bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insight into formation propensity of pseudocircular DNA G-hairpins
Authors: Živković Martina Lenarčič , Gajarský Martin , Beková Kateřina , Stadlbauer Petr , Vicherek Lukáš , Petrová Magdalena , Fiala Radovan , Rosenberg Ivan , Šponer Jiří , Plavec Janez , Trantírek Lukáš 
Published: January 2021

Abstract
We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their function in vivo and their applications in biotechnology, has not been elucidated. Here, we show that despite its ‘circular’ nature, PGHs tolerate single-stranded (ss) protrusions. High-resolution NMR structure of a novel member of PGH family reveals the atomistic details on a junction between ssDNA and PGH unit. Identification of new sequences capable of folding into one of the two forms of PGH helped in defining minimal sequence requirements for their formation. Our time-resolved NMR data indicate a possibility that PGHs fold via a complex kinetic partitioning mechanism and suggests the existence of K+ ion-dependent PGH folding intermediates. The data not only provide an explanation of cation-type-dependent formation of PGHs, but also explain the unusually large hysteresis between PGH melting and annealing noted in our previous study. Our findings have important implications for DNA biology and nanotechnology. Overrepresentation of sequences able to form PGHs in the evolutionary-conserved regions of the human genome implies their functionally important biological role(s).
Reversible chromatin condensation by the DNA repair and demethylation factor thymine DNA glycosylase
Authors: Deckard Charles E , Sczepanski Jonathan T 
Published: January 2021

Abstract
Chromatin structures (and modulators thereof) play a central role in genome organization and function. Herein, we report that thymine DNA glycosylase (TDG), an essential enzyme involved in DNA repair and demethylation, has the capacity to alter chromatin structure directly through its physical interactions with DNA. Using chemically defined nucleosome arrays, we demonstrate that TDG induces decompaction of individual chromatin fibers upon binding and promotes self-association of nucleosome arrays into higher-order oligomeric structures (i.e. condensation). Chromatin condensation is mediated by TDG’s disordered polycationic N-terminal domain, whereas its C-terminal domain antagonizes this process. Furthermore, we demonstrate that TDG-mediated chromatin condensation is reversible by growth arrest and DNA damage 45 alpha (GADD45a), implying that TDG cooperates with its binding partners to dynamically control chromatin architecture. Finally, we show that chromatin condensation by TDG is sensitive to the methylation status of the underlying DNA. This new paradigm for TDG has specific implications for associated processes, such as DNA repair, DNA demethylation, and transcription, and general implications for the role of DNA modification ‘readers’ in controlling chromatin organization.
Tribes of Trust or Distrust, “Attitude Roots” and Encouraging Scientific Participation in the Tobacco Harm-Reduction Debate
Authors: Kozlowski Lynn T 
Published: January 2021

Abstract
Implications This commentary provides an analysis of non-scientific influences on the tobacco harm reduction debate. It makes use of the “attitude roots” model and the issue of misplace trust and distrust. Greater participation in the debate by experts is encouraged, along with efforts to minimize the effects of non-scientific, biasing effects on judgments.
Vertical sexual habitat segregation in a wintering migratory songbird
Authors: Cooper Nathan W , Thomas Mark A , Marra Peter P 
Published: January 2021

AbstractSexual habitat segregation during the wintering period is a widespread phenomenon and has important implications for the ecology and conservation of migratory birds. We studied Black-and-white Warblers (Mniotilta varia) wintering in second-growth scrub and old-growth mangrove forest in Jamaica to quantify sexual habitat segregation and explore whether patterns of habitat occupation have consequences on physical condition. We used this information along with a body size analysis and simulated territorial intrusions to assess whether behavioral dominance or habitat specialization was responsible for habitat segregation. Based on standardized capture data, we found that females were more abundant than males in both scrub and mangrove forests. Foraging observations, however, suggested vertical segregation within each habitat, with females foraging primarily near the ground and males in the mid-canopy and canopy, indicating that our sex ratio estimates may be biased. Using 2 measures of body condition, we show that males were in better body condition than females, regardless of habitat. We found that males were on average slightly larger than females, and home range analysis and simulated territorial intrusions indicated that males were more territorial than females. We argue that the observed vertical sexual habitat segregation is likely caused by behavioral dominance rather than habitat specialization. Winter body condition is known to carry over to affect migration timing, reproductive success, and annual survival in other songbirds, and therefore sexual habitat segregation may have important implications for year-round population dynamics in Black-and-white Warblers.
Three-dimensional reconstructions of haustoria in two parasitic plant species in the Orobanchaceae
Authors: Masumoto Natsumi , Suzuki Yuki , Cui Songkui , Wakazaki Mayumi , Sato Mayuko , Kumaishi Kie , Shibata Arisa , Furuta Kaori M , Ichihashi Yasunori , Shirasu Ken , Toyooka Kiminori , Sato Yoshinobu , Yoshida Satoko 
Published: January 2021

