bluuebunny/crossref_metadata_2025_split huggingface dataset:
Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins?
Authors: Burak Okan Osman , Turgut Deniz , Atilgan Canan , Rana Atilgan Ali , Ozisik Rahmi 
Published: December 2021

Abstract
A direct way to spot structural features that are universally shared among proteins is to find analogues from simpler condensed matter systems. In the current study, the feasibility of creating ensembles of artificial structures that can automatically reproduce a large number of geometrical and topological descriptors of globular proteins is investigated. Towards this aim, a simple cubic (SC) arrangement is shown to provide the best background lattice after a careful analysis of the residue packing trends from 210 globular proteins. It is shown that a minimalistic set of rules imposed on this lattice is sufficient to generate structures that can mimic real proteins. In the proposed method, 210 such structures are generated by randomly removing residues (beads) from clusters that have a SC lattice arrangement such that all the generated structures have single connected components. Two additional sets are prepared from the initial structures via random relaxation and a reverse Monte Carlo simulated annealing algorithm, which targets the average radial distribution function (RDF) of 210 globular proteins. The initial and relaxed structures are compared to real proteins via RDF, bond orientational order parameters and several descriptors of network topology. Based on these features, results indicate that the structures generated with 40% occupancy closely resemble real residue networks. The structure generation mechanism automatically produces networks that are in the same topological class as globular proteins and reproduce small-world characteristics of high clustering and small shortest path lengths. Most notably, the established correspondence rules out icosahedral order as a relevant structural feature for residue networks in contrast to other amorphous systems where it is an inherent characteristic. The close correspondence is also observed in the vibrational characteristics as computed from the Anisotropic Network Model, therefore hinting at a non-superficial link between the proteins and the defect laden cubic crystalline order.
Benefits and Challenges of Implementing Telehealth in Rural Settings: A Mixed-Methods Study of Behavioral Medicine Providers
Authors: DeHart Dana , King L Bailey , Iachini Aidyn L , Browne Teri , Reitmeier Melissa 
Published: November 2021

Abstract
Social workers and other healthcare professionals face increasing pressure to expand access, efficiency, and quality of healthcare to rural patients. Telehealth has become a viable and necessary tool to address gaps in healthcare for rural areas. Unfortunately, little is known about the benefits and challenges of using these services to meet the needs of rural communities. This mixed-methods study examines telehealth implementation among healthcare organizations in a predominantly rural state. Seventeen providers from 11 organizations were interviewed. Most had used live video conferencing, and about a third used mobile technologies, but fewer providers had experience with store-and-forward or remote patient monitoring. Analyses of qualitative data collected via interviews revealed two main themes among benefits of telehealth implementation: (1) increased inter- and intra-agency coordination and (2) savings in time, travel, and efficiency. Three main themes emerged among barriers to telehealth: (1) organizational capacity, (2) patient skills and comfort, and (3) provider knowledge and skills. Recommendations are provided for social workers and other healthcare professionals related to expanding utilization of telehealth services to improve access to healthcare for rural populations.
TiO2 nano-coated thin film PV glazing with superior thermal resistance, self-cleaning, electricity generation and adaptive optical control
Authors: Cuce Erdem , Cuce Pinar Mert , Riffat Saffa 
Published: November 2021

Abstract
A unique nano-coated photovoltaic (PV) glazing technology with superior multifunctional features, thermally resistive PV glazing (TRPVG), is introduced, and for three different configurations of TRPVG (TRPVG-Air12, TRPVG-Ar12, TRPVG-Ar16), UVC/UVA absorption, noise reduction, thermal insulation, electricity generation, visible light and solar radiation control are evaluated through an extensive experimental methodology. Energy production and acoustic tests are conducted in a simulation house, whereas the rest of the experiments are carried out under real operating conditions. The results reveal that each sample is capable of blocking 100% of incoming UVC and UVA light. Visible light control of TRPVG-Ar12 (Glass 1) is found to be 94.4%, whereas it is 88.9% for TRPVG-Air12 (Glass 2) and 93.6% for TRPVG-Ar16 (Glass 3). Solar radiation blockage of Glasses 1–3 is found to be 93.5%, 90.9% and 94.8%, respectively. Average temperature difference between front and rear glazing is determined to be 21.3°C, 19.9°C and 21.7°C for Glasses 1, 2 and 3, respectively. A total of 25 independent acoustic tests are performed for Glass 3, and the sample is observed to reduce 33% of outdoor noise in dBA. Solar simulator tests reveal that Glass 3 can generate 102.6 W of electricity per square metre of PV module area.
Assessing community pharmacists’ attitudes towards identifying opportunities for deprescribing in clinical practice in Ireland
Authors: Heinrich Clara H , Donovan Maria D 
Published: November 2021

