bluuebunny/crossref_metadata_2025 huggingface dataset:
No evidence of canopy-scale leaf thermoregulation to cool leaves below air temperature across a range of forest ecosystems
Authors: Still Christopher J. , Page Gerald , Rastogi Bharat , Griffith Daniel M. , Aubrecht Donald M. , Kim Youngil , Burns Sean P. , Hanson Chad V. , Kwon Hyojung , Hawkins Linnia , Meinzer Frederick C. , Sevanto Sanna , Roberts Dar , Goulden Mike , Pau Stephanie , Detto Matteo , Helliker Brent , Richardson Andrew D.
Published: September 2022

Understanding and predicting the relationship between leaf temperature (

T
leaf

) and air temperature (

T
air

) is essential for projecting responses to a warming climate, as studies suggest that many forests are near thermal thresholds for carbon uptake. Based on leaf measurements, the limited leaf homeothermy hypothesis argues that daytime

T
leaf

is maintained near photosynthetic temperature optima and below damaging temperature thresholds. Specifically, leaves should cool below

T
air

at higher temperatures (i.e., > ∼25–30°C) leading to slopes <1 in

T
leaf

/

T
air

relationships and substantial carbon uptake when leaves are cooler than air. This hypothesis implies that climate warming will be mitigated by a compensatory leaf cooling response. A key uncertainty is understanding whether such thermoregulatory behavior occurs in natural forest canopies. We present an unprecedented set of growing season canopy-level leaf temperature (

T
can

) data measured with thermal imaging at multiple well-instrumented forest sites in North and Central America. Our data do not support the limited homeothermy hypothesis: canopy leaves are warmer than air during most of the day and only cool below air in mid to late afternoon, leading to

T
can

/

T
air

slopes >1 and hysteretic behavior. We find that the majority of ecosystem photosynthesis occurs when canopy leaves are warmer than air. Using energy balance and physiological modeling, we show that key leaf traits influence leaf-air coupling and ultimately the

T
can

/

T
air

relationship. Canopy structure also plays an important role in

T
can

dynamics. Future climate warming is likely to lead to even greater

T
can

, with attendant impacts on forest carbon cycling and mortality risk.
A kinase-independent function of cyclin-dependent kinase 6 promotes outer radial glia expansion and neocortical folding
Authors: Wang Lei , Park Jun Young , Liu Fengming , Olesen Kris M. , Hou Shirui , Peng Jamy C. , Infield Jordan , Levesque Anna C. , Wang Yong-Dong , Jin Hongjian , Fan Yiping , Connelly Patrick J. , Pruett-Miller Shondra M. , Hu Miaofen G. , Hinds Philip W. , Han Young-Goo
Published: September 2022

The neocortex, the center for higher brain function, first emerged in mammals and has become massively expanded and folded in humans, constituting almost half the volume of the human brain. Primary microcephaly, a developmental disorder in which the brain is smaller than normal at birth, results mainly from there being fewer neurons in the neocortex because of defects in neural progenitor cells (NPCs). Outer radial glia (oRGs), NPCs that are abundant in gyrencephalic species but rare in lissencephalic species, are thought to play key roles in the expansion and folding of the neocortex. However, how oRGs expand, whether they are necessary for neocortical folding, and whether defects in oRGs cause microcephaly remain important questions in the study of brain development, evolution, and disease. Here, we show that oRG expansion in mice, ferrets, and human cerebral organoids requires cyclin-dependent kinase 6 (CDK6), the mutation of which causes primary microcephaly via an unknown mechanism. In a mouse model in which increased Hedgehog signaling expands oRGs and intermediate progenitor cells and induces neocortical folding, CDK6 loss selectively decreased oRGs and abolished neocortical folding. Remarkably, this function of CDK6 in oRG expansion did not require its kinase activity, was not shared by the highly similar CDK4 and CDK2, and was disrupted by the mutation causing microcephaly. Therefore, our results indicate that CDK6 is conserved to promote oRG expansion, that oRGs are necessary for neocortical folding, and that defects in oRG expansion may cause primary microcephaly.
Quantum annealing with twisted fields
Authors: Imoto Takashi , Seki Yuya , Matsuzaki Yuichiro , Kawabata Shiro
Published: September 2022

Quantum annealing (QA) is a promising method for solving combinational optimization problems and performing quantum chemical calculations. The main sources of errors in QA are the effects of decoherence and non-adiabatic transition. We propose a method for suppressing both these effects using inhomogeneous twist operators corresponding to the twist angles of transverse fields applied to qubits. Furthermore, we adopt variational methods to determine the optimal inhomogeneous twist operator for minimizing the energy of the state after QA. Our approach is useful for increasing the energy gap and/or making the quantum states robust against decoherence during QA. In summary, our results can pave the way to a new approach for realizing practical QA.
Image recognition by FFT, artificial intelligence and k-nearest neighbors approach
Authors: Balabanova I S , Georgiev G I
Published: September 2022

