bluuebunny/crossref_metadata_2025 huggingface dataset:
Just a moment
Authors: Egan Thomas , Skogmo Siri Fürst
Published: August 2021

This chapter investigates two temporal lexemes, English moment and Norwegian øyeblikk, which
may encode either a point in time (‘x happened at time y’) or an interval of time (‘x lasted for time y’). The data for the
study comprise all instances of the two lexemes in the English and Norwegian original language texts and translations in the
English–Norwegian Parallel Corpus. While both lexemes are commonly used to encode time intervals, moment is
almost twice as likely as øyeblikk to refer to a point in time, suggesting that moment is
somewhat more polysemous. This impression is reinforced by the evidence of the translations, where moment is
more likely to be used to translate øyeblikk than vice versa.
Cross-disciplinary and cross-linguistic uses of tensed verb phrases in the
methods sections of master’s theses
Authors: Rørvik Sylvi
Published: August 2021

This study examines the distribution and functions of tensed verb phrases in the methods sections of master’s theses
produced at Norwegian universities. The material comprises texts written in both English and Norwegian within the disciplines
of chemistry, linguistics, and sociology. The method involved manual identification of tensed verb phrases, as well as a more
detailed investigation of their rhetorical functions. The findings indicate that there are cross-linguistic and
cross-disciplinary differences in both distribution and function, in line with findings from previous studies of student and
professional academic writing. These findings have implications for the teaching of academic writing, which should reflect the
conventions of the disciplinary communities of which the student writers are aspiring members.
Theory of Mind and children’s comforting behaviour (La Teoría de la Mente y el comportamiento infantil de consuelo)
Authors: López-Pérez Belén , Patel Hannah , Zuffianò Antonio
Published: August 2021

In order to comfort others, children need to exhibit Theory of Mind (ToM) skills. The goal of the present study was to investigate the role of ToM in association with children’s spontaneous comforting behaviour in a laboratory task. Forty-seven children between 26 and 57 months of age completed three ToM tasks: diverse desires, diverse beliefs and belief-emotion. To evaluate comforting, we used a previously evaluated procedure in which an experimenter drops a tower of blocks and pretends to be upset. The results showed a significant positive relationship between children’s understanding of their own and others’ desires and comforting. However, no relationships were found between comforting and understanding of one’s own and others’ beliefs or belief-emotion. The relationship between the different ToM tasks and age was also assessed, but it was non-significant. The implications of these findings for understanding the onset of spontaneous prosocial behaviour are discussed.
Quantitative measurements of singlet molecular oxygen in a low pressure ICP
Authors: Rogers Samuel D A , Bond Amelia , Peverall Robert , Hancock Gus , Western Colin M , Ritchie Grant A D
Published: August 2021

We present measurements of the densities and temperatures (rotational and translational) of the metastable a1Δg (v = 0) state of O2 in a cylindrically symmetric RF driven plasma operating in inductive mode at 100 mTorr total pressure and 300 W applied power. Line-of-sight absorption across the plasma region was determined by diode laser cavity ringdown spectroscopy on the (0, 0) vibrational band of the O2(b1Σg
+) ← O2(a1Δg) transition near 1.9 μm. Four rotational quantum states were studied, with a population distribution corresponding to a rotational temperature of 346 ± 38 K. The translational temperature was determined to be 359 ± 16 K from the width of the strongest absorption line, Q(12), and in equilibrium with the rotational distribution. The absolute concentration of O2(a1Δg, v = 0) was measured as (9.5 ± 1.3) × 1013 cm−3, and corresponds to an apparent (3.5 ± 0.45)% contribution to the total number density. Time-resolved CRDS measurements following plasma extinction were used to deduce a wall loss coefficient, γ, of (2.8 ± 0.3) × 10−3 on predominantly Al surfaces. Surmising reasonable concentrations for O2(b1Σg
+) and an upper limit for the vibrational temperature places the total contribution of O2(a1Δg) at between 3.6% and 5.85%. The variation of the O2(a1Δg, v = 0) state concentration with RF power shows a clear transition from the E to H mode excitation near an applied power of 150 W. Allan variance analysis yields a minimum measurable concentration of O2(a1Δg, v = 0) of 1.1 × 1012 cm−3 over 100 ringdown events, an order of magnitude more sensitive than previously reported.
Effect of interfacial conductivity on electrical characteristics of negative capacitance field effect transistors
Authors: Xiao Y G , Kang K C , Tian L Y , Xiong K , Li G , Tang M H , Li Z
Published: August 2021

In this article, an interfacial conductivity model for the surface potential and the drain current was proposed based on the metal-interface-ferroelectric-insulator-semiconductor (MIFIS) structure negative capacitance field effect transistor (NC-FET). The simulating results illustrate that the electrical conductivity (σ) of the interface layer between the electrode and ferroelectric thin film caused by lattice misfit plays an important role in the process of voltage amplifying and steep switching for the NC-FET. It is indicated that new device design rules should take into account this scenario.
Different reverse remodelling between left ventricle and right ventricle in fulminant heart failure due to giant cell myocarditis: a case report
Authors: Yokoyama Hiroaki , Yamaguchi Masashi , Tobita Kazuki , Saito Shigeru
Published: August 2021

Background

Giant cell myocarditis (GCM) is a rare cause of fulminant heart failure (HF). The most common presentation is progressive hemodynamic deterioration, and a few cases present with idiopathic complete atrioventricular block (cAVB). The prognosis of GCM is poor, and GCM patients usually die of HF and ventricular arrhythmia unless cardiac transplantation is performed. Few reports have described the effects of treatments such as immunosuppression and detailed reverse remodelling in GCM patients.

