bluuebunny/crossref_metadata_2025 huggingface dataset:
Caste, Ethnicity, and the State in Nepal
Authors: Gellner David N.
Published: January 2024

Caste in Nepal works and has worked according to much the same principles as in India. The introduction of party politics and regular elections after 1990 has led to increasing politicization of ethnicity and caste that parallels north India in some respects. However, the fact that Nepal never experienced colonialism directly means that deep processes of social and cultural change did not happen until after 1951 or indeed much later. The much larger proportion of Janajatis (formerly known as ‘hill tribes’) in Nepal than in north India means that the Janajatis occupy the political space that would in India belong to OBCs. Since 1990, five major ‘macro-categories’ (new social identities with new names, clubbing together distinct castes and ethnic groups) have emerged: Janajati, Dalit, Madheshi, Khas-Arya, and Other.
Caste and Mobility
Authors: Vaid Divya
Published: January 2024

Social mobility, closely tied to notions of inequality, is the intra-generational (over a person’s life time) or inter-generational (from one generation to another) movement between strata. This chapter explores both these forms, but focuses on inter-generational movement: first, by covering studies that have discussed the social class mobility of entire castes or the possibility of such movement; and second, by summarising work on the social class mobility of individuals from different castes. It then briefly discusses the significance of space and spatial mobility that either constrains or boosts social mobility. The chapter ends by looking at the experiences, aspirations, and anxieties tied to social mobility.
Caste and Gender
Authors: Kumar Pushpesh
Published: January 2024

Much before academic concerns, caste and women’s position in it emerged in India in the second half of the nineteenth century in anti-caste struggles. Phule, Periyar, Iyothee Thass, and Ambedkar, in their scathing attack on the privileged social order, imagined caste and gender discriminations as closely related phenomena. Until the 1980s, however, the feminist movements and kinship and gender literature in social anthropology failed to incorporate and foreground dalit women’s experiences in their concerns and analysis. The articulations of the complex and multiple marginalities of dalit women within Brahminical and dalit patriarchies and exploitative capitalist structures were made possible through the formation of dalit women’s organizations in the 1990s. The assertions of dalit women during the 1990s surfaced through their writings, including autobiographies, fictions, historical accounts, and poetry. Filled with the memorialization of the “untouchable” past, stigma, dispossession, back-breaking work, and violence, these literary sensibilities expose, satirize and critically reflect on upper caste customs as well as domination by their own (dalit) men. The concluding part of the chapter reflects on the issue of caste within sexuality movements in contemporary India.
GALAXY CRUISE: Spiral and ring classifications for bright galaxies at z = 0.01–0.3
Authors: Shimakawa Rhythm , Tanaka Masayuki , Ito Kei , Ando Makoto
Published: January 2024

This paper presents a morphology classification catalog of spiral and ring features of 59854 magnitude-limited galaxies (r < 17.8 mag, and additional 628005 subsamples down to r = 20 mag) at z = 0.01–0.3 based on the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program. We employ two deep-learning classifiers to determine the spiral and ring structures separately based on GALAXY CRUISE Data Release 1, which is dedicated to Hyper Suprime-Cam data. The number of spiral and ring galaxies contain 31864 and 8808 sources, respectively, which constitute 53% and 15% of the sample. A notable result of this study is the construction of a large sample of ring galaxies utilizing high-quality imaging data delivered by the Subaru Hyper Suprime-Cam. However, the accurate identification of ring galaxies remains difficult at a limited seeing resolution. Additionally, we confirm that most spiral galaxies are located on the star-forming main sequence, whereas ring galaxies preferentially reside in the green valley at stellar masses of 1010.5–1011 solar mass. Furthermore, decreasing fractions of spiral and ring galaxies are observed toward the centers of the galaxy clusters. The obtained morphology catalog is publicly available on the GALAXY CRUISE website.
Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model
Authors: Sinclair Matt , Stein Richard A , Sheehan Jonathan H , Hawes Emily M , O’Brien Richard M , Tajkhorshid Emad , Claxton Derek P
Published: January 2024

Mediating the terminal reaction of gluconeogenesis and glycogenolysis, the integral membrane protein glucose-6-phosphate catalytic subunit 1 (G6PC1) regulates hepatic glucose production by catalyzing hydrolysis of glucose-6-phosphate (G6P) within the lumen of the endoplasmic reticulum. Consistent with its vital contribution to glucose homeostasis, inactivating mutations in G6PC1 causes glycogen storage disease (GSD) type 1a characterized by hepatomegaly and severe hypoglycemia. Despite its physiological importance, the structural basis of G6P binding to G6PC1 and the molecular disruptions induced by missense mutations within the active site that give rise to GSD type 1a are unknown. In this study, we determine the atomic interactions governing G6P binding as well as explore the perturbations imposed by disease-linked missense variants by subjecting an AlphaFold2 G6PC1 structural model to molecular dynamics simulations and in silico predictions of thermodynamic stability validated with robust in vitro and in situ biochemical assays. We identify a collection of side chains, including conserved residues from the signature phosphatidic acid phosphatase motif, that contribute to a hydrogen bonding and van der Waals network stabilizing G6P in the active site. The introduction of GSD type 1a mutations modified the thermodynamic landscape, altered side chain packing and substrate-binding interactions, and induced trapping of catalytic intermediates. Our results, which corroborate the high quality of the AF2 model as a guide for experimental design and to interpret outcomes, not only confirm the active-site structural organization but also identify previously unobserved mechanistic contributions of catalytic and noncatalytic side chains.
Application of the Adverse Childhood Experiences Framework to the NICU
Authors: Malin Kathryn J. , Vittner Dorothy , Darilek Umber , McGlothen-Bell Kelly , Crawford Allison , Koerner Rebecca , Pados Britt Frisk , Cartagena Diana , McGrath Jacqueline M. , Vance Ashlee J.
Published: January 2024