This paper presents procedures of processing and recognition of color images by means of artificial intelligence and computer aided training. Two stages of processing have been applied with regard to extraction of features. Processing involves conversion of RGB images in grayscale and binary; and conversion of RGB, grayscale and binary into index formats. Spectral analysis is also applied in here with Fourier’s algorithm for fast conversion concerning indicated graphic formats and segmentation of the real and imaginary complex parts. Activities related with training, assessment and synthesis of feed-forward neural networks and probabilistic neural networks, based on Accuracy and Mean-Squared Error analysis. Special emphasis is made on a method for computer aided training k-nearest neighbors with Euclidean, Euclidean squared, Cityblock and Chebychev metric distances in relation to Cross-validation accuracy value. Some positive indications have been achieved in recognition of assigned graphic images by means of the employed mathematical apparatus.
Hand-held and UAV camera comparison in building thermal inspection process
Authors: Stokowiec K , Sobura S
Published: September 2022

Thermal building inspections indicate the growing interest among researchers due to the global climate changes resulting in legislations and policy contribution to low-energy consumption. The technologies applied during the experiments involve infrared cameras: both hand-held and on unmanned aerial vehicles. The research conducted in the public building in Kielce included the analysis of glass partition from the inside of the building by means of hand-held and UAV camera. The temperature distributions presented in the graphs proved that both methods are accurate in case of such investigations. However, during the experiments, it was concluded that hand-held camera is far more convenient.
Identification of building environment problems
Authors: Telejko M , Majewski G , Kotrys-Działak D
Published: September 2022

The indoor environment is an enclosed space where people tend to spend more and more time. Its atmosphere has a significant impact on room users. The article deals with the self – reported problems of volunteers related to the sick building syndrome (SBS). The tests were performed in the large lecture room of Kielce University of Technology, where 69 students took part in the questionnaire survey on indoor environment and health related problems. The results show that the students experienced SBS symptoms and that they might have an impact on their concentration during the lecture.
Contributions to an additive method for manufacturing solderless assembly for electronics
Authors: Varzaru G , Savu M , Mihailescu B , Ionescu C , Branzei M
Published: September 2022

The demand for more reliable electronic and affordable products has generated innovative activities in electronic packaging that have highlighted the great benefits of additive technologies. This approach requires new equipment for the electronic assembly line, such as 3D-printer, but especially new materials. Within the additive techniques, one that still keeps the assembly line is the Occam Process. This disruptive concept eliminates the use of solder alloy, and combines into one two technological processes: the manufacture of the printed circuit board and the electronic assembly. Following this concept, the paper presents the result of the research of a couple of electrically conductive adhesive materials and a method for their qualification in the manufacture of solderless electronic modules that can handle ultra high-frequency and microwave signals. A practical solution is to compare the frequency behavior of two identical test structures, one made by the adhesive material, and the other by copper. The comparative analysis showed that electrically conductive adhesives present a slightly better response at high frequencies than copper in terms of insertion loss and return loss in the range 0 to 10 GHz; the adhesive replacement for solder alloy to connect temperature-sensitive
components operating at high frequency is a good alternative.
Development of a fourfold dielectric-filled reentrant cavity as a beam position monitor (BPM) in a proton therapy facility
Authors: Srinivasan S. , Brandenburg S. , Schippers J.M. , Duperrex P.A.
Published: September 2022

At the Paul Scherrer Institute (PSI), the superconducting cyclotron “COMET” delivers a 250 MeV proton beam for radiation therapy in pulses of 1ns at the cyclotron-RF frequency of 72.85 MHz. Accurate measurement of the beam position at proton beam currents of 0.1–10 nA in the beam transport line downstream of the degrader is of crucial importance for the treatment safety and quality, beam alignment and feedback systems. This is essential for efficient operation and beam delivery. These measurements are usually performed with intercepting monitors such as ionization chambers (ICs). In this paper, we present a novel non-intercepting position sensitive cavity resonator. The resonant monitor, tuned to the second harmonic of the cyclotron's RF, is based on the detection of the transverse magnetic dipole mode of the EM field generated by the beam. This mode is only excited for off-center beam positions and is measured with the help of four floating cavities within a common grounded cylinder. This paper discusses the BPM fundamental characteristics, design optimization and the underlying parametric investigations involving the contribution of the different modes and crosstalk. We estimate the expected signals from the prototype BPM for position offsets from simulations and compare them with test-bench measurements and beam measurements with the prototype and the improvised BPM design. We conclude by summarizing the achieved position sensitivity, precision, and measurement bandwidth.
Systematic uncertainties in integrated luminosity measurement at CEPC
Authors: Smiljanic I. , Bozovic Jelisavcic I. , Kacarevic G. , Vukasinovic N. , Vidakovic I. , Rekovic V.
Published: September 2022

