bluuebunny/crossref_metadata_2025 huggingface dataset:
How to store a beetle larva? Comparing temporal effects of common fluid preservation methods on color, shape, and DNA quality
Authors: Novák Martin , Jakubec Pavel , Mahlerová Karolina , Montoya-Molina Santiago , Qubaiová Jarin
Published: December 2023

Proper fixing and long-term preservation of entomological evidence are essential in collections and research and crucial in applied fields such as forensic entomology. Incorrectly stored samples may lose important morphological features over time, rendering molecular analyses exceedingly difficult. The most effective method for preserving soft samples such as larvae is fluid preservation. It uses a combination of a wide range of fixatives and storage fluids. However, very little comparative work has been done to determine the effects of long-term storage on sample quality in terms of color, shape, and DNA stability. Moreover, the current golden standard in forensic entomology has been tailored for age estimation of larvae of Diptera, which differ from larvae of Coleoptera in morphology and subsequently in applied methods. We compared the effects of combinations of 6 commonly used fixatives and 6 commonly used storage fluids on midsized larvae of the forensically important beetle, Necrodes littoralis (Linnaeus, 1758), in terms of color, shape, and suitability for DNA analyses over a 2-yr period. We were looking for combinations that can preserve specimens in a satisfactory state, can be used on a regular basis, do not require advanced protection or skills of the personnel, and are not toxic or too harmful to the environment. We found not only several methods that scored significantly better in the tested parameters compared with the golden standard but also several common methods that should be avoided. The effects of agents on each tested category are discussed in detail.
Maternal serum concentrations of per- and polyfluoroalkyl substances and childhood acute lymphoblastic leukemia
Authors: Jones Rena R , Madrigal Jessica M , Troisi Rebecca , Surcel Heljä-Marja , Öhman Hanna , Kivelä Juha , Kiviranta Hannu , Rantakokko Panu , Koponen Jani , Medgyesi Danielle N , McGlynn Katherine A , Sampson Joshua , Albert Paul S , Ward Mary H
Published: December 2023

Background

Per- and polyfluoroalkyl substances (PFAS) are widespread and environmentally persistent chemicals with immunotoxic properties. Children are prenatally exposed through maternal transfer of PFAS to cord blood, but no studies have investigated the relationship with childhood leukemia.

Methods

We measured maternal serum levels of 19 PFAS in first-trimester samples collected in 1986-2010 and evaluated associations with acute lymphoblastic leukemia in full-term offspring (aged younger than 15 years) for 400 cases and 400 controls in the Finnish Maternity Cohort, matched on sample year, mother’s age, gestational age, birth order, and child’s sex. We analyzed continuous and categorical exposures, estimating odds ratios (ORs) and 95% confidence intervals (CIs) via conditional logistic regression adjusted for maternal smoking and correlated PFAS (ρ ≥ ±0.3). We also stratified by calendar period, mean diagnosis age, and the child’s sex.

Results

N-methyl-perfluorooctane sulfonamidoacetic acid was associated with acute lymphoblastic leukemia in continuous models (per each doubling in levels: ORperlog2 = 1.22, 95% CI = 1.07 to 1.39), with a positive exposure-response across categories (OR>90th percentile = 2.52, 95% CI = 1.33 to 4.78; Ptrend = .01). Although we found no relationship with perfluorooctane sulfonic acid overall, an association was observed in samples collected in 1986-1995, when levels were highest (median = 17.9 µg/L; ORperlog2 = 4.01, 95% CI = 1.62 to 9.93). A positive association with perfluorononanoic acid was suggested among first births (Pinteraction = .06). The N-methyl-perfluorooctane sulfonamidoacetic acid association was mainly limited to children diagnosed before age 5 years (Pinteraction = .02). We found no consistent patterns of association with other PFAS or differences by sex.

Conclusions

These novel data offer evidence of a relationship between some PFAS and risk of the most common childhood cancer worldwide, including associations with the highest levels of perfluorooctanesulfonic acid and with a precursor, N-methyl-perfluorooctane sulfonamidoacetic acid.
Progress in cancer control leads to a substantial number of cancer deaths avoided in Canada
Authors: Warkentin Matthew T , Ruan Yibing , Ellison Larry F , Billette Jean-Michel , Demers Alain A , Liu Fei-Fei , Brenner Darren R
Published: December 2023

It is currently not known how many more cancer deaths would have occurred among Canadians if cancer mortality rates were unchanged following various modern human interventions. The objective of this study was to estimate the number of cancer deaths that have been avoided in Canada since the age-standardized overall cancer mortality rate peaked in 1988. We applied the age-specific overall cancer mortality rates from 1988 to the Canadian population for all subsequent years to estimate the number of expected deaths. Avoided cancer deaths were estimated as the difference between the observed and expected number of cancer deaths for each year. Since 1988, there have been 372 584 (standardized mortality ratio = 0.77) and 120 045 (standardized mortality ratio = 0.90) avoided cancer deaths in males and females, respectively (492 629 total). Nearly half a million cancer deaths have been avoided in Canada since the overall cancer mortality rate peaked, which demonstrates the exceptional progress made in modern cancer control in Canada.
Least squares estimation of a quasiconvex regression function
Authors: Mukherjee Somabha , Patra Rohit K , Johnson Andrew L , Morita Hiroshi
Published: December 2023