Abstract

Objectives
The main objective of this study was to assess community pharmacists’ thoughts regarding the role they can play in effectively integrating deprescribing into clinical practice in Ireland. The aim was to assess pharmacists’ (1) knowledge of deprescribing, (2) confidence in deprescribing, (3) attitudes towards deprescribing and (4) barriers and facilitators to deprescribing in a community pharmacy setting.

Methods
An online questionnaire was disseminated to pharmacists currently registered with the Pharmaceutical Society of Ireland, with instruction only to complete if working in community pharmacy. Statistical analysis was conducted on the quantitative data, whereas thematic analysis was carried out on the open-ended responses.

Key findings
Results indicate good knowledge scores and positive attitudes surrounding deprescribing, with demographic factors having no significant effect on results. Although deprescribing knowledge is high, willingness to engage is hindered by obstacles such as time. Remuneration was identified as an enabler for deprescribing. Interdisciplinary educational opportunities and bidirectional communication channels with prescribers are viewed as the major facilitators of deprescribing.

Conclusions
Community pharmacists demonstrate that they possess sufficient knowledge, confidence and willingness to play a greater role in facilitating deprescribing. To enable this role expansion, enablers such as education and funding need to be implemented, to overcome barriers such as insufficient time. Further studies are required to assess community pharmacists’ deprescribing competence, to demonstrate their ability to fulfil this role in clinical practice in Ireland.
Epidemiology and Outcomes of Cooking- and Cookstove-Related Burn Injuries: A World Health Organization Global Burn Registry Report
Authors: Mehta Kajal , Thrikutam Nikhitha , Hoyte-Williams Paa Ekow , Falk Henry , Nakarmi Kiran , Stewart Barclay 
Published: December 2021

Abstract
Cooking- and cookstove-related burns (CSBs) comprise a large proportion of burn injuries globally, but there are limited data on cooking behavior patterns to inform prevention and advocacy. Therefore, we aimed to describe the epidemiology, risk factors, and outcomes of these injuries and highlight the potential of the World Health Organization (WHO) Global Burn Registry (GBR). Patients with cooking-related burns were identified in the WHO GBR. Patient demographics, cooking arrangement, injury characteristics, and outcomes were described and compared. Bivariate regression was performed to identify risk factors associated with CSBs. Analysis demonstrated that 25% of patients in the GBR sustained cooking-related burns (n = 1723). The cooking environment and cooking fuels used varied significantly by country income level ([electricity use: LIC 1.6 vs MIC 5.9 vs HIC 49.6%; P &lt; .001] [kerosene use: LIC 5.7 vs MIC 10.4 vs HIC 0.0%; P &lt; .001]). Of cooking-related burns, 22% were cookstove-related burns (CSBs; 311 burns). Patients with CSBs were more often female (65% vs 53%; P &lt; .001). CSBs were significantly larger in TBSA size (30%, IQR 15–45 vs 15%, IQR 10–25; P &lt; .001), had higher revised Baux scores (70, IQR 46–95 vs 28, IQR 10–25; P &lt; .001) and more often resulted in death (41 vs 11%; P &lt; .001) than other cooking burns. Patients with CSBs were more likely to be burned by fires (OR 4.74; 95% CI 2.99–7.54) and explosions (OR 2.91, 95% CI 2.03–4.18) than other cooking injuries. Kerosene had the highest odds of CSB compared to other cooking fuels (OR 2.37, 95% CI 1.52–3.69). In conclusion, CSBs specifically have different epidemiology than cooking-related burns. CSBs were more likely caused by structural factors (eg, explosion, fire) than behavioral factors (eg, accidental movements) when compared to other cooking burns. These differences suggest prevention interventions for CSBs may require distinctive efforts than typically deployed for cooking-related injuries, and necessarily involve cookstove design and safety regulations to prevent fires and explosions.
Visualization of three-dimensional stigmoid body in FFPE and ultrathin sections of mouse
Authors: Hirayama Masaya , Onouchi Takanori , Shiogama Kazuya , Katoh Yoshimitsu , Takahashi Kazuo , Abe Masato 
Published: November 2021