Background:

Infants and families requiring neonatal intensive care unit (NICU) care often experience significant stress and trauma during the earliest period of the infant's life, leading to increased risks for poorer infant and family outcomes. There is a need for frameworks to guide clinical care and research that account for the complex interactions of generational stress, pain, toxic stress, parental separation, and lifelong health and developmental outcomes for infants and families.

Purpose:

Apply the Adverse Childhood Experiences (ACEs) framework in the context of the NICU as a usable structure to guide clinical practice and research focused on infant neurodevelopment outcomes and parental attachment.

Methods:

An overview of ACEs is provided along with a detailed discussion of risk at each level of the ACEs pyramid in the context of the NICU. Supportive and protective factors to help mitigate the risk of the ACEs in the NICU are detailed.

Results:

NICU hospitalization may be considered the first ACE, or potentially an additional ACE, resulting in an increased risk for poorer health outcomes. The promotion of safe, stable, and nurturing relationships and implementation of trauma-informed care and individualized developmental care potentially counter the negative impacts of stress in the NICU.

Implications for Practice and Research:

Nurses can help balance the negative and positive stimulation of the NICU through activities such as facilitated tucking, skin-to-skin care, mother's milk, and active participation of parents in infant care. Future research can consider using the ACEs framework to explain cumulative risk for adverse health and well-being in the context of NICU care.
Reliable Prediction of Discharge Disposition Following Cervical Spine Surgery With Ensemble Machine Learning and Validation on a National Cohort
Authors: Feng Rui , Valliani Aly A. , Martini Michael L. , Gal Jonathan S. , Neifert Sean N. , Kim Nora C. , Geng Eric A. , Kim Jun S. , Cho Samuel K. , Oermann Eric K. , Caridi John M.
Published: January 2024

Study Design:

A retrospective cohort study.

Objective:

The purpose of this study is to develop a machine learning algorithm to predict nonhome discharge after cervical spine surgery that is validated and usable on a national scale to ensure generalizability and elucidate candidate drivers for prediction.

Summary of Background Data:

Excessive length of hospital stay can be attributed to delays in postoperative referrals to intermediate care rehabilitation centers or skilled nursing facilities. Accurate preoperative prediction of patients who may require access to these resources can facilitate a more efficient referral and discharge process, thereby reducing hospital and patient costs in addition to minimizing the risk of hospital-acquired complications.

Methods:

Electronic medical records were retrospectively reviewed from a single-center data warehouse (SCDW) to identify patients undergoing cervical spine surgeries between 2008 and 2019 for machine learning algorithm development and internal validation. The National Inpatient Sample (NIS) database was queried to identify cervical spine fusion surgeries between 2009 and 2017 for external validation of algorithm performance. Gradient-boosted trees were constructed to predict nonhome discharge across patient cohorts. The area under the receiver operating characteristic curve (AUROC) was used to measure model performance. SHAP values were used to identify nonlinear risk factors for nonhome discharge and to interpret algorithm predictions.

Results:

A total of 3523 cases of cervical spine fusion surgeries were included from the SCDW data set, and 311,582 cases were isolated from NIS. The model demonstrated robust prediction of nonhome discharge across all cohorts, achieving an area under the receiver operating characteristic curve of 0.87 (SD=0.01) on both the SCDW and nationwide NIS test sets. Anterior approach only, age, elective admission status, Medicare insurance status, and total Elixhauser Comorbidity Index score were the most important predictors of discharge destination.

Conclusions:

Machine learning algorithms reliably predict nonhome discharge across single-center and national cohorts and identify preoperative features of importance following cervical spine fusion surgery.
The Oxygen Therapy Tube as a Tool for Breast Squeezing during Pedicle De-epithelialization in Reduction Mammaplasty
Authors: Pau Alberto , Torresetti Matteo , Dragonetti Pietro , Di Benedetto Giovanni
Published: January 2024

During breast reduction, pedicle de-epithelialization, as meticulous as possible, is necessary to ensure satisfying breast sculpting and to avoid any epidermoid cyst. To perform an effective and rapid de-epithelialization, a good tension of the skin is mandatory. Several techniques to improve skin tension of the breast are described in the literature. We report a cheap, effective, and easily reproducible method, based on the use of an oxygen tube with nasal cannula.
A Modified Suturing Technique to Produce Temporary Scleral Buckling Effect for Noncomplex Rhegmatogenous Retinal Detachment
Authors: Zhang Zhaotian
Published: January 2024

Purpose:

To introduce a surgical technique for temporary scleral buckling (SB) of noncomplex rhegmatogenous retinal detachment (RRD) using a combination of non-absorbable and absorbable sutures that would induce minimal permanent refractive changes.

