bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of driver charge on wakefield characteristics in a plasma accelerator probed by femtosecond shadowgraphy
Authors: Schöbel Susanne , Pausch Richard , Chang Yen-Yu , Corde Sébastien , Couperus Cabadağ Jurjen , Debus Alexander , Ding Hao , Döpp Andreas , Foerster F Moritz , Gilljohann Max , Haberstroh Florian , Heinemann Thomas , Hidding Bernhard , Karsch Stefan , Köhler Alexander , Kononenko Olena , Kurz Thomas , Nutter Alastair , Steiniger Klaus , Ufer Patrick , Martinez de la Ossa Alberto , Schramm Ulrich , Irman Arie
Published: August 2022

We report on experimental investigations of plasma wave structures in a plasma wakefield acceleration (PWFA) stage which is driven by electron beams from a preceding laser plasma accelerator. Femtosecond optical probing is utilized to allow for direct visualization of the plasma dynamics inside the target. We compare two regimes in which the driver propagates either through an initially neutral gas, or a preformed plasma. In the first case, plasma waves are observed that quickly damp after a few oscillations and are located within a narrow plasma channel ionized by the driver, having about the same transverse size as the plasma wakefield cavities. In contrast, for the latter robust cavities are recorded sustained over many periods. Furthermore, here an elongation of the first cavity is measured, which becomes stronger with increasing driver beam charge. Since the cavity length is linked to the maximum accelerating field strength, this elongation implies an increased field strength. This observation is supported by 3D particle-in-cell simulations performed with PIConGPU. This work can be extended for the investigation of driver depletion by probing at different propagation distances inside the plasma, which is essential for the development of high energy efficiency PWFAs.
Gate fidelity, dephasing, and ‘magic’ trapping of optically trapped neutral atom
Authors: Yang Pengfei , Li Gang , Wang Zhihui , Zhang Pengfei , Zhang Tiancai
Published: August 2022

The fidelity of the gate operation and the coherence time of neutral atoms trapped in an optical dipole trap are figures of merit for the applications. The motion of the trapped atom is one of the key factors which influences the gate fidelity and coherence time. The motion has been considered as a classical oscillator in analyzing the influence. Here we treat the motion of the atom as a quantum oscillator. The population on the vibrational states of the atom are considered in analyzing the gate fidelity and decoherence. We show that the fidelity of a coherent rotation gate is dramatically limited by the temperature of a thermally trapped atom. We also show that the dephasing between the two hyperfine states due to the thermal motion of the atom could rephase naturally if the differential frequency shift is stable and the vibrational states do not change. The decoherence due to the fluctuations of the trap laser intensity is also discussed. Both the gate fidelity and coherence time can be dramatically enhanced by cooling the atom into vibrational ground states and/or by using a blue-detuned trap. More importantly, we propose a ‘magic’ trapping condition by preparing the atom into specific vibrational states.
Swampland dS conjecture in mimetic f(R, T) gravity
Authors: Noori Gashti S , Sadeghi J , Upadhyay S , Alipour M R
Published: August 2022

In this paper, we study a theory of gravity called mimetic f(R, T) in the presence of swampland dS conjecture. For this purpose, we introduce several inflation solutions of the Hubble parameter H(N) from f(R, T) = R + δ
T gravity model, in which R is Ricci scalar, and T denotes the trace of the energy–momentum tensor. Also, δ and N are the free parameter and a number of e-fold, respectively. Then we calculate quantities such as potential, Lagrange multiplier, slow-roll, and some cosmological parameters such as n

s
and r. Then we challenge the mentioned inflationary model from the swampland dS conjecture. We discuss the stability of the model and investigate the compatibility or incompatibility of this inflationary scenario with the latest Planck observable data.
The association of ambient temperature with depression in middle-aged and elderly people: a multicenter prospective repeat survey study in China
Authors: Jiang Ning , Ban Jie , Guo Yuming , Zhang Yi
Published: August 2022

Depression is the most common mental illness and contributes to a huge disease burden. However, few studies have examined the association between ambient temperature on depression. In this study, a three times repeated survey was conducted in 24 communities nationwide in China, through a face-to-face interview. Weather and air pollution data were collected from the European Centre for Medium-Range Weather Forecasts and the China National Environmental Monitoring Center, respectively. Depression was diagnosed by the 9-item Patient Health Questionnaire and generalized estimation equation models were used to examine the effects of ambient temperature on depression. Finally, 3811 individuals participated in the baseline survey, and a total of 9814 visits were completed during the three repeated survey periods. The relationship between ambient temperature and depression was linear. After adjusting for potential confounders, we observed that every 5 °C reduction in the two-week moving average temperature was associated with a 15.6% increase in depression (odds ratio (OR) = 1.156, 95% confidence interval (CI): 1.009–1.324, P= 0.038). Subgroup analyses showed that people aged ⩾65 years (OR = 1.269, 95% CI: 1.082–1.489, P< 0.01) were more vulnerable than those aged <65 years (OR = 0.873, 95% CI: 0.703–1.084, P= 0.22), while women (OR = 1.250, 95% CI: 1.054–1.483, P < 0.01) were more vulnerable than men (OR = 0.947, 95% CI: 0.771–1.162, P = 0.68). Results of the present study support an association between lower temperatures and increased risk of depression.
Improved efficiency for cross-arm comparisons via platform designs
Authors: Huang Tzu-Jung , Luedtke Alex ,   THE AMP INVESTIGATOR GROUP
Published: August 2022

