bluuebunny/crossref_metadata_2025 huggingface dataset:
Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats (
Neotoma
spp.)
Authors: Weinstein Sara B. , Martínez-Mota Rodolfo , Stapleton Tess E. , Klure Dylan M. , Greenhalgh Robert , Orr Teri J. , Dale Colin , Kohl Kevin D. , Dearing M. Denise
Published: November 2021

Significance

Understanding the factors that sculpt gut microbial communities in mammals is of great interest. Here, we studied a diverse clade of herbivorous rodents (woodrats,
Neotoma
) with variable but well-characterized diets and habitats to quantify the relative contributions of host genetics, geography, and diet, alongside neutral processes, in structuring the gut microbiome under natural and controlled conditions. While diet and geography made significant contributions to microbiome structure, host phylogeny explained the greatest proportion of observed variation. Provision of a common diet in captivity altered natural microbial communities, with communities from different species varying in their resistance to this perturbation. Captivity increased the amount of variation explained by host phylogeny, further emphasizing the extent to which host genetics structure mammalian microbiomes.
The use of smallwords in the speech of German learners of English
Authors: Rosen Anna
Published: November 2021

Based on data from the German component of LINDSEI and two native speaker corpora, this study investigates the consequences of language learning in an instructional setting versus additional natural exposure for the use of 18 fluency-enhancing smallwords. It thus complements previous studies of selected discourse markers in German learner English and offers a more in-depth analysis of individual differences in advanced learners’ speech in terms of frequency and appropriateness of use. Adding to earlier research, which has found that exposure to natural input is clearly beneficial to a more native-like use of discourse markers, the results of the present study also suggest that smallwords are teachable and that teaching in this area needs to be made more efficient.
Integrating corpus literacy into language teacher education
Authors: Callies Marcus
Published: November 2021

Despite the increasing popularization and availability of corpus tools and resources, the practice of English language teaching still seems to be only marginally affected by the corpus-linguistic turn, because comparatively few teachers were trained in corpus linguistics and use corpora or corpus software regularly themselves (Mukherjee 2004; Römer 2011). This chapter first reports on a recent survey that updates and largely confirms Mukherjee’s (2004) findings. It is argued that while university students of modern languages are increasingly familiarized with the research-based use of corpora in linguistic content classes, this research perspective is not sufficiently translated into a teaching perspective for corpora to be considered a useful addition to the toolbox of language teachers. The chapter then reports on the integration of corpus linguistics into the curriculum for English language teacher students by exposing them to the use of corpora and corpus methods from a researcher’s, teacher’s and learner’s perspective.
Fabrication and calibration of nanostructured vanadium-doped ZnO-based micromachined sensor with superior sensitive for underwater acoustic measurement
Authors: Gao Wei , Zhang Yu , Ma Binghe , Luo Jian , Deng Jinjun
Published: November 2021

A high-performance micromachined piezoelectric sensor based nanostructured vanadium-doped zinc oxide (ZnO) film with air-backing has been developed and characterized for underwater acoustic application. The sensing cell with a low foot-print of 2.0 mm × 2.0 mm is fabricated by Micro electro mechanical systems (MEMS) technology using a ZnO-on-silicon-on-insulator process platform. An optimal ratio of piezoelectric coefficient to the relative permittivity is obtained about 6.3 in the Zn0.98V0.02O sensing cell, improving by an order of magnitude compared with other notable piezoelectric films, plays a mainly dominant role in the enhanced piezoelectric response. Calibrations in the standard underwater instrument have demonstrated that the presented sensor could achieve an acoustic pressure sensitivity of −165 ± 2 dB (1 V μPa−1) over a bandwidth 10 Hz–10 kHz, outperforming the same kind of reported devices. The maximum non-linearity is no more than 0.3%, the sensitivity variation is no more than ±0.7 dB in the temperature range from 10 °C to 50 °C, indicating a better stability and higher reliability. The proposed sensor with a superior acoustic sensitivity gives a great application potential in underwater acoustic measurements.
Limit theorems for sums of products of consecutive partial quotients of continued fractions
Authors: Hu Hui , Hussain Mumtaz , Yu Yueli
Published: November 2021

Let [a
1(x), a
2(x), …, a

n
(x), …] be the continued fraction expansion of an irrational number x ∈ (0, 1). The study of the growth rate of the product of consecutive partial quotients a

n
(x)a

n+1(x) is associated with the improvements to Dirichlet’s theorem (1842). We establish both the weak and strong laws of large numbers for the partial sums

S

n

(

x

)

=

∑

i
=
1

n

a

i

(

x

)

a

i
+
1

(

x

)

as well as, from a multifractal analysis point of view, investigate its increasing rate. Specifically, we prove the following results:

• For any ϵ > 0, the Lebesgue measure of the set

x
∈

(

0
,
1

)

:

S

n

(

x

)

n

log

2

n

−

1

2

log

2

⩾
ϵ

tends to zero as n to infinity.

• For Lebesgue almost all x ∈ (0, 1),

lim

n
→
∞

S

n

(

x

)

−

max

1
⩽
i
⩽
n

a

i

(

x

)

a

i
+
1

(

x

)

n

log

2

n

=

1

2

log

2

.