Method:

Twenty consecutive patients (20 eyes) with noncomplex RRD were prospectively included. SB was performed in all eligible subjects, and encircling buckling (EB) was added when necessary. The silicone elements were fixed on the sclera with 5-0 non-absorbable sutures and tightened to form a ridge with 6-0 absorbable sutures. Best-corrected visual acuity (BCVA), scleral ridge status, axial length (AL), spherical diopter (SD), and cylinder diopter (CD) were collected.

Results:

All patients achieved primary retinal re-attachment with significant improvement of BCVA after surgery. Scleral ridge was obvious and in situ at the one-month follow-up but diminished at the three-month follow-up. At the one-month follow-up, AL increased from 24.78±2.14 mm preoperatively to 25.22±2.11 mm, and CD increased from –1.99±1.03 to –2.95±1.55 (both p<0.001). At the three-month follow-up, AL, SD, and CD decreased significantly compared with the values at the one-month follow-up (all p<0.05). No obvious complications were observed during the whole follow-up. Patients who underwent additional EB exhibited greater changes in AL and CD at the one-month follow-up (both P<0.001).

Conclusion:

The modified technique of SB with/without EB using both non-absorbable and absorbable sutures offers a safe and effective option to repair noncomplex RRD, which would offer an adequate temporary SB effect and induce minimal permanent refractive changes.
A Novel Reconstruction Technique to Reduce Stair-Step Artifacts in Sequential Mode Coronary CT Angiography
Authors: Moser Lukas Jakob , Mergen Victor , Allmendinger Thomas , Manka Robert , Eberhard Matthias , Alkadhi Hatem
Published: January 2024

Purpose

Prospective electrocardiography-triggering is one of the most commonly used cardiac computed tomography (CT) scan modes but can be susceptible to stair-step artifacts in the transition areas of an acquisition over multiple cardiac cycles. We evaluated a novel reconstruction algorithm to reduce the occurrence and severity of such artifacts in sequential coronary CT angiography.

Materials and Methods

In this institutional review board–approved, retrospective study, 50 consecutive patients (16 females; mean age, 58.9 ± 15.2) were included who underwent coronary CT angiography on a dual-source photon-counting detector CT in the sequential ultra-high-resolution mode with a detector collimation of 120 × 0.2 mm. Each scan was reconstructed without (hereafter called standard reconstruction) and with the novel ZeeFree reconstruction algorithm, which aims to minimize stair-step artifacts. The presence and extent of stair-step artifacts were rated by 2 independent, blinded readers on a 4-point discrete visual scale. The relationship between the occurrences of artifacts was correlated with the average and variability of heart rate and with patient characteristics.

Results

A total of 504 coronary segments were included into the analyses. In standard reconstructions, reader 1 reported stair-step artifacts in 40/504 (7.9%) segments, from which 12/504 led to nondiagnostic image quality (2.4% of all segments). Reader 2 reported 56/504 (11.1%) stair-step artifacts, from which 11/504 lead to nondiagnostic image quality (2.2% of all segments). With the ZeeFree algorithm, 9/12 (75%) and 8/11 (73%) of the nondiagnostic segments improved to a diagnostic quality for readers 1 and 2, respectively. The ZeeFree reconstruction algorithm significantly reduced the frequency and extent of stair-step artifacts compared with standard reconstructions for both readers (P < 0.001, each). Heart rate variability and body mass index were significantly related to the occurrence of stair-step artifacts (P < 0.05).

Conclusions

Our study demonstrates the feasibility and effectiveness of a novel reconstruction algorithm leading to a significant reduction of stair-step artifacts and, hence, a reduction of coronary segments with a nondiagnostic image quality in sequential ultra-high-resolution coronary photon-counting detector CT angiography.
Comparative Efficacy of Drug Interventions for Keloids
Authors: Yang Hsi-An , Jheng Wun-Long , Yu Jiaxin , Huang Jhao-Yu , Cheng Kai-Yuan , Lee Jian-Jr
Published: January 2024

Background

Keloids are common benign skin lesions originating from a disorganized fibroproliferative collagen response; these lesions often lead to both physical and psychological problems. The optimal treatment for keloids is yet to be standardized. Intralesional injection, which is simple and nontraumatic, is one of the most commonly used treatment modalities for these lesions. In this study, we compared 5 different drugs (intralesional injections) for the treatment of keloids in terms of efficacy.

Methods

We systemically searched relevant studies on PubMed, EMBASE, and Cochrane Library. Randomized clinical trials on the safety and efficacy of triamcinolone acetonide (TAC), 5-fluorouracil (5-FU), botulinum toxin A (BTA), verapamil, and bleomycin were included in this study.