Though platform trials have been touted for their flexibility and streamlined use of trial resources, their statistical efficiency is not well understood. We fill this gap by establishing their greater efficiency for comparing the relative efficacy of multiple interventions over using several separate, 2-arm trials, where the relative efficacy of an arbitrary pair of interventions is evaluated by contrasting their relative risks as compared to control. In theoretical and numerical studies, we demonstrate that the inference of such a contrast using data from a platform trial enjoys identical or better precision than using data from separate trials, even when the former enrolls substantially fewer participants. This benefit is attributed to the sharing of controls among interventions under contemporaneous randomization. We further provide a novel procedure for establishing the noninferiority of a given intervention relative to the most efficacious of the other interventions under evaluation, where this procedure is adaptive in the sense that it need not be a priori known which of these other interventions is most efficacious. Our numerical studies show that this testing procedure can attain substantially better power when the data arise from a platform trial rather than multiple separate trials. Our results are illustrated using data from two monoclonal antibody trials for the prevention of HIV.
Esophageal disease and loss to follow-up are common among patients who experience non-endoscopic resolution of food impaction
Authors: Hoversten Patrick , Lomeli Luis , Broman Aimee Teo , Gaumnitz Eric , Hillman Luke
Published: August 2022

Many patients who experience esophageal food impaction (EFI) will have non-endoscopic resolution (NER) of their EFI, but this population is poorly defined. The purpose of this study is to describe the outcomes of patients with NER of EFI. A retrospective chart review from 2007 to 2017 was performed at a single tertiary care center. There were 593 patients who presented to the emergency department with EFI, defined as recent soft food ingestion and inability to tolerate oral secretions. Adequate follow-up was defined as a gastroenterology clinic visit or EGD within 6 months of EFI. Out of these, 149 patients (25.1%) had NER of their EFI. Patients with NER were less likely to have adequate follow-up than those with ER (45.0% vs. 59.5%, P = 0.003). Of those without established esophageal disease and NER, 92.5% had significant esophageal pathology on endoscopy, including stricture (34.0%), features of eosinophilic esophagitis (30.2%), and esophagitis (22.6%). Recurrent EFI occurred at a similar rate between patients with NER and ER (9.4% vs. 14.6%, P = 0.14). Patients with established esophageal disease (odds ratio [OR]: 1.51, P = 0.04) and recommendation to follow-up at time of EFI (OR: 6.06, P < 0.001) were most likely to follow up after EFI. Approximately, a quarter of patients with EFI will experience NER of their EFI. Virtually, all patients (92.5%) were found to have esophageal disease warranting longitudinal care. Importantly, follow-up rates are significantly lower in those with NER than their counterparts requiring EGD. Our study highlights the need to develop standardized protocols that improve follow-up for patients after NER of EFI.
Changes in Burn Surgery Operative Volume and Metrics due to COVID-19
Authors: Yoon Joshua S , Khoo Kimberly H , Akhavan Arya A , Lagziel Tomer , Ha Michael , Cox Carrie A , Blanding Renee , Werthman Emily H , Caffrey Julie , Hultman C Scott
Published: August 2022

Due to COVID-19, hospitals underwent drastic changes to operating room policy to mitigate the spread of the disease. Given these unprecedented measures, we aimed to look at the changes in operative volume and metrics of the burn surgery service at our institution. A retrospective review was conducted for operative cases and metrics for the months of March to May for 2019, 2020, and 2021, which correspond with pre-COVID, early COVID (period without elective cases), and late COVID (period with resumed elective cases). Inclusion criteria were cases related to burns. Case types and operative metrics were compared amongst the three time-periods. Compared to the hospital, the burn service had a smaller decrease in volume during early COVID (28.7% vs 50.1%) and exceeded prepandemic volumes during late COVID (+21.8% vs -4.6%). There was a significant increase in excision and grafting cases in early and late COVID periods (P < .0001 and P < .002). There was a significant decrease in laser scar procedures that persisted even during late COVID (P < .0001). The projected and actual lengths of cases significantly increased and persisted into late COVID (P < .01). COVID-19 related operating room closures led to an expected decrease in the number of operative cases. However, there was no significant decline in the number of burn specific cases. The elective cases were largely replaced with excision and grafting cases and this shift has persisted even after elective cases have resumed. This change is also reflected in increased operative times.
Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern
Authors: Wood Dustin A , Richmond Jonathan Q , Escalona Merly , Marimuthu Mohan P A , Nguyen Oanh , Sacco Samuel , Beraut Eric , Westphal Michael , Fisher Robert N , Vandergast Amy G , Toffelmier Erin , Wang Ian J , Shaffer H Bradley
Published: August 2022