• The Hausdorff dimension of the set

E

(

ϕ

)

≔

x
∈

(

0
,
1

)

:

lim

n
→
∞

S

n

(

x

)

ϕ

(

n

)

=
1

is determined for a range of increasing functions

ϕ
:
N
→

R

+

.
An adaptive spot placement method on Cartesian grid for pencil beam scanning proton therapy
Authors: Lin Bowen , Fu Shujun , Lin Yuting , Rotondo Ronny L , Huang Weizhang , Li Harold H , Chen Ronald C , Gao Hao
Published: November 2021

Pencil beam scanning proton radiotherapy (RT) offers flexible proton spot placement near treatment targets for delivering tumoricidal radiation dose to tumor targets while sparing organs-at-risk. Currently the spot placement is mostly based on a non-adaptive sampling (NS) strategy on a Cartesian grid. However, the spot density or spacing during NS is a constant for the Cartesian grid that is independent of the geometry of tumor targets, and thus can be suboptimal in terms of plan quality (e.g. target dose conformality) and delivery efficiency (e.g. number of spots). This work develops an adaptive sampling (AS) spot placement method on the Cartesian grid that fully accounts for the geometry of tumor targets. Compared with NS, AS places (1) a relatively fine grid of spots at the boundary of tumor targets to account for the geometry of tumor targets and treatment uncertainties (setup and range uncertainty) for improving dose conformality, and (2) a relatively coarse grid of spots in the interior of tumor targets to reduce the number of spots for improving delivery efficiency and robustness to the minimum-minitor-unit (MMU) constraint. The results demonstrate that (1) AS achieved comparable plan quality with NS for regular MMU and substantially improved plan quality from NS for large MMU, using merely about 10% of spots from NS, where AS was derived from the same Cartesian grid as NS; (2) on the other hand, with similar number of spots, AS had better plan quality than NS consistently for regular and large MMU.
Deep learning-based 3D in vivo dose reconstruction with an electronic portal imaging device for magnetic resonance-linear accelerators: a proof of concept study
Authors: Li Yongbao , Xiao Fan , Liu Biaoshui , Qi Mengke , Lu Xingyu , Cai Jiajun , Zhou Linghong , Song Ting
Published: November 2021

Objective. To develop a novel deep learning-based 3D in vivo dose reconstruction framework with an electronic portal imaging device (EPID) for magnetic resonance-linear accelerators (MR-LINACs). Approach. The proposed method directly back-projected 2D portal dose into 3D patient coarse dose, which bypassed the complicated patient-to-EPID scatter estimation step used in conventional methods. A pre-trained convolutional neural network (CNN) was then employed to map the coarse dose to the final accurate dose. The electron return effect caused by the magnetic field was captured with the CNN model. Patient dose and portal dose datasets were synchronously generated with Monte Carlo simulation for 96 patients (78 cases for training and validation and 18 cases for testing) treated with fixed-beam intensity-modulated radiotherapy in four different tumor sites, including the brain, nasopharynx, lung, and rectum. Beam angles from the training dataset were further rotated 2–3 times, and doses were recalculated to augment the datasets. Results. The comparison between reconstructed doses and MC ground truth doses showed mean absolute errors <0.88% for all tumor sites. The averaged 3D γ-passing rates (3%, 2 mm) were 97.42%±2.66% (brain), 98.53%±0.95% (nasopharynx), 99.41%±0.46% (lung), and 98.63%±1.01% (rectum). The dose volume histograms and indices also showed good consistency. The average dose reconstruction time, including back projection and CNN dose mapping, was less than 3 s for each individual beam. Significance. The proposed method can be potentially used for accurate and fast 3D dosimetric verification for online adaptive radiotherapy using MR-LINACs.
Effect of voltage polarity and supply frequency on the properties of plasma contacting liquid electrodes and gold nanoparticle synthesis
Authors: Thai Van-Phuoc , Saito Nobuo , Nakamura Tsubasa , Takahashi Kazumasa , Sasaki Toru , Kikuchi Takashi
Published: November 2021

Plasma contacting with liquid (PCL) provides many charged particles and reactive species into the liquid. The difficulty in controlling or selecting each specific species has significantly limited its applications in industry. Here, we present a study on using voltage polarity to regulate the type of charged particles absorbing from the plasma into the liquid. A detailed understanding of the processes at the plasma–liquid interface and electrolysis due to switching in voltage polarity was determined via a visual pH observation, measuring the concentration of H2O2 and solvated electrons. The results indicated that changes in voltage polarity strongly affect the plasma properties, chemical properties and electrolysis process in liquid, and also in the types of reducing species for gold nanoparticle (GNP) synthesis. The results also showed that using a suitable frequency could improve the efficiency of absorption of H2O2 from plasma into the bulk liquid as well as the yield in the production of GNPs. The results provide a way to select desired species from the plasma to be transferred into the liquid for a distinct purpose and to accompany other properties in the system of PCL.
Noisy atomic magnetometry in real time
Authors: Amorós-Binefa Júlia , Kołodyński Jan
Published: November 2021

