bluuebunny/crossref_metadata_2025 huggingface dataset:
Family members’ conceptions of their supportive care needs across the colorectal cancer trajectory – A phenomenographic study
Authors: Samuelsson Maria , Jakobsson Jenny , Bengtsson Mariette , Lydrup Marie‐Louise , Wennick Anne
Published: June 2024

Aim

To describe the variations of family members' conceptions of their supportive care needs (SCN) across the colorectal cancer (CRC) trajectory.

Design

A descriptive qualitative study with a phenomenographic approach.

Method

Individual semi‐structured interviews were conducted from May 2022 to October 2022 with 23 family members of persons diagnosed with colorectal cancer. The interviews were analysed using phenomenographic analysis following the Consolidated criteria for reporting qualitative research (COREQ) checklist.

Results

The phenomenographic analysis resulted in five categories. Not of importance describes family members' needs as unimportant due to the good prognosis and the organization of care and in relation to the needs of others. Only satisfiable by professionals describes information possessed by the healthcare professionals as key, as well as the need for professional counselling for the family members to process their emotions. Managed by themselves describes family members preferring to manage their SCN themselves by turning to the appropriate social support and/or by using coping skills. Understood retrospectively describes SCN as only understandable when things have calmed down and as requiring one's own experience to understand. Left unmet describes SCN as unnoticed by the healthcare professionals or not brought to light by the family members, or family members not knowing where to turn for support.

Conclusion

Supportive care should involve individualized information, proactive and repeated assessments of needs across the trajectory, as well as encouragement of family members to reflect on their needs and to accept support when needed.

Impact

There is a gap in the literature regarding family members' SCN across the CRC trajectory which this study addresses. Findings show five categories of family members' conceptions of their SCN. Those findings could serve as a basis for the development of clinical colorectal supportive care across the cancer trajectory.

Implications for the Profession and/or Patient Care

Findings show that to offer family members of persons diagnosed with colorectal cancer support only at the time of diagnosis is insufficient. Instead, the healthcare team is recommended to proactively and repeatedly try to identify those in need and the characteristics of their needs. In addition, it is important to offer individualized information and strive to encourage family members to reflect on their situation and to not suppress their own needs if emerging.

Reporting Method

Reporting adheres to the consolidated criteria for reporting qualitative research (COREQ) checklist.

Patient or Public Contribution

No patient or public contribution.
Organisational culture in ‘better’ group homes for adults with intellectual and developmental disabilities in England: A qualitative study
Authors: Fox Diane , Beadle‐Brown Julie , Bradshaw Jill , Bigby Christine , Richardson Lisa
Published: June 2024

Background

Previous research identifies organisational culture as one of a number of factors associated with the quality of life outcomes of group home residents' with intellectual and developmental disabilities. This study aims to elaborate on the dimensions of group home culture in settings in England.

Method

Participant observations and semi‐structured interviews with staff were carried out in two group homes. Field‐notes, interview notes and transcripts were analysed using inductive thematic analysis by a researcher naïve to the project and the previous literature. Initial coding was re‐examined after sensitisation to theorised models in previous literature to identify the most parsimonious fit. The two settings were rated and compared using a five‐point Likert scale for each of the dimensions.

Results

The findings describe group home culture across seven dimensions. There were mixed ratings across the different dimensions reflecting inconsistencies in culture that were reflected in staff practice. The challenge in assigning a global rating of culture in group homes, which includes interactions across multiple staff and multiple residents over time, was highlighted.

Conclusion

The development of an observational measure of culture is highlighted as potentially helpful in understanding and responding to culture in services for individuals with intellectual and developmental disabilities.
Communities of metazoan parasites in seven sympatric skate species (Elasmobranchii, Rajidae) from the English Channel and Celtic Sea differing in conservation status
Authors: Gérard Claudia , Trochard Caroline , Hervé Maxime R. , Hamel Héloïse , Gay Mélanie , Barbier Michel , Trancart Thomas , Barreau Thomas
Published: June 2024

Elasmobranch populations are in steep decline mainly due to overfishing bycatch, but parasites may accelerate the collapse of vulnerable and/or highly parasitized species. We therefore studied metazoan parasites of Rajidae from the northeast Atlantic: vulnerable Leucoraja fullonica, near‐threatened Raja brachyura, Raja clavata, Raja microocellata and Raja undulata, and least‐concerned Raja montagui and Leucoraja naevus. Overall prevalence varied from 19% for R. montagui to 100% for L. fullonica. Parasite communities differed between skate species, and prevalence and abundance were higher for L. fullonica, R. microocellata, and R. undulata. We recorded 11 parasite taxa in the study: three nematodes, six cestodes, one monogenean, and one myxosporean. Whatever the skate species, the parasite component community comprised at least two nematode taxa among Phocanema spp., Proleptus sp. and Anisakis simplex. DNA‐sequencing revealed that Phocanema azarasi and Phocanema krabbei both occurred in R. microocellata and R. undulata. Phocanema spp. was first recorded in L. fullonica, L. naevus, R. microocellata, R. montagui, and R. undulata, as Proleptus sp. in L. fullonica, and A. simplex in L. fullonica and R. clavata, Rockacestus sp. and Nybelinia sp. in R. undulata, and gill‐myxosporeans on L. fullonica, L. naevus, R. microocellata, and R. undulata. The occurrence of 16 new host–parasite associations suggests potential environmental changes. Information provided by trophically transmitted helminths confirmed an opportunistic skate diet based on crustaceans and fish. We discuss results in terms of host fitness loss, bioindicator role of parasites, and anisakiasis risk. We recommend incorporating parasitology in research to improve elasmobranch conservation.
BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice
Authors: Li Zhen , Ye Junhua , Yuan Qiaoling , Zhang Mengchen , Wang Xingyu , Wang Jing , Wang Tianyi , Qian Hongge , Wei Xinghua , Yang Yaolong , Shang Lianguang , Feng Yue
Published: June 2024

Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss‐of‐function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2‐ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.
NETest in advanced high‐grade gastroenteropancreatic neuroendocrine neoplasms
Authors: Sorbye H. , Hjortland G. O. , Vestermark L. W. , Sundlov A. , Assmus J. , Couvelard A. , Perren A. , Langer S. W.
Published: June 2024

Molecular blood biomarkers are lacking for high‐grade (HG) gastroenteropancreatic (GEP) neuroendocrine neoplasms (NEN). To histologically distinguish between neuroendocrine carcinoma (NEC), neuroendocrine tumors G3 (NET G3), adenocarcinoma and MINEN is often challenging. The mRNA‐based NETest has diagnostic, prognostic and predictive value in neuroendocrine tumors G1‐2 but has not been studied in HG GEP‐NEN. Patients with advanced HG GEP‐NEN were prospectively included in an observational study. A blood sample was collected before the start of chemotherapy and pseudonymised before NETest was performed. NETest results are expressed as an activity index (NETest score) from 0 to 100. The normal score cut‐off is 20. Histological sections were pseudonymised before centralized pathological re‐evaluation. Samples from 60 patients were evaluable with the NETest. Main primary tumor sites were colon (14), rectum (12), pancreas (11) and esophagus (7). Re‐classification: 30 NEC, 12 NET G3, 3 HG‐NEN ambiguous morphology, 8 MiNEN, 3 adenocarcinomas with neuroendocrine differentiation (ADNE), 3 adenocarcinomas and 1 NET G2. Elevated NETest (>20) was seen in 38/45 (84%) HG GEP‐NEN, all 17 large‐cell NEC (100%), 11/13 (85%) small‐cell NEC, all ambiguous cases and 7/12 (64%) NET G3. NETest was elevated in 5/8 (63%) MiNEN, 2/3 ADNE, however not in 3 adenocarcinomas. Median survival was 10.2 months (9.6–10.8 95%CI) for evaluable HG GEP‐NEN treated with palliative chemotherapy (n = 39), and survival was significantly shorter in patients with NETest >60 with an OS of only 6.5 months. This is the first study to evaluate use of the NETest in advanced HG GEP‐NEN. The NETest was almost always elevated in GEP‐NEC and in all large‐cell NEC. The NETest was also frequently elevated in NET G3 and MiNEN, however cases were limited. Baseline NETest was not predictive for benefit of chemotherapy, however a NETest >60 was prognostic with a shorter survival for patients receiving chemotherapy.
Activities of cell‐wall‐degrading enzymes produced by Pestalotiopsis guepinii
Authors: Wu Sijun , Qiao Tianmin , Li Shujiang , Hu Binhong , Zhu Hanmingyue , Zhu Tianhui
Published: June 2024

Pestalotiopsis guepinii is a pathogenic fungus that causes grey blight on Camellia pitardii. In this study, we investigated the enzyme activity and kinetics of these cell‐wall‐degrading enzymes (CWDEs) produced by Pestalotiopsis guepinii in both C. pitardii leaves and culture medium. Our enzyme activity experiments revealed that the activities of xylanase, pectin methyl‐galacturonase (PMG), β‐1,4‐endoglucanase (Cx), and β‐glucosidase were high in both C. pitardii leaves and culture medium. These enzymes played a significant role in the pathogenic process. However, the activity of laccase was found to be very low and had a minor impact on the pathogenic process. Furthermore, our enzyme dynamics experiments demonstrated that the optimal reaction temperature for PMG and Cx was 50°C, while for β‐glucosidase and xylanase, it was 60°C. The optimal reaction pH for Cx, β‐glucosidase, and xylanase was 5.0, whereas for PMG, it ranged from 5.0 to 6.0. This indicates that these four enzymes prefer acidic conditions. Moreover, we observed that the activities of Cx, PMG, and xylanase decreased with increasing reaction time. On the other hand, the activity of β‐glucosidase initially increased sharply and then decreased slowly. The maximum reaction rates of the four cell‐wall‐degrading enzymes were ranked as follows: xylanase > PMG > β‐glucosidase > Cx. Additionally, the affinities of these enzymes with substrates were ranked as follows: PMG < Cx < xylanase < β‐glucosidase.
Vascular complications in extremities of physically restrained intensive care unit patients: A prospective, observational study
Authors: Yıldız İlknur , Özkaraman Ayse
Published: June 2024

Background

Physical restraint is used to prevent agitation, to continue treatments and to ensure safety in intensive care patients. Physical restraint has negative effects on physical and psychological health, and physical restraint should not be used unless necessary.