The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
An unusual case of abdominal compartment syndrome from a massive faecaloma
Authors: Chuang Fred Jui-Ju , Lim Aaron Er-Wynn , Cooper Michelle Louise , Townend Phillip , Parker David James
Published: August 2022

Severe constipation is a frequent presentation but progression into a life-threatening acute compartment syndrome (ACS) is few and far between. This case highlights the typical physiological manifestations of ACS and the immediate benefits of correcting these physiological imbalances through the disimpaction of a massive faecaloma. Furthermore, in adult patients with a history of colonic dysmotility, adult Hirschsprung’s disease should be considered.
Separating the effects of air and soil temperature on silver birch. Part I. Does soil temperature or resource competition determine the timing of root growth?
Authors: Kilpeläinen Jouni , Domisch Timo , Lehto Tarja , Piirainen Sirpa , Silvennoinen Raimo , Repo Tapani
Published: August 2022

The aboveground parts of boreal forest trees mostly grow earlier, and the roots later, in the growing season. We aimed to experimentally test whether the extrinsic driver of soil temperature or the intrinsic driver (resource competition between plant parts) is a more important control for the root and shoot growth of silver birch (Betula pendula Roth) seedlings. Sixteen two-year-old seedlings were grown in controlled environment rooms for two simulated growing seasons (GS1, GS2). In GS1, all the seedlings were acclimatized under the same conditions, but in GS2, the soil temperature treatments were: (i) constant 10 °C (Cool); (ii) constant 18 °C (Warm); (iii) early growing season at 10 °C, switched to 18 °C later (Early Cool Late Warm, ECLW) and (iv) early growing season 18 °C, switched to 10 °C later (Early Warm Late Cool, EWLC). The treatments did not affect growth allocation between shoots and roots. Warm soil benefitted shoot elongation as it slowed down in EWLC and accelerated in ECLW after the soil temperature switch. However, whole-tree biomasses were similar to Cool and the seedlings grew largest in Warm. Phenology was not strongly affected by soil temperature, and root and shoot growth did not usually peak simultaneously. Short root mortality increased strongly in ECLW and decreased in EWLC after the soil temperature switch. Long root longevity was not significantly affected but long root growth ceased earliest in ECLW. Soil warming increased foliar nutrient contents. Growth dynamics were not solely driven by soil temperature, but resource competition also played a significant role. The study showed the importance of soil temperature for fine root dynamics not only through root growth but also via root mortality, as soil warming increased mortality even more than growth. Soil temperature has complex effects on tree and soil functioning, which further affects carbon dynamics in forest ecosystems that have a climate feedback.
A Global Transcriptome and Co-expression Analysis Reveals Robust Host Defense Pathway Reprogramming and Identifies Key Regulators of Early Phases of Cicer-Ascochyta Interactions
Authors: Singh Ritu , Dwivedi Aditi , Singh Yeshveer , Kumar Kamal , Ranjan Aashish , Verma Praveen Kumar
Published: August 2022

Ascochyta blight (AB) caused by the filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive to date. Here, we investigated the comparative transcriptional dynamics of AB-resistant and -susceptible chickpea genotypes upon A. rabiei infection, to understand the early host defense response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared with a susceptible host. At the early stage (24 h postinoculation [hpi]), mainly cell-wall remodeling and secondary metabolite pathways were highly activated, while differentially expressed genes related to signaling components, such as protein kinases, transcription factors, and hormonal pathways, show a remarkable upsurge at 72 hpi, especially in the resistant genotype. Notably, our data suggest an imperative role of jasmonic acid, ethylene, and abscisic acid signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell-wall remodeling, signal transduction, and phytohormone pathways. Hub genes such as MYB14, PRE6, and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance and susceptibility at early Cicer-Ascochyta interactions but, also, offer a valuable resource for developing AB-resistant chickpea.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
A Phage Therapy Model for the Prevention of Pseudomonas syringae pv. actinidiae Infection of Kiwifruit Plants
Authors: Fiorillo Anna , Frezza Domenico , Di Lallo Gustavo , Visconti Sabina
Published: August 2022

Great efforts have been made with chemicals and pesticides to contain the spread of Pseudomonas syringae pv. actinidiae (Psa) responsible for kiwifruit canker. Unfortunately, only partial results were obtained for this bacterial pandemic, and alternative remedies were proposed to avoid soil pollution and the onset of antibiotic resistance. Among these, phage therapy represents a possible tool with low environmental impact and high specificity. Several phages have been isolated and tested for the capacity to kill Psa in vitro, but experiments to verify their efficacy in vivo are still lacking. In the present study, we demonstrated that the phage φPSA2 (previously characterized) contains the spread of Psa inside plant tissue and reduces the symptoms of the disease. Our data are a strong indication for the efficiency of this phage and open the possibility of developing a phage therapy based on φPSA2 to counteract the bacterial canker of kiwifruit.
3-Year Outcomes of XEN Implant Compared With Trabeculectomy, With or Without Phacoemulsification for Open Angle Glaucoma
Authors: Marcos-Parra María Teresa , Mendoza-Moreira Angi Lizbeth , Moreno-Castro Lucía , Mateos-Marcos Carlos , Salinas-López Javier Alejandro , Figuerola-García María Belén , González-Alonso Ángela , Pérez-Santonja Juan José
Published: August 2022

Précis:

Trabeculectomy (TRAB) surgery reduces the intraocular pressure (IOP) more than the XEN45 implant over 3 years. There is no difference in the number of antiglaucoma medications between the 2 procedures. The decision to perform either TRAB or XEN45 implantation must be evaluated on a case-by-case basis, taking into account the high rate of needling of the XEN45.