Continuously monitored atomic spin-ensembles allow, in principle, for real-time sensing of external magnetic fields beyond classical limits. Within the linear-Gaussian regime, thanks to the phenomenon of measurement-induced spin-squeezing, they attain a quantum-enhanced scaling of sensitivity both as a function of time, t, and the number of atoms involved, N. In our work, we rigorously study how such conclusions based on Kalman filtering methods change when inevitable imperfections are taken into account: in the form of collective noise, as well as stochastic fluctuations of the field in time. We prove that even an infinitesimal amount of noise disallows the error to be arbitrarily diminished by simply increasing N, and forces it to eventually follow a classical-like behaviour in t. However, we also demonstrate that, ‘thanks’ to the presence of noise, in most regimes the model based on a homodyne-like continuous measurement actually achieves the ultimate sensitivity allowed by the decoherence, yielding then the optimal quantum-enhancement. We are able to do so by constructing a noise-induced lower bound on the error that stems from a general method of classically simulating a noisy quantum evolution, during which the stochastic parameter to be estimated—here, the magnetic field—is encoded. The method naturally extends to schemes beyond the linear-Gaussian regime, in particular, also to ones involving feedback or active control.
Who’s Silenced? Who’s Not?
Authors: Allen Chadwick
Published: November 2021

This essay juxtaposes two stories of Indigenous-settler “first contact” in the twenty-first century. One describes an event of community-based research in coastal Maine in summer 2000; the other describes an event of community-based confrontation at the Serpent Mound earthworks site in Ohio on the winter solstice 2020. The stories overlap and intersect in surprising ways, and they prompt unresolved questions about the function of “American” literary criticism at the present time: What actually happens when Indigenous voices enter the structures of the settler academy? Who benefits, and whose interests are ultimately served? Within current conventions, is it possible to center Indigenous knowledges and research agendas, to address the pressing concerns of Indigenous communities? And what does it mean to pursue scholarship ostensibly focused on aspects of Indigenous cultures within social and political contexts that continue to allow or even to promote the settler erasure of Indigenous claims—not only to distant or recent histories but to ongoing presence? Is it enough for academic institutions to assume a neutral stance on such issues? Or are “Americanist” scholars obligated to pursue more rigorous forms of disrupting settler business as usual?
Corticofugal modulation of temporal and rate representations in the inferior colliculus of the awake marmoset
Authors: Wang Xiaohui , Zhang Yuanqing , Bai Siyi , Qi Runze , Sun Hao , Li Rui , Zhu Lin , Cao Xinyuan , Jia Guoqiang , Li Xinjian , Gao Lixia
Published: November 2021

Temporal processing is crucial for auditory perception and cognition, especially for communication sounds. Previous studies have shown that the auditory cortex and the thalamus use temporal and rate representations to encode slowly and rapidly changing time-varying sounds. However, how the primate inferior colliculus (IC) encodes time-varying sounds at the millisecond scale remains unclear. In this study, we investigated the temporal processing by IC neurons in awake marmosets to Gaussian click trains with varying interclick intervals (2–100 ms). Strikingly, we found that 28% of IC neurons exhibited rate representation with nonsynchronized responses, which is in sharp contrast to the current view that the IC only uses a temporal representation to encode time-varying signals. Moreover, IC neurons with rate representation exhibited response properties distinct from those with temporal representation. We further demonstrated that reversible inactivation of the primary auditory cortex modulated 17% of the stimulus-synchronized responses and 21% of the nonsynchronized responses of IC neurons, revealing that cortico-colliculus projections play a role, but not a crucial one, in temporal processing in the IC. This study has significantly advanced our understanding of temporal processing in the IC of awake animals and provides new insights into temporal processing from the midbrain to the cortex.
Randomized Trial of Metformin With Anti-Tuberculosis Drugs for Early Sputum Conversion in Adults With Pulmonary Tuberculosis
Authors: Padmapriydarsini Chandrasekaran , Mamulwar Megha , Mohan Anant , Shanmugam Prema , Gomathy N S , Mane Aarti , Singh Urvashi B , Pavankumar Nathella , Kadam Abhijeet , Kumar Hemanth , Suresh Chandra , Reddy Devaraju , Devi Poornaganga , Ramesh P M , Sekar Lakshmanan , Jawahar Shaheed , Shandil R K , Singh Manjula , Menon Jaykumar , Guleria Randeep
Published: November 2021

Background

Metformin, by reducing intracellular Mycobacterium tuberculosis growth, can be considered an adjunctive therapy to anti-tuberculosis treatment (ATT). We determined whether metformin with standard ATT reduces time to sputum culture conversion and tissue inflammation in adults with pulmonary tuberculosis (PTB).

Methods

In a randomized, 8-week, clinical trial, newly diagnosed, culture-positive PTB patients were randomized to standard ATT (HREZ = control arm) or standard ATT plus daily 1000 mg metformin (MET-HREZ = Metformin with Rifampicin [METRIF] arm) for 8 weeks during 2018–2020 at 5 sites in India. The primary end point was time to sputum culture conversion by liquid culture during 8 weeks of ATT. Plasma inflammatory markers were estimated in a subset. A Cox proportional hazard model was used to estimate time and predictors of culture conversion.

