bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limitations of antifungal prophylaxis in preventing invasive
Candida
surgical site infections after liver transplant surgery
Authors: Carugati M. , Arif S. , Yarrington M. E. , King L. Y. , Harris M. , Evans K. , Barbas A. S. , Sudan D. L. , Perfect J. R. , Miller R. A. , Alexander B. D. 
Published: February 2024

ABSTRACT

Invasive primary
Candida
surgical site infections (IP-SSIs) are a common complication of liver transplantation, and targeted antifungal prophylaxis is an efficient strategy to limit their occurrence. We performed a retrospective single-center cohort study among adult single liver transplant recipients at Duke University Hospital in the period between 1 January 2015 and 31 December 2020. The study aimed to determine the rate of
Candida
IP-SSI according to the peri-transplant antifungal prophylaxis received. Of 470 adult single liver transplant recipients, 53 (11.3%) received micafungin prophylaxis, 100 (21.3%) received fluconazole prophylaxis, and 317 (67.4%) did not receive systemic antifungal prophylaxis in the peri-transplant period. Ten
Candida
IP-SSIs occurred among 5 of 53 (9.4%) micafungin recipients, 1 of 100 (1.0%) fluconazole recipients, and 4 of 317 (1.3%) recipients who did not receive antifungal prophylaxis. Our study highlights the limitations of antifungal prophylaxis in preventing invasive
Candida
IP-SSI after liver transplant surgery. We hypothesize that pathogen, host, and pharmacokinetic-related factors contributed to the occurrence of
Candida
IP-SSI despite antifungal prophylaxis. Our study reinforces the need for a risk-based, multi-pronged approach to fungal prevention, including targeted antifungal administration in patients with risks for invasive candidiasis and close monitoring, especially among patients with surgically complex procedures, with timely control of surgical leaks.
Evolving mechanisms and presentations of cardiovascular disease in people with HIV: implications for management
Authors: Nazari Ilana , Feinstein Matthew J. 
Published: February 2024

SUMMARY
People with HIV (PWH) are at elevated risk for cardiovascular diseases (CVDs), including myocardial infarction, heart failure, and sudden cardiac death, among other CVD manifestations. Chronic immune dysregulation resulting in persistent inflammation is common among PWH, particularly those with sustained viremia and impaired CD4+ T cell recovery. This inflammatory milieu is a major contributor to CVDs among PWH, in concert with common comorbidities (such as dyslipidemia and smoking) and, to a lesser extent, off-target effects of antiretroviral therapy. In this review, we discuss the clinical and mechanistic evidence surrounding heightened CVD risks among PWH, implications for specific CVD manifestations, and practical guidance for management in the setting of evolving data.
Retrospective validation of MetaSystems’ deep-learning-based digital microscopy platform with assistance compared to manual fluorescence microscopy for detection of mycobacteria
Authors: Desruisseaux Claudine , Broderick Conor , Lavergne Valéry , Sy Kim , Garcia Duang-Jai , Barot Gaurav , Locher Kerstin , Porter Charlene , Caza Mélissa , Charles Marthe K. 
Published: February 2024

ABSTRACT

This study aimed to validate Metasystems’ automated acid-fast bacilli (AFB) smear microscopy scanning and deep-learning-based image analysis module (Neon Metafer) with assistance on respiratory and pleural samples, compared to conventional manual fluorescence microscopy (MM). Analytical parameters were assessed first, followed by a retrospective validation study. In all, 320 archived auramine-O-stained slides selected non-consecutively [85 originally reported as AFB-smear-positive, 235 AFB-smear-negative slides; with an overall mycobacterial culture positivity rate of 24.1% (77/320)] underwent whole-slide imaging and were analyzed by the Metafer Neon AFB Module (version 4.3.130) using a predetermined probability threshold (PT) for AFB detection of 96%. Digital slides were then examined by a trained reviewer blinded to previous AFB smear and culture results, for the final interpretation of assisted digital microscopy (a-DM). Paired results from both microscopic methods were compared to mycobacterial culture. A scanning failure rate of 10.6% (34/320) was observed, leaving 286 slides for analysis. After discrepant analysis, concordance, positive and negative agreements were 95.5% (95%CI, 92.4%–97.6%), 96.2% (95%CI, 89.2%–99.2%), and 95.2% (95%CI, 91.3%–97.7%), respectively. Using mycobacterial culture as reference standard, a-DM and MM had comparable sensitivities: 90.7% (95%CI, 81.7%–96.2%) versus 92.0% (95%CI, 83.4%–97.0%) (
P
-value = 1.00); while their specificities differed 91.9% (95%CI, 87.4%–95.2%) versus 95.7% (95%CI, 92.1%–98.0%), respectively (
P
-value = 0.03). Using a PT of 96%, MetaSystems’ platform shows acceptable performance. With a national laboratory staff shortage and a local low mycobacterial infection rate, this instrument when combined with culture, can reliably triage-negative AFB-smear respiratory slides and identify positive slides requiring manual confirmation and semi-quantification.