AbstractParasitic plants infect other plants by forming haustoria, specialized multicellular organs consisting of several cell types, each of which has unique morphological features and physiological roles associated with parasitism. Understanding the spatial organization of cell types is, therefore, of great importance in elucidating the functions of haustoria. Here, we report a three-dimensional (3-D) reconstruction of haustoria from two Orobanchaceae species, the obligate parasite Striga hermonthica infecting rice (Oryza sativa) and the facultative parasite Phtheirospermum japonicum infecting Arabidopsis (Arabidopsis thaliana). In addition, field-emission scanning electron microscopy observation revealed the presence of various cell types in haustoria. Our images reveal the spatial arrangements of multiple cell types inside haustoria and their interaction with host roots. The 3-D internal structures of haustoria highlight differences between the two parasites, particularly at the xylem connection site with the host. Our study provides cellular and structural insights into haustoria of S. hermonthica and P. japonicum and lays the foundation for understanding haustorium function.
A Retrospective Analysis of Gabapentinoid and Opioids to Opioid Monotherapy for Pain Relief in Patients with Chronic Neck and Low Back Pain
Authors: Knezevic Nebojsa Nick , Aijaz Tabish , Camacho-Ortega Alvaro , Candido Kenneth D 
Published: January 2021

Abstract

Objective
We compared the reduction in pain and opioid consumption in patients with chronic spinal pain on concomitant gabapentinoids and opioids with patients using opioids only.

Design
This was a retrospective chart review of patients with chronic neck or low back pain who were on opioids with at least a 24-month follow-up.

Setting
Single-center pain clinic in an urban setting.

Subjects
167 patients with chronic spinal pain lasting at least six months.

Methods
Patients on gabapentin or pregabalin were included in the gabapentinoid group, while the other patients were included in the non-gabapentinoid group. Primary outcome was assessment of pain scores measured via a numeric rating scale (NRS), and secondary outcomes were response to the treatment (&gt;2 point reduction on NRS) and daily opioid use measured in morphine milliequivalents.

Results
Pain scores were reduced in the first six months and plateaued after that in both groups. At the end of 24 months, the average pain score was 6.71 in the gabapentinoid group, while the average pain score was 7.18 in the non-gabapentinoid group. There was no statistical significance between the groups (p = 0.28). There was no difference in response to treatment in gabapentinoid group (33.3%) when compared with non-gabapentinoid group (32.7%). We also failed to find any significant difference in daily opioid usage between the two groups.

Conclusion
Gabapentinoids may not lead to reduction in pain or opioid consumption in patients with chronic spinal pain. A careful approach must be adopted while prescribing gabapentinoids in the chronic spinal pain patient population.
Evaluation of the Relationship Between Geographic Proximity and Treatment for People Referred to a Metropolitan Multidisciplinary Pain Clinic
Authors: Giummarra Melita J , Arnold Carolyn A , Beck Ben Ben 
Published: January 2021

Abstract

Objective
This study examined which patient characteristics are associated with traveling further to attend a metropolitan, publicly funded pain management service, and whether travel distance was associated with differences in treatment profile, duration, and percentage of appointments attended.

Design
Cross-sectional observational cohort study.

Method
Patients ≤70 years of age with a single referral between January 2014 and June 2018 who had not died within 12 months of their first appointment and who had a usual place of residence were included (N = 1,684; mean age = 47.2 years; 55.5% female). Travel distance was calculated with the HERE Routing API on the basis of historical travel times for each scheduled appointment.

Results
Median travel time was 27.5 minutes (Q1, Q3: 12.5, 46.2). Ordinal regression showed that women had 20% lower odds of traveling further, but people who were overweight or obese (odds ratio [OR] = 1.4–2.3), unemployed (OR = 1.27), or taking higher opioid dosages (OR = 1.79–2.82) had higher odds of traveling further. People traveling &gt;60 minutes had fewer treatment minutes (median = 143 minutes) than people living within 15 minutes of the pain clinic (median = 440 minutes), and a smaller proportion of those traveling &gt;60 minutes attended group programs vs. medical appointments only (n = 35, 17.0%) relative to those living within 15 minutes of their destination (n = 184, 32.6%). People living 16–30 minutes from the clinic missed the highest proportion of appointments.