Purpose:

The aim of this study was to compare the differences between the efficacy and safety of the XEN45 implant and TRAB, either alone or in combination with phacoemulsification (PHACO), in patients with open angle glaucoma (OAG) at 36 months.

Methods:

A retrospective, single-center and comparative study conducted on OAG patients who underwent XEN45 implantation or TRAB from 2016 to 2018. Patients were divided into 4 groups: group 1 (XEN45 alone), group 2 (XEN45+PHACO), group 3 (TRAB alone), and group 4 (TRAB+PHACO). For statistical purposes, groups 1 and 2 were combined (XEN45 implant), whereas groups 3 and 4 were also combined (TRAB surgery). IOP, number of glaucoma medications, and adverse events were evaluated. The main outcome measure was the reduction in IOP at 36 months postoperatively.

Results:

One hundred thirty-four patients (134 eyes; 63 XEN45 and 71 TRAB) were included. The mean (95% confidence interval) IOP reduction at the end of the study follow-up was −6.3 (−11.0 to −1.6 mm Hg, P=0.025, XEN45 alone), −8.9 (−11.0 to −6.8 mm Hg, P<0.001, TRAB alone), −2.5 (−4.5 to −0.4 mm Hg, P=0.019, XEN45+PHACO), and −5.6 (−7.7 to −3.4 mm Hg, P<0.001, TRAB±PHACO). The proportion of patients achieving an IOP≥6 and ≤16 mm Hg without treatment at the end of the 36-month follow-up were 50.8% (32/63) in the XEN45 implant and 49.3% (35/71) in the TRAB surgery group, P=0.863. The mean number of glaucoma medications was significantly reduced in all the study groups. The needling rate was 19% in XEN45 versus 5.6% in the TRAB group (P=0.030), and 2.81% and 36.6% of eyes in the TRAB group presented anterior chamber flattening and hyphema, respectively.

Conclusions:

TRAB surgery lowered IOP significantly more than XEN45 implant with or without phacoemulsification over 3 years and had a significantly lower need for additional needling surgery. Both procedures reduced glaucoma medications to a similar rate. These findings are relevant to the informed consent process and patient decisions for one procedure over the other.
Hand Hygiene Compliance Rates in 9 Pediatric Intensive Care Units Across Europe: Results from the Reducing Antimicrobial use and Nosocomial Infections in Kids Network
Authors: Kopsidas Ioannis , De Luca Maia , Bielicki Julia , Blázquez-Gamero Daniel , von Both Ulrich , Ciliento Gaetano , Epalza Cristina , Goycochea Validivia Walter Alfredo , Kolberg Laura , Lutsar Irja , Machaira Maria , Neth Olaf , Oletto Andrea , Tsolia Maria N. , Viltrop Anna-Liisa , Zaoutis Theoklis , Spyridis Nikos
Published: August 2022

A unified surveillance mechanism for hand hygiene and hospital-acquired infections for pediatric wards is lacking in Europe. We managed to setup such a mechanism in 9 pediatric intensive care units in 7 European countries, using World Health Organization’s definitions and common methodology which allows for benchmarking among units and countries. Median hand hygiene compliance was found high 82.3% (interquartile range 71.6–94.5%), but gaps in practices were identified.
Health effects of androgen abuse: a review of the HAARLEM study
Authors: Smit Diederik L. , Bond Peter , de Ronde Willem
Published: August 2022

Purpose of review

Data on the health effects of androgen abuse are mainly derived from lower level evidence, such as case series and cross-sectional studies. In the last few years a relatively large and prospective cohort initiative, the HAARLEM (health risks of anabolic androgenic steroid use by male amateur athletes) study, made an important contribution to current knowledge.

Recent findings

The HAARLEM study showed that all androgen abusers experience positive and negative effects, such as an increase in strength and acne and gynecomastia, respectively. Effects are generally reversible and acute life-threatening toxicity is rare. There is a distinct but limited impact on liver and kidney function. Gonadal function is disrupted but resumes normally after abuse is discontinued in the majority of athletes. The negative impact of androgens on cardiovascular parameters, such as blood pressure, hematocrit and lipid metabolism, as well as cardiac structure and function, seems to be the mechanism for premature atherosclerosis and cardiomyopathy, respectively, in long-term users.

