bluuebunny/crossref_metadata_2025 huggingface dataset:
Effective sequence similarity detection with strobemers
Authors: Sahlin Kristoffer
Published: October 2021

k-mer-based methods are widely used in bioinformatics for various types of sequence comparisons. However, a single mutation will mutate k consecutive k-mers and make most k-mer-based applications for sequence comparison sensitive to variable mutation rates. Many techniques have been studied to overcome this sensitivity, for example, spaced k-mers and k-mer permutation techniques, but these techniques do not handle indels well. For indels, pairs or groups of small k-mers are commonly used, but these methods first produce k-mer matches, and only in a second step, a pairing or grouping of k-mers is performed. Such techniques produce many redundant k-mer matches owing to the size of k. Here, we propose strobemers as an alternative to k-mers for sequence comparison. Intuitively, strobemers consist of two or more linked shorter k-mers, where the combination of linked k-mers is decided by a hash function. We use simulated data to show that strobemers provide more evenly distributed sequence matches and are less sensitive to different mutation rates than k-mers and spaced k-mers. Strobemers also produce higher match coverage across sequences. We further implement a proof-of-concept sequence-matching tool StrobeMap and use synthetic and biological Oxford Nanopore sequencing data to show the utility of using strobemers for sequence comparison in different contexts such as sequence clustering and alignment scenarios.
Decoding the function of bivalent chromatin in development and cancer
Authors: Kumar Dhirendra , Cinghu Senthilkumar , Oldfield Andrew J. , Yang Pengyi , Jothi Raja
Published: October 2021

Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Prevalent in embryonic stem cells (ESCs), bivalency is postulated to poise/prime lineage-controlling developmental genes for rapid activation during embryogenesis while maintaining a transcriptionally repressed state in the absence of activation cues; however, this hypothesis remains to be directly tested. Most gene promoters DNA hypermethylated in adult human cancers are bivalently marked in ESCs, and it was speculated that bivalency predisposes them for aberrant de novo DNA methylation and irreversible silencing in cancer, but evidence supporting this model is largely lacking. Here, we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. Genome-wide studies in differentiating ESCs reveal that activation of bivalent genes is no more rapid than that of other transcriptionally silent genes, challenging the premise that H3K4me3 is instructive for transcription. H3K4me3 at bivalent promoters—a product of the underlying DNA sequence—persists in nearly all cell types irrespective of gene expression and confers protection from de novo DNA methylation. Bivalent genes in ESCs that are frequent targets of aberrant hypermethylation in cancer are particularly strongly associated with loss of H3K4me3/bivalency in cancer. Altogether, our findings suggest that bivalency protects reversibly repressed genes from irreversible silencing and that loss of H3K4me3 may make them more susceptible to aberrant DNA methylation in diseases such as cancer. Bivalency may thus represent a distinct regulatory mechanism for maintaining epigenetic plasticity.
anaklasis: a compact software package for model-based analysis of specular neutron and X-ray reflectometry data sets
Authors: Koutsioubas Alexandros
Published: October 2021

anaklasis constitutes a set of open-source Python scripts that facilitate a range of specular neutron and X-ray reflectivity calculations, involving the generation of theoretical curves and the comparison/fitting of interfacial model reflectivity against experimental data sets. The primary focus of the software is twofold: on one hand to offer a more natural framework for model definition, requiring minimum coding literacy, and on the other hand to include advanced analysis methods that have been proposed in recent work. Particular attention is given to the ability to co-refine reflectivity data and to the estimation of model-parameter uncertainty and covariance using bootstrap analysis and Markov chain Monte Carlo sampling. The compactness and simplicity of model definition together with the streamlined analysis do not present a steep learning curve for the user, an aspect that may accelerate the generation of reproducible, easily readable and statistically accurate reports in future neutron and X-ray reflectivity related literature.
Integration in a mixed-method case study of construction phenomena: from data to theory
Authors: Amadi Alolote
Published: October 2021

Purpose

This study demonstrates integration within a mixed-methods case study of construction phenomena, whilst ensuring reliability and validity. This is in view of the established philosophical challenges in theory generation, whereby qualitative and quantitative methods are underpinned by divergent, almost incompatible, paradigmic assumptions.

Design/methodology/approach

The study uses a sample case study research on the phenomenon of cost overruns, supported by a coherent flow of well-articulated philosophical arguments to idealise the logic of integration. Issues of reliability and validity were resolved along these lines, by incorporating applicable criteria from both the qualitative and qualitative strands. A detailed outline and rationalisation of the stepwise approach to achieving integration are provided, from the point of design conceptualisation, data collection, analysis and further down to theory generation.

Findings

The study generated two level-1 theories by collecting numerical data on cost overruns, geotechnical index parameters and textual data on the geotechnical practices. Another level-1 theory was generated in reflexive adaptation to unanticipated social constructs emerging from the qualitative data. All level-1 theories from the quantitative and qualitative strands were triangulated to yield two “level-2 theories”: A log-regression model and a cognitive map. The approach to integration is thus explanatory sequential, and concurrent (at the second stage of transformation in the generation of level-2 theories).