The very forward region is one of the most challenging
regions to instrument at a future e
+
e
- collider. At CEPC,
machine-detector interface includes, among others, a calorimeter
dedicated for precision measurement of the integrated luminosity at
a per mill level or better. Here we review a feasibility of such
precision, from the point of view of systematic effects arising from
luminometer mechanical precision and positioning, beam-related
requirements and physics background from two-photon processes. The
impact of the beam energy spread and its uncertainty on the
integrated luminosity precision is also discussed, as well as the
achievable beam energy spread precision with the post-CDR CEPC
beams.
Y-systems for generalised Gibbs ensembles in integrable quantum field theory
Authors: Castro-Alvaredo Olalla A
Published: September 2022

The thermodynamic Bethe ansatz approach to the study of integrable quantum field theories was introduced in the early 90s. Since then it has been known that the thermodynamic Bethe ansatz equations can be recast in the form of Y-systems. These Y-systems have a number of interesting properties, notably in the high-temperature limit their solutions are constants from which the central charge of the ultraviolet fixed point can be obtained and they are typically periodic functions, with period proportional to the dimension of the perturbing field. In this letter we discuss the derivation of Y-systems when the standard thermodynamic Bethe ansatz equations are replaced by generalised versions, describing generalised Gibbs ensembles. We shown that for many integrable quantum field theories, there is a large class of distinct generalised Gibbs ensembles which share the same Y-system.
The Turn to Confession Bargaining in German Criminal Procedure: Causes and Comparisons with American Plea Bargaining
Authors: Langbein John H
Published: September 2022

In recent decades German criminal procedure has developed a practice of confession bargaining, in which defense counsel negotiates with the trial judge for the defendant to confess the charged offense in exchange for a milder sentence than would result if the defendant were to contest the charge. The German practice resembles American plea bargaining in many respects. This Article probes the similarities and the differences between the two systems of negotiated criminal justice. The Article discusses the origins of the German practice, its tensions with historic principles of the procedure system, and the troubled efforts of the courts and the legislature to justify and to regulate the practice.
Genome-wide characterization of twoAubrietataxa:Aubrieta canescenssubsp.canescensandAu. macrostyla(Brassicaceae)
Authors: Kaya Yasin , Aydın Zübeyde Uğurlu , Cai Xu , Wang Xiaowu , Dönmez Ali A
Published: September 2022

Aubrieta canescens complex is divided into two subspecies, Au. canescens subsp. canescens, Au. canescens subsp. cilicica and a distinct species, Au. macrostyla, based on molecular phylogeny. We generated a draft assembly of Au. canescens subsp. canescens and Au. macrostyla using paired-end shotgun sequencing. This is the first attempt at genome characterization for the genus. In the presented study, ~165 and ~157 Mbp of the genomes of Au. canescens subsp. canescens and Au. macrostyla were assembled, respectively, and a total of 32 425 and 31 372 gene models were predicted in the genomes of the target taxa, respectively. We corroborated the phylogenomic affinity of taxa with some core Brassicaceae species (Clades A and B) including Arabis alpina. The orthology-based tree suggested that Aubrieta species differentiated from A. alpina 1.3–2.0 mya (million years ago). The genome-wide syntenic comparison of two Aubrieta taxa revealed that Au. canescens subsp. canescens (46 %) and Au. macrostyla (45 %) have an almost identical syntenic gene pair ratio. These novel genome assemblies are the first steps towards the chromosome-level assembly of Au. canescens and understanding the genome diversity within the genus.
Comparison of metabolism and biological properties among positional isomers of quercetin glucuronide in LPS- and RANKL-challenged RAW264.7 cells
Authors: Nishikawa Miyu , Kada Yuriko , Kimata Mirai , Sakaki Toshiyuki , Ikushiro Shinichi
Published: September 2022

The major quercetin metabolite, quercetin-3-glucuronide, exerts various biological activities, including anti-inflammatory effects. This study aimed to evaluate the metabolic profiles and biological properties of the positional isomers of quercetin monoglucuronides (Q3G, Q7G, Q3’G, and Q4’G) in activated macrophages. In addition to quercetin aglycone, Q7G was more cytotoxic than the other quercetin monoglucuronides (QGs), which corresponded to its lower stability under neutral pH conditions. Q3G was most effective in inhibiting both LPS-dependent induction of IL-6 and RANKL-dependent activation of tartrate-resistant acid phosphatase; however, Q3’G and Q4’G may also help exert biological activities without potential cytotoxicity. The deconjugation efficacy to generate quercetin aglycone differed among QGs, with the highest efficacy in Q3G. These results suggest that the chemical or biological properties and metabolic profiles may depend on the stability of QGs to generate quercetin aglycone using β-glucuronidase.
Rice OsHAK5 is a major potassium transporter that functions in potassium uptake with high specificity but contributes less to cesium uptake
Authors: Uchiyama Minato , Fudaki Rika , Kobayashi Takuya , Adachi Yoshiko , Ukai Yuko , Yoshihara Toshihiro , Shimada Hiroaki
Published: September 2022

