bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein phosphatase 2A – structure, function and role in neurodevelopmental disorders
Authors: Sandal Priyanka , Jong Chian Ju , Merrill Ronald A. , Song Jianing , Strack Stefan
Published: July 2021

Neurodevelopmental disorders (NDDs), including intellectual disability (ID), autism and schizophrenia, have high socioeconomic impact, yet poorly understood etiologies. A recent surge of large-scale genome or exome sequencing studies has identified a multitude of mostly de novo mutations in subunits of the protein phosphatase 2A (PP2A) holoenzyme that are strongly associated with NDDs. PP2A is responsible for at least 50% of total Ser/Thr dephosphorylation in most cell types and is predominantly found as trimeric holoenzymes composed of catalytic (C), scaffolding (A) and variable regulatory (B) subunits. PP2A can exist in nearly 100 different subunit combinations in mammalian cells, dictating distinct localizations, substrates and regulatory mechanisms. PP2A is well established as a regulator of cell division, growth, and differentiation, and the roles of PP2A in cancer and various neurodegenerative disorders, such as Alzheimer's disease, have been reviewed in detail. This Review summarizes and discusses recent reports on NDDs associated with mutations of PP2A subunits and PP2A-associated proteins. We also discuss the potential impact of these mutations on the structure and function of the PP2A holoenzymes and the etiology of NDDs.
Total energy expenditure of bottlenose dolphins (Tursiops truncatus) of different ages
Authors: Rimbach Rebecca , Amireh Ahmad , Allen Austin , Hare Brian , Guarino Emily , Kaufman Chana , Salomons Hannah , Pontzer Herman
Published: July 2021

Marine mammals are thought to have an energetically expensive lifestyle because endothermy is costly in marine environments. However, measurements of total energy expenditure (TEE; kcal day−1) are available only for a limited number of marine mammals, because large body size and inaccessible habitats make TEE measurements expensive and difficult to obtain for many taxa. We measured TEE in 10 adult common bottlenose dolphins (Tursiops truncatus) living in natural seawater lagoons at two facilities (Dolphin Research Center and Dolphin Quest) using the doubly labeled water method. We assessed the relative effects of body mass, age and physical activity on TEE. We also examined whether TEE of bottlenose dolphins, and more generally of marine mammals, differs from that expected for their body mass compared with other eutherian mammals, using phylogenetic least squares (PGLS) regressions. There were no differences in body mass or TEE (unadjusted TEE and TEE adjusted for fat-free mass) between dolphins from the two facilities. Our results show that adjusted TEE decreased and fat mass increased with age. Different measures of activity were not related to age, body fat or adjusted TEE. Both PGLS and the non-phylogenetic linear regression indicate that marine mammals have an elevated TEE compared with that of terrestrial mammals. However, bottlenose dolphins expended 17.1% less energy than other marine mammals of similar body mass. The two oldest dolphins (>40 years) showed a lower TEE, similar to the decline in TEE seen in older humans. To our knowledge, this is the first study to show an age-related metabolic decline in a large non-human mammal.
Análise da eficiência em operações de vinícolas brasileiras e portuguesas: um estudo comparativo
Authors: Souza Santos Pedro Vieira , Viana Izabella Maria da Silva , Damasceno Naiane Talita dos Santos , Silva Eduína Carla da
Published: July 2021

A indústria vinícola está entre as que se destacam no contexto internacional: em 2019, os produtores de vinho de todo o mundo produziram entre 258,3 e 267,4 milhões de hectolitros do produto. Como se trata de um segmento com operações padronizadas, é suscetível o processo de avaliação de desempenho em termos de eficiência. O objetivo do presente estudo é avaliar e comparar a eficiência das operações de vinícolas localizadas no Brasil e em Portugal, por meio da aplicação da análise envoltória de dados. Com base nos dados gerados pelo modelo BCC-input, construiu-se a fronteira de eficiência para visualização e análise do desempenho entre as 18 empresas submetidas ao estudo. Foram obtidos dados de eficiência clássica, eficiência invertida, além de composta e normalizada. Tendo em vista a análise de eficiência composta normalizada, somente a empresa C manteve seu índice igual a um (1,0) ou 100%. Do conjunto inicial de 18 empresas que foram analisadas, esta é a única unidade de tomada de decisão homogênea (DMU) que se mostra eficiente nas operações. Em outras palavras, a DMU C tem uma boa performance nas métricas em que se destaca, além de não ter um desempenho ruim nas variáveis em que não se destaca. As demais DMUs ficaram no intervalo [0,230; 0,958].
Normalisation for Some Quite Interesting Many-Valued Logics
Authors: Kürbis Nils , Petrukhin Yaroslav
Published: July 2021

In this paper, we consider a set of quite interesting three- and four-valued logics and prove the normalisation theorem for their natural deduction formulations. Among the logics in question are the Logic of Paradox, First Degree Entailment, Strong Kleene logic, and some of their implicative extensions, including RM3 and RM3⊃. Also, we present a detailed version of Prawitz’s proof of Nelson’s logic N4 and its extension by intuitionist negation.
Estrategias de enseñanza para niños, niñas y adolescentes jornaleros agrícolas migrantes en México.
Authors: Juárez-Bolaños Diego , Solano-Becerril Luis Ernesto , Cervantes-Gómez Juana Isabel , Vega-Santos Luz Elena
Published: July 2021