Case summary

A 69-year-old female presented with cAVB. Transvenous pacemaker was implanted via the left subclavian vein. One and a half months later, she exhibited left ventricular dyssynchrony and lower left ventricular ejection fraction (LVEF), resulting in hospitalization for HF. She received cardiac resynchronization therapy; however, this had no apparently positive effects on her cardiac function. To investigate the cause of the lower LVEF, an endomyocardial biopsy was taken from the right ventricular septum. She was diagnosed with GCM and immediately received immunosuppression therapy with prednisolone and ciclosporin. This resulted in the functional recovery of the right ventricle; on the other hand, the left ventricle had still not recovered based on transthoracic echocardiography. Fortunately, she successfully recovered from severe HF without recurrence.

Discussion

This is a case of fulminant HF due to GCM which initially presented as cAVB. Moreover, this case demonstrates the quite difference of the functional recovery between the left ventricle and the right ventricle with immunosuppression therapy.
Enabling qualitative research data sharing using a natural language processing pipeline for deidentification: moving beyond HIPAA Safe Harbor identifiers
Authors: Gupta Aditi , Lai Albert , Mozersky Jessica , Ma Xiaoteng , Walsh Heidi , DuBois James M
Published: August 2021

Objective

Sharing health research data is essential for accelerating the translation of research into actionable knowledge that can impact health care services and outcomes. Qualitative health research data are rarely shared due to the challenge of deidentifying text and the potential risks of participant reidentification. Here, we establish and evaluate a framework for deidentifying qualitative research data using automated computational techniques including removal of identifiers that are not considered HIPAA Safe Harbor (HSH) identifiers but are likely to be found in unstructured qualitative data.

Materials and Methods

We developed and validated a pipeline for deidentifying qualitative research data using automated computational techniques. An in-depth analysis and qualitative review of different types of qualitative health research data were conducted to inform and evaluate the development of a natural language processing (NLP) pipeline using named-entity recognition, pattern matching, dictionary, and regular expression methods to deidentify qualitative texts.

Results

We collected 2 datasets with 1.2 million words derived from over 400 qualitative research data documents. We created a gold-standard dataset with 280K words (70 files) to evaluate our deidentification pipeline. The majority of identifiers in qualitative data are non-HSH and not captured by existing systems. Our NLP deidentification pipeline had a consistent F1-score of ∼0.90 for both datasets.

Conclusion

The results of this study demonstrate that NLP methods can be used to identify both HSH identifiers and non-HSH identifiers. Automated tools to assist researchers with the deidentification of qualitative data will be increasingly important given the new National Institutes of Health (NIH) data-sharing mandate.
Born on the Battlefield: Celebrating the Centennial of the Discovery of Epidural Anesthesia
Authors: Bowers Ensign Gerald M
Published: August 2021

The year 2021 marks the 100th anniversary of the discovery of epidural anesthesia by Spanish military surgeon Major Fidel Pagés. The idea for the technique was born from Pagés’ experiences in forward military hospitals in North Africa and Austria and would go on to revolutionize the fields of surgery and obstetrics.
Dual regulation of osteoclastogenesis and osteogenesis for osteoporosis therapy by iron oxide hydroxyapatite core/shell nanocomposites
Authors: Li Mengye , Fu Shengxiang , Cai Zhongyuan , Li Danyang , Liu Li , Deng Di , Jin Rongrong , Ai Hua
Published: August 2021

Osteoporosis is a skeletal disorder resulted in significant structural and functional changes, arousing a wide concern for the high prevalence and cost. Imbalance between osteoclastogenesis and osteogenesis have been verified as a main pathology etiology and considered an efficient therapy target in both clinical and pre-clinical studies. In recent years, inorganic nanomaterials have shown provable activities on osteoclastogenesis inhibition and osteogenesis promotion, respectively. Hence, in this study, a class of hydroxyapatite coated superparamagnetic iron oxide nanoparticles (SPIO@HA) were developed with a core−shell structure for targeting both osteoclastogenesis and osteogenesis. The optimal ratio of SPIO@15HA (Fe/Ca = 1:15, mol/mol) was screened to obtain dual function for inducing both bone formation and preventing bone resorption. The obtained nanocomposites significantly prevented the bone loss of ovariectomized (OVX) mice and increased bone mineral density (BMD) by 9.4%, exhibiting high bone accumulation in magnetic resonance imaging evaluation and reasonable biosafety profile. The mechanism study revealed that SPIO@15HA can suppress bone marrow monocyte derived osteoclast differentiation through TRAF6−p62−CYLD signaling complex regulation. Meanwhile, it could activate MSC osteogenic differentiation by TGF-β, PI3K-AKT and calcium signaling pathway regulation. Moreover, incubation of SPIO@15HA with MSC resulted in several cytokines overexpression such as osteoprotegerin (OPG), CSF2, CCL2 etc., which are responsible for maintaining the bone remodeling balance. The dual function of as-prepared SPIO@15HA may find a new way for designing of inorganic components containing core/shell nanomaterials for osteoporosis treatment.
Religion at the Frontline: How Religion Influenced the Response of Local Government Officials to the COVID-19 Pandemic
Authors: Adler Gary J , Ortiz Selena E , Plutzer Eric , Mayrl Damon , Coley Jonathan S , Sager Rebecca
Published: August 2021

