bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss
Authors: Pawlowski Katharina , Wibberg Daniel , Mehrabi Sara , Obaid Nadia Binte , Patyi András , Berckx Fede , Nguyen Han , Hagen Michelle , Lundin Daniel , Brachmann Andreas , Blom Jochen , Herrera-Belaroussi Aude , Abrouk Danis , Pujic Petar , Hahlin Ann-Sofi , Kalinowski Jörn , Normand Philippe , Sellstedt Anita 
Published: October 2024

Abstract
Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup−, while only one Hup− Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons. We analysed the distribution of different types of [NiFe] hydrogenase in the genomes of different Frankia species. Our results show that Frankia strains can contain four different [NiFe] hydrogenase syntons representing groups 1f, 1h, 2a, and 3b according to Søndergaard, Pedersen, and Greening (HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016;6:34212. https://doi.org/10.1038/srep34212.); no more than three types were found in any individual genome. The phylogeny of the structural proteins of groups 1f, 1h, and 2a follows Frankia phylogeny; the phylogeny of the accessory proteins does not consistently. An analysis of different [NiFe] hydrogenase types in Actinomycetia shows that under the most parsimonious assumption, all four types were present in the ancestral Frankia strain. Based on Hup activities analysed and the losses of syntons in different lineages of genome reduction, we can conclude that groups 1f and 2a are involved in recycling H2 formed by nitrogenase while group 1 h and group 3b are not.
Hepatitis B Virus RNA as a Biomarker for Safe Antiviral Discontinuation: A Prospective Study of Nucleos(t)ide Analogue Withdrawal
Authors: Terrault Norah A , Sterling Richard , Lok Anna S , Ghany Marc G , Feld Jordan J , Cloherty Gavin , Wahed Abdus S , Yang Xue 
Published: October 2024

Abstract

Background
Withdrawal of nucleos(t)ide analogue therapy is associated with hepatitis B surface antigen (HBsAg) loss and sustained off-therapy partial cure (normal alanine aminotransferase [ALT] ≤30 U/L for males and ≤20 U/L for females with hepatitis B virus [HBV] DNA &lt;2000 IU/mL) but should be offered only to those most likely to benefit. HBV RNA may be useful for risk stratification.

Methods
The Hepatitis B Research Network Immune-Active Trial prospectively evaluated treatment with tenofovir disoproxil fumarate (TDF) for 192 weeks ± peginterferon alfa-2a for the initial 24 weeks, followed by protocolized withdrawal of TDF among eligible participants (ClinicalTrials.gov NCT01369212). HBV RNA was evaluated as a predictor of ALT flares and sustained partial cure (HBV DNA &lt;2000 IU/mL) 48 weeks after TDF withdrawal.

Results
Of 93 participants discontinuing TDF (n = 52, TDF + peginterferon alfa-2a; n = 41, TDF alone), 52 (55.9%) had unquantifiable HBV RNA at end of treatment. ALT flares &gt;5 times the upper limit of normal at 48 weeks off therapy occurred in 33.3%, with pretreatment age (≥35 years) and quantifiable HBV RNA at end of treatment the best predictors (area under the receiver operating characteristic curves, 0.74 and 0.85 for training and test sets, respectively). A total of 26 (28.3%) had sustained partial cure, 3 (11.5%) with ALT flare. Nonquantifiable HBV RNA and quantitative HBsAg &lt;100 IU/mL at end of treatment were the best predictors of sustained partial cure (area under the receiver operating characteristic curves, 0.84 and 0.93 for training and test sets). If HBV RNA was quantifiable at end of treatment, the likelihood of sustained partial cure was only 3%, whereas if HBV RNA was unquantifiable and quantitative HBsAg was &lt;100 IU/mL, this likelihood was 73%.

Conclusions
HBV RNA is a useful biomarker in predicting likelihood of achieving sustained partial cure and safe withdrawal of nucleos(t)ide analogues.
Global emergence of Escherichia coli with PBP3 insertions
Authors: Long Haiyan , Zhao Feifei , Feng Yu , Zong Zhiyong 
Published: October 2024

Abstract

Objectives
Escherichia coli producing metallo-β-lactamases with penicillin-binding protein 3 (PBP3) insertions have reduced susceptibility to aztreonam–avibactam and cefiderocol. Here, we analysed high-quality E. coli genomes for PBP3 insertions.

Methods
E. coli genomes (n = 167 518) were retrieved from EnteroBase with CheckM2 for quality control, fastANI for species confirmation, multi-locus sequencing typing for sequence type (ST) determination and AMRFinderPlus for resistance gene identification. For PBP3 insertion analysis, we used Prokka for predicting coding sequences, BLAST+ for comparing resulted protein sequences and SnpEff for annotating variants.