Las familias que habitan de los territorios rurales desarrollan diversas estrategias para obtener ingresos económicos, tales como el trabajo en la propia tierra, la venta de artesanías, la migración nacional e internacional. En este sentido, existen miles de familias en México que realizan procesos temporales de migración interna, que viajan a campos agrícolas nacionales para trabajar en la cosecha de diversos productos durante algunos periodos de tiempo. Buena parte de estas familias migrantes son acompañadas por niños y adolescentes en edad escolar. La literatura sobre la educación formal de los niños, niñas y adolescentes jornaleros agrícolas migrantes (NNAJAM) se ha centrado en aspectos contextuales, en las acciones y programas de gobierno y en las condiciones escolares, pero poco se ha escrito sobre las estrategias de enseñanza en las aulas. El presente artículo tiene como objetivo sistematizar y examinar diversas estrategias de enseñanza que han sido aplicadas en escuelas que atienden a estas poblaciones en México. Los datos provienen de una investigación documental, a través de la cual identificó y sistematizó la literatura que, de manera central o secundaria, ha mencionado,descrito o examinado las estrategias de enseñanza para los NNAJAM. Los principales aportes del documento se centran en reunir, sistematizar y analizar diversas estrategias implementadas en escuelas en las áreas de lenguaje, razonamiento matemático, aprendizaje colaborativo, interculturalidad, uso del tiempo libre y alimentación y nutrición.
Decision Making Under Model Uncertainty: Fréchet–Wasserstein Mean Preferences
Authors: Petracou Electra V. , Xepapadeas Anastasios , Yannacopoulos Athanasios N.
Published: July 2021

This paper contributes to the literature on decision making under multiple probability models by studying a class of variational preferences. These preferences are defined in terms of Fréchet mean utility functionals, which are based on the Wasserstein metric in the space of probability models. In order to produce a measure that is the “closest” to all probability models in the given set, we find the barycenter of the set. We derive explicit expressions for the Fréchet–Wasserstein mean utility functionals and show that they can be expressed in terms of an expansion that provides a tractable link between risk aversion and ambiguity aversion. The proposed utility functionals are illustrated in terms of two applications. The first application allows us to define the social discount rate under model uncertainty. In the second application, the functionals are used in risk securitization. The barycenter in this case can be interpreted as the model that maximizes the probability that different decision makers will agree on, which could be useful for designing and pricing a catastrophe bond.

This paper was accepted by Manel Baucells, decision analysis.
DESORDENANDO O MONOPÓLIO TERRITORIAL ESTATAL: APORTES TEÓRICOS DA GEOGRAFIA CRÍTICA À RECONFIGURAÇÃO PLURINACIONAL DO ESTADO EQUATORIANO
Authors: Silveira Manuela Monarcha Murad da
Published: July 2021

Como parte de um esforço coletivo por construir uma nova geografia no Equador – e desejando que novas e plurais geo-grafias sejam possíveis –, sistematizamos neste artigo algumas reflexões que tiveram um papel central na práxis do Coletivo XX, voltado à defesa dos territórios dos povos e comunidades tradicionais, em uma conjuntura em que os avanços constitucionais relativos à plurinacionalidade do Estado não eram suficientes para frear os atropelos a esses territórios. Apresentamos, em primeiro lugar, uma leitura decolonial sobre o processo histórico de legitimação do monopólio territorial estatal, ressaltando o papel da associação naturalizada entre Estado, nação e território. Em seguida, fazemos uma revisão teórica sobre o conceito de território e de (des)ordenamento territorial, em sua relação com o processo de reconfiguração crítica da Geografia. Por fim, tecemos breves comentários sobre o processo de fomação territorial do Equador e as dinâmicas mais recentes que vêm ocasionando conflitos territoriais.
Characterization of Nutrients and Pilot Biofertilizer Production from Food Waste and Dairy Manure Digestates
Authors: Barzee Tyler J. , Edalati Abdolhossein , Rapport Joshua L. , El-Mashad Hamed M. , Zhang Ruihong
Published: July 2021

Highlights

N, P, Ca, and Mg were mainly localized to fine digestate solids (0.45 µm to 1 mm).

50% to 60% of NH4+-N was found in digestate solids between 0.45 and 75 µm.

K and Na were mainly transferred to the ultrafiltration permeate (<0.45 µm).

Mixing of coarse and fine solids can optimize nutrient and salt ratios in products.

Abstract. Food waste and dairy manure digestates from commercial digesters were characterized in the lab for particle and nutrient distributions before pilot-scale processing (vibratory screen, ultrafiltration, sun drying) to produce solid and liquid biofertilizer products. Experimental results showed that the elemental compositions of the two digestates were different but shared similarities. The coarse solids of both digestates had lower concentrations of nutrients than the liquid fractions, which contained most of the K and Na. The dairy manure digestate had a higher amount of fine solids between 0.4  and 75 µm than the food waste digestate, but the majority of TKN was contained in the fine solids of both digestates. An optimization analysis concluded that optimal combinations of digestate fractions included over 70% coarse solids to obtain desired nutrient and salt ratios. The solid and liquid fertilizer products derived from the pilot-scale processing were similar to those expected from the lab-scale investigation. Keywords: Biofertilizer formulation, Digestate, Nutrient distribution, Pilot-scale processing, Ultrafiltration, Value-added products.
Design of a Buffered Longitudinal Vibratory Picking Mechanism for Berry Shrub Fruits
Authors: Chen Jiayao , Wang Ying , Liang Dongtai , Xu Wenhao , Chen Yang
Published: July 2021

Highlights

A spring buffering system was added to a longitudinal vibration picking mechanism for berry shrub fruits.