We develop a new approach for the estimation of a multivariate function based on the economic axioms of quasiconvexity (and monotonicity). On the computational side, we prove the existence of the quasiconvex constrained least squares estimator (LSE) and provide a characterisation of the function space to compute the LSE via a mixed-integer quadratic programme. On the theoretical side, we provide finite sample risk bounds for the LSE via a sharp oracle inequality. Our results allow for errors to depend on the covariates and to have only two finite moments. We illustrate the superior performance of the LSE against some competing estimators via simulation. Finally, we use the LSE to estimate the production function for the Japanese plywood industry and the cost function for hospitals across the US.
Reflexive reciprocity under an ethics of care: Reflections from the field for refugee studies
Authors: Zadhy-Çepoğlu Aminath Nisha
Published: December 2023

By bringing reflexivity and reciprocity into conceptual dialogue in a discussion about the ethical framework of care in research, this article discusses how ‘reflexive reciprocity’ can be a research tool in migration studies. Taking reciprocity—the dynamics of giving and receiving—as an aspect contextually bound to the refugee experience, I propose that a relationship of giving and receiving helps undermine the inevitable power asymmetries in knowledge production. Reciprocity becomes all the more essential when researching refugee communities where narratives are prompted in a way that mirrors how refugees are elicited to give information within mechanisms of refugee governance, where they narrate their neediness, perform their vulnerability, and justify their deservingness in return for legal and humanitarian protection in traumatic processes that can be a distortion of the norms of reciprocity. This article invites researchers to address reciprocity in research, premised on the idea that an ethical framework of care should go beyond paying lip service to protect vulnerable and marginalized participants. Reflecting on my case study research with Syrian refugee women in Turkey, Ankara, I argue that reflexive reciprocity is both a tool for more rigorous data collection in a qualitative inquiry and a practical application of an ethical framework of care. In exploring instances where I could link reflexivity to action-oriented reciprocity through ‘everyday acts of caring’, I demonstrate that reflexive reciprocity can somewhat balance out the extractive nature of research and thereby contribute to the ongoing discussion about the ‘reflexive turn’ in migration studies.
[C ii] 158 μm emission as an indicator of galaxy star formation rate
Authors: Liang Lichen , Feldmann Robert , Murray Norman , Narayanan Desika , Hayward Christopher C , Anglés-Alcázar Daniel , Bassini Luigi , Richings Alexander J , Faucher-Giguère Claude-André , Chung Dongwoo T , Chan Jennifer Y H , Tolgay Doǧa , Çatmabacak Onur , Kereš Dušan , Hopkins Philip F
Published: December 2023

Observations of local star-forming galaxies (SFGs) show a tight correlation between their singly ionized carbon line luminosity ($L_{\rm [C\, {\small II}]}$) and star formation rate (SFR), suggesting that $L_{\rm [C\, {\small II}]}$ may be a useful SFR tracer for galaxies. Some other galaxy populations, however, are found to have lower $L_{\rm [C\, {\small II}]}{}/{}\rm SFR$ than local SFGs, including the infrared (IR)-luminous, starburst galaxies at low and high redshifts as well as some moderately SFGs at the epoch of re-ionization (EoR). The origins of this ‘$\rm [C\, {\small II}]$ deficit’ is unclear. In this work, we study the $L_{\rm [C\, {\small II}]}$–SFR relation of galaxies using a sample of z = 0–8 galaxies with $M_*\approx 10^7-5\times 10^{11}\, \mathrm{M}_\odot$ extracted from cosmological volume and zoom-in simulations from the Feedback in Realistic Environments (fire) project. We find a simple analytic expression for $L_{\rm [C\, {\small II}]}$/SFR of galaxies in terms of the following parameters: mass fraction of $\rm [C\, {\small II}]$-emitting gas ($f_{\rm [C\, {\small II}]}$), gas metallicity (Zgas), gas density (ngas), and gas depletion time ($t_{\rm dep}{}={}M_{\rm gas}{}/{}\rm SFR$). We find two distinct physical regimes: $\rm H_2$-rich galaxies, where tdep is the main driver of the $\rm [C\, {\small II}]$ deficit and $\rm H_2$-poor galaxies where Zgas is the main driver. The observed $\rm [C\, {\small II}]$ deficit of IR-luminous galaxies and early EoR galaxies, corresponding to the two different regimes, is due to short gas depletion time and low gas metallicity, respectively. Our result indicates that the $\rm [C\, {\small II}]$ deficit is a common phenomenon of galaxies, and caution needs to be taken when applying a constant $L_{\rm [C\, {\small II}]}$-to-SFR conversion factor derived from local SFGs to estimate cosmic SFR density at high redshifts and interpret data from upcoming $\rm [C\, {\small II}]$ line intensity mapping experiments.
Search for spectroscopic binaries using rotational velocities in five open clusters observed by ESO
Authors: Kovalev Mikhail , Ahmed Mariyam , Asa’d Randa
Published: December 2023