Research limitations/implications

The study empirically reinforces that ontological flexibility, achievable through the use of thoughtfully designed integrated mixed-methods case studies, permits the investigation of multidimensional construction phenomena in innovative ways, relevant to provide holistic theoretical and practice-based contributions.

Originality/value

The study practically signposts a bespoke stepwise approach to integration, in a mixed-methods case study of construction phenomena, against the contextual backdrop of its relative novelty and lack of studies delving in-depth into the theoretical nitty-gritty.
Proposing a multifaceted model for adopting prefabricated construction technology in the construction industry
Authors: Yuan Mengqi , Li Zhongfu , Li Xiaodong , Luo Xiaowei , Yin Xianfei , Cai Jin
Published: October 2021

Purpose

Although prefabricated construction (PC) technology has attracted considerable attention worldwide because of its significant role in the global fight against COVID-19, market-driven adoption is still limited. The mechanisms for PC technology adoption have yet to be defined, which inhibits its diffusion in the construction market. This study aims to reveal the intrinsic motivation and action mechanism for PC technology adoption.

Design/methodology/approach

Drawing on the technology acceptance model (TAM), the study integrates characteristics from the diffusion of innovation theory to propose a multifaceted model for explaining practitioners’ PC technology adoption behavior from technology, organization and environment contexts. The proposed theoretical model was empirically examined via a survey of 234 professionals in mainland China using the partial least squares-structural equation modeling technique.

Findings

The outcomes indicated that relative advantage, corporate social responsibility and market demand are significantly positively related to practitioners’ perceived usefulness from PC technology. Regulatory support and trading partner support have noticeable positive effects on practitioners’ perceived ease of use from PC technology. Perceived ease of use is found to positively influence perceived usefulness, and both of them have a positive influence on the attitude toward adopting PC technology. Attitude is further confirmed as an important predictor of adoption intention, which would lead to actual PC technology adoption behavior.

Originality/value

To the best of the authors’ knowledge, this paper is the first attempt to explore industry perceptions toward PC technology adoption, providing valuable guidance for the effective diffusion of PC technology and laying a reliable foundation for research on other construction innovation adoption in post-COVID-19.
Teamwork makes the net-work: participant-governed networks and athletics sustainability collaboration
Authors: Barrett Martin , Jones Gareth J. , Bunds Kyle S. , Casper Jonathan M. , Edwards Michael B.
Published: October 2021

Purpose

Athletic departments play an important role in sustainability-based collaborative processes due to their boundary spanning connections with both internal and external university stakeholders. As a result, athletic department representatives have become prominent members of university participant-governed network structures. The purpose of this study is to examine the role of dedicated “athletics green teams” as a unique form of control and coordination by considering how green team interactions support and augment the collaborative network of actors who are responsible for executing athletics sustainability practices on university campuses.

Design/methodology/approach

A sociocentric analysis is used to explore the network of a green team at a large American university. The analysis focuses on examining the size, composition and structure of relations involving green team members that facilitated various forms of information transmission and strategic action(s).

Findings

The results highlight how the presence of the athletic department in the green team provides heterophilous and multiplex relations across the collaborative network and how the green team itself provides a unique forum for planning and coordination, which is critical for providing more sophisticated, advanced structures for sustainability.

Practical implications

The findings of this study should reassure practitioners involved in convening green teams that such shared governance structures add value to athletics sustainability collaborative processes. In addition, subtle changes to the network governance structures has the potential to streamline the contribution of athletic departments to university sustainability initiatives and help project a more cohesive “Athletics” sustainability message that transmits across the collaborative network.

Originality/value

The outcomes of dedicated athletics green teams have been explored from a largely qualitative perspective. However, this study applies a novel relational approach to understand the shared governance value-added within a largely intra-organizational collaborative network.
Retrospective analysis of the clinical characteristics and patient‐reported outcomes in vulval lichen planus: Results from a single‐center study
Authors: Boch Katharina , Langan Ewan A. , Zillikens Detlef , Ludwig Ralf J. , Kridin Khalaf
Published: October 2021

Vulval lichen planus (VLP) is a rare, but often chronic, inflammatory disease whose symptoms include genital pain, discomfort, and dyspareunia. The clinical manifestations include erythema, erosions, and scarring. The aim of this study was to longitudinally investigate patient‐reported outcomes and clinical findings in patients with VLP. Patients (>18 years) with histologically confirmed VLP were included in the retrospective analysis. Patient demographics, clinical features, symptomatology, quality of life, management, clinical outcomes, and comorbidities associated with VLP were analyzed. Twenty‐four patients were identified with a mean (standard deviation [SD]) follow‐up time of 19.3 (13.8) months. Classical VLP with glazed erythema was found in seven (29.2%) patients, erosive VLP was present in 15 (62.5%) patients, and hypertrophic VLP in two (8.3%). Seven patients had additional cutaneous involvement, while six patients had both vulval and oral mucosal involvement. The labia minora was the most frequently affected anatomical site (83.3%), followed by the clitoris (58.3%). Scarring lesions were found in 62.5% (n = 15) of patients. All study participants received treatment with potent and/or superpotent topical corticosteroids but 50% required systemic therapy (acitretin, corticosteroids, or hydroxychloroquine). Five (20.8%) patients underwent surgery due to adhesions and scarring resulting from VLP. One patient was diagnosed with a vulval squamous cell carcinoma during long‐term follow‐up. The mean (SD) Dermatology Life Quality Index score was 8.4 (5.5) at presentation and 8.9 (6.8) at the end of follow‐up. In conclusion, VLP was associated with moderate quality of life impairments which persisted despite treatment, suggesting that current treatments for VLP are inadequate.
Phytoplankton diversity affects biomass and energy production differently during community development
Authors: Ghedini Giulia , Marshall Dustin J. , Loreau Michel
Published: October 2021