Results

Of the 322 patients randomized, 239 (74%) were male, and 212 (66%) had bilateral disease on chest radiograph with 54 (18%) showing cavitation. The median time to sputum culture conversion by liquid culture was 42 days in the METRIF arm and 41 days in the control arm (hazard ratio, 0.8; 95% confidence interval [CI], .624–1.019). After 8 weeks of ATT, cavitary lesions on X-ray (7, 5.3% vs 18, 12.9%; relative risk, 0.42; 95% CI, .18–.96; P = .041) and inflammatory markers were significantly lower in the METRIF arm. Higher body mass index and lower sputum smear grading were associated with faster sputum culture conversion.

Conclusions

The addition of metformin to standard ATT did not hasten sputum culture conversion but diminished excess inflammation, thus reducing lung tissue damage as seen by faster clearance on X-ray and reduced inflammatory markers.

Clinical Trials Registration

Clinical Trial Registry of India (CTRI/2018/01/011176)
Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Virus in Symptomatic Coronavirus Disease 2019 (COVID-19) Outpatients: Host, Disease, and Viral Correlates
Authors: Mollan Katie R , Eron Joseph J , Krajewski Taylor J , Painter Wendy , Duke Elizabeth R , Morse Caryn G , Goecker Erin A , Premkumar Lakshmanane , Wolfe Cameron R , Szewczyk Laura J , Alabanza Paul L , Loftis Amy James , Degli-Angeli Emily J , Brown Ariane J , Dragavon Joan A , Won John J , Keys Jessica , Hudgens Michael G , Fang Lei , Wohl David A , Cohen Myron S , Baric Ralph S , Coombs Robert W , Sheahan Timothy P , Fischer William A
Published: November 2021

Background

Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectious virus isolation in outpatients with coronavirus disease 2019 (COVID-19) has been associated with viral RNA levels and symptom duration, little is known about the host, disease, and viral determinants of infectious virus detection.

Methods

COVID-19 adult outpatients were enrolled within 7 days of symptom onset. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay.

Results

Among 204 participants with mild-to-moderate symptomatic COVID-19, the median nasopharyngeal viral RNA was 6.5 (interquartile range [IQR] 4.7–7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies (immunoglobulin (Ig)A, IgM, IgG, and/or total Ig) at baseline. Infectious virus was recovered in 7% of participants with SARS-CoV-2 antibodies compared to 58% of participants without antibodies (prevalence ratio [PR] = 0.12, 95% confidence interval [CI]: .04, .36; P = .00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log10, 95% CI: 2.2, 3.0; P < .0001) and fewer days since symptom onset (PR = 0.79, 95% CI: .71, .88 per day; P < .0001).

Conclusions

The presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus. Seropositivity and viral RNA levels are likely more reliable markers of infectious virus clearance than subjective measure of COVID-19 symptom duration. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion.

Clinical Trials Registration

NCT04405570.
Standardized Definitions of In Utero Human Immunodeficiency Virus and Antiretroviral Drug Exposure Among Children
Authors: Slogrove Amy L , Burmen Barbara , Davies Mary Ann , Edmonds Andrew , Abrams Elaine J , Chadwick Ellen G , Goetghebuer Tessa , Mofenson Lynne M , Paul Mary E , Thorne Claire , Williams Paige L , Vicari Marissa , Powis Kathleen M
Published: November 2021

In countries with high human immunodeficiency virus (HIV) prevalence, up to 30% of pregnant women are living with HIV, with fetal exposure to both HIV and antiretroviral therapy during pregnancy. In addition, pregnant women without HIV but at high risk of HIV acquisition are increasingly receiving HIV preexposure antiretroviral prophylaxis (PrEP). Investments are being made to establish and follow cohorts of children to evaluate the long-term effects of in utero HIV and antiretroviral exposure. Agreement on a key set of definitions for relevant exposures and outcomes is important both for interpreting individual study results and for comparisons across cohorts. Harmonized definitions of in utero HIV and antiretroviral drug (maternal treatment or PrEP) exposure will also facilitate improved classification of these exposures in future observational studies and clinical trials. The proposed definitions offer a uniform approach to facilitate the consistent description and estimation of effects of HIV and antiretroviral exposures on key child health outcomes.
Blood microbiome is associated with changes in portal hypertension after successful direct-acting antiviral therapy in patients with HCV-related cirrhosis
Authors: Virseda-Berdices Ana , Brochado-Kith Oscar , Díez Cristina , Hontañon Victor , Berenguer Juan , González-García Juan , Rojo David , Fernández-Rodríguez Amanda , Ibañez-Samaniego Luis , Llop-Herrera Elba , Olveira Antonio , Perez-Latorre Leire , Barbas Coral , Rava Marta , Resino Salvador , Jiménez-Sousa María Angeles
Published: November 2021

Background

Patients with a significant decrease in hepatic venous pressure gradient (HVPG) have a considerable reduction of liver complications and higher survival after HCV eradication.

Objectives

To evaluate the association between the baseline blood microbiome and the changes in HVPG after successful direct-acting antiviral (DAA) therapy in patients with HCV-related cirrhosis.