Results

This network meta-analysis included a total of 1114 patients from 20 randomized controlled trials. Botulinum toxin A alone and TAC plus 5-FU exhibited significantly better efficacy than did 5-FU, TAC, and verapamil. No significant difference in efficacy between BTA alone and TAC combined with 5-FU was observed. No significant differences were noted in the adverse event rate between BTA, TAC plus 5-FU, 5-FU, and TAC. Furthermore, we performed surface under the cumulative ranking curve analyses to predict the rank of each intervention (by efficacy and adverse event rate). The predicted ranking by efficacy was as follows: TAC plus 5-FU, BTA, bleomycin, TAC, 5-FU, and verapamil; the predicted ranking by adverse events was as follows: TAC, 5-FU, TAC plus 5-FU, and BTA. Funnel plot analysis revealed no publication bias.

Conclusions

Botulinum toxin A and TAC plus 5-FU appear to have outstanding therapeutic efficacy for keloids. The rate of adverse events was similar among BTA, TAC, 5-FU, and TAC plus 5-FU. Nonetheless, additional reviews of rigorous, large-scale randomized controlled trials are warranted for further validation of our findings.
Surgical Navigation Applied in Removal of Glass Located Under Zygomatic Arch
Authors: Liu Jaehong , Lee Jun Won , Jeong Hii Sun
Published: January 2024

The limited detection rate of plain radiography (as low as 75%) for glass particles within the softs renders the conventional C-arm visualization method ineffective in intraoperative scenarios. The authors report the successful use of intraoperative navigation to visualize and extract multiple small glass fragments located deep within the temporal fossa and beneath the zygomatic arch. A 25-year-old man presented with a deep facial laceration, suspected injury to the temporal branch of the facial nerve, and a 2×2 cm foreign body beneath the sphenoid bone near the left zygomatic arch. The initial surgery removed most of the glass; however, two 4 mm fragments remained near the skull base. Using intraoperative navigation, a 3 cm incision was made, and a navigating stylet was used to locate and remove the foreign bodies. In conclusion, intraoperative navigation is a precise method for removing small, imperceptible glass fragments from challenging anatomic areas, thus reducing the need for extensive dissection compared to conventional approaches.
Evaluation of the Anatomical and Radiological Morphometry of Optic Nerve and Cranium in Healthy Individuals
Authors: Tunç Mahmut , Polat Sema , Öksüzler Mahmut , Göker Pinar
Published: January 2024

This paper determined the morphometric measurements’ reference values and relationship of the optic nerve and cranium in Turkish healthy individuals according to age and sex. Five hundred fifty-nine (280 females and 279 males) patients aged from 2 to 90 years were included in this study. The measurements were taken from patients having brain magnetic resonance images in sagittal, axial, and coronal sections in the radiology department. Eyeball transverse diameter, optic nerve sheath thickness (ONST), optic chiasm length, optic chiasm width, and cranium morphometric measurements of all individuals who participated in the study were taken. Except for the width of the optic chiasm, all measurements showed significant differences between the sexes (P < 0.05). In contrast, all measurement values were higher in males than females, except for the clival angle. According to the result of Pearson correlation analysis, in which the existence of a relationship between ONST and craniometric measurements was evaluated, a low but significant correlation was found between ONST and craniometric measurements (r < 0.4; P < 0.05). In the post hoc test performed to compare the decades, it was seen that the most significant changes in our measurements were in the 2 to 10 age range and the measurement values decreased in old age. We think that revealing the age and sex-related changes in the optic nerve and cranium morphometry of our population anatomically and radiologically will be an important source in terms of creating reference values for our population.
Does YouTube Provide High-Quality Information for Patients Regarding Night Guards, Especially for Over-the-Counter Ones?
Authors: Haliloğlu Özkan Tuğba , Acar Ahmet Hüseyin , Özkan Enes
Published: January 2024

The aim of this study was to evaluate the quality of the information on YouTube regarding night guards (NGs). YouTube was systematically searched using the keyword “night guards.” Two independent reviewers examined the first 100 videos and exclusion criteria were applied. Descriptive characteristics of the remaining 60 videos were recorded. In addition, the purpose, target audience, and source of the included videos were collected. A 12-point content scale (CS) was used to evaluate video content, and the Global Quality Scale (GQS) was used to determine video quality. Statistical analyses were performed using the Kruskal-Wallis and Mann-Whitney tests, and the correlation between scores was evaluated using Spearman rho. Of the included videos, 50% were uploaded by dentists/health institutions, 26% by commercial sources and 24% by laypersons. The aim of 80% of the videos was to inform laypeople and 14% to inform professionals only. The content discussed the most (59.3%) was the production stages of NGs. The mean CS and GQS score of the videos were 2.06 ± 1.35 (poor) and 1.71 ± 0.88 (generally poor), respectively. A positive correlation was found between the CS and GQS scores (r = 0.447). YouTube videos were found to be poor in terms of both content and quality. Since NGs for treating bruxism will always be a trending topic for patients on social media, the content of YouTube videos should be checked and enriched by professionals so that patients can access accurate information, especially about NGs obtained over the counter.
Odontoid/Dens Fractures
Authors: Good Anthony E. , Ramponi Denise R.
Published: January 2024