Biodiversity determines the productivity and stability of ecosystems but some aspects of biodiversity–ecosystem functioning relationships remain poorly resolved. One key uncertainty is the inter‐relationship between biodiversity, energy and biomass production as communities develop over time. Energy production drives biomass accumulation but the ratio of the two processes can change during community development. How biodiversity affects these temporal patterns remains unknown.

We empirically assessed how species diversity mediates the rates of increase and maximum values of biomass and net energy production in experimental phytoplankton communities over 10 days in the laboratory. We used five phytoplankton species to assemble three levels of diversity (monocultures, bicultures and communities) and we quantify their changes in biomass production and energy fluxes (energy produced by photosynthesis, consumed by metabolism, and net energy production as their difference) as the cultures move from a low density, low competition system to a high density, high competition system.

We find that species diversity affects both biomass and energy fluxes but in different ways. Diverse communities produce net energy and biomass at faster rates, reaching greater maximum biomass but with no difference in maximum net energy production. Bounds on net energy production seem stronger than those on biomass because competition limits energy fluxes as biomass accumulates over time.

In summary, diversity initially enhances productivity by diffusing competitive interactions but metabolic density dependence reduces these positive effects as biomass accumulates in older communities. By showing how biodiversity affects both biomass and energy fluxes during community development, our results demonstrate a mechanism that underlies positive biodiversity effects and offer a framework for comparing biodiversity effects across systems at different stages of development and disturbance regimes.

A free Plain Language Summary can be found within the Supporting Information of this article.
Copy number variation of the SRY gene showed an association with disorders of sex development in Yorkshire Terrier dogs
Authors: Krzeminska P. , Nowacka‐Woszuk J. , Switonski M.
Published: October 2021

The molecular background of disorders of sex development (DSD) in dogs is poorly understood. Several copies of the SRY genes have been reported in the dog genome. We used droplet digital PCR with the aim of determining variability in SRY copy number and its association with DSD in dogs. Altogether 19 DSD male dogs (XY DSD) of 10 breeds and 87 control dogs of eight breeds were analyzed. Moreover, we performed a comparative analysis of SRY copy number in other canids: wolves (3), red foxes (16), and Chinese raccoon dogs (10). We found that the modal number of SRY copies in dogs, wolves, red foxes, and Chinese raccoon dogs was 3, 3, 1, and 3 respectively. Variability of copy number was only observed in Yorkshire Terriers (two or three copies) and red foxes (one or two copies). An analysis of six DSD Yorkshire Terriers and 38 control males of this breed showed that 50% of the DSD dogs had two copies, while the incidence of this variant was significantly lower in the control dogs (10.5%). Searching for the copy number of the coding and 5′‐flanking fragments revealed full concordance with the copy number. These fragments were also sequenced in DSD (19) and control (24) dogs, and no DNA variants were found. We conclude that, in the dog, two or three functional copies of the SRY gene are present, and a smaller number of copies showed an association with the risk of DSD phenotype in Yorkshire Terriers.
Nitric oxide (NO) synthase but not NO, HNO or H2O2 mediates endothelium‐dependent relaxation of resistance arteries from patients with cardiovascular disease
Authors: Matthies Maximilian , Rosenstand Kristoffer , Nissen Inger , Muitjens Stan , Riber Lars P. , De Mey Jo G. R. , Bloksgaard Maria
Published: October 2021

Background and Purpose

Superoxide anions can reduce the bioavailability and actions of endothelium‐derived NO. In human resistance‐sized arteries, endothelium‐dependent vasodilatation can be mediated by H2O2 instead of NO. Here, we tested the hypothesis that in resistance arteries from patients with cardiovascular disease, endothelium‐dependent vasodilatation is mediated by a reactive oxygen species and not impaired by oxidative stress.

Experimental Approach

Small arteries were isolated from biopsies of the parietal pericardium of patients undergoing elective cardiothoracic surgery and were studied using immunohistochemical and organ chamber techniques.

Key Results

NO synthases 1, 2 and 3, superoxide dismutase 1 and catalase proteins were observed in the microvascular wall. Relaxing responses to bradykinin were endothelium dependent. During submaximal depolarization‐induced contraction, bradykinin‐mediated relaxations were inhibited by inhibitors of NO synthases (NOS) and soluble guanylyl cyclase (sGC) but not by scavengers of NO or HNO, inhibitors of cyclooxygenases, neuronal NO synthase, superoxide dismutase or catalase, or by exogenous catalase. During contraction stimulated by endothelin‐1, these relaxations were not reduced by any of these interventions except DETCA, which caused a small reduction.