Methods

We performed a prospective study in 32 cirrhotic patients (21 HIV positive) with clinically significant portal hypertension (HVPG ≥10 mmHg). Patients were assessed at baseline and 48 weeks after HCV treatment completion. The clinical endpoint was a decrease in HVPG of ≥20% or HVPG <12 mmHg at the end of follow-up. Bacterial 16S ribosomal DNA was sequenced using MiSeq Illumina technology, inflammatory plasma biomarkers were investigated using ProcartaPlex immunoassays and the metabolome was investigated using GC-MS.

Results

During the follow-up, 47% of patients reached the clinical endpoint. At baseline, those patients had a higher relative abundance of Corynebacteriales and Diplorickettsiales order, Diplorickettsiaceae family, Corynebacterium and Aquicella genus and Undibacterium parvum species organisms and a lower relative abundance of Oceanospirillales and Rhodospirillales order, Halomonadaceae family and Massilia genus organisms compared with those who did not achieve the clinical endpoint according to the LEfSe algorithm. Corynebacteriales and Massilia were consistently found within the 10 bacterial taxa with the highest differential abundance between groups. Additionally, the relative abundance of the Corynebacteriales order was inversely correlated with IFN-γ, IL-17A and TNF-α levels and the Massilia genus with glycerol and lauric acid.

Conclusions

Baseline-specific bacterial taxa are related to an HVPG decrease in patients with HCV-related cirrhosis after successful DAA therapy.
Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)
Authors: Huang Yi , Escalona Merly , Morrison Glen , Marimuthu Mohan P A , Nguyen Oanh , Toffelmier Erin , Shaffer H Bradley , Litt Amy
Published: November 2021

Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.
NLR1 is a strong candidate for the Rm3 dominant green peach aphid (Myzus persicae) resistance trait in peach
Authors: Pan Lei , Lu Zhenhua , Yan Lele , Zeng Wenfang , Shen Zhijun , Yu Mingliang , Bu Lulu , Cui Guochao , Niu Liang , Wang Zhiqiang
Published: November 2021

The green peach aphid (GPA), Myzus persicae, is a polyphagous, sap-sucking aphid and a vector of many plant viruses. In peach, Prunus persica, three individual dominant GPA resistance loci have been genetically defined (Rm1–3), but knowledge of the underlying genes is limited. In this study, we focused on the Rm3 locus. Bulk segregant analysis (BSA) mapping in segregating progeny populations delimited Rm3 to an interval spanning 160 kb containing 21 genes on chromosome 1. RNA-seq data provided no evidence of candidate genes, but chromosomal structural variations were predicted around a nucleotide-binding site–leucine-rich repeat (NLR) gene (ppa000596m) within the Rm3 fine-mapping interval. Following bacterial artificial chromosome (BAC) library construction for a GPA-resistant peach cultivar and the sequencing of three target BAC clones, a chromosomal structural variation encompassing two novel TIR–NLR-class disease resistance (R) protein-coding genes was identified, and the expressed NLR gene (NLR1) was identified as a candidate for M. persicae resistance. Consistent with its proposed role in controlling GPA resistance, NLR1 was only expressed in the leaves of resistant peach phenotypes. A molecular marker that was designed based on the NLR1 sequence co-segregated with the GPA-resistant phenotype in four segregating populations, 162 peach cultivars, and 14 wild relatives, demonstrating the dominant inheritance of the Rm3 locus. Our findings can be exploited to facilitate future breeding for GPA-resistance in peach.
Author verification of Nahj Al-Balagha
Authors: Sarwar Raheem , Mohamed Emad
Published: November 2021

The primary purpose of this article is author verification of the Nahj Al-Balagha, a book attributed to Imam Ali and over which Sunni and Shi’i Muslims are proposing different theories. Given the morphologically complex nature of Arabic, we test whether morphological segmentation, applied to the book and works by the two authors suspected by Sunnis to have authored the texts, can be used for author verification of the Nahj Al-Balagha. Our findings indicate that morphological segmentation may lead to slightly better results than whole words and that regardless of the feature sets, the three sub-corpora cluster into three distinct groups using principal component analysis, hierarchical clustering, multi-dimensional scaling, and bootstrap consensus trees. Supervised classification methods such as Naive Bayes, Support Vector Machines, k Nearest Neighbours, Random Forests, AdaBoost, Bagging, and Decision Trees confirm the same results, which is a clear indication that (1) the book is internally consistent and can thus be attributed to a single person and (2) it was not authored by either of the suspected authors.
SDSS J1451 + 2709 a normal blue quasar but mis-classified as a H ii galaxy in the BPT diagram by flux ratios of narrow emission lines
Authors: Zhang X G
Published: November 2021