Results
Among the included 159 341 genomes, PBP3 insertions with 11 variants were found in 2.01% (n = 3198). The predominant variant is a duplication of 334–337 amino acids (aa) (94.75%, n = 3030), comprising YRIN (65.92%, n = 2108) and its single-aa-variant YRIK (28.83%, n = 922), followed by a similar PYRI duplication of 333–336 (4.16%, n = 133). The less common ones are a TIPY duplication of 331–334 (n = 24) and its single-aa-variant TVPY’s duplication: TVVPY (n = 1), TVPYTVPY (n = 1) and TVPYPVPY (n = 1). Rare duplications include VGDR of 106–109 (n = 3), ANALNIPL of 114–121 (n = 3), AL of 567–568 (n = 1) and TG of 584–585 (n = 1). Insertion variants were detected across 62 countries on six continents, primarily in human samples, and associated with 85 STs, concentrated in high-risk clones ST410 (29.18%, n = 1923), ST167 (23.40%, n = 1740) and ST405 (10.56%, n = 1334), with 83.32% (n = 2218) encoding metallo-β-lactamase NDM.

Conclusions
Global spread of E. coli harbouring PBP3 insertion, often with NDM β-lactamase, high-risk ST410, ST167 and ST405 clones and various hosts, underscores the escalating antimicrobial resistance crisis and the urgency for a ‘One Health’ strategy.
On Nelson’s conception of consistency
Authors: Lenzen Wolfgang 
Published: October 2024

Abstract
This paper scrutinizes Everett Nelson's conception of consistency by comparing it with the “standard” account of C. I. Lewis. This conflict surprisingly resembles a related controversy between the ancient logicians Chrysippus and Diodorus. Nelson's intuitions behind his peculiar conception of consistency are analysed and certain features of his logical system are critically examined. In particular, his objections against the law of the transitivity of implication and against the laws of conjunction and disjunction have to be discussed. Although Nelson's considerations contain interesting ideas in favour of a relevantist conception of logic, they fail to convincingly support the hardcore connexive thesis that even a selfcontradictory proposition doesn't entail its own negation.
Malassezia gallinae sp. nov., a new basidiomycetous yeast species isolated from skins of chickens
Authors: Zhao Yu-Jing , Ma Qin , Liu Miao-Miao , Wang Qi-Ming 
Published: October 2024

Abstract
Species of Malassezia are lipid-dependent yeasts and integral components of the skin microbiome. Most of the currently known species are isolated from mammals. However, the presence and distribution of Malassezia yeasts on the skin of avian species have not been fully understood or elucidated. During a survey on the occurrence of Malassezia species in chickens, 23 Malassezia strains isolated from the healthy skins of chickens may represent two candidate new species of this genus based on the sequence analysis of the internal transcribed spacer (ITS) (including 5.8S rRNA) and the D1/D2 domains of 26S rRNA. The combined ITS and D1/D2 phylogenetic analysis showed that those two candidate new species were closely related to Malassezia slooffiae, and differed from the type of M. slooffiae by 51–62 nucleotides in the ITS region and four nucleotides in the D1/D2 domains, respectively. Based on the phylogenetic analysis and the phenotypic comparison, we propose a new species, named M. gallinae sp. nov., to include the 21 isolated strains.
Twins in diversity: understanding circumstellar disc evolution in the twin clusters of W5 complex
Authors: Damian Belinda , Jose Jessy , Das Swagat R , Gupta Saumya , Vaikundaraman Vignesh , Ojha D K , Kartha Sreeja S , Panwar Neelam , Eswaraiah Chakali 
Published: October 2024