Conclusion and Implications

In resistance arteries from patients with cardiovascular disease, endothelium‐dependent relaxations seem not to be mediated by NO, HNO or H2O2, although NOS and sGC can be involved. These vasodilator responses continue during excessive oxidative stress.
Interleukin-17E, inducible nitric oxide synthase and arginase1 as new biomarkers in the identification of neutrophilic dermatoses
Authors: Stalder R. , Brembilla N. , Conrad C. , Yawalkar N. , Navarini A. , Boehncke WH. , Kaya G.
Published: October 2021

Background

Neutrophilic dermatoses (ND) are a heterogeneous group of diseases, but can often have a relatively similar histological appearance.

Aim

To identify a combination of biomarkers allowing a better differentiation of ND types.

Methods

Biopsies were obtained from normal human skin (NS; n = 4), chronic plaque-type psoriasis (PsO; n = 7), paradoxical psoriasis (PP; n = 8), generalized pustular psoriasis (GPP; n = 9), subcorneal pustular dermatosis of Sneddon–Wilkinson (SPD; n = 3), acute generalized exanthematous pustulosis (AGEP; n = 3), hidradenitis suppurativa (HS; n = 7), Sweet syndrome (SS; n = 8) and pyoderma gangrenosum (PG; n = 8). Samples were analysed by immunofluorescence using three biomarkers, interleukin (IL)-17E, inducible nitric oxide synthase (iNOS) and arginase1, each one in combination with two cell markers, myeloperoxidase (MPO) and CD68, which allow the identification of neutrophils and macrophages, respectively.

Results

We found that SS is characterized by high expression of IL-17E and iNOS in the epidermis, while PG exhibits low expression. The density of the neutrophil infiltrate helps to differentiate PP (high-density infiltrate) from PsO (low-density infiltrate). High expression of arginase1 in the granular layer of the epidermis is a hallmark of SPD. Finally, mature neutrophils and proinflammatory macrophages are readily detectable in PP, SPD and PG, whereas immature neutrophils and anti-inflammatory macrophages are more frequent in GPP, AGEP, HS and SS.

Conclusions

The analysis of ND by immunofluorescence using IL-17E, iNOS and arginase1 in combination with MPO and CD68 allows for characterization of differential expression patterns in the epidermis as well as the determination of the polarization status of the dermal neutrophils and macrophages. The appropriate markers may help in the differentiation of ND in clinical practice.
Assessing the extinction risk of insular, understudied marine species
Authors: Thomas Elin A. , Böhm Monika , Pollock Caroline , Chen Chong , Seddon Mary , Sigwart Julia D.
Published: October 2021

Hydrothermal vents are rare deep‐sea oases that house faunal assemblages with a similar density of life as coral reefs. Only approximately 600 of these hotspots are known worldwide, most only one‐third of a football field in size. With advancing development of the deep‐sea mining industry, there is an urgent need to protect these unique, insular ecosystems and their specialist endemic faunas. We applied the IUCN (International Union for the Conservation of Nature) Red List criteria to assess the extinction risk of vent‐endemic molluscs with varying exposure to potential deep‐sea mining. We assessed 31 species from three key areas under different regulatory frameworks in the Indian, West Pacific, and Southern Oceans. Three vent mollusc species were also examined as case studies of different threat contexts (protected or not from potential mining) to explore the interaction of local regulatory frameworks and IUCN Red List category assignment. We found that these assessments were robust even when there was some uncertainty in the total range of individual species, allowing assessment of species that have only recently been named and described. For vent‐endemic species, regulatory changes to area‐based management can have a greater impact on IUCN Red List assessment outcomes than incorporating additional data about species distributions. Our approach revealed the most useful IUCN Red List criteria for vent‐endemic species: criteria B and D2. This approach, combining regulatory framework and distribution, has the potential to rapidly gauge assessment outcomes for species in insular systems worldwide.
Multimodal opioid‐sparing pain management after lung transplantation and the impact of liposomal bupivacaine intercostal nerve block
Authors: Lewis Tyler C. , Sureau Kimberly , Katz Alyson , Fargnoli Anthony , Lesko Melissa , Rudym Darya , Angel Luis F. , Chang Stephanie H. , Kon Zachary N.
Published: October 2021

Opioid analgesics are commonly used post‐lung transplant, but have many side effects and are associated with worse outcomes. We conducted a retrospective review of all lung transplant recipients who were treated with a multimodal opioid‐sparing pain protocol. The use of liposomal bupivacaine intercostal nerve block was variable due to hospital restrictions. The primary objective was to describe opioid requirements and patient‐reported pain scores early post‐lung transplant and to assess the impact of intraoperative liposomal bupivacaine intercostal nerve block. We treated 64 lung transplant recipients with our protocol. Opioid utilization decreased to a mean of 43 milligram oral morphine equivalents by postoperative day 4. Median pain scores peaked at 4 on postoperative day 1 and decreased thereafter. Only three patients were discharged home with opioids, all of whom were taking opioid agonist therapy pre‐transplant for opioid use disorder. Patients who received liposomal bupivacaine intercostal nerve block in the operating room had a significant reduction in opioid consumption over postoperative day 1 through 4 (228 mg vs. 517 mg, P= .032). A multimodal opioid‐sparing pain management protocol is feasible and resulted in weaning of opioids prior to hospital discharge.
Dapsone in hidradenitis suppurativa: A case series of 56 patients
Authors: López‐Llunell Cristina , Riera‐Martí Núria , Gamissans Marta , Romaní Jorge
Published: October 2021