Abstract
Huntingtin-associated protein 1 (HAP1) is abundantly expressed in the neurons of the central nervous system and forms unique intracytoplasmic inclusions of unknown function called ‘stigmoid bodies’ (STBs). Transmission electron microscopy has revealed that the STBs are aggregates of granules containing cavities with a diameter of 0.5–3 µm. Small STBs fuse to form larger STBs, the size of which is said to vary depending on the developmental growth stage and brain region. Light microscopy can only reveal that these STBs have similar circular shapes due to its limited resolution. Therefore, light microscopy is only fit for the study of the STB distribution and quantitative changes. We, herein, suggest the adoption of correlative light and electron microscopy, which combines confocal laser scanning microscopy and scanning electron microscopy as the method allowing us to identify the huntingtin-associated protein 1–positive STBs in formalin-fixed paraffin-embedded (FFPE) sections. This approach allows us to study the three-dimensional morphology of immunolabeled objects in histopathological specimens. The STBs in FFPE sections of murine hypothalami reflected the transmission electron microscopic images of Epon-embedded STBs, although we were not able to observe any organelle covering the STBs of the FFPE sections. Furthermore, we were able to reconstruct the three-dimensional structure of the STB, and we identified it to be of spherical form, covered with mitochondria and rough endoplasmic reticulum, and bearing a cluster of cavities in the centre. In the future, we might gain new insights by comparing the three-dimensional structure of the STB between different neurons and under a variety of conditions.
Bilobed gallbladder discovered during laparoscopic cholecystectomy: a tale of two lobes and one duct
Authors: Plewman Devon , Kudrna Rachel , Rojas Oskar , Ford Jennifer , Smith-Singares Eduardo 
Published: November 2021

AbstractBilobed gallbladder (BG) is a rare congenital anomaly with just 24 cases documented in medical literature in the past 127 years. There are only three documented cases of BG’s managed with laparoscopic cholecystectomy, and in all three cases the bilobed anomaly was discovered preoperatively. We present a case of symptomatic cholelithiasis in a BG that was discovered intraoperatively. Both the surgical techniques used to ensure complete and safe removal of all gallbladder components and the elements associated with the preoperative diagnosis of these rare anomalies are discussed.
Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides
Authors: Achom Mingkee , Roy Proyash , Lagunas Beatriz , Picot Emma , Richards Luke , Bonyadi-Pour Roxanna , Pardal Alonso J , Baxter Laura , Richmond Bethany L , Aschauer Nadine , Fletcher Eleanor M , Rowson Monique , Blackwell Joseph , Rich-Griffin Charlotte , Mysore Kirankumar S , Wen Jiangqi , Ott Sascha , Carré Isabelle A , Gifford Miriam L 
Published: November 2021

Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.
MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events
Authors: Peterson Kevin J , Beavan Alan , Chabot Peter J , McPeek Mark A , Pisani Davide , Fromm Bastian , Simakov Oleg 
Published: November 2021

Abstract
Whole-genome duplications (WGDs) have long been considered the causal mechanism underlying dramatic increases to morphological complexity due to the neo-functionalization of paralogs generated during these events. Nonetheless, an alternative hypothesis suggests that behind the retention of most paralogs is not neo-functionalization, but instead the degree of the inter-connectivity of the intended gene product, as well as the mode of the WGD itself. Here, we explore both the causes and consequences of WGD by examining the distribution, expression, and molecular evolution of microRNAs (miRNAs) in both gnathostome vertebrates as well as chelicerate arthropods. We find that although the number of miRNA paralogs tracks the number of WGDs experienced within the lineage, few of these paralogs experienced changes to the seed sequence, and thus are functionally equivalent relative to their mRNA targets. Nonetheless, in gnathostomes, although the retention of paralogs following the 1R autotetraploidization event is similar across the two subgenomes, the paralogs generated by the gnathostome 2R allotetraploidization event are retained in higher numbers on one subgenome relative to the second, with the miRNAs found on the preferred subgenome showing both higher expression of mature miRNA transcripts and slower molecular evolution of the precursor miRNA sequences. Importantly, WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MicroRNA-106b overexpression suppresses synovial inflammation and alleviates synovial damage in patients with rheumatoid arthritis
Authors: Liu Linchen , Chen Haiyan , Jiang Ting , He Dongyi 
Published: December 2021

ABSTRACT

Objectives
To explore the effect of miR-106b on synovial inflammation and damage in rheumatoid arthritis (RA) patients and further to investigate its possible mechanism.