In the manuscript, we discuss properties of SDSS J1451 + 2709, a normal blue quasar but mis-classified as a H ii galaxy in the BPT diagram (called as a mis-classified quasar). The emission lines around H α and around H β are well measured by different model functions with broad Balmer lines described by Gaussian or Lorentz functions, in the SDSS spectrum in 2007 and in the KPNO spectrum in 1990. After considering variations of broad emission lines, different model functions lead to different determined fluxes of narrow emission lines, but the different narrow emission line flux ratios lead the SDSS J1451 + 2709 as a H ii galaxy in the BPT diagram. In order to explain the unique properties of the mis-classified quasar SDSS J1451+2709 in the BPT diagram, two methods are proposed, the starforming contributions and compressed NLRs with high electron densities near to critical densities of forbidden emission lines. Unfortunately, the two methods cannot be preferred in the SDSS J1451+2709, further efforts are necessary to find the physical origin of the unique properties of the mis-classified quasar SDSS J1451+2709 in the BPT diagram. Meanwhile, there are not quite different long-term variabilities of SDSS J1451+2709 from the normal quasars. The mis-classified quasar SDSS J1451 + 2709, an extremely unique case or a special case among the normal quasars, could provide further clues on the applications of BPT diagrams to the normal broad line AGN and to narrow emission line objects, indicating part of narrow emission line H ii galaxies actually harbouring central AGN activities.
The dynamical state of massive clumps
Authors: Lu Zu-Jia , Pelkonen Veli-Matti , Juvela Mika , Padoan Paolo , Haugbølle Troels , Nordlund Åke
Published: November 2021

The dynamical state of massive clumps is key to our understanding of the formation of massive stars. In this work, we study the kinematic properties of massive clumps using synthetic observations. We have previously compiled a very large catalogue of synthetic dust-continuum compact sources from our 250 pc, SN-driven, star formation simulation. Here, we compute synthetic $\rm N_{2}H^{+}$ line profiles for a subsample of those sources and compare their properties with the observations and with those of the corresponding three-dimensional (3D) clumps in the simulation. We find that the velocity dispersion of the sources estimated from the $\rm N_{2}H^{+}$ line is a good estimate of that of the 3D clumps, although its correlation with the source size is weaker than the velocity–size correlation of the 3D clumps. The relation between the mass of the 3D clumps, Mmain, and that of the corresponding synthetic sources, MSED, has a large scatter and a slope of 0.5, $M_{\rm main} \propto M_{\rm SED}^{0.5}$, due to uncertainties arising from the observational band-merging procedure and from projection effects along the line of sight. As a result, the virial parameters of the 3D clumps are not correlated with the clump masses, even if a negative correlation is found for the compact sources, and the virial parameter of the most massive sources may significantly underestimate that of the associated clumps.
The Bardeen–Petterson effect in accreting supermassive black hole binaries: disc breaking and critical obliquity
Authors: Nealon Rebecca , Ragusa Enrico , Gerosa Davide , Rosotti Giovanni , Barbieri Riccardo
Published: November 2021

The inspiral of supermassive black hole (BH) binaries in a gas-rich environment is driven by the presence of an accretion disc and viscous interactions tend to align the spin of the BHs with the orbital angular momentum of the disc. Recent work introduced a new iterative approach to describe the alignment process and the resulting non-linear evolution of the surrounding warped accretion disc. Their model predicted that BH spins reach either full alignment or a ‘critical obliquity’ where solutions to the warp equations cease to exist. In this paper, we show that this critical region corresponds to the disc breaking phenomenon, where the disc is disrupted into two or more discrete sections. We use 3D hydrodynamical simulations to (i) recover the predictions of the semi-analytic model and (ii) unveil a richer phenomenology where the disc exhibits either unsuccessful, single and multiple breaks. We additionally identify hydrodynamic effects such as spiral arms that are able to stabilize the disc against breaking beyond criticality. Our results show that when disc breaking occurs, the ability of BHs and disc to align is compromised and in some cases even prevented as the binary inspirals.
Dynamics and habitability of the TESS circumbinary systems TOI-1338 and TIC-172900988
Authors: Georgakarakos Nikolaos
Published: November 2021

Two circumbinary planets have been recently discovered by TESS. The main aim of this work is to explore whether it is possible, besides the discovered circumbinary planet, to have an Earth-like planet within the habitable zone of the system. We carry out numerical simulations over the whole range of the two habitable zones in order to see whether an Earth mass planet can exist there. We find that both systems seem to be able to host an additional planet in their habitable zone. We construct dynamically informed habitable zones and we find that a large percentage of the habitable zone can be suitable for a planet to retain liquid water on its surface no matter what its orbital evolution will be. Moreover, we investigate the possibility to detect an Earth-like planet in the habitable zone of the two systems. We find that for both systems, if such a planet existed, the radial velocity and astrometry signals would be rather small to be detected by our current instruments. Some discussion is also made for the dynamical evolution of the existing planet.
Probing the origin of 4FGL J0822.8–4207: cosmic ray illumination from the SNR Puppis A and the Herbig–Haro object HH219
Authors: Araya M , Gutiérrez L , Kerby S
Published: November 2021