Hidradenitis suppurativa (HS) is a chronic inflammatory disease with a challenging treatment. Current guidelines reserve dapsone as a third line agent for patients with mild to moderate HS. To our knowledge, only four small case series have been reported. The objective of this study was to assess the effectiveness and safety of dapsone in our clinical practice. A retrospective observational single‐center study of 56 HS patients who underwent treatment with dapsone from May 1, 2015, to June 1, 2021, was performed. The Hidradenitis Suppurativa Clinical Response (HiSCR) scale was used to evaluate the response to treatment. Fifty‐six patients were included, 66% of which were men, with a median age of 33 years. Most of them had mild or moderate disease and belonged to LC2 follicular phenotype. All patients had been refractory to first‐line treatments. Dapsone was prescribed at doses of 50–150 mg/day. 62.5% of the patients achieved HiSCR after 12 weeks of treatment. No serious adverse reactions were detected. The median duration of treatment was 8 months. After multivariate analysis, an association was found between the presence of fistulous tracts and the risk of non‐response to the drug. In four of the dapsone responders, oral retinoids were added to achieve a sustained response. Limitations include the retrospective and non‐controlled nature of this study. In conclusion, dapsone is an effective and well‐tolerated option for long‐term HS treatment, and in this series, it was mainly chosen for patients with LC2 phenotype. It would be interesting to study combination with retinoids and other management options.
Crystal structures of the SARS‐CoV‐2 nucleocapsid protein C‐terminal domain and development of nucleocapsid‐targeting nanobodies
Authors: Jia Zhenghu , Liu Chen , Chen Yuewen , Jiang Heng , Wang Zijing , Yao Jialu , Yang Jie , Zhu Jiaxing , Zhang Boqing , Yuchi Zhiguang
Published: October 2021

The ongoing outbreak of COVID‐19 caused by SARS‐CoV‐2 has resulted in a serious public health threat globally. Nucleocapsid protein is a major structural protein of SARS‐CoV‐2 that plays important roles in the viral RNA packing, replication, assembly, and infection. Here, we report two crystal structures of nucleocapsid protein C‐terminal domain (CTD) at resolutions of 2.0 Å and 3.1 Å, respectively. These two structures, crystallized under different conditions, contain 2 and 12 CTDs in asymmetric unit, respectively. Interestingly, despite different crystal packing, both structures show a similar dimeric form as the smallest unit, consistent with its solution form measured by the size‐exclusion chromatography, suggesting an important role of CTD in the dimerization of nucleocapsid proteins. By analyzing the surface charge distribution, we identified a stretch of positively charged residues between Lys257 and Arg262 that are involved in RNA‐binding. Through screening a single‐domain antibodies (sdAbs) library, we identified four sdAbs targeting different regions of nucleocapsid protein with high affinities that have future potential to be used in viral detection and therapeutic purposes.
Emerging roles of ferroptosis in infectious diseases
Authors: Bagayoko Salimata , Meunier Etienne
Published: October 2021

In living organisms, lipid peroxidation is a continuously occurring cellular process and therefore involved in various physiological and pathological contexts. Among the broad variety of lipids, polyunsaturated fatty acids (PUFA) constitute a major target of oxygenation either when released as mediators by phospholipases or when present in membranous phospholipids. The last decade has seen the characterization of an iron‐ and lipid peroxidation‐dependent cell necrosis, namely, ferroptosis, that involves the accumulation of peroxidized PUFA‐containing phospholipids. Further studies could link ferroptosis in a very large body of (physio)‐pathological processes, including cancer, neurodegenerative, and metabolic diseases. In this review, we mostly focus on the emerging involvement of lipid peroxidation‐driven ferroptosis in infectious diseases, and the immune consequences. We also discuss the putative ability of microbial virulence factors to exploit or to dampen ferroptosis regulatory pathways to their own benefit.
Systematic over‐crediting in California's forest carbon offsets program
Authors: Badgley Grayson , Freeman Jeremy , Hamman Joseph J. , Haya Barbara , Trugman Anna T. , Anderegg William R. L. , Cullenward Danny
Published: October 2021

Carbon offsets are widely used by individuals, corporations, and governments to mitigate their greenhouse gas emissions on the assumption that offsets reflect equivalent climate benefits achieved elsewhere. These climate‐equivalence claims depend on offsets providing real and additional climate benefits beyond what would have happened, counterfactually, without the offsets project. Here, we evaluate the design of California's prominent forest carbon offsets program and demonstrate that its climate‐equivalence claims fall far short on the basis of directly observable evidence. By design, California's program awards large volumes of offset credits to forest projects with carbon stocks that exceed regional averages. This paradigm allows for adverse selection, which could occur if project developers preferentially select forests that are ecologically distinct from unrepresentative regional averages. By digitizing and analyzing comprehensive offset project records alongside detailed forest inventory data, we provide direct evidence that comparing projects against coarse regional carbon averages has led to systematic over‐crediting of 30.0 million tCO2e (90% CI: 20.5–38.6 million tCO2e) or 29.4% of the credits we analyzed (90% CI: 20.1%–37.8%). These excess credits are worth an estimated $410 million (90% CI: $280–$528 million) at recent market prices. Rather than improve forest management to store additional carbon, California's forest offsets program creates incentives to generate offset credits that do not reflect real climate benefits.
Glass with hydration‐induced compressive stress profiles
Authors: Gross Timothy M. , Wu Jingshi , Aaldenberg Emily M. , Zheng Zheming , Sarafian Adam R. , Jones Joshua A. , Dimond Timothy E.
Published: October 2021