Frontline officials (such as mayors and commissioners) are responsible for local-level responses to the COVID-19 pandemic across the United States. Their actions and attitudes, either in support of or opposition to public health recommendations, have resulted in widespread variation in local-level pandemic response. Despite evidence that religion significantly impacts the general public’s response to the pandemic, the influence of religion on officials’ behaviors and attitudes is unknown. Using a unique, two-wave, representative survey of frontline officials, we examine how religion influenced officials’ reported personal health behaviors (mask wearing, social distancing) and attitudes toward institutional reopenings. Results show high levels of compliance with public health recommendations, but religious nationalism negatively influences all outcomes. Other religious factors, like affiliation and attendance, vary in their influence and even work differently among officials compared to the general public. Frontline officials are key for understanding how religion influences the pandemic and state action more generally.
Improvements in physical activity and some dietary behaviors in a community health worker-led diabetes self-management intervention for adults with low incomes: results from a randomized controlled trial
Authors: Gray Kristen E , Hoerster Katherine D , Taylor Leslie , Krieger James , Nelson Karin M
Published: August 2021

People with low incomes have a disproportionate prevalence of diabetes and its complications and experience many barriers to self-management, which community health workers (CHWs) may help address. We sought to examine the effects of an in-home CHW-led intervention for adults with diabetes and incomes <250% of the federal poverty line on self-management behaviors and test mediators and moderators. From 2010 to 2013, we randomized participants from three Washington State health systems with type 2 diabetes and hemoglobin A1c (HbA1c) ≥ 8% to the CHW intervention (N = 145) or usual care control (N = 142) arms. We examined effects on 12-month self-management: physical activity, dietary behaviors, medication taking, blood glucose monitoring, foot care, and tobacco use. For behaviors with significant intervention-control group differences, we tested mediation by self-efficacy and social support. We also investigated whether intervention-associated changes in behaviors varied by race/ethnicity, gender, and baseline values of HbA1c, diabetes distress, depression, and food insecurity (moderators). Compared to controls, intervention participants engaged in more physical activity and reported better dietary behaviors for some measures (general diet, frequency of skipping meals, and frequency of eating out) at 12-months, but there was no evidence of mediation by self-efficacy or social support. Evidence of moderation was limited: improvements in the frequency of skipping meals were restricted to participants with baseline HbA1c < 10%. Study findings suggest CHWs could be integrated into diabetes care to effectively support lifestyle changes around physical activity and some eating behaviors among adults with low incomes. More research is needed to understand mechanisms of change.
Implementing lung cancer screening in primary care: needs assessment and implementation strategy design
Authors: Reese Thomas J , Schlechter Chelsey R , Kramer Heidi , Kukhareva Polina , Weir Charlene R , Del Fiol Guilherme , Caverly Tanner , Hess Rachel , Flynn Michael C , Taft Teresa , Kawamoto Kensaku
Published: August 2021

Lung cancer screening with low-dose computed tomography (CT) could help avert thousands of deaths each year. Since the implementation of screening is complex and underspecified, there is a need for systematic and theory-based strategies. Explore the implementation of lung cancer screening in primary care, in the context of integrating a decision aid into the electronic health record. Design implementation strategies that target hypothesized mechanisms of change and context-specific barriers. The study had two phases. The Qualitative Analysis phase included semi-structured interviews with primary care physicians to elicit key task behaviors (e.g., ordering a low-dose CT) and understand the underlying behavioral determinants (e.g., social influence). The Implementation Strategy Design phase consisted of defining implementation strategies and hypothesizing causal pathways to improve screening with a decision aid. Three key task behaviors and four behavioral determinants emerged from 14 interviews. Implementation strategies were designed to target multiple levels of influence. Strategies included increasing provider self-efficacy toward performing shared decision making and using the decision aid, improving provider performance expectancy toward ordering a low-dose CT, increasing social influence toward performing shared decision making and using the decision aid, and addressing key facilitators to using the decision aid. This study contributes knowledge about theoretical determinants of key task behaviors associated with lung cancer screening. We designed implementation strategies according to causal pathways that can be replicated and tested at other institutions. Future research is needed to evaluate the effectiveness of these strategies and to determine the contexts in which they can be effectively applied.
Differences in psychosocial constructs among elementary school staff that implement physical activity programs: a step in designing implementation strategies
Authors: Szeszulski Jacob , Walker Timothy J , Robertson Michael C , Fernandez Maria E
Published: August 2021