It is beyond dispute that androgen abuse is harmful and much of the short-term toxicity is well documented. To prevent the long-term health hazards, there should be ample focus on preventive measures, both primary and secondary, and effective harm reduction strategies should be developed.
Assessing cardiovascular disease: looking beyond cholesterol
Authors: Kendrick Malcolm
Published: August 2022

Purpose of review

The low-density lipoprotein (LDL)-cholesterol level is a weak predictor of developing cardiovascular (CV) disease and can only explain a small proportion of CV risk. It is not used to determine CV risk on either the atherosclerotic cardiovascular disease (ASCVD) calculator in the United States, or the Qrisk3 in the UK.

A study in JAMA in 2022 suggested that ‘the absolute benefits of statins are modest and may not be strongly mediated through the degree of LDL reduction’. Perhaps it is time to look beyond cholesterol to a different causal model – the ‘thrombogenic’ model of ASCVD.

Recent findings

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) pandemic demonstrated that infectious agents damage the endothelium and the glycocalyx – the glycoprotein layer protecting underlying endothelial cells. There are numerous other conditions leading to this kind of damage, which can trigger thrombus formation, causing strokes and myocardial infarctions.

Although these are acute events, they highlight a mechanism for the development of ASCVD which centres on endothelial damage and thrombus formation as both the primary causal mechanism for acute events, and the driver behind progression towards atherosclerotic plaque development.

The cholesterol hypothesis, that a raised LDL is directly causal for ASCVD, does not adequately explain cardiovascular risk in individuals, or populations. An alternative ‘thrombogenic’ hypothesis is proposed as a more valid causal model.
Flexible use of contact calls in a species with high fission–fusion dynamics
Authors: Briseño-Jaramillo Margarita , Sosa-López José Roberto , Ramos-Fernández Gabriel , Lemasson Alban
Published: August 2022

The ‘social complexity hypothesis' posits that complex social systems (which entail high uncertainty) require complex communicative systems (with high vocal flexibility). In species with fission–fusion dynamics, where the fluid composition of temporary subgroups increases the uncertainty with which group members must manage their social relationships, vocal communication must be particularly flexible. This study assessed whether contact call rates vary with caller and audience characteristics in free-living spider monkeys, as well as with fission and fusion events. Adult females and immature individuals called more when in small audience settings, while audience size did not influence adult males. Adults called more when in the presence of the opposite sex, whereas immatures vocalized more in subgroups composed only by females. Females also called more when with their mature sons. We found higher call rates in periods during which fission and fusion events took place than in periods with more stable compositions and when the composition after a fission or fusion event changed from one sex to two sexes. A flexible use of contact calls allows individuals to identify themselves when they join others, particularly if they are members of the opposite sex. This socio-spatial cohesion function reduces the uncertainty about subgroup composition.

This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
An open-access T-BAS phylogeny for EmergingPhytophthoraspecies
Authors: Coomber Allison , Saville Amanda , Carbone Ignazio , Ristaino Jean Beagle
Published: August 2022

Phytophthoraspecies cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1875, it has expanded to comprise over 190 formally described species. There is a need for an open access bioinformatic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification ofPhytophthoraspecies. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genusPhytophthorausing sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood method. A search engine was also developed to identify genotypes ofP. infestansbased on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of allPhytophthoraspecies. Critically, this resource can be updated in real-time to keep pace with new species descriptions. The tool contains metadata such as clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the globalPhytophthoracommunity to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community ofPhytophthoraresearchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for diverse populations of pathogens.
Expansive growths with uniaxial gradients can explain formation of oblong diversity observed in two-dimensional leaf shapes
Authors: Nakamasu Akiko M.
Published: August 2022

Regulation of positional information in fields with different sizes are known as scaling in the area of morphogenesis, and enable integrated and robust developmental processes. Although it is known that interpretation of such scaled patterns leads to formations of relative shapes, the same positional information brings about diversities in morphogenesis.

In this research, a boundary of a two-dimensional shape was constructed by propagating points and segments connecting them for a description of a growing form. Cell expansion “with” or “without” cell proliferation were implemented using different simple algorithms, as “additive growth” and “expansive growth”, respectively. When the different types of growth algorithm with a biased restriction were calculated, the additive growth maintained a relative shape corresponding to the gradients with different lengths. However, diverse shapes were generated by the gradients in the cases of expansive growth and its combinations even with negate effects by additive growth. As an operative example of this attempt, leaf shapes with smooth margins were calculated using a combination of these growth algorithms.

Finally, we concluded that different algorithms brought different responses against the simple positional information, i.e., additive growth always governed by it or expansive growth can escape it. It was predicted theoretically that an expansive growth has a capacity to become a generator of diversity at least in leaf morphogenesis.