A novel potassium phospho‐aluminosilicate composition is described that can be strengthened by water vapor to achieve deep compressive stress (CS) profiles. Water vapor treatment at (A) 85°C and 85% relative humidity for 40 days results in a CS of 389 ± 20 MPa and a compressive depth of layer (DOL) of 18 ± 2 μm. When treated at (B) 160°C and 0.1 MPa for 7 days, a CS of 245 ± 20 MPa and a DOL of 40 ± 2 μm is achieved. Glasses with hydration‐induced stress profiles can provide high retained strength following flaw introduction compared with ion‐exchanged soda‐lime silicate glass. Sample treatment B also has an exemplary Vickers indentation cracking threshold value greater than 20 kgf. The hydration profile determined by secondary ion mass spectrometry (SIMS) is shown to closely match the stress profile for these samples. SIMS analysis also shows that the depth of water enrichment correlates well with the depletion depth of phosphorus. The high tendency towards water‐induced strengthening for this new type of glass even enables self‐strengthening by the generation of a near‐surface CS profile following exposure to ambient conditions.
The microbiome of dental and peri‐implant subgingival plaque during peri‐implant mucositis therapy: A randomized clinical trial
Authors: Philip Juliana , Buijs Mark J. , Pappalardo Vincent Y. , Crielaard Wim , Brandt Bernd W. , Zaura Egija
Published: October 2021

Aim

To assess the microbial effects of mechanical debridement in conjunction with a mouthrinse on sites with peri‐implant mucositis and gingivitis.

Materials and methods

Eighty‐nine patients with peri‐implant mucositis were included in a double‐blinded, randomized, placebo‐controlled trial with mechanical debridement and 1‐month use of either delmopinol, chlorhexidine (CHX), or a placebo mouthrinse. Submucosal and subgingival plaque samples of implants and teeth were collected at baseline and after 1 and 3 months, processed for 16S V4 rRNA gene amplicon sequencing, and analysed bioinformatically.

Results

The sites with peri‐implant mucositis presented with a less diverse and less anaerobic microbiome. Exposure to delmopinol or CHX, but not to the placebo mouthrinse resulted in microbial changes after 1 month. The healthy sites around the teeth harboured a more diverse and more anaerobe‐rich microbiome than the healthy sites around the implants.

Conclusions

Peri‐implant sites with mucositis harbour ecologically less complex and less anaerobic biofilms with lower biomass than patient‐matched dental sites with gingivitis while eliciting an equal inflammatory response. Adjunctive antimicrobial therapy in addition to mechanical debridement does affect both dental and peri‐implant biofilm composition in the short term, resulting in a less dysbiotic subgingival biofilm.
Perception, knowledge and attitudes on advance medical directives among hospital staff: Using mixed methodology
Authors: Park Mi Hee , Seong Mihyeon , Sok Sohyune
Published: October 2021

Background

It is necessary to examine the level of perception, knowledge and attitudes of the medical staff for advance medical directives, which are practical alternatives to good practice for end‐of‐life care in the actual medical field.

Purpose

This study was conducted to determine the degree of perception, knowledge and attitude of cancer hospital medical staff about advance medical directives, and to confirm the relationship between them. It also explored their experiences with advance medical directives.

Methods

This study used a convergent design to collect quantitative and qualitative data separately in the mixed methodology. This design adheres to the STROBE guidelines. Participants were a total of 140 subjects (70 doctors and 70 nurses) with more than 3 years and considered to have sufficient experience related to the study purpose. Focus group participants were a total 19 persons (9 doctors and 10 nurses).

Results

Mean score for perception was 35.40, which indicates lower perception when compared to the median value (37.50 points). Perception of advance medical directives had significant, positive relations with attitude of advance medical directives (p = .032). The perception on attitude of advance medical directives factor was significantly influencing (p = .021). As a result of the analysis based on qualitative research questions, six subjects and 11 categories were created by deriving meaningful sentences from the statements.

Conclusion

This study suggests that the perception of medical professionals about advance medical directives has a positive correlation with attitudes, as well as a causal relationship.