Vibration models of the picking part and side branch were established to obtain the vibration relationship.

Blueberry picking experiments were conducted to verify the performance of the picking mechanism.

Abstract. Current berry shrub picking mechanisms are generally rigid structures, which can easily cause the mechanism to jam and produce rigid impacts, damaging the berry shrub branches. In view of this situation, a longitudinal vibratory picking mechanism for berry shrub fruits is proposed in this study with a spring system added to provide a buffering effect. Vibration models were established for the picking part and for the berry shrub side branch, and analysis was performed to obtain the vibration relationships. Using blueberry as an example, suitable parameters were determined through calculation and then used in blueberry picking experiments with a prototype of the picking mechanism. The experiments verified that the vibration frequency calculated with the vibration relationships can meet the requirements for picking, and the performance of the longitudinal vibratory picking mechanism for berry shrub fruits was verified. Keywords: Berry shrub picking, Buffer, Longitudinal vibration, Vibration analysis.
Estimation of Corn Emergence Date Using UAV Imagery
Authors: Vong Chin Nee , Stewart Stirling A. , Zhou Jianfeng , Kitchen Newell R. , Sudduth Kenneth A.
Published: July 2021

Highlights

UAV imagery can be used to characterize newly-emerged corn plants.

Size and shape features used in a random forest model are able to predict days after emergence within a 3-day window.

Diameter and area were important size features for predicting DAE for the first, second, and third week of emergence.

Abstract. Assessing corn (Zea mays L.) emergence uniformity soon after planting is important for relating to grain production and making replanting decisions. Unmanned aerial vehicle (UAV) imagery has been used for determining corn densities at vegetative growth stage 2 (V2) and later, but not as a tool for quantifying emergence date. The objective of this study was to estimate days after corn emergence (DAE) using UAV imagery and a machine learning method. A field experiment was designed with four planting depths to obtain a range of corn emergence dates. UAV imagery was collected during the first, second, and third weeks after emergence. Acquisition height was approximately 5 m above ground level, which resulted in a ground sampling distance of 1.5 mm pixel-1. Seedling size and shape features derived from UAV imagery were used for DAE classification based on a random forest machine learning model. Results showed that 1-day DAE could be distinguished based on image features within the first week after initial corn emergence with a moderate overall classification accuracy of 0.49. However, for the second week and beyond, the overall classification accuracy diminished (0.20 to 0.35). When estimating DAE within a 3-day window (-1 to +1 day), the overall 3-day classification accuracies ranged from 0.54 to 0.88. Diameter, area, and the ratio of major axis length to area were important image features to predict corn DAE. Findings demonstrated that UAV imagery can detect newly-emerged corn plants and estimate their emergence date to assist in assessing emergence uniformity. Additional studies are needed for fine-tuning the image collection procedures and image feature identification to improve accuracy. Keywords: Corn emergence, Image features, Random forest, Unmanned aerial vehicle.
Granulated Poultry Litter Ash Acidulation and Physical Characteristics
Authors: Millsaps Clara R. , Reiter Mark S. , Whitehurst Brooks M. , Whitehurst Garnett B. , Maguire Rory O. , Thomason Wade E.
Published: July 2021

Highlights

Phosphoric acid (PA) increased water-soluble phosphorus (WSP) from 0.31 to 47.4 g P kg-1 in poultry litter ash (PLA).

Ideal granule size was identified at 29% acidulation (14.5 g acid to 50 g PLA) with granules averaging 3.14 mm.

Bulk fertilizer production needed 32% PA addition, and adequate mixing equipment is important for PA efficiency.

Granule size and strength were adequate as compared to industry standards and commercial fertilizers.

Abstract. Manure-to-energy systems effectively recycle poultry litter (PL) into poultry litter ash (PLA) that densifies and concentrates the phosphorus (P) content by a factor of 4 to 10. However, high conversion temperatures reduce nutrient solubility and produce small particulate materials. To redistribute manure nutrients beyond the original production location by improving the physical and chemical characteristics of PLA, the objectives of this research were to: (1) determine the phosphoric acid (H3PO4) acidifying effect on water-soluble P (WSP), measurable total P (TP), granulation point, and granule size and (2) conduct large-scale granulated poultry litter ash bulk (GPLA-B) granulation to determine the larger-scale formulations and granule physical characteristics produced. We measured bulk density, force and friction resistance, and granule size as compared to industry-standard triple superphosphate (TSP). Acidulation experiments were arranged in a completely randomized design with four replications per H3PO4 acidulation percentage. Increasing acidulation percentages from 0% to 50% H3PO4 (laboratory-grade white phosphoric acid) increased measurable TP from 50.63 to 116.90 g kg-1 and WSP from 0.31 to 47.4 g P kg-1 (LSD0.05 10.13 and 2.65 g P kg-1, respectively). Acidulation dose response relationships created simple linear regression equations to predict changes in measurable TP and WSP, pH, and exothermic reaction temperature, which all increased with acidulation. The loose (1.01 g cm-3) and packed (1.03 g cm3) bulk densities of GPLA-B were significantly less than those of TSP (1.14 and 1.30 g cm3, respectively) (LSD0.05 = 0.03 and 0.02 g cm-3). Compared to TSP particles (2.86 mm), GPLA particles (3.73 mm) were significantly larger (LSD0.05 = 0.61 mm); however, the force resistance of GPLA (4.53 kgf) was significantly less than that of TSP (5.95 kgf) (LSD0.05 = 0.61 kgf). Results showed that the physical characteristics of GPLA met industry standards and validated the adaptability of GPLA as an alternative P source. Furthermore, GPLA has higher elemental analysis, greater solubility, and improved form, which addresses the undesirable characteristics of ungranulated PLA and supports the use of GPLA for fertilizer and nutrient distribution. Keywords: Acidulation, Fertilizer, Granulation, Phosphorus, Poultry litter ash.
Deep learning classification of cervical dysplasia using depth-resolved angular light scattering profiles
Authors: Zhang Haoran , Kendall Wesley Y. , Jelly Evan T. , Wax Adam
Published: July 2021