ABSTRACT
Young star-forming regions in massive environments are ideal test beds to study the influence of surroundings on the evolution of discs around low-mass stars. We explore two distant young clusters, IC 1848-East and West located in the massive W5 complex. These clusters are unique due to their similar (distance, age and extinction) yet distinct (stellar density and far-ultraviolet radiation fields) physical properties. We use deep multiband photometry in optical, near-infrared and mid-infrared wavelengths complete down to the substellar limit in at least five bands. We trace the spectral energy distribution of the sources to identify the young pre-main sequence members in the region and derive their physical parameters. The disc fraction for the East and West clusters down to 0.1 M$_\odot$ was found to be $\sim 27\,\pm$ 2 per cent (N$_\mathrm{disc}$ = 184, N$_\mathrm{discless}$ = 492) and $\sim 17\,\pm$ 1 per cent (N$_\mathrm{disc}$ = 173, N$_\mathrm{discless}$ = 814), respectively. While no spatial variation in the disc fraction is observed, these values are lower than those in other nearby young clusters. Investigating the cause of this decrease, we find a correlation with the intense feedback from massive stars throughout the cluster area. We also identified the disc sources undergoing accretion and observed the mass accretion rates to exhibit a positive linear relationship with the stellar host mass and an inverse relationship with stellar age. Our findings suggest that the environment significantly influences the dissipation of discs in both clusters. These distant clusters, characterized by their unique attributes, can serve as templates for future studies in outer galaxy regions, offering insights into the influence of feedback mechanisms on star and planetary formation.
High-velocity outflows persist up to 1 Gyr after a starburst in recently quenched galaxies at z &gt; 1
Authors: Taylor Elizabeth , Maltby David , Almaini Omar , Merrifield Michael , Wild Vivienne , Rowlands Kate , Harrold Jimi 
Published: October 2024

ABSTRACT
High-velocity outflows are ubiquitous in star-forming galaxies at cosmic noon, but are not as common in passive galaxies at the same epoch. Using optical spectra of galaxies selected from the UKIDSS Ultra Deep Survey at $z\gt 1$, we perform a stacking analysis to investigate the transition in outflow properties along a quenching time sequence. To do this, we use Mg ii ($\lambda$2800 Å) absorption profiles to investigate outflow properties as a function of time since the last major burst of star formation (t$_{\textrm {burst}}$). We find evidence for high-velocity outflows in the star-forming progenitor population (v$_{\textrm {out}}$$\sim$ 1400 $\pm$ 210 km s$^{-1}$), for recently quenched galaxies with t$_{\textrm {burst}}$ &lt; 0.6 Gyr (v$_{\textrm {out}}$$\sim$ 990 $\pm$ 250 km s$^{-1}$), and for older quenched galaxies with 0.6 &lt; t$_{\textrm {burst}}$ &lt; 1 Gyr (v$_{\textrm {out}}$$\sim$ 1400 $\pm$ 220 km s$^{-1}$). The oldest galaxies (t$_{\textrm {burst}}$ &gt; 1 Gyr) show no evidence for significant outflows. Our samples show no signs of active galactic nucleus (AGN) in optical observations, suggesting that any AGN in these galaxies have very short duty cycles, and were ‘off’ when observed. The presence of significant outflows in the older quenched galaxies (t$_{\textrm {burst}}$ &gt; 0.6 Gyr) is difficult to explain with starburst activity, however, and may indicate energy input from episodic AGN activity as the starburst fades.
Revisiting dark photon constraints from CMB spectral distortions
Authors: Chluba Jens , Cyr Bryce , Johnson Matthew C 
Published: October 2024

ABSTRACT
Spectral distortions of the cosmic microwave background (CMB) provide stringent constraints on energy and entropy production in the post-BBN (big bang nucleosynthesis) era. This has been used to constrain dark photon models with COBE/FIRAS and forecast the potential gains with future CMB spectrometers. Here, we revisit these constraints by carefully considering the photon to dark photon conversion process and evolution of the distortion signal. Previous works only included the effect of CMB energy density changes but neglected the change to the photon number density. We clearly define the dark photon distortion signal and show that in contrast to previous analytic estimates the distortion has an opposite sign and a $\simeq 1.5$ times larger amplitude. We furthermore extend the treatment into the large distortion regime to also cover the redshift range $\simeq 2 \times 10^{6}-4 \times 10^{7}$ between the μ-era and the end of BBN using cosmotherm . This shows that the CMB distortion constraints for dark photon masses in the range $10^{-4}\, {\rm eV}\lesssim m_{\rm d}\lesssim 10^{-3}\, {\rm eV}$ were significantly underestimated. We demonstrate that in the small distortion regime the distortion caused by photon to dark photon conversion is extremely close to a μ-type distortion independent of the conversion redshift. This opens the possibility to study dark photon models using CMB distortion anisotropies and the correlations with CMB temperature anisotropies as we highlight here.
The Long Shadow of the Big Lie: How Beliefs about the Legitimacy of the 2020 Election Spill Over onto Future Elections
Authors: Levendusky Matthew , Patterson Shawn , Margolis Michele , Ophir Yotam , Walter Dror , Jamieson Kathleen Hall 
Published: October 2024