Aims

The purpose of this study was to evaluate the development of vascular complications in extremities of physically restrained patients hospitalized in the intensive care unit (ICU) and the associated factors.

Study Design

A prospective, observational study. The study was conducted between September 1, 2022, and March 31, 2023 in eight ICUs of a hospital located in the inner regions of Türkiye. The development of vascular complications (discolouration, distemperature, variations in capillary refill time, fluctuations in peripheral pulse, skin ulceration and oedema in the area of physical restraint) rate in patients hospitalized in the ICUs who were physically restrained. Independent sample t test, Mann–Whitney U test and Pearson‐χ2 test were used to analyse the data.

Results

During the study, 2409 patients were admitted to ICUs. Physical restraint was applied to 209 of these patients. Of the 209 patients, 112 patients who met the inclusion criteria were included in the study. The physical restraint site of the patients was evaluated an average of 230.12 times and physical restraint was terminated in 9.8% of the patients (n = 112) because of vascular complications that developed in the physical restraint site. The rate of vascular complications at the site of physical restraint was higher in patients with endotracheal tubes (p < .05), lower GCS scores (p < .05) and higher INR values (p < .05). Patients with skin ulceration at the restraint site received more massages and cream applications (%95CL = 1. 1.692–34.734, OR = 7.667, p = .032). It was determined that more massage was applied to patients with changes in skin temperature at the restraint site (%95Cl = 1.062–11.599, OR = 3.510, p = .032).

Conclusions

Vascular complications may develop at the restraint site in patients hospitalized in the ICU. This may be more common in ICU patients with endotracheal tube, lower GCS score and higher INR values.

Relevance to Clinical Practice

Nurses should closely monitor ICUs patients with endotracheal tube, lower GCS score and higher INR values, and implement care interventions to prevent the development of vascular complications.
Discriminative and exploitive stereotypes: Artificial intelligence generated images of aged care nurses and the impacts on recruitment and retention
Authors: Byrne Amy‐Louise , Mulvogue Jennifer , Adhikari Siju , Cutmore Ellie
Published: June 2024

This article uses critical discourse analysis to investigate artificial intelligence (AI) generated images of aged care nurses and considers how perspectives and perceptions impact upon the recruitment and retention of nurses. The article demonstrates a recontextualization of aged care nursing, giving rise to hidden ideologies including harmful stereotypes which allow for discrimination and exploitation. It is argued that this may imply that nurses require fewer clinical skills in aged care, diminishing the value of working in this area. AI relies on existing data sets, and thus represent existing stereotypes and biases. The discourse analysis has highlighted key issues which may further impact upon nursing recruitment and retention, and advocates for stronger ethical consideration, including the use of experts in data validation, for the way that aged care services and nurses are depicted and thus valued.
Reassembling nursing in the digital age: An actor‐network theory perspective
Authors: Wynn Matthew , Garwood‐Cross Lisa
Published: June 2024

This article explores the application of actor‐network theory (ANT) to the nursing profession, proposing a novel perspective in understanding nursing in the context of modern digital healthcare. Traditional grand nursing theories, while foundational, often fail to encapsulate the dynamic and complex nature of nursing, particularly in an era of rapid technological advancements and shifting societal dynamics. ANT, with its emphasis on the relationships between human and nonhuman actors, offers a framework to understand nursing beyond traditional paradigms. This article makes two key arguments: first, that nursing can be viewed as a highly organised social assemblage, where both human (nurses, patients and policymakers) and nonhuman actors (technologies, medical equipment, institutional policies) play a crucial role, and second, that ANT can be used to enhance existing nursing theory to better understand the role of technology in nursing practice. The article considers how ANT can provide a more holistic and adaptable model for describing the nursing profession, particularly in an era where technology plays an integral role in healthcare delivery. It discusses the implications of viewing nursing through ANT, highlighting the need for nursing education and practice to adapt to the interconnected and technologically advanced nature of modern healthcare. The article also acknowledges the limitations of ANT, particularly its potential oversimplification of the complex ethical dimensions inherent in nursing and its focus on observable phenomena.
Impact of histopathological parameters in prognosis of oral squamous cell carcinoma
Authors: Ekanayaka R. P. , Tilakaratne W. M.
Published: June 2024

Objective

Squamous cell carcinomas comprise approximately 90% of all oral malignancies. There is a wide geographical variation in the incidence of oral cancer, with South and South East Asia (SSEA) accounting for almost two third of new cases. The prognosis of oral cancer is influenced by a vast array of factors including demographic, clinical, histopathological and molecular factors. The objective this review is to analyse the impact of histopathological features assessed in hematoxylin and eosin stained sections on the prognosis of OSCC.

Materials and Methods

Medline and Scopus data base search was performed in order to identify related articles on histopathological parameters in predicting prognosis of oral squamous cell carcinoma. The primary emphasis is on the studies conducted in SSEA, with an accompanying comparison of their findings with those from research conducted in other parts of the world.