Multiple types of school staff members (e.g., classroom teachers, principals) are involved in implementing physical activity programs (e.g., classroom-based, gym), but factors specific to their job responsibilities may inhibit their ability to implement programming effectively. Thus, implementation strategies tailored by job type may be needed. We compare perceptions of behavioral constructs related to implementation of school-based physical activity programs, by job type, among school staff. School staff (n = 139), including principals/assistant principals (n = 21), physical education teachers (n = 41), and classroom teachers (n = 77), from elementary schools (n = 25), completed a cross-sectional survey measuring perceptions of attitudes, barriers, knowledge, and outcome expectations related to the implementation of physical activity programs. We compared constructs between job types using complex samples general linear models. Classroom teachers reported more perceived implementation barriers, lower physical activity knowledge, and lower outcome expectations than physical education teachers. Principals reported more perceived implementation barriers than physical education teachers. Classroom teachers reported lower physical activity knowledge than principals. Attitudes towards physical activity were not different by job type. Each job type has a unique constellation of factors affecting their capacity to implement physical activity programs. Understanding these differences enables tailoring of implementation strategies by job type.
Reactions of Winter Wheat, Spring Wheat, and Barley Cultivars to Mechanical Inoculation with Wheat Streak Mosaic Virus
Authors: McKelvy Uta , Brelsford Monica , Sherman Jamie , Burrows Mary
Published: August 2021

Wheat streak mosaic virus (WSMV) causes sporadic epidemics in Montana, which can threaten profitability of the state’s small grains production. One challenge for WSMV management in Montana is that most commercially available wheat and barley cultivars are susceptible to WSMV or their performance under WSMV pressure is unknown. In a 3-year field study from 2017 to 2019 winter wheat, spring wheat, and barley cultivars were evaluated for their susceptibility to WSMV and yield performance under WSMV pressure. Plants were mechanically inoculated, and WSMV incidence was assessed using double antibody sandwich ELISA. There was effective resistance to WSMV in breeding line CO12D922, which had consistently low WSMV incidence, highlighting promising efforts in the development of WSMV-resistant winter wheat cultivars. Moderate WSMV incidence and minor yield losses were observed from WSMV infection of commercial winter wheat ‘Brawl CL Plus’ and Montana State University breeding line MTV1681. Spring wheat cultivars in this study had high WSMV incidence of up to 100% in ‘Duclair,’ ‘Egan,’ and ‘McNeal.’ High WSMV incidence was associated with severe yield losses as high as 85% for Duclair and ‘WB9879CLP’ in 2019, demonstrating a high degree of susceptibility to WSMV inoculation. Barley cultivars had considerably lower WSMV incidence compared with spring and winter wheat. Grain yield response to WSMV inoculation was variable between barley cultivars. The study provided an experimental basis for cultivar recommendations for high WSMV pressure environments and identified breeding lines and cultivars with potential resistance traits of interest to breeding programs that aim to develop WSMV-resistant cultivars.
A-SMART Lifestyle Behaviors Model for health, wellbeing, and immune system enhancement
Authors: Downes Loureen , St. Hill Halcyon , Mays Traci
Published: August 2021

Healthy lifestyle behaviors and an optimally functioning immune system are essential for good health. We present evidence-based lifestyle behavior interventions that enhance immunity and wellbeing, with practical applications using the A-SMART Lifestyle Behaviors Model: Adopting healthy eating, stress management, moving more, alcohol avoidance, rest, and tobacco cessation.
Cystic fibrosis
Authors: Wendekier Camille , Wendekier-Raybuck Katheryn
Published: August 2021

Cystic fibrosis is an autosomal recessive genetic disorder that causes a lifetime of debilitating and potentially fatal complications affecting the lungs and other organ systems. Over 1,700 gene mutations that cause this rare disorder have been identified. This article describes the current treatment landscape for adults with CF, including the 2019 FDA approval of a breakthrough triple-drug combination therapy that may significantly improve the quality of life for an estimated 90% of patients with CF.
Chronic Quadriceps Tendon Rupture Reconstruction with Sartorius Muscle Transfer: A Report of Five Cases
Authors: Elhessy Ahmed H. , Alrabai Hamza M. , Eltayeby Hady H. , Gesheff Martin G. , Conway Janet D.
Published: August 2021

Disruption of the knee extensor mechanism is an unfavorable situation because efficient mobilization requires a functioning knee extensor apparatus. The purpose of this retrospective study was to report our technique of sartorius muscle transfer for restoration of extension mechanism function and the outcomes of five patients. Patients with ruptured knee extensor mechanism secondary to trauma or knee arthroplasty-related issues were studied retrospectively. In all patients, sartorius muscle was transferred to restore the quadriceps tension deficit. Increase in the knee active range of motion, increase in the extensor mechanism power by one grade on Medical Research Council scale, and improvement in the extension lag were observed in all patients. The sartorius muscle transfer can be a reliable option to restore the knee extensor mechanism in chronic quadriceps tendon injuries. Our initial results are promising and showed improvement of the extensor mechanism muscle power, increased knee active range of motion, and decreased knee extension lag. The complications we observed did not impair the successful outcome of the sartorius transfer and were anticipated given the complexity of the studied cases. We encourage additional studies of sartorius muscle transfer to treat chronic quadriceps tendon injuries.
Goldilocks Procedure without a Vertical Incision and a Comprehensive Literature Review
Authors: Becker Hilton , Vazquez Oscar Adrian , Komberg Jacob
Published: August 2021