We present a machine learning method for detecting and staging cervical dysplastic tissue using light scattering data based on a convolutional neural network (CNN) architecture. Depth-resolved angular scattering measurements from two clinical trials were used to generate independent training and validation sets as input of our model. We report 90.3% sensitivity, 85.7% specificity, and 87.5% accuracy in classifying cervical dysplasia, showing the uniformity of classification of a/LCI scans across different instruments. Further, our deep learning approach significantly improved processing speeds over the traditional Mie theory inverse light scattering analysis (ILSA) method, with a hundredfold reduction in processing time, offering a promising approach for a/LCI in the clinic for assessing cervical dysplasia.
An end-to-end network for segmenting the vasculature of three retinal capillary plexuses from OCT angiographic volumes
Authors: Guo Yukun , Hormel Tristan T. , Pi Shaohua , Wei Xiang , Gao Min , Morrison John C. , Jia Yali
Published: July 2021

The segmentation of en face retinal capillary angiograms from volumetric optical coherence tomographic angiography (OCTA) usually relies on retinal layer segmentation, which is time-consuming and error-prone. In this study, we developed a deep-learning-based method to segment vessels in the superficial vascular plexus (SVP), intermediate capillary plexus (ICP), and deep capillary plexus (DCP) directly from volumetric OCTA data. The method contains a three-dimensional convolutional neural network (CNN) for extracting distinct retinal layers, a custom projection module to generate three vascular plexuses from OCTA data, and three parallel CNNs to segment vasculature. Experimental results on OCTA data from rat eyes demonstrated the feasibility of the proposed method. This end-to-end network has the potential to simplify OCTA data processing on retinal vasculature segmentation. The main contribution of this study is that we propose a custom projection module to connect retinal layer segmentation and vasculature segmentation modules and automatically convert data from three to two dimensions, thus establishing an end-to-end method to segment three retinal capillary plexuses from volumetric OCTA without any human intervention.
Dantzig–Wolfe decomposition for the design of filterless optical networks
Authors: Jaumard Brigitte , Wang Yan , Coudert David
Published: July 2021

Filterless optical networks use passive splitters and combiners with coherent optics, providing wavelength selection in the digital domain, while forming a passive fiber-tree topology between nodes. In this study, we investigate the optimal design of filterless optical networks while minimizing the number of required wavelengths. We propose a Dantzig–Wolfe decomposition model in which each subproblem aims to generate a potential filterless optical subnetwork, with a directed tree topology. The master problem then selects the best combination of subnetworks. Numerical experiments demonstrate significant performance improvement over previous work, reducing previous computational results by a factor of 2 to 10, depending on the size of the data instances.
Generation of structured coherent extreme ultraviolet beams from an MgO crystal
Authors: Korobenko A. , Rashid S. , Heide C. , Naumov A. Yu. , Reis D. A. , Berini P. , Corkum P. B. , Vampa G.
Published: July 2021

Short wavelength high-harmonic sources are undergoing intense development for applications in spectroscopy and microscopy. Despite recent progress in peak and average power, spatial control over coherent extreme ultraviolet (XUV) beams remains a formidable challenge due to the lack of suitable optical elements for beam shaping and control. Here we demonstrate a robust and precise approach that structures XUV high-order harmonics in space as they are emitted from a nanostructured MgO crystal. Our demonstration paves the way for bridging the numerous applications of shaped light beams from the visible to the short wavelengths, with potential uses for applications in microscopy and nanoscale machining.
Improved performance of InGaAs/GaAs microdisk lasers epi-side down bonded onto a silicon board
Authors: Zubov Fedor , Maximov Mikhail , Moiseev Eduard , Vorobyev Alexandr , Mozharov Alexey , Berdnikov Yuri , Kaluzhnyy Nikolay , Mintairov Sergey , Kulagina Marina , Kryzhanovskaya Natalia , Zhukov Alexey
Published: July 2021