Cesium (Cs) in the environment is primarily absorbed by a potassium (K) transporter. OsHAK5 is a KT/HAK/KUP family K-transporter showing a high affinity for K. We created cultured rice cells whose OsHAK5 was knocked down by RNAi (named KD). In the medium containing 1.0 m m and less K, the growth of KD was significantly suppressed, suggesting that OsHAK5 greatly contributed to K absorption under limited K conditions. Although Cs suppressed the growth of KD and WT, stronger inhibition was observed on KD. Both KD and WT accumulated similar amounts of Cs when they were cultured in a medium containing Cs, whereas lower amounts of K were detected in KD. These results suggest that OsHAK5 was less involved in the absorption of Cs, although it was essential to K absorption under limited K conditions. In contrast, this means that another transporter may contribute to cesium uptake in rice.
Integrating multi-omics summary data using a Mendelian randomization framework
Authors: Jin Chong , Lee Brian , Shen Li , Long Qi ,   for the Alzheimer’s Disease Neuroimaging Initiative,   for the Alzheimer’s Disease Metabolomics Consortium
Published: September 2022

Mendelian randomization is a versatile tool to identify the possible causal relationship between an omics biomarker and disease outcome using genetic variants as instrumental variables. A key theme is the prioritization of genes whose omics readouts can be used as predictors of the disease outcome through analyzing GWAS and QTL summary data. However, there is a dearth of study of the best practice in probing the effects of multiple -omics biomarkers annotated to the same gene of interest. To bridge this gap, we propose powerful combination tests that integrate multiple correlated $P$-values without assuming the dependence structure between the exposures. Our extensive simulation experiments demonstrate the superiority of our proposed approach compared with existing methods that are adapted to the setting of our interest. The top hits of the analyses of multi-omics Alzheimer’s disease datasets include genes ABCA7 and ATP1B1.
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis
Authors: Han Wenkai , Cheng Yuqi , Chen Jiayang , Zhong Huawen , Hu Zhihang , Chen Siyuan , Zong Licheng , Hong Liang , Chan Ting-Fung , King Irwin , Gao Xin , Li Yu
Published: September 2022

We present a novel self-supervised Contrastive LEArning framework for single-cell ribonucleic acid (RNA)-sequencing (CLEAR) data representation and the downstream analysis. Compared with current methods, CLEAR overcomes the heterogeneity of the experimental data with a specifically designed representation learning task and thus can handle batch effects and dropout events simultaneously. It achieves superior performance on a broad range of fundamental tasks, including clustering, visualization, dropout correction, batch effect removal, and pseudo-time inference. The proposed method successfully identifies and illustrates inflammatory-related mechanisms in a COVID-19 disease study with 43 695 single cells from peripheral blood mononuclear cells.
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
Authors: Tian Simon Zhongyuan , Li Guoliang , Ning Duo , Jing Kai , Xu Yewen , Yang Yang , Fullwood Melissa J , Yin Pengfei , Huang Guangyu , Plewczynski Dariusz , Zhai Jixian , Dai Ziwei , Chen Wei , Zheng Meizhen
Published: September 2022

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.
Implementing the Social Care Workforce Race Equality Standard in England: Early Observations
Authors: Manthorpe Jill , Samsi Kritika
Published: September 2022

The implementation in England of a Social Care Workforce Race Equality Standard (SCWRES), initially confined to social work, started with a first set of eighteen volunteer local authorities (LAs) in 2021. This article discusses a rapid evaluation of the SCWRES during its first year. We used Normalization Process Theory (NPT) to better understand the implementation process of this initiative. Thirty-one interviews were undertaken in 2021. Transcripts were analysed using the constant comparative approach and emerging themes were then mapped onto the NPT framework and its four main constructs. Using these we found some lack of clarity over the aims and data demands of the SCWRES (coherence), but generally substantial personal and employer investment in the intervention (cognitive participation); implementation was assisted by personal support to the LAs from senior managers at national level (collective action); and there was general constructive reflection and positive feedback about the SCWRES (reflexive monitoring). Barriers to implementation of new initiatives might be expected during a global pandemic. However, support for the SCWRES was generally high and participants considered they had learned much in its first six months despite pandemic pressures. This article highlights aspects of implementation to be addressed in any further SCWRES rollout.
Neural signatures of default mode network in major depression disorder after electroconvulsive therapy
Authors: Li Yuanyuan , Yu Xiaohui , Ma Yingzi , Su Jing , Li Yue , Zhu Shunli , Bai Tongjian , Wei Qiang , Becker Benjamin , Ding Zhiyong , Wang Kai , Tian Yanghua , Wang Jiaojian
Published: September 2022