Background:

The Goldilocks technique is a postmastectomy breast reconstruction procedure adopted in 2012, which is performed by preserving and de-epithelializing the residual mastectomy flap to create an autologous tissue breast mound using an anchor, inverted T, or lateral incision. It is utilized in select patients along with the addition of a free nipple graft, fat grafting, and/or tattoo. A novel technique using the Goldilocks procedure offers promising postoperative results as a more aesthetic alternative. The purpose of this study was to perform a literature review on the healing outcomes and patient satisfaction of the Goldilocks procedure along with presenting our approach using a horizontal inframammary incision without a vertical incision.

Methods:

A retrospective chart review of patients presenting to a single surgeon for breast reconstruction surgery using the Goldilocks procedure without a vertical incision from March of 2018 to October of 2020 was performed. A narrative literature review on surgical techniques and outcomes was also conducted.

Results:

Three cases of breast reduction using the Goldilocks procedure without a vertical incision are described. From the literature search, 13 articles inclusive of 222 patients were identified.

Conclusions:

The Goldilocks procedure without a vertical incision can be performed in patients with large breasts for breast reconstruction postmastectomy. It is possible to utilize the superior flap in conjunction with the de-epithelialized inferior flap of the breast and obtain good projection with this method. Furthermore, avoidance of the vertical incision reduces breakdown at the T-junction and is aesthetically beneficial.
Dry Eye Symptoms in Individuals With Keratoconus Wearing Contact Lenses
Authors: Shorter Ellen , Harthan Jennifer , Nau Amy , Fogt Jennifer , Cao Dingcai , Schornack Muriel , Nau Cherie
Published: August 2021

Objectives:

To assess dry eye symptoms associated with different contact lens modalities in patients with keratoconus using a dry eye questionnaire.

Methods:

An online survey was distributed by the National Keratoconus Foundation. The survey asked participants to report demographic characteristics, current optical correction, age at the time of diagnosis of keratoconus, and contact lens history. The 12-item Ocular Surface Disease Index (OSDI) questionnaire was also completed. Data from participants wearing the same contact lens modality bilaterally were analyzed.

Results:

The survey was completed by 197 individuals wearing the same contact lens modality bilaterally. The average age of participants at the time of the survey was 47.2±14.8 years (range: 15–87 years), and the average age at which keratoconus was diagnosed was 26.1±9.9 years (range: 8–55 years). The mean overall OSDI score of all participants was 40.2±22.8 (range: 0–100). There was no difference in the mean OSDI scores based on current contact lens modality type (F=1.79; n=187; P=0.13). Based on an OSDI score of 33 or higher, 90% of participants reported symptoms indicative of dry eye disease. Scleral lens wearers reported less discomfort on the individual items related to windy and low-humidity conditions.

Conclusions:

Individuals with keratoconus, irrespective of contact lens modality, report a high incidence of dry eye symptoms.
A metastable attractor model of self–other integration (MEAMSO) in rhythmic synchronization
Authors: Heggli Ole Adrian , Konvalinka Ivana , Kringelbach Morten L. , Vuust Peter
Published: August 2021

Human interaction is often accompanied by synchronized bodily rhythms. Such synchronization may emerge spontaneously as when a crowd's applause turns into a steady beat, be encouraged as in nursery rhymes, or be intentional as in the case of playing music together. The latter has been extensively studied using joint finger-tapping paradigms as a simplified version of rhythmic interpersonal synchronization. A key finding is that synchronization in such cases is multifaceted, with synchronized behaviour resting upon different synchronization strategies such as mutual adaptation, leading–following and leading–leading. However, there are multiple open questions regarding the mechanism behind these strategies and how they develop dynamically over time. Here, we propose a metastable attractor model of self–other integration (MEAMSO). This model conceptualizes dyadic rhythmic interpersonal synchronization as a process of integrating and segregating signals of self and other. Perceived sounds are continuously evaluated as either being attributed to
self
-produced or
other
-produced actions. The model entails a metastable system with two particular attractor states: one where an individual maintains two separate predictive models for
self
- and
other
-produced actions, and the other where these two predictive models integrate into one. The MEAMSO explains the three known synchronization strategies and makes testable predictions about the dynamics of interpersonal synchronization both in behaviour and the brain.