We study the impact of improved heat removal on the performance of InGaAs/GaAs microdisk lasers epi-side down bonded onto a silicon substrate. Unlike the initial characteristics of microlasers on a GaAs substrate, the former’s bonding results in a decrease in thermal resistance by a factor of 2.3 (1.8) in microdisks with a diameter of 19 (31) µm, attributed to a thinner layered structure between the active region and the substrate and the better thermal conductivity of Si than GaAs. Bonded microdisk lasers show a 2.4–3.4-fold higher maximum output power, up to 21.7 mW, and an approximately 20% reduction in the threshold current. A record high 3 dB small-signal modulation bandwidth of 7.9 GHz for InGaAs/GaAs microdisk lasers is achieved.
Characterizing the spatial entanglement from laser modes analogous to quantum wave functions
Authors: Hsieh M. X. , Zheng X. L. , Yu Y. T. , Liang H. C. , Huang K. F. , Chen Y. F.
Published: July 2021

The Schmidt decomposition is exploited to study the spatial entanglement of laser transverse modes analogous to quantum Lissajous states. Based on the inverse Fourier transform, the stationary Lissajous state can be analytically derived as a coherent superposition of degenerate Hermite–Gaussian eigenmodes. With the derived stationary state, the Schmidt modes and the participation number

N

can be employed to evaluate the spatial localization and the quantum entanglement. The larger the participation number, the more localized is the stationary coherent state on the Lissajous figure. Moreover, the larger the participation number, the higher is the spatial entanglement.
Modeling the role of gap junctions between excitatory neurons in the developing visual cortex
Authors: Crodelle Jennifer , McLaughlin David W.
Published: July 2021

Recent experiments in the developing mammalian visual cortex have revealed that gap junctions couple excitatory cells and potentially influence the formation of chemical synapses. In particular, cells that were coupled by a gap junction during development tend to share an orientation preference and are preferentially coupled by a chemical synapse in the adult cortex, a property that is diminished when gap junctions are blocked. In this work, we construct a simplified model of the developing mouse visual cortex including spike-timing-dependent plasticity of both the feedforward synaptic inputs and recurrent cortical synapses. We use this model to show that synchrony among gap-junction-coupled cells underlies their preference to form strong recurrent synapses and develop similar orientation preference; this effect decreases with an increase in coupling density. Additionally, we demonstrate that gap-junction coupling works, together with the relative timing of synaptic development of the feedforward and recurrent synapses, to determine the resulting cortical map of orientation preference.
Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort
Authors: Datta Arghya , Flynn Noah R. , Barnette Dustyn A. , Woeltje Keith F. , Miller Grover P. , Swamidass S. Joshua
Published: July 2021

Drug-drug interactions account for up to 30% of adverse drug reactions. Increasing prevalence of electronic health records (EHRs) offers a unique opportunity to build machine learning algorithms to identify drug-drug interactions that drive adverse events. In this study, we investigated hospitalizations’ data to study drug interactions with non-steroidal anti-inflammatory drugs (NSAIDS) that result in drug-induced liver injury (DILI). We propose a logistic regression based machine learning algorithm that unearths several known interactions from an EHR dataset of about 400,000 hospitalization. Our proposed modeling framework is successful in detecting 87.5% of the positive controls, which are defined by drugs known to interact with diclofenac causing an increased risk of DILI, and correctly ranks aggregate risk of DILI for eight commonly prescribed NSAIDs. We found that our modeling framework is particularly successful in inferring associations of drug-drug interactions from relatively small EHR datasets. Furthermore, we have identified a novel and potentially hepatotoxic interaction that might occur during concomitant use of meloxicam and esomeprazole, which are commonly prescribed together to allay NSAID-induced gastrointestinal (GI) bleeding. Empirically, we validate our approach against prior methods for signal detection on EHR datasets, in which our proposed approach outperforms all the compared methods across most metrics, such as area under the receiver operating characteristic curve (AUROC) and area under the precision-recall curve (AUPRC).
Multitask learning over shared subspaces
Authors: Menghi Nicholas , Kacar Kemal , Penny Will
Published: July 2021

This paper uses constructs from machine learning to define pairs of learning tasks that either shared or did not share a common subspace. Human subjects then learnt these tasks using a feedback-based approach and we hypothesised that learning would be boosted for shared subspaces. Our findings broadly supported this hypothesis with either better performance on the second task if it shared the same subspace as the first, or positive correlations over task performance for shared subspaces. These empirical findings were compared to the behaviour of a Neural Network model trained using sequential Bayesian learning and human performance was found to be consistent with a minimal capacity variant of this model. Networks with an increased representational capacity, and networks without Bayesian learning, did not show these transfer effects. We propose that the concept of shared subspaces provides a useful framework for the experimental study of human multitask and transfer learning.
NuA4 and SAGA acetyltransferase complexes cooperate for repair of DNA breaks by homologous recombination
Authors: Cheng Xue , Côté Valérie , Côté Jacques
Published: July 2021