Functional abnormalities of default mode network (DMN) have been well documented in major depressive disorder (MDD). However, the association of DMN functional reorganization with antidepressant treatment and gene expression is unclear. Moreover, whether the functional interactions of DMN could predict treatment efficacy is also unknown. Here, we investigated the link of treatment response with functional alterations of DMN and gene expression with a comparably large sample including 46 individuals with MDD before and after electroconvulsive therapy (ECT) and 46 age- and sex-matched healthy controls. Static and dynamic functional connectivity (dFC) analyses showed increased intrinsic/static but decreased dynamic functional couplings of inter- and intra-subsystems and between nodes of DMN. The changes of static functional connections of DMN were spatially correlated with brain gene expression profiles. Moreover, static and dFC of the DMN before treatment as features could predict depressive symptom improvement following ECT. Taken together, these results shed light on the underlying neural and genetic basis of antidepressant effect of ECT and the intrinsic functional connectivity of DMN have the potential to serve as prognostic biomarkers to guide accurate personalized treatment.
Development and Analytical Validation of a 6-Plex Reverse Transcription Droplet Digital PCR Assay for the Absolute Quantification of Prostate Cancer Biomarkers in Circulating Tumor Cells of Patients with Metastatic Castration-Resistant Prostate Cancer
Authors: Zavridou Martha , Smilkou Stavroula , Tserpeli Victoria , Sfika Aggeliki , Bournakis Evangelos , Strati Areti , Lianidou Evi
Published: September 2022

Background

Gene expression in circulating tumor cells (CTCs) can be used as a predictive liquid biopsy test in metastatic castration-resistant prostate cancer (mCRPC). We developed a novel 6-plex reverse transcription droplet digital PCR (RT-ddPCR) assay for the absolute quantification of 4 prostate cancer biomarkers, a reference gene, and a synthetic DNA external control (DNA-EC) in CTCs isolated from mCRPC patients.

Methods

A novel 6-plex RT-ddPCR assay was developed for the simultaneous absolute quantification of AR-FL, AR-V7, PSA, and PSMA, HPRT (used as a reference gene), and a synthetic DNA-EC that was included for quality control. The assay was optimized and analytically validated using DNA synthetic standards for each transcript as positive controls. Epithelial cellular adhesion molecule (EpCAM)-positive CTC fractions isolated from 90 mCRPC patients and 11 healthy male donors were analyzed, and results were directly compared with reverse transcription quantitative PCR (RT-qPCR) for all markers in all samples.

Results

Linear dynamic range, limit of detection, limit of quantification, intra- and interassay precision, and analytical specificity were determined for each marker. Application of the assay in EpCAM-positive CTC showed positivity for AR-FL (71/90; 78.9%), AR-V7 (28/90; 31.1%), PSA (41/90; 45.6%), PSMA (38/90; 42.2%), and HPRT (90/90; 100%); DNA-EC concentration was constant across all samples. Direct comparison with RT-qPCR for the same markers in the same samples revealed RT-ddPCR to have superior diagnostic sensitivity.

Conclusions

Our 6-plex RT-ddPCR assay was highly sensitive, specific, and reproducible, and enabled simultaneous and absolute quantification of 5 gene transcripts in minute amounts of CTC-derived cDNA. Application of this assay in clinical samples gave diagnostic sensitivity and specificity comparable to, or better than, RT-qPCR.
Threshold Homomorphic Encryption From Provably Secure NTRU
Authors: Xu Kexin , Hong Meng Tan Benjamin , Wang Li-Ping , Mi Mi Aung Khin , Wang Huaxiong
Published: September 2022

Homomorphic Encryption (HE) supports computation on encrypted data without the need to decrypt, enabling secure outsourcing of computing to an untrusted cloud. Motivated by application scenarios where private information is offered by different data owners, Multi-Key Homomorphic Encryption (MKHE) and Threshold Homomorphic Encryption (ThHE) were proposed. Unlike MKHE, ThHE schemes do not require expensive ciphertext extension procedures and are therefore as efficient as their underlying single-key HE schemes. In this work, we propose a novel NTRU-type ThHE scheme which caters to the computation scenarios with pre-defined participants. In addition to inheriting the simplicity of NTRU scheme, our construction has no expensive relinearization and correspondingly no costly evaluation keys. Controlling noise to make it increase linearly and then using a wide key distribution, our scheme is immune to the subfield lattice attacks and its security follows from the hardness of the standard R-LWE problem. Finally, based on the {0,1}-linear secret sharing and noise flooding techniques, we design a single round distributed threshold decryption protocol, where the decryption is able to be completed even when only given a subset (say $t$-out-of-$k$) of partial decryptions. To the best of our knowledge, our construction is the first NTRU-type ThHE scheme.
Sinus plication technique for neoaorta dilation and regurgitation in patients with repaired congenital heart diseases
Authors: Kisamori Eiri , Kotani Yasuhiro , Suzuki Hiroyuki , Kasahara Shingo
Published: September 2022