Methods
Quantitative real-time polymerase chain reaction, immunofluorescence, in situ hybridization, and immunohistochemistry assay were used to verify the levels of miR-106b and cytokines. Pearson’s correlation analysis was conducted to examine bivariate relationship between miR-106b and cytokines or receptor activator of nuclear factor-κ B ligand (RANKL). Following the isolation of fibroblast-like synoviocytes (FLS), the cultured cells were separately transfected with or without miR-106b mimic. Thereafter, cell proliferation, invasion and migration were measured by Cell Counting Kit-8 assay and Transwell assay, respectively. Furthermore, concentration and expression of cytokines were separately detected by enzyme-linked immunosorbent assay and Western blot.

Results
Compared with osteoarthritis, RA patients had a lower level of miR-106b and higher levels of RANKL, tumour necrosis factor-a (TNF-a), and interleukin-6 (IL-6). The relative transcription of miR-106b level was negatively correlated to TNF-a, IL-6, and RNKAL levels in both patients (all P &lt; 0.05). Furthermore, miR-106b overexpression suppressed cell proliferation, migration, and invasion capacity of RA-FLS.

Conclusions
miR-106b overexpression suppresses synovial inflammation and alleviates synovial damage; thus, it may be served as a potential therapeutic target for RA patients.
SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning
Authors: Chandonia John-Marc , Guan Lindsey , Lin Shiangyi , Yu Changhua , Fox Naomi K , Brenner Steven E 
Published: November 2021

Abstract
The Structural Classification of Proteins—extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).
A novel role for gag as a cis-acting element regulating RNA structure, dimerization and packaging in HIV-1 lentiviral vectors
Authors: Vamva Eirini , Griffiths Alex , Vink Conrad A , Lever Andrew M L , Kenyon Julia C 
Published: November 2021

Abstract
Clinical usage of lentiviral vectors is now established and increasing but remains constrained by vector titer with RNA packaging being a limiting factor. Lentiviral vector RNA is packaged through specific recognition of the packaging signal on the RNA by the viral structural protein Gag. We investigated structurally informed modifications of the 5′ leader and gag RNA sequences in which the extended packaging signal lies, to attempt to enhance the packaging process by facilitating vector RNA dimerization, a process closely linked to packaging. We used in-gel SHAPE to study the structures of these mutants in an attempt to derive structure-function correlations that could inform optimized vector RNA design. In-gel SHAPE of both dimeric and monomeric species of RNA revealed a previously unreported direct interaction between the U5 region of the HIV-1 leader and the downstream gag sequences. Our data suggest a structural equilibrium exists in the dimeric viral RNA between a metastable structure that includes a U5–gag interaction and a more stable structure with a U5–AUG duplex. Our data provide clarification for the previously unexplained requirement for the 5′ region of gag in enhancing genomic RNA packaging and provide a basis for design of optimized HIV-1 based vectors.
Fecundity and density dependence can be estimated from mark–recapture data for making population projections
Authors: Şen Bilgecan , Akçakaya H Reşit 
Published: November 2021

Abstract
Forecasting changes in size and distributions of populations is an essential component of conservation assessments. Such forecasts are only useful for species conservation and management when they are based on robust estimators of fecundity, survival, and density dependence. While apparent survival estimation is the main focus of mark–recapture modeling, fecundity and density dependence are rarely the subject of these models. Here, we present a Bayesian hierarchical framework that can estimate fecundity and density dependence along with age-based survival using only robust-design capture–recapture data. We refer to this framework as RD-pop. We used simulated capture histories to demonstrate that RD-pop can estimate vital rates and their density dependence with little bias. We applied RD-pop to capture history data from Brown Creeper (Certhia americana) and showed that estimates of fecundity are consistent with the breeding biology of this species. Finally, we illustrate that density dependence, even when estimated with uncertainty in the RD-pop framework, regularizes population dynamics and reduces the frequent population extinctions and explosions observed under density-independent models. RD-pop is a useful addition to the current mark–recapture modeling toolbox especially when the goal is to build population models that can make medium- and long-term projections. It can be applied to any population for which long-term robust-design mark–recapture data are available, and with slight modifications (incorporation of weather and climate effects on vital rates) has the potential to facilitate demographic projections under climate change.