This article is part of the theme issue ‘Synchrony and rhythm interaction: from the brain to behavioural ecology’.
Pseudomonas capsici sp. nov., a plant-pathogenic bacterium isolated from pepper leaf in Georgia, USA
Authors: Zhao Mei , Koirala Santosh , Chen Hsiao-Chun , Gitaitis Ronald , Kvitko Brian , Dutta Bhabesh
Published: August 2021

Three phytopathogenic bacterial strains (Pc19-1T, Pc19-2 and Pc19-3) were isolated from seedlings displaying water-soaked, dark brown-to-black, necrotic lesions on pepper (Capsicum annuum) leaves in Georgia, USA. Upon isolation on King’s medium B, light cream-coloured colonies were observed and a diffusible fluorescent pigment was visible under ultraviolet light. Analysis of their 16S rRNA gene sequences showed that they belonged to the genus

Pseudomonas

, with the highest similarity to

Pseudomonas cichorii

ATCC 10857T (99.7 %). The fatty acid analysis revealed that the majority of the fatty acids were summed feature 3 (C16  :  1 ω7c/C16  :  1 ω6c), C16  :  0 and summed feature 8 (C18  :  1 ω7c/C18  :  1 ω6c). Phylogenomic analyses based on whole genome sequences demonstrated that the pepper strains belonged to the

Pseudomonas syringae

complex with

P. cichorii

as their closest neighbour, and formed a separate monophyletic clade from other species. Between the pepper strains and

P. cichorii

, the average nucleotide identity values were 91.3 %. Furthermore, the digital DNA–DNA hybridization values of the pepper strains when compared to their closest relatives, including

P. cichorii

, were 45.2 % or less. In addition, biochemical and physiological features were examined in this study and the results indicate that the pepper strains represent a novel

Pseudomonas

species. Therefore, we propose a new species Pseudomonas capsici sp. nov., with Pc19-1T (=CFBP 8884T=LMG 32209T) as the type strain. The DNA G+C content of the strain Pc19-1T is 58.4 mol%.
Categories of intimate partner violence and abuse (IPVA) among young women and men: Latent Class Analysis of psychological, physical, and sexual victimisation and perpetration in a UK birth cohort
Authors: Herbert Annie , Fraser Abigail , Howe Laura D. , Szilassy Eszter , Barnes Maria , Feder Gene , Barter Christine , Heron Jon
Published: August 2021

Background

In the UK, around one-third of young people are exposed to IPVA by 21 years old. However, types of IPVA victimisation in this population (psychological, physical, sexual), and their relationship with impact and perpetration are poorly understood.

Methods

Participants in a UK birth cohort reported IPVA victimisation and perpetration by age 21. We carried out a latent class analysis, where we categorised IPVA by types/frequency of victimisation, and then assigned individuals to their most probable class. Within these classes, we then estimated risks of reported: 1) types of negative impacts (sad, upset/unhappy, anxious, depressed, affected work/studies, angry/annoyed, drank/took drugs more); 2) types/frequency of perpetration.

Results

Among 2,130 women and 1,149 men, 32% and 24% reported IPVA victimisation (of which 89% and 73% reported negative impact); 21% and 16% perpetration. Victimisation responses were well represented by five classes, including three apparent in both sexes: No-low victimisation (characterised by low probabilities of all types of victimisation; average probabilities of women and men belonging to this class were 82% and 70%); Mainly psychological (15% and 12%); Psychological & physical victimisation (4% and 7%), and two classes that were specific to women: Psychological & sexual (7%); Multi-victimisation (frequent victimisation for all three types; 4%). In women, all types of negative impact were most common in the Psychological & sexual and Multi-victimisation classes; for men, the Psychological & physical class. In women, all types of perpetration were most common for the Mainly psychological, Psychological & physical, and Multi-victimisation classes; in men, the Mainly psychological and Psychological & physical classes.

Discussion

In this study of young people, we found categories of co-occurrence of types and frequency of IPVA victimisation associated with differential risks of negative impact and perpetrating IPVA. This is consistent with emerging evidence of IPVA differentiation and its variable impact in other populations.
Strong gamma frequency oscillations in the adolescent prefrontal cortex
Authors: Wang Zhengyang , Singh Balbir , Zhou Xin , Constantinidis Christos
Published: August 2021

Working memory ability continues to mature into adulthood in both humans and non-human primates. At the single neuron level, adolescent development is characterized by increased prefrontal firing rate in the delay period, but less is known about how coordinated activity between neurons is altered. Local field potentials (LFP) provide a window into the computation carried out by the local network. To address the effects of adolescent development on LFP activity, three male rhesus monkeys were trained to perform an oculomotor delayed response task and tested at both the adolescent and adult stage. Simultaneous single-unit and LFP signals were recorded from areas 8a and 46 of the dorsolateral prefrontal cortex (dlPFC). In both the cue and delay period, power relative to baseline increased in the gamma frequency range (32 - 128 Hz). In the adult stage, high-firing neurons were also more likely to reside at sites with strong gamma power increase from baseline. For both stages, the gamma power increase in the delay was selective for sites with neuron encoding stimulus information in their spiking. Gamma power and neuronal firing did not show stronger temporal correlations. Our results establish gamma power decrease to be a feature of prefrontal cortical maturation.