We report 3 cases in sinus plication technique utilized to repair aortic or neoaortic root dilation and valve regurgitation after congenital heart disease operation.
Nitrogen to phosphorus ratio shapes the bacterial communities involved in cellulose decomposition and copper contamination alters their stoichiometric demands
Authors: Wang Ziming , Cébron Aurélie , Baillard Vincent , Danger Michael
Published: September 2022

All living organisms theoretically have an optimal stoichiometric nitrogen: phosphorus (N: P) ratio, below and beyond which their growth is affected, but data remain scarce for microbial decomposers. Here, we evaluated optimal N: P ratios of microbial communities involved in cellulose decomposition and assessed their stability when exposed to copper Cu(II). We hypothesized that (1) cellulose decomposition is maximized for an optimal N: P ratio; (2) copper exposure reduces cellulose decomposition and (3) increases microbial optimal N: P ratio; and (4) N: P ratio and copper modify the structure of microbial decomposer communities. We measured cellulose disc decomposition by a natural inoculum in microcosms exposed to a gradient of N: P ratios at three copper concentrations (0, 1 and 15 µM). Bacteria were most probably the main decomposers. Without copper, cellulose decomposition was maximized at an N: P molar ratio of 4.7. Contrary to expectations, at high copper concentration, the optimal N: P ratio (2.8) and the range of N: P ratios allowing decomposition were significantly reduced and accompanied by a reduction of bacterial diversity. Copper contamination led to the development of tolerant taxa probably less efficient in decomposing cellulose. Our results shed new light on the understanding of multiple stressor effects on microbial decomposition in an increasingly stoichiometrically imbalanced world.
A chromosome-level assembly of the widely used Rockefeller strain of Aedes aegypti, the yellow fever mosquito
Authors: Fisher Cera R , Wilson Michael , Scott Jeffrey G
Published: September 2022

Aedes aegypti is the vector of important human diseases, and genomic resources are crucial in facilitating the study of A. aegypti and its ecosystem interactions. Several laboratory-acclimated strains of this mosquito have been established, but the most used strain in toxicology studies is “Rockefeller,” which was originally collected and established in Cuba 130 years ago. A full-length genome assembly of another reference strain, “Liverpool,” was published in 2018 and is the reference genome for the species (AaegL5). However, genetic studies with the Rockefeller strain are complicated by the availability of only the Liverpool strain as the reference genome. Differences between Liverpool and Rockefeller have been known for decades, particularly in the expression of genes relevant to mosquito behavior and vector control (e.g. olfactory). These differences indicate that AaegL5 is likely not fully representative of the Rockefeller genome, presenting potential impediments to research. Here, we present a chromosomal-level assembly and annotation of the Rockefeller genome and a comparative characterization vs the Liverpool genome. Our results set the stage for a pan-genomic approach to understanding evolution and diversity within this important disease vector.
Spatial structure alters the site frequency spectrum produced by hitchhiking
Authors: Min Jiseon , Gupta Misha , Desai Michael M , Weissman Daniel B
Published: September 2022

The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum left by hitchhiking in the genomic region of a sweep in a population occupying a 1D range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic 3-part site frequency spectrum at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly “surfed” on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the site frequency spectrum produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in 1D populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.
Comprehensive analysis of superconducting gravimeter data, GPS, and hydrology modelling in support of lunar laser ranging at Apache Point Observatory, New Mexico
Authors: Crossley D J , Murphy J T , Liang J
Published: September 2022

The Apache Point Observatory Lunar Laser-ranging Operation (APOLLO) project began in 2006 using a 3.5 m telescope on a high peak in the Sacramento Mountains of New Mexico. It has been one of the best performing (in terms of returned photons per viewing period and range uncertainty) of a handful of similar sites worldwide. The purpose of installing a superconducting gravimeter (SG) in 2009 was to improve the determination of local deformation, directly affecting the telescope motions, as part of an effort to reduce the error in lunar distance to the mm level. We have now accumulated 10 yr of gravity measurements, together with data from a nearby permanent GPS Plate Boundary Observatory (P027) site. This paper describes the traditional analysis of SG data to produce a local tidal model and to determine a number of necessary dynamic corrections that are specific to the site, of which local atmospheric and hydrology attraction and loading are the most important. Loading corrections are available through the Ecole et Observatoire des Sciences de la Terre (EOST) website as part of the International Earth Rotation Service, and we consider 12 different EOST loading series for global atmosphere and hydrology loading and attraction. Nonetheless, local hydrology can only be addressed at the required level of detail using local models determined directly from the gravity data. We devote a major portion of the paper to the development of several water storage and conceptual tank models that succeed in reducing the large seasonal variance of the SG residuals by more than 90 per cent. Yet there remain episodes in the corrected residuals that depart by up to 4 $\mu {\rm{Gal}}\,$ from the hydrological models, and the mean error of our fit remains between 1.5–2.0 $\mu {\rm{Gal}}\,$ for our two data sets, 2009–2012 and 2013–2018 respectively. Unfortunately the vertical GPS data relies on the UNAVCO processing, and has typically poor vertical accuracy. We find the correlation between the GPS and gravity residuals to be correspondingly weak, and then discuss briefly the incorporation of the displacement and gravity data into the Planetary Ephemeris Program for solving for the lunar distance.
Not for us, without us: examining horizontal coordination between the Ministry of Health and other sectors to advance health goals in Uganda
Authors: Ssennyonjo Aloysius , Van Belle Sara , Ssengooba Freddie , Titeca Kristof , Bakubi Rachael , Criel Bart
Published: September 2022