In this paper we detect double-lined spectroscopic binaries (SB2) in five open clusters: NGC 2243, NGC 2420, NGC 3532, NGC 6253, and NGC 6705 (M 11) using a method based on high values of the projected rotational velocity when they are fitted with single star spectral model. Observed spectra were obtained from the European Southern Observatory archive. The method was validated on the sets of synthetic spectra for the single and binary stars. It is able to reliably select spectroscopic binaries without confusing them with single stars, if the components in a binary rotate slowly and the radial velocity separation is sufficiently high. We found 60 SB2 candidates: two in NGC 2243, eight each in NGC 2420 and NGC 3532, 17 in NGC 6253, and 25 in NGC 6705. Comparison with literature confirms 18 of them, thus we found 42 new SB2 candidates.
The surprising lack of effect from stellar feedback on the gas stripping rate from massive jellyfish galaxies
Authors: Akerman Nina , Tonnesen Stephanie , Poggianti Bianca Maria , Smith Rory , Marasco Antonino , Kulier Andrea , Müller Ancla , Vulcani Benedetta
Published: December 2023

We study the role of star formation and stellar feedback in a galaxy being ram pressure (RP) stripped on its infall into a cluster. We use hydrodynamical wind-tunnel simulations of a massive galaxy (Mstar = 1011 M⊙) moving into a massive cluster (Mcluster = 1015 M⊙). We have two types of simulations: with and without star formation and stellar feedback, SF, and radiative cooling (RC), respectively. For each type, we simulate four realizations of the same galaxy: a face-on wind, edge-on wind, 45° angled wind, and a control galaxy not subject to RP. We directly compare the stripping evolution of galaxies with and without star formation. We find that stellar feedback has no direct effect on the stripping process, i.e. there is no enhancement in stripping via a velocity kick to the interstellar medium (ISM) gas. The main difference between RC and SF galaxies is due to the indirect effect of stellar feedback, which produces a smoother and more homogeneous ISM. Hence, while the average gas surface density is comparable in both simulation types, the scatter is broader in the RC galaxies. As a result, at the galaxy outskirts overdense clumps survive in RC simulation, and the stripping proceeds more slowly. At the same time, in the inner disc, underdense gas in the RC holes is removed faster than the smoothly distributed gas in the SF simulation. For our massive galaxy, we therefore find that the effect of feedback on the stripping rate is almost negligible, independent of wind angle.
Single-molecule visualization of twin-supercoiled domains generated during transcription
Authors: Janissen Richard , Barth Roman , Polinder Minco , van der Torre Jaco , Dekker Cees
Published: December 2023

Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and the regulation of genetic processes in all domains of life. It has become common knowledge that, during transcription, the DNA-dependent RNA polymerase (RNAP) induces positive supercoiling ahead of it (downstream) and negative supercoils in its wake (upstream), as rotation of RNAP around the DNA axis upon tracking its helical groove gets constrained due to drag on its RNA transcript. Here, we experimentally validate this so-called twin-supercoiled-domain model with in vitro real-time visualization at the single-molecule scale. Upon binding to the promoter site on a supercoiled DNA molecule, RNAP merges all DNA supercoils into one large pinned plectoneme with RNAP residing at its apex. Transcription by RNAP in real time demonstrates that up- and downstream supercoils are generated simultaneously and in equal portions, in agreement with the twin-supercoiled-domain model. Experiments carried out in the presence of RNases A and H, revealed that an additional viscous drag of the RNA transcript is not necessary for the RNAP to induce supercoils. The latter results contrast the current consensus and simulations on the origin of the twin-supercoiled domains, pointing at an additional mechanistic cause underlying supercoil generation by RNAP in transcription.
cGAS-STING signalling regulates microglial chemotaxis in genome instability
Authors: Talbot Emily J , Joshi Lisha , Thornton Peter , Dezfouli Mahya , Tsafou Kalliopi , Perkinton Michael , Khoronenkova Svetlana V
Published: December 2023

Defective DNA damage signalling and repair is a hallmark of age-related and genetic neurodegenerative disease. One mechanism implicated in disease progression is DNA damage-driven neuroinflammation, which is largely mediated by tissue-resident immune cells, microglia. Here, we utilise human microglia-like cell models of persistent DNA damage and ATM kinase deficiency to investigate how genome instability shapes microglial function. We demonstrate that upon DNA damage the cytosolic DNA sensing cGAS-STING axis drives chronic inflammation and a robust chemokine response, exemplified by production of CCL5 and CXCL10. Transcriptomic analyses revealed that cell migratory pathways were highly enriched upon IFN-β treatment of human iPSC-derived microglia, indicating that the chemokine response to DNA damage mirrors type I interferon signalling. Furthermore, we find that STING deletion leads to a defect in microglial chemotaxis under basal conditions and upon ATM kinase loss. Overall, this work provides mechanistic insights into cGAS-STING-dependent neuroinflammatory mechanisms and consequences of genome instability in the central nervous system.
An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex
Authors: Shannon Ashleigh , Chazot Aurélie , Feracci Mikael , Falcou Camille , Fattorini Véronique , Selisko Barbara , Good Steven , Moussa Adel , Sommadossi Jean-Pierre , Ferron François , Alvarez Karine , Canard Bruno
Published: December 2023

Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5′-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3′-to-5′ exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5′-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.
Behavior Change Intervention for Smokeless Tobacco Cessation Delivered Through Dentists in Dental Settings: A Pragmatic Pilot Trial
Authors: Rasool Shaista , Holliday Richard , Khan Zohaib , Dobbie Fiona , Bauld Linda
Published: December 2023

Introduction

Evidence on smokeless tobacco (ST) cessation interventions is scarce. The South Asian (SA) region that shares more than 90% of the burden of ST use is grossly underrepresented in research on ST cessation. This study aimed to assess the feasibility of delivering and investigating a behavioral support intervention for ST cessation in dental settings in Pakistan.