Odontoid fractures remain the most common C2 fracture and of those individuals older than 65 years. The type of optimal management remains in question given comorbidities, risk of nonunion, and limitations in mobility when surgical fusion is the treatment selected. These fractures are of particular importance, given the high incident of morbidity and mortality following an odontoid fracture. Overall quality of life remains a significant consideration when selecting the best intervention following careful examination and confirmation with radiographic imaging. The literature continues with controversies in the best treatment interventions for these fractures, resulting in a case-by-case decision-making process.
Assessment of the Diagnostic Accuracy and Reliability of the HEART Score Calculated by Ambulance Nurses Versus Emergency Physicians
Authors: van der Waarden Nancy W. P. L. , de Wolf G. Sander , van Meerten Kirsten F. , Backus Barbra E.
Published: January 2024

Chest pain is a common complaint for consultation of emergency medical services worldwide. Currently, ambulance nurses (AN) base their decision to transport a patient to the hospital on their own professional experience. The HEART score could improve prehospital risk stratification and patient treatment. The aim of this study is to investigate the interrater reliability and predictive accuracy of the HEART score between AN and emergency physicians (EP). A retrospective analysis on data of 569 patients 18 years and older included in two prehospital HEART score studies. The endpoints are interrater reliability (intraclass correlation [ICC]) and predictive accuracy for major adverse cardiac events within 30 days of the HEART score calculated by AN versus EP. Predictive accuracy is sensitivity, specificity, positive predicted value (PPV) and negative predicted value (NPV). Interrater reliability was good for total HEART score (ICC 0.78; 95% CI 0.75–0.81). However, focusing on the decision to transport a patient, the ICC dropped to 0.62 (95% CI 0.62–0.70). History and Risk factors caused the most variability. Predictive accuracy of HEART differed between AN and EP. The HEART score calculated by AN was sensitivity 91%, specificity 38%, PPV 26%, and NPV 95%. The HEART score calculated by EP was sensitivity 98%, specificity 32%, PPV −26%, and NPV 99%. With a cut-off value of 0–2 for a low HEART score, predictive accuracy significantly improved for the HEART score calculated by AN: sensitivity 98%, specificity 18%, PPV 22%, and NPV 98%. Our study shows a moderate interrater reliability and lower predictive accuracy of a HEART score calculated by AN versus EP. AN underestimate the risk of patients with acute chest pain, with the largest discrepancies in the elements History and Risk factors. Reconsidering the cut-off values of the low-risk HEART category, as well as a carefully developed training program, will possibly lead to a higher interrater reliability of the HEART score and higher predictive accuracy used by AN.
A proof of Specker’s principle
Authors: Bacciagaluppi Guido
Published: January 2024

Specker’s principle, the condition that pairwise orthogonal propositions must be jointly orthogonal (or rather, the ‘exclusivity principle’ that follows from it), has been much investigated recently within the programme of finding physical principles to characterize quantum mechanics. Specker’s principle, however, largely appears to lack a physical justification. In this paper, I present a proof of Specker’s principle from three assumptions (made suitably precise): the existence of ‘maximal entanglement’, the existence of ‘non-maximal measurements’ and no-signalling. I discuss these three assumptions and describe canonical examples of non-Specker sets of propositions satisfying any two of them. These examples display analogies with various approaches to the interpretation of quantum mechanics, including retrocausation. I also discuss connections with the work of Popescu & Rohrlich. The core of the proof (and the main example violating no-signalling) is illustrated by a variant of Specker’s tale of the seer of Nineveh, with which I open the paper.

This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
The quantum maxima for the basic graphs of exclusivity are not reachable in Bell scenarios
Authors: Porto Lucas E. A. , Rabelo Rafael , Terra Cunha Marcelo , Cabello Adán
Published: January 2024

A necessary condition for the probabilities of a set of events to exhibit Bell non-locality or Kochen–Specker contextuality is that the graph of exclusivity of the events contains induced odd cycles with five or more vertices, called odd holes, or their complements, called odd antiholes. From this perspective, events whose graph of exclusivity are odd holes or antiholes are the building blocks of contextuality. For any odd hole or antihole, any assignment of probabilities allowed by quantum theory can be achieved in specific contextuality scenarios. However, here we prove that, for any odd hole, the probabilities that attain the quantum maxima cannot be achieved in Bell scenarios. We also prove it for the simplest odd antiholes. This leads us to the conjecture that the quantum maxima for any of the building blocks cannot be achieved in Bell scenarios. This result sheds light on why the problem of whether a probability assignment is quantum is decidable, while whether a probability assignment within a given Bell scenario is quantum is, in general, undecidable. This also helps to understand why identifying principles for quantum correlations is simpler when we start by identifying principles for quantum sets of probabilities defined with no reference to specific scenarios.

This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Observer effect, quasi-probabilities and generalized Specker’s boxes
Authors: Onggadinata K. , Kaszlikowski D. , Kurzyński P.
Published: January 2024

Quantum non-locality and contextuality can be simulated with quasi-probabilities, i.e. probabilities that take negative values. Here, we show that another quantum phenomenon, the observer effect, admits a quasi-probabilistic description too. We also investigate post-quantum observer effects based on the Specker’s triangle scenario. This scenario comprises three observables, with the possibility of measuring two simultaneously. Represented as three boxes with a hidden ball, this scenario exhibits counterintuitive behaviour: regardless of the chosen pair of boxes, one box always contains the ball. Moreover, the scenario demonstrates a strong observer effect. When an observer selects and opens the first box, finding it empty, the ball is guaranteed to be in the second box, thereby allowing the observer to determine the ball’s location among the remaining two boxes. We extend this scenario to include additional boxes and multiple balls. By employing negative probabilities, we demonstrate amplification of the observer effect.