Summary statement

Explanation of different responses against single positional information by different algorithms for two types of growth modes.
ATG5- and ATG7-mediated autophagy regulates pollen tube guidance and male fertility in Arabidopsis thaliana
Authors: Yan He , Du Xiaojuan , Yang Mingkang , Li Nianle , Li Xuequan , Ni Zailue , Huang Wei , Wu Hong , Zhao Lifeng , Wang Hao
Published: August 2022

Autophagy functions as a crucial cellular scavenger by targeting cytoplasmic cargo to specific lysosome/vacuole for degradation. Autophagy-related (ATG) core proteins including ATG5 and ATG7 are evolutionarily conserved factors that are spatiotemporally orchestrated to regulate multiple processes of autophagy in yeast, mammalian and plant cells. However, autophagy is believed to be functionally dispensable in Arabidopsis thaliana since severe defects during plant growth, development and reproduction have not been observed in most of the ATG loss-of-function mutants, including atg5 and atg7, under standard cultivation conditions. In this study, we report that autophagy does in fact play roles in regulating pollen tube growth guidance and male fertility in Arabidopsis thaliana. A detailed re-assessment of atg5 and atg7 mutants revealed greatly reduced autophagy activity in germinated pollens and the seed formation within siliques is partially abolished. Next, we demonstrated that both the pollen germination ratio and pollen tube length of the mutants decreased at the beginning of germination by time-lapse tracking of pollen germination in vitro and in vivo. Additionally, we observed occurrences of pollen tube twisting and stacking during their growth towards the ovules. Finally, we found abnormal pollen grains containing only a single sperm cell or an undivided generative nucleus. Collectively, these results indicate that ATG5- and ATG7-mediated autophagy is functionally involved in regulating pollen germination, tube growth guidance and sperm cell development in Arabidopsis thaliana.
Different modality-specific mechanisms mediate perceptual history effects in vision and audition
Authors: Togoli Irene , Fornaciai Michele , Bueti Domenica
Published: August 2022

Perceptual history plays an important role in sensory processing and decision making, shaping how we perceive and judge external objects and events. Indeed, past stimuli can bias what we are currently seeing in an attractive fashion, making a current stimulus to appear more similar to its preceding one than it actually is. Such attractive effects across successive stimuli appear to be ubiquitous, affecting almost every aspect of perception – from very basic visual attributes (i.e., orientation) to more complex features (i.e., face identity) – suggesting that they may reflect a fundamental principle of brain processing. However, it is unclear whether the ubiquitous nature of these effects is due to an underlying centralised mechanism mediating all of them, or by the existence of separate mechanisms implemented independently in different perceptual pathways. Here we address this question by assessing the behavioural and neural signature of perceptual history in audition and vision, in the context of time perception. Our results first show a double dissociation between the two modalities, whereby the behavioural effect of perceptual history shows opposite patterns of selectivity for the features and position of the stimuli. Electroencephalography results further support a difference between audition and vision, demonstrating that the signature of perceptual history unfolds according to different dynamics in the two modalities and show different relations with the behavioural effect. Overall, our results suggest that the effect of perceptual history may be mediated by different and at least partially independent mechanisms based on the same computational principle, implemented in different sensory pathways.

SIGNIFICANCE STATEMENT

The recent history of stimulation, or perceptual history, plays a fundamental role in perception, shaping what we see according to what we saw in the past. The brain mechanisms mediating the integration of past and present perceptual information are however still unclear. In this study we asked whether perceptual history operates via a centralized mechanism shared across sensory modalities, or via distinct modality-specific mechanisms. Our findings show a double dissociation in attractive perceptual history effects across vision and audition, while EEG data show neural signatures of perceptual history with distinct dynamics and properties. Overall, we thus demonstrate that perceptual history affects sensory processing starting from the earliest level of processing, within distinct modality-specific sensory pathways.
The transcribed intergenic regions exhibit lower frequency of nucleotide polymorphism than the untranscribed intergenic regions in the genomes of Escherichia coli and Salmonella enterica
Authors: Beura Pratyush Kumar , Sen Piyali , Aziz Ruksana , Satapathy Siddhartha Shankar , Ray Suvendra Kumar
Published: August 2022