IMPORTANCE
This manuscript presents a full validation of MetaSystems’ automated acid-fast bacilli (AFB) smear microscopy scanning and deep-learning-based image analysis module using a probability threshold of 96% including accuracy, precision studies, and evaluation of limit of AFB detection on respiratory samples when the technology is used with assistance. This study is complementary to the conversation started by Tomasello et al. on the use of image analysis artificial intelligence software in routine mycobacterial diagnostic activities within the context of high-throughput laboratories with low incidence of tuberculosis.
The intersection of host
in vivo
metabolism and immune responses to infection with kinetoplastid and apicomplexan parasites
Authors: Ewald Sarah , Nasuhidehnavi Azadeh , Feng Tzu-Yu , Lesani Mahbobeh , McCall Laura-Isobel 
Published: February 2024

SUMMARY

Protozoan parasite infection dramatically alters host metabolism, driven by immunological demand and parasite manipulation strategies. Immunometabolic checkpoints are often exploited by kinetoplastid and protozoan parasites to establish chronic infection, which can significantly impair host metabolic homeostasis. The recent growth of tools to analyze metabolism is expanding our understanding of these questions. Here, we review and contrast host metabolic alterations that occur
in vivo
during infection with
Leishmania
, trypanosomes,
Toxoplasma
,
Plasmodium,
and
Cryptosporidium
. Although genetically divergent, there are commonalities among these pathogens in terms of metabolic needs, induction of the type I immune responses required for clearance, and the potential for sustained host metabolic dysbiosis. Comparing these pathogens provides an opportunity to explore how transmission strategy, nutritional demand, and host cell and tissue tropism drive similarities and unique aspects in host response and infection outcome and to design new strategies to treat disease.
Draft genome sequence ofDietziasp. strain CH92 isolated from oil reservoir
Authors: Xiang Wei , Zhang Quan , Wang Jianxin , Xue Yanfen , Yu Bo 
Published: February 2024

ABSTRACTWe report the draft genome sequence ofDietziasp. strain CH92, isolated from a high temperature oil well in Baolige oilfield, China. The estimated genome is 3.73 Mb, with 3,479 protein-coding sequences.
Differential analysis of IBV-infected primary chicken embryonic fibroblasts and immortalized DF-1
Authors: Yang Qingcheng , Gong Huiling , Liu Song , Huang Siyu , Yan Wenjun , Wang Kailu , Li Hao , Lei Chang-Wei , Wang Hong-Ning , Yang Xin 
Published: February 2024

ABSTRACT

Infectious bronchitis virus (IBV), the causative agent of infectious bronchitis, is responsible for major economic losses in the poultry industry worldwide. While IBVs can usually be passaged in primary chicken embryonic fibroblasts (CEFs), most of the wild ones cannot adapt to passaged cell lines. In this study, the wild strain CK/CH/MY/2020 was used to infect primary CEF and immortalize DF-1 CEF cells. Results indicated that IBV was able to cause lesions and pass onto CEF, but not DF-1. Indeed, the virus could enter DF-1 cells and synthesize the associated structural gene but could not assemble into complete viral particles for release. Furthermore, transcriptome sequencing analysis showed significant differences in gene expression between CEF and DF-1 cells after viral infection, although the corresponding antiviral responses could be activated in both cell types. The biggest difference was in terms of the amino acid biosynthesis pathway and the cytokine receptor interaction pathway, which were significantly and specifically activated in CEF. This could actually explain why intact viruses can be assembled but not in DF-1. In addition,
SLBP
and
P2RX7
affect the replication of IBV’s structural genes to some extent. Overall, IBV can enter CEF and DF-1 cells, but the complex intracellular cytokine interactions affect the assembly and release of viral particles. The insight will be useful for the study of IBV through
in vitro
transmission and pathogenesis.