Methods

A multicenter, pilot, two-armed parallel-group, individually randomized control trial, with a 1:1 allocation ratio, was conducted at two dental hospitals. Eligibility criteria included being an ST user seeking dental treatment and not currently accessing cessation support. All participants were provided written self-help ST cessation material. The intervention group also received a dentist-delivered, bespoke behavioral support intervention for ST cessation developed for users of SA origin. Participants were followed up telephonically at 3 and 6 months. Self-reported 6-month abstinence was verified by salivary cotinine. Analysis was descriptive, with 95% confidence intervals presented where appropriate.

Results

One hundred participants were successfully recruited from the selected hospitals. Of these, 78% continued to engage throughout the study duration and provided primary outcome data, whereas 63% completed all hospital visits. The outcome measures were successfully collected. Biochemically verified 6-month abstinence in the intervention and control groups was 10% and 4%.

Conclusions

It was feasible to deliver and evaluate a dentist-delivered behavioral support intervention for ST cessation in Pakistan. The data suggested that the intervention may improve ST quit rates. The findings of this study will be useful in informing the design of future definitive studies.

Implications

To our knowledge, this is the first pragmatic pilot trial on ST cessation in dental settings in Pakistan and the first trial on dentist-delivered structured behavioral support intervention for ST cessation. It adds to the scarce, trial evidence based on ST cessation interventions. The findings suggest behavioral support intervention for ST cessation may improve quit rates. The trial was conducted in a country with poor ST control measures, where ST products are not taxed, the products are sold openly to and by minors, and the users are offered negligible cessation support. The findings may, therefore, be generalizable to low–middle-income countries, particularly SA countries, with similar policy backgrounds.
Drought as a trigger of the rapid rise of professional skateboarding in 1970s Southern California
Authors: Büntgen Ulf , Oppenheimer Clive , Li Paco , Frachetti Michael , Esper Jan , Torbenson Max C A , Krusic Paul J
Published: December 2023

In 1977 California, authorities responded to an extreme drought with an unprecedented state order to drastically reduce domestic water usage and leave countless newly built swimming pools empty. These curved pools became “playgrounds” for inspired surfers to develop professional vertical skateboarding in the Los Angeles area. Industrial production of polyurethane, and the advent of digital photography, laser printing, and high gloss mass media further contributed to the explosive popularization of skateboarding, creating a global subculture and multibillion-dollar industry that still impacts music, fashion, and lifestyle worldwide. Our interdisciplinary investigation demonstrates that neither the timing nor the location of the origin of professional skateboarding was random. This modern case study highlights how environmental changes can affect human behavior, transform culture, and engender technical innovation in the Anthropocene.
Autocratic Legalism, Partisanship, and Popular Legitimation in Authoritarian Cameroon
Authors: Letsa Natalie Wenzell , Morse Yonatan L
Published: December 2023

Authoritarian regimes regularly turn to the law to justify repression. This article examines whether invoking legal institutions has a persuasive effect on public perceptions of repression, and whether that effect is shaped by partisanship. The article uses the case of Cameroon’s Special Criminal Tribunal, created in 2011 to prosecute high-profile corruption cases. A survey experiment was designed that describes the arrest and trial of a suspected corrupt oppositional minister and reminds a treatment group about the Special Criminal Tribunal. The results show that neither regime nor opposition partisans are swayed by legal justifications for repression. By contrast, nonpartisans respond negatively to autocratic legalism, particularly those with low levels of regime trust. The article clarifies when autocratic legalism might be used for public legitimation, suggests that partisanship is a useful lens for understanding public opinion in an autocracy, and elaborates upon the meaning of nonpartisanship in electoral authoritarian regimes.
The Reverse Backlash: How the Success of Populist Radical Right Parties Relates to More Positive Immigration Attitudes
Authors: Dennison James , Kustov Alexander
Published: December 2023

What is the relationship between the electoral success of populist radical right parties (PRRPs) and public attitudes toward immigration? Previous research suggests that PRRP success can lead to more negative attitudes due to the breaking down of antiprejudice norms and more prominent anti-immigration party cues. However, we argue that greater PRRP success could have a positive relationship with immigration attitudes, reflecting negative partisanship, polarization, and a desire to reemphasize antiprejudice norms, which we call a “reverse backlash effect.” Using the best available electoral and public opinion data across the last thirty years in twenty-four European countries, our TSCS analyses show the predominance of such “reverse backlash effects” across several operationalizations of PRRP success. Our argument has important consequences for the understanding of possible PRRP effects on public opinion, as well as attitudinal formation via party cueing and social norms more generally.
Disjunctivism and the Paradox of Tragedy
Authors: Gaskin Richard
Published: December 2023