The temporary exposure of single-stranded regions in the genome during the process of replication and transcription makes the region vulnerable to cytosine deamination resulting higher rate of C→T transitions. Intra-operon intergenic regions undergo transcription along with adjacent co-transcribed genes in an operon, whereas inter-operon intergenic regions only undergo replication. Hence these two types of intergenic regions (IGRs) can be compared to find out the contribution of replication-associated mutations (RAM) and transcription-associated mutations (TrAM) towards bringing variation in genomes. In our work, we performed a polymorphism spectra comparison between intra-operon IGRs and inter-operon IGRs in genomes of two well-known closely related bacteria such as Escherichia coli and Salmonella enterica. In general, the size of intra-operon IGRs was smaller than that of inter-operon IGRs in these bacteria. Interestingly, the polymorphism frequency at intra-operon IGRs was 2.5-fold lesser than that in the inter-operon IGRs in E. coli genome. Similarly, the polymorphism frequency at intra-operon IGRs was 2.8-fold lesser than that in the inter-operon IGRs in S. enterica genome. Therefore, the intra-operon IGRs were often observed to be more conserved. In the case of inter-operon IGRs, the T→C transition frequency was a minimum of two times more than T→A transversion frequency whereas in the case of intra-operon IGRs, T→C transition frequency was similar to that of T→A transversion frequency. The polymorphism was purine biased and keto biased more in intra-operon IGRs than the inter-operon IGRs. In E. coli, the Ti/Tv ratio was observed as 1.639 and 1.338 in inter-operon and in intra-operon IGRs, respectively. In S. enterica, the Ti/Tv ratio was observed as 2.134 and 2.780 in inter-operon and in intra-operon IGRs, respectively. The observation in this study indicates that transcribed IGRs might not always have higher polymorphism frequency than the untranscribed IGRs. The lower polymorphism frequency at intra-operon IGRs might be attributed to different events such as the transcription-coupled DNA repair, sequences facilitating translation initiation and avoidance of rho-dependent transcription termination.
A tripartite complex HIV-1 Tat-cyclophilin A-capsid protein enables Tat encapsidation that is required for HIV-1 infectivity
Authors: Schatz Malvina , Marty Laetitia , Ounadjela Camille , Tong Phuoc Bao Viet , Cardace Ilaria , Mettling Clément , Milhiet Pierre-Emmanuel , Costa Luca , Godefroy Cédric , Pugnière Martine , Guichou Jean-François , Mesnard Jean-Michel , Blaise Mickaël , Beaumelle Bruno
Published: August 2022

HIV-1 Tat is a key viral protein that stimulates several steps of viral gene expression. Tat is especially required for the transcription of viral genes but it is still not clear if and how Tat is incorporated into HIV-1 virions. Cyclophilin A (CypA) is a prolylisomerase that binds to HIV-1 capsid protein (CA) and is thereby encapsidated. Here we found that a Tat-CypA-CA tripartite complex assembles in HIV-1 infected cells. Biochemical and biophysical studies showed that high affinity interactions drive the assembly of this complex. Virions devoid of encapsidated Tat showed a 5-10 fold decrease in HIV-infectivity and, conversely, encapsidating Tat into ΔTat viruses greatly enhanced infectivity. The absence of encapsidated Tat decreases the efficiency of retrotranscription by ∼50% and transcription by 99%. We thus identified a Tat-CypA-CA complex that enables Tat encapsidation and showed that encapsidated Tat is required to initiate robust HIV-1 infection and viral production.
Pericyte Heterogeneity Identified by 3D Ultrastructural Analysis of the Microvessel Wall
Authors: Abdelazim Hanaa , Payne Laura Beth , Nolan Kyle , Paralkar Karan , Bradley Vanessa , Kanodia Ronak , Gude Rosalie , Ward Rachael , Monavarfeshani Aboozar , Fox Michael A. , Chappell John C.
Published: August 2022

ABSTRACT/SUMMARY

Unequivocal pericyte identification remains a limitation in the field of vascular biology given the lack of unique molecular marker. Compounding this challenge are the recently described heterogeneities in pericyte morphology across microvascular networks. Here, we found further support on the ultrastructural level for classifying pericytes into sub-types – “thin-strand” (TSPs), mesh (MP), and ensheathing (EP) pericytes – based on their architecture in the mouse brain microcirculation. We also observed several instances of an additional cell type in the medial layer between endothelial cells and pericytes, specifically associated with EPs. A conserved characteristic across PC subtypes was extracellular matrix (ECM) encompassing the vascular unit and dispersed among neighboring cells. ECM thicknesses fell within a specific range depending on vessel location, and only thinned where cells were in closer proximity. Pericytes and endothelial cells formed “peg-and-socket” structures at these locations, providing another distinguishing feature across PC subtypes. Unique contact locations seemed to be present between medial and endothelial cells, as well as between vascular cells and the brain parenchyma. The ECM surrounding EPs exhibited another notable configuration in that thin extensions radiated out from the vessel wall into the surrounding parenchyma, suggesting mechanical and/or biochemical roles. Considering these data together, ultrastructural observations may provide an orthogonal perspective on pericyte heterogeneity and the presence of medial cells in cerebrovascular walls as well as assessing ECM coverage as a criterion for PC identification and exploring PC-associated ECM extensions that may have unique relevance in health and disease.
Teacher–researcher partnership in the translation and implementing of PALS (Peer‐Assisted Learning Strategies): An international perspective
Authors: Vardy Emma J. , Al Otaiba Stephanie , Breadmore Helen L. , Kung Shu‐Hsuan , Pétursdóttir Anna‐Lind , Zaru Mai W. , McMaster Kristen L.
Published: August 2022