Chromatin modifying complexes play important yet not fully defined roles in DNA repair processes. The essential NuA4 histone acetyltransferase (HAT) complex is recruited to double-strand break (DSB) sites and spreads along with DNA end resection. As predicted, NuA4 acetylates surrounding nucleosomes upon DSB induction and defects in its activity correlate with altered DNA end resection and Rad51 recombinase recruitment. Importantly, we show that NuA4 is also recruited to the donor sequence during recombination along with increased H4 acetylation, indicating a direct role during strand invasion/D-loop formation after resection. We found that NuA4 cooperates locally with another HAT, the SAGA complex, during DSB repair as their combined action is essential for DNA end resection to occur. This cooperation of NuA4 and SAGA is required for recruitment of ATP-dependent chromatin remodelers, targeted acetylation of repair factors and homologous recombination. Our work reveals a multifaceted and conserved cooperation mechanism between acetyltransferase complexes to allow repair of DNA breaks by homologous recombination.
Aging-related upregulation of the homeobox gene caudal represses intestinal stem cell differentiation in Drosophila
Authors: Wu Kun , Tang Yiming , Zhang Qiaoqiao , Zhuo Zhangpeng , Sheng Xiao , Huang Jingping , Ye Jie’er , Li Xiaorong , Liu Zhiming , Chen Haiyang
Published: July 2021

The differentiation efficiency of adult stem cells undergoes a significant decline in aged animals, which is closely related to the decline in organ function and age-associated diseases. However, the underlying mechanisms that ultimately lead to this observed decline of the differentiation efficiency of stem cells remain largely unclear. This study investigatedDrosophilamidguts and identified an obvious upregulation ofcaudal(cad), which encodes a homeobox transcription factor. This factor is traditionally known as a central regulator of embryonic anterior-posterior body axis patterning. This study reports that depletion ofcadin intestinal stem/progenitor cells promotes quiescent intestinal stem cells (ISCs) to become activate and produce enterocytes in the midgut under normal gut homeostasis conditions. However, overexpression ofcadresults in the failure of ISC differentiation and intestinal epithelial regeneration after injury. Moreover, this study suggests thatcadprevents intestinal stem/progenitor cell differentiation by modulating the Janus kinase/signal transducers and activators of the transcription pathway and Sox21a-GATAe signaling cascade. Importantly, the reduction ofcadexpression in intestinal stem/progenitor cells restrained age-associated gut hyperplasia inDrosophila. This study identified a function of the homeobox genecadin the modulation of adult stem cell differentiation and suggested a potential gene target for the treatment of age-related diseases induced by age-related stem cell dysfunction.
Distinct spermiogenic phenotypes underlie sperm elimination in the Segregation Distorter meiotic drive system
Authors: Herbette Marion , Wei Xiaolu , Chang Ching-Ho , Larracuente Amanda M. , Loppin Benjamin , Dubruille Raphaëlle
Published: July 2021

Segregation Distorter (SD) is a male meiotic drive system in Drosophila melanogaster. Males heterozygous for a selfish SD chromosome rarely transmit the homologous SD+ chromosome. It is well established that distortion results from an interaction between Sd, the primary distorting locus on the SD chromosome and its target, a satellite DNA called Rsp, on the SD+ chromosome. However, the molecular and cellular mechanisms leading to post-meiotic SD+ sperm elimination remain unclear. Here we show that SD/SD+ males of different genotypes but with similarly strong degrees of distortion have distinct spermiogenic phenotypes. In some genotypes, SD+ spermatids fail to fully incorporate protamines after the removal of histones, and degenerate during the individualization stage of spermiogenesis. In contrast, in other SD/SD+ genotypes, protamine incorporation appears less disturbed, yet spermatid nuclei are abnormally compacted, and mature sperm nuclei are eventually released in the seminal vesicle. Our analyses of different SD+ chromosomes suggest that the severity of the spermiogenic defects associates with the copy number of the Rsp satellite. We propose that when Rsp copy number is very high (> 2000), spermatid nuclear compaction defects reach a threshold that triggers a checkpoint controlling sperm chromatin quality to eliminate abnormal spermatids during individualization.
Uncovering phylogenetic relationships and genetic diversity of water dropwort using phenotypic traits and SNP markers
Authors: Ji Qun , Zhu Honglian , Huang Xinfang , Zhou Kai , Liu Zhengwei , Sun Yalin , Wang Zhixin , Ke Weidong
Published: July 2021

The water dropwortsOenanthe linearisWall. ex DC. andO.javanica(Blume) DC. are aquatic perennial herbs that have been used in China as vegetables and traditional medicines. However, their phylogenetic relationships and genetic diversity are poorly understood. Here, we presented the phenotypic traits and genome-wide DNA marker-based analysis of 158 water dropwort accessions representing both species. The analysis revealed thatOenanthe lineariswas readily segregated into linear-leaf and deep-cleft leaf water dropworts according to their leaf shapes at flowering.Oenanthe javanicawas classified by clustering analysis into two clusters based mainly on the morphological characteristics of their ultimate segments (leaflets). A set of 11 493 high-quality single-nucleotide polymorphisms was identified and used to construct a phylogenetic tree. There was strong discrimination betweenO.linearisandO.javanica, which was consistent with their phenotype diversification. The population structure and phylogenetic tree analyses suggested that theO.linearisaccessions formed two major groups, corresponding to the linear-leaf and deep-cleft leaf types. The most obvious phenotypic differences between them were fully expressed at the reproductive growth stage. A single-nucleotide polymorphism-based analysis revealed that theO.javanicaaccessions could be categorized into groups I andII. However, this finding did not entirely align with the clusters revealed by morphological classification. Landraces were clustered into one group along with the remaining wild accessions. Hence, water dropwort domestication was short in duration. The level of genetic diversity forO.linearis(π = 0.1902) was slightly lower than that which was estimated forO.javanica(π = 0.2174). There was a low level of genetic differentiation betweenO.linearisandO.javanica(Fst = 0.0471). The mean genetic diversity among accessions ranged from 0.1818 for the linear-leaf types to 0.2318 for the groupII accessions. The phenotypic traits and the single-nucleotide polymorphism markers identified here lay empirical foundation for future genomic studies on water dropwort.
Magnitude and determinants of adequate antenatal care service utilization among mothers in Southern Ethiopia
Authors: Gebrekirstos Lielt Gebreselassie , Wube Tsiyon Birhanu , Gebremedhin Meron Hadis , Lake Eyasu Alem
Published: July 2021