Results

It has been shown that the number of studies conducted in SSEA is not proportionate to the high prevalence of Oral Cancer in the region. There is no significant difference between the findings from SSEA compared to the rest of the world. It is clearly shown that most histopathological parameters can be accurately used to predict nodal metastasis and prognosis.

Conclusions

Histopathological parameters can be used reliably in planning treatment of Oral cancer. Clinicians should combine clinical and histopathological parameters in drawing treatment plan for Oral Cancer.
Left versus right ventricular pacing during TAVR and balloon aortic valvuloplasty: A systematic review and meta‐analysis
Authors: Khalefa Basma Badrawy , Ayyad Mohammed , Albandak Maram , Ayyad Alaa , Yassin Mazen Negmeldin Aly , Awad Ahmed K.
Published: July 2024

Introduction

While right ventricular pacing (RVP) is the conventional temporary pacing modality used for transcatheter aortic valve replacement (TAVR), this approach possesses inherent risks and procedural challenges. We aim to assess and compare the safety and efficacy of left ventricular pacing (LVP) and RVP during TAVR and balloon aortic valvuloplasty (BAV).

Methods

Following PRISMA guidelines, a comprehensive literature search was conducted in four databases from inception to December 15th, 2023. We included observational studies and clinical trials comparing LVP with RVP during TAVR and BAV procedures. Primary outcomes included short‐term mortality, mortality due to cardiac tamponade, and procedural complications including bleeding, vascular complications, and cardiac tamponade. Secondary outcomes comprised procedure duration and length of hospital stay.

Results

Five studies involving 830 patients with RVP and 1577 with LVP were included. Short‐term mortality was significantly higher in the RVP group (RR 2.32, 95% CI: [1.37–3.93], P = .002), as was the incidence of cardiac tamponade (RR 2.19, 95% CI: [1.11–4.32], P = .02). LVP demonstrated shorter hospital stays (MD = 1.34 d, 95% CI: [0.90, 1.78], P < .001) and reduced procedure duration (MD = 7.75 min, 95% CI: [5.08, 10.41], P < .00001) compared to RVP. New pacemaker implantation was higher in the RVP group (RR 2.23, 95% CI: [1.14, 4.39], P = .02).

Conclusion

LVP during TAVR and BAV emerges a safer alternative to RVP, offering reduced mortality, hospital stays, and procedure durations.
From bedside to genetic analysis: New insights into pathophysiology of melanoma, basal cell carcinoma, and other cancers
Authors: Zemtsov Alexander
Published: June 2024

Objective

Patients with myotonic muscular dystrophy (MMD) were observed to have numerous basal cell carcinoma (BCC) and abnormal dysplastic nevi (DN) on non‐sun exposed skin. Simultaneously a large study published in the Journal of American Medical Association (JAMA) illustrated that patients with MMD have “overall” an increased risk for cancer development. Based on these findings, this author in 2010 postulated that dysregulation of RNA binding proteins (RBP), responsible for clinical manifestations of MMD, is also responsible for the development of BCC and melanoma.

Methods

To report new research elucidating the etiology of melanoma, BCC, MMD‐induced cancers, and potentially other environmentally induced malignancies.

Results

Dysregulation of RBP induces aberrant mRNA splicing; recent data indicates that abnormal mRNA splicing not just plays a key role in the pathogenesis of melanoma but is a hallmark of essentially all human malignancies.

Conclusion

The author's hypothesis is that ultraviolet (UV) radiation induces DNA damage in intronic regions of a variety of genes. Furthermore, these UV‐induced abnormal DNA dimers, repeats and mutations interfere with normal mRNA splicing thus producing abnormal proteins. These abnormal proteins in turn activate oncogenic pathways such as hedgehog, MAP kinase, and WNT.
Blood donor return behavior in South Africa and the United States before and during the COVID‐19 pandemic
Authors: Jagirdar Huzbah , Nwobi Nkasiobi H. , Swanevelder Ronel , Cockeran Riana , Bruhn Roberta , Kaidarova Zhanna , Bravo Marjorie D. , van den Berg Karin , Custer Brian S. , Vassallo Ralph , Ding Yichuan , Panagiotoglou Dimitra , Russell W. Alton
Published: June 2024

Background

Studies preceding the COVID‐19 pandemic found that slower time‐to‐return was associated with first‐time, deferred, and mobile drive blood donors. How donor return dynamics changed during the COVID‐19 pandemic is not well understood.

Methods

We analyzed visits by whole blood donors from 2017 to 2022 in South Africa (SA) and the United States (US) stratified by mobile and fixed environment, first‐time and repeat donor status, and pre‐COVID19 (before March 2020) and intra‐COVID19. We used Kaplan–Meier curves to characterize time‐to‐return, cumulative incidence functions to analyze switching between donation environments, and Cox proportional hazards models to analyze factors influencing time‐to‐return.