Conclusions
Although people traveling further for treatment may be seeking predominantly medical treatment, particularly opioid medications, the present findings highlight the need to further explore patient triage and program models of care to ensure that people living with persistent disabling pain can access the same level of care, regardless of where they live.
A dynamical study of fusion hindrance with the Nakajima–Zwanzig projection method
Authors: Abe Yasuhisa , Boilley David , Hourdillé Quentin , Shen Caiwan 
Published: January 2021

Abstract
A new framework is proposed for the study of collisions between very heavy ions which lead to the synthesis of Super-Heavy Elements (SHE), to address the fusion hindrance phenomenon. The dynamics of the reaction is studied in terms of collective degrees of freedom undergoing relaxation processes with different time scales. The Nakajima–Zwanzig projection operator method is employed to eliminate fast variables and derive a dynamical equation for the reduced system with only slow variables. There, the time evolution operator is renormalised and an inhomogeneous term appears, which represents a propagation of the given initial distribution. The term results in a slip to the initial values of the slow variables. We expect that gives a dynamical origin for the so-called “injection point $s$” introduced by Swiatecki et al. in order to reproduce absolute values of measured cross sections for SHE. A formula for the slip is given in terms of physical parameters of the system, which confirms the results recently obtained with a Langevin equation, and permits us to compare various incident channels.
Physical and mental health of older people while cocooning during the COVID-19 pandemic
Authors: Bailey L , Ward M , DiCosimo A , Baunta S , Cunningham C , Romero-Ortuno R , Kenny R A , Purcell R , Lannon R , McCarroll K , Nee R , Robinson D , Lavan A , Briggs R 
Published: January 2021

Summary

Background
Cocooning or shielding, i.e. staying at home and reducing face-to-face interaction with other people, was an important part of the response to the COVID-19 pandemic for older people. However, concerns exist regarding the long-term adverse effects cocooning may have on their physical and mental health.

Aim
To examine health trajectories and healthcare utilization while cocooning in a cohort of community-dwelling people aged ≥70 years.

Design
Survey of 150 patients (55% female, mean age 80 years and mean Clinical Frailty Scale Score 4.8) attending ambulatory medical services in a large urban university hospital.

Methods
The survey covered four broad themes: access to healthcare services, mental health, physical health and attitudes to COVID-19 restrictions. Survey data were presented descriptively.

Results
Almost 40% (59/150) reported that their mental health was ‘worse’ or ‘much worse’ while cocooning, while over 40% (63/150) reported a decline in their physical health. Almost 70% (104/150) reported exercising less frequently or not exercising at all. Over 57% (86/150) of participants reported loneliness with 1 in 8 (19/150) reporting that they were lonely ‘very often’. Half of participants (75/150) reported a decline in their quality of life. Over 60% (91/150) agreed with government advice for those ≥70 years but over 40% (61/150) reported that they disliked the term ‘cocooning’.

Conclusions
Given the likelihood of further restrictions in coming months, clear policies and advice for older people around strategies to maintain social engagement, manage loneliness and continue physical activity and access timely medical care and rehabilitation services should be a priority.
Distinct transcriptional profile of blood mononuclear cells in Behçet’s disease: insights into the central role of neutrophil chemotaxis
Authors: Verrou Kleio-Maria , Vlachogiannis Nikolaos I , Ampatziadis-Michailidis Giannis , Moulos Panagiotis  , Pavlopoulos Georgios A , Hatzis Pantelis , Kollias George , Sfikakis Petros P 
Published: January 2021

Abstract

Objectives
Both innate and adaptive immune responses are reportedly increased in Behçet’s disease (BD), a chronic, relapsing systemic vasculitis lying at the intersection between autoinflammation and autoimmunity. To further study pathophysiologic molecular mechanisms operating in BD, we searched for transcriptome-wide changes in blood mononuclear cells from these patients.

Methods
We performed 3ʹ mRNA next-generation sequencing-based genome-wide transcriptional profiling followed by analysis of differential expression signatures, Kyoto Encyclopedia of Genes and Genomes pathways, GO biological processes and transcription factor signatures.

Results
Differential expression analysis clustered the transcriptomes of 13 patients and one healthy subject separately from those of 10 healthy age/gender-matched controls and one patient. Among the total of 17 591 expressed protein-coding genes, 209 and 31 genes were significantly upregulated and downregulated, respectively, in BD vs controls by at least 2-fold. The most upregulated genes comprised an abundance of CC- and CXC-chemokines. Remarkably, the 5 out of top 10 upregulated biological processes involved leucocyte recruitment to peripheral tissues, especially for neutrophils. Moreover, NF-kB, TNF and IL-1 signalling pathways were prominently enhanced in BD, while transcription factor activity analysis suggested that the NF-kB p65/RELA subunit action underlies the observed differences in the BD transcriptome.

