) ordination and an Analysis of Similarities (ANOSIM) using the Bray–Curtis index of similarity. Diversity (1D, 2D) but not species richness (0D) differed between forest types (P = 0.01 and 0.66, respectively). IVI was highest for the legume family Fabaceae, followed by the Moraceae and Malvaceae (27.8, 11.1 and 10.5, respectively). Vachellia pennatula, Guazuma ulmifolia and Bursera simaruba had IVIs >30%, the former two being the most abundant trees in all forest types. An analysis of community similarity revealed that each forest type had a distinct composition (P < 0.01, R2 = 0.30), thereby underlining the importance of conserving all these different types of land cover.
Letermovir for Cytomegalovirus Prevention in Adolescent Patients Following Hematopoietic Cell Transplantation
Authors: P Daukshus Nicole , Cirincione Anthony , Siver Molly , Mathew Sherry , Kunvarjee Binni , Chan Amelia , Boelens Jaap Jan , Seo Susan K , Papanicolaou Genovefa A , Kernan Nancy A
Published: March 2022

There are limited data for letermovir as primary cytomegalovirus (CMV) prophylaxis in patients less than 18 years of age. We report 9 adolescent patients who received letermovir following hematopoietic cell transplantation. No patients developed clinically significant CMV while taking letermovir. Letermovir was well tolerated and efficacious in preventing CMV infections.
Biogenesis, conservation, and function of miRNA in liverworts
Authors: Pietrykowska Halina , Sierocka Izabela , Zielezinski Andrzej , Alisha Alisha , Carrasco-Sanchez Juan Carlo , Jarmolowski Artur , Karlowski Wojciech M , Szweykowska-Kulinska Zofia
Published: March 2022

MicroRNAs (miRNAs) are small non-coding endogenous RNA molecules, 18–24 nucleotides long, that control multiple gene regulatory pathways via post-transcriptional gene silencing in eukaryotes. To develop a comprehensive picture of the evolutionary history of miRNA biogenesis and action in land plants, studies on bryophyte representatives are needed. Here, we review current understanding of liverwort MIR gene structure, miRNA biogenesis, and function, focusing on the simple thalloid Pellia endiviifolia and the complex thalloid Marchantia polymorpha. We review what is known about conserved and non-conserved miRNAs, their targets, and the functional implications of miRNA action in M. polymorpha and P. endiviifolia. We note that most M. polymorpha miRNAs are encoded within protein-coding genes and provide data for 23 MIR gene structures recognized as independent transcriptional units. We identify M. polymorpha genes involved in miRNA biogenesis that are homologous to those identified in higher plants, including those encoding core microprocessor components and other auxiliary and regulatory proteins that influence the stability, folding, and processing of pri-miRNAs. We analyzed miRNA biogenesis proteins and found similar domain architecture in most cases. Our data support the hypothesis that almost all miRNA biogenesis factors in higher plants are also present in liverworts, suggesting that they emerged early during land plant evolution.
Anticardiolipin IgA as a Potential Risk Factor for Pregnancy Morbidity in Patients with Antiphospholipid Syndrome
Authors: Zhai Xiaodan , Yang Shuo , Cui Liyan
Published: March 2022

Background

Antiphospholipid syndrome (APS) is an autoimmune disorder that is characterized by venous or arterial thrombosis and/or obstetric morbidity in the constant presence of persistent antiphospholipid antibodies (aPLs). In patients with APS, the relationship between production of immunoglobulin (Ig)A antiphospholipid antibodies and adverse events in pregnancy is still unclear. As a result of massive trials, the clinical efficiency of IgA-aPLs is used to evaluate pregnancy outcomes in patients with APS.

Methods

We enrolled 381 female patients with APS and 93 healthy pregnant women. Silica clotting time ratio, dilute Russell viper venom time (dRVVT) ratio, and 6 aPLs, including IgA/IgG/IgM isotypes aβ2GPI and IgA/IgG/IgM isotypes anticardiolipin (aCL), were detected using commercial kits.

Results

We found no significant differences in laboratory parameters between patients with APS and the control group. The total prevalence of aCL IgA was 2.9%; the prevalence of aβ2GPI IgA was 3.4%. Only 1.3% of the individuals who tested aCL-positive (5/381) had isolated aCL IgA. Similarly, isolated aβ2GPI IgA was present in only 0.8% (3/381) of the aβ2GPI-positive subjects. Meanwhile, aCL IgA showed the maximum area under the curve (AUC) of 0.666 (95% CI, 0.60–0.73; P < .001), followed by dRVVT ratio (AUC = 0.649; 0.58–0.72; P < .001).