Background

Mortality from preventable pregnancy-related complications remains high in Ethiopia. Antenatal care remains a major public health intervention that prevents maternal and neonatal mortality. Thus, this study aimed to assess the magnitude and determinants of adequate antenatal care utilization in Southern Ethiopia.

Methods

A community-based cross-sectional study was conducted between November and December 2019. A systematic random sampling technique was used to select 670 women. Data were collected using a pre-tested structured questionnaire administered with a digital survey tool (open data kit) and directly exported to STATA version 15 for analysis. Descriptive statistics followed by a multivariable logistic regression analysis were performed. Both crude and adjusted odds ratios (ORs) with 95% confidence intervals were reported.

Results

The magnitude of adequate antenatal care utilization was 23.13%. Tertiary and above education (AOR,4.15;95%CI: 1.95, 8.83), having the best friend who used maternal care (AOR,2.01;95%CI: 1.18,3.41), husband support (AOR,3.84; 95%CI: 1.05, 14.08), high wealth index (AOR,3.61; 95%CI: 1.86, 6.99), follow-up in private health facilities (AOR, 2.27;95% CI:1.33, 3.88), having a history of risky pregnancy (AOR,2.59; 95%CI: 1.55, 4.35), and planned pregnancy (AOR,2.60;95% CI: 1.35, 4.99) were significant determinants of overall adequate ANC service utilization.

Conclusion

The utilization of adequate antenatal care services is quite low. The study findings suggest that interventions should be in place to improve husband’s support, social networks, and women’s education. There is also a need to counsel women to utilize family planning.
Genotyping versus phenotyping of non-ABO erythrocyte antigens in patients with the Mediterranean hemopathic syndromes: Effect of transfusion therapy
Authors: NasrEldin Eman , Khaled Safaa A. A. , Abdelhameed Nada O. , Atwa Maha , Thabet Marwa M. , Elsayh Khalid I. , Elgammal Sahar A.
Published: July 2021

The Mediterranean hemopathic syndromes (MHS) are the most prevalent hemoglobinopathies in the Mediterranean basin. Transfusion therapy is the main therapy for these disorders, particularly for severe forms of the disease. Currently, pre-transfusion serological typing of erythrocyte antigens is the standard tool for reducing complications of transfusion in those patients. This study compared genotyping with phenotyping of non-ABO erythrocyte antigens in patients with MHS and assessed the effect of transfusion therapy on their results. One-hundred ninety-eight MHS patients were recruited, screened, and proven negative for allo-antibodies. They were grouped into two groups: (1) 20 newly diagnosed patients with no transfusion history and (2) 178 previously diagnosed patients undergoing transfusion therapy. Patients were interviewed and clinically examined. Full blood count (FBC) and high performance liquid chromatography (HPLC) were done for group 1 only. Genotyping and phenotyping of non-ABO erythrocyte antigens were performed for group 1, and 25 patients out of group 2 were propensity score-matched (PSM) with group 1. Both groups were gender and age matched; 55% and 74% of groups 1 and 2 had major disease, respectively. Insignificant differences were observed between genotyping and phenotyping of non-ABO erythrocyte antigens in group 1, while significant discrepancies and mixed field results were noted in group 2 patients. Discrepancies were obvious with JKa, JKb, and little c antigens. Conclusively, molecular typing is a powerful tool for pre-transfusion testing in chronically transfused MHS patients. This testing reduces incidence of transfusion reactions. JKa, JKband little c antigens are the most clinically significant non-ABO erythrocyte antigens.
Mortality and morbidity of asthma and chronic obstructive pulmonary disease associated with ambient environment in metropolitans in Taiwan
Authors: Zafirah Yasmin , Lin Yu-Kai , Andhikaputra Gerry , Deng Li-Wen , Sung Fung-Chang , Wang Yu-Chun
Published: July 2021

Background

This study investigated risks of mortality from and morbidity (emergency room visits (ERVs) and outpatient visits) of asthma and chronic obstructive pulmonary disease (COPD) associated with extreme temperatures, fine particulate matter (PM2.5), and ozone (O3) by sex, and age, from 2005 to 2016 in 6 metropolitan cities in Taiwan.

Methods

The distributed lag non-linear model was employed to assess age (0–18, 19–39, 40–64, and 65 years and above), sex-cause-specific deaths, ERVs, and outpatient visits associated with extreme high (99thpercentile) and low (5thpercentile) temperatures and PM2.5and O3concentrations at 90thpercentile. Random-effects meta-analysis was adopted to investigate cause-specific pooled relative risk (RR) and 95% confidence intervals (CI) for the whole studied areas.