Abstract
Has the “big lie”—the false claim that the 2020 election was stolen from Donald Trump—shaped citizens’ views of the legitimacy of other US elections? We argue that it has. Those who believe Trump’s claim, whom we call election skeptics, lack confidence in elections for two interrelated reasons. First, because they think 2020 was inaccurately and unfairly conducted, they think that other elections will suffer a similar fate, and hence think these elections are illegitimate even before any votes are cast. Second, while most voters think elections are less legitimate when their preferred candidate loses, this effect will be especially large for election skeptics, because voter fraud gives them a mechanism to explain their candidate’s loss. Using an original panel dataset spanning the 2020 and 2022 elections, we show strong support for these hypotheses. This has important implications for our elections, and their legitimacy, moving forward.
Comparison of Ultrasound-guided Single-injection Erector Spinae Plane Block, Retrolaminar Block, and Paravertebral Block for Postoperative Analgesia in Single-incision Video-assisted Thoracoscopic Surgery
Authors: Zhu Yuyang , Yang Yi , Zhang Qinyu , Li Xuan , Xue Wenqiang , Liu Yuan , Zhao Yufei , Xu Wenxia , Yan Peng , Li Shuang , Fang Yu , Huang Jie 
Published: October 2024

Objective:
Effective postoperative analgesia is critical for thoracic surgery. This study compares the analgesic efficacy of the erector spinae plane block (ESPB), retrolaminar block (RLB), and paravertebral block (TPVB) in single-incision video-assisted thoracoscopic surgery (SITS).

Methods:
Seventy-six patients underwent general anesthesia followed by ultrasound-guided nerve blocks with 20 mL of 0.5% ropivacaine. Primary outcomes included the area under the curve (AUC) of numeric rating scale (NRS) scores during rest and coughing over 24 hours. Secondary outcomes included perioperative opioid use, plasma biomarkers, and postoperative recovery measures.

Results:
The AUC for NRS was 107.8±10.53 in the ESPB group, 104.8±8.05 in the RLB group, and 103.6±10.42 in the TPVB group, demonstrating noninferiority for ESPB (difference: 4.2±3.0, 95% CI: −1.82 to 10.22) and RLB (difference: 1.2±2.6, 95% CI: −3.97 to 6.37) compared with TPVB. No statistically significant differences were observed in opioid use, plasma biomarkers, QoR-15 scores, or adverse events.

Discussion:
ESPB and RLB provide noninferior analgesia compared with TPVB in SITS patients and are effective alternatives that enhance safety.
Use of Commercial Bacon to Extract Maggots from an Infested Chronic Wound
Authors: Fenati Gregory , Youssoffi Santana , Vejendla Shriya , Neeki Cameron C. , Nguyen Vinh T. , Dong Fanglong , Neeki Michael M. 
Published: October 2024

ABSTRACT
Maggot therapy, also known as larval therapy or biosurgery, is the use of live, sterilized maggots to debride necrotic tissue. Alternatively, wound infestation by maggots, known as myiasis, can occur in patients with poor wound management, particularly in those living in poor socioeconomic conditions. In the case of myiasis, various maggot extraction solutions are used to encourage the live larvae to emerge from the wound on their own. Current recommendations include the use of hypochlorous acid, sodium hypochlorite solutions, isopropyl alcohol, betadine, and hydrogen peroxide for wound cleansing. This case report focuses on a unique utilization of commercial bacon strips for the extraction of maggots in an infested necrotic wound. The use of commercial bacon strips in selective patients as a noninvasive technique for the removal of maggots from necrotic wounds can be an additional tool for medical providers.
Restorative Treatments for Cervical Spinal Cord Injury, a Narrative Review
Authors: Kaleem Muhammad I. , Javeed Saad , Plog Benjamin A. , Gupta Vivek P. , Ray Wilson Z. 
Published: October 2024

Study Design:
A narrative review.

Objective:
To summarize relevant data from representative studies investigating upper limb restorative therapies for cervical spinal cord injury.

Summary of Background Data:
Cervical spinal cord injury (SCI) is a debilitating condition resulting in tetraplegia, lifelong disability, and reduced quality of life. Given the dependence of all activities on hand function, patients with tetraplegia rank regaining hand function as one of their highest priorities. Recovery from cervical SCI is heterogeneous and often incomplete; currently, various novel therapies are under investigation to improve neurological function and eventually better quality of life in patients with tetraplegia.

Methods:
In this article, a narrative literature review was performed to identify treatment options targeting the restoration of function in patients with cervical SCI. Studies were included from available literature based on the availability of clinical data and whether they are applicable to restoration of arm and hand function in patients with cervical SCI.