Conclusion

Positive aCL IgA and aβ2GPI IgA ratios were extremely low for each isolated isotype of aPLs. For patients with APS who experienced fetal loss, aCL IgA may be utilized as a risk factor for pregnancy loss among patients with APS. Establishing a standardized diagnosis of IgA aPLs is also important for these patients.
A robust RFI identification for radio interferometry based on a convolutional neural network
Authors: Sun Haomin , Deng Hui , Wang Feng , Mei Ying , Xu Tingting , Smirnov Oleg , Deng Linhua , Wei Shoulin
Published: March 2022

The rapid development of new generation radio interferometers such as the Square Kilometer Array (SKA) has opened up unprecedented opportunities for astronomical research. However, anthropogenic radio frequency interference (RFI) from communication technologies and other human activities severely affects the fidelity of observational data. It also significantly reduces the sensitivity of the telescopes. We proposed a robust convolutional neural network (CNN) model to identify RFI based on machine-learning methods. We overlaid RFI on the simulation data of SKA1-LOW to construct three visibility function data sets. One data set was used for modelling, and the other two were used for validating the model’s usability. The experimental results show that the area under the curve reaches 0.93, with satisfactory accuracy and precision. We then further investigated the effectiveness of the model by identifying the RFI in the actual observational data from LOFAR and MeerKAT. The results show that the model performs well. The overall effectiveness is comparable to AOFlagger software and provides an improvement over existing methods in some instances.
The widths of magnetized filaments in molecular clouds
Authors: Priestley F D , Whitworth A P
Published: March 2022

Filaments are an ubiquitous feature of molecular clouds, and appear to play a critical role in assembling the material to form stars. The dominant filaments are observed to have a rather narrow range of widths around $\sim 0.1 \, {\rm pc}$, and to be preferentially aligned perpendicularly to the direction of the local magnetic field. We have previously argued that the observed filament widths can be explained if filaments are formed by converging, mildly supersonic flows, resulting from large-scale turbulent motions in the parent molecular cloud. Here we demonstrate that the introduction of a magnetic field perpendicular to the filament long axis does not greatly alter this conclusion, as long as the mass-to-flux ratio is supercritical. The distribution of widths for supercritical magnetized filaments formed via this mechanism is peaked at slightly higher values, and is slightly broader, than for non-magnetized filaments, but still reproduces the basic properties of the width distributions derived from far-infrared observations of molecular clouds. In contrast, subcritical filaments have width distributions with a fundamentally different shape, and typically have much larger widths than those observed. Both subcritical and supercritical filaments are consistent with the observed lack of correlation between filament widths and filament surface densities.
Self-consistent modelling of the Milky Way’s nuclear stellar disc
Authors: Sormani Mattia C , Sanders Jason L , Fritz Tobias K , Smith Leigh C , Gerhard Ortwin , Schödel Rainer , Magorrian John , Neumayer Nadine , Nogueras-Lara Francisco , Feldmeier-Krause Anja , Mastrobuono-Battisti Alessandra , Schultheis Mathias , Shahzamanian Banafsheh , Vasiliev Eugene , Klessen Ralf S , Lucas Philip , Minniti Dante
Published: March 2022

The nuclear stellar disc (NSD) is a flattened high-density stellar structure that dominates the gravitational field of the Milky Way at Galactocentric radius $30\, {\rm pc}\lesssim R\lesssim 300\, {\rm pc}$. We construct axisymmetric self-consistent equilibrium dynamical models of the NSD in which the distribution function is an analytic function of the action variables. We fit the models to the normalized kinematic distributions (line-of-sight velocities + VIRAC2 proper motions) of stars in the NSD survey of Fritz et al., taking the foreground contamination due to the Galactic Bar explicitly into account using an N-body model. The posterior marginalized probability distributions give a total mass of $M_{\rm NSD} = 10.5^{+1.1}_{-1.0} \times 10^8 \, \, \rm M_\odot$, roughly exponential radial and vertical scale lengths of $R_{\rm disc} = 88.6^{+9.2}_{-6.9} \, {\rm pc}$ and $H_{\rm disc}=28.4^{+5.5}_{-5.5} \, {\rm pc}$, respectively, and a velocity dispersion $\sigma \simeq 70\, {\rm km\, s^{-1}}$ that decreases with radius. We find that the assumption that the NSD is axisymmetric provides a good representation of the data. We quantify contamination from the Galactic Bar in the sample, which is substantial in most observed fields. Our models provide the full 6D (position + velocity) distribution function of the NSD, which can be used to generate predictions for future surveys. We make the models publicly available as part of the software package agama.
IgA vasculitis following COVID-19 vaccination
Authors: Nishimura Naoya , Shiomichi Yasuko , Takeuchi Satoshi , Akamine Shun , Yoneda Reiko , Yoshizawa Seiji
Published: March 2022