Results

Only the mortality risk of COPD in the elderly men was significantly associated with the extreme low temperatures. Exposure to the 90thpercentile PM2.5was associated with outpatient visits for asthma in 0–18 years old boys [RR = 1.15 (95% CI: 1.09–1.22)]. Meanwhile, significant elevation of ERVs of asthma for females aged 40–64 years was associated with exposure to ozone, with the highest RR of 1.21 (95% CI: 1.05–1.39).

Conclusions

This study identified vulnerable subpopulations who were at risk to extreme events associated with ambient environments deserving further evaluation for adaptation.
Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome
Authors: Srikanth Sujata , Jain Lavanya , Zepeda-Mendoza Cinthya , Cascio Lauren , Jones Kelly , Pauly Rini , DuPont Barb , Rogers Curtis , Sarasua Sara , Phelan Katy , Morton Cynthia , Boccuto Luigi
Published: July 2021

Phelan-McDermid syndrome (PMS) is a multi-system disorder characterized by significant variability in clinical presentation. The genetic etiology is also variable with differing sizes of deletions in the chromosome 22q13 region and types of genetic abnormalities (e.g., terminal or interstitial deletions, translocations, ring chromosomes, or SHANK3 variants). Position effects have been shown to affect gene expression and function and play a role in the clinical presentation of various genetic conditions. This study employed a topologically associating domain (TAD) analysis approach to investigate position effects of chromosomal rearrangements on selected candidate genes mapped to 22q13 in 81 individuals with PMS. Data collected were correlated with clinical information from these individuals and with expression and metabolic profiles of lymphoblastoid cells from selected cases. The data confirmed TAD predictions for genes encompassed in the deletions and the clinical and molecular data indicated clear differences among individuals with different 22q13 deletion sizes. The results of the study indicate a positive correlation between deletion size and phenotype severity in PMS and provide evidence of the contribution of other genes to the clinical variability in this developmental disorder by reduced gene expression and altered metabolomics.
CBAG: Conditional biomedical abstract generation
Authors: Sybrandt Justin , Safro Ilya
Published: July 2021

Biomedical research papers often combine disjoint concepts in novel ways, such as when describing a newly discovered relationship between an understudied gene with an important disease. These concepts are often explicitly encoded as metadata keywords, such as the author-provided terms included with many documents in the MEDLINE database. While substantial recent work has addressed the problem of text generation in a more general context, applications, such as scientific writing assistants, or hypothesis generation systems, could benefit from the capacity to select the specific set of concepts that underpin a generated biomedical text. We propose a conditional language model following the transformer architecture. This model uses the “encoder stack” to encode concepts that a user wishes to discuss in the generated text. The “decoder stack” then follows the masked self-attention pattern to perform text generation, using both prior tokens as well as the encoded condition. We demonstrate that this approach provides significant control, while still producing reasonable biomedical text.
Optimizing COVID-19 vaccine distribution across the United States using deterministic and stochastic recurrent neural networks
Authors: Davahli Mohammad Reza , Karwowski Waldemar , Fiok Krzysztof
Published: July 2021

Optimizing COVID-19 vaccine distribution can help plan around the limited production and distribution of vaccination, particularly in early stages. One of the main criteria for equitable vaccine distribution is predicting the geographic distribution of active virus at the time of vaccination. This research developed sequence-learning models to predict the behavior of the COVID-19 pandemic across the US, based on previously reported information. For this objective, we used two time-series datasets of confirmed COVID-19 cases and COVID-19 effective reproduction numbers from January 22, 2020 to November 26, 2020 for all states in the US. The datasets have 310 time-steps (days) and 50 features (US states). To avoid training the models for all states, we categorized US states on the basis of their similarity to previously reported COVID-19 behavior. For this purpose, we used an unsupervised self-organizing map to categorize all states of the US into four groups on the basis of the similarity of their effective reproduction numbers. After selecting a leading state (the state with earliest outbreaks) in each group, we developed deterministic and stochastic Long Short Term Memory (LSTM) and Mixture Density Network (MDN) models. We trained the models with data from each leading state to make predictions, then compared the models with a baseline linear regression model. We also remove seasonality and trends from a dataset of non-stationary COVID-19 cases to determine the effects on prediction. We showed that the deterministic LSTM model trained on the COVID-19 effective reproduction numbers outperforms other prediction methods.
Simultaneous confidence intervals for all pairwise comparisons of the means of delta-lognormal distributions with application to rainfall data
Authors: Maneerat Patcharee , Niwitpong Sa-Aat , Niwitpong Suparat
Published: July 2021

Natural disasters such as flooding and landslides are important unexpected events during the rainy season in Thailand, and how to direct action to avoid their impacts is the motivation behind this study. The differences between the means of natural rainfall datasets in different areas can be estimated using simultaneous confidence intervals (SCIs) for pairwise comparisons of the means of delta-lognormal distributions. Our proposed methods are based on a parametric bootstrap (PB), a fiducial generalized confidence interval (FGCI), the method of variance estimates recovery (MOVER), and Bayesian credible intervals based on mixed (BCI-M) and uniform (BCI-U) priors. Their coverage probabilities, lower and upper error probabilities, and relative average lengths were used to evaluate and compare their SCI performances through Monte Carlo simulation. The results show that BCI-U and PB work well in different situations, even with large differences in variancesσj2. All of the methods were applied to estimate pairwise differences between the means of natural rainfall data from five areas in Thailand during the rainy season to determine their abilities to predict occurrences of flooding and landslides.