4FGL J0822.8–4207 is a point source found in the 4FGL-DR2 catalogue by the gamma-ray observatory Fermi-LAT and has no known association. We carry out X-ray observations of 4FGL J0822.8–4207 to help understand its nature. We explore two scenarios for the origin of 4FGL J0822.8–4207 . In the first case, we study the possibility that cosmic rays from the supernova remnant (SNR) Puppis A, seen nearby in the sky, reach the dense gas at the location of the source and produce the gamma-rays through inelastic proton–proton collisions. We apply a standard model for particle diffusion in the interstellar medium and derive the required physical parameters. We find that this scenario for the gamma-rays is possible if the gas is located at a distance that is not higher than ∼40 pc from Puppis A, unless the SNR is older than 7 kyr or the diffusion coefficient is higher than typical Galactic values, and relatively low-energy cosmic rays are currently escaping from the SNR. In the second scenario, we consider the protostellar jet HH219 as the origin of the GeV source and find the very interesting possibility that particles could be accelerated up to energies of at least several TeV in HH219. This would make this system the first known of its kind to produce gamma-ray emission extending up to hundreds of GeV without any apparent cut-off and an excellent laboratory to study the process of particle acceleration.
Survival and mass growth of cold gas in a turbulent, multiphase medium
Authors: Gronke Max , Oh S Peng , Ji Suoqing , Norman Colin
Published: November 2021

Astrophysical gases are commonly multiphase and highly turbulent. In this work, we investigate the survival and growth of cold gas in such a turbulent, multiphase medium using three-dimensional hydrodynamical simulations. Similar to previous work simulating coherent flow (winds), we find that cold gas survives if the cooling time of the mixed gas is shorter than the Kelvin–Helmholtz time of the cold gas clump (with some weak additional Mach number dependence). However, there are important differences. Near the survival threshold, the long-term evolution is highly stochastic, and subject to the existence of sufficiently large clumps. In a turbulent flow, the cold gas continuously fragments, enhancing its surface area. This leads to exponential mass growth, with a growth time given by the geometric mean of the cooling and the mixing time. The fragmentation process leads to a large number of small droplets which follow a scale-free dN/dm ∝ m−2 mass distribution, and dominate the area covering fraction. Thus, whilst survival depends on the presence of large ‘clouds’, these in turn produce a ‘fog’ of smaller droplets tightly coupled to the hot phase which are probed by absorption line spectroscopy. We show with the aid of Monte Carlo simulations that the simulated mass distribution emerges naturally due to the proportional mass growth and the coagulation of droplets. We discuss the implications of our results for convergence criteria of larger scale simulations and observations of the circumgalactic medium.
A temporal scale to track the spectral transitions in low-mass X-ray binaries
Authors: Sonbas E , Mohamed K , Dhuga K S , Göğüş E
Published: November 2021

The results of a temporal analysis of observations for a sample of nine low-mass X-ray binaries (LMXBs) are presented. Of these sources, five host a neutron star (NS) primary (4U1608−52, Aql X-1, 4U1705−44, GX17+2-, and Cyg X-2), and four host a black hole (BH) (GX339-4, XTE J1859+226, H1743−322, and MAXI J1659−152). The NS group includes three Atolls and two Z-type sources. We utilized archival Proportional Counter Array (PCA)/RXTE data to construct high-resolution light-curves. A wavelet transform of the light curves is deployed to extract a minimal time-scale (MTS) associated with the spectral state of the sources. The MTS, together with the fractional root-mean-square (rms) and hardness ratios, is used to construct RMS–MTS and hardness–MTS diagrams that enable a direct comparison of the evolution of spectral transitions in the target sources. Observations with high fractional rms and high hardness cluster in a broad region occupied jointly by BH and NS sources. For low fractional rms observations, the Atolls exhibit large MTS whereas Z-type sources exhibit small MTS. This new feature raises the possibility of discriminating between these two types of sources. Moreover, in the hardness–MTS plane, BH sources are the sole occupiers of the low-hardness and small-MTS domain thus potentially signalling a unique property for distinguishing BH and NS hosts in LMXBs.
Lenses In VoicE (LIVE): searching for strong gravitational lenses in the VOICE@VST survey using convolutional neural networks
Authors: Gentile Fabrizio , Tortora Crescenzo , Covone Giovanni , Koopmans Léon V E , Spiniello Chiara , Fan Zuhui , Li Rui , Liu Dezi , Napolitano Nicola R , Vaccari Mattia , Fu Liping
Published: November 2021

We present a sample of 16 likely strong gravitational lenses identified in the VST Optical Imaging of the CDFS and ES1 fields (VOICE survey) using convolutional neural networks (CNNs). We train two different CNNs on composite images produced by superimposing simulated gravitational arcs on real Luminous Red Galaxies observed in VOICE. Specifically, the first CNN is trained on single-band images and more easily identifies systems with large Einstein radii, while the second one, trained on composite RGB images, is more accurate in retrieving systems with smaller Einstein radii. We apply both networks to real data from the VOICE survey, taking advantage of the high limiting magnitude (26.1 in the r band) and low PSF FWHM (0.8 arcsec in the r band) of this deep survey. We analyse ∼21 200 images with magr < 21.5, identifying 257 lens candidates. To retrieve a high-confidence sample and to assess the accuracy of our technique, nine of the authors perform a visual inspection. Roughly 75 per cent of the systems are classified as likely lenses by at least one of the authors. Finally, we assemble the LIVE sample (Lenses In VoicE) composed by the 16 systems passing the chosen grading threshold. Three of these candidates show likely lensing features when observed by the Hubble Space Telescope. This work represents a further confirmation of the ability of CNNs to inspect large samples of galaxies searching for gravitational lenses. These algorithms will be crucial to exploit the full scientific potential of forthcoming surveys with the Euclid satellite and the Vera Rubin Observatory.
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process
Authors: Calle García Joan , Guadagno Anna , Paytuvi-Gallart Andreu , Saera-Vila Alfonso , Amoroso Ciro Gianmaria , D’Esposito Daniela , Andolfo Giuseppe , Aiese Cigliano Riccardo , Sanseverino Walter , Ercolano Maria Raffaella
Published: November 2021