This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Corrected Bell and non-contextuality inequalities for realistic experiments
Authors: Vallée Kim , Emeriau Pierre-Emmanuel , Bourdoncle Boris , Sohbi Adel , Mansfield Shane , Markham Damian
Published: January 2024

Contextuality is a feature of quantum correlations. It is crucial from a foundational perspective as a non-classical phenomenon, and from an applied perspective as a resource for quantum advantage. It is commonly defined in terms of hidden variables, for which it forces a contradiction with the assumptions of parameter-independence and determinism. The former can be justified by the empirical property of non-signalling or non-disturbance, and the latter by the empirical property of measurement sharpness. However, in realistic experiments neither empirical property holds exactly, which leads to possible objections to contextuality as a form of non-classicality, and potential vulnerabilities for supposed quantum advantages. We introduce measures to quantify both properties, and introduce quantified relaxations of the corresponding assumptions. We prove the continuity of a known measure of contextuality, the contextual fraction, which ensures its robustness to noise. We then bound the extent to which these relaxations can account for contextuality, via corrections terms to the contextual fraction (or to any non-contextuality inequality), culminating in a notion of genuine contextuality, which is robust to experimental imperfections. We then show that our result is general enough to apply or relate to a variety of established results and experimental set-ups.

This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Parachitinimonas caeni gen. nov., sp. nov., a novel member of family Burkholderiaceae isolated from activated sludge collected in Shenzhen, PR China
Authors: Wang Xin , Chen Han , Wang Jing , Yuan Siliang , Jiao Dian , Wang Shanhui , Liu Yaqi , Li Yan , Dai Jingcheng , Li Shuyang , Qiu Dongru
Published: January 2024

A Gram-stain-negative, strictly aerobic and filamentous bacterial strain, designated as DQS-5T, was isolated from the activated sludge of a municipal sewage treatment plant in Shenzhen, PR China. Optimal growth was observed at 28 °C and pH 7.5. Catalase and oxidase activities were detected. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DQS-5T was most closely related to the genera

Chitinimonas

and

Chitinivorax

(91.0–93.4 % and 92.5 % 16S rRNA gene sequence similarity, respectively) and was close to the member of the family

Burkholderiaceae

. The complete genome sequence of strain DQS-5T contains 5 653 844 bp and 57.3 mol% G+C. The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values between the genome of strain DQS-5T and those of its close relatives were 75.9–77.2, 19.0–20.3 and 57.2–61.8 %, respectively. Chemotaxonomic analysis of strain DQS-5T indicated that the sole respiratory quinone was ubiquinone-8, the predominant cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrate that strain DQS-5T represents a novel species in a novel genus within the family

Burkholderiaceae

, for which the name Parachitinimonas caeni gen. nov., sp. nov., is proposed. Strain DQS-5T (=KCTC 92788T=CCTCC AB 2022320T) is the type and only strain of P. caeni.
Spathaspora quercus f.a., sp. nov., a novel yeast isolated from rotting wood and a lichen sample in Kyushu region, Japan
Authors: Hamaguchi Ayuki , Umeshita Katsuhiro , Taguchi Hisataka , Sasano Yu
Published: January 2024

A corrigendum of this article has been published full details can be found at

https://doi.org/10.1099/ijsem.0.006492

Four novel d-xylose assimilation yeast strains were isolated from rotting wood and a lichen sample collected in the Kyushu region of Japan. Species identifications were performed by analysing the internal transcribed spacer 5.8S region sequences and the D1/D2 variable domain of the large subunit rRNA gene. Phylogenetic analysis suggested that these isolates are closely related to Spathaspora species isolated in China, such as S. jiuxiensis and S. parajiuxiensis. These isolates also showed sequence similarity to deposited sequences labelled as Schwanniomyces. They did not produce asci and ascospores under any of the test conditions. Based on phylogenetic analysis and phenotypic differences, Spathaspora quercus f.a., sp. nov. is proposed to accommodate these isolates. The holotype of Spathaspora quercus f.a., sp. nov. is NBRC 116146T (CBS18366). This species is able to ferment d-xylose, and a d-xylose fermentation test revealed that this species produces a considerable amount of xylitol.
Three novel Luteimonas species from a root and rhizosphere soil of Kalidium cuspidatum: Luteimonas endophytica sp. nov., Luteimonas rhizosphaericola sp. nov. and Luteimonas kalidii sp. nov.
Authors: Wei Hua-Mei , Xu Lian , Zhang Xu , Sun Ji-Quan
Published: January 2024

Three Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RD2P54T, M1R5S18T and M1R5S59T, were isolated from a root and rhizosphere soil of Kalidium cuspidatum, in Baotou, PR China. The three strains showed 94.1–98.7 % 16S rRNA gene sequence similarities to

Luteimonas

strains, indicating they belonged to the genus

Luteimonas

. The phylogenomic tree based on core genomes showed that strain RD2P54T tightly clustered with