The Ministry or Department of Health (M/DoH) is the mandated government agency for health in all countries. However, achieving good health and wellbeing requires the health sector to coordinate with other sectors such as the environment, agriculture and education. Little is known about the coordination relationship between MoH and other sectors to advance health and development goals in low- and middle-income countries (LMICs). Our study examined the coordination relationship between MoH and other government ministries, departments and agencies (MDAs) at the national level in Uganda. This was an embedded case study nested in a study on intragovernmental coordination at the central government in Uganda. A qualitative approach used document review and key informant interviews with government officials and non-state actors. Data were analysed thematically using a multitheoretical framework. The coordination relationship was characterized by interdependencies generally framed lopsidedly in terms of health sector goals and not vice versa. Actor opportunism and asymmetrical interests interacted with structural–institutional factors contributing to variable influence on internal and external coordination within and beyond MOH. Supportive mechanisms include (a) diverse health sector legal–institutional frameworks, (b) their alignment to broader government efforts and (c) the MOH’s agency to leverage government-wide efforts. Constraints arose from (a) gaps in the legal-institutional framework, (b) demands on resources due to the ‘broad’ MOH mandate and (c) the norms of the MOH’s professional bureaucracy and the predominance of medical professionals. This study underlines critical actions needed to improve coordination between the health and non-health sectors. Introspection within the MOH is vital to inform efforts to modify MOH’s internal functioning and positioning within the broader government to strategically advance MOH’s (development) aspirations. The nature of MoH’s role in multisectoral efforts should be contingent. Consideration of mutual sectoral interdependencies and interactions with and within broader government systems is critical.
Longitudinal characterization of determinants associated with obesogenic growth patterns in early childhood
Authors: Michael Navin , Gupta Varsha , Fogel Anna , Huang Jonathan , Chen Li , Sadananthan Suresh Anand , Ong Yi Ying , Aris Izzuddin M , Pang Wei Wei , Yuan Wen Lun , Loy See Ling , Thway Tint Mya , Tan Kok Hian , Chan Jerry Ky , Chan Shiao-Yng , Shek Lynette Pei-Chi , Yap Fabian , Godfrey Keith , Chong Yap Seng , Gluckman Peter , Velan S Sendhil , Forde Ciarán G , Lee Yung Seng , Eriksson Johan G , Karnani Neerja
Published: September 2022

Background

Longitudinal assessment of the determinants of obesogenic growth trajectories in childhood can suggest appropriate developmental windows for intervention.

Methods

Latent class growth mixture modelling was used to identify body mass index (BMI) z-score trajectories from birth to age 6 years in 994 children from a prospective mother–offspring cohort (Chinese, Indian and Malay ethnicities) based in Singapore. We evaluated the early-life determinants of the trajectories as well as their associations with cardiometabolic risk markers at age 6 years.

Results

Five BMI z-score trajectory patterns were identified, three within the healthy weight range, alongside early-acceleration and late-acceleration obesogenic trajectories. The early-acceleration pattern was characterized by elevated fetal abdominal circumference growth velocity, BMI acceleration immediately after birth and crossing of the obesity threshold by age 2 years. The late-acceleration pattern had normal fetal growth and BMI acceleration after infancy, and approached the obesity threshold by age 6 years. Abdominal fat, liver fat, insulin resistance and odds of pre-hypertension/hypertension were elevated in both groups. Indian ethnicity, high pre-pregnancy BMI, high polygenic risk scores for obesity and shorter breastfeeding duration were common risk factors for both groups. Malay ethnicity and low maternal educational attainment were uniquely associated with early BMI acceleration, whereas nulliparity and obesogenic eating behaviours in early childhood were uniquely associated with late BMI acceleration.

Conclusion

BMI acceleration starting immediately after birth or after infancy were both linked to early cardiometabolic alterations. The determinants of these trajectories may be useful for developing early risk stratification and intervention approaches to counteract metabolic adversities linked to childhood obesity.
The US Food and Drug Administration Sentinel System: a national resource for a learning health system
Authors: Brown Jeffrey S , Mendelsohn Aaron B , Nam Young Hee , Maro Judith C , Cocoros Noelle M , Rodriguez-Watson Carla , Lockhart Catherine M , Platt Richard , Ball Robert , Dal Pan Gerald J , Toh Sengwee
Published: September 2022