Results

Overall time‐to‐return was shorter in SA. Pre‐COVID19, the proportion of donors returning within a year of becoming eligible was lower for deferred donors in both countries regardless of donation environment and deferral type. Intra‐COVID19, the gap between deferred and non‐deferred donors widened in the US but narrowed in SA, where efforts to schedule return visits from deferred donors were intensified, particularly for non‐hemoglobin‐related deferrals. Intra‐COVID19, the proportion of donors returning within a year in SA was higher for deferred first‐time donors (>81%) than for successful first‐time donors (80% at fixed sites; 69% at mobile drives).

Conclusions

The pandemic complicated efforts to recruit new donors and schedule returning visits after completed donations. Concerted efforts to improve time‐to‐return for deferred donors helped mitigate donation loss in SA during the public health emergency.
Feasibility of open cholangioscopy with disposable flexible endoscopes
Authors: Chik Colin , Buote Nicole J.
Published: June 2024

Objective

To determine the feasibility of open cholangioscopy using disposable flexible endoscopes in canine cadavers and describe the surgical approach.

Study design

Ex vivo experimental cadaveric study.

Sample population

Eight canine cadavers.

Methods

Cadavers ranging from 5.8 to 43.8 kg underwent open transcholecystic cholangioscopy using a disposable flexible endoscope with a 3.8 mm outer diameter and 1.2 mm working channel and the surgical approach was described. The most distal anatomical region of the biliary tree towards the duodenal papilla that was visualized with the endoscope was recorded in each cadaver. A 2.7 mm rigid endoscope and a 1.9 mm flexible endoscope were also trialed and findings recorded. Endoscopic tools were trialed and their usage recorded.

Results

The disposable flexible endoscope was feasible for visualization of the junction of the common bile duct, cystic duct, and hepatic ducts in all eight dogs. Cholangioscopy using a 2.7 mm rigid endoscope did not provide further distal visualization. The 1.9 mm flexible endoscope was able to traverse down to the level of the major duodenal papilla in a 43.8 kg cadaver. Use of certain endoscopic tools can be considered through the disposable flexible endoscope although fluid instillation was affected.

Conclusion

A 3.8 mm disposable flexible endoscope could be placed through an open transcholecystic approach to provide intraluminal endoscopic evaluation up to the level of the junction of the common bile duct, cystic duct, and hepatic ducts in dogs without cholecystic disease.

Clinical significance

Open transcholecystic cholangioscopy with a disposable flexible endoscope could provide a low‐cost diagnostic and therapeutic tool in cases of obstructive biliary disease up to the level of the common bile duct.
Analysis on Power Flow of Lamb Waves Generated by Laser Illumination in Carbon Fiber-Reinforced Plastic Laminates
Authors: Zhang Zeping , Saito Osamu , Okabe Yoji
Published: July 2024

Laser ultrasonics using guided waves excited by laser irradiation has attracted attention as an efficient nondestructive inspection method for carbon fiber-reinforced plastic (CFRP) composite laminates. In this article, to clarify the properties of laser-excited Lamb waves, we investigate the power flow of Lamb waves in an anisotropic CFRP laminate. The temperature rising caused by laser absorption is analytically calculated, and the derived thermal force is input to a finite element model to simulate the generation of Lamb waves. It is found that the power flow has an obvious directivity in a quasi-isotropic CFRP laminate. The power flow is smaller in the direction parallel to the carbon fibers of the surface layer and is larger in the perpendicular direction, but the maximum is in a slightly different direction; this result was validated by an experiment. Such directivity pattern is determined by two factors: the distribution of thermal force and the stacking sequence of CFRP laminates. Moreover, we investigate the different simulation models (metal-coated CFRP and cross-ply CFRP) to discuss the influence of each factor on the distribution of power flow separately.
Thresholds for the distributed surface code in the presence of memory decoherence
Authors: de Bone Sébastian , Möller Paul , Bradley Conor E. , Taminiau Tim H. , Elkouss David
Published: July 2024

In the search for scalable, fault-tolerant quantum computing, distributed quantum computers are promising candidates. These systems can be realized in large-scale quantum networks or condensed onto a single chip with closely situated nodes. We present a framework for numerical simulations of a memory channel using the distributed toric surface code, where each data qubit of the code is part of a separate node, and the error-detection performance depends on the quality of four-qubit Greenberger–Horne–Zeilinger (GHZ) states generated between the nodes. We quantitatively investigate the effect of memory decoherence and evaluate the advantage of GHZ creation protocols tailored to the level of decoherence. We do this by applying our framework for the particular case of color centers in diamond, employing models developed from experimental characterization of nitrogen-vacancy centers. For diamond color centers, coherence times during entanglement generation are orders of magnitude lower than coherence times of idling qubits. These coherence times represent a limiting factor for applications, but previous surface code simulations did not treat them as such. Introducing limiting coherence times as a prominent noise factor makes it imperative to integrate realistic operation times into simulations and incorporate strategies for operation scheduling. Our model predicts error probability thresholds for gate and measurement reduced by at least a factor of three compared to prior work with more idealized noise models. We also find a threshold of 4×102 in the ratio between the entanglement generation and the decoherence rates, setting a benchmark for experimental progress.
Performance of biological food processing interfaces: Perspectives on the science of mollusc radula
Authors: Krings Wencke , Gorb Stanislav N.
Published: June 2024