Conclusion
This RNA-sequencing analysis in peripheral blood mononuclear cells derived from patients with BD does not support a major pathogenetic role for adaptive immunity-driven mechanisms, but clearly points to the action of aberrant innate immune responses with a central role played by upregulated neutrophil chemotaxis.
POTENTIAL EXPOSURE LEVELS FROM BROADCAST TRANSMITTERS IN GHANA
Authors: Deatanyah P , Menyeh A , Amoako J K , Abavare E K K , Osei-Donkor A , Quarshie E 
Published: January 2021

Abstract
The protection of man and his environment from undue exposure from radio frequency electromagnetic field requires identification of the location where exposures are likely to be higher than safe levels established by international safety standards. A wideband measurement with a spectrum analyzer and a log-periodic antenna in conjunction with the three-point spatial average method was used. The results ranged from 16.21 to 2907.00 mVm−1 and complied with a maximum of 1.08% of the ICNIRP reference level. Private frequency modulation (FM) sources were identified as the major source of exposure to the public with a mean value of 337.70 ± 133.70 mVm−1 against 122.30 ± 36.47 mVm−1 for the public FM transmitters. Even though the result was lower than a workplace assessment, it was, however, higher than similar works conducted in Africa and Palestine. Finally, four sensitive locations were identified for further research work.
The brain network in support of social semantic accumulation
Authors: Zhang Guangyao , Xu Yangwen , Zhang Meimei , Wang Shaonan , Lin Nan 
Published: January 2021

Abstract
Some studies have indicated that a specific ‘social semantic network’ represents the social meanings of words. However, studies of the comprehension of complex materials, such as sentences and narratives, have indicated that the same network supports the online accumulation of connected semantic information. In this study, we examined the hypothesis that this network does not simply represent the social meanings of words but also accumulates connected social meanings from texts. We defined the social semantic network by conducting a meta-analysis of previous studies on social semantic processing and then examined the effects of social semantic accumulation using a functional Magnetic Resonance Imaging (fMRI) experiment. Two important findings were obtained. First, the social semantic network showed a stronger social semantic effect in sentence and narrative reading than in word list reading, indicating the amplitude of social semantic activation can be accumulated in the network. Second, the activation of the social semantic network in sentence and narrative reading can be better explained by the holistic social-semantic-richness rating scores of the stimuli than by those of the constitutive words, indicating the social semantic contents can be integrated in the network. These two findings convergently indicate that the social semantic network supports the accumulation of connected social meanings.
Vicarious praise and pain: parental neural responses to social feedback about their adolescent child
Authors: van Houtum Lisanne A E M , Wever Mirjam C M , Janssen Loes H C , van Schie Charlotte C , Will Geert-Jan , Tollenaar Marieke S , Elzinga Bernet M 
Published: January 2021

AbstractSocial feedback, such as praise or critique, profoundly impacts our mood and social interactions. It is unknown, however, how parents experience praise and critique about their child and whether their mood and neural responses to such ‘vicarious’ social feedback are modulated by parents’ perceptions of their child. Parents (n = 60) received positive, intermediate and negative feedback words (i.e. personality characteristics) about their adolescent child during a magnetic resonance imaging scan. After each word, parents indicated their mood. After positive feedback their mood improved and activity in ventromedial prefrontal cortex and posterior cingulate cortex/precuneus increased. Negative feedback worsened parents’ mood, especially when perceived as inapplicable to their child, and increased activity in anterior cingulate cortex, anterior insula, dorsomedial prefrontal cortex and precuneus. Parents who generally viewed their child more positively showed amplified mood responses to both positive and negative feedback and increased activity in dorsal striatum, inferior frontal gyrus and insula in response to negative feedback. These findings suggest that vicarious feedback has similar effects and engages similar brain regions as observed during feedback about the self and illustrates this is dependent on parents’ beliefs of their child’s qualities and flaws. Potential implications for parent–child dynamics and children’s own self-views are discussed.
Testing the effects of species interactions and water limitation on tree seedling biomass allocation and physiology
Authors: Kerr Kelly L , Zenes Nicole , Trugman Anna T , Anderegg William R L 
Published: January 2021

AbstractSpecies interactions mediate tree responses to water limitation because competition and/or facilitation alter plant physiology and growth. However, because it is difficult to isolate the effects of plant–plant interactions and water limitation from other environmental factors, the mechanisms underlying tree physiology and growth in coexisting plants under drought are poorly understood. We investigated how species interactions and water limitation impact the physiology and growth of trembling aspen (Populus tremuloides), narrowleaf cottonwood (Populus angustifolia) and ponderosa pine (Pinus ponderosa) seedlings in a controlled environment growth chamber, using aspen as a focal species. Seedlings were grown in pots alone or with a con- or hetero-specific seedling, and were subjected to a water limitation treatment. Growth, water status and physiological traits were measured before, during and after the treatment. Under well-watered conditions, the presence of another seedling affected growth or biomass allocation in all species, but did not impact the physiological traits we measured. Under water limitation, the presence of a competing seedling had a marginal impact on seedling growth and physiological traits in all species. Throughout the study, the magnitude and direction of seedling responses were complex and often species-specific. Our study serves as an important step toward testing how species’ interactions modify physiological responses and growth in well-watered and water-limited periods.