The paper offers a disjunctivist solution to the paradox of tragedy. The first part of the paper defends a version of disjunctivism as that doctrine is understood in the epistemology of perception, and contrasts it with its rival, conjunctivism. In the second part of the paper, it is argued that the traditional paradox of tragedy—the question why tragedy gives pleasure—can be solved by adopting a disjunctivist approach to the relevant felt emotions. The tragic audience does not really feel ‘sorrow, terror, anxiety’ (so Hume), but simulacra thereof, emotions which resemble the originals in certain respects but which have quite different connections with action. A conjunctivist approach to the paradox discerns a ‘highest common factor’ in both non-fictional and fictional scenarios: but this is not only phenomenologically implausible; it decouples the agent from the actions that are essentially keyed to particular emotions, and so splits the self.
Cancer risks in patients with ankylosing spondylitis and the effects of biologic agents: a population-based study
Authors: Eom Sang-Yong , Jang Hyun-a , Im Yo Han , Choi Kyung-Hwa , Kim Ji Hyoun
Published: December 2023

Objective

The objective of this study was to conduct a population-based analysis of the malignancy risks of patients with AS.

Methods

A total of 1796 patients with AS and 7184 age- and sex-matched controls (1:4 ratio) were selected from the Korea National Health Insurance Service–National Sample Cohort database. Data of patients diagnosed with AS (code M45) according to the International Classification of Diseases (ICD) 10th edition, between 2002 and 2019, were reviewed. These data were extracted based on the ICD codes assigned to cancer patients.

Results

Cancer developed in 168/1796 patients (9.3%) after the AS diagnosis. After adjusting for confounders, the cancer risk of patients with AS was not significantly increased compared with that of controls [adjusted hazard ratio (HR): 1.1; 95% CI: 0.93–1.31]. However, the risks for upper gastrointestinal (GI) cancer (adjusted HR: 1.51; 95% CI: 1.07–2.12) and haematologic malignancy (adjusted HR: 2.36; 95% CI: 1.2–4.65) were significantly higher in patients with AS than in controls. There were no significant differences in the risks for other major cancers between patients with AS and controls. Regarding medication for AS, the HR of upper GI cancer was higher in patients with AS compared with controls (adjusted HR: 1.51; 95% CI: 1.00–2.29).

Conclusion

The overall cancer risk in patients with AS was not significantly different compared with that in the controls. However, while the effect of NSAIDs on upper GI cancer cannot be ruled out, patients with AS exhibited a significant increase in the risk of both upper GI cancer and haematologic malignancy.
Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa
Authors: Wang Mianzhi , Wei Jingyi , Jiang Lei , Jiang Li , Zhang Junxuan , He Xiaolu , Ren Yiwen , Wang Zixuan , Sun Yongxue , Wang Zhiqiang
Published: December 2023

Antibiotic-resistant bacteria are current threats to available antibiotic therapies, and this has renewed interest in the therapeutic use of phage as an alternative. However, development of phage resistance has led to unsuccessful therapeutic outcomes. In the current study, we applied phage training to minimize bacterial phage resistance and to improve treatment outcome by adapting the phage to their target hosts during co-evolution. We isolated and characterized a novel Pseudomonas aeruginosa N4-like lytic phage (PWJ) from wastewater in Yangzhou, China. PWJ is a double-stranded DNA podovirus that can efficiently lyse the model strain ATCC 27,853 and opportunistic pathogen PAO1. Genome sequencing of PWJ revealed features similar to those of the N4-like P. aeruginosa phage YH6. We used PWJ to screen for an evolved trained phage (WJ_Ev14) that restored infectivity to PWJ phage bacterial resisters. BLASTN analysis revealed that WJ_Ev14 is identical to its ancestor PWJ except for the amino acid substitution R1051S in its tail fiber protein. Moreover, phage adsorption tests and transmission electron microscopy of resistant bacteria demonstrated that the R1051S substitution was most likely the reason WJ_Ev14 could re-adsorb and regain infectivity. Furthermore, phage therapy assays in vitro and in a mouse P. aeruginosa lung infection model demonstrated that PWJ treatment resulted in improved clinical results and a reduction in lung bacterial load whereas the joint phage cocktail (PWJ+ WJ_Ev14) was better able to delay the emergence of resister bacteria. The phage cocktail (PWJ +WJ_Ev14) represents a promising candidate for inclusion in phage cocktails developed for clinical applications.
The first record of the genus Prosantorhinus (Perissodactyla: Rhinocerotidae) of East Asia
Authors: Sun Danhui , Deng Tao , Wang Shiqi
Published: December 2023