Luteimonas salinisoli

SJ-92T, while strains M1R5S18T and M1R5S59T clustered with each other and with Luteimonas viscosa XBU10T and

Luteimonas saliphila

SJ-9T. Though strains M1R5S18T and M1R5S59T showed high 16S rRNA similarity (99.4 %) to each other, the low average nucleotide identity based on blast (ANIb; 88.6 %) and digital DNA–DNA hybridization (dDDH; 31.6 %) values between them indicated that they belonged to two different species. The ANIb and dDDH values of strains RD2P54T, M1R5S18T and M1R5S59T with their closely neighbours are well below the delineation threshold values for identifying strains as representing different species. All three strains take iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1
 ω9c) as major fatty acids, and ubiquinone-8 as the sole respiratory quinone. The major polar lipids of all three strains are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on phenotypic and phylogenetic data, these three strains should be considered to represent three novel species of the genus

Luteimonas

, for which the names Luteimonas endophytica sp. nov. (type strain RD2P54T=CGMCC 1.61535T =KCTC 92470T), Luteimonas rhizosphaericola sp. nov. (type strain M1R5S18T=CGMCC 1.61537T =KCTC 92469T) and Luteimonas kalidii sp. nov. (type strain M1R5S59T=CGMCC 1.61536T =KCTC 92471T) are proposed.
PERFORATION-TYPE ANCHORS INSPIRED BY SKIN LIGAMENT FOR THE ROBOTIC FACE COVERED WITH LIVING SKIN
Authors: Kawai M. , Nie M. , Oda H. , Takeuchi S.
Published: January 2024

Skin equivalent, a living skin model composed of cells and extracellular matrix, possesses the potential as an ideal covering material for robots due to their biological functionalities. To employ skin equivalents as a coverage material for robots, a secure method for attaching them to the underlying structure is required. In this study, we developed a perforation-type anchor inspired by the structure of skin ligaments as a technique to effectively adhere skin equivalent to robotic surfaces, ensuring a smooth and non-protrusive integration, akin to natural skin adherence. We showed the effectiveness of plasma treatment for collagen-gel penetration within the perforation-type anchor. In characterizing the anchoring system, we investigated the impact of anchor diameter on preventing contraction and changes in holding strength. To showcase the versatility of perforation-type anchors in three-dimensional (3D) coverage applications, a 3D facial mold with intricate surface structure was covered with skin equivalent. Furthermore, we constructed a robotic face covered with dermis equivalent, capable of expressing smiles with the actuation to the skin equivalent through perforation-type anchors.

This research introduces an approach for the adhesion and actuation of skin equivalent with perforation-type anchors, potentially contributing to advancements in biohybrid robotics technology.
Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-dependent Spectral Features
Authors: Burr David J. , Drauschke Janina , Kanevche Katerina , Kümmel Steffen , Stryhanyuk Hryhoriy , Heberle Joachim , Perfumo Amedea , Elsaesser Andreas
Published: January 2024

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP-nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science and cancer research.
Loss of NAT10 disrupts enhancer organization via p300 mislocalization and suppresses transcription of genes necessary for metastasis progression
Authors: Amin Ruhul , Ha Ngoc-Han , Qiu Tinghu , Holewinski Ronald , Lam Khiem C. , Lopès Amélie , Liu Huaitian , Tran Andy D. , Lee Maxwell P. , Gamage Supuni Thalalla , Andresson Thorkell , Goldszmid Romina S. , Meier Jordan L. , Hunter Kent W.
Published: January 2024

Acetylation of protein and RNA represent a critical event for development and cancer progression. NAT10 is the only known RNA acetylase that catalyzes the N4-actylcytidine (ac4C) modification of RNAs. Here, we show that the loss of NAT10 significantly decreases lung metastasis in allograft and genetically engineered mouse models of breast cancer. NAT10 interacts with a mechanosensitive, metastasis susceptibility protein complex at the nuclear pore. In addition to its canonical role in RNA acetylation, we find that NAT10 interacts with p300 at gene enhancers. NAT10 loss is associated with p300 mislocalization into heterochromatin regions. NAT10 depletion disrupts enhancer organization, leading to alteration of gene transcription necessary for metastatic progression, including reduced myeloid cell-recruiting chemokines that results in a less metastasis-prone tumor microenvironment. Our study uncovers a distinct role of NAT10 in enhancer organization of metastatic tumor cells and suggests its involvement in the tumor-immune crosstalk dictating metastatic outcomes.
Ligand supplementation restores the cancer therapy efficacy of an antirheumatic drug auranofin from serum inactivation
Authors: Wang Yuan , Cao Bei , Wang Qianqian , Fang Xin , Wang Junjian , Chan Albert S. C. , Xiong Xiaolin , Zou Taotao
Published: January 2024