Immunoglobulin A (IgA) vasculitis is generally triggered by infectious causes, but it has also been reported after immunisation with various vaccines. Herein, we report two cases of IgA vasculitis after receiving the first or second dose of the Pfizer-BioNTech BNT16B2b2 mRNA vaccine. Two men, aged 22 and 30 years, developed palpable purpura on the extremities and arthritis. One patient also complained of fever and gastrointestinal symptoms. Laboratory findings revealed mild leucocytosis and slightly elevated C-reactive protein levels, although the platelet count and coagulation profile were within normal levels in both cases. Proteinuria and microhaematuria were seen in one patient. Skin biopsies were performed in both patients and revealed leucocytoclastic vasculitis. The deposits of IgA and C3 were shown in immunofluorescence studies in one patient. Both patients were diagnosed with IgA vasculitis and treated with prednisolone, and their symptoms resolved within 1 week after initiation of treatment. The coronavirus disease 2019 mRNA vaccine could trigger IgA vasculitis; however, a coincidence cannot be ruled out.
Identification of Distinct Long COVID Clinical Phenotypes Through Cluster Analysis of Self-Reported Symptoms
Authors: Kenny Grace , McCann Kathleen , O’Brien Conor , Savinelli Stefano , Tinago Willard , Yousif Obada , Lambert John S , O’Broin Cathal , Feeney Eoin R , De Barra Eoghan , Doran Peter , Mallon Patrick W G ,   All-Ireland Infectious Diseases (AIID) Cohort Study Group, Cotter A , Muldoon E , Sheehan G , McGinty T , Lambert J S , Green S , Leamy K , Kenny G , McCann K , McCann R , O’Broin C , Waqas S , Savinelli S , Feeney E , Mallon P W G , Garcia Leon A , Miles S , Alalwan D , Negi R , de Barra E , McConkey S , Hurley K , Sulaiman I , Horgan M , Sadlier C , Eustace J , Kelly C , Bracken T , Whelan B , Low J , Yousif O , McNicholas B , Courtney G , Gavin P
Published: March 2022

Background

We aimed to describe the clinical presentation of individuals presenting with prolonged recovery from coronavirus disease 2019 (COVID-19), known as long COVID.

Methods

This was an analysis within a multicenter, prospective cohort study of individuals with a confirmed diagnosis of COVID-19 and persistent symptoms >4 weeks from onset of acute symptoms. We performed a multiple correspondence analysis (MCA) on the most common self-reported symptoms and hierarchical clustering on the results of the MCA to identify symptom clusters.

Results

Two hundred thirty-three individuals were included in the analysis; the median age of the cohort was 43 (interquartile range [IQR], 36–54) years, 74% were women, and 77.3% reported a mild initial illness. MCA and hierarchical clustering revealed 3 clusters. Cluster 1 had predominantly pain symptoms with a higher proportion of joint pain, myalgia, and headache; cluster 2 had a preponderance of cardiovascular symptoms with prominent chest pain, shortness of breath, and palpitations; and cluster 3 had significantly fewer symptoms than the other clusters (2 [IQR, 2–3] symptoms per individual in cluster 3 vs 6 [IQR, 5–7] and 4 [IQR, 3–5] in clusters 1 and 2, respectively; P < .001). Clusters 1 and 2 had greater functional impairment, demonstrated by significantly longer work absence, higher dyspnea scores, and lower scores in SF-36 domains of general health, physical functioning, and role limitation due to physical functioning and social functioning.

Conclusions

Clusters of symptoms are evident in long COVID patients that are associated with functional impairments and may point to distinct underlying pathophysiologic mechanisms of disease.