Prosantorhinus is a genus of small extinct teleoceratine rhinoceroses with shortened limb bones, widely distributed in Europe. However, the Asian evolution of the teleoceratine Prosantorhinus has remained unclear because of a scarcity of fossil records of the genus. Here, we report the first record of Prosantorhinus in East Asia from the Middle Miocene of Tongxin, Ningxia. The new specimen is characterized by a concave dorsal skull profile and elevated nasals; short and stout nasal bones with drooping margins on both sides; the thickened, enlarged, and roughened nasal extremity supporting a small horn; the semi-molarized upper premolars with a lingual bridge between the protocone and hypocone; the metaloph constriction present on P2–4; the protocone equal to the hypocone on P2; the crista present on P3; and the cement on the cheek teeth developed. With all the morphological evidence considered, we establish a new species, Prosantorhinus yei sp. nov.. A phylogenetic analysis based on 282 morphological characters scored for 36 taxa reveals that Prosantorhinus yei sp. nov. is a relatively derived taxon in the genus. We hypothesize that Prosantorhinus yei sp. nov. lived in relatively moist environments.
Gene Expression Clusters Suggest Potential Mechanisms of Resistance to Powdery Mildew in Hop (Humulus lupulus)
Authors: Eriksen Renée L. , Wiseman Michele S. , Magana Armando Alcazar , Dhar Nikhilesh , Reed Ralph L. , Stevens Jan F. , Gent David H. , Henning John A.
Published: December 2023

Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop in the Pacific Northwest of the United States. Resistant cultivars exist; however, recently, the pathogen has overcome two sources of resistance in popular cultivars. Breeding for new, emerging races of the pathogen is thus a continuing priority. We used RNA-seq to understand gene expression trends in a resistant (cv. USDA Nugget) and a susceptible (cv. Symphony) hop cultivar along a time series following inoculation. We found stronger transcriptional reprogramming in the resistant cultivar than the susceptible cultivar. Transcripts that increased in expression within 12 h post-inoculation in the resistant cultivar included genes in the jasmonic acid biosynthesis pathway, as well as phenylpropanoid biosynthesis. Transcripts that had a positive correlation with time post-inoculation in the resistant cultivar included genes involved in phosphorylation, cell-surface signaling pathways, and response to jasmonic acid. We used untargeted HPLC–HR-MS/MS analysis and confirmed an increase in jasmonic acid and several phenolic compounds. We hypothesize that resistance to powdery mildew in cv. Nugget may be at least partially due to perception of the pathogen outside of the cell, and transcriptional and metabolic reprogramming is mediated by jasmonic acid signaling. At least part of that transcriptional and metabolic reprogramming involves changes to lignin production, which might reinforce the cell wall. The multi-omics approach to describe the contrasting responses of a resistant and a susceptible hop cultivar following inoculation with this important pathogen may indicate new strategies for developing resistant germplasm and control methods.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Impact of Surge Strain and Pandemic Progression on Prognostication by an Established COVID-19–Specific Severity Score
Authors: Yek Christina , Wang Jing , Fintzi Jonathan , Mancera Alex G. , Keller Michael B. , Warner Sarah , Kadri Sameer S.
Published: December 2023

IMPORTANCE:

Many U.S. State crisis standards of care (CSC) guidelines incorporated Sequential Organ Failure Assessment (SOFA), a sepsis-related severity score, in pandemic triage algorithms. However, SOFA performed poorly in COVID-19. Although disease-specific scores may perform better, their prognostic utility over time and in overcrowded care settings remains unclear.

OBJECTIVES:

We evaluated prognostication by the modified 4C (m4C) score, a COVID-19–specific prognosticator that demonstrated good predictive capacity early in the pandemic, as a potential tool to standardize triage across time and hospital-surge environments.

DESIGN:

Retrospective observational cohort study.

SETTING:

Two hundred eighty-one U.S. hospitals in an administrative healthcare dataset.

PARTICIPANTS:

A total of 298,379 hospitalized adults with COVID-19 were identified from March 1, 2020, to January 31, 2022. m4C scores were calculated from admission diagnosis codes, vital signs, and laboratory values.

MAIN OUTCOMES AND MEASURES:

Hospital-surge index, a severity-weighted measure of COVID-19 caseload, was calculated for each hospital-month. Discrimination of in-hospital mortality by m4C and surge index-adjusted models was measured by area under the receiver operating characteristic curves (AUC). Calibration was assessed by training models on early pandemic waves and measuring fit (deviation from bisector) in subsequent waves.

RESULTS:

From March 2020 to January 2022, 298,379 adults with COVID-19 were admitted across 281 U.S. hospitals. m4C adequately discriminated mortality in wave 1 (AUC 0.779 [95% CI, 0.769–0.789]); discrimination was lower in subsequent waves (wave 2: 0.772 [95% CI, 0.765–0.779]; wave 3: 0.746 [95% CI, 0.743–0.750]; delta: 0.707 [95% CI, 0.702–0.712]; omicron: 0.729 [95% CI, 0.721–0.738]). m4C demonstrated reduced calibration in contemporaneous waves that persisted despite periodic recalibration. Performance characteristics were similar with and without adjustment for surge.