The Plant Resistance Genes database (PRGdb; http://prgdb.org/prgdb4/) has been greatly expanded, keeping pace with the increasing amount of available knowledge and data (sequenced proteomes, cloned genes, public analysis data, etc.). The easy-to-use style of the database website has been maintained, while an updated prediction tool, more data and a new section have been added. This new section will contain plant resistance transcriptomic experiments, providing additional easy-to-access experimental information. DRAGO3, the tool for automatic annotation and prediction of plant resistance genes behind PRGdb, has been improved in both accuracy and sensitivity, leading to more reliable predictions. PRGdb offers 199 reference resistance genes and 586.652 putative resistance genes from 182 sequenced proteomes. Compared to the previous release, PRGdb 4.0 has increased the number of reference resistance genes from 153 to 199, the number of putative resistance genes from 177K from 76 proteomes to 586K from 182 sequenced proteomes. A new section has been created that collects plant-pathogen transcriptomic data for five species of agricultural interest. Thereby, with these improvements and data expansions, PRGdb 4.0 aims to serve as a reference to the plant scientific community and breeders worldwide, helping to further study plant resistance mechanisms that contribute to fighting pathogens.
Heterozygous COL4A3/COL4A4 mutations: the hidden part of the iceberg?
Authors: Mastrangelo Antonio , Madeira Catarina , Castorina Pierangela , Giani Marisa , Montini Giovanni
Published: November 2021

Background

Single mutations in COL4A3/COL4A4 genes have been described in patients with autosomal dominant Alport syndrome and thin basement membrane nephropathy, without a shared definition of these patients within the medical community. We aimed to better categorize this clinical entity by examining clinical manifestations, family history, pathological features and genetics.

Methods

We retrospectively analyzed patients with causative heterozygous COL4A3/COL4A4 mutations referred to us between 1990 and 2019. Index cases were defined as children who were the first to be diagnosed in their families.

Results

The study included 24 index cases and 29 affected relatives, belonging to 25 families with a heterozygous mutation in the COL4A3/COL4A4 genes. During the follow-up, nine patients developed proteinuria [median age 15.7 years (range 5.6–33)], six at clinical diagnosis and four with progression toward chronic kidney disease (CKD) (three required kidney replacement therapy at 25, 45 and 53 years and one had CKD Stage 2 at 46 years). Extrarenal involvement was observed in 24.5% of patients. Hematuria was transmitted in consecutive generations, while CKD was reported in nonconsecutive generations of 11 families [median age 53 years (range 16–80)]. Seventeen patients (32%) underwent kidney biopsy: findings were consistent with Alport syndrome in 12 cases and with thin basement membrane nephropathy in 5 cases.

Conclusions

Despite the benign course for these patients described in the literature, a significant percentage is at risk for disease progression. Consequently, we suggest that the assessment of these patients must take into account family history, genetic analysis and pathologic findings. After comparison with the literature, our data suggest that a different definition for Alport syndrome must be considered.
Healthcare utilization and economic burden in systemic sclerosis: a systematic review
Authors: Martin Calderon Leonardo , Chaudhary Mitali , Pope Janet E
Published: November 2021

Objective

Systemic sclerosis (SSc) is characterized by vasculopathy, fibrosis of skin and internal organs, and autoimmunity with complications including interstitial lung disease, pulmonary hypertension, and digital ulcers with substantial morbidity and disability. Patients with SSc may require considerable healthcare resources with economic impact. The purpose of this systematic review was to provide a narrative synthesis of the economic impact and healthcare resource utilization associated with SSc.

Methods

MEDLINE and EMBASE were searched from inception to 20 January 2021. Studies were included if they provided information regarding the total, direct and indirect cost of SSc. The cost of SSc subtypes and associated complications was determined. Risk of bias assessments through the Joanna Briggs Institute cross-sectional and case series checklists, and the Newcastle–Ottawa Cohort and Case–Control study scales were performed. A narrative synthesis of included studies was planned.

Results

The number of publications retrieved was 1778, of which 34 were included representing 20 cross-sectional, 11 cohort, and three case–control studies. Studies used various methods of calculating cost including prevalence-based cost-of-illness approach and health resource units cost analysis. Overall SSc total annual cost ranged from USD $14 959 to $23 268 in USA, CAD $10 673 to $18 453 in Canada, €4607 to €30 797 in Europe, and AUD $7060 to $11 607 in Oceania. Annual cost for SSc-associated interstitial lung disease and pulmonary hypertension was USD $31 285–55 446 and $44 454–63 320, respectively.

Conclusion

Cost-calculation methodology varied greatly between included studies. SSc represents a significant patient and health resource economic burden. SSc-associated complications increase economic burden and are variable depending on geographical location and access.