The Mollusca comprises a diverse range of organisms, with the class Gastropoda alone boasting approximately 80 000 extant species. Their adaptability across various habitats is facilitated by the evolution of the radula, a key structure for food acquisition. The radula’s composition and mechanical properties, including its chitinous membrane, teeth, and supporting structures, enable efficient food gathering and processing. Through adaptive tooth morphology and composition, an interplay between radular components is facilitated, which results in collective effects to withstand forces encountered during feeding and reduce structural failure, with the broad range of variations reflecting ecological niches. Furthermore, teeth consist of composite materials with sometimes high contents of iron, calcium, or silicon to reduce wear. During interaction with the food, the radula performs complex three-dimensional motions, challenging to document. Here, we provide a review on the morphology, the mechanical properties, the composition, and various other parameters that contribute to radular performance. Due to, e.g., the smallness of these structures, there are, however, limitations to radular research. However, numerical simulations and physical models tested on substrates offer avenues for further understanding radular function and performance during feeding. These studies not only advance our knowledge of molluscan biology and ecology but also provide inspirations for biomimetic design and further advances in materials engineering.
Regulation of blood-brain barrier integrity by
Dmp1
-expressing astrocytes through mitochondrial transfer
Authors: Liu Delin , Liao Peng , Li Hao , Tong Sihan , Wang Bingqi , Lu Yafei , Gao Youshui , Huang Yigang , Zhou Hao , Shi Linjing , Papadimitriou John , Zong Yao , Yuan Jun , Chen Peilin , Chen Ziming , Ding Peng , Zheng Yongqiang , Zhang Changqing , Zheng Minghao , Gao Junjie
Published: June 2024

The blood-brain barrier (BBB) acts as the crucial physical filtration structure in the central nervous system. Here, we investigate the role of a specific subset of astrocytes in the regulation of BBB integrity. We showed that
Dmp1-
expressing astrocytes transfer mitochondria to endothelial cells via their endfeet for maintaining BBB integrity. Deletion of the Mitofusin 2 (
Mfn2
) gene in
Dmp1
-expressing astrocytes inhibited the mitochondrial transfer and caused BBB leakage. In addition, the decrease of MFN2 in astrocytes contributes to the age-associated reduction of mitochondrial transfer efficiency and thus compromises the integrity of BBB. Together, we describe a mechanism in which astrocytes regulate BBB integrity through mitochondrial transfer. Our findings provide innnovative insights into the cellular framework that underpins the progressive breakdown of BBB associated with aging and disease.
Frictional instabilities in clay illuminate the origin of slow earthquakes
Authors: Volpe Giuseppe , Collettini Cristiano , Taddeucci Jacopo , Marone Chris , Pozzi Giacomo
Published: June 2024

The shallowest regions of subduction megathrusts mainly deform aseismically, but they can sporadically host slow-slip events (SSEs) and tsunami earthquakes, thus representing a severe hazard. However, the mechanisms behind these remain enigmatic because the frictional properties of shallow subduction zones, usually rich in clay, do not allow earthquake slip according to standard friction theory. We present experimental data showing that clay-rich faults with bulk rate-strengthening behavior and null healing rate, typically associated with aseismic creep, can contemporaneously creep and nucleate SSE. Our experiments document slow ruptures occurring within thin shear zones, driven by structural and stress heterogeneities of the experimental faults. We propose that bulk rate-strengthening frictional behavior promotes long-term aseismic creep, whereas localized frictional shear allows slow rupture nucleation and quasi-dynamic propagation typical of rate-weakening behavior. Our results provide additional understanding of fault friction and illustrate the complex behavior of clay-rich faults, providing an alternative paradigm for interpretation of the spectrum of fault slip including SSEs and tsunami earthquakes.
TGR5 deficiency in excitatory neurons ameliorates Alzheimer’s pathology by regulating APP processing
Authors: Li Chenli , Wang Liangjie , Xie Wenting , Chen Erqu , Chen Yanbing , Li Huifang , Can Dan , Lei Aiyu , Wang Yue , Zhang Jie
Published: June 2024

Bile acids (BAs) metabolism has a significant impact on the pathogenesis of Alzheimer’s disease (AD). We found that deoxycholic acid (DCA) increased in brains of AD mice at an early stage. The enhanced production of DCA induces the up-regulation of the bile acid receptor Takeda G protein-coupled receptor (TGR5), which is also specifically increased in neurons of AD mouse brains at an early stage. The accumulation of exogenous DCA impairs cognitive function in wild-type mice, but not in TGR5 knockout mice. This suggests that TGR5 is the primary receptor mediating these effects of DCA. Furthermore, excitatory neuron-specific knockout of TGR5 ameliorates Aβ pathology and cognition impairments in AD mice. The underlying mechanism linking TGR5 and AD pathology relies on the downstream effectors of TGR5 and the APP production, which is succinctly concluded as a “p-STAT3–APH1–γ-secretase” signaling pathway. Our studies identified the critical role of TGR5 in the pathological development of AD.
Dissecting infectious bronchitis virus-induced host shutoff at the translation level
Authors: Zhao Jing , Huang Yahui , Liukang Chengyin , Yang Ruihua , Tang Lihua , Sun Lu , Zhao Ye , Zhang Guozhong
Published: June 2024