CONCLUSIONS AND RELEVANCE:

Mortality prediction by the m4C score remained robust to surge strain, making it attractive for when triage is most needed. However, score performance has deteriorated in recent waves. CSC guidelines relying on defined prognosticators, especially for dynamic disease processes like COVID-19, warrant frequent reappraisal to ensure appropriate resource allocation.
A Case of Superficial Papular Neuroma: A Rare Neural Neoplasm
Authors: Suzuki Shuji , Fukumoto Takuya , Hiraki Tsubasa , Goldberg Lynne J.
Published: December 2023

A case of 67-year-old male patient with superficial papular neuroma (SPN) on the occiput is reported. This is the second report of SPN and the first with clinical images. Histologically, in the superficial dermis and periadnexa, the specimen exhibits a nodule of bland spindle cells with an S-shaped and spindle nucleus, surrounded by eosinophilic collagen fibers and scattered mast cells, which forms focally peripheral nerve-like structures. Lichen simplex chronicus-like changes are observed. Immunostaining result revealed that the tumor cells are positive for S-100, neurofilament, collagen IV, and CD34 but negative for Melan A, epithelial membrane antigen, and glial fibrillary acidic protein. Histological differential diagnosis includes prurigo nodularis, neurotized nevus, benign peripheral nerve sheath tumor, such as neurofibroma or schwannoma, a type of neuroma, such as traumatic neuroma, mucosal neuroma, and palisaded encapsulated neuroma, or a type of neural hamartoma. A careful histological investigation will enable dermatopathologists to make a diagnosis of SPN.
Long COVID and Chronic Conditions in the US Workforce
Authors: Bonner Carole , Ghouralal Sera-Leigh
Published: December 2023

Objective

This study examines how long COVID, chronic conditions, and work outcomes affect the general workforce.

Methods

It examines the prevalence of long COVID and its associations with chronic conditions, and other sociodemographic characteristics using 2022 National Health Interview Survey data.

Results

Long COVID affected work attendance and disability risk, especially in those with mental health issues, angina, stroke, cancer, diabetes, chronic lung conditions, and musculoskeletal conditions.

Conclusion

This study reveals the relationships between long COVID, chronic conditions, and work outcomes.
Total versus proximal gastrectomy for proximal gastric cancer after neoadjuvant chemotherapy: a multicenter retrospective propensity score-matched cohort study
Authors: Yuan Zhen , Cui Hao , Xu Qixuan , Gao Jingwang , Liang Wenquan , Cao Bo , Lin Xia , Song Liqiang , Huang Jun , Zhao Ruiyang , Li Hanghang , Yu Zhiyuan , Du Jiajun , Wang Shuyuan , Chen Lin , Cui Jianxin , Zhao Yongliang , Wei Bo
Published: December 2023

Background:

This study aimed to analyze and compare the short-term and long-term outcomes of proximal gastrectomy (PG) and total gastrectomy (TG) in patients with locally advanced proximal gastric cancer (GC) following neoadjuvant chemotherapy (NACT).

Method:

A multicenter retrospective cohort study and propensity score matching (PSM) were employed. We examined 367 patients with proximal GC who received NACT followed by PG (n=164) or TG (n=203) at two Chinese medical institutions between December 2009 and December 2022. Clinical and pathological parameters, postoperative complications, and 5-year overall survival (OS) and recurrence-free survival (RFS) were compared between the two groups. The dissection status and metastasis rate of each lymph node station were assessed.

Results:

After PSM, 80 patients were enrolled in both TG and PG group, and baseline characteristics were comparable between the groups (all P>0.05). The TG group had a higher total number of lymph nodes retrived (P<0.001) and longer operative time (P=0.007) compared to the PG group. The incidence of Clavien-Dindo grade II or higher postoperative complications was similar between the TG group (21.3%, 17/80) and the PG group (23.8%, 19/80) (P=0.850). The 5-year OS rates were 68.4% for the PG group and 66.0% for the TG group (P=0.881), while the 5-year RFS rates were 64.8% and 61.9%, respectively (P=0.571), with no statistically significant differences. Metastasis rates at lymph node stations #4d, #5, #6, and #12a were notably low in the TG group, with values of 2.74%, 0.67%, 1.33%, and 1.74%, respectively.

Conclusion:

For proximal GC patients following NACT, PG maintains comparable curative potential and oncological efficacy to TG, making it a safe option.
Hemostasis after transradial coronary intervention by rotary compression device with sterile gauze is associated with more adverse events: a retrospective study
Authors: Fan Rong , Yang Zixuan , Wang Ruiping , Liu Haoqi , Feng Can , Wu Feng , Fan Min
Published: December 2023

Objective

We investigated the relationship between using a rotary compression device (RCD) with or without sterile gauze and adverse events in transradial access (TRA) for coronary intervention.

Methods

In this study involving 933 patients at Yueyang Hospital, we recorded TRA-related adverse events, such as bleeding, forearm hematoma, swollen palms, radial artery occlusion (RAO) and others. Logistic regression was applied to assess the association.

Results

Of the 933 patients (66.7% males, average age 67.8 years), 511 used RCD with sterile gauze, whereas 422 used RCD without sterile gauze. The most common adverse events were radial artery hemorrhage (7.4%), hand swelling (4.8%) and RAO (4.6%). Logistic regression analysis revealed that the use of RCD with sterile gauze was associated with a higher prevalence of adverse events [odds ratio (OR), 1.74; 95% confidence interval (CI), 1.22–2.49), even with the adjustment of potential confounders (OR, 1.71; 95% CI, 1.19–2.45). Moreover, patients who used RCD with sterile gauze exhibited an increased risk of radial artery hemorrhage (OR, 1.83; 95% CI, 1.07–3.12), swelling of the hand (OR, 1.96; 95% CI, 1.02–3.75) and RAO (OR, 3.17; 95% CI, 1.49–6.72).