IMPORTANCE
Infectious bronchitis virus (IBV) is responsible for high morbidity and mortality as well as substantial economic losses worldwide. Transcriptome sequencing of IBV-infected chicken embryonic fibroblast and DF-1 cells revealed that the virus elicits antiviral immunity in cells after viral infection, but IBV cannot activate DF-1 cells to produce sufficient amounts of viral structures to assemble into complete virions, which may be caused by the interactions between cytokines. The study of IBV cellular adaptations is important for vaccine development and investigation of the pathogenesis of IBV.
Bulldoze and rebuild: Modifying cratonic lithosphere via removal and replacement induced by continental subduction
Authors: Meng Lingtong , Chu Yang , Lin Wei , Mitchell Ross N. , Zhao Liang 
Published: February 2024

Abstract
Establishing the mechanisms for craton modification is critical for understanding cratonic stability and architecture. It is well known that oceanic subduction and mantle plumes can destroy and destabilize the overriding cratonic lithosphere, but the role of continental subduction in craton modification remains unclear. In the North China craton (NCC), which experienced deep continental subduction of the Yangtze block (YB) during the early Mesozoic, we report the presence of the YB crust embedded in the overriding craton. Combining our new results with previous observations, we argue that during 250–220 Ma, a 200-km-long tract of the NCC lithosphere was bulldozed by the subducted YB, resulting in a lithospheric suture far from the suture zone at the surface. This lithospheric removal occurred at middle-lower crustal levels (16–20 km depth)—much shallower than previously thought possible. The bulldozed NCC lithosphere was replenished by the subducted YB continental lithosphere rather than the asthenosphere, thus terminating the lithosphere modification. With essentially no net loss of lithosphere during deep continental subduction, the NCC maintained its stability until Early Cretaceous paleo-Pacific oceanic subduction. This “bulldoze and rebuild” model can thus account for how a craton maintains stability during a collision with another continental plate.
UK endoscopy trainer survey: perspectives on current endoscopy training delivery, experience, barriers and opportunities
Authors: Brown Fraser , Weidner Alice , Wells Christopher , Ghumman Rumneet , McConnell Susan , Ngu Wee Sing , Ratcliffe Elizabeth , Subramaniam Sharmila , Barbour Jamie 
Published: February 2024

ObjectiveUK endoscopy training is delivered by trainers possessing well developed endoscopy and teaching skills to help learners perform high-quality endoscopy. Train The Trainer (TTT) courses are effective, but additional trainer support is variable with little formal quality assurance. We performed a survey to map UK endoscopy training, assess trainer perspectives on training delivery and identify factors that would enhance training.Design/MethodAn online survey was designed by trainer representatives, in collaboration with the JAG training committee, and collected responses from trainers registered on JAG endoscopy training system e-portfolio from April to June 2022.ResultsThere were 1024 responses from all trainer disciplines, with 813 (79%) completing TTT courses and 584 (57%) having job planned dedicated training lists (DTLs). Clinical endoscopists most frequently had job-planned DTLs (71%), and DTLs occurring at least weekly (58%). 293 (29%) respondents participated as course faculty. Trainers reported high levels of pre-procedure preparation, effective dialogue and frequent feedback. The DOPS forms were ‘always/often’ completed by 81% of clinical endoscopists, 73% of gastroenterologist and 58% of surgeons. 435 (42%) trainers never had peer feedback. Responses suggested training could improve by protecting training time, attending courses, participating as faculty and receiving feedback from experienced trainers.ConclusionThis survey demonstrates substantial proportions of highly motivated UK trainers who value time spent teaching and learning how to teach. Skills taught on the TTT courses are often actively used in everyday training. Improved trainer course access, protected training time and formal use of existing feedback tools by peers were highlighted as measures that could support trainers’ development.
Endovascular therapy of acute vertebrobasilar occlusions: influence of first-line strategy in the Endovascular Treatment in Ischemic Stroke (ETIS) Registry
Authors: Bekri Imen , Finitsis Stefanos , Pizzuto Silvia , Maier Benjamin , Piotin Michel , Eker Omer F , Marnat Gaultier , Sibon Igor , Dargazanli Cyril , Bourcier Romain , Lapergue Bertrand , Pop Raoul , Caroff Jildaz , Gory Benjamin , Pico Fernando , Consoli Arturo 
Published: February 2024

Background
The choice of the first-line technique in vertebrobasilar occlusions (VBOs) remains challenging. We aimed to report outcomes in a large cohort of patients and to compare the efficacy and safety of contact aspiration (CA) and combined technique (CoT) as a first-line endovascular technique in patients with acute VBOs.

Methods
We retrospectively analyzed clinical and neuroradiological data of patients with VBOs from the prospective, multicenter, observational Endovascular Treatment in Ischemic Stroke (ETIS) Registry in France between January 2015 and August 2023. The primary outcome was the first pass effect (FPE) rate, whereas modified Thrombolysis In Cerebral Infarction (mTICI) 2b-3 and 2c-3, number of passes, need for rescue strategy, modified Rankin Scale (mRS) 0–2, mortality, and symptomatic intracranial hemorrhage (sICH) were secondary outcomes. We performed univariate and multivariate analyses to investigate differences between the two groups.