Relevance to clinical practice

Based on the finding from this study, concrete strategies and interventions to improve the perception of advance medical directives among cancer hospital medical staff are needed.
Why and Under What Conditions Does Loss Aversion Emerge?1
Authors: Nagaya Kazuhisa
Published: October 2021

A person's propensity to attribute more weight to a loss than a gain of equal magnitude is known as “loss aversion.” Loss aversion is a component of the prospect theory (which provides a descriptive account of a person's value judgments) and has broad effects in terms of market transactions, intrapersonal decision‐making, and behavioral regulations. Previous studies have considered loss aversion as an omnipresent fundamental psychological bias; however, recent studies have highlighted the limitations of its impact. Accordingly, this paper summarizes the process and boundary conditions of loss aversion in decision‐making under risk, considering four distinct approaches: the absolute magnitude of losses, the bias of attentional allocation, the ranking of losses relative to gains, and the preference for inaction. A comprehensive overview of studies that examined loss aversion from these different perspectives reveals detailed boundary conditions for loss aversion and provides an in‐depth perspective on the mechanism of its occurrence. Based on these findings, specific directions for future loss‐aversion studies are discussed.
Telomerase activity in ecological studies: What are its consequences for individual physiology and is there evidence for effects and trade‐offs in wild populations
Authors: Smith Steve , Hoelzl Franz , Zahn Sandrine , Criscuolo François
Published: October 2021

Increasing evidence at the cellular level is helping to provide proximate explanations for the balance between investment in growth, reproduction and somatic maintenance in wild populations. Studies of telomere dynamics have informed researchers about the loss and gain of telomere length both on a seasonal scale and across the lifespan of individuals. In addition, telomere length and telomere rate of loss seems to have evolved differently among taxonomic groups, and relate differently to organismal diversity of lifespan. So far, the mechanisms behind telomere maintenance remain elusive, although many studies have inferred a role for telomerase, an enzyme/RNA complex known to induce telomere elongation from laboratory studies. Exciting further work is also emerging that suggests telomerase (and/or its individual component parts) has a role in fitness that goes beyond the maintenance of telomere length. Here, we review the literature on telomerase biology and examine the evidence from ecological studies for the timing and extent of telomerase activation in relation to life history events associated with telomere maintenance. We suggest that the underlying mechanism is more complicated than originally anticipated, possibly involves several complimentary pathways, and is probably associated with high energetic costs. Potential pathways for future research are numerous and we outline what we see as the most promising prospects to expand our understanding of individual differences in immunity or reproduction efficiency.
Three cases of GFAP astrocytopathy, one with bilateral ovarian teratoma
Authors: Osakada Yosuke , Omote Yoshio , Taira Yuki , Matsuoka Chika , Ikegami Ken , Tadokoro Koh , Nomura Emi , Kawahara Yuko , Sato Kota , Terasawa Yuka , Hishikawa Nozomi , Morihara Ryuta , Takemoto Mami , Kimura Akio , Shimohata Takayoshi , Yamashita Toru , Abe Koji
Published: October 2021

Glial fibrillary acidic protein (GFAP) astrocytopathy is a novel autoimmune meningoencephalomyelitis. Case 1 is a 26–year‐old (yo) woman with a bilateral ovarian teratoma. She presented neck stiffness, hyperreflexia, bilateral postural tremor, and urinary retention. Three courses of a methylprednisolone pulse and subsequent enucleation of the bilateral ovarian teratoma improved her neurological symptoms with no recurrence. Case 2 is a 46‐year‐old man who showed infectious‐like symptoms with elevated creatine kinase. Case 3 is a 76‐year‐old man with preceding weight loss, a hyperintensity lesion in the hypothalamus, and increased uptake of the spinal cord, assessed by Fluorine18 fluorodeoxyglucose positron emission tomography (18F‐FDG PET). We compared the clinical features of the present three cases with previous reports. Consciousness disturbance, neck stiffness, tremors, and urinary dysfunction were observed in all three cases. These findings suggest widespread damage of the brain and spinal cord.
Cellulose synthase‐like protein OsCSLD4 plays an important role in the response of rice to salt stress by mediating abscisic acid biosynthesis to regulate osmotic stress tolerance
Authors: Zhao Hui , Li Zixuan , Wang Yayun , Wang Jiayi , Xiao Minggang , Liu Hai , Quan Ruidang , Zhang Haiwen , Huang Rongfeng , Zhu Li , Zhang Zhijin
Published: October 2021

Cell wall polysaccharide biosynthesis enzymes play important roles in plant growth, development and stress responses. The functions of cell wall polysaccharide synthesis enzymes in plant growth and development have been well studied. In contrast, their roles in plant responses to environmental stress are poorly understood. Previous studies have demonstrated that the rice cell wall cellulose synthase‐like D4 protein (OsCSLD4) is involved in cell wall polysaccharide synthesis and is important for rice growth and development. This study demonstrated that the OsCSLD4 function‐disrupted mutant nd1 was sensitive to salt stress, but insensitive to abscisic acid (ABA). The expression of some ABA synthesis and response genes was repressed in nd1 under both normal and salt stress conditions. Exogenous ABA can restore nd1‐impaired salt stress tolerance. Moreover, overexpression of OsCSLD4 can enhance rice ABA synthesis gene expression, increase ABA content and improve rice salt tolerance, thus implying that OsCSLD4‐regulated rice salt stress tolerance is mediated by ABA synthesis. Additionally, nd1 decreased rice tolerance to osmotic stress, but not ion toxic tolerance. The results from the transcriptome analysis showed that more osmotic stress‐responsive genes were impaired in nd1 than salt stress‐responsive genes, thus indicating that OsCSLD4 is involved in rice salt stress response through an ABA‐induced osmotic response pathway. Intriguingly, the disruption of OsCSLD4 function decreased grain width and weight, while overexpression of OsCSLD4 increased grain width and weight. Taken together, this study demonstrates a novel plant salt stress adaptation mechanism by which crops can coordinate salt stress tolerance and yield.
Counterpossibles
Authors: Kocurek Alexander W.
Published: October 2021