Conclusions:

The use of RCD with sterile gauze in TRA is associated with a higher incidence of adverse events.
Impact of Diplopia and Ptosis From Lingering Third Nerve Palsy After Treatment of Cerebral Aneurysms
Authors: Shapiro Jeremy N. , Delott Lindsey B. , Trobe Jonathan D.
Published: December 2023

Background:

Third nerve palsies (TNPs) may not resolve after intervention for intracranial aneurysms that have compressed the nerve. The disability related to this lingering condition has not been assessed with the support of patient self-report.

Methods:

A single-institutional retrospective study of patients with TNP who had undergone interventions for intracranial aneurysms. We used residual primary-position diplopia, a narrow zone of single binocular vision, and vision-obscuring ptosis to divide TNP recovery into complete, incomplete nondisabling, and incomplete disabling outcomes based on medical record documentation and patient self-report derived from telephonic interviews.

Results:

In a cohort of 33 patients, 13 (39%) had complete TNP recovery. There were 11 patients (33%) with lingering visual disability from diplopia or ptosis present before ophthalmic interventions. Of the 6 patients who underwent ophthalmic interventions, visual disability was relieved in only 2 patients, leaving 9 patients (27%) with lingering impairment in instrumental activities of daily living. Telephonic interviews of 23 patients (70% of the cohort) confirmed that the outcome criteria we applied were accurate in assessing visual disability in 17 patients (74%). Univariate analysis using the Fisher exact test showed that aneurysmal clipping as a treatment modality was the only clinical feature associated with a favorable TNP outcome.

Conclusions:

In applying a novel method of assessing disability, this study showed that more than one-quarter of patients undergoing procedures for brain aneurysms had lingering disability from third nerve palsy–associated diplopia or ptosis, despite later ophthalmic interventions. Patient self-report gleaned from telephonic interviews was valuable in largely validating the assessment method derived from medical records and in revealing differences between physician and patient estimation of disability.
Impact of swab removal in the detection of SARS-CoV-2 weakly-positive specimens
Authors: Zorzoli Azul , Bennett-Slater Susan , MacLean Alasdair , McAllister Gina , Gunson Rory , Templeton Kate
Published: December 2023

Graphical Abstract

Early removal of swabs can accelerate laboratory work and enhance quality by decreasing contamination and errors in downstream procedures. This article aims to compare the traditional testing workflow in a diagnostic laboratory (red), with manual swab removal and aliquoting vs a swab-out laboratory workflow (blue).
Halothiobacillus diazotrophicus sp. nov., a chemolithoautotrophic sulphur-oxidizing and nitrogen-fixing bacterium isolated from freshwater
Authors: Dai Chenming , Li Jihan , Yan Hongshan , Lin Weitie , Luo Jianfei
Published: December 2023

A sulphur-oxidizing and nitrogen-fixing bacterium, designated strain LS2T, was isolated from freshwater collected from the Pearl River in Guangzhou, PR China. The strain was an obligate chemolithoautotroph, utilizing reduced sulphur compounds (sulphide, sulphite, elemental sulphur, thiosulphate and tetrathionate) as energy sources and electron donors. Diazotrophic growth of strain LS2T was observed at 15–40 °C, pH 5–9, with a NaCl concentration range of 0–0.68 mol l−1 and with oxygen content higher than 21 %. The major cellular fatty acids were summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The DNA G+C content of the complete genome sequence was 60.7 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LS2T formed a lineage within the family

Halothiobacillaceae

, showing gene sequence identity of 96.8 % with its closest relative

Halothiobacillus neapolitanus

c2. The genome of strain LS2T contains multiple genes encoding sulphur-oxidizing enzymes that catalyse the oxidation of reduced sulphur compounds and an nif complex encoding enzymes for nitrogen fixation. In addition, the genome contains genes encoding cbb3
-type cytochrome c oxidase, aa3
-type cytochrome c oxidase, bd-type quinol oxidase and cytochrome o oxidase, which enable the survival strain LS2T under oxic and microaerophilic conditions. On the basis of phenotypic, genotypic and phylogenetic data, strain LS2T is considered to represent a novel species of the genus

Halothiobacillus

, for which the name Halothiobacillus diazotrophicus sp. nov. is proposed. The type strain is LS2T (=GDMCC 1.4095T=JCM 39442T).
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications
Authors: Timme Ruth E. , Karsch-Mizrachi Ilene , Waheed Zahra , Arita Masanori , MacCannell Duncan , Maguire Finlay , Petit III Robert , Page Andrew J. , Mendes Catarina Inês , Nasar Muhammad Ibtisam , Oluniyi Paul , Tyler Andrea D. , Raphenya Amogelang R. , Guthrie Jennifer L. , Olawoye Idowu , Rinck Gabriele , O’Cathail Colman , Lees John , Cochrane Guy , Cummins Carla , Brister J. Rodney , Klimke William , Feldgarden Michael , Griffiths Emma
Published: December 2023

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.

To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.