Results
Among the 583 included patients (mean age 66.2 years, median National Institutes of Health Stroke Scale (NIHSS) 13, median posterior circulation Alberta Stroke Program Early CT Score (pc-ASPECTS) 8), 393 were treated with CA alone and 190 with CoT. Procedures performed with CA were shorter compared with CoT (28 vs 47 min, P<0.0001); however, no differences were observed in terms of FPE (CA 43.3% vs CoT 38.4%, P=0.99), and successful final recanalization (mTICI 2b-3, CA 92.4% vs CoT 91.8%, P=0.74) did not differ between the two groups. Functional independence and sICH rates were also similar, whereas mortality was significantly lower in the CA group (34.5% vs 42.9%; OR 1.79, 95% CI 1.03 to 3.11).

Conclusions
We observed no differences in FPE, mTICI 2b-3, sICH, and functional independence between the two study groups. First-line CA was associated with shorter procedures and lower mortality rates than CoT.
$$B_{(s)}$$ to light $$2^{--}$$ tensor meson form factors via LCSR in HQEFT and relevant semileptonic decays
Authors: Zuo Ya-Bing , Zhu Jia-Li , Hu Shan-Shan , Liu Cheng-Cheng , Zou Jia-Yu 
Published: February 2024

AbstractIn this study, the form factors of $$B_{(s)}$$

B

(
s
)

to light D-wave tensor mesons with $$J^{PC} = 2^{--}$$

J

PC

=

2

-
-

($$\rho _2$$

ρ
2

, $$\omega _2$$

ω
2

, $$K_2$$

K
2

and $$\phi _2$$

ϕ
2

) are calculated via the light cone sum rules (LCSR) in the framework of heavy quark effective eld theory (HQEFT). Firstly, the expressions of form factors in terms of the light cone distribution amplitudes (LCDAs) of tensor mesons are derived via the LCSR at the leading order of heavy quark expansion. Similar to the case of $$2^{++}$$

2

+
+

tensor mesons, the penguin type form factors can be obtained directly from the corresponding semileptonic ones. Considering the light tensor meson LCDAs to twist-3 and quark mass corrections, we give the numerical results of form factors systematically. Based on the form factors given here, we investigate the branching ratios, longitudinal polarization fractions and forward-backward asymmetries of relevant charged current induced semileptonic decays. Our results may be tested by more precise experiments in the future.
Heavy quark dominance in orbital excitation of singly and doubly heavy baryons
Authors: Li Zhen-Yu , Yu Guo-Liang , Wang Zhi-Gang , Gu Jian-Zhong 
Published: February 2024

AbstractA mechanism of the heavy quark dominance in the orbital excitation is proposed in this paper which is testified to be reasonable for singly and doubly heavy baryons. In the relativistic quark model, an analysis of the Hamiltonian figures out the mechanism that the excitation mode with lower energy levels is always associated with the heavy quark(s), and the splitting of the energy levels is suppressed by the heavy quark(s). So, the heavy quarks dominate the orbital excitation of singly and doubly heavy baryons. Furthermore, a physical understanding of this mechanism is given in a semi-classical way. Accordingly, the predicted mass spectra of singly and doubly heavy baryons confirm the rationality of this mechanism. In addition, an interesting consequence of this mechanism is that a heavy-light meson is more likely to be produced in the strong decay of the high-orbital excited states, which is supported by experiments. This mechanism is rooted in the breakdown of the mass symmetry. Therefore, it may be also valid for other multi-quark systems, such as the tetraquarks Qqqq and QQqq, or the pentaquarks Qqqqq and QQqqq.
Is There a Correlation between the Radiological and Clinical Outcome after Core Decompression of the Radius for Kienböck Disease?
Authors: MANIGLIO Mauro , ZAIDENBERG Ezequiel E. , RONER Simon , HABIB Nermine , BORETTO Jorge , DE CARLI Pablo 
Published: February 2024