Viruses have evolved a range of strategies to utilize or manipulate the host’s cellular translational machinery for efficient infection, although the mechanisms by which infectious bronchitis virus (IBV) manipulates the host translation machinery remain unclear. In this study, we firstly demonstrate that IBV infection causes host shutoff, although viral protein synthesis is not affected. We then screened 23 viral proteins, and identified that more than one viral protein is responsible for IBV-induced host shutoff, the inhibitory effects of proteins Nsp15 were particularly pronounced. Ribosome profiling was used to draw the landscape of viral mRNA and cellular genes expression model, and the results showed that IBV mRNAs gradually dominated the cellular mRNA pool, the translation efficiency of the viral mRNAs was lower than the median efficiency (about 1) of cellular mRNAs. In the analysis of viral transcription and translation, higher densities of RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) reads were observed for structural proteins and 5′ untranslated regions, which conformed to the typical transcriptional characteristics of nested viruses. Translational halt events and the number of host genes increased significantly after viral infection. The translationally paused genes were enriched in translation, unfolded-protein-related response, and activation of immune response pathways. Immune- and inflammation-related mRNAs were inefficiently translated in infected cells, and IBV infection delayed the production of IFN-β and IFN-λ. Our results describe the translational landscape of IBV-infected cells and demonstrate new strategies by which IBV induces host gene shutoff to promote its replication.

IMPORTANCE

Infectious bronchitis virus (IBV) is a γ-coronavirus that causes huge economic losses to the poultry industry. Understanding how the virus manipulates cellular biological processes to facilitate its replication is critical for controlling viral infections. Here, we used Ribo-seq to determine how IBV infection remodels the host’s biological processes and identified multiple viral proteins involved in host gene shutoff. Immune- and inflammation-related mRNAs were inefficiently translated, the translation halt of unfolded proteins and immune activation-related genes increased significantly, benefitting IBV replication. These data provide new insights into how IBV modulates its host’s antiviral responses.
Molecular insights into type I interferon suppression and enhanced pathogenicity by species B human adenoviruses B7 and B14
Authors: Graves Drayson , Akkerman Nikolas , Fulham Lauren , Helwer Rafe , Pelka Peter
Published: June 2024

Human adenoviruses (HAdVs) are small DNA viruses that generally cause mild disease. Certain strains, particularly those belonging to species B HAdVs, can cause severe pneumonia and have a relatively high mortality rate. Little is known about the molecular aspects of how these highly pathogenic species affect the infected cell and how they suppress innate immunity. The present study provides molecular insights into how species B adenoviruses suppress the interferon signaling pathway. Our study shows that these viruses, unlike HAdV-C2, are resistant to type I interferon. This resistance likely arises due to the highly efficient suppression of interferon-stimulated gene expression. Unlike in HAdV-C2, HAdV-B7 and B14 sequester STAT2 and RNA polymerase II from interferon-stimulated gene promoters in infected cells. This results in suppressed interferon- stimulated gene activation. In addition, we show that RuvBL1 and RuvBL2, cofactors important for RNA polymerase II recruitment to promoters and interferon-stimulated gene activation, are redirected to the cytoplasm forming high molecular weight complexes that, likely, are unable to associate with chromatin. Proteomic analysis also identified key differences in the way these viruses affect the host cell, providing insights into species B-associated high pathogenicity. Curiously, we observed that at the level of protein expression changes to the infected cell, HAdV-C2 and B7 were more similar than those of the same species, B7 and B14. Collectively, our study represents the first such study of innate immune suppression by the highly pathogenic HAdV-B7 and B14, laying an important foundation for future investigations.

IMPORTANCE

Human adenoviruses form a large family of double-stranded DNA viruses known for a variety of usually mild diseases. Certain strains of human adenovirus cause severe pneumonia leading to much higher mortality and morbidity than most other strains. The reasons for this enhanced pathogenicity are unknown. Our study provides a molecular investigation of how these highly pathogenic strains might inactivate the interferon signaling pathway, highlighting the lack of sensitivity of these viruses to type I interferon in general while providing a global picture of how viral changes in cellular proteins drive worse disease outcomes.
Metagenomic sequences from anaerobic chloroform and dichloromethane degrading microbial communities
Authors: Bulka Olivia , Edwards Elizabeth A.
Published: July 2024

Here, we present metagenomes from two cultures derived from an anaerobic microbial consortium used for bioremediation. One culture dechlorinates chloroform to dichloromethane, which is further mineralized to CO
2
. A second subculture was amended with only dichloromethane. We sought draft genomes of key microorganisms to identify metabolic potential in these consortia.
Bacillus coagulans
restores pathogen-induced intestinal dysfunction via acetate–FFAR2–NF-κB–MLCK–MLC axis in
Apostichopus japonicus
Authors: Song Mingshan , Zhang Shanshan , Zhang Zhen , Guo Liyuan , Liang Weikang , Li Chenghua , Wang Zhonghua
Published: June 2024