Acounterpossibleis a counterfactual with an impossible antecedent. Counterpossibles present a puzzle for standard theories of counterfactuals, which predict that all counterpossibles are semantically vacuous. Moreover, counterpossibles play an important role in many debates within metaphysics and epistemology, including debates over grounding, causation, modality, mathematics, science, and even God. In this article, we will explore various positions on counterpossibles as well as their potential philosophical consequences.
Moral Testimony, Knowledge and Understanding
Authors: Viswanathan Kumar
Published: October 2021

This article explains why relying on moral testimony leaves an agent short of moral understanding. Hills’ version of that thesis and Sliwa’s contrary thesis are criticised, and their whole debate about whether moral knowledge is necessary and sufficient for moral understanding is found questionable. Following a line of thinking in Gaita’s philosophy, the assumption that the object of moral understanding must be a true proposition is rebutted and a more personal approach to moral understanding is developed. Relying on testimony for your moral beliefs leaves you short of moral understanding because you fail to make the beliefs your own.
Solvent‐ and Wavelength‐Dependent Photolysis of Estrone
Authors: Adriano Natalie , Ahearn Ceilidh , Black Cory , Cracchiolo Michael , Ghere Daniel , Nuñez Alexandra , Olivan Lars , Patel Raj , Saner Stephanie , Smith Krista R. , Watkins Barbie , Hare Patrick M.
Published: October 2021

The direct photolysis of estrone in solvents ranging from water to cyclohexane is reported. The photodegradation is dominated by lumiestrone, an epimer of estrone resulting from the inversion of the methyl group at carbon 13, regardless of solvent and photolysis wavelength in the range 254–320 nm. Solvent addition products are also observed in lesser amounts. The photodegradation rate in water is an order of magnitude slower than in nonaqueous solvents. Short wavelength excitation enhances photodegradation. Together, these results suggest complicated photophysics underlie the photochemistry with implications for the remediation of environmental estrogens.
Handgrip strength as a simple measure for screening prediabetes and type 2 diabetes mellitus risk among adults in Malawi: A cross‐sectional study
Authors: Manda Chrispin Mahala , Nakanga Wisdom P. , Mkandawire Joseph , Muula Adamson S. , Nyirenda Moffat J. , Crampin Amelia Catherine , Wagatsuma Yukiko
Published: October 2021

OBJECTIVE

Handgrip strength, a simple measure of muscle strength, has been reported as a predictor of both prediabetes and type 2 diabetes mellitus (T2DM) and has been suggested for screening prediabetes and T2DM risk. This study examined the relationship of handgrip strength with prediabetes and T2DM among rural‐ and urban‐dwelling adults in Malawi.

METHODS

This was a cross‐sectional study nested in a follow‐up study of prediabetic and prehypertensive individuals identified during an extensive noncommunicable disease survey in Malawi. A total of 261 participants (women: 64%) were recruited. Univariate and multivariate binary logistic regression analyses were performed to examine the association of prediabetes and T2DM with relative handgrip strength.

RESULTS

The mean (SD) age of the participants was 49.7 (13.6) years, and 54.0% were between the ages of 40 and 59 years. The mean (SD) absolute handgrip strength and relative handgrip strength were 28.8 (7.3) kg and 1.16 (0.40) kg/BMI, respectively, and the mean relative handgrip strength differed significantly (p < 0.001) by T2DM status. In unadjusted model, the odds ratio (OR) of prediabetes and T2DM per unit increase in relative handgrip strength was 0.12 [95% CI; 0.04–0.33]. The result remained significant after adjusting for age (continuous), sex, place of study, hypertension, dyslipidaemia and level of education (aOR [95% CI]; 0.19 [0.03–0.95]).

CONCLUSIONS

The findings suggest that handgrip strength could be a relatively inexpensive, noninvasive measure for contributing to risk scores to identify high‐risk individuals for screening diabetes in SSA.
Effect of Wear on Thermoelastic Instability Involving Friction Pair Thickness in Automotive Clutches
Authors: Qiao Yijun , Yi Yun-Bo , Wang Tie , Cui Hongwei , Lian Zisheng
Published: October 2021

Wear is an inevitable phenomenon in the working process of clutch and brake system. With the increase of transmission speed and power density, the thermoelastic instability (TEI) of clutch and brake system is becoming more serious over time. It is difficult to obtain the practical solution for conventional materials of clutches and brakes and their actual geometry with finite thickness using the existing analytical method. To study the comprehensive effects of wear and friction pair thickness on TEI, Archard Wear Law is combined with the Fourier Reduction Method to develop a finite element model, the accuracy of which is validated using the existing analytical method. Within the usual ranges of thickness and wear coefficient of friction pair, the increase of friction material thickness or the decrease of steel material thickness will suppress the TEI. Nonetheless, if the wear-rate is increased significantly, the effect of friction material thickness will be reversed. The worst thickness, which must be avoided in the design, and the local optimum thickness exist for the steel material.