Auranofin, an FDA-approved antirheumatic gold drug, has gained ongoing interest in clinical studies for treating advanced or recurrent tumors. However, gold ion’s dynamic thiol exchange nature strongly attenuates its bioactivity due to the fast formation of covalent albumin-gold adducts. Here we report that newly-added thiols can modulate the dynamic albumin-gold binding and recover the therapeutic efficacy. Initially, we found that auranofin supplemented with its own thiol ligand, TGTA (1-thio-β-D-glucose tetraacetate), significantly restored the anticancer activities in cells and patient-derived xenograft models. Then, screening a collection of ligand fragments followed by machine learning evaluation unveiled diverse synergizing thiols, including pantethine that effectuates auranofin at a low dosage used for rheumatoid arthritis. Interestingly, the thiol exchange inside cells accounts for a cuproptosis-like phenotype induced by auranofin. Together, we believe the ligand-enabled dynamic modulation strategy is of value to researchers and clinicians contemplating metallodrugs and ligand-like molecules in cancer therapy.
Activated fibroblasts drive cellular interactions in end-stage pediatric hypertrophic cardiomyopathy
Authors: Tadros Hanna J. , Turaga Diwakar , Zhao Yi , Tsai Chang-Ru , Adachi Iki A. , Li Xiao , Martin James F.
Published: January 2024

Hypertrophic cardiomyopathy (HCM) is a relatively rare but debilitating diagnosis in the pediatric population and patients with end-stage HCM require heart transplantation. In this study, we performed single-nucleus RNA sequencing on pediatric HCM and control myocardium. We identified distinct underling cellular processes in pediatric, end-stage HCM in cardiomyocytes, fibroblasts, endothelial cells, and myeloid cells, compared to controls. Pediatric HCM was enriched in cardiomyocytes exhibiting “stressed” myocardium gene signatures and underlying pathways associated with cardiac hypertrophy. Cardiac fibroblasts exhibited clear activation signatures and heightened downstream processes associated with fibrosis, more so than adult counterparts. There was notable depletion of tissue-resident macrophages, and increased vascular remodeling in endothelial cells. Our analysis provides the first single nuclei analysis focused on end-stage pediatric HCM.
Undoing the ‘nasty: dissecting touch-sensitive stigma movement (thigmonasty) and its loss in self-pollinating monkeyflowers
Authors: Fishman Lila , McIntosh Mariah , Nelson Thomas C. , Baesen Kailey , Finseth Findley R. , Stark-Dykema Evan
Published: January 2024

Rapid touch-sensitive stigma closure is a novel plant reproductive trait found in hundreds of Lamiales species. The origins, mechanisms, and functions of stigma closure remain poorly understood, but its repeated loss in self-fertilizing taxa and direct tests implicate adaptive roles in animal-mediated cross-pollination. Here, we document several additional losses of stigma closure in monkeyflowers (Mimulus), then use quantitative trait locus (QTL) mapping and gene expression analyses to provide a first glimpse into the genetic and molecular basis of stigma mechanosensing and movement. Variation in stigma closure in hybrids between selfer/non-closerMimulus nasutusand outcrosser/fast-closerM. guttatushas a moderately complex genetic basis, with four QTLs together explaining ∼70% of parental divergence.Loss of stigma closure inM. nasutusappears genetically independent from other aspects of the floral selfing syndrome and from a parallel loss in M. parishii. Analyses of stylar gene expression in closerM. guttatus,M. nasutus, and a rareM. guttatusnon-closer genotype identify functional candidates involved in mechanosensing, turgor regulation, and cell wall remodeling. Together, these analyses reveal a polygenic genetic architecture underlying gain and loss of a novel plant movement, illuminate selfer-outcrosser reproductive divergence, and initiate mechanistic investigations of an unusually visible manifestation of plant intelligence.
Sounds of the underground reflect soil biodiversity dynamics across a grassy woodland restoration chronosequence
Authors: Robinson Jake M. , Taylor Alex F. , Fickling Nicole W. , Sun Xin , Breed Martin F.
Published: January 2024

Fifty-nine percent of the world’s species inhabit the soil. However, soils are degrading at unprecedented rates, necessitating efficient, cost-effective, and minimally intrusive biodiversity monitoring methods to aid in their restoration. Ecoacoustics is emerging as a promising tool for detecting and monitoring soil biodiversity, recently proving effective in a temperate forest restoration context. However, understanding the efficacy of soil ecoacoustics in other ecosystems and bioregions is essential. Here, we applied ecoacoustics tools and indices (Acoustic Complexity Index, Bioacoustic Index, Normalised Difference Soundscape Index) to measure soil biodiversity in an Australian grassy woodland restoration chronosequence. We collected 240 soil acoustic samples from two cleared plots (continuously cleared through active management), two woodland restoration plots (revegetated 14-15 years ago), and two remnant vegetation plots over 5 days at Mount Bold, South Australia. We used a below-ground sampling device and sound attenuation chamber to record soil invertebrate communities, which were also manually counted. We show that acoustic complexity and diversity were significantly higher in revegetated and remnant plots than in cleared plots, both in-situ and in sound attenuation chambers. Acoustic complexity and diversity were also strongly positively associated with soil invertebrate abundance and richness, and each chronosequence age class supported distinct invertebrate communities. Our results provide support that soil ecoacoustics can effectively measure soil biodiversity in woodland restoration contexts. This technology holds promise in addressing the global need for effective soil biodiversity monitoring methods and protecting our planet’s most diverse ecosystems.