Results:
We describe relevant studies including indications and outcomes with a focus on arm and hand function. Different treatment modalities described include nerve transfers, tendon transfers, spinal cord stimulation, functional electrical stimulation, non-invasive brain stimulation, brain-machine interfaces and neuroprosthetics, stem cell therapy, and immunotherapy. As the authors’ institution leads one of the largest clinical trials on nerve transfers for cervical SCI, we also describe how patients undergoing nerve transfers are managed and followed at our center.

Conclusions:
While complete recovery from cervical spinal cord injury may not be possible, novel therapies aimed at the restoration of upper limb motor function have made significant progress toward the realization of complete recovery.
Three-Dimensional Fluoroscopic System to Assess Robotically Placed Pedicle Screws
Authors: Lebovic Jordan , Trudeau Maxwell , Charalambous Lefko T. , Venkat Nitya , Gallina Jason , Goldstein Jeffrey A. 
Published: October 2024

Study Design:
Retrospective cohort study.

Objective:
The purpose of this study is to determine the utility of advanced imaging to confirm the placement of robotic pedicle screws.

Summary of Background Data:
With increasing robotic adoption, certain institutions and surgeons have developed protocols for obtaining 3D intraoperative imaging after robotic pedicle screw placement to ensure proper hardware placement. No studies have assessed the utility of these protocols relative to the potential risks of increased radiation exposure and operative time. The purpose of this study is to determine if we should be obtaining advanced imaging to confirm the placement of robotic pedicle screws.

Methods:
This is a single institution retrospective cohort study of patients from May 2022 to July 2023 who underwent lumbar spinal fusion by a high-volume orthopedic spine surgeon at a level 1 metropolitan hospital. All cases used combined robotics and navigation systems for pedicle screw placement and intraoperative 3D imaging for evaluation of screw position. Pedicle screw accuracy was assessed using the Gertzbein and Robbins system (GRS). Acceptable pedicle screw position was defined as GRS A or B.

Results:
Seventy patients with 354 robotically placed pedicle screws were assessed with intraoperative 3D fluoroscopy. All pedicle screws were placed in either a GRS type A or type B position. Three hundred fifty-one were placed in a GRS A classification (99.2%, 351/354), and 3 were placed in a GRS B classification (0.08% 3/354). No patients had screw-related complications. The average radiation dosage of 3D imaging was 289.7±164.6 mGy.

Conclusion:
The robotic system places pedicle screws accurately without 3D intraoperative imaging. Given the increased radiation and operative time associated with 3D imaging protocols 3D imaging scans should only be obtained in cases with heightened clinical concern.

Level of Evidence:
Level IV.
SOX-10 and Melan-A Immunostaining in Areas of Focal Acantholytic Dyskeratosis and Epidermolytic Hyperkeratosis Within Dysplastic Nevi Biopsies: An Observational Study
Authors: Erickson Kayley L. , Tripathi Raghav , Rohr Bethany R. 
Published: October 2024

Background:
Focal acantholytic dyskeratosis (FAD) and epidermolytic hyperkeratosis (EHK) are common incidental epidermal histologic findings within dysplastic nevi biopsies. We evaluate whether areas of FAD and EHK within dysplastic nevi biopsies stain with immunostains used to characterize melanocytic neoplasms.

Methods:
In this case series, a natural language search of histopathology reports from our institution in the past year (2020–2021) identified dysplastic nevus biopsies with concurrent FAD and/or EHK. Tissue samples were examined for positive melanocytic immunostaining with SOX-10 and Melan-A in areas of FAD and EHK.

Results:
Out of 32 biopsies, 20 of 26 FAD specimens (76.9%) and 2 of 6 EHK specimens (33.3%) showed unexpected suprabasal layer staining with a melanocytic marker that did not correspond to definitively identified melanocytes on the H&E-stained sections. The immunohistochemical staining of FAD and EHK was observed in 2 forms: nonspecific background staining or “true” staining (ie, seemed nuclear on SOX-10 or cytoplasmic on Melan-A).

Conclusions:
This pilot examination provides evidence that areas of incidental FAD within dysplastic nevi biopsies demonstrate unexpected suprabasal layer staining with melanocytic markers. When dermatopathologists evaluate melanocytic neoplasms with melanocytic markers, it is possible the presence of incidental FAD could lead to over diagnosing pagetoid scatter within these lesions. This study is a proof of concept with mild to moderately dysplastic nevi that do not typically incur the use of melanocytic stains; however, the implication of this unexpected staining pattern would be important when using melanocytic markers on borderline melanocytic neoplasms that have incidental FAD. Close correlation with H&E is imperative to prevent misinterpretation in these cases.