Skin ulceration syndrome (SUS) is currently the main disease threatening
Apostichopus japonicus
aquaculture due to its higher mortality rate and infectivity, which is caused by
Vibrio splendidus
. Our previous studies have demonstrated that SUS is accompanied by intestinal microbiota (IM) dysbiosis, alteration of short-chain fatty acids (SCFAs) content and the damage to the intestinal barrier. However, the mediating effect of IM on intestine dysfunction is largely unknown. Herein, we conducted comprehensive intestinal microbiota transplantation (IMT) to explore the link between IM and SUS development. Furthermore, we isolated and identified a
Bacillus coagulans
strain with an ability to produce acetic acid from both healthy individual and SUS individual with IM from healthy donors. We found that dysbiotic IM and intestinal barrier function in SUS recipients
A. japonicus
could be restored by IM from healthy donors. The
B. coagulans
strain could restore IM community and intestinal barrier function. Consistently, acetate supply also restores intestinal homeostasis of SUS-diseased and
V. splendidus
-infected
A. japonicus
. Mechanically, acetate was found to specifically bind to its receptor-free fatty acid receptor 2 (FFAR2) to mediate IM structure community and intestinal barrier function. Knockdown of FFAR2 by transfection of specific FFAR2 siRNA could hamper acetate-mediated intestinal homeostasis
in vivo
. Furthermore, we confirmed that acetate/FFAR2 could inhibit
V. splendidus
-activated NF-κB–MLCK–MLC signaling pathway to restore intestinal epithelium integrity and upregulated the expression of ZO-1 and Occludin. Our findings provide the first evidence that
B. coagulans
restores pathogen-induced intestinal barrier dysfunction via acetate/FFAR2–NF-κB–MLCK–MLC axis, which provides new insights into the control and prevention of SUS outbreak from an ecological perspective.

IMPORTANCE

Skin ulceration syndrome (SUS) as a main disease in
Apostichopus japonicus
aquaculture has severely restricted the developmental
A. japonicus
aquaculture industry. Intestinal microbiota (IM) has been studied extensively due to its immunomodulatory properties. Short-chain fatty acids (SCFAs) as an essential signal molecule for microbial regulation of host health also have attracted wide attention. Therefore, it is beneficial to explore the link between IM and SUS for prevention and control of SUS. In the study, the contribution of IM to SUS development has been examined. Additionally, our research further validated the restoration of SCFAs on intestinal barrier dysfunction caused by SUS via isolating SCFAs-producing bacteria. Notably, this restoration might be achieved by inhibition of NF-κB–MLCK–MLC signal pathway, which could be activated by
V. splendidus
. These findings may have important implications for exploration of the role of IM in SUS occurrence and provide insight into the SUS treatment.
Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in
Chlamydia trachomatis
persistence
Authors: Chowdhury Niaz Bahar , Pokorzynski Nick , Rucks Elizabeth A. , Ouellette Scot P. , Carabeo Rey A. , Saha Rajib
Published: June 2024

Upon nutrient starvation,
Chlamydia trachomatis
serovar L2 (CTL) shifts from its normal growth to a non-replicating form, termed persistence. It is unclear if persistence reflects an adaptive response or a lack thereof. To understand this, transcriptomics data were collected for CTL grown under nutrient-replete and nutrient-starved conditions. Applying K-means clustering on transcriptomics data revealed a global transcriptomic rewiring of CTL under stress conditions in the absence of any canonical global stress regulator. This is consistent with previous data that suggested that CTL’s stress response is due to a lack of an adaptive response mechanism. To investigate the impact of this on CTL metabolism, we reconstructed a genome-scale metabolic model of CTL (iCTL278) and contextualized it with the collected transcriptomics data. Using the metabolic bottleneck analysis on contextualized iCTL278, we observed that phosphoglycerate mutase (
pgm
) regulates the entry of CTL to the persistence state. Our data indicate that
pgm
has the highest thermodynamics driving force and lowest enzymatic cost. Furthermore, CRISPRi-driven knockdown of
pgm
in the presence or absence of tryptophan revealed the importance of this gene in modulating persistence. Hence, this work, for the first time, introduces thermodynamics and enzyme cost as tools to gain a deeper understanding on CTL persistence.

IMPORTANCE

This study uses a metabolic model to investigate factors that contribute to the persistence of
Chlamydia trachomatis
serovar L2 (CTL) under tryptophan and iron starvation conditions. As CTL lacks many canonical transcriptional regulators, the model was used to assess two prevailing hypotheses on persistence—that the chlamydial response to nutrient starvation represents a passive response due to the lack of regulators or that it is an active response by the bacterium. K-means clustering of stress-induced transcriptomics data revealed striking evidence in favor of the lack of adaptive (i.e., a passive) response. To find the metabolic signature of this, metabolic modeling pin-pointed pgm as a potential regulator of persistence. Thermodynamic driving force, enzyme cost, and CRISPRi knockdown of pgm supported this finding. Overall, this work introduces thermodynamic driving force and enzyme cost as a tool to understand chlamydial persistence, demonstrating how systems biology-guided CRISPRi can unravel complex bacterial phenomena.