Significance Statement

Gamma-frequency oscillations in extracellular field recordings (such as LFP or EEG) are a marker of normal interactions between excitatory and inhibitory neurons in neural circuits. Abnormally low gamma power during working memory is seen in conditions such as schizophrenia. We sought to examine whether the immature prefrontal cortex similarly exhibits lower power in the gamma frequency range during working memory, in a non-human primate model of adolescence. Contrary to this expectation, the adolescent PFC exhibited stronger gamma power during the maintenance of working memory. Our findings reveal an unknown developmental maturation trajectory of gamma band oscillations and raise the possibility that schizophrenia represent an excessive state of prefrontal maturation.
Probing the orientation specificity of excitatory and inhibitory circuitries in the primary motor cortex with multi-channel TMS
Authors: Souza Victor Hugo , Nieminen Jaakko O. , Tugin Sergei , Koponen Lari , Baffa Oswaldo , Ilmoniemi Risto J.
Published: August 2021

Background

The electric field orientation is a crucial parameter for optimizing the excitation of neuronal tissue in transcranial magnetic stimulation (TMS). Yet, the effects of stimulus orientation on the short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) paradigms are poorly known, mainly due to significant technical challenges in manipulating the TMS-induced stimulus orientation within milliseconds.

Objective

Our aim is to assess the effect of the TMS-induced stimulus orientation on the SICI and ICF paradigms and search for the optimal orientations to maximize the facilitation and suppression of the motor evoked potentials (MEP).

Methods

We applied paired-pulse multi-channel TMS in healthy subjects to generate SICI and ICF with conditioning and test pulses in the same, opposite, and perpendicular orientations to each other. The conditioning- and test-stimulus intensities were 80% and 110% of the resting motor threshold, respectively.

Results

Both SICI and ICF were significantly affected by the conditioning- and test-stimulus orientation. MEP suppression and facilitation were strongest with both pulses delivered in the same direction. SICI with a 2.5-ms and ICF with a 6.0-ms interstimulus interval (ISI) were more sensitive to changes in stimulus orientation compared with SICI at 0.5- and ICF at 8.0-ms ISIs, respectively.

Conclusion

Our findings provide evidence that SICI and ICF at specific ISIs are mediated by distinct mechanisms. Such mechanisms exhibit a preferential orientation depending on the anatomical and morphological arrangement of inhibitory and excitatory neuronal populations. We also demonstrate that the SICI and ICF can be maximized by adjusting the TMS-induced electric field orientation.
The complexities of inferring symbiont function: Paraburkholderia symbiont dynamics in social amoeba populations and their impacts on the amoeba microbiota
Authors: DuBose James G. , Robeson Michael S. , Hoogshagen Mackenzie , Olsen Hunter , Haselkorn Tamara S.
Published: August 2021

The relationship between the social amoeba Dictyostelium discoideum and its endosymbiotic bacteria Paraburkholderia provides a model system for studying the development of symbiotic relationships. Laboratory experiments have shown that any of three species of Paraburkholderia symbiont allow D. discoideum food bacteria to persist through the amoeba lifecycle and survive in amoeba spores, rather than being fully digested. This phenomenon is termed “farming”, as it potentially allows spores dispersed to food poor locations to grow their own. The occurrence and impact of farming in natural populations, however, has been a challenge to measure. Here, we surveyed natural D. discoideum populations and found that only one of the three symbiont species, P. agricolaris, remained prevalent. We then explored the effect of Paraburkholderia on the amoeba microbiota, expecting that by facilitating bacterial food carriage it would diversify the microbiota. Contrary to our expectations, Paraburkholderia tended to infectiously dominate the D. discoideum microbiota, in some cases decreasing diversity. Similarly, we found little evidence for Paraburkholderia facilitating the carriage of particular food bacteria. These findings highlight the complexities of inferring symbiont function in nature and suggest the possibility that Paraburkholderia could be playing multiple roles for its host.
A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins
Authors: Stadelmann Tobias , Heid Daniel , Jendrusch Michael , Mathony Jan , Rosset Stéphane , Correia Bruno E. , Niopek Dominik
Published: August 2021

Deep mutational scanning is a powerful method to explore the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins, which are natural CRISPR-Cas inhibitors and key players in the co-evolution of microbes and phages, would facilitate their in-depth characterization and optimization. Here, we developed a robust anti-CRISPR deep mutational scanning pipeline inEscherichia colicombining synthetic gene circuits based on CRISPR interference with flow cytometry-coupled sequencing and mathematical modeling. Using this pipeline, we created and characterized comprehensive single point mutation libraries for AcrIIA4 and AcrIIA5, two potent inhibitors ofStreptococcus pyogenesCas9. The resulting mutational fitness landscapes revealed that both Acrs possess a considerable mutational tolerance as well as an intrinsic redundancy with respect to Cas9 inhibitory features, suggesting evolutionary pressure towards high plasticity and robustness. Finally, to demonstrate that our pipeline can inform the optimization and fine-tuning of Acrs for genome editing applications, we cross-validated a subset of AcrIIA4 mutants via gene editing assays in mammalian cells andin vitroaffinity measurements. Together, our work establishes deep mutational scanning as powerful method for anti-CRISPR protein characterization and optimization.
Resting Parasympathetic Nervous System Activity is Associated with Greater Antiviral Gene Expression
Authors: Rahal Danny , Tashjian Sarah M. , Karan Maira , Eisenberger Naomi , Galván Adriana , Fuligni Andrew J. , Cole Steve W.
Published: August 2021