Peer‐Assisted Learning Strategies (PALS) is a class‐wide structured supplementary paired reading programme to support learners with their reading (Fuchs et al., 1997). What remains at the core of implementing PALS in any given location is the co‐creation with teachers to ensure PALS fits with that educational context. This paper discusses the involvement of teachers as co‐creators in the process of adapting PALS in England, United Arab Emirates (UAE), Taiwan and Iceland. The aim is to demonstrate the importance of careful adaptation when implementing a programme adopted from another country. Each adaption used a different methodological approach to co‐creation. For example, in England, field notes, informal conversations and interviews were utilised for co‐creation. In Iceland, preschool and elementary teachers were instrumental in translating and adapting the PALS materials to the Icelandic context. From each adaption, the teachers supported the development of a literacy programme that was suitable for classroom use. In England, teachers' involvement resulted in the removal of the motivational point system. For the UAE context, PALS began in English to support second language learning, but the instructional routines were a good ‘fit’ for the school culture and were developed in Arabic. For the Taiwan context, PALS provided an empirical basis for a model of differentiated instruction to enhance the reading literacy of Chinese‐speaking elementary students. In Iceland, teachers trained other teachers in PALS as a research‐based and efficient approach to meeting diverse learning needs of students, especially those with Icelandic as an additional language. Careful adaptation, piloting and the involvement of key stakeholders is important for the successful implementation of a reading programme.
Non‐cigarette combustible tobacco use and its associations with subsequent cessation of smoking among daily cigarette smokers: findings from the International Tobacco Control Four Country Smoking and Vaping Surveys (2016–20)
Authors: Li Lin , Borland Ron , Cummings K. Michael , Hyland Andrew , Le Grande Michael , Fong Geoffrey T. , McNeill Ann
Published: August 2022

Aims

To examine whether polyuse of cigarettes and other smoked products (polysmoking) is predictive of quit attempts and quit success.

Design

A prospective multi‐country cohort design.

Setting

Australia, Canada, England and the United States.

Participants

A total of 3983 adult daily cigarette smokers were surveyed in 2016 (wave 1 of data collection) and were re‐contacted in 2018 (wave 2) (i.e. waves 1–2 cohort) in the International Tobacco Control Four Country Smoking and Vaping (ITC 4CV) surveys; and 3736 smokers were surveyed in 2018 and re‐contacted in 2020 (wave 3) (i.e. waves 2–3 cohort).

Measurements

Participants were asked about their cigarette smoking and use of cigars, cigarillos, pipes and waterpipes. Outcomes were quit attempts between two survey waves and success, defined as having quit smoking all the combustible tobacco at the subsequent survey for 1 month or more.

Findings

Levels of polysmoking were 12.7% in the waves 1–2 cohort and 10.5% for the waves 2–3 cohort. Compared with cigarette‐only smokers, polysmokers were more likely to attempt to quit between waves 1 and 2 [54.9 versus 42.7%, adjusted odds ratio (aOR) = 1.37, 95% confidence interval (CI) = 1.08–1.74, P < 0.01], but not between waves 2 and 3 (43.8 versus 40.1%, aOR = 0.94, 95% CI = 0.72–1.22). Polysmoking predicted reduced likelihood of success in both cohorts among attempters and the overall samples. Between waves 2 and 3 there were significantly more transitions to non‐daily smoking among the polysmokers (12.4 versus 5.3%, χ2 = 40.4, P < 0.001).

Conclusions

There is a consistent association between polysmoking (use of cigarettes together with other smoked products) and reduced quit success for combustible tobacco, but it is probably due to increased likelihood of transitioning to non‐daily use rather than complete cessation.
Immediate possible adverse event rates in infants treated with oral propranolol for infantile haemangiomas at an Australian urban tertiary hospital between 2016 and 2019
Authors: Adams Lucinda , Ryan Emma
Published: August 2022

Background/Objectives

Infantile haemangiomas (IH) are common benign tumours of childhood. The current guideline recommended treatment is oral propranolol, the use of which for IH is relatively recent and there are no safety audits in Australian children published. As a result, it is a primarily inpatient initiated treatment. The aim of this study was to examine the short‐term complication rates in infants treated with oral propranolol for IH.

Methods

Retrospective case note review of IH patients initiated on oral propranolol admitted to the day‐unit of tertiary metropolitan hospital in an Australia capital city, from January 2016 to December 2019.

Results

Overall, 72 children were included in the study. Mean age at time of admission was 3.8 ± 2 months. Eight patients (11.1%) experienced complications during their initiation admission. Pulmonary complications (oxygen desaturation, wheeze, increased respiratory rate) was the most common type. No children required high‐dependency or intensive care unit admission. The children who experienced complications had a mean age of 2.4 ± 1.2 months; t‐test of equality of means found a relationship between propranolol‐associated complication rate and age (p = 0.007). All other patient or admission characteristics were not associated with complication events (all p > 0.05).

Conclusions

Propranolol is a safe, effective and well‐tolerated treatment in Australian children with IH. This study demonstrates younger infants will most likely benefit from inpatient initiation. More research needs to be done to characterise the risk profile of propranolol initiation for IH.
Editorial: pegylated interferon combined with bulevirtide for chronic hepatitis delta—new life for an old timer? Authors' reply
Authors: Jachs Mathias , Reiberger Thomas , Ferenci Peter
Published: August 2022

LINKED CONTENT

This article is linked to Jachs et al papers. To view these articles, visit https://doi.org/10.1111/apt.16945 and https://doi.org/10.1111/apt.16115