Background: Despite the good clinical results in the treatment of Kienböck disease with distal radius core decompression, a radiological progression to a certain degree in the long-term follow-up is possible. Is there a negative correlation between the clinical improvement of the patients and the radiological progression? Methods: We retrospectively reviewed the radiological and clinical results of 24 patients (mean age: 38 years; 10 women) treated with core decompression for Kienböck disease. The mean follow-up was 10 years. Results: A radiologic progression in the Lichtman classification was seen in nine patients. The Spearman correlation did not show any correlation between this radiological progression and the clinical outcome. Namely −0.06 between Mayo and Lichtman classification and 0.16 between VAS and Lichtman classification. Conclusions: We found that the clinical outcomes do not deteriorate despite a radiological progression of patients treated with core decompression for Kienböck disease Level of Evidence: Level IV (Therapeutic)
Association Between Thenar Musculature and Carpal Tunnel Syndrome
Authors: HALPERN Robert A. , HUANG Shengnan , DUNHAM Kevin , PETCHPRAPA Catherine , WOLLSTEIN Ronit 
Published: February 2024

Background: Dynamic forces acting on the transverse carpal ligament (TCL) may influence the mechanics of the carpal tunnel (CT), thus affecting the occurrence of CT syndrome (CTS). Previous studies demonstrated an association between muscle overlying the CT and the diagnosis of CTS. Understanding the location of insertion/origin of the thenar musculature will allow mechanical analysis of the forces applied to the TCL during performance of individual tasks. Our purpose was to determine the location of muscle overlying the CT on magnetic resonance imaging (MRI) in CTS and controls. Methods: Case-control study of 21 normal adult wrist MRI scans. MRI measurements were performed on an axial cut at the level of the hook-of-hamate. Median nerve cross-sectional area (CSA), median nerve shape and increased signal intensity within the CT were associated with CTS. The amount and length of muscle crossing the midline and the CT on the same cut was measured and the association with the occurrence of CTS was analysed. Results: We found an inverse relationship between the amount of muscle crossing the midline and the size of the CT, and a direct relationship with occurrence of CTS p less than 0.01, but no differences regarding length of muscle crossing the midline. Conclusions: This study supports an association between the thenar musculature location relative to the CT and the predictors of CTS on MRI. Since the location of muscle origin/insertion is variable, their effect may differ accordingly, therefore, further study is needed to describe the exact location of origin/insertion and its differential dynamic or static effect on the pathogenesis of CTS. Level of Evidence: Level IV (Diagnostic)
Cytogenetic and Molecular Associations with Outcomes in Higher-Risk Myelodysplastic Syndromes Treated with Hypomethylating Agents plus Venetoclax
Authors: Bazinet Alexandre , Desikan Sai Prasad , Li Ziyi , Rodriguez-Sevilla Juan Jose , Venugopal Sangeetha , Urrutia Samuel , Montalban-Bravo Guillermo , Sasaki Koji , Chien Kelly S. , Hammond Danielle , Kanagal-Shamanna Rashmi , Ganan-Gomez Irene , Kadia Tapan M. , Borthakur Gautam , DiNardo Courtney D. , Daver Naval G. , Jabbour Elias J. , Ravandi Farhad , Kantarjian Hagop , Garcia-Manero Guillermo 
Published: February 2024

Abstract

Purpose:
Hypomethylating agents (HMA) combined with venetoclax are an emerging therapeutic strategy for higher-risk myelodysplastic syndromes (HR-MDS). The cytogenetic and molecular factors associated with outcomes with this combination for HR-MDS are incompletely understood.

Experimental Design:
We pooled patient data from 3 prospective trials evaluating HMA–venetoclax in HR-MDS to study associations between cytogenetic and molecular factors and overall response rate (ORR), overall survival (OS), and event-free survival (EFS). The Kaplan–Meier method was used to estimate time-to-event endpoints. Univariate and multivariate analyses using logistic regression (for ORR) or the Cox proportional hazards model (for OS and EFS) were used to identify associations between clinical, cytogenetic, and molecular factors and outcomes.

Results:
A total of 80 patients (52 HMA-naïve, 28 HMA-failure) were included. ORR was 90% in HMA-naïve and 57% in HMA-failure. Median OS was 28.2 and 8.3 months in HMA-naïve and HMA-failure, respectively. Median EFS was 17.9 and 5.5 months in HMA-naïve and HMA-failure, respectively. In addition, 24/52 (46%) of the HMA-naïve and 3/28 (11%) of the HMA-failure patients proceeded to allogeneic stem cell transplantation (SCT). Factors associated with inferior outcomes were prior HMA failure, complex cytogenetics, trisomy 8, TP53 mutations, and RAS pathway mutations. Mutations in RNA splicing, DNA methylation, and ASXL1 appeared favorable. Blast percentage was not predictive of outcomes.

Conclusions:
Knowledge of cytogenetic and molecular alterations may help identify which patients with HR-MDS benefit the most from venetoclax.