Parasympathetic nervous system activity can downregulate inflammation, but it remains unclear how parasympathetic nervous system activity relates to antiviral activity. The present study examined associations between parasympathetic nervous system activity and cellular antiviral gene regulation in 90 adolescents (Mage= 16.3,SD= 0.7; 51.1% female) who provided blood samples and measures of cardiac respiratory sinus arrhythmia (RSA), twice, five weeks apart. Using a multilevel analytic framework, we found that higher RSA (an indicator of higher parasympathetic nervous system activity)—both at rest and during paced breathing—was associated with higher expression of Type I interferon (IFN) response genes in circulating leukocytes, even after adjusting for demographic and biological covariates. RSA was not associated with a parallel measure of inflammatory gene expression. These results identify a previously unrecognized immunoregulatory aspect of autonomic nervous system function and highlight a potential biological pathway by which parasympathetic nervous system activity may relate to health.
Deciphering spatial domains from spatially resolved transcriptomics with adaptive graph attention auto-encoder
Authors: Dong Kangning , Zhang Shihua
Published: August 2021

Recent advances in spatially resolved transcriptomics have enabled comprehensive measurements of gene expression patterns while retaining the spatial context of the tissue microenvironment. Deciphering the spatial context of spots in a tissue needs to use their spatial information carefully. To this end, we developed a graph attention auto-encoder framework STAGATE to accurately identify spatial domains by learning low-dimensional latent embeddings via integrating spatial information and gene expression profiles. To better characterize the spatial similarity at the boundary of spatial domains, STAGATE adopts an attention mechanism to adaptively learn the similarity of neighboring spots, and an optional cell type-aware module through integrating the pre-clustering of gene expressions. We validated STAGATE on diverse spatial transcriptomics datasets generated by different platforms with different spatial resolutions. STAGATE could substantially improve the identification accuracy of spatial domains, and denoise the data while preserving spatial expression patterns. Importantly, STAGATE could be extended to multiple consecutive sections to reduce batch effects between sections and extracting three-dimensional (3D) expression domains from the reconstructed 3D tissue effectively.
DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity
Authors: Quintana Felix M. , Kong Zhaoming , He Lifang , Chen Brian Y.
Published: August 2021

Amino acids that play a role in binding specificity can be identified with many methods, but few techniques identify the biochemical mechanisms by which they act. To address a part of this problem, we present DeepVASP-E, an algorithm that can suggest electrostatic mechanisms that influence specificity. DeepVASP-E uses convolutional neural networks to classify an electrostatic representation of ligand binding sites into specificity categories. It also uses class activation mapping to identify regions of electrostatic potential that are salient for classification. We hypothesize that electrostatic regions that are salient for classification are also likely to play a biochemical role in achieving specificity. Our findings, on two families of proteins with electrostatic influences on specificity, demonstrate that large salient regions can identify amino acids that have an electrostatic role in binding, and that DeepVASP-E is an effective classifier of ligand binding sites.
Communities of tropical soil fungi differ between burned and unburned forest, with corresponding changes in plant community composition, litter and soil chemistry
Authors: Calvert Jed , McTaggart Alistair , Carvalhais Lília C. , Drenth André , Shivas Roger
Published: August 2021

Fire is predicted to be more severe and frequent in forests of the Australian Monsoon Tropics over the coming decades. The way in which groups of ecologically important soil fungi respond to disturbance caused by fire has not been studied in Australian tropical forest ecosystems. Ectomycorrhizal (EM) fungi are important tree symbionts and saprotrophic fungi drive soil nutrient cycles. We analysed both publicly-available environmental DNA sequence data as well as soil chemistry data to test a hypothesis that burned areas in a contiguous tropical forest have different community composition and diversity of EM and saprotrophic soil fungi relative to nearby unburned sites. We tested this hypothesis by measuring community-level taxonomic composition, fungal diversity, species richness and evenness. We determined whether changes in fungal communities were associated with fire-altered soil chemical/physical properties, vegetation types, or the direct effect of fire. Soil fungi differed in abundance and community phylogenetic structure between forest sites that had experienced fire, and sites dominated by unburned forest. EM community composition differed between unburned and burned sites, which had more mycorrhizal hosts including Corymbia intermedia, Acacia flavescens and Acacia midgleyi. Lower diversity of saprotrophic fungi was correlated with lower soil nutrient levels and different litter composition at burned sites. Pyrophilic, truffle-like EM fungi that rely on mycophagous mammals for dispersal were abundant at recently burned sites. We conclude that EM fungi show different patterns of diversity in burned tropical forest, likely driven by changing plant communities, whereas differences in saprotrophic fungal communities of burned sites may be driven by by reduced soil nutrient levels and altered litter composition.

Graphical abstract