The US Food and Drug Administration (FDA) created the Sentinel System in response to a requirement in the FDA Amendments Act of 2007 that the agency establish a system for monitoring risks associated with drug and biologic products using data from disparate sources. The Sentinel System has completed hundreds of analyses, including many that have directly informed regulatory decisions. The Sentinel System also was designed to support a national infrastructure for a learning health system. Sentinel governance and guiding principles were designed to facilitate Sentinel’s role as a national resource. The Sentinel System infrastructure now supports multiple non-FDA projects for stakeholders ranging from regulated industry to other federal agencies, international regulators, and academics. The Sentinel System is a working example of a learning health system that is expanding with the potential to create a global learning health system that can support medical product safety assessments and other research.
Examining the impact of sex differences and the COVID-19 pandemic on health and health care: findings from a national cross-sectional study
Authors: Ye Jiancheng , Ren Zhimei
Published: September 2022

Objective

To examine the association of the coronavirus disease 2019 (COVID-19) pandemic, the association of sex, and the joint association of sex and the COVID-19 pandemic with health communication, physical activity, mental health, and behavioral health.

Materials and Methods

We drew data from the National Cancer Institute's 2020 Health Information National Trends Survey. We described and compared the characteristics of social determinants of health, physical activity, mental health, alcohol use, patterns of social networking service use, and health information data sharing. Analyses were weighted to provide nationally representative estimates. Multivariate models (multiple linear regression, multiple logistic regression, and multinomial logistic model) were used to assess the sole and joint association with sex and pandemic. In addition, we applied the Bonferroni correction to adjust P values to decrease the risks of type I errors when making multiple statistical tests.

Results

Females were more likely to use mobile health and health communication technologies than males, and the difference increased after the pandemic. The association between sex and mental health was significant after the COVID-19 pandemic. Females were more likely to experience depression or anxiety disorders. Both males and females had a slight decrease in terms of the quantity and intensity of physical activity and females were less likely to perform moderate exercise and strength training regularly. Males were likely to drink more alcohol than females.

Conclusion

The COVID-19 pandemic amplifies the differences between males and females in health communication, physical activity, mental health, and behavioral health. Intersectional analyses of sex are integral to addressing issues that arise and mitigating the exacerbation of inequities. Responses to the pandemic should consider diverse perspectives, including sex and gender.
Waste, Fertilising Product, or Something Else? EU Regulation of Biochar
Authors: Štrubelj Luka
Published: September 2022

The Intergovernmental Panel on Climate Change Sixth Assessment Report (report) on mitigation of climate change brought greenhouse gas removals (GGRs) under the spotlight. The report relied on the use of GGRs in all models suggesting how to comply with the Paris Agreement’s temperature targets. The EU has adopted specific legislation to address one of the more technologically mature GGR methodologies—biochar—and its waste status dilemma. Here, biochar is analysed in more detail, focusing on the EU waste regime and the potential absolution of biochar from EU’s waste obligations. Additionally, the recently enacted Fertilising Products Regulation (EU/2019/1009) is investigated, and its approach to label biochar a fertilising product. Ultimately, this study identifies regulatory inconsistencies and shortfalls of EU law as pertains to biochar’s waste status, and recognises the need to establish a more comprehensive regulatory treatment of biochar that acknowledges its multifaceted nature, including helping the EU, and its member states to reach net zero.
Emerging hybrid networks of verification, accountability, and institutional resilience: the U.S. Capitol Riot and the work of open-source investigation
Authors: Reese Stephen D , Chen Bin
Published: September 2022

The violent spectacle of the January 6, 2021, U.S. Capitol riot provides a case study of how online open-source investigation helped identify members of the mob and provide deeper understanding of the day’s events. Considering this form of investigation as an emerging network for the hybrid institution of journalism, an assemblage extending beyond the newsroom, this study takes a mixed-method, networked ethnography approach to map out this open-source space. Using a network analysis of open-source investigators based on Twitter data shows that the recently emerged Bellingcat organization and similar open-source groups serve a liaison function, bridging professional journalists and largely anonymous citizen “sleuthers.” Using this network as a guide, depth interviews were conducted with key participants, showing that the community was organized around an accountability ethos and a methodology of verification. We argue that this interlocking network has potential to strengthen the resilience of the journalistic institution, build citizen trust and resist politicized historical revisionism.
Mixed epithelial and stromal tumor—adult cystic nephroma of the kidney: a case report with immunohistochemical analysis
Authors: Karasavvidou Foteini , Mitrakas Lampros , Tzika Styliani , Zachos Ioannis , Anagnostou Athanasios , Tzortzis Vassilios
Published: September 2022

The mixed epithelial and stromal tumor family of kidney contain neoplasms with biphasic epithelial and stromal component. According to the 2016 World Health Organization Classification, they encompasses a spectrum of tumors ranging from predominantly cystic tumors (adult cystic nephroma) to tumors that are variably solid (Mixed epithelial and stromal tumor-MESTs). We present the case of a 20-year-old woman with an adult cystic nephroma which was verified by immunohistochemical examination.